Publications

the wheat agc kinase taagc1 is a positive contributor to host resistance to the necrotrophic pathogen rhizoctonia cerealis.	considerable progress has been made in understanding the roles of agc kinases in mammalian systems. however, very little is known about the roles of agc kinases in wheat (triticum aestivum). the necrotrophic fungus rhizoctonia cerealis is the major pathogen of the destructive disease sharp eyespot of wheat. in this study, the wheat agc kinase gene taagc1, responding to r. cerealis infection, was isolated, and its properties and role in wheat defence were characterized. r. cerealis-resistant whea ...	2015	26220083
plant immune receptors mimic pathogen virulence targets.		2015	26219337
spatial dissection of the arabidopsis thaliana transcriptional response to downy mildew using fluorescence activated cell sorting.	changes in gene expression form a crucial part of the plant response to infection. in the last decade, whole-leaf expression profiling has played a valuable role in identifying genes and processes that contribute to the interactions between the model plant arabidopsis thaliana and a diverse range of pathogens. however, with some pathogens such as downy mildew caused by the biotrophic oomycete pathogen hyaloperonospora arabidopsidis (hpa), whole-leaf profiling may fail to capture the complete ara ...	2015	26217372
role of proline and pyrroline-5-carboxylate metabolism in plant defense against invading pathogens.	pyrroline-5-carboxylate (p5c) is an intermediate product of both proline biosynthesis and catabolism. recent evidences indicate that proline-p5c metabolism is tightly regulated in plants, especially during pathogen infection and abiotic stress. however, role of p5c and its metabolism in plants has not yet been fully understood. studies indicate that p5c synthesized in mitochondria has a role in both resistance (r)-gene-mediated and non-host resistance against invading pathogens. proline dehydrog ...	2015	26217357
temperature-dependent expression of virulence genes in fish-pathogenic bacteria.	virulence gene expression in pathogenic bacteria is modulated by environmental parameters. a key factor in this expression is temperature. its effect on virulence gene expression in bacteria infecting warm-blooded hosts is well documented. transcription of virulence genes in these bacteria is induced upon a shift from low environmental to a higher host temperature (37°c). interestingly, host temperatures usually correspond to the optimum for growth of these pathogenic bacteria. on the contrary, ...	2015	26217329
genome mining and metabolic profiling of the rhizosphere bacterium pseudomonas sp. sh-c52 for antimicrobial compounds.	the plant microbiome represents an enormous untapped resource for discovering novel genes and bioactive compounds. previously, we isolated pseudomonas sp. sh-c52 from the rhizosphere of sugar beet plants grown in a soil suppressive to the fungal pathogen rhizoctonia solani and showed that its antifungal activity is, in part, attributed to the production of the chlorinated 9-amino-acid lipopeptide thanamycin (mendes et al., 2011). to get more insight into its biosynthetic repertoire, the genome o ...	2015	26217324
auto-acetylation on k289 is not essential for hopz1a-mediated plant defense suppression.	the pseudomonas syringae type iii-secreted effector hopz1a is a member of the hopz/yopj superfamily of effectors that triggers immunity in arabidopsis. we have previously shown that hopz1a suppresses both local [effector-triggered immunity (eti)] and systemic immunity [systemic acquired resistance (sar)] triggered by the heterologous effector avrrpt2. hopz1a has been shown to possess acetyltransferase activity, and this activity is essential to trigger immunity in arabidopsis. hopz1a acetyltrans ...	2015	26217317
the effects of silver nanoparticles on intact wastewater biofilms.	silver nanoparticles (ag-nps) have strong antibacterial properties, which may adversely affect biological wastewater treatment processes. to determine the overall effect, intact biofilm samples were collected from the rotating biological contactor at the local wastewater treatment plant and treated with 200 mg ag/l ag-nps for 24 h. the biofilm uptake of ag-nps was monitored with transmission electron microscopy. forty-five minutes after ag-np application, ag-nps were seen in the biofilm extracel ...	2015	26217316
representing virus-host interactions and other multi-organism processes in the gene ontology.	the gene ontology project is a collaborative effort to provide descriptions of gene products in a consistent and computable language, and in a species-independent manner. the gene ontology is designed to be applicable to all organisms but up to now has been largely under-utilized for prokaryotes and viruses, in part because of a lack of appropriate ontology terms.	2015	26215368
pre-mrna splicing in plants: in vivo functions of rna-binding proteins implicated in the splicing process.	alternative pre-messenger rna splicing in higher plants emerges as an important layer of regulation upon exposure to exogenous and endogenous cues. accordingly, mutants defective in rna-binding proteins predicted to function in the splicing process show severe phenotypic alterations. among those are developmental defects, impaired responses to pathogen threat or abiotic stress factors, and misregulation of the circadian timing system. a suite of splicing factors has been identified in the model ...	2015	26213982
characterization of para-nitrophenol-degrading bacterial communities in river water by using functional markers and stable isotope probing.	microbial degradation is a major determinant of the fate of pollutants in the environment. para-nitrophenol (pnp) is an epa-listed priority pollutant with a wide environmental distribution, but little is known about the microorganisms that degrade it in the environment. we studied the diversity of active pnp-degrading bacterial populations in river water using a novel functional marker approach coupled with [(13)c6]pnp stable isotope probing (sip). culturing together with culture-independent ter ...	2015	26209677
origin of the outbreak in france of pseudomonas syringae pv. actinidiae biovar 3, the causal agent of bacterial canker of kiwifruit, revealed by a multilocus variable-number tandem-repeat analysis.	the first outbreaks of bacterial canker of kiwifruit caused by pseudomonas syringae pv. actinidiae biovar 3 were detected in france in 2010. p. syringae pv. actinidiae causes leaf spots, dieback, and canker that sometimes lead to the death of the vine. p. syringae pv. actinidifoliorum, which is pathogenic on kiwi as well, causes only leaf spots. in order to conduct an epidemiological study to track the spread of the epidemics of these two pathogens in france, we developed a multilocus variable-n ...	2015	26209667
novel glucose-1-phosphatase with high phytase activity and unusual metal ion activation from soil bacterium pantoea sp. strain 3.5.1.	phosphorus is an important macronutrient, but its availability in soil is limited. many soil microorganisms improve the bioavailability of phosphate by releasing it from various organic compounds, including phytate. to investigate the diversity of phytate-hydrolyzing bacteria in soil, we sampled soils of various ecological habitats, including forest, private homesteads, large agricultural complexes, and urban landscapes. bacterial isolate pantoea sp. strain 3.5.1 with the highest level of phytas ...	2015	26209662
a single-step purification of cauliflower lysozyme and its dual role against bacterial and fungal plant pathogens.	a novel lysozyme from cauliflower was purified in a single step, for the first time, using sephadex g100 column chromatography. the purified lysozyme exhibited a homogenized single band in sodium dodecyl sulfate polyacrylamide gel electrophoresis (sds-page), and its molecular mass was calculated to be 22.0 kda. the purified lysozyme showed activity between 30 to 60 °c with 40 °c as the optimum temperature for its maximal activity. although the purified lysozyme was functional at ph ranges betwee ...	2015	26208688
pseudomonas syringae effector avirulence protein e localizes to the host plasma membrane and down-regulates the expression of the nonrace-specific disease resistance1/harpin-induced1-like13 gene required for antibacterial immunity in arabidopsis.	many bacterial pathogens of plants and animals deliver effector proteins into host cells to promote infection. elucidation of how pathogen effector proteins function not only is critical for understanding bacterial pathogenesis but also provides a useful tool in discovering the functions of host genes. in this study, we characterized the pseudomonas syringae pv tomato dc3000 effector protein avirulence protein e (avre), the founding member of a widely distributed, yet functionally enigmatic, bac ...	2015	26206852
pseudomonas syringae enhances herbivory by suppressing the reactive oxygen burst in arabidopsis.	plant-herbivore interactions have evolved in the presence of plant-colonizing microbes. these microbes can have important third-party effects on herbivore ecology, as exemplified by drosophilid flies that evolved from ancestors feeding on plant-associated microbes. leaf-mining flies in the genus scaptomyza, which is nested within the paraphyletic genus drosophila, show strong associations with bacteria in the genus pseudomonas, including pseudomonas syringae. adult females are capable of vectori ...	2015	26205072
pseudomonas syringae enhances herbivory by suppressing the reactive oxygen burst in arabidopsis.	plant-herbivore interactions have evolved in the presence of plant-colonizing microbes. these microbes can have important third-party effects on herbivore ecology, as exemplified by drosophilid flies that evolved from ancestors feeding on plant-associated microbes. leaf-mining flies in the genus scaptomyza, which is nested within the paraphyletic genus drosophila, show strong associations with bacteria in the genus pseudomonas, including pseudomonas syringae. adult females are capable of vectori ...	2015	26205072
cross kingdom activators of five classes of bacterial effectors.		2015	26203905
conserved nematode signalling molecules elicit plant defenses and pathogen resistance.	plant-defense responses are triggered by perception of conserved microbe-associated molecular patterns (mamps), for example, flagellin or peptidoglycan. however, it remained unknown whether plants can detect conserved molecular patterns derived from plant-parasitic animals, including nematodes. here we show that several genera of plant-parasitic nematodes produce small molecules called ascarosides, an evolutionarily conserved family of nematode pheromones. picomolar to micromolar concentrations ...	2015	26203561
high levels of cyclic-di-gmp in plant-associated pseudomonas correlate with evasion of plant immunity.	the plant innate immune system employs plasma membrane-localized receptors that specifically perceive pathogen/microbe-associated molecular patterns (pamps/mamps). this induces a defence response called pattern-triggered immunity (pti) to fend off pathogen attack. commensal bacteria are also exposed to potential immune recognition and must employ strategies to evade and/or suppress pti to successfully colonize the plant. during plant infection, the flagellum has an ambiguous role, acting as both ...	2015	26202381
high levels of cyclic-di-gmp in plant-associated pseudomonas correlate with evasion of plant immunity.	the plant innate immune system employs plasma membrane-localized receptors that specifically perceive pathogen/microbe-associated molecular patterns (pamps/mamps). this induces a defence response called pattern-triggered immunity (pti) to fend off pathogen attack. commensal bacteria are also exposed to potential immune recognition and must employ strategies to evade and/or suppress pti to successfully colonize the plant. during plant infection, the flagellum has an ambiguous role, acting as both ...	2015	26202381
unearthing the genomes of plant-beneficial pseudomonas model strains wcs358, wcs374 and wcs417.	plant growth-promoting rhizobacteria (pgpr) can protect plants against pathogenic microbes through a diversity of mechanisms including competition for nutrients, production of antibiotics, and stimulation of the host immune system, a phenomenon called induced systemic resistance (isr). in the past 30 years, the pseudomonas spp. pgpr strains wcs358, wcs374 and wcs417 of the willie commelin scholten (wcs) collection have been studied in detail in pioneering papers on the molecular basis of pgpr-me ...	2015	26198432
tolerance of an antarctic bacterium to multiple environmental stressors.	a population of cold-tolerant antarctic bacteria was screened for their ability to tolerate other environmental stress factors. besides low temperature, they were predominantly found to be tolerant to alkali. attempt was also made to postulate a genetic basis of their multistress-tolerance. transposon mutagenesis of an isolate pseudomonas syringae lz4w was performed, and mutants with delayed growth at low temperature were further screened for sensitivity to some other stress factors. a number of ...	2015	26198412
phosphorylation of the plant immune regulator rpm1-interacting protein4 enhances plant plasma membrane h⁺-atpase activity and inhibits flagellin-triggered immune responses in arabidopsis.	the pseudomonas syringae effector avrb targets multiple host proteins during infection, including the plant immune regulator rpm1-interacting protein4 (rin4) and rpm1-induced protein kinase (ripk). in the presence of avrb, ripk phosphorylates rin4 at thr-21, ser-160, and thr-166, leading to activation of the immune receptor rpm1. here, we investigated the role of rin4 phosphorylation in susceptible arabidopsis thaliana genotypes. using circular dichroism spectroscopy, we show that rin4 is a diso ...	2015	26198070
an arabidopsis plasma membrane proton atpase modulates ja signaling and is exploited by the pseudomonas syringae effector protein avrb for stomatal invasion.	stomata are natural openings through which many pathogenic bacteria enter plants. successful bacterial pathogens have evolved various virulence factors to promote stomatal opening. here, we show that the pseudomonas syringae type iii effector protein avrb induces stomatal opening and enhances bacterial virulence in a manner dependent on rpm1-interacting4 (rin4), which promotes stomatal opening by positively regulating the arabidopsis plasma membrane h(+)-atpase (aha1), which is presumed to direc ...	2015	26198069
large-scale phenomics identifies primary and fine-tuning roles for crks in responses related to oxidative stress.	cysteine-rich receptor-like kinases (crks) are transmembrane proteins characterized by the presence of two domains of unknown function 26 (duf26) in their ectodomain. the crks form one of the largest groups of receptor-like protein kinases in plants, but their biological functions have so far remained largely uncharacterized. we conducted a large-scale phenotyping approach of a nearly complete crk t-dna insertion line collection showing that crks control important aspects of plant development an ...	2015	26197346
feng shao: getting a sense for the defense.		2015	26195661
lessons in fundamental mechanisms and diverse adaptations from the 2015 bacterial locomotion and signal transduction meeting.	in response to rapid changes in their environment, bacteria control a number of processes, including motility, cell division, biofilm formation, and virulence. research presented in january 2015 at the biennial bacterial locomotion and signal transduction (blast) meeting in tucson, az, illustrates the elegant complexity of the nanoarrays, nanomachines, and networks of interacting proteins that mediate such processes. studies employing an array of biophysical, genetic, cell biology, and mathemati ...	2015	26195592
stress-responsive expression, subcellular localization and protein-protein interactions of the rice metacaspase family.	metacaspases, a class of cysteine-dependent proteases like caspases in animals, are important regulators of programmed cell death (pcd) during development and stress responses in plants. the present study was focused on comprehensive analyses of expression patterns of the rice metacaspase (osmc) genes in response to abiotic and biotic stresses and stress-related hormones. results indicate that members of the osmc family displayed differential expression patterns in response to abiotic (e.g., dro ...	2015	26193260
secretion systems and signal exchange between nitrogen-fixing rhizobia and legumes.	the formation of symbiotic nitrogen-fixing nodules on the roots and/or stem of leguminous plants involves a complex signal exchange between both partners. since many microorganisms are present in the soil, legumes and rhizobia must recognize and initiate communication with each other to establish symbioses. this results in the formation of nodules. rhizobia within nodules exchange fixed nitrogen for carbon from the legume. symbiotic relationships can become non-beneficial if one partner ceases t ...	2015	26191069
oxylipins in moss development and defense.	oxylipins are oxygenated fatty acids that participate in plant development and defense against pathogen infection, insects, and wounding. initial oxygenation of substrate fatty acids is mainly catalyzed by lipoxygenases (loxs) and α-dioxygenases but can also take place non-enzymatically by autoxidation or singlet oxygen-dependent reactions. the resulting hydroperoxides are further metabolized by secondary enzymes to produce a large variety of compounds, including the hormone jasmonic acid (ja) a ...	2015	26191067
bacterial extracellular polysaccharides in biofilm formation and function.	microbes produce a biofilm matrix consisting of proteins, extracellular dna, and polysaccharides that is integral in the formation of bacterial communities. historical studies of polysaccharides revealed that their overproduction often alters the colony morphology and can be diagnostic in identifying certain species. the polysaccharide component of the matrix can provide many diverse benefits to the cells in the biofilm, including adhesion, protection, and structure. aggregative polysaccharides ...	2015	26185074
plant myb transcription factors: their role in drought response mechanisms.	water scarcity is one of the major causes of poor plant performance and limited crop yields worldwide and it is the single most common cause of severe food shortage in developing countries. several molecular networks involved in stress perception, signal transduction and stress responses in plants have been elucidated so far. transcription factors are major players in water stress signaling. in recent years, different myb transcription factors, mainly in arabidopsis thaliana (l.) heynh. but also ...	2015	26184177
bacteria murmur: application of an acoustic biosensor for plant pathogen detection.	a multi-targeting protocol for the detection of three of the most important bacterial phytopathogens, based on their scientific and economic importance, was developed using an acoustic biosensor (the quartz crystal microbalance) for dna detection. acoustic detection was based on a novel approach where dna amplicons were monitored and discriminated based on their length rather than mass. experiments were performed during real time monitoring of analyte binding and in a direct manner, i.e. without ...	2015	26177507
calmodulin-like protein cml37 is a positive regulator of aba during drought stress in arabidopsis.	plants need to adapt to various stress factors originating from the environment. signal transduction pathways connecting the recognition of environmental cues and the initiation of appropriate downstream responses in plants often involve intracellular ca(2+) concentration changes. these changes must be deciphered into specific cellular signals. calmodulin-like proteins, cmls, act as ca(2+) sensors in plants and are known to be involved in various stress reactions. here, we show that in arabidops ...	2015	26176898
early lotus japonicus root transcriptomic responses to symbiotic and pathogenic fungal exudates.	the objective of this study is to evaluate lotus japonicus transcriptomic responses to arbuscular mycorrhizal (am) germinated spore exudates (gses), responsible for activating nuclear ca(2+) spiking in plant root epidermis. a microarray experiment was performed comparing gene expression in lotus rootlets treated with gse or water after 24 and 48 h. the transcriptional pattern of selected genes that resulted to be regulated in the array was further evaluated upon different treatments and timings. ...	2015	26175746
proteomic analysis of apoplastic fluid of coffea arabica leaves highlights novel biomarkers for resistance against hemileia vastatrix.	a proteomic analysis of the apoplastic fluid (apf) of coffee leaves was conducted to investigate the cellular processes associated with incompatible (resistant) and compatible (susceptible) coffea arabica-hemileia vastatrix interactions, during the 24-96 hai period. the apf proteins were extracted by leaf vacuum infiltration and protein profiles were obtained by 2-de. the comparative analysis of the gels revealed 210 polypeptide spots whose volume changed in abundance between samples (control, r ...	2015	26175744
exploration of micrornas and their targets engaging in the resistance interaction between wheat and stripe rust.	wheat stripe rust, caused by puccinia striiformis f. sp. tritici (pst), is one of the most destructive diseases of wheat worldwide. mirnas are important regulators, they play very central roles in plant organ development, vegetable phase change and defense responses. in this study, two mirna libraries from wheat cultivar xingzi 9104 (xz) challenged with the avirulent pst race cyr32 and sterile water were constructed, respectively. a total of 596 mirna candidates were obtained. 420 wheat-specific ...	2015	26175740
the alternative respiratory pathway is involved in brassinosteroid-induced environmental stress tolerance in nicotiana benthamiana.	brassinosteroids (brs), plant steroid hormones, play essential roles in modulating cell elongation, vascular differentiation, senescence, and stress responses. however, the mechanisms by which brs regulate plant mitochondria and resistance to abiotic stress remain largely unclear. mitochondrial alternative oxidase (aox) is involved in the plant response to a variety of environmental stresses. in this report, the role of aox in br-induced tolerance against cold, polyethylene glycol (peg), and hig ...	2015	26175355
structural features reminiscent of atp-driven protein translocases are essential for the function of a type iii secretion-associated atpase.	many bacterial pathogens and symbionts utilize type iii secretion systems to interact with their hosts. these machines have evolved to deliver bacterial effector proteins into eukaryotic target cells to modulate a variety of cellular functions. one of the most conserved components of these systems is an atpase, which plays an essential role in the recognition and unfolding of proteins destined for secretion by the type iii pathway. here we show that structural features reminiscent of other atp-d ...	2015	26170413
the sulfur/sulfonates transport systems in xanthomonas citri pv. citri.	the xanthomonas citri pv. citri (x. citri) is a phytopathogenic bacterium that infects different species of citrus plants where it causes canker disease. the adaptation to different habitats is related to the ability of the cells to metabolize and to assimilate diverse compounds, including sulfur, an essential element for all organisms. in escherichia coli, the necessary sulfur can be obtained by a set of proteins whose genes belong to the cys regulon. although the cys regulon proteins and their ...	2015	26169280
genome-wide profiling of histone modifications (h3k9me2 and h4k12ac) and gene expression in rust (uromyces appendiculatus) inoculated common bean (phaseolus vulgaris l.).	histone modifications such as methylation and acetylation play a significant role in controlling gene expression in unstressed and stressed plants. genome-wide analysis of such stress-responsive modifications and genes in non-model crops is limited. we report the genome-wide profiling of histone methylation (h3k9me2) and acetylation (h4k12ac) in common bean (phaseolus vulgaris l.) under rust (uromyces appendiculatus) stress using two high-throughput approaches, chromatin immunoprecipitation sequ ...	2015	26167691
plant immune receptor decoy: pathogens in their own trap.		2015	26164080
tomato slrbohb, a member of the nadph oxidase family, is required for disease resistance against botrytis cinerea and tolerance to drought stress.	nadph oxidases (also known as respiratory burst oxidase homologs, rbohs) are key enzymes that catalyze the generation of reactive oxygen species (ros) in plants. in the present study, eight slrboh genes were identified in tomato and their possible involvement in resistance to botrytis cinerea and drought tolerance was examined. expression of slrbohs was induced by b. cinerea and pseudomonas syringae pv. tomato but displayed distinct patterns. virus-induced gene silencing based silencing of slrbo ...	2015	26157450
extra-large g proteins expand the repertoire of subunits in arabidopsis heterotrimeric g protein signaling.	heterotrimeric g proteins, consisting of gα, gβ, and gγ subunits, are a conserved signal transduction mechanism in eukaryotes. however, g protein subunit numbers in diploid plant genomes are greatly reduced as compared with animals and do not correlate with the diversity of functions and phenotypes in which heterotrimeric g proteins have been implicated. in addition to gpa1, the sole canonical arabidopsis (arabidopsis thaliana) gα subunit, arabidopsis has three related proteins: the extra-large ...	2015	26157115
function of aba in stomatal defense against biotic and drought stresses.	the plant hormone abscisic acid (aba) regulates many key processes involved in plant development and adaptation to biotic and abiotic stresses. under stress conditions, plants synthesize aba in various organs and initiate defense mechanisms, such as the regulation of stomatal aperture and expression of defense-related genes conferring resistance to environmental stresses. the regulation of stomatal opening and closure is important to pathogen defense and control of transpirational water loss. re ...	2015	26154766
catalytic mechanisms of fe(ii)- and 2-oxoglutarate-dependent oxygenases.	mononuclear non-heme fe(ii)- and 2-oxoglutarate (2og)-dependent oxygenases comprise a large family of enzymes that utilize an fe(iv)-oxo intermediate to initiate diverse oxidative transformations with important biological roles. here, four of the major types of fe(ii)/2og-dependent reactions are detailed: hydroxylation, halogenation, ring formation, and desaturation. in addition, an atypical epimerization reaction is described. studies identifying several key intermediates in catalysis are conci ...	2015	26152721
gntr family of bacterial transcription factors and their dna binding motifs: structure, positioning and co-evolution.	the gntr family of transcription factors (tfs) is a large group of proteins present in diverse bacteria and regulating various biological processes. here we use the comparative genomics approach to reconstruct regulons and identify binding motifs of regulators from three subfamilies of the gntr family, fadr, hutc, and ytra. using these data, we attempt to predict dna-protein contacts by analyzing correlations between binding motifs in dna and amino acid sequences of tfs. we identify pairs of pos ...	2015	26151451
microbial species delineation using whole genome sequences.	increased sequencing of microbial genomes has revealed that prevailing prokaryotic species assignments can be inconsistent with whole genome information for a significant number of species. the long-standing need for a systematic and scalable species assignment technique can be met by the genome-wide average nucleotide identity (gani) metric, which is widely acknowledged as a robust measure of genomic relatedness. in this work, we demonstrate that the combination of gani and the alignment fracti ...	2015	26150420
novel properties of γ-glutamyltransferase from pseudomonas syringae with β-aspartyltransferase activity.	gene cloning, purification, and characterization of γ-glutamyltransferase from pseudomonas syringae (psggt) were performed in escherichia coli.	2015	26149579
characterization of ice-nucleating bacteria using on-line electron impact ionization aerosol mass spectrometry.	the mass spectral signatures of airborne bacteria were measured and analyzed in cloud simulation experiments at the aida (aerosol interaction and dynamics in the atmosphere) facility. suspensions of cultured cells in pure water were sprayed into the aerosol and cloud chambers forming an aerosol which consisted of intact cells, cell fragments and residual particles from the agar medium in which the bacteria were cultured. the aerosol particles were analyzed with a high-resolution time-of-flight a ...	2015	26149110
visualizing the relevance of bacterial blue- and red-light receptors during plant-pathogen interaction.	the foliar pathogen pseudomonas syringae pv. tomato dc3000 (pst) leads to consistent losses in tomato crops, urging to multiply investigations on the physiological bases for its infectiveness. as other p. syringae pathovars, pst is equipped with photoreceptors for blue and red light, mimicking the photosensing ability of host plants. in this work we have investigated pst strains lacking the genes for a blue-light sensing protein (pstlov), for a bacteriophytochrome (pstbph1) or for heme-oxygenase ...	2015	26147514
comparative genomic analyses of multiple pseudomonas strains infecting corylus avellana trees reveal the occurrence of two genetic clusters with both common and distinctive virulence and fitness traits.	the european hazelnut (corylus avellana) is threatened in europe by several pseudomonads which cause symptoms ranging from twig dieback to tree death. a comparison of the draft genomes of nine pseudomonas strains isolated from symptomatic c. avellana trees was performed to identify common and distinctive genomic traits. the thorough assessment of genetic relationships among the strains revealed two clearly distinct clusters: p. avellanae and p. syringae. the latter including the pathovars avella ...	2015	26147218
lamp assay and rapid sample preparation method for on-site detection of flavescence dorée phytoplasma in grapevine.	in europe the most devastating phytoplasma associated with grapevine yellows (gy) diseases is a quarantine pest, flavescence dorée (fdp), from the 16srv taxonomic group. the on-site detection of fdp with an affordable device would contribute to faster and more efficient decisions on the control measures for fdp. therefore, a real-time isothermal lamp assay for detection of fdp was validated according to the eppo standards and miqe guidelines. the lamp assay was shown to be specific and extremely ...	2014	26146413
lamp assay and rapid sample preparation method for on-site detection of flavescence dorée phytoplasma in grapevine.	in europe the most devastating phytoplasma associated with grapevine yellows (gy) diseases is a quarantine pest, flavescence dorée (fdp), from the 16srv taxonomic group. the on-site detection of fdp with an affordable device would contribute to faster and more efficient decisions on the control measures for fdp. therefore, a real-time isothermal lamp assay for detection of fdp was validated according to the eppo standards and miqe guidelines. the lamp assay was shown to be specific and extremely ...	2014	26146413
molecular characterization of lubx: functional divergence of the u-box fold by legionella pneumophila.	lubx is part of the large arsenal of effectors in legionella pneumophila that are translocated into the host cytosol during infection. despite such unique features as the presence of two u-box motifs and its targeting of another effector sidh, the molecular basis of lubx activity remains poorly understood. here we show that the n terminus of lubx is able to activate an extended number of ubiquitin-conjugating (e2) enzymes including ube2w, ubel6, and all tested members of ube2d and ube2e families ...	2015	26146184
genetic variation for induced and basal resistance against leaf pathogen pseudomonas syringae pv. tomato dc3000 among arabidopsis thaliana accessions.	in arabidopsis thaliana, significant efforts to determine the effect of naturally occurring variation between phenotypically divergent accessions on different biotic or abiotic stresses are underway. although it is usually assumed that induced systemic resistance (isr) against pathogen will covary with plant genetic variation, this assumption has not been tested rigorously in previous experiments. here, we investigated heritable variation in resistance as well as penicillium simplicissimum gp17- ...	2015	26140260
spatial and temporal regulation of biosynthesis of the plant immune signal salicylic acid.	the plant hormone salicylic acid (sa) is essential for local defense and systemic acquired resistance (sar). when plants, such as arabidopsis, are challenged by different pathogens, an increase in sa biosynthesis generally occurs through transcriptional induction of the key synthetic enzyme isochorismate synthase 1 (ics1). however, the regulatory mechanism for this induction is poorly understood. using a yeast one-hybrid screen, we identified two transcription factors (tfs), ntm1-like 9 (ntl9) a ...	2015	26139525
tight regulation of plant immune responses by combining promoter and suicide exon elements.	effector-triggered immunity (eti) is activated when plant disease resistance (r) proteins recognize the presence of pathogen effector proteins delivered into host cells. the eti response generally encompasses a defensive 'hypersensitive response' (hr) that involves programmed cell death at the site of pathogen recognition. while many r protein and effector protein pairs are known to trigger hr, other components of the eti signaling pathway remain elusive. effector genes regulated by inducible pr ...	2015	26138488
the hidden world within plants: ecological and evolutionary considerations for defining functioning of microbial endophytes.	all plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. these microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, and diversification. the increasing awareness of and information on endophytes provide insight into the complexity of the plant microbiome. the nature of plant-endophyte interactions ranges from mutualism to pathogenicity. this depends on a set of abiotic and bi ...	2015	26136581
identification of mirnas and their targets in cotton inoculated with verticillium dahliae by high-throughput sequencing and degradome analysis.	micrornas (mirnas) are a group of endogenous small non-coding rnas that play important roles in plant growth, development, and stress response processes. verticillium wilt is a vascular disease in plants mainly caused by verticillium dahliae kleb., the soil-borne fungal pathogen. however, the role of mirnas in the regulation of verticillium defense responses is mostly unknown. this study aimed to identify new mirnas and their potential targets that are involved in the regulation of verticillium ...	2015	26133244
a circadian oscillator in the fungus botrytis cinerea regulates virulence when infecting arabidopsis thaliana.	the circadian clock of the plant model arabidopsis thaliana modulates defense mechanisms impacting plant-pathogen interactions. nevertheless, the effect of clock regulation on pathogenic traits has not been explored in detail. moreover, molecular description of clocks in pathogenic fungi--or fungi in general other than the model ascomycete neurospora crassa--has been neglected, leaving this type of question largely unaddressed. we sought to characterize, therefore, the circadian system of the pl ...	2015	26124115
ltp3 contributes to disease susceptibility in arabidopsis by enhancing abscisic acid (aba) biosynthesis.	several plant lipid transfer proteins (ltps) act positively in plant disease resistance. here, we show that ltp3 (at5g59320), a pathogen and abscisic acid (aba)-induced gene, negatively regulates plant immunity in arabidopsis. the overexpression of ltp3 (ltp3-ox) led to an enhanced susceptibility to virulent bacteria and compromised resistance to avirulent bacteria. on infection of ltp3-ox plants with pseudomonas syringae pv. tomato, genes involved in aba biosynthesis, nced3 and aao3, were highl ...	2016	26123657
small rnas--the secret agents in the plant-pathogen interactions.	eukaryotic regulatory small rnas (srnas) that induce rna interference (rnai) are involved in a plethora of biological processes, including host immunity and pathogen virulence. in plants, diverse classes of srnas contribute to the regulation of host innate immunity. these immune-regulatory srnas operate through distinct rnai pathways that trigger transcriptional or post-transcriptional gene silencing. similarly, many pathogen-derived srnas also regulate pathogen virulence. remarkably, the influe ...	2015	26123395
bean 2.0: an integrated web resource for the identification and functional analysis of type iii secreted effectors.	gram-negative pathogenic bacteria inject type iii secreted effectors (t3ses) into host cells to sabotage their immune signaling networks. because t3ses constitute a meeting-point of pathogen virulence and host defense, they are of keen interest to host-pathogen interaction research community. to accelerate the identification and functional understanding of t3ses, we present bean 2.0 as an integrated web resource to predict, analyse and store t3ses. bean 2.0 includes three major components. first ...	2015	26120140
chloroplast stromules function during innate immunity.	inter-organellar communication is vital for successful innate immune responses that confer defense against pathogens. however, little is known about how chloroplasts, which are a major production site of pro-defense molecules, communicate and coordinate with other organelles during defense. here we show that chloroplasts send out dynamic tubular extensions called stromules during innate immunity or exogenous application of the pro-defense signals, hydrogen peroxide (h2o2) and salicylic acid. int ...	2015	26120031
plant and animal organelles in cell death.		2015	26116839
type iii secretion system translocon component eseb forms filaments on and mediates autoaggregation of and biofilm formation by edwardsiella tarda.	the type iii secretion system (t3ss) of edwardsiella tarda plays an important role in infection by translocating effector proteins into host cells. eseb, a component required for effector translocation, is reported to mediate autoaggregation of e. tarda. in this study, we demonstrate that eseb forms filamentous appendages on the surface of e. tarda and is required for biofilm formation by e. tarda in dulbecco's modified eagle's medium (dmem). biofilm formation by e. tarda in dmem does not requir ...	2015	26116669
nicotinate o-glucosylation is an evolutionarily metabolic trait important for seed germination under stress conditions in arabidopsis thaliana.	the glycosylation of nicotinate (na), a key intermediate of the nad salvage pathway, occurs widely in land plants. however, the physiological function of na glycosylation is not well understood in planta, and no gene encoding na glycosyltransferase has been reported to date. na glycosylation in arabidopsis thaliana occurs at either the n- or the o-position of the na molecule, and o-glucosylation appears to be unique to the brassicaceae. using gene-enzyme correlations focused on family 1 glycosyl ...	2015	26116607
genome, proteome and structure of a t7-like bacteriophage of the kiwifruit canker phytopathogen pseudomonas syringae pv. actinidiae.	pseudomonas syringae pv. actinidiae is an economically significant pathogen responsible for severe bacterial canker of kiwifruit (actinidia sp.). bacteriophages infecting this phytopathogen have potential as biocontrol agents as part of an integrated approach to the management of bacterial canker, and for use as molecular tools to study this bacterium. a variety of bacteriophages were previously isolated that infect p. syringae pv. actinidiae, and their basic properties were characterized to pro ...	2015	26114474
isolation and characterization of a novel pathogenesis-related protein gene (gmprp) with induced expression in soybean (glycine max) during infection with phytophthora sojae.	pathogenesis-related proteins (pr proteins) play crucial roles in the plant defense system. a novel prp gene was isolated from highly resistant soybean infected with phytophthora sojae (p. sojae) and was named gmprp (genbank accession number: km506762). the amino acid sequences of gmprp showed identities of 74%, 73%, 72% and 69% with prp proteins from vitis vinifera, populus trichocarpa, citrus sinensis and theobroma cacao, respectively. quantitative real-time reverse transcription pcr (qrt-pcr) ...	2015	26114301
a cupin domain-containing protein with a quercetinase activity (vdqase) regulates verticillium dahliae's pathogenicity and contributes to counteracting host defenses.	we previously identified rutin as part of potato root responses to its pathogen verticillium dahliae. rutin was directly toxic to the pathogen at doses greater than 160 μm, a threshold below which many v. dahliae pathogenicity-related genes were up-regulated. we identified and characterized a cupin domain-containing protein (vdqase) with a dioxygenase activity and a potential role in v. dahliae-potato interactions. the pathogenicity of vdqase knock-out mutants generated through agrobacterium tum ...	2015	26113857
the olive knot disease as a model to study the role of interspecies bacterial communities in plant disease.	there is an increasing interest in studying interspecies bacterial interactions in diseases of animals and plants as it is believed that the great majority of bacteria found in nature live in complex communities. plant pathologists have thus far mainly focused on studies involving single species or on their interactions with antagonistic competitors. a bacterial disease used as model to study multispecies interactions is the olive knot disease, caused by pseudomonas savastanoi pv. savastanoi (ps ...	2015	26113855
a geminivirus betasatellite damages the structural and functional integrity of chloroplasts leading to symptom formation and inhibition of photosynthesis.	geminivirus infection often causes severe vein clearing symptoms in hosts. recently a betasatellite has emerged as a key regulator of symptom induction. to understand the host-betasatellite interactions in the process of symptom development, a systematic study was carried out involving symptoms induced by a betasatellite associated with radish leaf curl disease (ralcb) in nicotiana benthamiana. it has been found that βc1 protein localized to chloroplasts of host cells, and ralcb lacking βc1, whi ...	2015	26113193
a comprehensive quantitative phosphoproteome analysis of rice in response to bacterial blight.	rice is a major crop worldwide. bacterial blight (bb) caused by xanthomonas oryzae pv. oryzae (xoo) has become one of the most devastating diseases for rice. it has been clear that phosphorylation plays essential roles in plant disease resistance. however, the role of phosphorylation is poorly understood in rice-xoo system. here, we report the first study on large scale enrichment of phosphopeptides and identification of phosphosites in rice before and 24 h after xoo infection.	2015	26112675
cellulose production in pseudomonas syringae pv. syringae: a compromise between epiphytic and pathogenic lifestyles.	genome sequencing and annotation have revealed a putative cellulose biosynthetic operon in the strain pseudomonas syringae pv. syringae umaf0158, the causal agent of bacterial apical necrosis. bioinformatics analyses and experimental methods were used to confirm the functionality of the cellulose biosynthetic operon. in addition, the results showed the contribution of the cellulose operon to important aspects of p. syringae pv. syringae biology, such as the formation of biofilms and adhesion to ...	2015	26109133
phytohormone involvement in the ustilago maydis- zea mays pathosystem: relationships between abscisic acid and cytokinin levels and strain virulence in infected cob tissue.	ustilago maydis is the causative agent of common smut of corn. early studies noted its ability to synthesize phytohormones and, more recently these growth promoting substances were confirmed as cytokinins (cks). cytokinins comprise a group of phytohormones commonly associated with actively dividing tissues. lab analyses identified variation in virulence between u. maydis dikaryon and solopathogen infections of corn cob tissue. samples from infected cob tissue were taken at sequential time points ...	2015	26107181
transcriptome analysis of the compatible interaction of tomato with verticillium dahliae using rna-sequencing.	tomato verticillium wilt is a soil-borne vascular disease caused by the necrotrophic fungus verticillium dahliae. although some understanding of plant defense mechanisms against v. dahliae infection has been gained for incompatible interactions, including identification of inducible resistant genes and defense signaling pathways, the genes and signaling pathways involved in the compatible interaction remain unclear. to investigate the molecular basis of the compatible interaction between tomato ...	2015	26106404
re-analysis of rna-seq transcriptome data reveals new aspects of gene activity in arabidopsis root hairs.	root hairs, tubular-shaped outgrowths from root epidermal cells, play important roles in the acquisition of nutrients and water, interaction with microbe, and in plant anchorage. as a specialized cell type, root hairs, especially in arabidopsis, provide a pragmatic research system for various aspects of studies. here, we re-analyzed the rna-seq transcriptome profile of arabidopsis root hair cells by tophat software and used cufflinks program to mine the differentially expressed genes. results sh ...	2015	26106402
two serine residues in pseudomonas syringae effector hopz1a are required for acetyltransferase activity and association with the host co-factor.	gram-negative bacteria inject type iii secreted effectors (t3ses) into host cells to manipulate the immune response. the yopj family effector hopz1a produced by the plant pathogen pseudomonas syringae possesses acetyltransferase activity and acetylates plant proteins to facilitate infection. using mass spectrometry, we identified a threonine residue, t346, as the main autoacetylation site of hopz1a. two neighboring serine residues, s349 and s351, are required for the acetyltransferase activity o ...	2015	26103463
pseudomonas putida-a versatile host for the production of natural products.	the biosynthesis of natural products by heterologous expression of biosynthetic pathways in amenable production strains enables biotechnological access to a variety of valuable compounds by conversion of renewable resources. pseudomonas putida has emerged as a microbial laboratory work horse, with elaborated techniques for cultivation and genetic manipulation available. beyond that, this bacterium offers several particular advantages with regard to natural product biosynthesis, notably a versati ...	2015	26099332
the methylome of soybean roots during the compatible interaction with the soybean cyst nematode.	the soybean cyst nematode (scn; heterodera glycines) induces the formation of a multinucleated feeding site, or syncytium, whose etiology includes massive gene expression changes. nevertheless, the genetic networks underlying gene expression control in the syncytium are poorly understood. dna methylation is a critical epigenetic mark that plays a key role in regulating gene expression. to determine the extent to which dna methylation is altered in soybean (glycine max) roots during the susceptib ...	2015	26099268
redox rhythm reinforces the circadian clock to gate immune response.	recent studies have shown that in addition to the transcriptional circadian clock, many organisms, including arabidopsis, have a circadian redox rhythm driven by the organism's metabolic activities. it has been hypothesized that the redox rhythm is linked to the circadian clock, but the mechanism and the biological significance of this link have only begun to be investigated. here we report that the master immune regulator npr1 (non-expressor of pathogenesis-related gene 1) of arabidopsis is a s ...	2015	26098366
epi-fingerprinting and epi-interventions for improved crop production and food quality.	increasing crop production at a time of rapid climate change represents the greatest challenge facing contemporary agricultural research. our understanding of the genetic control of yield derives from controlled field experiments designed to minimize environmental variance. in spite of these efforts there is substantial residual variability among plants attributable to genotype × environment interactions. recent advances in the field of epigenetics have revealed a plethora of gene control mechan ...	2015	26097484
a salt-regulated peptide derived from the cap superfamily protein negatively regulates salt-stress tolerance in arabidopsis.	high salinity has negative impacts on plant growth through altered water uptake and ion-specific toxicities. plants have therefore evolved an intricate regulatory network in which plant hormones play significant roles in modulating physiological responses to salinity. however, current understanding of the plant peptides involved in this regulatory network remains limited. here, we identified a salt-regulated peptide in arabidopsis. the peptide was 11 aa and was derived from the c terminus of a c ...	2015	26093145
temporal transcriptome profiling reveals expression partitioning of homeologous genes contributing to heat and drought acclimation in wheat (triticum aestivum l.).	hexaploid wheat (triticum aestivum) is a globally important crop. heat, drought and their combination dramatically reduce wheat yield and quality, but the molecular mechanisms underlying wheat tolerance to extreme environments, especially stress combination, are largely unknown. as an allohexaploid, wheat consists of three closely related subgenomes (a, b, and d), and was reported to show improved tolerance to stress conditions compared to tetraploid. but so far very little is known about how wh ...	2015	26092253
global transcriptional analysis of burkholderia pseudomallei high and low biofilm producers reveals insights into biofilm production and virulence.	chronic bacterial infections occur as a result of the infecting pathogen's ability to live within a biofilm, hence escaping the detrimental effects of antibiotics and the immune defense system. burkholderia pseudomallei, a gram-negative facultative pathogen, is distinctive in its ability to survive within phagocytic and non-phagocytic cells, to persist in vivo for many years and subsequently leading to relapse as well as the development of chronic disease. the capacity to persist has been attrib ...	2015	26092034
rna-seq analysis of resistant and susceptible potato varieties during the early stages of potato virus y infection.	potato virus y (pvy) is one of the most important plant viruses affecting potato production. the interactions between potato and pvy are complex and the outcome of the interactions depends on the potato genotype, the pvy strain, and the environmental conditions. a potato cultivar can induce resistance to a specific pvy strain, yet be susceptible to another. how a single potato cultivar responds to pvy in both compatible and incompatible interactions is not clear.	2015	26091899
hydrolysis of phytate and formation of inositol phosphate isomers without or with supplemented phytases in different segments of the digestive tract of broilers.	the objective was to characterise degradation of myo-inositol 1,2,3,4,5,6-hexakis (dihydrogen phosphate) (insp6) and formation of inositol phosphate (insp) isomers in different segments of the broiler digestive tract. influence of an aspergillus niger (phya) and two escherichia coli-derived (phye1 and phye2) phytases was also investigated. a total of 600 16-d-old broilers were allocated to forty floor pens (ten pens per treatment). low-p (5·2 g/kg dm) maize-soyabean meal-based diets were fed wit ...	2015	26090091
the knottin-like blufensin family regulates genes involved in nuclear import and the secretory pathway in barley-powdery mildew interactions.	plants have evolved complex regulatory mechanisms to control a multi-layered defense response to microbial attack. both temporal and spatial gene expression are tightly regulated in response to pathogen ingress, modulating both positive and negative control of defense. blufensins, small knottin-like peptides in barley, wheat, and rice, are highly induced by attack from fungal pathogens, in particular, the obligate biotrophic fungus, blumeria graminis f. sp. hordei (bgh), causal agent of barley p ...	2015	26089830
phylogenomics of xanthomonas field strains infecting pepper and tomato reveals diversity in effector repertoires and identifies determinants of host specificity.	bacterial spot disease of pepper and tomato is caused by four distinct xanthomonas species and is a severely limiting factor on fruit yield in these crops. the genetic diversity and the type iii effector repertoires of a large sampling of field strains for this disease have yet to be explored on a genomic scale, limiting our understanding of pathogen evolution in an agricultural setting. genomes of 67 xanthomonas euvesicatoria (xe), xanthomonas perforans (xp), and xanthomonas gardneri (xg) strai ...	2015	26089818
genome sequences of pseudomonas amygdali pv. tabaci strain atcc 11528 and pv. lachrymans strain 98a-744.	certain pathovars of pseudomonas amygdali, which is newly reclassified from pseudomonas syringae by dna-dna hybridization and ribotyping, cause many serious diseases of major crop plants. herein, we present draft genome sequences of p. amygdali pv. tabaci strain atcc 11528 and p. amygdali pv. lachrymans strain 98a-744.	2015	26089433
genome sequence of rhizobacterium serratia marcescens strain 90-166, which triggers induced systemic resistance and plant growth promotion.	the rhizobacterium serratia marcescens strain 90-166 elicits induced systemic resistance against plant pathogens and herbivores and promotes plant growth under greenhouse and field conditions. strain 90-166 secretes volatile compounds, siderophores, salicylic acid, and quorum-sensing autoinducers as bacterial determinants toward plant health. herein, we present its draft genome sequence.	2015	26089427
impact of plant domestication on rhizosphere microbiome assembly and functions.	the rhizosphere microbiome is pivotal for plant health and growth, providing defence against pests and diseases, facilitating nutrient acquisition and helping plants to withstand abiotic stresses. plants can actively recruit members of the soil microbial community for positive feedbacks, but the underlying mechanisms and plant traits that drive microbiome assembly and functions are largely unknown. domestication of plant species has substantially contributed to human civilization, but also cause ...	2015	26085172
impact of plant domestication on rhizosphere microbiome assembly and functions.	the rhizosphere microbiome is pivotal for plant health and growth, providing defence against pests and diseases, facilitating nutrient acquisition and helping plants to withstand abiotic stresses. plants can actively recruit members of the soil microbial community for positive feedbacks, but the underlying mechanisms and plant traits that drive microbiome assembly and functions are largely unknown. domestication of plant species has substantially contributed to human civilization, but also cause ...	2015	26085172
microrna-mediated regulation of gene expression in the response of rice plants to fungal elicitors.	micrornas (mirnas) are small non-coding rnas that have important regulatory functions in plant growth, development, and response to abiotic stress. increasing evidence also supports that plant mirnas contribute to immune responses to pathogens. here, we used deep sequencing of small rna libraries for global identification of rice mirnas that are regulated by fungal elicitors. we also describe 9 previously uncharacterized mirnas in rice. combined small rna and degradome analyses revealed regulato ...	2015	26083154
mitogen-activated protein kinase kinase 3 is required for regulation during dark-light transition.	plant growth and development are coordinately orchestrated by environmental cues and phytohormones. light acts as a key environmental factor for fundamental plant growth and physiology through photosensory phytochromes and underlying molecular mechanisms. although phytochromes are known to possess serine/threonine protein kinase activities, whether they trigger a signal transduction pathway via an intracellular protein kinase network remains unknown. in analyses of mitogen-activated protein kina ...	2015	26082029
a macrophage subversion factor is shared by intracellular and extracellular pathogens.	pathogenic bacteria have developed strategies to adapt to host environment and resist host immune response. several intracellular bacterial pathogens, including salmonella enterica and mycobacterium tuberculosis, share the horizontally-acquired mgtc virulence factor that is important for multiplication inside macrophages. mgtc is also found in pathogenic pseudomonas species. here we investigate for the first time the role of mgtc in the virulence of an extracellular pathogen, pseudomonas aerugin ...	2015	26080006
identification of the arabidopsis ram/mor signalling network: adding new regulatory players in plant stem cell maintenance and cell polarization.	the ram/mor signalling network of eukaryotes is a conserved regulatory module involved in co-ordination of stem cell maintenance, cell differentiation and polarity establishment. to date, no such signalling network has been identified in plants.	2015	26078466
layering genetic circuits to build a single cell, bacterial half adder.	gene regulation in biological systems is impacted by the cellular and genetic context-dependent effects of the biological parts which comprise the circuit. here, we have sought to elucidate the limitations of engineering biology from an architectural point of view, with the aim of compiling a set of engineering solutions for overcoming failure modes during the development of complex, synthetic genetic circuits.	2015	26078033