Publications

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
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
phylogenetic and variable-number tandem-repeat analyses identify nonpathogenic xanthomonas arboricola lineages lacking the canonical type iii secretion system.	xanthomonas arboricola is conventionally known as a taxon of plant-pathogenic bacteria that includes seven pathovars. this study showed that x. arboricola also encompasses nonpathogenic bacteria that cause no apparent disease symptoms on their hosts. the aim of this study was to assess the x. arboricola population structure associated with walnut, including nonpathogenic strains, in order to gain a better understanding of the role of nonpathogenic xanthomonads in walnut microbiota. a multilocus ...	2015	26048944
camalexin contributes to the partial resistance of arabidopsis thaliana to the biotrophic soilborne protist plasmodiophora brassicae.	camalexin has been reported to play defensive functions against several pathogens in arabidopsis. in this study, we investigated the possible role of camalexin accumulation in two arabidopsis genotypes with different levels of basal resistance to the compatible eh strain of the clubroot agent plasmodiophora brassicae. camalexin biosynthesis was induced in infected roots of both col-0 (susceptible) and bur-0 (partially resistant) accessions during the secondary phase of infection. however, the le ...	2015	26257750
feng shao: getting a sense for the defense.		2015	26195661
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
comparative secretomics reveals novel virulence-associated factors of vibrio parahaemolyticus.	vibrio parahaemolyticus is a causative agent of serious human seafood-borne gastroenteritis disease and even death. in this study, for the first time, we obtained the secretomic profiles of seven v. parahaemolyticus strains of clinical and food origins. the strains exhibited various toxic genotypes and phenotypes of antimicrobial susceptibility and heavy metal resistance, five of which were isolated from aquatic products in shanghai, china. fourteen common extracellular proteins were identified ...	2015	26236293
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
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
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
commentary: the absence of protein y4ys affects negatively the abundance of t3ss mesorhizobium loti secretin, rhcc2, in bacterial membranes.		2015	26236295
keeping control: the role of senescence and development in plant pathogenesis and defense.	many plant pathogens show interactions with host development. pathogens may modify plant development according to their nutritional demands. conversely, plant development influences pathogen growth. biotrophic pathogens often delay senescence to keep host cells alive, and resistance is achieved by senescence-like processes in the host. necrotrophic pathogens promote senescence in the host, and preventing early senescence is a resistance strategy of plants. for hemibiotrophic pathogens both patte ...	2015	27135337
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
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
the proteome of the outer membrane vesicles of an antarctic bacterium pseudomonas syringae lz4w.	outer membrane vesicles (omvs) of gram-negative bacteria are released during all growth phases and play an important role in bacterial physiology. they consist of lipids, proteins, lipopolysaccharides and other molecules. the omvs of the antarctic bacterium pseudomonas syringae lz 4w were isolated and identified their proteins. the mass spectral data set deposited with pride, accession number pxd 000221 is presented in this report. the proteins identified from the omvs of p. syringae lz4w, data ...	2015	26306312
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
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
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
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
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
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
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
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
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
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
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
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
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
structural and functional characterization of recombinant isoforms of the lentil lipid transfer protein.	the recombinant isoforms lc-ltp1 and lc-ltp3 of the lentil lipid transfer protein were overexpressed in e. coli cells. it was confirmed that both proteins are stabilized by four disulfide bonds and characterized by a high proportion of the α-helical structure. it was found that lc-ltp1 and lc-ltp3 possess antimicrobial activity and can bind fatty acids. both isoforms have the ability to bind specific ige from sera of patients with food allergies, which recognize similar epitopes of the major pea ...	2015	26483961
chemical products induce resistance to xanthomonas perforans in tomato.	the bacterial spot of tomato, caused by xanthomonas spp., is a very important disease, especially in the hot and humid periods of the year. the chemical control of the disease has not been very effective for a number of reasons. this study aimed to evaluate, under greenhouse conditions, the efficacy of leaf-spraying chemicals (acibenzolar-s-methyl (asm) (0.025 g.l(-1)), fluazinam (0.25 g.l(-1)), pyraclostrobin (0.08 g.l(-1)), pyraclostrobin + methiran (0.02 g.l(-1) + 2.2 g.l(-1)), copper oxychlo ...	2015	26413050
characterization of the hrpz gene from pseudomonas syringae pv. maculicola m2.	pseudomonas syringae pv. maculicola is a natural pathogen of members of the brassicaceae plant family. using a transposon-based mutagenesis strategy in pseudomonas syringaepv. maculicola m2 (psmm2), we conducted a genetic screen to identify mutants that were capable of growing in m9 medium supplemented with a crude extract from the leaves of arabidopsis thaliana. a mutant containing a transposon insertion in the hrpz gene (psmmut8) was unable to infect adult plants from arabidopsis thaliana or b ...	2015	26413080
profiling of spatial metabolite distributions in wheat leaves under normal and nitrate limiting conditions.	the control and interaction between nitrogen and carbon assimilatory pathways is essential in both photosynthetic and non-photosynthetic tissue in order to support metabolic processes without compromising growth. physiological differences between the basal and mature region of wheat (triticum aestivum) primary leaves confirmed that there was a change from heterotrophic to autotrophic metabolism. fourier transform infrared (ft-ir) spectroscopy confirmed the suitability and phenotypic reproducibil ...	2015	25680480
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
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
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
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
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
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
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
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 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
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
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
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
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
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
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
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
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
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
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
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
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
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
negative regulation of aba signaling by wrky33 is critical for arabidopsis immunity towards botrytis cinerea 2100.	the arabidopsis mutant wrky33 is highly susceptible to botrytis cinerea. we identified >1680 botrytis-induced wrky33 binding sites associated with 1576 arabidopsis genes. transcriptional profiling defined 318 functional direct target genes at 14 hr post inoculation. comparative analyses revealed that wrky33 possesses dual functionality acting either as a repressor or as an activator in a promoter-context dependent manner. we confirmed known wrky33 targets involved in hormone signaling and phy ...	2015	26076231
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
high-throughput sequencing identifies novel and conserved cucumber (cucumis sativus l.) micrornas in response to cucumber green mottle mosaic virus infection.	seedlings of cucumis sativus l. (cv. 'zhongnong 16') were artificially inoculated with cucumber green mottle mosaic virus (cgmmv) at the three-true-leaf stage. leaf and flower samples were collected at different time points post-inoculation (10, 30 and 50 d), and processed by high throughput sequencing analysis to identify candidate mirna sequences. bioinformatic analysis using screening criteria, and secondary structure prediction, indicated that 8 novel and 23 known mirnas (including 15 mirnas ...	2015	26076360
tomato sl3-mmp, a member of the matrix metalloproteinase family, is required for disease resistance against botrytis cinerea and pseudomonas syringae pv. tomato dc3000.	matrix metalloproteinases (mmps) are a family of zinc-dependent endopeptidases. mmps have been characterized in detail in mammals and shown to play key roles in many physiological and pathological processes. although mmps in some plant species have been identified, the function of mmps in biotic stress responses remains elusive.	2015	26070456
maize embryo sac family peptides interact differentially with pollen tubes and fungal cells.	embryo sac1-4 (es1-4) peptides belong to the defensin subgroup of cysteine-rich peptides known to mediate pollen tube burst in zea mays (maize). es1-4 are reported here to also be capable of inhibiting germination and growth of the maize fungal pathogens fusarium graminearum and ustilago maydis at higher concentrations. dividing the peptides into smaller pieces showed that a 15-amino-acid peptide located in a highly variable loop region lacking similarity to other defensins or defensin-like pept ...	2015	26071527
salicylic acid biosynthesis is enhanced and contributes to increased biotrophic pathogen resistance in arabidopsis hybrids.	heterosis, the phenotypic superiority of a hybrid over its parents, has been demonstrated for many traits in arabidopsis thaliana, but its effect on defence remains largely unexplored. here, we show that hybrids between some a. thaliana accessions show increased resistance to the biotrophic bacterial pathogen pseudomonas syringae pv. tomato (pst) dc3000. comparisons of transcriptomes between these hybrids and their parents after inoculation reveal that several key salicylic acid (sa) biosynthesi ...	2015	26065719
widespread occurrence of n6-methyladenosine in bacterial mrna.	n(6)-methyladenosine (m(6)a) is the most abundant internal modification in eukaryotic messenger rna (mrna). recent discoveries of demethylases and specific binding proteins of m(6)a as well as m(6)a methylomes obtained in mammals, yeast and plants have revealed regulatory functions of this rna modification. although m(6)a is present in the ribosomal rna of bacteria, its occurrence in mrna still remains elusive. here, we have employed ultra-high pressure liquid chromatography coupled with triple- ...	2015	26068471
the ida/ida-like and pip/pip-like gene families in arabidopsis: phylogenetic relationship, expression patterns, and transcriptional effect of the pipl3 peptide.	peptide ligands play crucial roles in the life cycle of plants by modulating the innate immunity against pathogens and regulating growth and developmental processes. one well-studied example is inflorescence deficient in abscission (ida), which controls floral organ abscission and lateral root emergence in arabidopsis thaliana. ida belongs to a family of five additional ida-like (idl) members that have all been suggested to be involved in regulation of arabidopsis development. here we present th ...	2015	26062745
pseudomonas syringae pv. tomato dc3000 type iii secretion effector polymutants reveal an interplay between hopad1 and avrptob.	the bacterial pathogen pseudomonas syringae pv. tomato dc3000 suppresses the two-tiered plant innate immune system by injecting a complex repertoire of type iii secretion effector (t3e) proteins. beyond redundancy and interplay, individual t3es may interact with multiple immunity-associated proteins, rendering their analysis challenging. we constructed a pst dc3000 polymutant lacking all 36 t3es and restored individual t3es or their mutants to explore the interplay among t3es. the weakly express ...	2015	26067603
copper tolerance and virulence in bacteria.	copper (cu) is an essential trace element for all aerobic organisms. it functions as a cofactor in enzymes that catalyze a wide variety of redox reactions due to its ability to cycle between two oxidation states, cu(i) and cu(ii). this same redox property of copper has the potential to cause toxicity if copper homeostasis is not maintained. studies suggest that the toxic properties of copper are harnessed by the innate immune system of the host to kill bacteria. to counter such defenses, bacteri ...	2015	25652326
specific detection and identification of american mulberry-infecting and italian olive-associated strains of xylella fastidiosa by polymerase chain reaction.	xylella fastidiosa causes bacterial leaf scorch in many landscape trees including elm, oak, sycamore and mulberry, but methods for specific identification of a particular tree host species-limited strain or differentiation of tree-specific strains are lacking. it is also unknown whether a particular landscape tree-infecting x. fastidiosa strain is capable of infecting multiple landscape tree species in an urban environment. we developed two pcr primers specific for mulberry-infecting strains of ...	2015	26061051
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
localization and expression of eds5h a homologue of the sa transporter eds5.	an important signal transduction pathway in plant defence depends on the accumulation of salicylic acid (sa). sa is produced in chloroplasts and the multidrug and toxin extrusion transporter enhanced disease susceptibility5 (eds5; at4g39030) is necessary for the accumulation of sa after pathogen and abiotic stress. eds5 is localized at the chloroplast and functions in transporting sa from the chloroplast to the cytoplasm. eds5 has a homologue called eds5h (eds5 homologue; at2g21340) but its rela ...	2015	26055508
plant and animal organelles in cell death.		2015	26116839
cpsf30 at the interface of alternative polyadenylation and cellular signaling in plants.	post-transcriptional processing, involving cleavage of precursor messenger rna (pre mrna), and further incorporation of poly(a) tail to the 3' end is a key step in the expression of genetic information. alternative polyadenylation (apa) serves as an important check point for the regulation of gene expression. recent studies have shown widespread prevalence of apa in diverse systems. a considerable amount of research has been done in characterizing different subunits of so-called cleavage and pol ...	2015	26061761
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
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
subfamily-specific fluorescent probes for cysteine proteases display dynamic protease activities during seed germination.	cysteine proteases are an important class of enzymes implicated in both developmental and defense-related programmed cell death and other biological processes in plants. because there are dozens of cysteine proteases that are posttranslationally regulated by processing, environmental conditions, and inhibitors, new methodologies are required to study these pivotal enzymes individually. here, we introduce fluorescence activity-based probes that specifically target three distinct cysteine protease ...	2015	26048883
virulence factors of erwinia amylovora: a review.	erwinia amylovora, a gram negative bacteria of the enterobacteriaceae family, is the causal agent of fire blight, a devastating plant disease affecting a wide range of host species within rosaceae and a major global threat to commercial apple and pear production. among the limited number of control options currently available, prophylactic application of antibiotics during the bloom period appears the most effective. pathogen cells enter plants through the nectarthodes of flowers and other natur ...	2015	26057748
comparative transcriptome and itraq proteome analyses of citrus root responses to candidatus liberibacter asiaticus infection.	root samples of 'sanhu' red tangerine trees infected with and without candidatus liberibacter asiaticus (clas) were collected at 50 days post inoculation and subjected to rna-sequencing and isobaric tags for relative and absolute quantification (itraq) to profile the differentially expressed genes (degs) and proteins (deps), respectively. quantitative real-time pcr was subsequently used to confirm the expression of 16 selected degs. results showed that a total of 3956 genes and 78 proteins were ...	2015	26046530
the first complete chloroplast genome sequences in actinidiaceae: genome structure and comparative analysis.	actinidia chinensis is an important economic plant belonging to the basal lineage of the asterids. availability of a complete actinidia chloroplast genome sequence is crucial to understanding phylogenetic relationships among major lineages of angiosperms and facilitates kiwifruit genetic improvement. we report here the complete nucleotide sequences of the chloroplast genomes for actinidia chinensis and a. chinensis var deliciosa obtained through de novo assembly of illumina paired-end reads prod ...	2015	26046631
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
correction for bartoli et al., whole-genome sequencing of 10 pseudomonas syringae strains representing different host range spectra.		2015	26044440
draft genome sequence of pseudomonas syringae pv. persicae ncppb 2254.	pseudomonas syringae pv. persicae is a pathogen that causes bacterial decline of stone fruit. here, we report the draft genome sequence for p. syringae pv. persicae, which was isolated from prunus persica.	2015	26044420
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
protein phosphatase 2a regulatory subunits affecting plant innate immunity, energy metabolism, and flowering time--joint functions among b'η subfamily members.	protein phosphatase 2a (pp2a) is a heterotrimeric complex comprising a catalytic, scaffolding, and regulatory subunit. the regulatory subunits are essential for substrate specificity and localization of the complex and are classified into b/b55, b', and b" non-related families in higher plants. in arabidopsis thaliana, the close paralogs b'η, b'θ, b'γ, and b'ζ were further classified into a subfamily of b' called b'η. here we present results that consolidate the evidence for a role of the b'η su ...	2015	26039486
the arabidopsis thaliana tcp transcription factors: a broadening horizon beyond development.	the tcp family of transcription factors is named after the first 4 characterized members, namely teosinte branched1 (tb1) from maize (zea mays), cycloidea (cyc) from snapdragon (antirrhinum majus), as well as proliferating cell nuclear antigen factor1 (pcf1) and pcf2 from rice (oryza sativa). phylogenic analysis of this plant-specific protein family unveils a conserved bhlh-containing dna-binding motif known as the tcp domain. in accordance with the structure of this shared domain, tcp proteins ...	2015	26039357
oomycete interactions with plants: infection strategies and resistance principles.	the oomycota include many economically significant microbial pathogens of crop species. understanding the mechanisms by which oomycetes infect plants and identifying methods to provide durable resistance are major research goals. over the last few years, many elicitors that trigger plant immunity have been identified, as well as host genes that mediate susceptibility to oomycete pathogens. the mechanisms behind these processes have subsequently been investigated and many new discoveries made, ma ...	2015	26041933
in silico identification of ampylating enzymes and study of their divergent evolution.	ampylation is a novel post-translational modification (ptm) involving covalent attachment of an amp moiety to threonine/tyrosine side chains of a protein. ampylating enzymes belonging to three different families, namely fic/doc, gs-atase and drra have been experimentally characterized. involvement of these novel enzymes in a myriad of biological processes makes them interesting candidates for genome-wide search. we have used svm and hmm to develop a computational protocol for identification of a ...	2015	26039278
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
overexpression of an ap2/erf type transcription factor oserebp1 confers biotic and abiotic stress tolerance in rice.	ap2/erf-type transcription factors regulate important functions of plant growth and development as well as responses to environmental stimuli. a rice ap2/erf transcription factor, oserebp1 is a downstream component of a signal transduction pathway in a specific interaction between rice (oryza sativa) and its bacterial pathogen, xoo (xanthomonas oryzae pv. oryzae). constitutive expression of oserebp1 in rice driven by maize ubiquitin promoter did not affect normal plant growth. microarray analysi ...	2015	26035591
investigating the association between flowering time and defense in the arabidopsis thaliana-fusarium oxysporum interaction.	plants respond to pathogens either by investing more resources into immunity which is costly to development, or by accelerating reproductive processes such as flowering time to ensure reproduction occurs before the plant succumbs to disease. in this study we explored the link between flowering time and pathogen defense using the interaction between arabidopsis thaliana and the root infecting fungal pathogen fusarium oxysporum. we report that f. oxysporum infection accelerates flowering time and ...	2015	26034991
screening currency notes for microbial pathogens and antibiotic resistance genes using a shotgun metagenomic approach.	fomites are a well-known source of microbial infections and previous studies have provided insights into the sojourning microbiome of fomites from various sources. paper currency notes are one of the most commonly exchanged objects and its potential to transmit pathogenic organisms has been well recognized. approaches to identify the microbiome associated with paper currency notes have been largely limited to culture dependent approaches. subsequent studies portrayed the use of 16s ribosomal rna ...	2015	26035208
the arabidopsis pep-pepr system is induced by herbivore feeding and contributes to ja-mediated plant defence against herbivory.	a number of plant endogenous elicitors have been identified that induce pattern-triggered immunity upon perception. in arabidopsis thaliana eight small precursor proteins, called propeps, are thought to be cleaved upon danger to release eight peptides known as the plant elicitor peptides peps. as the expression of some propeps is induced upon biotic stress and perception of any of the eight peps triggers a defence response, they are regarded as amplifiers of immunity. besides the induction of de ...	2015	26034129
induced autoprocessing of the cytopathic makes caterpillars floppy-like effector domain of the vibrio vulnificus martx toxin.	the multifunctional-autoprocessing repeats-in-toxin (martx(vv)) toxin that harbours a varied repertoire of effector domains is the primary virulence factor of vibrio vulnificus. although ubiquitously present among biotype i toxin variants, the 'makes caterpillars floppy-like' effector domain (mcf(vv)) is previously unstudied. using transient expression and protein delivery, mcf(vv) and mcf(ah) from the aeromonas hydrophila martx(ah)) toxin are shown for the first time to induce cell rounding. al ...	2015	25912102
the udp-glucose: glycoprotein glucosyltransferase (uggt), a key enzyme in er quality control, plays a significant role in plant growth as well as biotic and abiotic stress in arabidopsis thaliana.	udp-glucose: glycoprotein glucosyltransferase (uggt) is a key player in the quality control mechanism (er-qc) that newly synthesized glycoproteins undergo in the er. it has been shown that the uggt arabidopsis orthologue is involved in er-qc; however, its role in plant physiology remains unclear.	2015	26017403
capping protein integrates multiple mamp signalling pathways to modulate actin dynamics during plant innate immunity.	plants and animals perceive diverse microbe-associated molecular patterns (mamps) via pattern recognition receptors and activate innate immune signalling. the actin cytoskeleton has been suggested as a target for innate immune signalling and a key transducer of cellular responses. however, the molecular mechanisms underlying actin remodelling and the precise functions of these rearrangements during innate immunity remain largely unknown. here we demonstrate rapid actin remodelling in response to ...	2015	26018794
phosphatidic acid produced by phospholipase d promotes rna replication of a plant rna virus.	eukaryotic positive-strand rna [(+)rna] viruses are intracellular obligate parasites replicate using the membrane-bound replicase complexes that contain multiple viral and host components. to replicate, (+)rna viruses exploit host resources and modify host metabolism and membrane organization. phospholipase d (pld) is a phosphatidylcholine- and phosphatidylethanolamine-hydrolyzing enzyme that catalyzes the production of phosphatidic acid (pa), a lipid second messenger that modulates diverse intr ...	2015	26020241
alginate-modifying enzymes: biological roles and biotechnological uses.	alginate denotes a group of industrially important 1-4-linked biopolymers composed of the c-5-epimers β-d-mannuronic acid (m) and α-l-guluronic acid (g). the polysaccharide is manufactured from brown algae where it constitutes the main structural cell wall polymer. the physical properties of a given alginate molecule, e.g., gel-strength, water-binding capacity, viscosity and biocompatibility, are determined by polymer length, the relative amount and distribution of g residues and the acetyl cont ...	2015	26074905
mechanisms and ecological consequences of plant defence induction and suppression in herbivore communities.	plants are hotbeds for parasites such as arthropod herbivores, which acquire nutrients and energy from their hosts in order to grow and reproduce. hence plants are selected to evolve resistance, which in turn selects for herbivores that can cope with this resistance. to preserve their fitness when attacked by herbivores, plants can employ complex strategies that include reallocation of resources and the production of defensive metabolites and structures. plant defences can be either prefabricate ...	2015	26019168