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downy mildew resistance induced by trichoderma harzianum t39 in susceptible grapevines partially mimics transcriptional changes of resistant genotypes.downy mildew, caused by plasmopara viticola, is one of the most severe diseases of grapevine and is commonly controlled by fungicide treatments. the beneficial microorganism trichoderma harzianum t39 (t39) can induce resistance to downy mildew, although the molecular events associated with this process have not yet been elucidated in grapevine. a next generation rna sequencing (rna-seq) approach was used to study global transcriptional changes associated with resistance induced by t39 in vitis v ...201223173562
genome sequence of the necrotrophic fungus penicillium digitatum, the main postharvest pathogen of citrus.penicillium digitatum is a fungal necrotroph causing a common citrus postharvest disease known as green mold. in order to gain insight into the genetic bases of its virulence mechanisms and its high degree of host-specificity, the genomes of two p. digitatum strains that differ in their antifungal resistance traits have been sequenced and compared with those of 28 other pezizomycotina.201223171342
conservation of nlr-triggered immunity across plant lineages.the nucleotide-binding domain and leucine-rich repeat (nlr) family of plant receptors detects pathogen-derived molecules, designated effectors, inside host cells and mediates innate immune responses to pathogenic invaders. genetic evidence revealed species-specific coevolution of many nlrs with effectors from host-adapted pathogens, suggesting that the specificity of these nlrs is restricted to the host or closely related plant species. however, we report that an nlr immune receptor (mla1) from ...201223175786
ethylene synthesis and regulated expression of recombinant protein in synechocystis sp. pcc 6803.the ethylene-forming enzyme (efe) from pseudomonas syringae catalyzes the synthesis of ethylene which can be easily detected in the headspace of closed cultures. a synthetic codon-optimized gene encoding n-terminal his-tagged efe (efeh) was expressed in synechocystis sp. pcc 6803 (synechocystis) and escherichia coli (e. coli) under the control of diverse promoters in a self-replicating broad host-range plasmid. ethylene synthesis was stably maintained in both organisms in contrast to earlier wor ...201223185630
synergies between rna degradation and trans-translation in streptococcus pneumoniae: cross regulation and co-transcription of rnase r and smpb.ribonuclease r (rnase r) is an exoribonuclease that recognizes and degrades a wide range of rna molecules. it is a stress-induced protein shown to be important for the establishment of virulence in several pathogenic bacteria. rnase r has also been implicated in the trans-translation process. transfer-messenger rna (tmrna/ssra rna) and smpb are the main effectors of trans-translation, an rna and protein quality control system that resolves challenges associated with stalled ribosomes on non-stop ...201223167513
gel-based and gel-free quantitative proteomics approaches at a glance.two-dimensional gel electrophoresis (2-de) is widely applied and remains the method of choice in proteomics; however, pervasive 2-de-related concerns undermine its prospects as a dominant separation technique in proteome research. consequently, the state-of-the-art shotgun techniques are slowly taking over and utilising the rapid expansion and advancement of mass spectrometry (ms) to provide a new toolbox of gel-free quantitative techniques. when coupled to ms, the shotgun proteomic pipeline can ...201223213324
identification of two novel endoplasmic reticulum body-specific integral membrane proteins.the endoplasmic reticulum (er) body, a large compartment specific to the brassicales, accumulates β-glucosidase and possibly plays a role in the defense against pathogens and herbivores. although the er body is a subdomain of the er, it is unclear whether any er body-specific membrane protein exists. in this study, we identified two integral membrane proteins of the er body in arabidopsis (arabidopsis thaliana) and termed them membrane protein of endoplasmic reticulum body1 (meb1) and meb2. in a ...201223166355
identification of two novel endoplasmic reticulum body-specific integral membrane proteins.the endoplasmic reticulum (er) body, a large compartment specific to the brassicales, accumulates β-glucosidase and possibly plays a role in the defense against pathogens and herbivores. although the er body is a subdomain of the er, it is unclear whether any er body-specific membrane protein exists. in this study, we identified two integral membrane proteins of the er body in arabidopsis (arabidopsis thaliana) and termed them membrane protein of endoplasmic reticulum body1 (meb1) and meb2. in a ...201223166355
the ubiquitin ligase pub22 targets a subunit of the exocyst complex required for pamp-triggered responses in arabidopsis.plant pathogens are perceived by pattern recognition receptors, which are activated upon binding to pathogen-associated molecular patterns (pamps). ubiquitination and vesicle trafficking have been linked to the regulation of immune signaling. however, little information exists about components of vesicle trafficking involved in immune signaling and the mechanisms that regulate them. in this study, we identified arabidopsis thaliana exo70b2, a subunit of the exocyst complex that mediates vesicle ...201223170036
transcription factor-dependent nuclear localization of a transcriptional repressor in jasmonate hormone signaling.the plant hormone jasmonate (ja) plays an important role in regulating growth, development and immunity. a key step in ja signaling is ligand-dependent assembly of a coreceptor complex consisting of the f-box protein coi1 and jaz transcriptional repressors. assembly of this receptor complex results in proteasome-mediated degradation of jaz repressors, which at resting state bind to and repress the myc transcription factors. although the ja receptor complex is believed to function within the nucl ...201223169619
co-expression analysis identifies putative targets for cbp60g and sard1 regulation.salicylic acid is a critical signalling component in plant defence responses. in arabidopsis, isochorismate synthase encoded by sid2 is essential for the biosynthesis of salicylic acid in response to biotic challenges. recently, both the calmodulin binding protein cbp60g and its closest homolog, the non-calmodulin binding sard1, have been shown to bind to the promoter region of sid2. loss of both cbp60g and sard1 severely impacts the plants ability to produce sa in response to bacterial inoculat ...201223153277
nitric oxide-dependent posttranslational modification in plants: an update.nitric oxide (no) has been demonstrated as an essential regulator of several physiological processes in plants. the understanding of the molecular mechanism underlying its critical role constitutes a major field of research. no can exert its biological function through different ways, such as the modulation of gene expression, the mobilization of second messengers, or interplays with protein kinases. besides this signaling events, no can be responsible of the posttranslational modifications (ptm ...201223203119
a u-box e3 ubiquitin ligase, pub20, interacts with the arabidopsis g-protein β subunit, agb1.an arabidopsis u-box e3 ubiquitin ligase plant u-box 20 (pub20; alternatively called atcmpg1) was identified as a possible interactor of the arabidopsis g-protein β subunit, agb1, by yeast two-hybrid screening. a bimolecular fluorescence complementation (bifc) assay showed that pub20 interacted with agb1 in the nuclei and the cytosol. the expression levels of pub20 and its closest homolog, pub21 were stable under many conditions. gus driven by the pub20 promoter was active in anthers, pollen, pr ...201223166612
the impact of global change factors on redox signaling underpinning stress tolerance. 201223151347
the impact of global change factors on redox signaling underpinning stress tolerance. 201223151347
structure of the type iii secretion effector protein exou in complex with its chaperone spcu.disease causing bacteria often manipulate host cells in a way that facilitates the infectious process. many pathogenic gram-negative bacteria accomplish this by using type iii secretion systems. in these complex secretion pathways, bacterial chaperones direct effector proteins to a needle-like secretion apparatus, which then delivers the effector protein into the host cell cytosol. the effector protein exou and its chaperone spcu are components of the pseudomonas aeruginosa type iii secretion sy ...201223166655
linking ligand perception by pepr pattern recognition receptors to cytosolic ca2+ elevation and downstream immune signaling in plants.little is known about molecular steps linking perception of pathogen invasion by cell surface sentry proteins acting as pattern recognition receptors (prrs) to downstream cytosolic ca(2+) elevation, a critical step in plant immune signaling cascades. some prrs recognize molecules (such as flagellin) associated with microbial pathogens (pathogen-associated molecular patterns, pamps), whereas others bind endogenous plant compounds (damage-associated molecular patterns, damps) such as peptides rele ...201223150556
structure of the catalytic domain of the salmonella virulence factor ssei.ssei is secreted into host cells by salmonella and contributes to the establishment of systemic infections. the crystal structure of the c-terminal domain of ssei has been solved to 1.70 å resolution, revealing it to be a member of the cysteine protease superfamily with a catalytic triad consisting of cys178, his216 and asp231 that is critical to its virulence activities. structure-based analysis revealed that ssei is likely to possess either acyl hydrolase or acyltransferase activity, placing t ...201223151626
arabidopsis actin-depolymerizing factor-4 links pathogen perception, defense activation and transcription to cytoskeletal dynamics.the primary role of actin-depolymerizing factors (adfs) is to sever filamentous actin, generating pointed ends, which in turn are incorporated into newly formed filaments, thus supporting stochastic actin dynamics. arabidopsis adf4 was recently shown to be required for the activation of resistance in arabidopsis following infection with the phytopathogenic bacterium pseudomonas syringae pv. tomato dc3000 (pst) expressing the effector protein avrpphb. herein, we demonstrate that the expression of ...201223144618
the blade-on-petiole genes of arabidopsis are essential for resistance induced by methyl jasmonate.npr1 is a gene of arabidopsis thaliana required for the perception of salicylic acid. this perception triggers a defense response and negatively regulates the perception of jasmonates. surprisingly, the application of methyl jasmonate also induces resistance, and npr1 is also suspected to be relevant. since an allelic series of npr1 was recently described, the behavior of these alleles was tested in response to methyl jasmonate.201223116333
the salicylic acid dependent and independent effects of nmd in plants.in eukaryotes, nonsense-mediated mrna decay (nmd) targets aberrant and selected non-aberrant mrnas for destruction. a recent screen for mrnas showing increased abundance in arabidopsis nmd-deficient mutants revealed that most are associated with the salicylic acid (sa)-mediated defense pathway. mrnas with conserved peptide upstream open reading frames (cpuorfs or cuorfs) are hugely overrepresented among the smaller class of nmd-regulated transcripts not associated with sa. here we show that the ...201222990450
the maize cystatin cc9 interacts with apoplastic cysteine proteases.in a recent study we identified corn cystain9 (cc9) as a novel compatibility factor for the interaction of the biotrophic smut fungus ustilago maydis with its host plant maize. cc9 is transcriptionally induced during the compatible interaction with u. maydis and localizes in the maize apoplast where it inhibits apoplastic papain-like cysteine proteases. the proteases are activated during incompatible interaction and salicylic acid (sa) treatment and, in turn, are sufficient to induce sa signalin ...201222960758
chemical inhibitors of the type three secretion system: disarming bacterial pathogens.the recent and dramatic rise of antibiotic resistance among bacterial pathogens underlies the fear that standard treatments for infectious disease will soon be largely ineffective. resistance has evolved against nearly every clinically used antibiotic, and in the near future, we may be hard-pressed to treat bacterial infections previously conquered by "magic bullet" drugs. while traditional antibiotics kill or slow bacterial growth, an important emerging strategy to combat pathogens seeks to blo ...201222850518
probing, by self-assembly, the number of potential binding sites for minor protein subunits in the procapsid of double-stranded rna bacteriophage φ6.the double-stranded rna bacteriophage φ6 is an extensively studied prokaryotic model system for virus assembly. there are established in vitro assembly protocols available for the φ6 system for obtaining infectious particles from purified protein and rna constituents. the polymerase complex is a multifunctional nanomachine that replicates, transcribes, and translocates viral rna molecules in a highly specific manner. the complex is composed of (i) the major structural protein (p1), forming a t=1 ...201222933292
characterization of a ferrous iron-responsive two-component system in nontypeable haemophilus influenzae.nontypeable haemophilus influenzae (nthi), an opportunistic pathogen that is commonly found in the human upper respiratory tract, has only four identified two-component signal transduction systems. one of these, an ortholog to the qsebc (quorum-sensing escherichia coli) system, was characterized. this system, designated firrs, was found to be transcribed in an operon with a gene encoding a small, predicted periplasmic protein with an unknown function, ygiw. the ygiw-firrs operon exhibited a uniq ...201222961857
constitutive expression of mammalian nitric oxide synthase in tobacco plants triggers disease resistance to pathogens.nitric oxide (no) is known for its role in the activation of plant defense responses. to examine the involvement and mode of action of no in plant defense responses, we introduced calmodulin-dependent mammalian neuronal nitric oxide synthase (nnos), which controls the camv35s promoter, into wild-type and nahg tobacco plants. constitutive expression of nnos led to no production and triggered spontaneous induction of leaf lesions. transgenic plants accumulated high amounts of h(2)o(2), with catala ...201223124383
constitutively active mitogen-activated protein kinase versions reveal functions of arabidopsis mpk4 in pathogen defense signaling.plant mitogen-activated protein kinases (mapks) are involved in important processes, including stress signaling and development. in a functional yeast screen, we identified mutations that render arabidopsis thaliana mapks constitutively active (ca). importantly, ca-mapks maintain their specificity toward known activators and substrates. as a proof-of-concept, arabidopsis mapk4 (mpk4) function in plant immunity was investigated. in agreement with the phenotype of mpk4 mutants, ca-mpk4 plants were ...201223115249
sulfonamides identified as plant immune-priming compounds in high-throughput chemical screening increase disease resistance in arabidopsis thaliana.plant activators are agrochemicals that protect crops from diseases by activating the plant immune system. to isolate lead compounds for use as practical plant activators, we screened two different chemical libraries composed of various bioactive substances by using an established screening procedure that can selectively identify immune-priming compounds. we identified and characterized a group of sulfonamide compounds - sulfameter, sulfamethoxypyridazine, sulfabenzamide, and sulfachloropyridazi ...201223118736
ter-dependent stress response systems: novel pathways related to metal sensing, production of a nucleoside-like metabolite, and dna-processing.the mode of action of the bacterial ter cluster and tela genes, implicated in natural resistance to tellurite and other xenobiotic toxic compounds, pore-forming colicins and several bacteriophages, has remained enigmatic for almost two decades. using comparative genomics, sequence-profile searches and structural analysis we present evidence that the ter gene products and their functional partners constitute previously underappreciated, chemical stress response and anti-viral defense systems of b ...201223044854
systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks.physiological responses, developmental programs, and cellular functions rely on complex networks of interactions at different levels and scales. systems biology brings together high-throughput biochemical, genetic, and molecular approaches to generate omics data that can be analyzed and used in mathematical and computational models toward uncovering these networks on a global scale. various approaches, including transcriptomics, proteomics, interactomics, and metabolomics, have been employed to ...201223110892
dynamics of membrane potential variation and gene expression induced by spodoptera littoralis, myzus persicae, and pseudomonas syringae in arabidopsis.biotic stress induced by various herbivores and pathogens invokes plant responses involving different defense mechanisms. however, we do not know whether different biotic stresses share a common response or which signaling pathways are involved in responses to different biotic stresses. we investigated the common and specific responses of arabidopsis thaliana to three biotic stress agents: spodoptera littoralis, myzus persicae, and the pathogen pseudomonas syringae.201223118859
glutamate receptor homologs in plants: functions and evolutionary origins.the plant glutamate-like receptor homologs (glrs) are homologs of mammalian ionotropic glutamate receptors (iglurs) which were discovered more than 10 years ago, and are hypothesized to be potential amino acid sensors in plants. although initial progress on this gene family has been hampered by gene redundancy and technical issues such as gene toxicity; genetic, pharmacological, and electrophysiological approaches are starting to uncover the functions of this protein family. in parallel, there h ...201223115559
silencing and innate immunity in plant defense against viral and non-viral pathogens.the frontline of plant defense against non-viral pathogens such as bacteria, fungi and oomycetes is provided by transmembrane pattern recognition receptors that detect conserved pathogen-associated molecular patterns (pamps), leading to pattern-triggered immunity (pti). to counteract this innate defense, pathogens deploy effector proteins with a primary function to suppress pti. in specific cases, plants have evolved intracellular resistance (r) proteins detecting isolate-specific pathogen effec ...201223202495
diuretics prime plant immunity in arabidopsis thaliana.plant activators are agrochemicals that activate the plant immune system, thereby enhancing disease resistance. due to their prophylactic and durable effects on a wide spectrum of diseases, plant activators can provide synergistic crop protection when used in combination with traditional pest controls. although plant activators have achieved great success in wet-rice farming practices in asia, their use is still limited. to isolate novel plant activators applicable to other crops, we screened a ...201223144763
nad: not just a pawn on the board of plant-pathogen interactions.many metabolic processes that occur in living cells involve oxido-reduction (redox) chemistry underpinned by redox compounds such as glutathione, ascorbate and/or pyridine nucleotides. among these redox carriers, nicotinamide adenine dinucleotide (nad) is the cornerstone of cellular oxidations along catabolism and is therefore essential for plant growth and development. in addition to its redox role, there is now compelling evidence that nad is a signal molecule controlling crucial functions lik ...201223104110
nad: not just a pawn on the board of plant-pathogen interactions.many metabolic processes that occur in living cells involve oxido-reduction (redox) chemistry underpinned by redox compounds such as glutathione, ascorbate and/or pyridine nucleotides. among these redox carriers, nicotinamide adenine dinucleotide (nad) is the cornerstone of cellular oxidations along catabolism and is therefore essential for plant growth and development. in addition to its redox role, there is now compelling evidence that nad is a signal molecule controlling crucial functions lik ...201223104110
putative role of proteins involved in detoxification of reactive oxygen species in the early response to gravitropic stimulation of poplar stems.gravity perception and gravitropic response are essential for plant development. in herbaceous species it is widely accepted that one of the primary events in gravity perception involves the displacement of amyloplasts within specialized cells. however the signaling cascade leading to stem reorientation is not fully known especially in woody species in which primary and secondary growth occur. several different second messengers and proteins have been suggested to be involved in signal transduct ...201223104108
putative role of proteins involved in detoxification of reactive oxygen species in the early response to gravitropic stimulation of poplar stems.gravity perception and gravitropic response are essential for plant development. in herbaceous species it is widely accepted that one of the primary events in gravity perception involves the displacement of amyloplasts within specialized cells. however the signaling cascade leading to stem reorientation is not fully known especially in woody species in which primary and secondary growth occur. several different second messengers and proteins have been suggested to be involved in signal transduct ...201223104108
plant plasma membrane-bound staphylococcal-like dnases as a novel class of eukaryotic nucleases.the activity of degradative nucleases responsible for genomic dna digestion has been observed in all kingdoms of life. it is believed that the main function of dna degradation occurring during plant programmed cell death is redistribution of nucleic acid derived products such as nitrogen, phosphorus and nucleotide bases. plant degradative nucleases that have been studied so far belong mainly to the s1-type family and were identified in cellular compartments containing nucleic acids or in the org ...201223102437
phylogeny of cirsium spp. in north america: host specificity does not follow phylogeny.weedy invasive cirsium spp. are widespread in temperate regions of north america and some of their biological control agents have attacked native cirsium spp. a phylogenetic tree was developed from dna sequences for the internal transcribed spacer and external transcribed spacer regions from native and non-native great plains cirsium spp. and other thistles to determine if host specificity follows phylogeny. the monophyly of cirsium spp. and carduus within the tribe cardinae was confirmed with n ...201227137640
regulation of plant immune receptors by ubiquitination.from pathogen perception and the activation of signal transduction cascades to the deployment of defense responses, protein ubiquitination plays a key role in the modulation of plant immunity. ubiquitination is mediated by three enzymes, of which the e3 ubiquitin ligases, the substrate determinants, have been the major focus of attention. accumulating evidence suggests that ubiquitination modulates signaling mediated by pattern recognition receptors and is important for the accumulation of nucle ...201223109936
involvement of bacterial tonb-dependent signaling in the generation of an oligogalacturonide damage-associated molecular pattern from plant cell walls exposed to xanthomonas campestris pv. campestris pectate lyases.efficient perception of attacking pathogens is essential for plants. plant defense is evoked by molecules termed elicitors. endogenous elicitors or damage-associated molecular patterns (damps) originate from plant materials upon injury or pathogen activity. while there are comparably well-characterized examples for damps, often oligogalacturonides (ogas), generated by the activity of fungal pathogens, endogenous elicitors evoked by bacterial pathogens have been rarely described. in particular, t ...201223082751
tricking the guard: exploiting plant defense for disease susceptibility.typically, pathogens deploy virulence effectors to disable defense. plants defeat effectors with resistance proteins that guard effector targets. we found that a pathogen exploits a resistance protein by activating it to confer susceptibility in arabidopsis. the guard mechanism of plant defense is recapitulated by interactions among victorin (an effector produced by the necrotrophic fungus cochliobolus victoriae), trx-h5 (a defense-associated thioredoxin), and lov1 (an arabidopsis susceptibility ...201223087001
aux/lax family of auxin influx carriers-an overview.auxin regulates several aspects of plant growth and development. auxin is unique among plant hormones for exhibiting polar transport. indole-3-acetic acid (iaa), the major form of auxin in higher plants, is a weak acid and its intercellular movement is facilitated by auxin influx and efflux carriers. polarity of auxin movement is provided by asymmetric localization of auxin carriers (mainly pin efflux carriers). pin-formed (pin) and p-glycoprotein (pgp) family of proteins are major auxin efflux ...201223087694
proteomic analysis of grapevine resistance induced by trichoderma harzianum t39 reveals specific defence pathways activated against downy mildew.downy mildew is caused by the oomycete plasmopara viticola and is one of the most serious diseases of grapevine. the beneficial microorganism trichoderma harzianum t39 (t39) has previously been shown to induce plant-mediated resistance and to reduce the severity of downy mildew in susceptible grapevines. in order to better understand the cellular processes associated with t39-induced resistance, the proteomic and histochemical changes activated by t39 in grapevine were investigated before and 1 ...201223105132
arabidopsis thaliana mterf proteins: evolution and functional classification.organellar gene expression (oge) is crucial for plant development, photosynthesis, and respiration, but our understanding of the mechanisms that control it is still relatively poor. thus, oge requires various nucleus-encoded proteins that promote transcription, splicing, trimming, and editing of organellar rnas, and regulate translation. in metazoans, proteins of the mitochondrial transcription termination factor (mterf) family interact with the mitochondrial chromosome and regulate transcriptio ...201223087700
the arabidopsis mediator complex subunit16 positively regulates salicylate-mediated systemic acquired resistance and jasmonate/ethylene-induced defense pathways.systemic acquired resistance (sar) is a long-lasting plant immunity against a broad spectrum of pathogens. biological induction of sar requires the signal molecule salicylic acid (sa) and involves profound transcriptional changes that are largely controlled by the transcription coactivator nonexpressor of pathogenesis-related genes1 (npr1). however, it is unclear how sar signals are transduced from the npr1 signaling node to the general transcription machinery. here, we report that the arabidops ...201223064320
non-recognition-of-bth4, an arabidopsis mediator subunit homolog, is necessary for development and response to salicylic acid.salicylic acid (sa) signaling acts in defense and plant development. the only gene demonstrated to be required for the response to sa is arabidopsis thaliana non-expresser of pathogenesis-related gene 1 (npr1), and npr1 mutants are insensitive to sa. by focusing on the effect of analogs of sa on plant development, we identified mutants in additional genes acting in the sa response. in this work, we describe a gene necessary for the sa non-recognition-of-bth4 (nrb4). three nrb4 alleles recovered ...201223064321
14-3-3 proteins sgf14c and sgf14l play critical roles during soybean nodulation.the soybean (glycine max) genome contains 18 members of the 14-3-3 protein family, but little is known about their association with specific phenotypes. here, we report that the glyma0529080 soybean g-box factor 14-3-3c (sgf14c) and glyma08g12220 (sgf14l) genes, encoding 14-3-3 proteins, appear to play essential roles in soybean nodulation. quantitative reverse transcription-polymerase chain reaction and western-immunoblot analyses showed that sgf14c mrna and protein levels were specifically inc ...201223060368
cauliflower mosaic virus protein p6 inhibits signaling responses to salicylic acid and regulates innate immunity.cauliflower mosaic virus (camv) encodes a multifunctional protein p6 that is required for translation of the 35s rna and also acts as a suppressor of rna silencing. here we demonstrate that p6 additionally acts as a pathogenicity effector of an unique and novel type, modifying npr1 (a key regulator of salicylic acid (sa)- and jasmonic acid (ja)-dependent signaling) and inhibiting sa-dependent defence responses we find that that transgene-mediated expression of p6 in arabidopsis and transient exp ...201223071821
one-shot nmr analysis of microbial secretions identifies highly potent proteasome inhibitor.natural products represent valuable lead structures for drug discovery. however, for most bioactive compounds no cellular target is yet identified and many substances predicted from genome analysis are inaccessible due to their life stage-dependent biosynthesis, which is not reflected in common isolation procedures. in response to these issues, an nmr-based and target-directed protease assay for inhibitor detection of the proteasome was developed. the methodology is suitable for one-shot identif ...201223091006
expression of the gene for resistance to phaseolotoxin (argk) depends on the activity of genes phtabc in pseudomonas syringae pv. phaseolicola.the bacterium pseudomonas syringae pv. phaseolicola produces phaseolotoxin in a temperature dependent manner, being optimally produced between 18°c and 20°c, while no detectable amounts are present above 28°c. phaseolotoxin is an effective inhibitor of ornithine carbamoyltransferase (octase) activity from plant, mammalian and bacterial sources and causes a phenotypic requirement for arginine. to protect the cell from its own toxin, p. syringae pv. phaseolicola synthesizes a phaseolotoxin-resista ...201223056465
acyl coa binding proteins are required for cuticle formation and plant responses to microbes.fatty acids (fa) and lipids are well known regulators of plant defense. our previous studies have shown that components of prokaryotic (plastidal) fa biosynthesis pathway regulate various aspects of plant defense. here, we investigated the defense related roles of the soluble acyl coa binding proteins (acbps), which are thought to facilitate the intracellular transport of fa/lipids. we show that acbp3 and 4 are required for maintaining normal lipid levels and that acbp3 contributes to the lipid ...201223060893
catecholate siderophores protect bacteria from pyochelin toxicity.bacteria produce small molecule iron chelators, known as siderophores, to facilitate the acquisition of iron from the environment. the synthesis of more than one siderophore and the production of multiple siderophore uptake systems by a single bacterial species are common place. the selective advantages conferred by the multiplicity of siderophore synthesis remains poorly understood. however, there is growing evidence suggesting that siderophores may have other physiological roles besides their ...201223071628
how membranes shape plant symbioses: signaling and transport in nodulation and arbuscular mycorrhiza.as sessile organisms that cannot evade adverse environmental conditions, plants have evolved various adaptive strategies to cope with environmental stresses. one of the most successful adaptations is the formation of symbiotic associations with beneficial microbes. in these mutualistic interactions the partners exchange essential nutrients and improve their resistance to biotic and abiotic stresses. in arbuscular mycorrhiza (am) and in root nodule symbiosis (rns), am fungi and rhizobia, respecti ...201223060892
disruption of abscisic acid signaling constitutively activates arabidopsis resistance to the necrotrophic fungus plectosphaerella cucumerina.plant resistance to necrotrophic fungi is regulated by a complex set of signaling pathways that includes those mediated by the hormones salicylic acid (sa), ethylene (et), jasmonic acid (ja), and abscisic acid (aba). the role of aba in plant resistance remains controversial, as positive and negative regulatory functions have been described depending on the plant-pathogen interaction analyzed. here, we show that aba signaling negatively regulates arabidopsis (arabidopsis thaliana) resistance to t ...201223037505
imprimatinc1, a novel plant immune-priming compound, functions as a partial agonist of salicylic acid.plant activators are agrochemicals that protect crops from pathogens. they confer durable resistance to a broad range of diseases by activating intrinsic immune mechanisms in plants. to obtain leads regarding useful compounds, we have screened a chemical library using an established method that allows selective identification of immune-priming compounds. here, we report the characterisation of one of the isolated chemicals, imprimatinc1, and its structural derivative imprimatinc2. imprimatinc1 f ...201223050089
chemical methods to interrogate bacterial quorum sensing pathways.bacteria frequently manifest distinct phenotypes as a function of cell density in a phenomenon known as quorum sensing (qs). this intercellular signalling process is mediated by "chemical languages" comprised of low-molecular weight signals, known as autoinducers, and their cognate receptor proteins. as many of the phenotypes regulated by qs can have a significant impact on the success of pathogenic or mutualistic prokaryotic-eukaryotic interactions, there is considerable interest in methods to ...201222948815
length bias correction in gene ontology enrichment analysis using logistic regression.when assessing differential gene expression from rna sequencing data, commonly used statistical tests tend to have greater power to detect differential expression of genes encoding longer transcripts. this phenomenon, called "length bias", will influence subsequent analyses such as gene ontology enrichment analysis. in the presence of length bias, gene ontology categories that include longer genes are more likely to be identified as enriched. these categories, however, are not necessarily biolog ...201223056249
a boolean model of the cardiac gene regulatory network determining first and second heart field identity.two types of distinct cardiac progenitor cell populations can be identified during early heart development: the first heart field (fhf) and second heart field (shf) lineage that later form the mature heart. they can be characterized by differential expression of transcription and signaling factors. these regulatory factors influence each other forming a gene regulatory network. here, we present a core gene regulatory network for early cardiac development based on published temporal and spatial e ...201223056457
a bacterial effector targets the traf6-nfκb pathway to modulate the acute inflammatory response to bacterial invasion of epithelial cells. 201223076286
the role of g-proteins in plant immunity.heterotrimeric g-proteins play an important regulatory role in multiple physiological processes, including the plant immune response, and substantial progress has been made in elucidating the g-protein-mediated defense-signaling network. this mini-review discusses the importance of g-proteins in plant immunity. we also provide an overview of how g-proteins affect plant cell death and stomatal movement. our recent studies demonstrated that g-proteins are involved in signal transduction and induct ...201222895102
multiple calmodulin-like proteins in arabidopsis are induced by insect-derived (spodoptera littoralis) oral secretion.in plant cells, diverse environmental changes often induce transient elevation in the intracellular calcium concentrations, which are involved in signaling pathways leading to the respective cellular reactions. therefore, these calcium elevations need to be deciphered into specific downstream responses. calmodulin-like-proteins (cmls) are calcium-sensing proteins present only in higher plants. they are involved in signaling processes induced by both abiotic as well as biotic stress factors. howe ...201222902684
nucleoporins nup160 and seh1 are required for disease resistance in arabidopsis.arabidopsis nup160 and seh1, encoding two predicted nucleoporins of the nup107-160 nuclear pore sub-complex, were identified in a reverse genetics screen based on their requirement for basal disease resistance. both genes also contribute to immunity conferred by toll interleukin 1 receptor/nucleotide-binding/leucine-rich repeat (tnl)-type r proteins and constitutive resistance activated in the deregulated tnl mutant, snc1. protein amounts of eds1, a central regulator of tnl-triggered resistance, ...201222902705
genome sequence of the plant pathogen pseudomonas syringae pv. panici lmg 2367.pseudomonas syringae pv. panici is a phytopathogenic bacterium causing brown stripe disease in economically important crops worldwide. here, we announce the draft genome sequence of pseudomonas syringae pv. panici lmg2367 to provide further valuable insights for comparison of the pathovars among species pseudomonas syringae.201223012277
direct and indirect regulation of the ycnkji operon involved in copper uptake through two transcriptional repressors, ycnk and csor, in bacillus subtilis.northern blot and primer extension analyses revealed that the ycnkji operon and the ycnl gene of bacillus subtilis are transcribed from adjacent promoters that are divergently oriented. the ycnk and ycnj genes encode a deor-type transcriptional regulator and a membrane protein involved in copper uptake, respectively. dna binding experiments showed that the ycnk protein specifically binds to the ycnk-ycnl intergenic region, including a 16-bp direct repeat that is essential for the high binding af ...201222904286
engineering ecosystems and synthetic ecologies.microbial ecosystems play an important role in nature. engineering these systems for industrial, medical, or biotechnological purposes are important pursuits for synthetic biologists and biological engineers moving forward. here we provide a review of recent progress in engineering natural and synthetic microbial ecosystems. we highlight important forward engineering design principles, theoretical and quantitative models, new experimental and manipulation tools, and possible applications of micr ...201222722235
arabidopsis defense against botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis.transcriptional reprogramming forms a major part of a plant's response to pathogen infection. many individual components and pathways operating during plant defense have been identified, but our knowledge of how these different components interact is still rudimentary. we generated a high-resolution time series of gene expression profiles from a single arabidopsis thaliana leaf during infection by the necrotrophic fungal pathogen botrytis cinerea. approximately one-third of the arabidopsis genom ...201223023172
the destructive citrus pathogen, 'candidatus liberibacter asiaticus' encodes a functional flagellin characteristic of a pathogen-associated molecular pattern.huanglongbing (hlb) is presently the most devastating citrus disease worldwide. as an intracellular plant pathogen and insect symbiont, the hlb bacterium, 'candidatus liberibacter asiaticus' (las), retains the entire flagellum-encoding gene cluster in its significantly reduced genome. las encodes a flagellin and hook-associated protein (fla) of 452 amino acids that contains a conserved 22 amino acid domain (flg22) at positions 29 to 50 in the n-terminus. the phenotypic alteration in motility of ...201223029520
glyphosate effects on plant mineral nutrition, crop rhizosphere microbiota, and plant disease in glyphosate-resistant crops.claims have been made recently that glyphosate-resistant (gr) crops sometimes have mineral deficiencies and increased plant disease. this review evaluates the literature that is germane to these claims. our conclusions are: (1) although there is conflicting literature on the effects of glyphosate on mineral nutrition on gr crops, most of the literature indicates that mineral nutrition in gr crops is not affected by either the gr trait or by application of glyphosate; (2) most of the available da ...201223013354
an amino acid substitution inhibits specialist herbivore production of an antagonist effector and recovers insect-induced plant defenses.plants respond to insect herbivory through the production of biochemicals that function as either direct defenses or indirect defenses via the attraction of natural enemies. while attack by closely related insect pests can result in distinctive levels of induced plant defenses, precise biochemical mechanisms responsible for differing responses remain largely unknown. cowpea (vigna unguiculata) responds to fall armyworm (spodoptera frugiperda) herbivory through the detection of fragments of chlor ...201223008466
dispersion by pseudomonas aeruginosa requires an unusual posttranslational modification of bdla.dispersion enables biofilm bacteria to transit from the biofilm to the planktonic growth state and to spawn novel communities in new locales. although the chemotaxis protein bdla plays a role in the dispersion of pseudomonas aeruginosa biofilms in response to environmental cues, little is known about regulation of bdla activity or how bdla modulates the dispersion response. here, we demonstrate that bdla in its native form is inactive and is activated upon nonprocessive proteolysis at a clpp-pro ...201223012421
immunity's fourth dimension: approaching the circadian-immune connection.the circadian system ensures the generation and maintenance of self-sustained ~24-h rhythms in physiology that are linked to internal and environmental changes. in mammals, daily variations in light intensity and other cues are integrated by a hypothalamic master clock that conveys circadian information to peripheral molecular clocks that orchestrate physiology. multiple immune parameters also vary throughout the day and disruption of circadian homeostasis is associated with immune-related disea ...201223000010
application of synthetic biology in cyanobacteria and algae.cyanobacteria and algae are becoming increasingly attractive cell factories for producing renewable biofuels and chemicals due to their ability to capture solar energy and co(2) and their relatively simple genetic background for genetic manipulation. increasing research efforts from the synthetic biology approach have been made in recent years to modify cyanobacteria and algae for various biotechnological applications. in this article, we critically review recent progresses in developing genetic ...201223049529
involvement of microrna-mediated gene expression regulation in the pathological development of stem canker disease in populus trichocarpa.micrornas (mirnas), a type of short (21-23 nucleotides), non-coding rna molecule, mediate repressive gene regulation through rna silencing at the post-transcriptional level, and play an important role in defense and response to abiotic and biotic stresses. in the present study, affymetrix® mirna array, real-time quantitative pcr (qpcr) for mirnas and their targets, and mirna promoter analysis were used to validate the gene expression patterns of mirnas in populus trichocarpa plantlets induced wi ...201223028709
comparison of intact arabidopsis thaliana leaf transcript profiles during treatment with inhibitors of mitochondrial electron transport and tca cycle.plant mitochondria signal to the nucleus leading to altered transcription of nuclear genes by a process called mitochondrial retrograde regulation (mrr). mrr is implicated in metabolic homeostasis and responses to stress conditions. mitochondrial reactive oxygen species (mtros) are a mrr signaling component, but whether all mrr requires ros is not established. inhibition of the cytochrome respiratory pathway by antimycin a (aa) or the tca cycle by monofluoroacetate (mfa), each of which initiates ...201223028523
diversities in virulence, antifungal activity, pigmentation and dna fingerprint among strains of burkholderia glumae.burkholderia glumae is the primary causal agent of bacterial panicle blight of rice. in this study, 11 naturally avirulent and nine virulent strains of b. glumae native to the southern united states were characterized in terms of virulence in rice and onion, toxofalvin production, antifungal activity, pigmentation and genomic structure. virulence of b. glumae strains on rice panicles was highly correlated to virulence on onion bulb scales, suggesting that onion bulb can be a convenient alternati ...201223028972
genome wide identification of chilling responsive micrornas in prunus persica.micrornas (mirnas) are small rnas (srnas) approximately 21 nucleotides in length that negatively control gene expression by cleaving or inhibiting the translation of target gene transcripts. within this context, mirnas and sirnas are coming to the forefront as molecular mediators of gene regulation in plant responses to annual temperature cycling and cold stress. for this reason, we chose to identify and characterize the conserved and non-conserved mirna component of peach (prunus persica (l.) b ...201222978558
identification of a coding sequence and structure modeling of a glycine-rich rna-binding protein (cmgrp1) from chelidonium majus l.the family of glycine-rich plant proteins (grps) is a large and complex group of proteins that share, as a common feature, the presence of glycine-rich domains arranged in (gly)n-x repeats that are suggested to be involved in protein-protein interactions, rna binding, and nucleolar targeting. these proteins are implicated in several independent physiological processes. some are components of cell walls of many higher plants, while others are involved in molecular responses to environmental stres ...201224415842
identification of a coding sequence and structure modeling of a glycine-rich rna-binding protein (cmgrp1) from chelidonium majus l.the family of glycine-rich plant proteins (grps) is a large and complex group of proteins that share, as a common feature, the presence of glycine-rich domains arranged in (gly)n-x repeats that are suggested to be involved in protein-protein interactions, rna binding, and nucleolar targeting. these proteins are implicated in several independent physiological processes. some are components of cell walls of many higher plants, while others are involved in molecular responses to environmental stres ...201224415842
ubiquitin initiates sorting of golgi and plasma membrane proteins into the vacuolar degradation pathway.in yeast and mammals, many plasma membrane (pm) proteins destined for degradation are tagged with ubiquitin. these ubiquitinated proteins are internalized into clathrin-coated vesicles and are transported to early endosomal compartments. there, ubiquitinated proteins are sorted by the endosomal sorting complex required for transport (escrt) machinery into the intraluminal vesicles of multivesicular endosomes. degradation of these proteins occurs after endosomes fuse with lysosomes/lytic vacuoles ...201222970698
organelle signaling: how stressed chloroplasts communicate with the nucleus.plastids are able to relay information to the nucleus to regulate stress responses. a new genetic screen has identified an isoprenoid intermediate that accumulates in stressed plastids and acts as a novel retrograde signal.201222974998
rhamnolipids elicit defense responses and induce disease resistance against biotrophic, hemibiotrophic, and necrotrophic pathogens that require different signaling pathways in arabidopsis and highlight a central role for salicylic acid.plant resistance to phytopathogenic microorganisms mainly relies on the activation of an innate immune response usually launched after recognition by the plant cells of microbe-associated molecular patterns. the plant hormones, salicylic acid (sa), jasmonic acid, and ethylene have emerged as key players in the signaling networks involved in plant immunity. rhamnolipids (rls) are glycolipids produced by bacteria and are involved in surface motility and biofilm development. here we report that rls ...201222968829
homology modeling and functional characterization of pr-1a protein of hordeum vulgare subsp. vulgare.pathogenesis-related protein 1a of hordeum vulgare subsp. vulgare (hvpr-1a) is induced by various pathogens and stress related factors. it plays important roles in plant defense system. since the discovery of hvpr-1a a great deal of research has been focused on its isolation and characterization. however, three dimensional structure of hvpr-1a is still unknown. 3d structure can be used for determining protein function, and identifying novel protein folds and potential targets for regulation. the ...201223139589
hdt701, a histone h4 deacetylase, negatively regulates plant innate immunity by modulating histone h4 acetylation of defense-related genes in rice.histone acetylation and deacetylation play an important role in the modification of chromatin structure and regulation of gene expression in eukaryotes. chromatin acetylation status is modulated antagonistically by histone acetyltransferases and histone deacetylases (hdacs). in this study, we characterized the function of histone deacetylase701 (hdt701), a member of the plant-specific hd2 subfamily of hdacs, in rice (oryza sativa) innate immunity. transcription of hdt701 is increased in the comp ...201222968716
genome-wide identification and analysis of the tify gene family in grape.the tify gene family constitutes a plant-specific group of genes with a broad range of functions. this family encodes four subfamilies of proteins, including zml, tify, ppd and jasmonate zim-domain (jaz) proteins. jaz proteins are targets of the scf(coi1) complex, and function as negative regulators in the ja signaling pathway. recently, it has been reported in both arabidopsis and rice that tify genes, and especially jaz genes, may be involved in plant defense against insect feeding, wounding, ...201222984514
alternative oxidase in resistance to biotic stresses: nicotiana attenuata aox contributes to resistance to a pathogen and a piercing-sucking insect but not manduca sexta larvae.the role of the alternative respiratory pathway in the protection of plants against biotic stress was examined in transgenic tobacco (nicotiana attenuata) plants (iraox) silenced in the expression of alternative oxidase (aox) gene. wild-type and iraox plants were independently challenged with (1) chewing herbivores (manduca sexta), (2) piercing-sucking insects (empoasca spp.), and (3) bacterial pathogens (pseudomonas syringae pv tomato dc3000), showing that all these treatments can strongly elic ...201222961128
novel plant immune-priming compounds identified via high-throughput chemical screening target salicylic acid glucosyltransferases in arabidopsis.plant activators are compounds, such as analogs of the defense hormone salicylic acid (sa), that protect plants from pathogens by activating the plant immune system. although some plant activators have been widely used in agriculture, the molecular mechanisms of immune induction are largely unknown. using a newly established high-throughput screening procedure that screens for compounds that specifically potentiate pathogen-activated cell death in arabidopsis thaliana cultured suspension cells, ...201222960909
rosette iron deficiency transcript and microrna profiling reveals links between copper and iron homeostasis in arabidopsis thaliana.iron (fe) is an essential plant micronutrient, and its deficiency limits plant growth and development on alkaline soils. under fe deficiency, plant responses include up-regulation of genes involved in fe uptake from the soil. however, little is known about shoot responses to fe deficiency. using microarrays to probe gene expression in kas-1 and tsu-1 ecotypes of arabidopsis thaliana, and comparison with existing col-0 data, revealed conserved rosette gene expression responses to fe deficiency. f ...201222962679
dual targeting and retrograde translocation: regulators of plant nuclear gene expression can be sequestered by plastids.changes in the developmental or metabolic state of plastids can trigger profound changes in the transcript profiles of nuclear genes. many nuclear transcription factors were shown to be controlled by signals generated in the organelles. in addition to the many different compounds for which an involvement in retrograde signaling is discussed, accumulating evidence suggests a role for proteins in plastid-to-nucleus communication. these proteins might be sequestered in the plastids before they act ...201223109840
ectopic expression of hrf1 enhances bacterial resistance via regulation of diterpene phytoalexins, silicon and reactive oxygen species burst in rice.harpin proteins as elicitor derived from plant gram negative bacteria such as xanthomonas oryzae pv. oryzae (xoo), erwinia amylovora induce disease resistance in plants by activating multiple defense responses. however, it is unclear whether phytoalexin production and ros burst are involved in the disease resistance conferred by the expression of the harpin(xoo) protein in rice. in this article, ectopic expression of hrf1 in rice enhanced resistance to bacterial blight. accompanying with the act ...201222970151
characterization of copper-resistant bacteria and bacterial communities from copper-polluted agricultural soils of central chile.copper mining has led to cu pollution in agricultural soils. in this report, the effects of cu pollution on bacterial communities of agricultural soils from valparaiso region, central chile, were studied. denaturing gradient gel electrophoresis (dgge) of the 16s rrna genes was used for the characterization of bacterial communities from cu-polluted and non-polluted soils. cu-resistant bacterial strains were isolated from cu-polluted soils and characterized.201222950448
constitutive expression of transgenes encoding derivatives of the synthetic antimicrobial peptide bp100: impact on rice host plant fitness.the biopeptide bp100 is a synthetic and strongly cationic α-helical undecapeptide with high, specific antibacterial activity against economically important plant-pathogenic bacteria, and very low toxicity. it was selected from a library of synthetic peptides, along with other peptides with activities against relevant bacterial and fungal species. expression of the bp100 series of peptides in plants is of major interest to establish disease-resistant plants and facilitate molecular farming. speci ...201222947243
identification of novel type iii effectors using latent dirichlet allocation.among the six secretion systems identified in gram-negative bacteria, the type iii secretion system (t3ss) plays important roles in the disease development of pathogens. t3ss has attracted a great deal of research interests. however, the secretion mechanism has not been fully understood yet. especially, the identification of effectors (secreted proteins) is an important and challenging task. this paper adopts machine learning methods to identify type iii secreted effectors (t3ses). we extract fe ...201222997537
mpk11-a fourth elicitor-responsive mitogen-activated protein kinase in arabidopsis thaliana.recognition of pathogen attack or elicitation with pathogen-associated molecular patterns (pamps) leads to defense signaling that includes activation of the three mitogen-activated protein kinases (mpks), mpk3, mpk4 and mpk6 in arabidopsis. recently, we demonstrated the activation of a fourth mpk, mpk11, after treatment with flg22, a 22 amino acid pamp derived from bacterial flagellin. here, we extended the study by examining elicitation with two other pamps, elf18 (derived from bacterial elonga ...201222899057
sgt1b is required for hopz3-mediated suppression of the epiphytic growth of pseudomonas syringae on n. benthamiana.type iii secreted effectors shape the potential of bacterial pathogens to cause disease on plants. some effectors affect pathogen growth only in specific niches. for example, hopz3 causes reduced epiphytic growth of pseudomonas syringae strain b728a on nicotiana benthamiana. this raises the question of whether genes important for effector-triggered disease resistance are needed for responses to effectors whose major effect is in the epiphytic niche. we report that sgt1b, a protein known to be im ...201222899059
cml9, a multifunctional arabidopsis thaliana calmodulin-like protein involved in stress responses and plant growth?plants have evolved complex signaling networks to respond to their fluctuating environment and adapt their growth and development. calcium-dependent signaling pathways play key role in the onset of these adaptive responses. in plant cells, the intracellular calcium transients are triggered by numerous stimuli and it is supposed that the large repertory of calcium sensors present in higher plants could contribute to integrate these signals in physiological responses. here, we present data on cml9 ...201222899061
plant erd2s self-interact and interact with gtpase-activating proteins and adp-ribosylation factor 1.erd2s (er luminal protein receptors)-mediated retrograde transport is one of the most substantial processes to maintain the endoplasmic reticulum (er) homeostasis. it is completed by the recognition of the escaped er luminal proteins, the gathering into cop i vesicle, and the fusion and releasing into the er. erd2s can recognize hdel/kdel motifs at the c-terminal of the escaped er luminal proteins at the golgi to initiate the retrograde transport. however, these mechanisms remain largely unknown ...201222899072
disease resistance to pectobacterium carotovorum is negatively modulated by the arabidopsis lectin receptor kinase lecrk-v.5.plant stomata function in disease resistance by restricting bacteria entry inside leaves. during plant-bacteria interactions, stomatal closure is initiated by the recognition of microbe-associated molecular patterns (mamps). recently, we have shown that the lectin receptor kinase v.5 (lecrk-v.5) negatively regulates bacterium- and mamp-induced stomatal closure upstream of reactive oxygen species (ros) production mediated by abscisic acid signaling. closed stomata in lecrk-v.5 mutants are correla ...201222899085
gene discovery using mutagen-induced polymorphisms and deep sequencing: application to plant disease resistance.next-generation sequencing technologies are accelerating gene discovery by combining multiple steps of mapping and cloning used in the traditional map-based approach into one step using dna sequence polymorphisms existing between two different accessions/strains/backgrounds of the same species. the existing next-generation sequencing method, like the traditional one, requires the use of a segregating population from a cross of a mutant organism in one accession with a wild-type (wt) organism in ...201222714407
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