Publications

activation and manipulation of host responses by a gram-positive bacterium.	the interaction between tomato plants and clavibacter michiganensis subsp. michiganensis (cmm) represents a model pathosystem to study the interplay between the virulence determinants of a gram-positive bacterium and the attempt of a crop plant to counteract pathogen invasion. to investigate plant responses activated during this compatible interaction, we recently analyzed gene expression profiles of tomato stems infected with cmm. this analysis revealed activation of basal defense responses tha ...	2008	19704516
blocking and triggering of plant immunity by pseudomonas syringae effector avrpto.	bacterial effectors are double-edged swords that enhance bacterial virulence in susceptible plants while trigger resistance in plants carrying cognate resistance proteins. a well-known example of this is pseudomonas syringae protein avrpto that is delivered into plant cells through the type iii secretion system. avrpto inhibits immune responses in arabidopsis plants but triggers resistance in some tomato plants carrying cognate resistance proteins pto, a serine/threonine kinase, and prf, a nucle ...	2008	19704476
downstream targets of wrky33.	innate immunity signaling pathways in both animals and plants are regulated by mitogen-activated protein kinase (mapk) cascades. in a recent publication we show that mpk4 and its substrate mks1 interact with wrky33 in vivo, and that wrky33 is released from complexes with mpk4 upon infection. transcriptome analysis of a wrky33 loss-of-function mutant identified a subset of defense-related genes as putative targets of wrky33. these genes include pad3 and cyp71a13, which encode cytochrome p450 mono ...	2008	19704444
a draft genome sequence and functional screen reveals the repertoire of type iii secreted proteins of pseudomonas syringae pathovar tabaci 11528.	pseudomonas syringae is a widespread bacterial pathogen that causes disease on a broad range of economically important plant species. pathogenicity of p. syringae strains is dependent on the type iii secretion system, which secretes a suite of up to about thirty virulence 'effector' proteins into the host cytoplasm where they subvert the eukaryotic cell physiology and disrupt host defences. p. syringae pathovar tabaci naturally causes disease on wild tobacco, the model member of the solanaceae, ...	2009	19703286
nuclear pore complex component mos7/nup88 is required for innate immunity and nuclear accumulation of defense regulators in arabidopsis.	plant immune responses depend on dynamic signaling events across the nuclear envelope through nuclear pores. nuclear accumulation of certain resistance (r) proteins and downstream signal transducers are critical for their functions, but it is not understood how these processes are controlled. here, we report the identification, cloning, and analysis of arabidopsis thaliana modifier of snc1,7 (mos7-1), a partial loss-of-function mutation that suppresses immune responses conditioned by the autoact ...	2009	19700630
at4g24160, a soluble acyl-coenzyme a-dependent lysophosphatidic acid acyltransferase.	human cgi-58 (for comparative gene identification-58) and ylr099c, encoding ict1p in saccharomyces cerevisiae, have recently been identified as acyl-coa-dependent lysophosphatidic acid acyltransferases. sequence database searches for cgi-58 like proteins in arabidopsis (arabidopsis thaliana) revealed 24 proteins with at4g24160, a member of the alpha/beta-hydrolase family of proteins being the closest homolog. at4g24160 contains three motifs that are conserved across the plant species: a gxsxg li ...	2009	19700561
a pair of allelic wrky genes play opposite roles in rice-bacteria interactions.	although allelic diversity of genes has been reported to play important roles in different physiological processes, information on allelic diversity of defense-responsive genes in host-pathogen interactions is limited. here, we report that a pair of allelic genes, oswrky45-1 and oswrky45-2, which encode proteins with a 10-amino acid difference, play opposite roles in rice (oryza sativa) resistance against bacterial pathogens. bacterial blight caused by xanthomonas oryzae pv oryzae (xoo), bacteri ...	2009	19700558
gene regulation in parthenocarpic tomato fruit.	parthenocarpy is potentially a desirable trait for many commercially grown fruits if undesirable changes to structure, flavour, or nutrition can be avoided. parthenocarpic transgenic tomato plants (cv microtom) were obtained by the regulation of genes for auxin synthesis (iaam) or responsiveness (rolb) driven by defh9 or the inner no outer (ino) promoter from arabidopsis thaliana. fruits at a breaker stage were analysed at a transcriptomic and metabolomic level using microarrays, real-time rever ...	2009	19700496
why so repressed? turning off transcription during plant growth and development.	to ensure correct patterns of gene expression, eukaryotes use a variety of strategies to repress transcription. the transcriptional regulators mediating this repression can be broadly categorized as either passive or active repressors. while passive repressors rely on mechanisms such as steric hindrance of transcriptional activators to repress gene expression, active repressors display inherent repressive abilities commonly conferred by discrete repression domains. recent studies have indicated ...	2009	19700365
microarray comparative genomic hybridisation analysis incorporating genomic organisation, and application to enterobacterial plant pathogens.	microarray comparative genomic hybridisation (acgh) provides an estimate of the relative abundance of genomic dna (gdna) taken from comparator and reference organisms by hybridisation to a microarray containing probes that represent sequences from the reference organism. the experimental method is used in a number of biological applications, including the detection of human chromosomal aberrations, and in comparative genomic analysis of bacterial strains, but optimisation of the analysis is desi ...	2009	19696881
the wound hormone jasmonate.	plant tissues are highly vulnerable to injury by herbivores, pathogens, mechanical stress, and other environmental insults. optimal plant fitness in the face of these threats relies on complex signal transduction networks that link damage-associated signals to appropriate changes in metabolism, growth, and development. many of these wound-induced adaptive responses are triggered by de novo synthesis of the plant hormone jasmonate (ja). recent studies provide evidence that ja mediates systemic wo ...	2009	19695649
determinants for the activation and autoinhibition of the diguanylate cyclase response regulator wspr.	the bacterial second messenger bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-gmp) controls secretion, cell adhesion, and motility, leading to biofilm formation and increased cytotoxicity. diguanylate cyclases containing ggdef and phosphodiesterases containing eal or hd-gyp domains have been identified as the enzymes controlling cellular c-di-gmp levels, yet less is known regarding the molecular mechanisms governing regulation and signaling specificity. we recently determined a product ...	2009	19695263
forward and reverse genetics to identify genes involved in the age-related resistance response in arabidopsis thaliana.	summary age-related resistance (arr) occurs in numerous plant species, often resulting in increased disease resistance as plants mature. arr in arabidopsis to pseudomonas syringae pv. tomato is associated with intercellular salicylic acid (sa) accumulation and the transition to flowering. forward and reverse genetic screens were performed to identify genes required for arr and to investigate the mechanism of the arr response. infiltration of sa into the intercellular space of the arr-defective m ...	2009	19694953
the role of the conserved phenylalanine in the sigma54-interacting gaftga motif of bacterial enhancer binding proteins.	sigma(54)-dependent transcription requires activation by bacterial enhancer binding proteins (bebps). bebps are members of the aaa+ (atpases associated with various cellular activities) protein family and typically form hexameric structures that are crucial for their atpase activity. the precise mechanism by which the energy derived from atp hydrolysis is coupled to biological output has several unknowns. here we use escherichia coli pspf, a model bebp involved in the transcription of stress res ...	2009	19692583
protein-protein interactions of tandem affinity purified protein kinases from rice.	eighty-eight rice (oryza sativa) cdnas encoding rice leaf expressed protein kinases (pks) were fused to a tandem affinity purification tag (tap-tag) and expressed in transgenic rice plants. the tap-tagged pks and interacting proteins were purified from the t1 progeny of the transgenic rice plants and identified by tandem mass spectrometry. forty-five tap-tagged pks were recovered in this study and thirteen of these were found to interact with other rice proteins with a high probability score. in ...	2009	19690613
salmonella type iii secretion effector slrp is an e3 ubiquitin ligase for mammalian thioredoxin.	salmonella enterica encodes two virulence-related type iii secretion systems in salmonella pathogenicity islands 1 and 2, respectively. these systems mediate the translocation of protein effectors into the eukaryotic host cell, where they alter cell signaling and manipulate host cell functions. however, the precise role of most effectors remains unknown. using a genetic screen, we identified the small, reduction/oxidation-regulatory protein thioredoxin as a mammalian binding partner of the salmo ...	2009	19690162
advances in maize genomics and their value for enhancing genetic gains from breeding.	maize is an important crop for food, feed, forage, and fuel across tropical and temperate areas of the world. diversity studies at genetic, molecular, and functional levels have revealed that, tropical maize germplasm, landraces, and wild relatives harbor a significantly wider range of genetic variation. among all types of markers, snp markers are increasingly the marker-of-choice for all genomics applications in maize breeding. genetic mapping has been developed through conventional linkage map ...	2009	19688107
a locus conferring resistance to colletotrichum higginsianum is shared by four geographically distinct arabidopsis accessions.	colletotrichum higginsianum is a hemibiotrophic fungal pathogen that causes anthracnose disease on arabidopsis and other crucifer hosts. by exploiting natural variation in arabidopsis we identified a resistance locus that is shared by four geographically distinct accessions (ws-0, kondara, gifu-2 and can-0). a combination of quantitative trait loci (qtl) and mendelian mapping positioned this locus within the major recognition gene complex mrc-j on chromosome 5 containing the toll-interleukin-1 r ...	2009	19686535
improved phosphate biosorption by bacterial surface display of phosphate-binding protein utilizing ice nucleation protein.	the conventional enhanced biological phosphorus removal (ebpr) system often deteriorates at low chemical oxygen demand (cod) or under aeration conditions. a new approach that incorporates phosphate-eutrophic wastewater remediation was introduced through immobilization of an intracellular phosphate-binding protein (pbp) onto the surface of pseudomonas putida or escherichia coli, using the n-terminal anchor (inaq-n) of a newly identified ice nucleation protein from pseudomonas syringae. a green fl ...	2009	19686343
aeromonas hydrophila ah-3 type iii secretion system expression and regulatory network.	the aeromonas hydrophila type iii secretion system (t3ss) has been shown to play a crucial role in this pathogen's interactions with its host. we previously described the genetic organization of the t3ss cluster and the existence of at least one effector, called aext, in a. hydrophila strain ah-3. in this study, we analyzed the expression of the t3ss regulon by analyzing the activity of the aopn-aopd and aext promoters (t3ss machinery components and effector, respectively) by means of two differ ...	2009	19684162
microbial telesensing: probing the environment for friends, foes, and food.	bacterial-sensing circuits may be triggered by molecules originating from the environment (e.g., nutrients and chemoattractants). bacteria also actively probe the environment for information by releasing molecular probes to measure conditions beyond the cell surface: a process known as telesensing. perceiving the environment beyond is achieved by sensing environmentally induced changes in those probes, as occurs when a siderophore chelates an iron atom or a quorum-sensing signal is inactivated b ...	2009	19683678
expression and functional characterization of two pathogenesis-related protein 10 genes from zea mays.	a novel pr10 gene (zmpr10.1) was isolated from maize and its expression and function were compared with the previous zmpr10. zmpr10.1 shares 89.8% and 85.7% identity to zmpr10 at the nucleotide and amino acid sequence level, respectively. zmpr10 and zmpr10.1 were mainly expressed in root tissue with low expression in other tissues. zmpr10.1 had significantly lower expression than zmpr10 in all tissues examined. the expression of both zmpr10 and zmpr10.1 was induced by most abiotic stresses inclu ...	2010	19682768
an f-box gene, cpr30, functions as a negative regulator of the defense response in arabidopsis.	arabidopsis gain-of-resistance mutants, which show hr-like lesion formation and sar-like constitutive defense responses, were used well as tools to unravel the plant defense mechanisms. we have identified a novel mutant, designated constitutive expresser of pr genes 30 (cpr30), that exhibited dwarf morphology, constitutive resistance to the bacterial pathogen pseudomonas syringae and the dramatic induction of defense-response gene expression. the cpr30-conferred growth defect morphology and defe ...	2009	19682297
recombineering and stable integration of the pseudomonas syringae pv. syringae 61 hrp/hrc cluster into the genome of the soil bacterium pseudomonas fluorescens pf0-1.	many gram-negative bacteria use a type iii secretion system (t3ss) to establish associations with their hosts. the t3ss is a conduit for direct injection of type-iii effector proteins into host cells, where they manipulate the host for the benefit of the infecting bacterium. for plant-associated pathogens, the variations in number and amino acid sequences of type-iii effectors, as well as their functional redundancy, make studying type-iii effectors challenging. to mitigate this challenge, we de ...	2009	19682294
a "repertoire for repertoire" hypothesis: repertoires of type three effectors are candidate determinants of host specificity in xanthomonas.	the genetic basis of host specificity for animal and plant pathogenic bacteria remains poorly understood. for plant pathogenic bacteria, host range is restricted to one or a few host plant species reflecting a tight adaptation to specific hosts.	2009	19680562
efflux-mediated drug resistance in bacteria: an update.	drug efflux pumps play a key role in drug resistance and also serve other functions in bacteria. there has been a growing list of multidrug and drug-specific efflux pumps characterized from bacteria of human, animal, plant and environmental origins. these pumps are mostly encoded on the chromosome, although they can also be plasmid-encoded. a previous article in this journal provided a comprehensive review regarding efflux-mediated drug resistance in bacteria. in the past 5 years, significant pr ...	2009	19678712
loss of calmodulin binding to bax inhibitor-1 affects pseudomonas-mediated hypersensitive response-associated cell death in arabidopsis thaliana.	bax inhibitor-1 (bi-1) is a cell death suppressor protein conserved across a variety of organisms. the arabidopsis atbi1-1 plant is a mutant in which the c-terminal 6 amino acids of the expressed bi-1 protein have been replaced by t-dna insertion. this mutant bi-1 protein (atbi-cm) produced in escherichia coli can no longer bind to calmodulin. a promoter-reporter assay demonstrated compartmentalized expression of bi-1 during hypersensitive response, introduced by the inoculation of pseudomonas s ...	2009	19674971
occidiofungin, a unique antifungal glycopeptide produced by a strain of burkholderia contaminans.	bacterial strain burkholderia contaminans ms14 was isolated from soil that suppressed brown patch disease of lawn grass. an antifungal compound was purified from the liquid culture of this bacterium. in this study, complete covalent structures of two purified closely related antifungal compounds were determined by the experiments of tocsy, noesy, roesy, 13c hsqc 2d nmr, and esi-ms and gc. the analysis of monoisotopic masses of the purified preparation indicated the presence of two related compou ...	2009	19673482
are small gtpases signal hubs in sugar-mediated induction of fructan biosynthesis?	external sugar initiates biosynthesis of the reserve carbohydrate fructan, but the molecular processes mediating this response remain obscure. previously it was shown that a phosphatase and a general kinase inhibitor hamper fructan accumulation. we use various phosphorylation inhibitors both in barley and in arabidopsis and show that the expression of fructan biosynthetic genes is dependent on pp2a and different kinases such as tyr-kinases and pi3-kinases. to further characterize the phosphoryla ...	2009	19672308
proteolysis of a negative regulator of innate immunity is dependent on resistance genes in tomato and nicotiana benthamiana and induced by multiple bacterial effectors.	rpm1-interacting protein 4 (rin4), a negative regulator of the basal defense response in plants, is targeted by multiple bacterial virulence effectors. we show that rin4 degradation is induced by the effector avrpto from pseudomonas syringae and that this degradation in solanaceous plants is dependent on the resistance protein, pto, a protein kinase, and prf, a nucleotide binding site-leucine-rich repeat protein. our data demonstrate overlap between two of the best-characterized pathways for rec ...	2009	19671880
the expression patterns of atbsmt1 and atsagt1 encoding a salicylic acid (sa) methyltransferase and a sa glucosyltransferase, respectively, in arabidopsis plants with altered defense responses.	we reported previously that overexpression of a salicylic acid (sa) methyltransferase1 gene from rice (osbsmt1) or a sa glucosyltransferase1 gene from arabidopsis thaliana (atsagt1) leads to increased susceptibility to pseudomonas syringae due to reduced sa levels. to further examine their roles in the defense responses, we assayed the transcript levels of atbsmt1 or atsagt1 in plants with altered levels of sa and/or other defense components. these data showed that atsagt1 expression is regulate ...	2009	19669626
transcriptional and functional studies of acidithiobacillus ferrooxidans genes related to survival in the presence of copper.	the acidophilic acidithiobacillus ferrooxidans can resist exceptionally high copper (cu) concentrations. this property is important for its use in biomining processes, where cu and other metal levels range usually between 15 and 100 mm. to learn about the mechanisms that allow a. ferrooxidans cells to survive in this environment, a bioinformatic search of its genome showed the presence of at least 10 genes that are possibly related to cu homeostasis. among them are three genes coding for putativ ...	2009	19666734
biophysical investigations on the aggregation and thermal unfolding of harpin(pss) and identification of leucine-zipper-like motifs in harpins.	harpins are heat-stable, glycine-rich proteins secreted by gram-negative bacteria, which induce hypersensitive response (hr) in non-host plants. in this study, the thermal unfolding and aggregation of harpin(pss) from pseudomonas syringae pv. syringae have been investigated by biophysical approaches. differential scanning calorimetric studies indicate that thermal unfolding of harpin(pss) is a complex process involving three distinct transitions. cd spectroscopy revealed that the secondary struc ...	2009	19665594
improve bioavailability of harpin protein on plant use plga based nanoparticle.	harpins can induce systemic acquired resistance (sar) pathway on scores of non-host plant, provide protection against a range of pathogens. in this study, we demonstrated that applied recombinant harpinz pseudomonas syringae pv. tomato (rhrpz) on tobacco with three kinds of methods: infiltrating from micro-pore into leaf; injecting into petiole, and spraying on leaf, there is great difference in assimilation of protein because of the poor osmosis of tobacco leaves, and with multi-application of ...	2009	19665501
brucella regulators: self-control in a hostile environment.	brucella is an important zoonotic pathogen for which no human vaccine exists. in an infected host, brucella resides in macrophages but must coordinate expression of multiple virulence factors for successful cell entry and trafficking to acquire this replicative niche. brucella responds to environmental signals to regulate virulence strategies that circumvent or blunt the host immune response. the brucella quorum sensing system is a nexus of control for several brucella virulence factors includin ...	2009	19660951
r/bhc: fast bayesian hierarchical clustering for microarray data.	although the use of clustering methods has rapidly become one of the standard computational approaches in the literature of microarray gene expression data analysis, little attention has been paid to uncertainty in the results obtained.	2009	19660130
quantitative fitness effects of infection in a gene-for-gene system.	* it is often assumed that pathogen infection decreases plant fitness, thereby driving the evolution of plant resistance (r) genes. however, the impact of bacterial pathogens on fitness has been shown to be relatively subtle, ranging from positive to negative. * in this study, we focus on the rps5-mediated resistance in arabidopsis thaliana and examine the fitness effects of resistance by experimentally infecting resistant (r) and susceptible (s) plants with a natural avirulent pseudomonas syrin ...	2009	19659661
active dna demethylation mediated by dna glycosylases.	active dna demethylation is involved in many vital developmental and physiological processes of plants and animals. recent genetic and biochemical studies in arabidopsis have demonstrated that a subfamily of dna glycosylases function to promote dna demethylation through a base excision-repair pathway. these specialized bifunctional dna glycosylases remove the 5-methylcytosine base and then cleave the dna backbone at the abasic site, resulting in a gap that is then filled with an unmethylated cyt ...	2009	19659441
focus: plant interactions with bacterial pathogens.		2009	19656918
systemic acquired resistance in soybean is regulated by two proteins, orthologous to arabidopsis npr1.	systemic acquired resistance (sar) is induced in non-inoculated leaves following infection with certain pathogenic strains. sar is effective against many pathogens. salicylic acid (sa) is a signaling molecule of the sar pathway. the development of sar is associated with the induction of pathogenesis related (pr) genes. arabidopsis non-expressor of pr1 (npr1) is a regulatory gene of the sa signal pathway 123. sar in soybean was first reported following infection with colletotrichum trancatum that ...	2009	19656407
the majority of the type iii effector inventory of pseudomonas syringae pv. tomato dc3000 can suppress plant immunity.	the pseudomonas syringae type iii protein secretion system (t3ss) and the type iii effectors it injects into plant cells are required for plant pathogenicity and the ability to elicit a hypersensitive response (hr). the hr is a programmed cell death that is associated with effector-triggered immunity (eti). a primary function of p. syringae type iii effectors appears to be the suppression of eti and pathogen-associated molecular pattern-triggered immunity (pti), which is induced by conserved mol ...	2009	19656042
overexpression of a rice gene encoding a small c2 domain protein ossmcp1 increases tolerance to abiotic and biotic stresses in transgenic arabidopsis.	plant growth and crop production are limited by environmental stress. we used a large population of transgenic arabidopsis expressing rice full-length cdnas to isolate the rice genes that improve the tolerance of plants to environmental stress. by sowing t2 seeds of the transgenic lines under conditions of salinity stress, the salt-tolerant line r07047 was isolated. it expressed a rice gene, ossmcp1, which encodes a small protein with a single c2 domain, a ca(2+)-dependent membrane-targeting dom ...	2009	19653105
the bordetella type iii secretion system effector btea contains a conserved n-terminal motif that guides bacterial virulence factors to lipid rafts.	the bordetella type iii secretion system (t3ss) effector protein btea is necessary and sufficient for rapid cytotoxicity in a wide range of mammalian cells. we show that btea is highly conserved and functionally interchangeable between bordetella bronchiseptica, bordetella pertussis and bordetella parapertussis. the identification of btea sequences required for cytotoxicity allowed the construction of non-cytotoxic mutants for localization studies. btea derivatives were targeted to lipid rafts a ...	2009	19650828
regulation of defense gene expression by arabidopsis srfr1.	reduced growth and viability is a common phenotype of plants with constitutively activated pathogen defenses. one branch of the plant innate immunity system, effector-triggered immunity, is especially potent and requires tight control to enable normal plant development. while some facets of this control that directly regulate resistance protein abundance or activity have been documented, general control of effector-triggered signaling sensitivity is poorly understood. we recently identified supp ...	2009	19649196
two different signaling pathways for thaxtomin a-induced cell death in arabidopsis and tobacco by2.	thaxtomin a (txt) is a phytotoxin produced by all plant-pathogenic streptomyces scabies involved in the potato scab disease. their pathogenicity was previously correlated with the production of txt. calcium is known to be an essential second messenger associated with pathogen-induced plant responses and cell death. we have effectively shown that in arabidopsis thaliana cell suspensions, txt induces an early short lived ca(2+) influx which is involved in the cell death process and other txt-induc ...	2009	19649193
very long chain fatty acid and lipid signaling in the response of plants to pathogens.	recent findings indicate that lipid signaling is essential for plant resistance to pathogens. besides oxylipins and unsaturated fatty acids known to play important signaling functions during plant-pathogen interactions, the very long chain fatty acid (vlcfa) biosynthesis pathway has been recently associated to plant defense through different aspects. vlcfas are indeed required for the biosynthesis of the plant cuticle and the generation of sphingolipids. elucidation of the roles of these lipids ...	2009	19649180
internalization of salmonella enterica in leaves is induced by light and involves chemotaxis and penetration through open stomata.	outbreaks of salmonellosis related to consumption of fresh produce have raised interest in salmonella-plant interactions leading to plant colonization. incubation of gfp-tagged salmonella enterica with iceberg lettuce leaves in the light resulted in aggregation of bacteria near open stomata and invasion into the inner leaf tissue. in contrast, incubation in the dark resulted in a scattered attachment pattern and very poor stomatal internalization. forcing stomatal opening in the dark by fusicocc ...	2009	19648358
the arabidopsis pleiotropic drug resistance8/abcg36 atp binding cassette transporter modulates sensitivity to the auxin precursor indole-3-butyric acid.	plants have developed numerous mechanisms to store hormones in inactive but readily available states, enabling rapid responses to environmental changes. the phytohormone auxin has a number of storage precursors, including indole-3-butyric acid (iba), which is apparently shortened to active indole-3-acetic acid (iaa) in peroxisomes by a process similar to fatty acid beta-oxidation. whereas metabolism of auxin precursors is beginning to be understood, the biological significance of the various pre ...	2009	19648296
the high light response in arabidopsis involves aba signaling between vascular and bundle sheath cells.	previously, it has been shown that arabidopsis thaliana leaves exposed to high light accumulate hydrogen peroxide (h2o2) in bundle sheath cell (bsc) chloroplasts as part of a retrograde signaling network that induces ascorbate peroxidase2 (apx2). abscisic acid (aba) signaling has been postulated to be involved in this network. to investigate the proposed role of aba, a combination of physiological, pharmacological, bioinformatic, and molecular genetic approaches was used. aba biosynthesis is ini ...	2009	19638476
whole-genome analyses reveal genetic instability of acetobacter pasteurianus.	acetobacter species have been used for brewing traditional vinegar and are known to have genetic instability. to clarify the mutability, acetobacter pasteurianus nbrc 3283, which forms a multi-phenotype cell complex, was subjected to genome dna sequencing. the genome analysis revealed that there are more than 280 transposons and five genes with hyper-mutable tandem repeats as common features in the genome consisting of a 2.9-mb chromosome and six plasmids. there were three single nucleotide muta ...	2009	19638423
jasmonate-dependent plant defense restricts thrips performance and preference.	the western flower thrips (frankliniella occidentalis [pergande]) is one of the most important insect herbivores of cultivated plants. however, no pesticide provides complete control of this species, and insecticide resistance has emerged around the world. we previously reported the important role of jasmonate (ja) in the plant's immediate response to thrips feeding by using an arabidopsis leaf disc system. in this study, as the first step toward practical use of ja in thrips control, we analyze ...	2009	19635132
diversity and evolution of effector loci in natural populations of the plant pathogen melampsora lini.	genetic variation for pathogen infectivity is an important driver of disease incidence and prevalence in both natural and managed systems. here, we use the interaction between the rust pathogen, melampsora lini, and two host plants, linum marginale and linum usitatissimum, to examine how host-pathogen interactions influence the maintenance of polymorphism in genes underlying pathogen virulence. extensive sequence variation at two effector loci (avrp123, avrp4) was found in m. lini isolates colle ...	2009	19633228
role of the twin-arginine translocation pathway in staphylococcus.	in staphylococcus, the twin-arginine translocation (tat) pathway is present only in some species and is composed of tata and tatc. the tatac operon is associated with the fepabc operon, which encodes homologs to an iron-binding lipoprotein, an iron-dependent peroxidase (fepb), and a high-affinity iron permease. the fepb protein has a typical twin-arginine (rr) signal peptide. the tat and fep operons constitute an entity that is not present in all staphylococcal species. our analysis was focused ...	2009	19633084
productive steps toward an antimicrobial targeting virulence.	targeting virulence factors has gained increasing attention as a potential approach to new antibiotics. small molecule inhibitors of virulence have been shown to change the course of disease in whole organism infection models. recently, key advances in the field include the identification of novel targets within cell signaling pathways, a new class of anti-virulence compounds that target bacterial defenses against host immunity, and a growing body of in vivo data to support the general approach ...	2009	19631578
two prp19-like u-box proteins in the mos4-associated complex play redundant roles in plant innate immunity.	plant resistance (r) proteins play an integral role in defense against pathogen infection. a unique gain-of-function mutation in the r gene snc1, snc1, results in constitutive activation of plant immune pathways and enhanced resistance against pathogen infection. we previously found that mutations in mos4 suppress the autoimmune phenotypes of snc1, and that mos4 is part of a nuclear complex called the mos4-associated complex (mac) along with the transcription factor atcdc5 and the wd-40 protein ...	2009	19629177
receptor-mediated signalling in plants: molecular patterns and programmes.	a highly evolved surveillance system in plants is able to detect a broad range of signals originating from pathogens, damaged tissues, or altered developmental processes, initiating sophisticated molecular mechanisms that result in defence, wound healing, and development. microbe-associated molecular pattern molecules (mamps), damage-associated molecular pattern molecules (damps), virulence factors, secreted proteins, and processed peptides can be recognized directly or indirectly by this survei ...	2009	19628572
the arabidopsis resurrection1 gene regulates a novel antagonistic interaction in plant defense to biotrophs and necrotrophs.	we report a role for the arabidopsis (arabidopsis thaliana) resurrection1 (rst1) gene in plant defense. the rst1 mutant exhibits enhanced susceptibility to the biotrophic fungal pathogen erysiphe cichoracearum but enhanced resistance to the necrotrophic fungal pathogens botrytis cinerea and alternaria brassicicola. rst1 encodes a novel protein that localizes to the plasma membrane and is predicted to contain 11 transmembrane domains. disease responses in rst1 correlate with higher levels of jasm ...	2009	19625635
interaction of the tobacco mosaic virus replicase protein with a nac domain transcription factor is associated with the suppression of systemic host defenses.	an interaction between the helicase domain of the tobacco mosaic virus (tmv) 126-/183-kda replicase protein(s) and the arabidopsis thaliana nac domain transcription factor ataf2 was identified via yeast two-hybrid and in planta immunoprecipitation assays. ataf2 is transcriptionally induced in response to tmv infection, and its overexpression significantly reduces virus accumulation. proteasome inhibition studies suggest that ataf2 is targeted for degradation during virus infection. the transcrip ...	2009	19625399
downy mildew resistance in arabidopsis by mutation of homoserine kinase.	plant disease resistance is commonly triggered by early pathogen recognition and activation of immunity. an alternative form of resistance is mediated by recessive downy mildew resistant 1 (dmr1) alleles in arabidopsis thaliana. map-based cloning revealed that dmr1 encodes homoserine kinase (hsk). six independent dmr1 mutants each carry a different amino acid substitution in the hsk protein. amino acid analysis revealed that dmr1 mutants contain high levels of homoserine that is undetectable in ...	2009	19622802
arabidopsis wrky2 transcription factor mediates seed germination and postgermination arrest of development by abscisic acid.	plant wrky dna-binding transcription factors are key regulators in certain developmental programs. a number of studies have suggested that wrky genes may mediate seed germination and postgermination growth. however, it is unclear whether wrky genes mediate aba-dependent seed germination and postgermination growth arrest.	2009	19622176
sporicidal activity of synthetic antifungal undecapeptides and control of penicillium rot of apples.	the antifungal activity of cecropin a(2-8)-melittin(6-9) hybrid undecapeptides, previously reported as active against plant pathogenic bacteria, was studied. a set of 15 sequences was screened in vitro against fusarium oxysporum, penicillium expansum, aspergillus niger, and rhizopus stolonifer. most compounds were highly active against f. oxysporum (mic < 2.5 microm) but were less active against the other fungi. the best peptides were studied for their sporicidal activity and for sytox green upt ...	2009	19617390
p2cs: a two-component system resource for prokaryotic signal transduction research.	with the escalation of high throughput prokaryotic genome sequencing, there is an ever-increasing need for databases that characterise, catalogue and present data relating to particular gene sets and genomes/metagenomes. two-component system (tcs) signal transduction pathways are the dominant mechanisms by which micro-organisms sense and respond to external as well as internal environmental changes. these systems respond to a wide range of stimuli by triggering diverse physiological adjustments, ...	2009	19604365
overexpression of the soybean gmerf3 gene, an ap2/erf type transcription factor for increased tolerances to salt, drought, and diseases in transgenic tobacco.	a new member of the ap2/erf transcription factor family, gmerf3, was isolated from soybean. sequence analysis showed that gmerf3 contained an ap2/erf domain of 58 amino acids and two putative nuclear localization signal (nls) domains. it belonged to a group iv protein in the erf (ethylene response factor) subfamily as typified by a conserved n-terminal motif [mcggai(i/l)]. expression of gmerf3 was induced by treatments with high salinity, drought, abscisic acid (aba), salicylic acid (sa), jasmon ...	2009	19602544
the gacs/gaca signal transduction system of pseudomonas aeruginosa acts exclusively through its control over the transcription of the rsmy and rsmz regulatory small rnas.	we report here the results of an analysis of the regulatory range of the gacs/gaca two-component system in pseudomonas aeruginosa. using microarrays, we identified a large number of genes that are regulated by the system, and detected a near complete overlap of these genes with those regulated by two small rnas (srnas), rsmy and rsmz, suggesting that the expression of all gaca-regulated genes is rsmy/z-dependent. using genome-wide dna-protein interaction analyses, we identified only two genomic ...	2009	19602144
protein nitration during defense response in arabidopsis thaliana.	nitric oxide and reactive oxygen species play a key role in the plant hypersensitive disease resistance response, and protein tyrosine nitration is emerging as an important mechanism of their co-operative interaction. up to now, the proteins targeted by this post-translational modification in plants are still totally unknown. in this study, we analyzed for the first time proteins undergoing nitration during the hypersensitive response by analyzing via 1d- and 2d-western blot the protein extracts ...	2009	19598157
extracellular atp is a regulator of pathogen defence in plants.	in healthy plants extracellular atp (eatp) regulates the balance between cell viability and death. here we show an unexpected critical regulatory role of eatp in disease resistance and defensive signalling. in tobacco, enzymatic depletion of eatp or competition with non-hydrolysable atp analogues induced pathogenesis-related (pr) gene expression and enhanced resistance to tobacco mosaic virus and pseudomonas syringae pv. tabaci. artificially increasing eatp concentrations triggered a drop in lev ...	2009	19594709
genome-scale identification of legionella pneumophila effectors using a machine learning approach.	a large number of highly pathogenic bacteria utilize secretion systems to translocate effector proteins into host cells. using these effectors, the bacteria subvert host cell processes during infection. legionella pneumophila translocates effectors via the icm/dot type-iv secretion system and to date, approximately 100 effectors have been identified by various experimental and computational techniques. effector identification is a critical first step towards the understanding of the pathogenesis ...	2009	19593377
gida posttranscriptionally regulates rhl quorum sensing in pseudomonas aeruginosa.	the opportunistic pathogen pseudomonas aeruginosa utilizes two interconnected acyl-homoserine lactone quorum-sensing (acyl-hsl qs) systems, lasri and rhlri, to regulate the expression of hundreds of genes. the qs circuitry itself is integrated into a complex network of regulation by other factors. however, our understanding of this network is still unlikely to be complete, as a comprehensive, saturating approach to identifying regulatory components has never been attempted. here, we utilized a n ...	2009	19592591
pseudomonas syringae pv. phaseolicola mutants compromised for type iii secretion system gene induction.	pseudomonas syringae bacteria utilize the type iii secretion system (t3ss) to deliver effector proteins into host cells. the t3ss and t3 effector genes (together called the t3 genes hereafter) are repressed in nutrient-rich medium but rapidly induced after the bacteria are transferred into minimal medium or infiltrated into plants. the induction of the t3 genes is mediated by hrpl, an alternative sigma factor that recognizes the conserved hrp box motif in the t3 gene promoters. the induction of ...	2009	19589072
enhanced disease susceptibility 1 and salicylic acid act redundantly to regulate resistance gene-mediated signaling.	resistance (r) protein-associated pathways are well known to participate in defense against a variety of microbial pathogens. salicylic acid (sa) and its associated proteinaceous signaling components, including enhanced disease susceptibility 1 (eds1), non-race-specific disease resistance 1 (ndr1), phytoalexin deficient 4 (pad4), senescence associated gene 101 (sag101), and eds5, have been identified as components of resistance derived from many r proteins. here, we show that eds1 and sa fulfill ...	2009	19578402
gene ontology for type iii effectors: capturing processes at the host-pathogen interface.	disease development is determined by the interplay of host defense processes and pathogen factors that subvert defenses and remodel the host for parasitic benefit. the goal of the plant-associated microbe gene ontology (pamgo) interest group is the development of gene ontology (go) terms that capture the range of biological processes occurring between hosts and symbionts (from mutualists to pathogens). here, the application of the new go terms to type iii effector proteins (t3es) from the plant ...	2009	19576777
differential expression proteomics to investigate responses and resistance to orobanche crenata in medicago truncatula.	parasitic angiosperm orobanche crenata infection represents a major constraint for the cultivation of legumes worldwide. the level of protection achieved to date is either incomplete or ephemeral. hence, an efficient control of the parasite requires a better understanding of its interaction and associated resistance mechanisms at molecular levels.	2009	19575787
oxi1 protein kinase is required for plant immunity against pseudomonas syringae in arabidopsis.	expression of the arabidopsis oxidative signal-inducible1 (oxi1) serine/threonine protein kinase gene (at3g25250) is induced by oxidative stress. the kinase is required for root hair development and basal defence against the oomycete pathogen hyaloperonospora parasitica, two separate h(2)o(2)-mediated processes. in this study, the role of oxi1 during pathogenesis was characterized further. null oxi1 mutants are more susceptible to both virulent and avirulent strains of the biotrophic bacterial p ...	2009	19574254
abscisic acid has a key role in modulating diverse plant-pathogen interactions.	we isolated an activation-tagged arabidopsis (arabidopsis thaliana) line, constitutive disease susceptibility2-1d (cds2-1d), that showed enhanced bacterial growth when challenged with various pseudomonas syringae strains. systemic acquired resistance and systemic pathogenesis-related gene1 induction were also compromised in cds2-1d. the t-dna insertion adjacent to nine-cis-epoxycarotenoid dioxygenase5 (nced5), one of six genes encoding the abscisic acid (aba) biosynthetic enzyme nced, caused a m ...	2009	19571312
comparative large-scale analysis of interactions between several crop species and the effector repertoires from multiple pathovars of pseudomonas and ralstonia.	bacterial plant pathogens manipulate their hosts by injection of numerous effector proteins into host cells via type iii secretion systems. recognition of these effectors by the host plant leads to the induction of a defense reaction that often culminates in a hypersensitive response manifested as cell death. genes encoding effector proteins can be exchanged between different strains of bacteria via horizontal transfer, and often individual strains are capable of infecting multiple hosts. host p ...	2009	19571308
the multifunctional enzyme cyp71b15 (phytoalexin deficient3) converts cysteine-indole-3-acetonitrile to camalexin in the indole-3-acetonitrile metabolic network of arabidopsis thaliana.	accumulation of camalexin, the characteristic phytoalexin of arabidopsis thaliana, is induced by a great variety of plant pathogens. it is derived from trp, which is converted to indole-3-acetonitrile (ian) by successive action of the cytochrome p450 enzymes cyp79b2/b3 and cyp71a13. extracts from wild-type plants and camalexin biosynthetic mutants, treated with silver nitrate or inoculated with phytophthora infestans, were comprehensively analyzed by ultra-performance liquid chromatography elect ...	2009	19567706
rin4 functions with plasma membrane h+-atpases to regulate stomatal apertures during pathogen attack.	pathogen perception by the plant innate immune system is of central importance to plant survival and productivity. the arabidopsis protein rin4 is a negative regulator of plant immunity. in order to identify additional proteins involved in rin4-mediated immune signal transduction, we purified components of the rin4 protein complex. we identified six novel proteins that had not previously been implicated in rin4 signaling, including the plasma membrane (pm) h(+)-atpases aha1 and/or aha2. rin4 int ...	2009	19564897
a membrane-bound matrix-metalloproteinase from nicotiana tabacum cv. by-2 is induced by bacterial pathogens.	plant matrix metalloproteinases (mmp) are conserved proteolytic enzymes found in a wide range of monocotyledonous and dicotyledonous plant species. acting on the plant extracellular matrix, they play crucial roles in many aspects of plant physiology including growth, development and the response to stresses such as pathogen attack.	2009	19563670
recent advances in pamp-triggered immunity against bacteria: pattern recognition receptors watch over and raise the alarm.		2009	19561123
underexplored niches in research on plant pathogenic bacteria.		2009	19561122
synthetic ultrashort cationic lipopeptides induce systemic plant defense responses against bacterial and fungal pathogens.	a new family of synthetic, membrane-active, ultrashort lipopeptides composed of only four amino acids linked to fatty acids was tested for the ability to induce systemic resistance and defense responses in plants. we found that two peptides wherein the third residue is a d-enantiomer (italic), c16-kkkk and c16-kllk, can induce medium alkalinization of tobacco suspension-cultured cells and expression of defense-related genes in cucumber and arabidopsis seedlings. moreover, these compounds can pri ...	2009	19542326
the tomato pto kinase uses shared and unique surfaces to recognize divergent avirulence proteins.		2009	19542294
site-directed mutagenesis identifies a molecular switch involved in copper sensing by the histidine kinase cins in pseudomonas putida kt2440.	in the presence of copper, pseudomonas putida activates transcription of cinaq via the two-component system cins-cinr. the cins-cinr tcs was responsive to 0.5 microm copper and was specifically activated only by copper and silver. modeling studies of cins identified a potential copper binding site containing h37 and h147. cins mutants with h37r and h147r mutations had an almost 10-fold reduced copper-dependent induction of cinaq compared to the wild type.	2009	19542288
slya, a marr family transcriptional regulator, is essential for virulence in dickeya dadantii 3937.	slya, a marr family transcriptional regulator, controls an assortment of biological functions in several animal-pathogenic bacteria. in order to elucidate the functions of slya in the phytopathogen dickeya dadantii (formerly erwinia chrysanthemi) 3937, a slya gene deletion mutant (denoted deltaslya) was constructed. the mutant exhibited increased sensitivity to sodium hypochlorite, the cationic antimicrobial peptide polymyxin b, and oxidative stress. the mutant showed reduced production of pecta ...	2009	19542281
mapping of heterologous expressed sequence tags as an alternative to microarrays for study of defense responses in plants.	microarray technology helped to accumulate an immense pool of data on gene expression changes in response to different environmental factors. yet, computer- generated gene profiling using expressed sequence tags (est) represents a valuable alternative to microarrays, which allows efficient discovery of homologous sequences in evolutionarily different species and comparison of gene sets on the whole genome scale. in this study, we used publicly available est database derived from different plant ...	2009	19538747
cellular biophysics during freezing of rat and mouse sperm predicts post-thaw motility.	though cryopreservation of mouse sperm yields good survival and motility after thawing, cryopreservation of rat sperm remains a challenge. this study was designed to evaluate the biophysics (membrane permeability) of rat in comparison to mouse to better understand the cooling rate response that contributes to cryopreservation success or failure in these two sperm types. in order to extract subzero membrane hydraulic permeability in the presence of ice, a differential scanning calorimeter (dsc) m ...	2009	19535788
hormonometer: a tool for discerning transcript signatures of hormone action in the arabidopsis transcriptome.	plant hormones regulate growth and responses to environmental change. hormone action ultimately modifies cellular physiological processes and gene activity. to facilitate transcriptome evaluation of novel mutants and environmental responses, there is a need to rapidly assess the possible contribution of hormone action to changes in the levels of gene transcripts. we developed a vector-based algorithm that rapidly compares lists of transcripts yielding correlation values. the application as descr ...	2009	19535475
calcium and calmodulin-mediated regulation of gene expression in plants.	sessile plants have developed a very delicate system to sense diverse kinds of endogenous developmental cues and exogenous environmental stimuli by using a simple ca2+ ion. calmodulin (cam) is the predominant ca2+ sensor and plays a crucial role in decoding the ca2+ signatures into proper cellular responses in various cellular compartments in eukaryotes. a growing body of evidence points to the importance of ca2+ and cam in the regulation of the transcriptional process during plant responses to ...	2009	19529824
diverse transcriptional programs associated with environmental stress and hormones in the arabidopsis receptor-like kinase gene family.	the genome of arabidopsis thaliana encodes more than 600 receptor-like kinase (rlk) genes, by far the dominant class of receptors found in land plants. although similar to the mammalian receptor tyrosine kinases, plant rlks are serine/threonine kinases that represent a novel signaling innovation unique to plants and, consequently, an excellent opportunity to understand how extracellular signaling evolved and functions in plants as opposed to animals. rlks are predicted to be major components of ...	2009	19529822
common themes in the design and function of bacterial effectors.	central to the biology of many pathogenic bacteria are a number of specialized machines, known as type iii, type iv, or type vi protein secretion systems. these machines have specifically evolved to deliver bacterial effector proteins into host cells with the capacity to modulate a variety of cellular functions. the identification of the biochemical activities of many effector proteins, coupled with a better understanding of their potential contribution to pathogenesis, has revealed common theme ...	2009	19527884
autophagy, immunity, and microbial adaptations.	autophagy adjusts cellular biomass and function in response to diverse stimuli, including infection. autophagy plays specific roles in shaping immune system development, fueling host innate and adaptive immune responses, and directly controlling intracellular microbes as a cell-autonomous innate defense. as an evolutionary counterpoint, intracellular pathogens have evolved to block autophagic microbicidal defense and subvert host autophagic responses for their survival or growth. the ability of ...	2009	19527881
prediction of type iii secretion signals in genomes of gram-negative bacteria.	pathogenic bacteria infecting both animals as well as plants use various mechanisms to transport virulence factors across their cell membranes and channel these proteins into the infected host cell. the type iii secretion system represents such a mechanism. proteins transported via this pathway ("effector proteins") have to be distinguished from all other proteins that are not exported from the bacterial cell. although a special targeting signal at the n-terminal end of effector proteins has bee ...	2009	19526054
resistance to the pseudomonas syringae effector hopa1 is governed by the tir-nbs-lrr protein rps6 and is enhanced by mutations in srfr1.	the pseudomonas syringae-arabidopsis (arabidopsis thaliana) interaction is an extensively studied plant-pathogen system. arabidopsis possesses approximately 150 putative resistance genes encoding nucleotide binding site (nbs) and leucine-rich repeat (lrr) domain-containing proteins. the majority of these belong to the toll/interleukin-1 receptor (tir)-nbs-lrr (tnl) class. comparative studies with the coiled-coil-nbs-lrr genes rps2, rpm1, and rps5 and isogenic p. syringae strains expressing singl ...	2009	19525323
mining the arabidopsis and rice genomes for cyclophilin protein families.	cyclophilins, which possess peptidyl-prolyl isomerase activity, are cellular targets of immunosuppressant drugs and involved in a wide variety of functions. while the arabidopsis thaliana genome contains the largest number of cyclophilins, the number of plant cyclophilins available in databases is small compared to that of other organisms. it implies that many cyclophilins are yet to be identified in plants. in order to identify cyclophilin candidates from available plant sequence data, we exami ...	2009	19525202
bacterial growth restriction during host resistance to pseudomonas syringae is associated with leaf water loss and localized cessation of vascular activity in arabidopsis thaliana.	the physiological mechanisms by which plants limit the growth of bacterial pathogens during gene-for-gene resistance are poorly understood. we characterized early events in the arabidopsis thaliana-pseudomonas syringae pathosystem to identify physiological changes for which the kinetics are consistent with bacterial growth restriction. using a safranine-o dye solution to detect vascular activity, we demonstrated that a. thaliana col-0 resistance to p. syringae pv. tomato dc3000 cells expressing ...	2009	19522568
systemic acquired resistance.	upon infection with necrotizing pathogens many plants develop an enhanced resistance to further pathogen attack also in the uninoculated organs. this type of enhanced resistance is referred to as systemic acquired resistance (sar). in the sar state, plants are primed (sensitized) to more quickly and more effectively activate defense responses the second time they encounter pathogen attack. since sar depends on the ability to access past experience, acquired disease resistance is a paradigm for t ...	2006	19521483
nitric oxide production in plants: facts and fictions.	there is now general agreement that nitric oxide (no) is an important and almost universal signal in plants. nevertheless, there are still many controversial observations and opinions on the importance and function of no in plants. partly, this may be due to the difficulties in detecting and even more in quantifying no. here, we summarize major pathways of no production in plants, and briefly discuss some methodical problems.	2006	19521475
rrs1 and rps4 provide a dual resistance-gene system against fungal and bacterial pathogens.	colletotrichum higginsianum is a fungal pathogen that infects a wide variety of cruciferous plants, causing important crop losses. we have used map-based cloning and natural variation analysis of 19 arabidopsis ecotypes to identify a dominant resistance locus against c. higginsianum. this locus named rch2 (for recognition of c. higginsianum) maps in an extensive cluster of disease-resistance loci known as mrc-j in the arabidopsis ecotype ws-0. by analyzing natural variations within the mrc-j reg ...	2009	19519800
lifestyles of the effector rich: genome-enabled characterization of bacterial plant pathogens.		2009	19515788
arabidopsis gh3.5 regulates salicylic acid-dependent and both npr1-dependent and independent defense responses.	the cross-talk between plant disease resistance and development is fundamental to understanding systemic physiological processes during pathogen attack. our previous study showed that the arabidopsis gh3.5 gene acts as a bifunctional modulator of the salicylic acid (sa)-mediated resistance and the auxin-mediated susceptibility during the arabidopsis-pseudomonas syringae interaction as well as development. here, we further study the role and mechanism of gh3.5 involved in the sa-dependent defense ...	2008	19513247