Publications

2-amino-3-(oxirane-2,3-dicarboxamido)-propanoyl-valine, an effective peptide antibiotic from the epiphyte pantoea agglomerans 48b/90.	the epiphyte pantoea agglomerans 48b/90, which has been isolated from soybean leaves, belongs to the enterobacteriaceae, as does the plant pathogen erwinia amylovora, which causes fire blight on rosaceous plants such as apples and leads to severe economic losses. since p. agglomerans efficiently antagonizes phytopathogenic bacteria, the p. agglomerans strain c9-1 is used as a biocontrol agent (blightban c9-1). here we describe the bioassay-guided isolation of a peptide antibiotic that is highly ...	2009	19820144
crystal structures of pseudomonas syringae pv. tomato dc3000 quinone oxidoreductase and its complex with nadph.	zeta-crystallin-like quinone oxidoreductase is nad(p)h-dependent and catalyzes one-electron reduction of certain quinones to generate semiquinone. here we present the crystal structures of zeta-crystallin-like quinone oxidoreductase from pseudomonas syringae pv. tomato dc3000 (ptoqor) and its complexes with nadph determined at 2.4 and 2.01a resolutions, respectively. ptoqor forms as a homologous dimer, each monomer containing two domains. in the structure of the ptoqor-nadph complex, nadph locat ...	2009	19818736
oligonucleotide array discovery of polymorphisms in cultivated tomato (solanum lycopersicum l.) reveals patterns of snp variation associated with breeding.	cultivated tomato (solanum lycopersicum l.) has narrow genetic diversity that makes it difficult to identify polymorphisms between elite germplasm. we explored array-based single feature polymorphism (sfp) discovery as a high-throughput approach for marker development in cultivated tomato.	2009	19818135
molecular characterization of a defense-related amp-binding protein gene, osbiabp1, from rice.	we cloned and characterized a rice gene osbiabp1 encoding an amp-binding protein. the full-length cdna of osbiabp1 is 1912-bp long and is predicted to encode a 558-aa protein. osbiabp1 contains a typical amp-binding signature motif and shows high similarity to members of amp-binding protein family. osbiabp1 is expressed in stems, leaves and flowers of rice plants, but is not expressed, or expressed at a very low level, in rice roots. the expression of osbiabp1 was induced by some defense-related ...	2009	19816997
unraveling the roles of sphingolipids in plant innate immunity.		2009	19816144
retraction of : "the multilevel and dynamic interplay between plant and pathogen".		2009	19816134
the lysm receptor kinase cerk1 mediates bacterial perception in arabidopsis.		2009	19816132
biosynthesis of salicylic acid in plants.	salicylic acid (sa) is an important signal molecule in plants. two pathways of sa biosynthesis have been proposed in plants. biochemical studies using isotope feeding have suggested that plants synthesize sa from cinnamate produced by the activity of phenylalanine ammonia lyase (pal). silencing of pal genes in tobacco or chemical inhibition of pal activity in arabidopsis, cucumber and potato reduces pathogen-induced sa accumulation. genetic studies, on the other hand, indicate that the bulk of s ...	2009	19816125
the missing link?: arabidopsis spch is a mapk specificity factor that controls entry into the stomatal lineage.	mitogen activated protein kinase (mapk) signaling modules that incorporate atmpk3 and atmpk6 control critical aspects of arabidopsis biology including stress responses, development, cell division and cell death. arabidopsis stomatal development is negatively regulated by the yda-mkk4/5-mpk3/6 mapk module and follows a three step pathway of asymmetric and symmetric divisions followed by terminal differentiation. we have identified the bhlh transcription factor spch, which controls entry into the ...	2009	19816100
defects in flagellin glycosylation affect the virulence of pseudomonas syringae pv. tabaci 6605.	flagellar motility and its glycosylation are indispensable for the virulence of pseudomonas syringae pv. tabaci 6605. six serine residues of the flagellin protein at positions 143, 164, 176, 183, 193 and 201 are glycosylated, and the glycan structure at 201 was determined to consist of a trisaccharide of two l-rhamnosyl residues and a modified 4-amino-4,6-dideoxyglucosyl (viosamine) residue. to investigate the glycan structures attached to the other serine residues and to identify the glycans im ...	2010	19815579
substrate positioning controls the partition between halogenation and hydroxylation in the aliphatic halogenase, syrb2.	the alpha-ketoglutarate-dependent hydroxylases and halogenases employ similar reaction mechanisms involving hydrogen-abstracting fe(iv)-oxo (ferryl) intermediates. in the halogenases, the carboxylate residue from the his(2)(asp/glu)(1) "facial triad" of iron ligands found in the hydroxylases is replaced by alanine, and a halide ion (x(-)) coordinates at the vacated site. halogenation is thought to result from "rebound" of the halogen radical from the x-fe(iii)-oh intermediate produced by hydroge ...	2009	19815524
unsupervised meta-analysis on diverse gene expression datasets allows insight into gene function and regulation.	over the past years, microarray databases have increased rapidly in size. while they offer a wealth of data, it remains challenging to integrate data arising from different studies. here we propose an unsupervised approach of a large-scale meta-analysis on arabidopsis thaliana whole genome expression datasets to gain additional insights into the function and regulation of genes. applying kernel principal component analysis and hierarchical clustering, we found three major groups of experimental ...	2008	19812781
crosstalks between myo-inositol metabolism, programmed cell death and basal immunity in arabidopsis.	although it is a crucial cellular process required for both normal development and to face stress conditions, the control of programmed cell death in plants is not fully understood. we previously reported the isolation of atxr5 and atxr6, two pcna-binding proteins that could be involved in the regulation of cell cycle or cell death. a yeast two-hybrid screen using atxr5 as bait captured atips1, an enzyme which catalyses the committed step of myo-inositol (mi) biosynthesis. atips1 mutants form sp ...	2009	19812700
airborne induction and priming of plant defenses against a bacterial pathogen.	herbivore-induced plant volatiles affect the systemic response of plants to local damage and hence represent potential plant hormones. these signals can also lead to "plant-plant communication," a defense induction in yet undamaged plants growing close to damaged neighbors. we observed this phenomenon in the context of disease resistance. lima bean (phaseolus lunatus) plants in a natural population became more resistant against a bacterial pathogen, pseudomonas syringae pv syringae, when located ...	2009	19812184
hexanoic acid-induced resistance against botrytis cinerea in tomato plants.	we have demonstrated that root treatment with hexanoic acid protects tomato plants against botrytis cinerea. hexanoic acid-induced resistance (hx-ir) was blocked in the jasmonic acid (ja)-insensitive mutant jai1 (a coi1 homolog) and in the abscisic acid (aba)-deficient mutant flacca (flc). upon infection, the loxd gene as well as the oxylipin 12-oxo-phytodienoic acid and the bioactive molecule ja-ile were clearly induced in treated plants. however, the basal aba levels were not altered. hexanoic ...	2009	19810814
the pepper calmodulin gene cacam1 is involved in reactive oxygen species and nitric oxide generation required for cell death and the defense response.	calcium signaling has emerged as an important signal transduction pathway of higher plants in response to biotic and abiotic stresses. ca2+-bound calmodulin (cam) plays a critical role in decoding and transducing stress signals by activating specific targets. here, we isolated and functionally characterized the pathogen-responsive cam gene, capsicum annuum calmodulin 1 (cacam1), from pepper (c. annuum) plants. the cellular function of cacam1 was verified by agrobacterium spp.-mediated transient ...	2009	19810808
pseudomonas syringae pv. tomato dc3000 type iii effector hopaa1-1 functions redundantly with chlorosis-promoting factor pspto4723 to produce bacterial speck lesions in host tomato.	the ability of pseudomonas syringae pv. tomato dc3000 to cause bacterial speck disease in tomato is dependent on the injection, via the type iii secretion system, of approximately 28 avr/hop effector proteins. hopaa1-1 is encoded in the conserved effector locus (cel) of the p. syringae hrp pathogenicity island. transiently expressed hopaa1-1 acts inside saccharomyces cerevisiae and plant cells to elicit cell death. hopaa1 homologs were cloned and sequenced from the cel of seven p. syringae strai ...	2009	19810804
a non-hydrolyzable atp derivative generates a stable complex in a light-inducible two-component system.	isothermal calorimetry (itc) measurements yielded the binding constants during complex formation of light-inducible histidine kinases (hk) and their cognate chey-type response regulators (rr). hk-rr interactions represent the core function of the bacterial two-component system, which is also present in many bacterial phytochromes. here, we have studied the recombinant forms of phytochromes cpha and cphb from the cyanobacterium tolypothrix pcc7601 and their cognate rrs rcpa and rcpb. the interact ...	2009	19808667
first-principles study of non-heme fe(ii) halogenase syrb2 reactivity.	we present here a computational study of reactions at a model complex of the syrb2 enzyme active site. syrb2, which chlorinates l-threonine in the syringomycin biosynthetic pathway, belongs to a recently discovered class of alpha-ketoglutarate (alphakg), non-heme fe(ii)-dependent halogenases that share many structural and chemical similarities with hydroxylases. namely, halogenases and hydroxylases alike decarboxylate the alphakg co-substrate, facilitating formation of a high-energy ferryl-oxo i ...	2009	19807187
the atp-dependent amide ligases ddag and ddaf assemble the fumaramoyl-dipeptide scaffold of the dapdiamide antibiotics.	the enzymes ddag and ddaf, encoded in the pantoea agglomerans dapdiamide antibiotic biosynthetic gene cluster, when expressed in escherichia coli, form the tandem amide bonds of the dapdiamide scaffold at the expense of atp cleavage. ddag uses fumarate, 2,3-diaminopropionate (dap), and atp to make fumaroyl-amp transiently on the way to the n(beta)-fumaroyl-dap regioisomer. then ddaf acts as a second atp-dependent amide ligase, but this enzyme cleaves atp to adp and p(i) during amide bond formati ...	2009	19807062
the phytohormone precursor opda is isomerized in the insect gut by a single, specific glutathione transferase.	oxylipins play important roles in stress signaling in plants. the compound 12-oxophytodienoic acid (cis-opda) is an early biosynthetic precursor of jasmonic acid (ja), the key phytohormone orchestrating the plant anti-herbivore defense. when consumed by feeding lepidopteran larvae, plant-derived cis-opda suffers rapid isomerization to iso-opda in the midgut and is excreted in the frass. unlike opda epimerization (yielding trans-opda), the formation of iso-opda is enzyme-dependent, and is catalyz ...	2009	19805297
conserved synteny at the protein family level reveals genes underlying shewanella species' cold tolerance and predicts their novel phenotypes.	bacteria of the genus shewanella can thrive in different environments and demonstrate significant variability in their metabolic and ecophysiological capabilities including cold and salt tolerance. genomic characteristics underlying this variability across species are largely unknown. in this study, we address the problem by a comparison of the physiological, metabolic, and genomic characteristics of 19 sequenced shewanella species. we have employed two novel approaches based on association of a ...	2010	19802638
conserved synteny at the protein family level reveals genes underlying shewanella species' cold tolerance and predicts their novel phenotypes.	bacteria of the genus shewanella can thrive in different environments and demonstrate significant variability in their metabolic and ecophysiological capabilities including cold and salt tolerance. genomic characteristics underlying this variability across species are largely unknown. in this study, we address the problem by a comparison of the physiological, metabolic, and genomic characteristics of 19 sequenced shewanella species. we have employed two novel approaches based on association of a ...	2010	19802638
mutations in arabidopsis fatty acid amide hydrolase reveal that catalytic activity influences growth but not sensitivity to abscisic acid or pathogens.	fatty acid amide hydrolase (faah) terminates the endocannabinoid signaling pathway that regulates numerous neurobehavioral processes in animals by hydrolyzing n-acylethanolamines (naes). recently, an arabidopsis faah homologue (atfaah) was identified, and several studies, especially those using atfaah overexpressing and knock-out lines, have suggested an in vivo role for faah in the catabolism of naes in plants. we previously reported that overexpression of atfaah in arabidopsis resulted in acce ...	2009	19801664
top hits in contemporary jaz: an update on jasmonate signaling.	the phytohormone jasmonate (ja) regulates a wide range of growth, developmental, and defense-related processes during the plant life cycle. identification of the jaz family of proteins that repress ja responses has facilitated rapid progress in understanding how this lipid-derived hormone controls gene expression. recent analysis of jaz proteins has provided insight into the nature of the ja receptor, the chemical specificity of signal perception, and cross-talk between ja and other hormone resp ...	2009	19800644
deciphering cgmp signatures and cgmp-dependent pathways in plant defence.		2009	19794847
the multilevel and dynamic interplay between plant and pathogen.	phytopathogens invade into plant apoplast and proliferate by assimilating nutrition from plant cells. plants depend on sophisticated defensive strategies to resist this invasion. therefore, pathogenic disease and plant disease resistance are two opposite phases. fascinating molecular mechanisms uncovered that interactions between plant and pathogen are multilevel and dynamic processes. on one side, plant immunity system contains multiple layers mainly including the perception of common pathogen- ...	2009	19794843
in planta expression screens of phytophthora infestans rxlr effectors reveal diverse phenotypes, including activation of the solanum bulbocastanum disease resistance protein rpi-blb2.	the irish potato famine pathogen phytophthora infestans is predicted to secrete hundreds of effector proteins. to address the challenge of assigning biological functions to computationally predicted effector genes, we combined allele mining with high-throughput in planta expression. we developed a library of 62 infection-ready p. infestans rxlr effector clones, obtained using primer pairs corresponding to 32 genes and assigned activities to several of these genes. this approach revealed that 16 ...	2009	19794118
agrobacterium tumefaciens promotes tumor induction by modulating pathogen defense in arabidopsis thaliana.	agrobacterium tumefaciens causes crown gall disease by transferring and integrating bacterial dna (t-dna) into the plant genome. to examine the physiological changes and adaptations during agrobacterium-induced tumor development, we compared the profiles of salicylic acid (sa), ethylene (et), jasmonic acid (ja), and auxin (indole-3-acetic acid [iaa]) with changes in the arabidopsis thaliana transcriptome. our data indicate that host responses were much stronger toward the oncogenic strain c58 th ...	2009	19794116
actin-depolymerizing factor2-mediated actin dynamics are essential for root-knot nematode infection of arabidopsis.	reorganization of the actin and microtubule networks is known to occur in targeted vascular parenchymal root cells upon infection with the nematode meloidogyne incognita. here, we show that actin-depolymerizing factor (adf) is upregulated in the giant feeding cells of arabidopsis thaliana that develop upon nematode infection and that knockdown of a specific adf isotype inhibits nematode proliferation. analysis of the levels of transcript and the localization of seven adf genes shows that five ar ...	2009	19794115
phosphorylation of the pseudomonas syringae effector avrpto is required for fls2/bak1-independent virulence activity and recognition by tobacco.	the type iii effector protein avrpto from pseudomonas syringae pv. tomato is secreted into plant cells where it promotes bacterial growth and enhances symptoms of speck disease on susceptible tomato plants. the virulence activity of avrpto is due, in part, to its interaction with components of host pattern recognition receptor complexes, which disrupts pathogen-associated molecular pattern-triggered immunity. this disruption mechanism requires a structural element of the avrpto protein, the cd l ...	2010	19793077
micrornas in the rhizobia legume symbiosis.		2009	19789286
negative regulation of stress-activated mapk signaling in arabidopsis.		2009	19789279
map kinase phosphatase1 and protein tyrosine phosphatase1 are repressors of salicylic acid synthesis and snc1-mediated responses in arabidopsis.	mitogen-activated protein (map) kinase phosphatases are important negative regulators of the levels and kinetics of map kinase activation that modulate cellular responses. the dual-specificity phosphatase map kinase phosphatase1 (mkp1) was previously shown to regulate map kinase6 (mpk6) activation levels and abiotic stress responses in arabidopsis thaliana. here, we report that the mkp1 null mutation in the columbia (col) accession results in growth defects and constitutive biotic defense respon ...	2009	19789277
lights, rhythms, infection: the role of light and the circadian clock in determining the outcome of plant-pathogen interactions.	the importance of light with respect to the outcome of plant-pathogen interactions is becoming increasingly evident: light affects both the host response and the virulence of some pathogens. the response of plants to environmental signals and stresses is modulated by the circadian clock, and it is apparent that this may include immune responses. photo and temporal regulation of immune responses may allow plants to anticipate and react more effectively to particular pathogen infections. these asp ...	2009	19789275
genetic analysis of genes involved in synthesis of modified 4-amino-4,6-dideoxyglucose in flagellin of pseudomonas syringae pv. tabaci.	glycosylation of flagellin contributes to swimming and swarming motilities, adhesion ability, and consequently virulence in pseudomonas syringae pv. tabaci 6605. glycans attached to six serine residues are located in the central region of the flagellin polypeptide. the glycan structure at position ser 201 was recently revealed to consist of two l-rhamnoses and one modified 4-amino-4,6-dideoxyglucose (viosamine). to clarify the mechanisms for glycosylation of modified viosamine, genes encoding dt ...	2009	19787374
2-de analysis indicates that acinetobacter baumannii displays a robust and versatile metabolism.	acinetobacter baumannii is a nosocomial pathogen that has been associated with outbreak infections in hospitals. despite increasing awareness about this bacterium, its proteome remains poorly characterised, however recently the complete genome of a. baumannii reference strain atcc 17978 has been sequenced. here, we have used 2-de and maldi-tof/tof approach to characterise the proteome of this strain.	2009	19785748
contribution of mangotoxin to the virulence and epiphytic fitness of pseudomonas syringae pv. syringae.	mangotoxin is an antimetabolite toxin that inhibits ornithine acetyl transferase, a key enzyme in the biosynthetic pathway of ornithine and arginine and recently reported in strains of pseudomonas syringae pv. syringae (pss) isolated from mango. since symptoms on mango tissues are very difficult to reproduce, in this study the role of mangotoxin in pss virulence was addressed by analyzing the in planta growth and development of disease symptoms on tomato leaflets. inoculation experiments were ca ...	2009	19784928
imaging of multi-color fluorescence emission from leaf tissues.	multi-color fluorescence emission from leaf tissues is presented as a powerful reporter on plant biochemistry and physiology that can be applied both at macro- and micro-scales. the blue-green fluorescence emission is typically excited by ultraviolet (uv) excitation. however, this approach cannot be applied in investigating intact leaf interior because the uv photons are largely absorbed in the epidermis of the leaf surface. this methodological barrier is eliminated by replacing the uv photon ex ...	2009	19784795
distribution and phylogeny of light-oxygen-voltage-blue-light-signaling proteins in the three kingdoms of life.	plants and fungi respond to environmental light stimuli via the action of different photoreceptor modules. one such class, responding to the blue region of light, is constituted by photoreceptors containing so-called light-oxygen-voltage (lov) domains as sensor modules. four major lov families are currently identified in eukaryotes: (i) the plant phototropins, regulating various physiological effects such as phototropism, chloroplast relocation, and stomatal opening; (ii) the aureochromes, media ...	2009	19783626
comparative genome and phenotypic analysis of clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium.	the continued rise of clostridium difficile infections worldwide has been accompanied by the rapid emergence of a highly virulent clone designated pcr-ribotype 027. to understand more about the evolution of this virulent clone, we made a three-way genomic and phenotypic comparison of an 'historic' non-epidemic 027 c. difficile (cd196), a recent epidemic and hypervirulent 027 (r20291) and a previously sequenced pcr-ribotype 012 strain (630).	2009	19781061
a nomadic subtelomeric disease resistance gene cluster in common bean.	the b4 resistance (r) gene cluster is one of the largest clusters known in common bean (phaseolus vulgaris [pv]). it is located in a peculiar genomic environment in the subtelomeric region of the short arm of chromosome 4, adjacent to two heterochromatic blocks (knobs). we sequenced 650 kb spanning this locus and annotated 97 genes, 26 of which correspond to coiled-coil-nucleotide-binding-site-leucine-rich-repeat (cnl). conserved microsynteny was observed between the pv b4 locus and correspondin ...	2009	19776165
autophagy negatively regulates cell death by controlling npr1-dependent salicylic acid signaling during senescence and the innate immune response in arabidopsis.	autophagy is an evolutionarily conserved intracellular process for vacuolar degradation of cytoplasmic components. in higher plants, autophagy defects result in early senescence and excessive immunity-related programmed cell death (pcd) irrespective of nutrient conditions; however, the mechanisms by which cells die in the absence of autophagy have been unclear. here, we demonstrate a conserved requirement for salicylic acid (sa) signaling for these phenomena in autophagy-defective mutants (atg m ...	2009	19773385
genotypic comparison of pantoea agglomerans plant and clinical strains.	pantoea agglomerans strains are among the most promising biocontrol agents for a variety of bacterial and fungal plant diseases, particularly fire blight of apple and pear. however, commercial registration of p. agglomerans biocontrol products is hampered because this species is currently listed as a biosafety level 2 (bl2) organism due to clinical reports as an opportunistic human pathogen. this study compares plant-origin and clinical strains in a search for discriminating genotypic/phenotypic ...	2009	19772624
pseudomonas benzenivorans sp. nov. and pseudomonas saponiphila sp. nov., represented by xenobiotics degrading type strains.	two strains of gram-negative bacteria isolated because of their abilities to decompose xenobiotic compounds were subjected to a polyphasic taxonomic study. on the basis of 16s rrna gene sequence analysis, the two strains were found to belong to the genus pseudomonas. benzene degrading strain dsm 8628(t) was moderately related to p. flavescens ncpp 3063(t) (98.3% similarity), p. monteilii cip 104883(t), and p. plecoglossicida fpc 951(t) (98.1%). strain dsm 9751(t) capable to grow with cetyltrimet ...	2010	19771475
mediators of lipid a modification, rna degradation, and central intermediary metabolism facilitate the growth of legionella pneumophila at low temperatures.	legionella pneumophila is an aquatic bacterium that is also the agent of legionnaires' disease pneumonia. since l. pneumophila is transmitted directly from the environment to the lung, it is important to understand how legionellae survive at low temperatures. to identify genes that are needed for l. pneumophila growth at low temperature, we screened a population of mutagenized legionellae for strains that are specifically impaired for growth at 17 degrees c. from the 7,400 mutants tested, 11 dis ...	2010	19768502
mediators of lipid a modification, rna degradation, and central intermediary metabolism facilitate the growth of legionella pneumophila at low temperatures.	legionella pneumophila is an aquatic bacterium that is also the agent of legionnaires' disease pneumonia. since l. pneumophila is transmitted directly from the environment to the lung, it is important to understand how legionellae survive at low temperatures. to identify genes that are needed for l. pneumophila growth at low temperature, we screened a population of mutagenized legionellae for strains that are specifically impaired for growth at 17 degrees c. from the 7,400 mutants tested, 11 dis ...	2010	19768502
zinc-independent folate biosynthesis: genetic, biochemical, and structural investigations reveal new metal dependence for gtp cyclohydrolase ib.	gtp cyclohydrolase i (gcyh-i) is an essential zn(2+)-dependent enzyme that catalyzes the first step of the de novo folate biosynthetic pathway in bacteria and plants, the 7-deazapurine biosynthetic pathway in bacteria and archaea, and the biopterin pathway in mammals. we recently reported the discovery of a new prokaryotic-specific gcyh-i (gcyh-ib) that displays no sequence identity to the canonical enzyme and is present in approximately 25% of bacteria, the majority of which lack the canonical ...	2009	19767425
structural characterization of an o-linked tetrasaccharide from pseudomonas syringae pv. tabaci flagellin.	the flagellin of pseudomonas syringae pv. tabaci is a glycoprotein that contains o-linked oligosaccharides composed of rhamnosyl and 4,6-dideoxy-4-(3-hydroxybutanamido)-2-o-methylglucosyl residues. these o-linked glycans are released by hydrazinolysis and then labeled at their reducing ends with 2-aminopyridine (pa). a pa-labeled trisaccharide and a pa-labeled tetrasaccharide are isolated by normal-phase high-performance liquid chromatography. these oligosaccharides are structurally characterize ...	2009	19766989
concentrations of host-specific and generic fecal markers measured by quantitative pcr in raw sewage and fresh animal feces.	we measured the concentrations of four host-specific (human, dog, cow, and horse bacteroidales), four generic fecal (16s total bacteroidales and escherichia coli, 23s enterococcus and uida e. coli,) and two universal bacterial (16s universal and rpob universal) dna targets by qpcr in raw sewage and pooled fecal samples from dogs, cows, horses, and canada geese. a spiking protocol using the non-fecal bacterium pseudomonas syringae pph 6 was developed to estimate the recovery of dna from fecal and ...	2009	19765792
receptor quality control in the endoplasmic reticulum for plant innate immunity.	pattern recognition receptors in eukaryotes initiate defence responses on detection of microbe-associated molecular patterns shared by many microbe species. the leu-rich repeat receptor-like kinases fls2 and efr recognize the bacterial epitopes flg22 and elf18, derived from flagellin and elongation factor-tu, respectively. we describe arabidopsis 'priority in sweet life' (psl) mutants that show de-repressed anthocyanin accumulation in the presence of elf18. efr accumulation and signalling, but n ...	2009	19763087
control of the pattern-recognition receptor efr by an er protein complex in plant immunity.	in plant innate immunity, the surface-exposed leucine-rich repeat receptor kinases efr and fls2 mediate recognition of the bacterial pathogen-associated molecular patterns ef-tu and flagellin, respectively. we identified the arabidopsis stromal-derived factor-2 (sdf2) as being required for efr function, and to a lesser extent fls2 function. sdf2 resides in an endoplasmic reticulum (er) protein complex with the hsp40 erdj3b and the hsp70 bip, which are components of the er-quality control (er-qc) ...	2009	19763086
functional analysis of alpha-dox2, an active alpha-dioxygenase critical for normal development in tomato plants.	plant alpha-dioxygenases initiate the synthesis of oxylipins by catalyzing the incorporation of molecular oxygen at the alpha-methylene carbon atom of fatty acids. previously, alpha-dox1 has been shown to display alpha-dioxygenase activity and to be implicated in plant defense. in this study, we investigated the function of a second alpha-dioxygenase isoform, alpha-dox2, in tomato (solanum lycopersicum) and arabidopsis (arabidopsis thaliana). recombinant slalpha-dox2 and atalpha-dox2 proteins ca ...	2009	19759339
the type iii secretion system is involved in the invasion and intracellular survival of escherichia coli k1 in human brain microvascular endothelial cells.	type iii secretion systems (t3sss) have been documented in many gram-negative bacteria, including enterohemorrhagic escherichia coli. we have previously shown the existence of a putative t3ss in meningitis-causing e. coli k1 strains, referred to as e. coli type iii secretion 2 (ett2). the sequence of ett2 in meningitis-causing e. coli k1 strain ec10 (o7:k1) revealed that ett2 comprises the epr, epa and eiv genes, but bears mutations, deletions and insertions. we constructed the ec10 mutants dele ...	2009	19758329
corruption of innate immunity by bacterial proteases.	the innate immune system of the human body has developed numerous mechanisms to control endogenous and exogenous bacteria and thus prevent infections by these microorganisms. these mechanisms range from physical barriers such as the skin or mucosal epithelium to a sophisticated array of molecules and cells that function to suppress or prevent bacterial infection. many bacteria express a variety of proteases, ranging from non-specific and powerful enzymes that degrade many proteins involved in in ...	2009	19756242
surface display of heterologous proteins in bacillus thuringiensis using a peptidoglycan hydrolase anchor.	abstract:	2009	19754974
comparative in vivo gene expression of the closely related bacteria photorhabdus temperata and xenorhabdus koppenhoeferi upon infection of the same insect host, rhizotrogus majalis.	photorhabdus and xenorhabdus are gram-negative, phylogenetically related, enterobacteria, forming mutualism with the entomopathogenic nematodes heterorhabditis and steinernema, respectively. the mutualistic bacteria living in the intestines of the nematode infective juveniles are pathogenic to the insect upon release by the nematodes into the insect hemolymph. such a switch needs activation of genes that promote bacterial virulence. we studied in vivo gene expression in photorhabdus temperata an ...	2009	19754939
reverse-engineering the arabidopsis thaliana transcriptional network under changing environmental conditions.	understanding the molecular mechanisms plants have evolved to adapt their biological activities to a constantly changing environment is an intriguing question and one that requires a systems biology approach. here we present a network analysis of genome-wide expression data combined with reverse-engineering network modeling to dissect the transcriptional control of arabidopsis thaliana. the regulatory network is inferred by using an assembly of microarray data containing steady-state rna express ...	2009	19754933
ectopic expression of mgsm1, a cerato-platanin family protein from magnaporthe grisea, confers broad-spectrum disease resistance in arabidopsis.	proteins belonging to the newly identified cerato-platanin (cp) family have been shown to have elicitor activity in inducing disease resistance responses in various plants. in this study, we characterized a gene, mgsm1, from magnaporthe grisea, encoding a putative small protein belonging to the cp family. mgsm1 was constitutively expressed not only in different fungal growth stages but also during its infection process in rice plants. agrobacterium-mediated transient expression of mgsm1 in arabi ...	2009	19754836
expression of bacterial genes in transgenic tobacco: methods, applications and future prospects.	tobacco is the most commonly used plant for expression of transgenes from a variety of organisms, because it is easily grown and transformed, it provides abundant amounts of fresh tissue and has a well-established cell culture system. many bacterial proteins involved in the synthesis of commercial products are currently engineered for production in tobacco. bacterial enzymes synthesized in tobacco can enhance protection against abiotic stresses and diseases, and provide a system to test applied ...	2007	19750137
combination of chromogenic differential medium and esta-specific pcr for isolation and detection of phytopathogenic xanthomonas spp.	a xanthomonad differential medium (designated xan-d medium) was developed, on which streaks and colonies of xanthomonads, including 13 species of the genus xanthomonas, turned wet-shining yellow-green and were surrounded with a smaller milky zone and a bigger clear zone in 3 to 4 days. the characteristics could easily be differentiated from those of yellow nonxanthomonads and other bacteria. the mechanism of color change and formation of a milky zone on the medium are mainly due to the tween 80 ...	2009	19749062
motility and flagellar glycosylation in clostridium difficile.	in this study, intact flagellin proteins were purified from strains of clostridium difficile and analyzed using quadrupole time of flight and linear ion trap mass spectrometers. top-down studies showed the flagellin proteins to have a mass greater than that predicted from the corresponding gene sequence. these top-down studies revealed marker ions characteristic of glycan modifications. additionally, diversity in the observed masses of glycan modifications was seen between strains. electron tran ...	2009	19749038
one for all: the receptor-associated kinase bak1.	the plant receptor kinase bak1/serk3 has been identified as a partner of ligand-binding leucine-rich repeat receptor kinases, in particular the brassinosteroid receptor bri1 and the immune receptor fls2. bak1 positively regulates bri1 receptor function via physical interaction and transphosphorylation. since its first description in 2001, several independent groups have discovered bak1/serk3 as a component of diverse processes, including brassinosteroid signaling, light responses, cell death, an ...	2009	19748302
bacterial evolution by genomic island transfer occurs via dna transformation in planta.	our understanding of the evolution of microbial pathogens has been advanced by the discovery of "islands" of dna that differ from core genomes and contain determinants of virulence. the acquisition of genomic islands (gis) by horizontal gene transfer (hgt) is thought to have played a major role in microbial evolution. there are, however, few practical demonstrations of the acquisition of genes that control virulence, and, significantly, all have been achieved outside the animal or plant host. lo ...	2009	19747826
pyrroloquinoline quinone biogenesis: demonstration that pqqe from klebsiella pneumoniae is a radical s-adenosyl-l-methionine enzyme.	biogenesis of pyrroloquinoline quinone (pqq) in klebsiella pneumoniae requires the expression of six genes (pqqa-f). one of these genes (pqqe) encodes a 43 kda protein (pqqe) that plays a role in the initial steps in pqq formation [veletrop, j. s., et al. (1995) j. bacteriol. 177, 5088-5098]. pqqe contains two highly conserved cysteine motifs at the n- and c-termini, with the n-terminal motif comprised of a cx(3)cx(2)c consensus sequence that is unique to a family of proteins known as radical s- ...	2009	19746930
assay for pathogen-associated molecular pattern (pamp)-triggered immunity (pti) in plants.	to perceive potential pathogens in their environment, plants use pattern recognition receptors (prrs) present on their plasma membranes. prrs recognize conserved microbial features called pathogen-associated molecular patterns (pamps) and this detection leads to pamp-triggered immunity (pti), which effectively prevents colonization of plant tissues by non-pathogens(1,2). the most well studied system in pti is the fls2-dependent pathway(3). fls2 recognizes the pamp flg22 that is a component of ba ...	2009	19741586
the arabidopsis ataf1, a nac transcription factor, is a negative regulator of defense responses against necrotrophic fungal and bacterial pathogens.	transcription factors of the nac family are known to be involved in various growth or developmental processes and in regulation of response to environmental stresses. in the present study, we report that arabidopsis ataf1 is a negative regulator of defense responses against both necrotrophic fungal and bacterial pathogens. expression of ataf1 was downregulated after infection with botrytis cinerea or pseudomonas syringae pv. tomato or after treatment with salicylic acid (sa), jasmonic acid, and ...	2009	19737096
characterization of rimo, a new member of the methylthiotransferase subclass of the radical sam superfamily.	rimo, encoded by the ylig gene in escherichia coli, has been recently identified in vivo as the enzyme responsible for the attachment of a methylthio group on the beta-carbon of asp88 of the small ribosomal protein s12 [anton, b. p., saleh, l., benner, j. s., raleigh, e. a., kasif, s., and roberts, r. j. (2008) proc. natl. acad. sci. u.s.a. 105, 1826-1831]. to date, it is the only enzyme known to catalyze methylthiolation of a protein substrate; the four other naturally occurring methylthio modi ...	2009	19736993
mutations that disrupt either the pqq or the gdh gene of rahnella aquatilis abolish the production of an antibacterial substance and result in reduced biological control of grapevine crown gall.	rahnella aquatilis hx2, a biocontrol agent for grapevine crown gall caused by agrobacterium vitis, produces an antibacterial substance that inhibits the growth of a. vitis in vitro. in this study, we show that mh15 and mh16, two tn5-induced mutants of hx2, have lost their abilities to inhibit a. vitis and have reduced biocontrol activities; they grow in logarithmic phase at a rate similar to that of the wild type and have single tn5 insertions. they are also impaired in producing pyrroloquinolin ...	2009	19734331
comparative analyses of genotype dependent expressed sequence tags and stress-responsive transcriptome of chickpea wilt illustrate predicted and unexpected genes and novel regulators of plant immunity.	the ultimate phenome of any organism is modulated by regulated transcription of many genes. characterization of genetic makeup is thus crucial for understanding the molecular basis of phenotypic diversity, evolution and response to intra- and extra-cellular stimuli. chickpea is the world's third most important food legume grown in over 40 countries representing all the continents. despite its importance in plant evolution, role in human nutrition and stress adaptation, very little ests and diffe ...	2009	19732460
molecular analysis of menadione-induced resistance against biotic stress in arabidopsis.	menadione sodium bisulphite (msb) is a water-soluble derivative of vitamin k3, or menadione, and has been previously demonstrated to function as a plant defence activator against several pathogens in several plant species. however, there are no reports of the role of this vitamin in the induction of resistance in the plant model arabidopsis thaliana. in the current study, we demonstrate that msb induces resistance by priming in arabidopsis against the virulent strain pseudomonas syringae pv. tom ...	2009	19732380
phytochrome b and histone deacetylase 6 control light-induced chromatin compaction in arabidopsis thaliana.	natural genetic variation in arabidopsis thaliana exists for many traits and often reflects acclimation to local environments. studying natural variation has proven valuable in the characterization of phenotypic traits and, in particular, in identifying genetic factors controlling these traits. it has been previously shown that chromatin compaction changes during development and biotic stress. to gain more insight into the genetic control of chromatin compaction, we investigated the nuclear phen ...	2009	19730687
n-acylhomoserine lactones involved in quorum sensing control the type vi secretion system, biofilm formation, protease production, and in vivo virulence in a clinical isolate of aeromonas hydrophila.	in this study, we delineated the role of n-acylhomoserine lactone(s) (ahls)-mediated quorum sensing (qs) in the virulence of diarrhoeal isolate ssu of aeromonas hydrophila by generating a double knockout delta ahyri mutant. protease production was substantially reduced in the delta ahyri mutant when compared with that in the wild-type (wt) strain. importantly, based on western blot analysis, the delta ahyri mutant was unable to secrete type vi secretion system (t6ss)-associated effectors, namely ...	2009	19729404
three-dimensional structure of the enveloped bacteriophage phi12: an incomplete t = 13 lattice is superposed on an enclosed t = 1 shell.	bacteriophage phi12 is a member of the cystoviridae, a unique group of lipid containing membrane enveloped bacteriophages that infect the bacterial plant pathogen pseudomonas syringae pv. phaseolicola. the genomes of the virus species contain three double-stranded (dsrna) segments, and the virus capsid itself is organized in multiple protein shells. the segmented dsrna genome, the multi-layered arrangement of the capsid and the overall viral replication scheme make the cystoviridae similar to th ...	2009	19727406
dual roles of reactive oxygen species and nadph oxidase rbohd in an arabidopsis-alternaria pathosystem.	arabidopsis (arabidopsis thaliana) nadph oxidases have been reported to suppress the spread of pathogen- and salicylic acid-induced cell death. here, we present dual roles of rbohd (for respiratory burst oxidase homolog d) in an arabidopsis-alternaria pathosystem, suggesting either initiation or prevention of cell death dependent on the distance from pathogen attack. our data demonstrate that a rbohd knockout mutant exhibits increased spread of cell death at the macroscopic level upon inoculatio ...	2009	19726575
legume transcription factor genes: what makes legumes so special?		2009	19726573
involvement of coronatine-inducible reactive oxygen species in bacterial speck disease of tomato.		2009	19721761
a possible role of class 1 plant hemoglobin at the early stage of legume-rhizobium symbiosis.		2009	19721749
mechanism-based tuning of a lov domain photoreceptor.	phototropin-like lov domains form a cysteinyl-flavin adduct in response to blue light but show considerable variation in output signal and the lifetime of the photo-adduct signaling state. mechanistic studies of the slow-cycling fungal lov photoreceptor vivid (vvd) reveal the importance of reactive cysteine conformation, flavin electronic environment and solvent accessibility for adduct scission and thermal reversion. proton inventory, ph effects, base catalysis and structural studies implicate ...	2009	19718042
ethylene insensitive3 and ethylene insensitive3-like1 repress salicylic acid induction deficient2 expression to negatively regulate plant innate immunity in arabidopsis.	pathogen/microbe-associated molecular patterns (pamps/mamps) trigger plant immunity that forms the first line inducible defenses in plants. the regulatory mechanism of mamp-triggered immunity, however, is poorly understood. here, we show that arabidopsis thaliana transcription factors ethylene insensitive3 (ein3) and ethylene insensitive3-like1 (eil1), previously known to mediate ethylene signaling, also negatively regulate pamp-triggered immunity. plants lacking ein3 and eil1 display enhanced p ...	2009	19717619
the arabidopsis coronatine insensitive1 protein is a jasmonate receptor.	jasmonates play a number of diverse roles in plant defense and development. coronatine insensitive1 (coi1), an f-box protein essential for all the jasmonate responses, interacts with multiple proteins to form the scf(coi1) e3 ubiquitin ligase complex and recruits jasmonate zim-domain (jaz) proteins for degradation by the 26s proteasome. to determine which protein directly binds to jasmonoyl-isoleucine (ja-ile)/coronatine (cor) and serves as a receptor for jasmonate, we built a high-quality struc ...	2009	19717617
a novel insertion sequence derepresses efflux pump expression and preadapts pseudomonas putida s12 for extreme solvent stress.	a multidrug efflux pump, srpabc, plays a key role in pseudomonas putida s12 tolerance to toxic organic solvents. srprs are putative regulators of the srpabc efflux pump encoded upstream of the srpabc structural genes, and previous studies suggest that srps is a repressor of srpabc expression. an s12 isolate able to withstand extreme solvent stress carries a novel insertion sequence, isppu21, interrupting srps. this insertion preadapts s12 to extreme solvent conditions through constitutive srpabc ...	2009	19717594
specific er quality control components required for biogenesis of the plant innate immune receptor efr.	plant innate immunity depends in part on recognition of pathogen-associated molecular patterns (pamps), such as bacterial flagellin, ef-tu, and fungal chitin. recognition is mediated by pattern-recognition receptors (prrs) and results in pamp-triggered immunity. ef-tu and flagellin, and the derived peptides elf18 and flg22, are recognized in arabidopsis by the leucine-rich repeat receptor kinases (lrr-rk), efr and fls2, respectively. to gain insights into the molecular mechanisms underlying pti, ...	2009	19717464
active-site dynamics of spvc virulence factor from salmonella typhimurium and density functional theory study of phosphothreonine lyase catalysis.	the newly discovered spvc effector protein from salmonella typhimurium interferes with the host immune response by dephosphorylating mitogen-activated protein kinases (mapks) with a beta-elimination mechanism. to understand this unique phosphothreonine lyase catalysis, the dynamics of the enzyme-substrate complex of the spvc effector is investigated with a 3.2 ns molecular dynamics simulation, which reveals that the phosphorylated peptide substrate is tightly held in the active site by a hydroge ...	2009	19715325
the cyst nematode sprysec protein rbp-1 elicits gpa2- and rangap2-dependent plant cell death.	plant nb-lrr proteins confer robust protection against microbes and metazoan parasites by recognizing pathogen-derived avirulence (avr) proteins that are delivered to the host cytoplasm. microbial avr proteins usually function as virulence factors in compatible interactions; however, little is known about the types of metazoan proteins recognized by nb-lrr proteins and their relationship with virulence. in this report, we demonstrate that the secreted protein rbp-1 from the potato cyst nematode ...	2009	19714238
the colletotrichum orbiculare ssd1 mutant enhances nicotiana benthamiana basal resistance by activating a mitogen-activated protein kinase pathway.	plant basal resistance is activated by virulent pathogens in susceptible host plants. a colletotrichum orbiculare fungal mutant defective in the ssd1 gene, which regulates cell wall composition, is restricted by host basal resistance responses. here, we identified the nicotiana benthamiana signaling pathway involved in basal resistance by silencing the defense-related genes required for restricting the growth of the c. orbiculare mutant. only silencing of map kinase kinase2 or of both salicylic ...	2009	19706796
the involvement of the arabidopsis crt1 atpase family in disease resistance protein-mediated signaling.	resistance (r) gene-mediated immunity provides plants with rapid and strain-specific protection against pathogen infection. our recent study using the genetically tractable arabidopsis and turnip crinkle virus (tcv) pathosystem revealed a novel component, named crt1 (compromised for recognition of the tcv cp), that is involved in general r gene-mediated signaling, including that mediated by hrt, an r gene against tcv. the arabidopsis crt1 gene family contains six additional members, of which two ...	2008	19704828
oviposition-induced changes in arabidopsis genome expression: anticipating your enemy?	plants have evolved exquisite ways to detect their enemies and are able to induce defenses responses tailored to their specific aggressors. insect eggs deposited on a leaf represent a future threat as larvae hatching from the egg will ultimately feed on the plant. although direct and indirect defenses towards oviposition have been documented, our knowledge of the molecular changes triggered by egg deposition is limited. using a whole-genome microarray, we recently analyzed the expression profile ...	2007	19704745
considerations on post-translational modification and protein targeting in the arabidopsis defense proteome.	the immune response of plants to potential pathogens consists of two levels of defense; basal resistance triggered by pattern recognition (pti) and effector triggered immunity (eti). recent analysis of the arabidopsis proteome after challenge by three strains of pseudomonas syringae identified proteins implicated in the establishment of disease, pti and eti. in this addendum we discuss the significance of some of the putative post-translational modifications and the predicted localisation of the ...	2007	19704740
the role of atnudt7, a nudix hydrolase, in the plant defense response.	nudix hydrolases constitute a large family of proteins that hydrolyze nucleoside diphosphate derivatives. some nudix hydrolases act as 'housecleaning' enzymes whereas others may function to sense and modulate the levels of their substrates to maintain physiological homeostasis. the arabidopsis genome encodes 32 nudix proteins (atnudts). however, their physiological substrates and biological functions are little known. atnudt7 has been identified as a negative regulator of the defense response an ...	2008	19704728
homoserine lactones: do plants really listen to bacterial talk?	the bacterial quorum sensing signals n-acyl-l-homoserine lactones (ahl) enable bacterial cells to regulate gene expression depending on population density, which eventually leads to invasion of hosts. only little is known about the molecular ways of plants reacting to these bacterial signals. recently, we showed that the contact of arabidopsis thaliana roots with n-hexanoyl-dl-homoserine-lactone (hhl) resulted in distinct transcriptional changes in roots and shoots, respectively. in addition, we ...	2009	19704707
host-derived signals activate plant innate immunity.	oligogalacturonides (ogs) are endogenous elicitors of defense responses released after partial degradation of pectin in the plant cell wall. despite ogs cannot be considered true pathogen-associated molecular patterns, such as flg22, they can be considered host-associated molecular patterns that are generated by the host cell during the infection process, and that stimulate the plant innate immune system. we have previously shown that, in arabidopsis, ogs increase resistance to botrytis cinerea ...	2009	19704701
manipulation of plant programmed cell death pathways during plant-pathogen interactions.	the interaction of plants with bacterial pathogens involves the manipulation of programmed cell death (pcd) pathways. during a resistance interaction pcd is induced in a process termed the hypersensitive response (hr) which may function to limit pathogen spread. in a susceptible plant-pathogen interactions, the pathogen both inhibits and/or induces host pcd depending on the infection stage and lifestyle of the pathogen. genes/pathways regulating pcd in plants have been difficult to identify due ...	2007	19704693
regulation of plant innate immunity by sumo e3 ligase.	reversible posttranslational modification of proteins by the action of small ubiquitin-like modifier (sumo) peptide (sumoylation) has been known to participate in various biological processes in eukaryotes. however, much less is known about the role of sumoylation in plants. in our recent paper to which we write this addendum, we show that loss of siz1, a sumo e3 ligase, results in a highly increased sa-mediated defense signaling through a pad4-dependent pathway. this signaling leads to constitu ...	2007	19704670
arabidopsis thaliana root surface chemistry regulates in planta biofilm formation of bacillus subtilis.	among the various rhizospheric interactions, plant root-microbe interactions are very important both economically and ecologically. the interaction of plant roots with plant growth promoting rhizobacteria (pgpr) have been studied in case of symbiotic organisms. however, the knowledge on interaction with other pgprs such as biocontrol bacillus sps. is vastly unexplored. especially the complex root surface chemistry and its effect on modulating the bacterial growth and association with the root sy ...	2007	19704655
the arabidopsis map kinase kinase 7: a crosstalk point between auxin signaling and defense responses?	plant-pathogen interaction induces a complex host response that coordinates various signaling pathways through multiple signal molecules. besides the well-documented signal molecules salicylic acid (sa), ethylene and jasmonic acid, auxin is emerging as an important player in this response. we recently characterized an arabidopsis activation-tagged mutant, bud1, in which the expression of the map kinase kinase 7 (atmkk7) gene is increased. the bud1 mutant plants accumulate elevated levels of sa a ...	2008	19704652
roles of iron in plant defence and fungal virulence.	iron is an essential component of various proteins and pigments for both plants and pathogenic fungi. however, redox cycling between the ferric and ferrous forms of iron can also catalyse the production of dangerous free radicals and iron homeostasis is therefore tightly regulated. our work has indicated that monocot plants challenged by pathogenic fungi redistribute cellular iron to the apoplast in a controlled manner to activate both intracellular and extracellular defences. in the apoplast, t ...	2007	19704628
beta-1,3-glucanases: plasmodesmal gate keepers for intercellular communication.	plasmodesmata (pd), coaxial membranous channels that connect adjacent plant cells, are not static, but show a dynamic nature and can be opened or closed. these controlled changes in pd conductivity regulate plant symplasmic permeability and play a role both in development and defense processes. one of the mechanisms shown to produce these changes is the deposition and hydrolysis of callose by beta-1-3-synthase and glucanase, respectively. recently we have identified the first beta-1,3-glucanase ...	2007	19704615
plants under attack: multiple interactions with insects and microbes.	to defend themselves, plants activate inducible defense mechanisms that are effective against the invader that is encountered. there is partial overlap in the defense signaling pathways that are induced by insect herbivores and microbial pathogens that may result in cross-resistance. we have previously shown that infestation by tissue-chewing pieris rapae larvae induces resistance in arabidopsis thaliana against subsequent attack by the microbial pathogens pseudomonas syringae pv. tomato (pst), ...	2007	19704549
gene silencing to investigate the roles of receptor-like proteins in arabidopsis.	receptor-like proteins (rlps) are cell surface receptors that play important roles in various processes. in several plant species rlps have been found to play a role in disease resistance, including the tomato cf and ve proteins and the apple hcrvf proteins that mediate resistance against the fungal pathogens cladosporium fulvum, verticillium spp., and venturia inaequalis, respectively. the arabidopsis genome contains 57 atrlp genes. two of these, clv2 (atrlp10) and tmm (atrlp17), have well-char ...	2008	19704533