Publications

the role of ndr1 in pathogen perception and plant defense signaling.	the biochemical and cellular function of ndr1 in plant immunity and defense signaling has long remained elusive. herein, we describe a novel role for ndr1 in both pathogen perception and plant defense signaling, elucidated by exploring a broader, physiological role for ndr1 in general stress responses and cell wall adhesion. based on our predictive homology modeling, coupled with a structure-function approach, we found that ndr1 shares a striking similarity to mammalian integrins, well-character ...	2011	21758001
recognition events and host-pathogen co-evolution in gene-for-gene resistance to flax rust.	the outcome of infection of individual plants by pathogenic organisms is governed by complex interactions between the host and pathogen. these interactions are the result of long-term co-evolutionary processes involving selection and counterselection between plants and their pathogens. these processes are ongoing, and occur at many spatio-temporal scales, including genes and gene products, cellular interactions within host individuals, and the dynamics of host and pathogen populations. however, ...	2009	21760756
sinorhizobium fredii usda257 and s. fredii usda191, cultivar-specific and non-specific symbionts of soybean, produce distinct cell surface appendages.	sinorhizobium fredii usda257 and s. fredii usda191 are fast-growing rhizobia that form nitrogen-fixing nodules on soybean roots. in contrast to usda191, usda257 exhibits cultivar specificity and can form nodules only on primitive soybean cultivars. in response to flavonoids released from soybean roots these two rhizobia secrete nodulation outer proteins (nop) to the extracellular milieu through a type iii secretion system. in spite of the fact that nop proteins are known to regulate legume nodul ...	2011	21764962
subcellular targeting of salmonella virulence proteins by host-mediated s-palmitoylation.	several pathogenic bacteria utilize type iii secretion systems (ttss) to deliver into host cells bacterial virulence proteins with the capacity to modulate a variety of cellular pathways. once delivered into host cells, the accurate targeting of bacterial effectors to specific locations is critical for their proper function. however, little is known about the mechanisms these virulence effectors use to reach their subcellular destination. here we show that the salmonella ttss effector proteins s ...	2011	21767808
inducing salt tolerance in mung bean through coinoculation with rhizobia and plant-growth-promoting rhizobacteria containing 1-aminocyclopropane-1-carboxylate deaminase.	twenty-five strains of plant-growth-promoting rhizobacteria (pgpr) containing 1-aminocyclopropane-1-carboxylate (acc) deaminase and 10 strains of rhizobia were isolated from rhizosphere soil samples and nodules of mung bean. they were screened in separate trials under salt-stressed axenic conditions. the three most effective strains of pgpr (mk1, pseudomonas syringae ; mk20, pseudomonas fluorescens ; and mk25, pseudomonas fluorescens biotype g) and rhizobium phaseoli strains m1, m6, and m9 were ...	2011	21770816
arabidopsis nitrate reductase activity is stimulated by the e3 sumo ligase atsiz1.	small ubiquitin-related modifier (sumo) is a small polypeptide that modulates protein activity and regulates hormone signalling, abiotic and biotic responses in plants. here we show that atsiz regulates nitrogen assimilation in arabidopsis through its e3 sumo ligase function. dwarf plants of siz1-2 flower early, show abnormal seed development and have high salicylic acid content and enhanced resistance to bacterial pathogens. these mutant phenotypes are reverted to wild-type phenotypes by exogen ...	2011	21772271
interactions of bacterial proteins with host eukaryotic ubiquitin pathways.	ubiquitination is a post-translational modification in which one or more 76 amino acid polypeptide ubiquitin molecules are covalently linked to the lysine residues of target proteins. ubiquitination is the main pathway for protein degradation that governs a variety of eukaryotic cellular processes, including the cell-cycle, vesicle trafficking, antigen presentation, and signal transduction. not surprisingly, aberrations in the system have been implicated in the pathogenesis of many diseases incl ...	2011	21772834
bacterial effector-involved temporal and spatial regulation by hijack of the host ubiquitin pathway.	ubiquitination is one of the most conserved post-translational modifications of proteins, and is involved in essential eukaryotic cellular processes. these include protein degradation, transcriptional regulation, cell-cycle progression, and signaling. microbial pathogens have evolved sophisticated systems to hijack host cellular functions for their own benefit. central to these systems are protein transport machineries; many pathogenic bacteria inject "effector proteins" to modulate host cellula ...	2011	21772836
functional analysis of the type 3 effector nopl from rhizobium sp. ngr234: symbiotic effects, phosphorylation and interference with mapk signaling.	pathogenic bacteria use type 3 secretion systems to deliver virulence factors (type 3 effector proteins) directly into eukaryotic host cells. similarly, type 3 effectors of certain nitrogen-fixing rhizobial strains affect nodule formation in the symbiosis with host legumes. nodulation outer protein l (nopl) of rhizobium sp. strain ngr234 is a rhizobium-specific type 3 effector. nodulation tests and microscopic analysis showed that distinct necrotic areas were rapidly formed in ineffective nodule ...	2011	21775427
vibrio parahaemolyticus cell biology and pathogenicity determinants.	vibrio parahaemolyticus is a significant cause of gastroenteritis worldwide. characterization of this pathogen has revealed a unique repertoire of virulence factors that allow for colonization of the human host and disease. the following describes the known pathogenicity determinants while establishing the need for continued research.	2011	21782964
two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic xanthomonas spp.	xanthomonas is a large genus of bacteria that collectively cause disease on more than three hundred plant species. the broad host range of the genus contrasts with stringent host and tissue-specificity for individual species and pathovars. whole genome sequences of x. campestris pv. raphani strain 756c and x. oryzae pv. oryzicola strain bls256, pathogens that infect the mesophyll tissue of the leading models for plant biology, arabidopsis thaliana and rice, respectively, were determined that pro ...	2011	21784931
characterization of the fur regulon in pseudomonas syringae pv. tomato dc3000.	the plant pathogen pseudomonas syringae pv. tomato dc3000 (dc3000) is found in a wide variety of environments and must monitor and respond to various environmental signals such as the availability of iron, an essential element for bacterial growth. an important regulator of iron homeostasis is fur (ferric uptake regulator) and here we present the first study of the fur regulon in dc3000. using chromatin immunoprecipitation followed by massively parallel sequencing (chip-seq), 312 chromosomal reg ...	2011	21784947
perturbation of arabidopsis amino acid metabolism causes incompatibility with the adapted biotrophic pathogen hyaloperonospora arabidopsidis.	reliance of biotrophic pathogens on living plant tissues to propagate implies strong interdependence between host metabolism and nutrient uptake by the pathogen. however, factors determining host suitability and establishment of infection are largely unknown. we describe a loss-of-inhibition allele of aspartate kinase2 and a loss-of-function allele of dihydrodipicolinate synthase2 identified in a screen for arabidopsis thaliana mutants with increased resistance to the obligate biotrophic oomycet ...	2011	21784950
analysis of a range of catabolic mutants provides evidence that phytanoyl-coenzyme a does not act as a substrate of the electron-transfer flavoprotein/electron-transfer flavoprotein:ubiquinone oxidoreductase complex in arabidopsis during dark-induced senescence.	the process of dark-induced senescence in plants is not fully understood, however, the functional involvement of an electron-transfer flavoprotein/electron-transfer flavoprotein:ubiquinone oxidoreductase (etf/etfqo), has been demonstrated. recent studies have revealed that the enzymes isovaleryl-coenzyme a (coa) dehydrogenase and 2-hydroxyglutarate dehydrogenase act as important electron donors to this complex. in addition both enzymes play a role in the breakdown of cellular carbon storage rese ...	2011	21788362
hyaloperonospora arabidopsidis atr1 effector is a repeat protein with distributed recognition surfaces.	the in planta association of the hyaloperonospora arabidopsidis effector atr1 with the cognate arabidopsis thaliana rpp1 immune receptor activates a disease-resistance signaling pathway that inhibits pathogen growth. to define the molecular events specifying effector recognition by rpp1, we determined the crystal structure of atr1 and assayed in planta the effects of surface polymorphisms that are critical to activating plant immunity. atr1 adopts an elongated, all-helical, two-domain, seahorse- ...	2011	21788488
a novel manganese efflux system, yebn, is required for virulence by xanthomonas oryzae pv. oryzae.	manganese ions (mn(2+)) play a crucial role in virulence and protection against oxidative stress in bacterial pathogens. such pathogens appear to have evolved complex mechanisms for regulating mn(2+) uptake and efflux. despite numerous studies on mn(2+) uptake, however, only one efflux system has been identified to date. here, we report on a novel mn(2+) export system, yebn, in xanthomonas oryzae pv. oryzae (xoo), the causative agent of bacterial leaf blight. compared with wild-type pxo99, the y ...	2011	21789199
metabolic versatility and antibacterial metabolite biosynthesis are distinguishing genomic features of the fire blight antagonist pantoea vagans c9-1.	pantoea vagans is a commercialized biological control agent used against the pome fruit bacterial disease fire blight, caused by erwinia amylovora. compared to other biocontrol agents, relatively little is currently known regarding pantoea genetics. better understanding of antagonist mechanisms of action and ecological fitness is critical to improving efficacy.	2011	21789243
the plant growth-promoting fungus aspergillus ustus promotes growth and induces resistance against different lifestyle pathogens in arabidopsis thaliana.	to deal with pathogens, plants have evolved sophisticated mechanisms including constitutive and induced defense mechanisms. phytohormones play important roles in plant growth and development, as well as in the systemic response induced by beneficial and pathogen microorganisms. in this work, we identified an aspergillus ustus isolate that promotes growth and induces developmental changes in solanum tuberosum and arabidopsis thaliana. a. ustus inoculation on a. thaliana and s. tuberosum roots ind ...	2011	21791954
identification of a host 14-3-3 protein that interacts with xanthomonas effector avrrxv.	avrrxv is a member of a family of pathogen effectors present in pathogens of both plant and mammalian species. xanthomonas campestris pv. vesicatoria strains carrying avrrxv induce a hypersensitive response (hr) in the tomato cultivar hawaii 7998. using a yeast two-hybrid screen, we identified a 14-3-3 protein from tomato that interacts with avrrxv called avrrxv interactor 1 (ari1). the interaction was confirmed in vitro with affinity chromatography. using mutagenesis, we identified a 14-3-3-bin ...	2008	21796232
independently evolved virulence effectors converge onto hubs in a plant immune system network.	plants generate effective responses to infection by recognizing both conserved and variable pathogen-encoded molecules. pathogens deploy virulence effector proteins into host cells, where they interact physically with host proteins to modulate defense. we generated an interaction network of plant-pathogen effectors from two pathogens spanning the eukaryote-eubacteria divergence, three classes of arabidopsis immune system proteins, and ~8000 other arabidopsis proteins. we noted convergence of eff ...	2011	21798943
dynamic evolution of pathogenicity revealed by sequencing and comparative genomics of 19 pseudomonas syringae isolates.	closely related pathogens may differ dramatically in host range, but the molecular, genetic, and evolutionary basis for these differences remains unclear. in many gram- negative bacteria, including the phytopathogen pseudomonas syringae, type iii effectors (ttes) are essential for pathogenicity, instrumental in structuring host range, and exhibit wide diversity between strains. to capture the dynamic nature of virulence gene repertoires across p. syringae, we screened 11 diverse strains for nove ...	2011	21799664
reconstructing host range evolution of bacterial plant pathogens using pseudomonas syringae pv. tomato and its close relatives as a model.	several lines of evidence suggest that highly virulent bacterial human pathogens evolved from less virulent wider host range animal pathogens since human migration out of africa. to investigate evolution of host specificity of bacterial plant pathogens, here we report a molecular evolutionary analysis of the model plant pathogen pseudomonas syringae pv. tomato dc3000 and of close relatives that are pathogens of a diverse set of crop plants. extensive host range tests on five different plant spec ...	2011	21802528
plant ferredoxin-like protein (pflp) outside chloroplast in arabidopsis enhances disease resistance against bacterial pathogens.	protection of crops against bacterial disease is an important issue in agricultural production. one of the strategies to lead plants become resistant against bacterial pathogens is employing a transgene, like plant ferredoxin-like protein (pflp). pflp is a photosynthetic type ferredoxin isolated from sweet pepper and contains a signal peptide for targeting towards chloroplasts. our previous reports indicated that transgenic plants with this protein are more resistant against bacterial pathogens. ...	2010	21802603
oxyr is necessary for the hydrogen peroxide stress response and full virulence in ralstonia solanacearum.	the plant pathogen ralstonia solanacearum, which causes bacterial wilt disease, is exposed to reactive oxygen species (ros) during tomato infection and expresses diverse oxidative stress response (osr) genes during mid-stage disease on tomato. the r. solanacearum genome predicts that the bacterium produces multiple and redundant ros-scavenging enzymes, but only one known oxidative stress response regulator, oxyr. an r. solanacearum oxyr mutant had no detectable catalase activity, did not grow in ...	2011	21803891
choline uptake in agrobacterium tumefaciens by the high-affinity choxwv transporter.	agrobacterium tumefaciens is a facultative phytopathogen that causes crown gall disease. for successful plant transformation a. tumefaciens requires the membrane lipid phosphatidylcholine (pc), which is produced via the methylation and the pc synthase (pcs) pathways. the latter route is dependent on choline. although choline uptake has been demonstrated in a. tumefaciens, the responsible transporter(s) remained elusive. in this study, we identified the first choline-transport system in a. tumefa ...	2011	21803998
comparative analyses imply that the enigmatic sigma factor 54 is a central controller of the bacterial exterior.	sigma-54 is a central regulator in many pathogenic bacteria and has been linked to a multitude of cellular processes like nitrogen assimilation and important functional traits such as motility, virulence, and biofilm formation. until now it has remained obscure whether these phenomena and the control by sigma-54 share an underlying theme.	2011	21806785
genome-wide comparison of nucleotide-binding site-leucine-rich repeat-encoding genes in arabidopsis.	plants, like animals, use several lines of defense against pathogen attack. prominent among genes that confer disease resistance are those encoding nucleotide-binding site-leucine-rich repeat (nb-lrr) proteins. likely due to selection pressures caused by pathogens, nb-lrr genes are the most variable gene family in plants, but there appear to be species-specific limits to the number of nb-lrr genes in a genome. allelic diversity within an individual is also increased by obligatory outcrossing, wh ...	2011	21810963
protein secretion systems in pseudomonas aeruginosa: an essay on diversity, evolution, and function.	protein secretion systems are molecular nanomachines used by gram-negative bacteria to thrive within their environment. they are used to release enzymes that hydrolyze complex carbon sources into usable compounds, or to release proteins that capture essential ions such as iron. they are also used to colonize and survive within eukaryotic hosts, causing acute or chronic infections, subverting the host cell response and escaping the immune system. in this article, the opportunistic human pathogen ...	2011	21811488
defining the pseudomonas genus: where do we draw the line with azotobacter?	the genus pseudomonas has gone through many taxonomic revisions over the past 100 years, going from a very large and diverse group of bacteria to a smaller, more refined and ordered list having specific properties. the relationship of the pseudomonas genus to azotobacter vinelandii is examined using three genomic sequence-based methods. first, using 16s rrna trees, it is shown that a. vinelandii groups within the pseudomonas close to pseudomonas aeruginosa. genomes from other related organisms ( ...	2011	21811795
defining the pseudomonas genus: where do we draw the line with azotobacter?	the genus pseudomonas has gone through many taxonomic revisions over the past 100 years, going from a very large and diverse group of bacteria to a smaller, more refined and ordered list having specific properties. the relationship of the pseudomonas genus to azotobacter vinelandii is examined using three genomic sequence-based methods. first, using 16s rrna trees, it is shown that a. vinelandii groups within the pseudomonas close to pseudomonas aeruginosa. genomes from other related organisms ( ...	2011	21811795
enzymatic timing and tailoring of macrolactamization in syringolin biosynthesis.	the enzymatic activation of 3,4-dehydrolysine and subsequent formation of the 12-membered syringolin macrolactam were investigated. the timing of the desaturation was elucidated through the analysis of the initial adenylation domain of syld. the syld-tte didomain was characterized and demonstrated to be the catalyst for formation of 12-membered macrocycles. when the syld thioesterase domain was reacted with a family of acyclic coa both natural and unnatural macrocycles were generated.	2011	21812451
cytokinins mediate resistance against pseudomonas syringae in tobacco through increased antimicrobial phytoalexin synthesis independent of salicylic acid signalling.	cytokinins are phytohormones that are involved in various regulatory processes throughout plant development, but are also produced by pathogens and known to modulate plant immunity. a novel transgenic approach enabling autoregulated cytokinin synthesis in response to pathogen infection showed that cytokinins mediate enhanced resistance against the virulent hemibiotrophic pathogen pseudomonas syringae pv. tabaci. this was confirmed by two additional independent transgenic approaches to increase e ...	2011	21813654
genome engineering using targeted oligonucleotide libraries and functional selection.	the ? phage red proteins greatly enhance homologous recombination in escherichia coli. red-mediated recombination or "recombineering" can be used to construct targeted gene deletions as well as to introduce point mutations into the genome. here, we describe our method for scanning mutagenesis using recombineered oligonucleotide libraries. this approach entails randomization of specific codons within a target gene, followed by functional selection to isolate mutants. oligonucleotide library mutag ...	2011	21815087
identification of host genes involved in geminivirus infection using a reverse genetics approach.	geminiviruses, like all viruses, rely on the host cell machinery to establish a successful infection, but the identity and function of these required host proteins remain largely unknown. tomato yellow leaf curl sardinia virus (tylcsv), a monopartite geminivirus, is one of the causal agents of the devastating tomato yellow leaf curl disease (tylcd). the transgenic 2irgfp n. benthamiana plants, used in combination with virus induced gene silencing (vigs), entail an important potential as a tool i ...	2011	21818318
Levansucrases from Pseudomonas syringae pv. tomato and P. chlororaphis subsp. aurantiaca: Substrate specificity, polymerizing properties and usage of different acceptors for fructosylation.	Levansucrases of Pseudomonas syringae pv. tomato DC3000 (Lsc3) and Pseudomonas chlororaphis subsp. aurantiaca (also Pseudomonas aurantiaca) (LscA) have 73% identity of protein sequences, similar substrate specificity and kinetic properties. Both enzymes produce levan and fructooligosaccharides (FOS) of varied length from sucrose, raffinose and sugar beet molasses. A novel high-throughput chip-based nanoelectrospray mass spectrometric method was applied to screen alternative fructosyl acceptors f ...	2011	21820018
a cry for help from leaf to root: above ground insect feeding leads to the recruitment of rhizosphere microbes for plant self-protection against subsequent diverse attacks.	plants have evolved general and specific defense mechanisms to protect themselves from diverse enemies, including herbivores and pathogens. to maintain fitness in the presence of enemies, plant defense mechanisms are aimed at inducing systemic resistance: in response to the attack of pathogens or herbivores, plants initiate extensive changes in gene expression to activate "systemic acquired resistance" against pathogens and "indirect defense" against herbivores. recent work revealed that leaf in ...	2011	21822064
chromatin configuration as a battlefield in plant-bacteria interactions.		2011	21825106
regulation of stomatal tropism and infection by light in cercospora zeae-maydis: evidence for coordinated host/pathogen responses to photoperiod?	cercospora zeae-maydis causes gray leaf spot of maize, which has become one of the most widespread and destructive diseases of maize in the world. c. zeae-maydis infects leaves through stomata, which is predicated on the ability of the pathogen to perceive stomata and reorient growth accordingly. in this study, the discovery that light was required for c. zeae-maydis to perceive stomata and infect leaves led to the identification of crp1, a gene encoding a putative blue-light photoreceptor homol ...	2011	21829344
quantitative and qualitative stem rust resistance factors in barley are associated with transcriptional suppression of defense regulons.	stem rust (puccinia graminis f. sp. tritici; pgt) is a devastating fungal disease of wheat and barley. pgt race ttksk (isolate ug99) is a serious threat to these triticeae grain crops because resistance is rare. in barley, the complex rpg-ttksk locus on chromosome 5h is presently the only known source of qualitative resistance to this aggressive pgt race. segregation for resistance observed on seedlings of the q21861 +ù sm89010 (qsm) doubled-haploid (dh) population was found to be predominantly ...	2011	21829384
sequencing and validation of the genome of a campylobacter concisus reveals intra-species diversity.	campylobacter concisus is an emerging pathogen of the human gastrointestinal tract. its role in different diseases remains a subject of debate; this may be due to strain to strain genetic variation. here, we sequence and analyze the genome of a c. concisus from a biopsy of a child with crohn's disease (unswcd); the second such genome for this species. a 1.8 mb genome was assembled with paired-end reads from a next-generation sequencer. this genome is smaller than the 2.1 mb c. concisus reference ...	2011	21829448
harpin(pss)-mediated enhancement in growth and biological control of late leaf spot in groundnut by a chlorothalonil-tolerant bacillus thuringiensis sfc24.	chemical and biological approaches have been adopted to increase the growth and yield of crops and reduce loss due to diseases. we have adopted an integrated approach, where both direct antagonism and induced resistance were combined to reduce the incidence of late leaf spot (lls) disease in groundnut caused by phaeoisariopsis personata. chitinolytic chlorothalonil-tolerant soil bacterium bacillus thuringiensis sfc24 (bt sfc24) was manipulated in vitro to express secretable form of elicitor prot ...	2011	21831618
an ecf sigma factor mediated cell surface signaling system in pseudomonas syringae pv. tomato dc3000 regulates gene expression in response to heterologous siderophores.	the diversity of regulatory systems encoded by bacteria provides an indication of the variety of stresses and interactions that these organisms encounter in nature. we have been investigating how the plant pathogen pseudomonas syringae pv. tomato dc3000 responds to iron limitation and have focused on the iron starvation (is) sigma factors to identify regulon members and to explore the mechanistic details of genetic control for this class of regulators. in this report we used chromatin immunoprec ...	2011	21840980
microarray based analysis of inca/c plasmid associated genes from multidrug resistant salmonella enterica.	in enterobacteriaceae, plasmids have been classified according to 27 incompatibility (inc) or replicon types which are based on the inability of different plasmids with the same replication mechanism to co-exist in the same cell. certain replicon types such as inca/c are associated with multidrug resistance (mdr). we developed a microarray that contains 286 unique 70 mer oligonucleotide probes based on sequences from five inca/c plasmids: pyr1 (yersinia ruckeri), ppip1202 (yersinia pestis), pp99 ...	2011	21841024
differential bacteriophage mortality on exposure to copper.	many studies report that copper can be used to control microbial growth, including that of viruses. we determined the rates of copper-mediated inactivation for a wide range of bacteriophages. we used two methods to test the effect of copper on bacteriophage survival. one method involved placing small volumes of bacteriophage lysate on copper and stainless steel coupons. following exposure, metal coupons were rinsed with lysogeny broth and the resulting fluid was serially diluted and plated on ag ...	2011	21841029
transcription dynamics in plant immunity.	plant cells maintain sophisticated gene transcription programs to regulate their development, communication, and response to the environment. environmental stress cues, such as pathogen encounter, lead to dramatic reprogramming of transcription to favor stress responses over normal cellular functions. transcription reprogramming is conferred by the concerted action of myriad transcription (co)factors that function directly or indirectly to recruit or release rna polymerase ii. to establish an ef ...	2011	21841124
antimicrobial peptides: modes of mechanism, modulation of defense responses.	complicated schemes of classical breeding and their drawbacks, environmental risks imposed by agrochemicals, decrease of arable land, and coincident escalating damages of pests and pathogens have accentuated the necessity for highly efficient measures to improve crop protection. during co-evolution of host-microbe interactions, antimicrobial peptides (amps) have exhibited a brilliant history in protecting host organisms against devastation by invading pathogens. since the 1980s, a plethora of am ...	2011	21847025
The role of effectors of biotrophic and hemibiotrophic fungi in infection.	Biotrophic and hemibiotrophic fungi are successful groups of plant pathogens that require living plant tissue to survive and complete their life cycle. Members of these groups include the rust fungi and powdery mildews and species in the Ustilago, Cladosporium and Magnaporthe genera. Collectively, they represent some of the most destructive plant parasites, causing huge economic losses and threatening global food security. During plant infection, pathogens synthesize and secrete effector protein ...	2011	21848815
transport genes and chemotaxis in laribacter hongkongensis: a genome-wide analysis.	abstract:	2011	21849034
Transcript and metabolite analysis of the Trichoderma-induced systemic resistance response to Pseudomonas syringae in Arabidopsis thaliana.	In the present study we have assessed, by transcriptional and metabolic profiling, the systemic defence response of Arabidopsis thaliana plants to the leaf pathogen Pseudomonas syringae pv. tomato DC3000 (Pst) induced by the beneficial fungus Trichoderma asperelloides T203. Expression analysis (qPCR) of a set of 137 Arabidopsis genes related to Pst defence responses showed that T203 root colonization is not associated with major detectable transcriptomic changes in leaves. However, plants challe ...	2012	21852347
Free sphingobases induce RBOHD-dependent reactive oxygen species production in Arabidopsis leaves.	Sphingolipids are implied in several regulatory processes, including cell death. Levels of the free sphingobase t18:0 (phytosphingosine) increase in Arabidopsis in response to the bacterial pathogen Pseudomonas syringae. To gain information on sphingobase-induced signaling, we determined kinetics of leaf reactive oxygen species (ROS) levels and cell death in response to specific sphingobases. t18:0, d18:0 and d17:1, but not d20:0, induced ROS and cell death within 1.5-2h. Early sphingobase-induc ...	2011	21856300
vprfp1, a novel c4c4-type ring finger protein gene from chinese wild vitis pseudoreticulata, functions as a transcriptional activator in defence response of grapevine.	ring finger proteins comprise a large family and play important roles in regulation of growth and development, hormone signalling, and responses to biotic and abiotic stresses in plants. in this study, the identification and functional characterization of a c4c4-type ring finger protein gene from the chinese wild grapevine vitis pseudoreticulata (designated vprfp1) are reported. vprfp1 was initially identified as an expressed sequence tag (est) from a cdna library constructed from leaves of v. p ...	2011	21862480
bik1 function in plant growth and defense signaling.		2011	21862709
biochemical and genetic requirements for function of the immune response regulator botrytis-induced kinase1 in plant growth, ethylene signaling, and pamp-triggered immunity in arabidopsis.	arabidopsis thaliana botrytis-induced kinase1 (bik1) regulates immune responses to a distinct class of pathogens. here, mechanisms underlying bik1 function and its interactions with other immune response regulators were determined. we describe bik1 function as a component of ethylene (et) signaling and pamp-triggered immunity (pti) to fungal pathogens. bik1 in vivo kinase activity increases in response to flagellin peptide (flg22) and the et precursor 1-aminocyclopropane-1-carboxylic acid (acc) ...	2011	21862710
the arabidopsis thaliana dna-binding protein ahl19 mediates verticillium wilt resistance.	verticillium spp. are destructive soilborne fungal pathogens that cause vascular wilt diseases in a wide range of plant species. verticillium wilts are particularly notorious, and genetic resistance in crop plants is the most favorable means of disease control. in a gain-of-function screen using an activation-tagged arabidopsis mutant collection, we identified four mutants, a1 to a4, which displayed enhanced resistance toward the vascular wilt species verticillium dahliae, v. albo-atrum and v. l ...	2011	21864046
the involvement of jasmonates and ethylene in alternaria alternata f. sp. lycopersici toxin-induced tomato cell death.	previous studies have shown that an ethylene (et)-dependent pathway is involved in the cell death signalling triggered by alternaria alternata f. sp. lycopersici (aal) toxin in detached tomato (solanum lycopersicum) leaves. in this study, the role of jasmonic acid (ja) signalling in programmed cell death (pcd) induced by aal toxin was analysed using a 35s::prosystemin transgenic line (35s::prosys), a ja-deficient mutant spr2, and a ja-insensitive mutant jai1. the results indicated that ja biosyn ...	2011	21865178
the glutamine synthetase gene family in populus.	glutamine synthetase (gs; ec: 6.3.1.2, l-glutamate: ammonia ligase adp-forming) is a key enzyme in ammonium assimilation and metabolism of higher plants. the current work was undertaken to develop a more comprehensive understanding of molecular and biochemical features of gs gene family in poplar, and to characterize the developmental regulation of gs expression in various tissues and at various times during the poplar perennial growth.	2011	21867507
hla-dr3 restricted t cell epitope mimicry in induction of autoimmune response to lupus-associated antigen smd.	although systemic lupus erythematosus (sle) is a multigenic autoimmune disorder, hla-d is the most dominant genetic susceptibility locus. this study was undertaken to investigate the hypothesis that microbial peptides bind hla-dr3 and activate t cells reactive with lupus autoantigens. using hla-dr3 transgenic mice and lupus-associated autoantigen smd protein, smd(79-93) was identified to contain a dominant hla-dr3 restricted t cell epitope. this t cell epitope was characterized by using a t-t hy ...	2011	21868195
concerted action of two avirulent spore effectors activates reaction to puccinia graminis 1 (rpg1)-mediated cereal stem rust resistance.	the barley stem rust resistance gene reaction to puccinia graminis 1 (rpg1), encoding a receptor-like kinase, confers durable resistance to the stem rust pathogen puccinia graminis f. sp. tritici. the fungal urediniospores form adhesion structures with the leaf epidermal cells within 1 h of inoculation, followed by hyphae and haustorium formation. the rpg1 protein is constitutively expressed and not phosphorylated. on inoculation with avirulent urediniospores, it is phosphorylated in vivo within ...	2011	21873196
stability of plant immune-receptor resistance proteins is controlled by skp1-cullin1-f-box (scf)-mediated protein degradation.	the nucleotide-binding domain and leucine-rich repeats containing proteins (nlrs) serve as immune receptors in both plants and animals. overaccumulation of nlrs often leads to autoimmune responses, suggesting that the levels of these immune receptors must be tightly controlled. however, the mechanism by which nlr protein levels are regulated is unknown. here we report that the f-box protein cpr1 controls the stability of plant nlr resistance proteins. loss-of-function mutations in cpr1 lead to h ...	2011	21873230
the pal2 promoter activities in relation to structural development and adaptation in arabidopsis thaliana.	phenylalanine ammonia lyase (pal) plays a major role in plant growth, development and adaptation. in arabidopsis thaliana, the enzyme is encoded by four genes, namely pal1, pal2, pal3, and pal4 with pal1 and pal2 being closely related phylogenetically and functionally. pal1 promoter activities are associated with plant development and are inducible by various stress agents. however, pal2 promoter activities have not been functionally analysed. here, we show that the pal2 promoter activities are ...	2011	21874349
gebp/gpl transcription factors regulate a subset of cpr5-dependent processes.	the constitutive expressor of pathogenesis-related genes5 (cpr5) gene of arabidopsis (arabidopsis thaliana) encodes a putative membrane protein of unknown biochemical function and displays highly pleiotropic functions, particularly in pathogen responses, cell proliferation, cell expansion, and cell death. here, we demonstrate a link between cpr5 and the glabra1 enhancer binding protein (gebp) family of transcription factors. we investigated the primary role of the gebp/gebp-like (gpl) genes usin ...	2011	21875893
the 3-hydroxy-2-butanone pathway is required for pectobacterium carotovorum pathogenesis.	pectobacterium species are necrotrophic bacterial pathogens that cause soft rot diseases in potatoes and several other crops worldwide. gene expression data identified pectobacterium carotovorum subsp. carotovorum budb, which encodes the α-acetolactate synthase enzyme in the 2,3-butanediol pathway, as more highly expressed in potato tubers than potato stems. this pathway is of interest because volatiles produced by the 2,3-butanediol pathway have been shown to act as plant growth promoting molec ...	2011	21876734
soybean homologs of mpk4 negatively regulate defense responses and positively regulate growth and development.	mitogen-activated protein kinase (mapk) cascades play important roles in disease resistance in model plant species such as arabidopsis (arabidopsis thaliana) and tobacco (nicotiana tabacum). however, the importance of mapk signaling pathways in the disease resistance of crops is still largely uninvestigated. to better understand the role of mapk signaling pathways in disease resistance in soybean (glycine max), 13, nine, and 10 genes encoding distinct mapks, mapkks, and mapkkks, respectively, we ...	2011	21878550
Tandem translation generates a chaperone for the Salmonella type III secretion system protein SsaQ.	Type III secretion systems (T3SSs) of bacterial pathogens involve the assembly of a surface-localized needle complex, through which translocon proteins are secreted to form a pore in the eukaryotic cell membrane. This enables the transfer of effector proteins from the bacterial cytoplasm to the host cell. A structure known as the C-ring is thought to have a crucial role in secretion by acting as a cytoplasmic sorting platform at the base of the T3SS. Here, we studied SsaQ, an FliN-like putative ...	2011	21878641
a tomato lysm receptor-like kinase promotes immunity and its kinase activity is inhibited by avrptob.	resistance in tomato (solanum lycopersicum) to infection by pseudomonas syringae involves both detection of pathogen-associated molecular patterns (pamps) and recognition by the host pto kinase of pathogen effector avrptob which is translocated into the host cell and interferes with pamp-triggered immunity (pti). the n-terminal portion of avrptob is sufficient for its virulence activity and for recognition by pto. an amino acid substitution in avrptob, f173a, abolishes these activities. to inves ...	2012	21880077
a tomato lysm receptor-like kinase promotes immunity and its kinase activity is inhibited by avrptob.	resistance in tomato (solanum lycopersicum) to infection by pseudomonas syringae involves both detection of pathogen-associated molecular patterns (pamps) and recognition by the host pto kinase of pathogen effector avrptob which is translocated into the host cell and interferes with pamp-triggered immunity (pti). the n-terminal portion of avrptob is sufficient for its virulence activity and for recognition by pto. an amino acid substitution in avrptob, f173a, abolishes these activities. to inves ...	2012	21880077
a eukaryotic-type signalling system of pseudomonas aeruginosa contributes to oxidative stress resistance, intracellular survival and virulence.	the genome of pseudomonas aeruginosa contains at least three genes encoding eukaryotic-type ser/thr protein kinases, one of which, ppka, has been implicated in p. aeruginosa virulence. together with the adjacent pppa phosphatase gene, they belong to the type vi secretion system (h1-t6ss) locus, which is important for bacterial pathogenesis. to determine the biological function of this protein pair, we prepared a pppa-ppka double mutant and characterised its phenotype and transcriptomic profiles.	2011	21880152
oligogalacturonide-auxin antagonism does not require posttranscriptional gene silencing or stabilization of auxin response repressors in arabidopsis.	α-1-4-linked oligogalacturonides (ogs) derived from plant cell walls are a class of damage-associated molecular patterns and well-known elicitors of the plant immune response. early transcript changes induced by ogs largely overlap those induced by flg22, a peptide derived from bacterial flagellin, a well-characterized microbe-associated molecular pattern, although responses diverge over time. ogs also regulate growth and development of plant cells and organs, due to an auxin-antagonistic activi ...	2011	21880931
comparison of biosurfactant detection methods reveals hydrophobic surfactants and contact-regulated production.	biosurfactants are diverse molecules with numerous biological functions and industrial applications. a variety of environments were examined for biosurfactant-producing bacteria including soil, water and leaf surfaces. biosurfactant production was assessed with an atomized oil assay for a large number of bacterial isolates and compared with a commonly used drop collapse assay from broth and plate cultures. the atomized oil assay detected every strain that produced a biosurfactant detectable by t ...	2011	21883788
genomic analysis and temperature-dependent transcriptome profiles of the rhizosphere originating strain pseudomonas aeruginosa m18.	our previously published reports have described an effective biocontrol agent named pseudomonas sp. m18 as its 16s rdna sequence and several regulator genes share homologous sequences with those of p. aeruginosa, but there are several unusual phenotypic features. this study aims to explore its strain specific genomic features and gene expression patterns at different temperatures.	2011	21884571
the universally conserved prokaryotic gtpases.	members of the large superclass of p-loop gtpases share a core domain with a conserved three-dimensional structure. in eukaryotes, these proteins are implicated in various crucial cellular processes, including translation, membrane trafficking, cell cycle progression, and membrane signaling. as targets of mutation and toxins, gtpases are involved in the pathogenesis of cancer and infectious diseases. in prokaryotes also, it is hard to overestimate the importance of gtpases in cell physiology. nu ...	2011	21885683
surface structures involved in plant stomata and leaf colonization by shiga-toxigenic escherichia coli o157:h7.	shiga-toxigenic escherichia coli (stec) o157:h7 uses a myriad of surface adhesive appendages including pili, flagella, and the type 3 secretion system (t3ss) to adhere to and inflict damage to the human gut mucosa. consumption of contaminated ground beef, milk, juices, water, or leafy greens has been associated with outbreaks of diarrheal disease in humans due to stec. the aim of this study was to investigate which of the known stec o157:h7 adherence factors mediate colonization of baby spinach ...	2011	21887151
Diversity in the architecture of ATLs, a family of plant ubiquitin-ligases, leads to recognition and targeting of substrates in different cellular environments.	Ubiquitin-ligases or E3s are components of the ubiquitin proteasome system (UPS) that coordinate the transfer of ubiquitin to the target protein. A major class of ubiquitin-ligases consists of RING-finger domain proteins that include the substrate recognition sequences in the same polypeptide; these are known as single-subunit RING finger E3s. We are studying a particular family of RING finger E3s, named ATL, that contain a transmembrane domain and the RING-H2 finger domain; none of the member o ...	2011	21887349
evolution of the deaminase fold and multiple origins of eukaryotic editing and mutagenic nucleic acid deaminases from bacterial toxin systems.	the deaminase-like fold includes, in addition to nucleic acid/nucleotide deaminases, several catalytic domains such as the jab domain, and others involved in nucleotide and adp-ribose metabolism. using sensitive sequence and structural comparison methods, we develop a comprehensive natural classification of the deaminase-like fold and show that its ancestral version was likely to operate on nucleotides or nucleic acids. consequently, we present evidence that a specific group of jab domains are l ...	2011	21890906
a novel antimicrobial protein for plant protection consisting of a xanthomonas oryzae harpin and active domains of cecropin a and melittin.	discoveries about antimicrobial peptides and plant defence activators have made possible the de novo and rational design of novel peptides for use in crop protection. here we report a novel chimeric protein, hcm1, which was made by linking the active domains of cecropin a and melittin to the hypersensitive response (hr)-elicitor hpa1 of xanthomonas oryzae pv. oryzicola, the causal agent of rice bacterial leaf streak. the resulting chimeric protein maintained not only the hr-inducing property of ...	2011	21895994
Localization of DIR1 at the tissue, cellular and subcellular levels during Systemic Acquired Resistance in Arabidopsis using DIR1:GUS and DIR1:EGFP reporters.	Systemic Acquired Resistance (SAR) is an induced resistance response to pathogens, characterized by the translocation of a long-distance signal from induced leaves to distant tissues to prime them for increased resistance to future infection. DEFECTIVE in INDUCED RESISTANCE 1 (DIR1) has been hypothesized to chaperone a small signaling molecule to distant tissues during SAR in Arabidopsis.	2011	21896186
a special pair of phytohormones controls excitability, slow closure, and external stomach formation in the venus flytrap.	venus flytrap's leaves can catch an insect in a fraction of a second. since the time of charles darwin, scientists have struggled to understand the sensory biology and biomechanics of this plant, dionaea muscipula. here we show that insect-capture of dionaea traps is modulated by the phytohormone abscisic acid (aba) and jasmonates. water-stressed dionaea, as well as those exposed to the drought-stress hormone aba, are less sensitive to mechanical stimulation. in contrast, application of 12-oxo-p ...	2011	21896747
revealing plant defense signaling: getting more sophisticated with phosphoproteomics.	the regulation mechanisms of any plant-pathogen interaction are complex and dynamic. a proteomic approach is necessary in understanding regulatory networks because it identifies new proteins in relation to their function and ultimately aims to clarify how their expression, accumulation and modification is controlled. one of the major control mechanisms for protein activity in plant-pathogen interactions is protein phosphorylation, and an understanding of the significance of protein phosphorylati ...	2011	21897123
for security and stability: sgt1 in plant defense and development.	sgt1 (suppressor of g-two allele of skp1) is highly conserved among all eukaryotes. in plants, sgt1 interacts with various proteins, including molecular chaperones (hsp70 and hsp90) and certain scf ubiquitin ligases, and hence sgt1 likely functions in protein folding and stability. since these protein complexes are involved in many aspects of plant biology, plants with a defective sgt1 display a plethora of phenotypic alterations. in this review we highlight the interaction between sgt1 with oth ...	2011	21897126
effect of glutaraldehyde fixation on bacterial cells observed by atomic force microscopy.	atomic force microscopy (afm) is a promising microscopy technique that can provide high-resolution images of bacterial cells without fixation. three species of bacteria, xanthomonas campestris, pseudomonas syringae, and bacillus subtilis, were used in this study. afm images were obtained from unfixed and glutaraldehyde-fixed cells, and cell height was measured. the mean height of bacterial cells prepared by fixation was higher than that of those prepared by nonfixation. however, the height chang ...	2011	21898456
genetic dissection of salicylic acid-mediated defense signaling networks in arabidopsis.	properly coordinated defense signaling networks are critical for the fitness of plants. one hub of the defense networks is centered on salicylic acid (sa), which plays a key role in activating disease resistance in plants. however, while a number of genes are known to affect sa-mediated defense, relatively little is known about how these gene interact genetically with each other. here we exploited the unique defense-sensitized arabidopsis mutant accelerated cell death (acd) 6-1 to dissect functi ...	2011	21900271
brush and spray: a high-throughput systemic acquired resistance assay suitable for large-scale genetic screening.	systemic acquired resistance (sar) is a defense mechanism induced in the distal parts of plants after primary infection. it confers long-lasting protection against a broad spectrum of microbial pathogens. lack of high-throughput assays has hampered the forward genetic analysis of sar. here, we report the development of an easy and efficient assay for sar and its application in a forward genetic screen for sar-deficient mutants in arabidopsis (arabidopsis thaliana). using the new assay for sar, w ...	2011	21900483
transcriptome analysis of arabidopsis thaliana plants in response to kin and stranger recognition.	recent reports have demonstrated that arabidopsis thaliana has the ability to alter its growth differentially when grown in the presence of secretions from other a. thaliana plants that are kin or strangers, however, little knowledge has been gained as to the physiological processes involved in these plant-plant interactions. therefore, we examined the root transcriptome of a. thaliana plants exposed to stranger versus kin secretions to determine genes involved in these processes. we conducted a ...	2011	21900741
Constitutive expression of MKS1 confers susceptibility to Botrytis cinerea infection independent of PAD3 expression.	Signal transduction through MAPK cascades is essential for eukaryotic cell response to various extracellular stimuli, such as the induction of innate immune responses. Arabidopsis thaliana relies in particular on three of its 20 MAPKs, MPK3,-4,-6, for a proper immune response. Recently we showed that one MPK4-substrate, MKS1, is required for basal resistance against the virulent Pseudomonas syringae and the oomycete Hyaloperonospora arabidopsidis. Overexpression of MKS1 (35S-MKS1) led to increas ...	2011	21900742
The plant pathogen pseudomonas syringae pv. tomato is genetically monomorphic and under strong selection to evade tomato immunity.	Recently, genome sequencing of many isolates of genetically monomorphic bacterial human pathogens has given new insights into pathogen microevolution and phylogeography. Here, we report a genome-based micro-evolutionary study of a bacterial plant pathogen, Pseudomonas syringae pv. tomato. Only 267 mutations were identified between five sequenced isolates in 3,543,009 nt of analyzed genome sequence, which suggests a recent evolutionary origin of this pathogen. Further analysis with genome-derived ...	2011	21901088
pseudomonas evades immune recognition of flagellin in both mammals and plants.	the building blocks of bacterial flagella, flagellin monomers, are potent stimulators of host innate immune systems. recognition of flagellin monomers occurs by flagellin-specific pattern-recognition receptors, such as toll-like receptor 5 (tlr5) in mammals and flagellin-sensitive 2 (fls2) in plants. activation of these immune systems via flagellin leads eventually to elimination of the bacterium from the host. in order to prevent immune activation and thus favor survival in the host, bacteria s ...	2011	21901099
Functional diversification of the GALA type III effector family contributes to Ralstonia solanacearum adaptation on different plant hosts.	Type III effectors from phytopathogenic bacteria exhibit a high degree of functional redundancy, hampering the evaluation of their precise contribution to pathogenicity. This is illustrated by the GALA type III effectors from Ralstonia solanacearum, which have been shown to be collectively, but not individually, required for disease on Arabidopsis thaliana and tomato. We investigated evolution, redundancy and diversification of this family in order to understand the individual contribution of th ...	2011	21902695
crystal structures of multicopper oxidase cueo bound to copper(i) and silver(i): functional role of a methionine-rich sequence.	the multicopper oxidase cueo oxidizes toxic cu(i) and is required for copper homeostasis in escherichia coli. like many proteins involved in copper homeostasis, cueo has a methionine-rich segment that is thought to be critical for copper handling. how such segments function is poorly understood. here, we report the crystal structure of cueo at 1.1 å with the 45-residue methionine-rich segment fully resolved, revealing an n-terminal helical segment with methionine residues juxtaposed for cu(i) li ...	2011	21903583
negative regulation of pathogenesis in pseudomonas syringae pv. tabaci 11528 by atp-dependent lon protease.	pseudomonas syringae pv. tabaci causes wildfire disease in tobacco plants. the hrp pathogenicity island (hrp pai) of p. syringae pv. tabaci encodes a type iii secretion system (ttss) and its regulatory system, which are required for pathogenesis in plants. three important regulatory proteins-hrpr, hrps, and hrpl-have been identified to activate hrp pai gene expression. the bacterial lon protease regulates the expression of various genes. to investigate the regulatory mechanism of the lon proteas ...	2011	21904881
relevant uses of surface proteins - display on self-organized biological structures.	proteins are often found attached to surfaces of self-assembling biological units such as whole microbial cells or subcellular structures, e.g. intracellular inclusions. in the last two decades surface proteins were identified that could serve as anchors for the display of foreign protein functions. extensive protein engineering based on structure-function data enabled efficient display of technically and/or medically relevant protein functions. small size, diversity of the anchor protein as wel ...	2011	21906264
mutation of l-2,3-diaminopropionic acid synthase genes blocks staphyloferrin b synthesis in staphylococcus aureus.	staphylococcus aureus synthesizes two siderophores, staphyloferrin a and staphyloferrin b, that promote iron-restricted growth. previous work on the biosynthesis of staphyloferrin b has focused on the role of the synthetase enzymes, encoded from within the sbna-i operon, which build the siderophore from the precursor molecules citrate, alpha-ketoglutarate and l-2,3-diaminopropionic acid. however, no information yet exists on several other enzymes, expressed from the biosynthetic cluster, that ar ...	2011	21906287
Comparative genomic analysis of Xanthomonas axonopodis pv. citrumelo F1, which causes citrus bacterial spot disease, and related strains provides insights into virulence and host specificity.	Xanthomonas axonopodis pv. citrumelo is a citrus pathogen causing citrus bacterial spot disease that is geographically restricted within the state of Florida. Illumina, 454 sequencing, and optical mapping were used to obtain a complete genome sequence of X. axonopodis pv. citrumelo strain F1, 4.9 Mb in size. The strain lacks plasmids, in contrast to other citrus Xanthomonas pathogens. Phylogenetic analysis revealed that this pathogen is very close to the tomato bacterial spot pathogen X. campest ...	2011	21908674
chalcone synthase and its functions in plant resistance.	chalcone synthase (chs, ec 2.3.1.74) is a key enzyme of the flavonoid/isoflavonoid biosynthesis pathway. besides being part of the plant developmental program the chs gene expression is induced in plants under stress conditions such as uv light, bacterial or fungal infection. chs expression causes accumulation of flavonoid and isoflavonoid phytoalexins and is involved in the salicylic acid defense pathway. this review will discuss chs and its function in plant resistance.	2011	21909286
expanded functions for a family of plant intracellular immune receptors beyond specific recognition of pathogen effectors.	plants and animals deploy intracellular immune receptors that perceive specific pathogen effector proteins and microbial products delivered into the host cell. we demonstrate that the adr1 family of arabidopsis nucleotide-binding leucine-rich repeat (nb-lrr) receptors regulates accumulation of the defense hormone salicylic acid during three different types of immune response: (i) adrs are required as "helper nb-lrrs" to transduce signals downstream of specific nb-lrr receptor activation during e ...	2011	21911370
sumo and sumoylation in plants.	the traditional focus on the central dogma of molecular biology, from gene through rna to protein, has now been replaced by the recognition of an additional mechanism. the new regulatory mechanism, post-translational modifications to proteins, can actively alter protein function or activity introducing additional levels of functional complexity by altering cellular and sub-cellular location, protein interactions and the outcome of biochemical reaction chains. modifications by ubiquitin (ub) and ...	2011	21912873
Conservation of Salmonella infection mechanisms in plants and animals.	Salmonella virulence in animals depends on effectors injected by Type III Secretion Systems (T3SSs). In this report we demonstrate that Salmonella mutants that are unable to deliver effectors are also compromised in infection of Arabidopsis thaliana plants. Transcriptome analysis revealed that in contrast to wild type bacteria, T3SS mutants of Salmonella are compromised in suppressing highly conserved Arabidopsis genes that play a prominent role during Salmonella infection of animals. We also fo ...	2011	21915285
evaluation of methods for de novo genome assembly from high-throughput sequencing reads reveals dependencies that affect the quality of the results.	recent developments in high-throughput sequencing technology have made low-cost sequencing an attractive approach for many genome analysis tasks. increasing read lengths, improving quality and the production of increasingly larger numbers of usable sequences per instrument-run continue to make whole-genome assembly an appealing target application. in this paper we evaluate the feasibility of de novo genome assembly from short reads (≤100 nucleotides) through a detailed study involving genomic se ...	2011	21915294
Phosphorylcholine Phosphatase: A Peculiar Enzyme of Pseudomonas aeruginosa.	Pseudomonas aeruginosa synthesizes phosphorylcholine phosphatase (PchP) when grown on choline, betaine, dimethylglycine or carnitine. In the presence of Mg(2+) or Zn(2+), PchP catalyzes the hydrolysis of p-nitrophenylphosphate (p-NPP) or phosphorylcholine (Pcho). The regulation of pchP gene expression is under the control of GbdR and NtrC; dimethylglycine is likely the metabolite directly involved in the induction of PchP. Therefore, the regulation of choline metabolism and consequently PchP syn ...	2011	21915373
Biosynthesis and defensive function of Nd-acetylornithine, a jasmonate-induced Arabidopsis metabolite.	Since research on plant interactions with herbivores and pathogens is often constrained by the analysis of already known compounds, there is a need to identify new defense-related plant metabolites. The uncommon nonprotein amino acid N(d)-acetylornithine was discovered in a targeted search for Arabidopsis thaliana metabolites that are strongly induced by the phytohormone methyl jasmonate (MeJA). Stable isotope labeling experiments show that, after MeJA elicitation, Arg, Pro, and Glu are converte ...	2011	21917546
the xanthomonas type iii effector xopd targets the arabidopsis transcription factor myb30 to suppress plant defense.	plant and animal pathogens inject type iii effectors (t3es) into host cells to suppress host immunity and promote successful infection. xopd, a t3e from xanthomonas campestris pv vesicatoria, has been proposed to promote bacterial growth by targeting plant transcription factors and/or regulators. here, we show that xopd from the b100 strain of x. campestris pv campestris is able to target myb30, a transcription factor that positively regulates arabidopsis thaliana defense and associated cell dea ...	2011	21917550