Publications

azospirillum brasilense produces the auxin-like phenylacetic acid by using the key enzyme for indole-3-acetic acid biosynthesis.	an antimicrobial compound was isolated from azospirillum brasilense culture extracts by high-performance liquid chromatography and further identified by gas chromatography-mass spectrometry as the auxin-like molecule, phenylacetic acid (paa). paa synthesis was found to be mediated by the indole-3-pyruvate decarboxylase, previously identified as a key enzyme in indole-3-acetic acid (iaa) production in a. brasilense. in minimal growth medium, paa biosynthesis by a. brasilense was only observed in ...	2005	15812004
xanthomonas axonopodis pv. phaseoli var. fuscans is aggregated in stable biofilm population sizes in the phyllosphere of field-grown beans.	the occurrence of "xanthomonas axonopodis pv. phaseoli var. fuscans" (proposed name) populations as biofilms on bean leaves was investigated during three field experiments on plots established with naturally contaminated bean seeds. behavior of aggregated versus solitary populations was determined by quantification of culturable cells in different fractions of the epiphytic population separated by particle size. x. axonopodis pv. phaseoli var. fuscans population dynamic studies confirmed an asym ...	2005	15812033
whole-genome sequence analysis of pseudomonas syringae pv. phaseolicola 1448a reveals divergence among pathovars in genes involved in virulence and transposition.	pseudomonas syringae pv. phaseolicola, a gram-negative bacterial plant pathogen, is the causal agent of halo blight of bean. in this study, we report on the genome sequence of p. syringae pv. phaseolicola isolate 1448a, which encodes 5,353 open reading frames (orfs) on one circular chromosome (5,928,787 bp) and two plasmids (131,950 bp and 51,711 bp). comparative analyses with a phylogenetically divergent pathovar, p. syringae pv. tomato dc3000, revealed a strong degree of conservation at the ge ...	2005	16159782
novel nirk cluster genes in nitrosomonas europaea are required for nirk-dependent tolerance to nitrite.	nitrite reductase (nirk) of nitrosomonas europaea confers tolerance to nitrite (no2-). the nirk gene is clustered with three genes of unknown physiological function: ncgabc. at present, this organization is unique to nitrifying bacteria. here we report that the ncgabc gene products facilitate nirk-dependent no2- tolerance by reversing the negative physiological effect that is associated with the activity of nirk in their absence. we hypothesize that the ncg gene products are involved in the deto ...	2005	16166549
signal signature and transcriptome changes of arabidopsis during pathogen and insect attack.	plant defenses against pathogens and insects are regulated differentially by cross-communicating signaling pathways in which salicylic acid (sa), jasmonic acid (ja), and ethylene (et) play key roles. to understand how plants integrate pathogen- and insect-induced signals into specific defense responses, we monitored the dynamics of sa, ja, and et signaling in arabidopsis after attack by a set of microbial pathogens and herbivorous insects with different modes of attack. arabidopsis plants were e ...	2005	16167763
the type iii secretion system of biocontrol pseudomonas fluorescens kd targets the phytopathogenic chromista pythium ultimum and promotes cucumber protection.	the type iii secretion system (ttss) is used by proteobacteria for pathogenic or symbiotic interaction with plant and animal hosts. recently, ttss genes thought to originate from the phytopathogen pseudomonas syringae were evidenced in pseudomonas fluorescens kd, which protects cucumber from the oomycete pythium ultimum (kingdom chromista/stramenopila). however, it is not known whether the ttss contributes to plant protection by the bacterium and, if so, whether it targets the plant or the phyto ...	2005	16167769
pseudomonas syringae pv. tomato type iii effectors avrpto and avrptob promote ethylene-dependent cell death in tomato.	the type iii secretion system (ttss) of pseudomonas syringae pv. tomato (pst) injects into the plant cell effector proteins that play an essential role in the formation of bacterial speck disease. to investigate the molecular roles of ttss effectors in disease formation, we used a cdna microarray to analyze the expression of approximately 8600 random tomato genes in response to wild-type pst strain dc3000 and a mutant lacking a functional ttss. many of the differentially expressed genes identifi ...	2005	16167902
the development and endophytic nature of the fungus heteroconium chaetospira.	the root endophytic fungus heteroconium chaetospira was isolated from roots of chinese cabbage grown in field soil in japan. this fungus penetrates through the outer epidermal cells of its host, passes into the inner cortex, and grows throughout the cortical cells, including those of the root tip region, without causing apparent pathogenic symptoms. there are no ultrastructural signs of host resistance responses. h. chaetospira has been recovered from 19 plant species in which there was no disru ...	2005	16168582
diversity in domain architectures of ser/thr kinases and their homologues in prokaryotes.	ser/thr/tyr kinases (styks) commonly found in eukaryotes have been recently reported in many bacterial species. recent studies elucidating their cellular functions have established their roles in bacterial growth and development. however functions of a large number of bacterial styks still remain elusive. the organisation of domains in a large dataset of bacterial styks has been investigated here in order to recognise variety in domain combinations which determine functions of bacterial styks.	2005	16171520
identification of new secreted effectors in salmonella enterica serovar typhimurium.	a common theme in bacterial pathogenesis is the secretion of bacterial products that modify cellular functions to overcome host defenses. gram-negative bacterial pathogens use type iii secretion systems (ttsss) to inject effector proteins into host cells. the genes encoding the structural components of the type iii secretion apparatus are conserved among bacterial species and can be identified by sequence homology. in contrast, the sequences of secreted effector proteins are less conserved and a ...	2005	16177297
role of an alginate lyase for alginate transport in mucoid pseudomonas aeruginosa.	the opportunistic pathogen pseudomonas aeruginosa secretes a capsule-like polysaccharide called alginate that is important for evasion of host defenses, especially during chronic pulmonary disease of patients with cystic fibrosis (cf). most proteins for alginate biosynthesis are encoded by the 12-gene algd operon. interestingly, this operon also encodes algl, a lyase that degrades alginate. mutants lacking algg, algk, or algx, also encoded by the operon, synthesize alginate polymers that are dig ...	2005	16177314
homologues of insecticidal toxin complex genes in yersinia enterocolitica biotype 1a and their contribution to virulence.	yersinia enterocolitica is an enteric pathogen that consists of six biotypes: 1a, 1b, 2, 3, 4, and 5. strains of the latter five biotypes can carry a virulence plasmid, known as pyv, and several well-characterized chromosomally encoded virulence determinants. y. enterocolitica strains of biotype 1a lack the virulence-associated markers of pyv-bearing strains and were once considered to be avirulent. there is growing epidemiological, clinical, and experimental evidence, however, to suggest that s ...	2005	16177365
pseudotrienic acids a and b, two bioactive metabolites from pseudomonas sp. mf381-iods.	bioassay-guided fractionation of the liquid culture broth of pseudomonas sp. mf381-iods yielded two new antimicrobial substances, identified as (2e,4e,6e)-9-[((2s,3r)-3-hydroxy-4-{[(3e,5e,7rs)-7-hydroxy-4-methylhexadeca-3,5-dienoyl]amino}-2-methylbutanoyl)amino]nona-2,4,6-trienoic acid and the tetradeca equivalent, named pseudotrienic acids a (1) and b (2), respectively. the compounds are prone to lactone formation, and their structures suggest them to be derived from ring opening of a macrolide ...	2005	16180818
repressor- and activator-type ethylene response factors functioning in jasmonate signaling and disease resistance identified via a genome-wide screen of arabidopsis transcription factor gene expression.	to identify transcription factors (tfs) involved in jasmonate (ja) signaling and plant defense, we screened 1,534 arabidopsis (arabidopsis thaliana) tfs by real-time quantitative reverse transcription-pcr for their altered transcript at 6 h following either methyl ja treatment or inoculation with the incompatible pathogen alternaria brassicicola. we identified 134 tfs that showed a significant change in expression, including many apetala2/ethylene response factor (ap2/erf), myb, wrky, and nac tf ...	2005	16183832
pseudomonas fluorescens and glomus mosseae trigger dmi3-dependent activation of genes related to a signal transduction pathway in roots of medicago truncatula.	plant genes induced during early root colonization of medicago truncatula gaertn. j5 by a growth-promoting strain of pseudomonas fluorescens (c7r12) have been identified by suppressive subtractive hybridization. ten m. truncatula genes, coding proteins associated with a putative signal transduction pathway, showed an early and transient activation during initial interactions between m. truncatula and p. fluorescens, up to 8 d after root inoculation. gene expression was not significantly enhanced ...	2005	16183836
bioactive metabolites from the fungus nectria galligena, the main apple canker agent in chile.	the phytopathogenic fungus nectria galligena bres. is the most common canker disease agent of hardwood trees. the terpenoids colletochlorin b, colletorin b, ilicicolin c, e, and f, as well as the phytotoxin alpha,beta-dehydrocurvularin have been isolated from liquid cultures of n. galligena obtained from the xylem of infected apple trees in central chile. ilicicolin c and f and alpha,beta-dehydrocurvularin were active against pseudomonas syringae with ic50 values of 28.5, 28.5, and 14.2 microg/m ...	2005	16190620
crystal structures of delta1-piperideine-2-carboxylate/delta1-pyrroline-2-carboxylate reductase belonging to a new family of nad(p)h-dependent oxidoreductases: conformational change, substrate recognition, and stereochemistry of the reaction.	delta(1)-piperideine-2-carboxylate/delta(1)-pyrroline-2-carboxylate reductase from pseudomonas syringae pv. tomato belongs to a novel sub-class in a large family of nad(p)h-dependent oxidoreductases distinct from the conventional mdh/ldh superfamily characterized by the rossmann fold. we have determined the structures of the following three forms of the enzyme: the unliganded form, the complex with nadph, and the complex with nadph and pyrrole-2-carboxylate at 1.55-, 1.8-, and 1.7-a resolutions, ...	2005	16192274
biosynthesis of active bacillus subtilis urease in the absence of known urease accessory proteins.	bacillus subtilis contains urease structural genes but lacks the accessory genes typically required for gtp-dependent incorporation of nickel. nevertheless, b. subtilis was shown to possess a functional urease, and the recombinant enzyme conferred low levels of nickel-dependent activity to escherichia coli. additional investigations of the system lead to the suggestion that b. subtilis may use unidentified accessory proteins for in vivo urease activation.	2005	16199586
role of the ssu and seu genes of corynebacterium glutamicum atcc 13032 in utilization of sulfonates and sulfonate esters as sulfur sources.	corynebacterium glutamicum atcc 13032 was found to be able to utilize a broad range of sulfonates and sulfonate esters as sulfur sources. the two gene clusters potentially involved in sulfonate utilization, ssud1cba and ssui-seuabc-ssud2, were identified in the genome of c. glutamicum atcc 13032 by similarity searches. while the ssu genes encode proteins resembling ssu proteins from escherichia coli or bacillus subtilis, the seu gene products exhibited similarity to the dibenzothiophene-degradin ...	2005	16204527
trichoderma mitogen-activated protein kinase signaling is involved in induction of plant systemic resistance.	the role of a mitogen-activated protein kinase (mapk) tmka in inducing systemic resistance in cucumber against the bacterial pathogen pseudomonas syringae pv. lacrymans was investigated by using tmka loss-of-function mutants of trichoderma virens. in an assay where trichoderma spores were germinated in proximity to cucumber roots, the mutants were able to colonize the plant roots as effectively as the wild-type strain but failed to induce full systemic resistance against the leaf pathogen. inter ...	2005	16204544
intracellular screen to identify metagenomic clones that induce or inhibit a quorum-sensing biosensor.	the goal of this study was to design and evaluate a rapid screen to identify metagenomic clones that produce biologically active small molecules. we built metagenomic libraries with dna from soil on the floodplain of the tanana river in alaska. we extracted dna directly from the soil and cloned it into fosmid and bacterial artificial chromosome vectors, constructing eight metagenomic libraries that contain 53,000 clones with inserts ranging from 1 to 190 kb. to identify clones of interest, we de ...	2005	16204555
production of an engineered killer peptide in nicotiana benthamiana by using a potato virus x expression system.	the decapeptide killer peptide (kp) derived from the sequence of a single-chain, anti-idiotypic antibody acting as a functional internal image of a microbicidal, broad-spectrum yeast killer toxin (kt) was shown to exert a strong microbicidal activity against human pathogens. with the aim to exploit this peptide to confer resistance to plant pathogens, we assayed its antimicrobial activity against a broad spectrum of phytopathogenic bacteria and fungi. synthetic kp exhibited antimicrobial activit ...	2005	16204558
[genetic diversity in pseudomonads associated with cereal cultures infected with basal bacteriosis].	the genetic properties of 45 pseudomonad strains isolated from cereal cultures exhibiting symptoms of basal bacteriosis have been investigated. considerable genetic diversity has been demonstrated using dna fingerprints obtained by amplification with rep, eric, and box primers. restriction analysis of the 16s-23s internal transcribed spacer (its1) allowed the strains to be subdivided into two major groups. in a phylogenetic tree, the its1s of these groups fell into two clusters, which also inclu ...	2005	16211859
regulation of plant defense responses in arabidopsis by edr2, a ph and start domain-containing protein.	we have identified an arabidopsis mutant that displays enhanced disease resistance (edr2) to the biotrophic powdery mildew pathogen erysiphe cichoracearum. inhibition of fungal growth on edr2 mutant leaves occurred at a late stage of the infection process and coincided with formation of necrotic lesions approximately 5 days after inoculation. double-mutant analysis revealed that edr2-mediated resistance is suppressed by mutations that inhibit salicylic acid (sa)-induced defense signaling, includ ...	2005	16212604
a duplicated pair of arabidopsis ring-finger e3 ligases contribute to the rpm1- and rps2-mediated hypersensitive response.	the arabidopsis rpm1 protein confers resistance to disease caused by pseudomonas syringae strains delivering either the avrrpm1 or avrb type iii effector proteins into host cells. we characterized two closely related rpm1-interacting proteins, rin2 and rin3. rin2 and rin3 encode ring-finger type ubiquitin ligases with six apparent transmembrane domains and an ubiquitin-binding cue domain. rin2 and rin3 are orthologs of the mammalian autocrine motility factor receptor, a cytokine receptor localiz ...	2005	16212605
basal resistance against bacteria in nicotiana benthamiana leaves is accompanied by reduced vascular staining and suppressed by multiple pseudomonas syringae type iii secretion system effector proteins.	basal resistance in plants is induced by flagellin and several other common bacterial molecules and is implicated in the immunity of plants to most bacteria and other microbes. however, basal resistance can be suppressed by effector proteins that are injected by the type iii secretion system (ttss) of pathogens such as pseudomonas syringae. this study demonstrates that basal resistance in the leaves of nicotiana benthamiana is accompanied by reduced vascular flow into minor veins. reduced vascul ...	2005	16212612
comparative phylogenomics of the food-borne pathogen campylobacter jejuni reveals genetic markers predictive of infection source.	campylobacter jejuni is the predominant cause of bacterial gastroenteritis worldwide, but traditional typing methods are unable to discriminate strains from different sources that cause disease in humans. we report the use of genomotyping (whole-genome comparisons of microbes using dna microarrays) combined with bayesian-based algorithms to model the phylogeny of this major food-borne pathogen. in this study 111 c. jejuni strains were examined by genomotyping isolates from humans with a spectrum ...	2005	16230626
insights into genome plasticity and pathogenicity of the plant pathogenic bacterium xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence.	the gram-negative plant-pathogenic bacterium xanthomonas campestris pv. vesicatoria is the causative agent of bacterial spot disease in pepper and tomato plants, which leads to economically important yield losses. this pathosystem has become a well-established model for studying bacterial infection strategies. here, we present the whole-genome sequence of the pepper-pathogenic xanthomonas campestris pv. vesicatoria strain 85-10, which comprises a 5.17-mb circular chromosome and four plasmids. th ...	2005	16237009
multiple and interconnected pathways for l-lysine catabolism in pseudomonas putida kt2440.	l-lysine catabolism in pseudomonas putida kt2440 was generally thought to occur via the aminovalerate pathway. in this study we demonstrate the operation of the alternative aminoadipate pathway with the intermediates d-lysine, l-pipecolate, and aminoadipate. the simultaneous operation of both pathways for the use of l-lysine as the sole carbon and nitrogen source was confirmed genetically. mutants with mutations in either pathway failed to use l-lysine as the sole carbon and nitrogen source, alt ...	2005	16237033
the incp island in the genome of brucella suis 1330 was acquired by site-specific integration.	an 18,228-bp region containing open reading frames predicted to be derived from the incp plasmid or phage ancestors is present in the genomes of brucella suis biovars 1 to 4, b. canis, b. neotomae, and strains isolated from marine mammals, but not in b. melitensis, b. abortus, b. ovis, and b. suis biovar 5. the presence of circular excision intermediates and the results of an analysis of sequenced bacterial genomes suggest that the region downstream of the guaa gene is a hotspot for site-specifi ...	2005	16239585
calmodulin-like proteins from arabidopsis and tomato are involved in host defense against pseudomonas syringae pv. tomato.	complex signal transduction pathways underlie the myriad plant responses to attack by pathogens. ca(2+) is a universal second messenger in eukaryotes that modulates various signal transduction pathways through stimulus-specific changes in its intracellular concentration. ca(2+)-binding proteins such as calmodulin (cam) detect ca(2+) signals and regulate downstream targets as part of a coordinated cellular response to a given stimulus. here we report the characterization of a tomato gene (apr134) ...	2005	16240180
oligomerization of sulfolobus solfataricus signature amidase is promoted by acidic ph and high temperature.	the recombinant amidase from the hyperthermophylic archaeon sulfolobus solfataricus (ssam) a signature amidase, was cloned, purified and characterized. the enzyme is active on a large number of aliphatic and aromatic amides over the temperature range 60-95 degrees c and at ph values between 4.0 and 9.5, with an optimum at ph 5.0. the recombinant enzyme is in the form of a dimer of about 110 kd that reversibly associates into an octamer in a ph-dependent reaction. the ph dependence of the state o ...	2005	16243781
ascorbic acid deficiency activates cell death and disease resistance responses in arabidopsis.	programmed cell death, developmental senescence, and responses to pathogens are linked through complex genetic controls that are influenced by redox regulation. here we show that the arabidopsis (arabidopsis thaliana) low vitamin c mutants, vtc1 and vtc2, which have between 10% and 25% of wild-type ascorbic acid, exhibit microlesions, express pathogenesis-related (pr) proteins, and have enhanced basal resistance against infections caused by pseudomonas syringae. the mutants have a delayed senesc ...	2005	16244149
increased calcium levels and prolonged shelf life in tomatoes expressing arabidopsis h+/ca2+ transporters.	here we demonstrate that fruit from tomato (lycopersicon esculentum) plants expressing arabidopsis (arabidopsis thaliana) h(+)/cation exchangers (cax) have more calcium (ca2+) and prolonged shelf life when compared to controls. previously, using the prototypical cax1, it has been demonstrated that, in yeast (saccharomyces cerevisiae) cells, cax transporters are activated when the n-terminal autoinhibitory region is deleted, to give an n-terminally truncated cax (scax), or altered through specifi ...	2005	16244156
analysis of the cdnas of hypothetical genes on arabidopsis chromosome 2 reveals numerous transcript variants.	in the fully sequenced arabidopsis (arabidopsis thaliana) genome, many gene models are annotated as "hypothetical protein," whose gene structures are predicted solely by computer algorithms with no support from either expressed sequence matches from arabidopsis, or nucleic acid or protein homologs from other species. in order to confirm their existence and predicted gene structures, a high-throughput method of rapid amplification of cdna ends (race) was used to obtain their cdna sequences from 1 ...	2005	16244158
[cloning and characterization of an harpin-encoding gene from xanthomonas axonopodis pv. glycines required for hypersensitive response on nonhost plant tobacco].	an hpa1 gene was cloned into an expression vector, pet30a(+), from the genomic dna of xanthomonas axonopodis pv. glycines (xag), the causal agent of soybean bacterial pustule, with degenerated primers by polymerase amplification reaction (pcr). the gene product was extracted from the conjugate (bhr-3) of bl21 (des) with the recombined vector phr3 after the engineering strain was induced by iptg in lb medium. the sds-page gel showed that the gene product was 15.1kd. the product was heat-stable (1 ...	2005	16245857
evolution of mutational robustness in an rna virus.	mutational (genetic) robustness is phenotypic constancy in the face of mutational changes to the genome. robustness is critical to the understanding of evolution because phenotypically expressed genetic variation is the fuel of natural selection. nonetheless, the evidence for adaptive evolution of mutational robustness in biological populations is controversial. robustness should be selectively favored when mutation rates are high, a common feature of rna viruses. however, selection for robustne ...	2005	16248678
horizontal transfer of iturin a operon, itu, to bacillus subtilis 168 and conversion into an iturin a producer.	iturin a and its derivatives are lipopeptide antibiotics produced by bacillus subtilis and several closely related bacteria. three iturin group operons (i.e., iturin a, mycosubtilin, and bacillomycin d) of those antibiotic-producing strains have been cloned and sequenced thus far, strongly implying the horizontal transfer of these operons. to examine the nature of such horizontal transfer in terms of antibiotic production, a 42-kb region of the b. subtilis rb14 genome, which contains a complete ...	2005	16251307
natural variation in the arabidopsis response to the avirulence gene hoppsya uncouples the hypersensitive response from disease resistance.	the plant hypersensitive response (hr) is tightly associated with gene-for-gene resistance and has been proposed to function in containing pathogens at the invasion site. this tight association has made it difficult to unequivocally evaluate the importance of hr for plant disease resistance. here, hoppsya from pseudomonas syringae pv. syringae 61 is identified as a new avirulence gene for arabidopsis that triggers resistance in the absence of macroscopic hr. resistance to p. syringae pv. tomato ...	2005	16255244
extracytoplasmic function sigma factors in pseudomonas syringae.	genome analyses of the plant pathogens pseudomonas syringae pv. tomato dc3000, pv. syringae b728a and pv. phaseolicola 1448a reveal fewer extracytoplasmic function (ecf) sigma factors than in related pseudomonads with different lifestyles. we highlight the presence of a p. syringae-specific ecf sigma factor that is an interesting target for future studies because of its potential role in the adaptation of p. syringae to its specialized phytopathogenic lifestyle.	2005	16257528
novel virulence gene of pseudomonas syringae pv. tomato strain dc3000.	previously, we conducted a mutant screen of pseudomonas syringae pv. tomato strain dc3000 to identify genes that contribute to virulence on arabidopsis thaliana plants. here we describe the characterization of one mutant strain, db4h2, which contains a single tn5 insertion in pspto3576, an open reading frame that is predicted to encode a protein belonging to the tetr family of transcriptional regulators. we demonstrate that pspto3576 is necessary for virulence in dc3000 and designate the encoded ...	2005	16267304
reciprocal regulation of pyoluteorin production with membrane transporter gene expression in pseudomonas fluorescens pf-5.	pyoluteorin is a chlorinated polyketide antibiotic secreted by the rhizosphere bacterium pseudomonas fluorescens pf-5. genes encoding enzymes and transcriptional regulators involved in pyoluteorin production are clustered in the genome of pf-5. sequence analysis of genes adjacent to the known pyoluteorin biosynthetic gene cluster revealed the presence of an abc transporter system. we disrupted two putative abc transporter genes by inserting transcriptional fusions to an ice nucleation reporter g ...	2005	16269724
evidence for horizontal transfer of 1-aminocyclopropane-1-carboxylate deaminase genes.	pcr was used to rapidly identify and isolate 1-aminocyclopropane-1-carboxylate (acc) deaminase genes from bacteria. the shimodaira-hasegawa test was used to assess whether phylogenetically anomalous gene placements suggestive of horizontal gene transfer (hgt) were significantly favored over vertical transmission. the best maximum likelihood (ml) acc deaminase tree was significantly more likely than four alternative ml trees, suggesting hgt.	2005	16269802
characterization of sr3 reveals abundance of non-ltr retrotransposons of the rte clade in the genome of the human blood fluke, schistosoma mansoni.	it is becoming apparent that perhaps as much as half of the genome of the human blood fluke schistosoma mansoni is constituted of mobile genetic element-related sequences. non-long terminal repeat (ltr) retrotransposons, related to the line elements of mammals, comprise much of this repetitive component of the schistosome genome. of more than 12 recognized clades of non-ltr retrotransposons, only members of the cr1, rte, and r2 clades have been reported from the schistosome genome.	2005	16271150
structural basis for transcription inhibition by tagetitoxin.	tagetitoxin (tgt) inhibits transcription by an unknown mechanism. a structure at a resolution of 2.4 a of the thermus thermophilus rna polymerase (rnap)-tgt complex revealed that the tgt-binding site within the rnap secondary channel overlaps that of the stringent control effector ppgpp, which partially protects rnap from tgt inhibition. tgt binding is mediated exclusively through polar interactions with the beta and beta' residues whose substitutions confer resistance to tgt in vitro. important ...	2005	16273103
identification of erwinia amylovora genes induced during infection of immature pear tissue.	the enterobacterium erwinia amylovora is a devastating plant pathogen causing necrotrophic fire blight disease of apple, pear, and other rosaceous plants. in this study, we used a modified in vivo expression technology system to identify e. amylovora genes that are activated during infection of immature pear tissue, a process that requires the major pathogenicity factors of this organism. we identified 394 unique pear fruit-induced (pfi) genes on the basis of sequence similarity to known genes a ...	2005	16291682
genome-wide association mapping in arabidopsis identifies previously known flowering time and pathogen resistance genes.	there is currently tremendous interest in the possibility of using genome-wide association mapping to identify genes responsible for natural variation, particularly for human disease susceptibility. the model plant arabidopsis thaliana is in many ways an ideal candidate for such studies, because it is a highly selfing hermaphrodite. as a result, the species largely exists as a collection of naturally occurring inbred lines, or accessions, which can be genotyped once and phenotyped repeatedly. fu ...	2005	16292355
proposed guidelines for a unified nomenclature and phylogenetic analysis of type iii hop effector proteins in the plant pathogen pseudomonas syringae.	pathovars of pseudomonas syringae interact with their plant hosts via the action of hrp outer protein (hop) effector proteins, injected into plant cells by the type iii secretion system (ttss). recent availability of complete genome sequences for a number of p. syringae pathovars has led to a significant increase in the rate of effector discovery. however, lack of a systematic nomenclature has resulted in multiple names being assigned to the same hop, unrelated hops designated by the same alphab ...	2005	15828679
oligonucleotide microarray analysis of the sala regulon controlling phytotoxin production by pseudomonas syringae pv. syringae.	the sala gene is a key regulatory element for syringomycin production by pseudomonas syringae pv. syringae and encodes a member of the luxr regulatory protein family. previous studies revealed that sala, a member of the gacs/gaca signal transduction system, was required for bacterial virulence, syringomycin production, and expression of the syrb1 synthetase gene. to define the sala regulon, the spotted oligonucleotide microarray was constructed using gene-specific 70-mer oligonucleotides of all ...	2005	15828684
arabidopsis ssi2-conferred susceptibility to botrytis cinerea is dependent on eds5 and pad4.	loss of a stearoyl-acp desaturase activity in the arabidopsis thaliana ssi2 mutant confers susceptibility to the necrotroph, botrytis cinerea. in contrast, the ssi2 mutant exhibits enhanced resistance to pseudomonas syringae, peronospora parasitica, and cucumber mosaic virus. the altered basal resistance to these pathogens in the ssi2 mutant plant is accompanied by the constitutive accumulation of elevated salicylic acid (sa) level and expression of the pathogenesis-related 1 (pr1) gene, the ina ...	2005	15828688
molecular pathogenesis, epidemiology, and clinical manifestations of respiratory infections due to bordetella pertussis and other bordetella subspecies.	bordetella respiratory infections are common in people (b. pertussis) and in animals (b. bronchiseptica). during the last two decades, much has been learned about the virulence determinants, pathogenesis, and immunity of bordetella. clinically, the full spectrum of disease due to b. pertussis infection is now understood, and infections in adolescents and adults are recognized as the reservoir for cyclic outbreaks of disease. dtap vaccines, which are less reactogenic than dtp vaccines, are now in ...	2005	15831828
the dotl protein, a member of the trag-coupling protein family, is essential for viability of legionella pneumophila strain lp02.	legionella pneumophila is able to survive inside phagocytic cells by an internalization route that bypasses fusion of the nascent phagosome with the endocytic pathway to allow formation of a replicative phagosome. the dot/icm genes, a major virulence system of l. pneumophila, encode a type ivb secretion system that is required for intracellular growth. one dot protein, dotl, has sequence similarity to type iv secretion system coupling proteins (t4cps). in other systems, coupling proteins are not ...	2005	15838018
autoinduction in erwinia amylovora: evidence of an acyl-homoserine lactone signal in the fire blight pathogen.	erwinia amylovora causes fire blight disease of apple, pear, and other members of the rosaceae. here we present the first evidence for autoinduction in e. amylovora and a role for an n-acyl-homoserine lactone (ahl)-type signal. two major plant virulence traits, production of extracellular polysaccharides (amylovoran and levan) and tolerance to free oxygen radicals, were controlled in a bacterial-cell-density-dependent manner. two standard autoinducer biosensors, agrobacterium tumefaciens ntl4 an ...	2005	15838048
identification of a large cluster of coiled coil-nucleotide binding site--leucine rich repeat-type genes from the rps1 region containing phytophthora resistance genes in soybean.	fifteen rps genes confer resistance against the oomycete pathogen phytophthora sojae, which causes root and stem rot disease in soybean. we have isolated a disease resistance gene-like sequence from the genomic region containing rps1-k. four classes of cdna of the sequence were isolated from etiolated hypocotyl tissues that express the rps1-k-encoded phytophthora resistance. sequence analyses of a cdna clone showed that the sequence is a member of the coiled coil-nucleotide binding site-leucine ...	2005	15841357
sipk signaling controls multiple components of harpin-induced cell death in tobacco.	harpin from pseudomonas syringae pv. phaseolicola (hrpz) elicits a rapid cell death response in tobacco plants. multiple signaling components, including mitogen-activated protein kinase (mapk), reactive oxygen species (ros) and salicylic acid (sa), have been reported to be involved in this cell death process, but the interaction between these molecules is poorly understood. here we show through utilizing plants manipulated in sipk expression levels that lack of sipk results in increased sensitiv ...	2005	15842625
the pseudomonas syringae effector avrrpt2 cleaves its c-terminally acylated target, rin4, from arabidopsis membranes to block rpm1 activation.	plant pathogenic pseudomonas syringae deliver type iii effector proteins into the host cell, where they function to manipulate host defense and metabolism to benefit the extracellular bacterial colony. the activity of these virulence factors can be monitored by plant disease resistance proteins deployed to "guard" the targeted host proteins. the arabidopsis rin4 protein is targeted by three different type iii effectors. specific manipulation of rin4 by each of them leads to activation of either ...	2005	15845764
crystal structure of levansucrase from the gram-negative bacterium gluconacetobacter diazotrophicus.	the endophytic gram-negative bacterium gluconacetobacter diazotrophicus srt4 secretes a constitutively expressed levansucrase (lsda, ec 2.4.1.10), which converts sucrose into fructooligosaccharides and levan. the enzyme is included in gh (glycoside hydrolase) family 68 of the sequence-based classification of glycosidases. the three-dimensional structure of lsda has been determined by x-ray crystallography at a resolution of 2.5 a (1 a=0.1 nm). the structure was solved by molecular replacement us ...	2005	15869470
production of rhamnolipids by pseudomonas chlororaphis, a nonpathogenic bacterium.	rhamnolipids, naturally occurring biosurfactants constructed of rhamnose sugar molecules and beta-hydroxyalkanoic acids, have a wide range of potential commercial applications. in the course of a survey of 33 different bacterial isolates, we have identified, using a phenotypic assay for rhamnolipid production, a strain of the nonpathogenic bacterial species pseudomonas chlororaphis that is capable of producing rhamnolipids. rhamnolipid production by p. chlororaphis was achieved by growth at room ...	2005	15870313
utilization of the plant hormone indole-3-acetic acid for growth by pseudomonas putida strain 1290.	we have isolated from plant surfaces several bacteria with the ability to catabolize indole-3-acetic acid (iaa). one of them, isolate 1290, was able to utilize iaa as a sole source of carbon, nitrogen, and energy. the strain was identified by its 16s rrna sequence as pseudomonas putida. activity of the enzyme catechol 1,2-dioxygenase was induced during growth on iaa, suggesting that catechol is an intermediate of the iaa catabolic pathway. this was in agreement with the observation that the oxyg ...	2005	15870323
reduced genetic variation occurs among genes of the highly clonal plant pathogen xanthomonas axonopodis pv. vesicatoria, including the effector gene avrbs2.	the bacterial plant pathogen xanthomonas axonopodis pv. vesicatoria, also known as xanthomonas campestris pv. vesicatoria group a, is the causal agent of bacterial spot in pepper and tomato. in order to test different models that may explain the coevolution of avrbs2 with its host plants, we sequenced avrbs2 and six chromosomal loci (total of 5.5 kb per strain) from a global sample of 55 x. axonopodis pv. vesicatoria strains collected from diseased peppers. we found an extreme lack of genetic va ...	2005	15870329
construction of a cloning system for the mass production of a virus-binding protein specific for poliovirus type 1.	in our previous study, virus-binding proteins (vbps) demonstrating the ability to strongly bind poliovirus type 1 (pv1) were recovered from a bacterial culture derived from activated sludge. the isolated vbps would be useful as viral adsorbents for water and wastewater treatments. the vbp gene of activated sludge bacteria was isolated, and the cloning system of the vbp was established. the isolation of the vbp gene from dna libraries for activated sludge bacteria was achieved with the colony hyb ...	2005	15870352
production of autoinducer 2 in salmonella enterica serovar thompson contributes to its fitness in chickens but not on cilantro leaf surfaces.	food-borne illness caused by salmonella enterica has been linked traditionally to poultry products but is associated increasingly with fresh fruits and vegetables. we have investigated the role of the production of autoinducer 2 (ai-2) in the ability of s. enterica serovar thompson to colonize the chicken intestine and the cilantro phyllosphere. a mutant of s. enterica serovar thompson that is defective in ai-2 production was constructed by insertional mutagenesis of luxs. the population size of ...	2005	15870357
an sos-regulated operon involved in damage-inducible mutagenesis in caulobacter crescentus.	dna polymerases of the y-family, such as escherichia coli umuc and dinb, are specialized enzymes induced by the sos response, which bypass lesions allowing the continuation of dna replication. umudc orthologs are absent in caulobacter crescentus and other bacteria, raising the question about the existence of sos mutagenesis in these organisms. here, we report that the c.crescentus dinb ortholog is not involved in damage-induced mutagenesis. however, an operon composed of two hypothetical genes a ...	2005	15886391
formation of a novel surface structure encoded by salmonella pathogenicity island 2.	the type iii secretion system (t3ss) encoded by salmonella pathogenicity island 2 (spi2) is essential for virulence and intracellular proliferation of salmonella enterica. we have previously identified spi2-encoded proteins that are secreted and function as a translocon for the injection of effector proteins. here, we describe the formation of a novel spi2-dependent appendage structure in vitro as well as on the surface of bacteria that reside inside a vacuole of infected host cells. in contrast ...	2005	15889142
an ancestral oomycete locus contains late blight avirulence gene avr3a, encoding a protein that is recognized in the host cytoplasm.	the oomycete phytophthora infestans causes late blight, the potato disease that precipitated the irish famines in 1846 and 1847. it represents a reemerging threat to potato production and is one of >70 species that are arguably the most devastating pathogens of dicotyledonous plants. nevertheless, little is known about the molecular bases of pathogenicity in these algae-like organisms or of avirulence molecules that are perceived by host defenses. disease resistance alleles, products of which re ...	2005	15894622
phytohormones mediate volatile emissions during the interaction of compatible and incompatible pathogens: the role of ethylene in pseudomonas syringae infected tobacco.	interactions between the phytohormones ethylene, salicylic acid (sa), and jasmonic acid (ja) are thought to regulate the specificity of induced plant defenses against microbial pathogens and herbivores. however, the nature of these interactions leading to induced plant volatile emissions during pathogen infection is unclear. we previously demonstrated that a complex volatile blend including (e)-beta-ocimene, methyl salicylate (mesa), and numerous sesquiterpenes was released by tobacco plants, ni ...	2005	15898494
purification and characterization of allophanate hydrolase (atzf) from pseudomonas sp. strain adp.	atzf, allophanate hydrolase, is a recently discovered member of the amidase signature family that catalyzes the terminal reaction during metabolism of s-triazine ring compounds by bacteria. in the present study, the atzf gene from pseudomonas sp. strain adp was cloned and expressed as a his-tagged protein, and the protein was purified and characterized. atzf had a deduced subunit molecular mass of 66,223, based on the gene sequence, and an estimated holoenzyme molecular mass of 260,000. the acti ...	2005	15901697
prediction of functional modules based on comparative genome analysis and gene ontology application.	we present a computational method for the prediction of functional modules encoded in microbial genomes. in this work, we have also developed a formal measure to quantify the degree of consistency between the predicted and the known modules, and have carried out statistical significance analysis of consistency measures. we first evaluate the functional relationship between two genes from three different perspectives--phylogenetic profile analysis, gene neighborhood analysis and gene ontology ass ...	2005	15901854
role of core promoter sequences in the mechanism of swarmer cell-specific silencing of gyrb transcription in caulobacter crescentus.	each caulobacter crescentus cell division yields two distinct cell types: a flagellated swarmer cell and a non-motile stalked cell. the swarmer cell is further distinguished from the stalked cell by an inability to reinitiate dna replication, by the physical properties of its nucleoid, and its discrete program of gene expression. specifically, with regard to the latter feature, many of the genes involved in dna replication are not transcribed in swarmer cells.	2005	15904494
antimicrobial activity and membrane selective interactions of a synthetic lipopeptide msi-843.	lipopeptide msi-843 consisting of the nonstandard amino acid ornithine (oct-oolloolool-nh2) was designed with an objective towards generating non-lytic short antimicrobial peptides, which can have significant pharmaceutical applications. octanoic acid was coupled to the n-terminus of the peptide to increase the overall hydrophobicity of the peptide. msi-843 shows activity against bacteria and fungi at micromolar concentrations. it permeabilizes the outer membrane of gram-negative bacterium and a ...	2005	15904663
electrophysiological characterization of the arabidopsis avrrpt2-specific hypersensitive response in the absence of other bacterial signals.	the hypersensitive response (hr) is defined as rapid cell collapse at the infection site and often accompanies plant resistance. the physiological processes leading to hr are not well understood. here, we report an electrophysiological characterization of bacterial hr caused by a single avirulence gene in the absence of other bacterial signals. we used dexamethasone (dex)-inducible transgenic arabidopsis (arabidopsis thaliana) plants containing the avrrpt2 gene from pseudomonas syringae pv tomat ...	2005	15908609
gene expression analysis of six gc-rich gram-negative phytopathogens.	predicted highly expressed (phx) genes are comparatively analyzed for six gc-rich gram-negative phytopathogens, i.e., ralstonia solanacearum, agrobacterium tumefaciens, xanthomonas campestris pv. campestris (xcc), xanthomonas axonopodis pv. citri (xac), pseudomonas syringae pv. tomato, and xylella fastidiosa. enzymes involved in energy metabolism, such as atp synthase, and genes involved in tca cycle, are phx in most bacteria except x. fastidiosa, which prefers an anaerobic environment. most pat ...	2005	15910748
a central role for s-nitrosothiols in plant disease resistance.	animal s-nitrosoglutathione reductase (gsnor) governs the extent of cellular s-nitrosylation, a key redox-based posttranslational modification. mutations in atgsnor1, an arabidopsis thaliana gsnor, modulate the extent of cellular s-nitrosothiol (sno) formation in this model plant species. loss of atgsnor1 function increased sno levels, disabling plant defense responses conferred by distinct resistance (r) gene subclasses. furthermore, in the absence of atgsnor1, both basal and nonhost disease re ...	2005	15911759
microarray analysis of the gene expression profile induced by the endophytic plant growth-promoting rhizobacteria, pseudomonas fluorescens fpt9601-t5 in arabidopsis.	pseudomonas fluorescens fpt9601-t5 was originally identified as an endophytic plant growth-promoting rhizobacteria (pgpr) on tomato. to perform a molecular dissecttion of physiological and biochemical changes occurring in the host triggered by p. fluorescens fpt9601-t5 colonization, the model plant arabidopsis was used in this study. root colonization of arabidopsis with p. fluorescens fpt9601-t5 promoted plant growth later than three weeks after inoculation and partially suppressed disease symp ...	2005	15915637
functional characterization of ntcef1, an ap2/erebp-type transcriptional activator highly expressed in tobacco callus.	using pcr-select cdna subtraction, we identified the genes that are predominantly expressed in the shooty callus induced by suppression of the chrk1 receptor-like kinase gene. one of the identified genes encoded a novel ap2/erebp-type transcription factor, and it was highly expressed in various types of tobacco callus including the chrk1 transgenic callus, hence designated as nicotiana tabacum callus-expressing factor 1 ntcef1. the ntcef1-gfp fusion protein was localized in the nucleus. the full ...	2005	15918028
structural complexity, differential response to infection, and tissue specificity of indolic and phenylpropanoid secondary metabolism in arabidopsis roots.	levels of indolic and phenylpropanoid secondary metabolites in arabidopsis (arabidopsis thaliana) leaves undergo rapid and drastic changes during pathogen defense, yet little is known about this process in roots. using arabidopsis wild-type and mutant root cultures as an experimental system, and the root-pathogenic oomycete, pythium sylvaticum, for infections, we analyzed the aromatic metabolite profiles in soluble extracts from uninfected and infected roots, as well as from the surrounding medi ...	2005	15923335
an arabidopsis homeodomain transcription factor, overexpressor of cationic peroxidase 3, mediates resistance to infection by necrotrophic pathogens.	the mechanisms controlling plant resistance to necrotrophic fungal pathogens are poorly understood. we previously reported on ep5c, a gene shown to be induced by the h(2)o(2) generated during a plant-pathogen interaction. to identify novel plant components operating in pathogen-induced signaling cascades, we initiated a large-scale screen using arabidopsis thaliana plants carrying the beta-glucuronidase reporter gene under control of the h(2)o(2)-responsive ep5c promoter. here, we report the ide ...	2005	15923348
improved degradation of organophosphorus nerve agents and p-nitrophenol by pseudomonas putida js444 with surface-expressed organophosphorus hydrolase.	pseudomonas putida js444, isolated from p-nitrophenol (pnp) contaminated waste sites, was genetically engineered to simultaneously degrade organophosphorus pesticides (op) and pnp. a surface anchor system derived from the ice-nucleation protein (inp) from pseudomonas syringae was used to target the organophosphorus hydrolase (oph) onto the surface of pseudomonas putida js444, reducing the potential substrate uptake limitation. engineered cells were capable of targeting oph onto the cell surface ...	2005	15932242
complete genome sequence of phihsic, a pseudotemperate marine phage of listonella pelagia.	the genome for the marine pseudotemperate member of the siphoviridae phihsic has been sequenced using a combination of linker amplification library construction, restriction digest library construction, and primer walking. phihsic enters into a pseudolysogenic relationship with its host, listonella pelagia, characterized by sigmoidal growth curves producing >10(9) cells/ml and >10(11) phage/ml. the genome (37,966 bp; g+c content, 44%) contained 47 putative open reading frames (orfs), 17 of which ...	2005	15933034
two pseudomonas syringae type iii effectors inhibit rin4-regulated basal defense in arabidopsis.	plant cells have two defense systems that detect bacterial pathogens. one is a basal defense system that recognizes complex pathogen-associated molecular patterns (pamps). a second system uses disease-resistance (r) proteins to recognize type lll effector proteins that are delivered into the plant cell by the pathogen's type iii secretion system. here we show that these two pathways are linked. we find that two pseudomonas syringae type iii effectors, avrrpt2 and avrrpm1, inhibit pamp-induced si ...	2005	15935761
suppression of host defense in compatible plant-pseudomonas syringae interactions.	despite impressive advances in the study of plant resistance to pathogens, little is known about the molecular basis of plant susceptibility to virulent pathogens. recent progress in susceptible plant-pseudomonas syringae interactions has provided a glimpse into the battles fought between plants and bacterial pathogens. a key step for pathogenesis appears to be the suppression of host defenses. suppression of host defenses, including basal defense, gene-for-gene resistance and nonhost resistance ...	2005	15936244
analysis of pseudomonas putida kt2440 gene expression in the maize rhizosphere: in vivo [corrected] expression technology capture and identification of root-activated promoters.	pseudomonas putida kt2440, a paradigm organism in biodegradation and a good competitive colonizer of the maize rhizosphere, was the subject of studies undertaken to establish the genetic determinants important for its rhizospheric lifestyle. by using in vivo expression technology (ivet) to positively select single cell survival, we identified 28 rap genes (root-activated promoters) preferentially expressed in the maize rhizosphere. the ivet system had two components: a mutant affected in asparta ...	2005	15937166
pseudomonas syringae type iii chaperones shco1, shcs1, and shcs2 facilitate translocation of their cognate effectors and can substitute for each other in the secretion of hopo1-1.	the pseudomonas syringae type iii secretion system (ttss) translocates effector proteins into plant cells. several p. syringae effectors require accessory proteins called type iii chaperones (ttcs) to be secreted via the ttss. we characterized the hopo1-1, hops1, and hops2 operons in p. syringae pv. tomato dc3000; these operons encode three homologous ttcs, shco1, shcs1, and shcs2. shco1, shcs1, and shcs2 facilitated the type iii secretion and/or translocation of their cognate effectors hopo1-1, ...	2005	15937188
systemic acquired tolerance to virulent bacterial pathogens in tomato.	recent studies on the interactions between plants and pathogenic microorganisms indicate that the processes of disease symptom development and pathogen growth can be uncoupled. thus, in many instances, the symptoms associated with disease represent an active host response to the presence of a pathogen. these host responses are frequently mediated by phytohormones. for example, ethylene and salicylic acid (sa) mediate symptom development but do not influence bacterial growth in the interaction be ...	2005	15937273
natural variation in the pto pathogen resistance gene within species of wild tomato (lycopersicon). i. functional analysis of pto alleles.	disease resistance to the bacterial pathogen pseudomonas syringae pv. tomato (pst) in the cultivated tomato, lycopersicon esculentum, and the closely related l. pimpinellifolium is triggered by the physical interaction between plant disease resistance protein, pto, and the pathogen avirulence protein, avrpto. to investigate the extent to which variation in the pto gene is responsible for naturally occurring variation in resistance to pst, we determined the resistance phenotype of 51 accessions f ...	2005	15944360
the tetr family of transcriptional repressors.	we have developed a general profile for the proteins of the tetr family of repressors. the stretch that best defines the profile of this family is made up of 47 amino acid residues that correspond to the helix-turn-helix dna binding motif and adjacent regions in the three-dimensional structures of tetr, qacr, cprb, and ethr, four family members for which the function and three-dimensional structure are known. we have detected a set of 2,353 nonredundant proteins belonging to this family by scree ...	2005	15944459
a census of membrane-bound and intracellular signal transduction proteins in bacteria: bacterial iq, extroverts and introverts.	analysis of complete microbial genomes showed that intracellular parasites and other microorganisms that inhabit stable ecological niches encode relatively primitive signaling systems, whereas environmental microorganisms typically have sophisticated systems of environmental sensing and signal transduction.	2005	15955239
evasion of toll-like receptor 5 by flagellated bacteria.	toll-like receptor 5 (tlr5) recognizes an evolutionarily conserved site on bacterial flagellin that is required for flagellar filament assembly and motility. the alpha and epsilon proteobacteria, including the important human pathogens campylobacter jejuni, helicobacter pylori, and bartonella bacilliformis, require flagellar motility to efficiently infect mammalian hosts. in this study, we demonstrate that these bacteria make flagellin molecules that are not recognized by tlr5. we map the site r ...	2005	15956202
recd plays an essential function during growth at low temperature in the antarctic bacterium pseudomonas syringae lz4w.	the antarctic psychrotrophic bacterium pseudomonas syringae lz4w has been used as a model system to identify genes that are required for growth at low temperature. transposon mutagenesis was carried out to isolate mutant(s) of the bacterium that are defective for growth at 4 degrees but normal at 22 degrees . in one such cold-sensitive mutant (cs1), the transposon-disrupted gene was identified to be a homolog of the recd gene of several bacteria. trans-complementation and freshly targeted gene d ...	2005	15956672
resistance to fusarium oxysporum 1, a dominant arabidopsis disease-resistance gene, is not race specific.	arabidopsis thaliana ecotypes differ in their susceptibility to fusarium wilt diseases. ecotype taynuilt-0 (ty-0) is susceptible to fusarium oxysporum forma specialis (f.) matthioli whereas columbia-0 (col-0) is resistant. segregation analysis of a cross between ty-0 and col-0 revealed six dominant resistance to fusarium oxysporum (rfo) loci that significantly contribute to f. matthioli resistance in col-0 relative to ty-0. we refer to the locus with the strongest effect as rfo1. ty-0 plants in ...	2005	15965251
two new sinorhizobium meliloti lysr-type transcriptional regulators required for nodulation.	the establishment of an effective nitrogen-fixing symbiosis between sinorhizobium meliloti and its legume host alfalfa (medicago sativa) depends on the timely expression of nodulation genes that are controlled by lysr-type regulators. ninety putative genes coding for lysr-type transcriptional regulators were identified in the recently sequenced s. meliloti genome. all 90 putative lysr genes were mutagenized using plasmid insertions as a first step toward determining their roles in symbiosis. two ...	2005	15968067
rotting softly and stealthily.	the soft rot erwiniae, which are plant pathogens on potato and other crops world-wide, synthesize and secrete large quantities of plant cell wall degrading enzymes that are responsible for the soft rot phenotype, earning them the epithet 'brute force' pathogens. they have been distinguished from classic 'stealth' pathogens, such as pseudomonas syringae, which possesses an extensive battery of type iii secreted effector proteins and phytotoxins to manipulate and suppress host defences. however, r ...	2005	15970273
molecular cloning of a phytase gene (phy m) from pseudomonas syringae mok1.	a phytase gene (phy m) was cloned from pseudomonas syringae mok1 by two steps of degenerate pcr and inverse pcr. this gene consists of 1,287 nucleotides and encodes a polypeptide of 428 amino acids with a deduced molecular mass of 46,652 kda. based on its amino acid sequence, the phy m shares the active site rhgxrxp and hd sequence motifs, typically characterized by histidine acid phosphatases familly. each phy m gene fragment encoding mature phy m with its own signal sequence (pepss) and withou ...	2005	15971093
role of motility and flagellin glycosylation in the pathogenesis of pseudomonas aeruginosa burn wound infections.	in this study, we tested the contribution of flagellar motility, flagellin structure, and its glycosylation in pseudomonas aeruginosa using genetically defined flagellar mutants. all mutants and their parent strains were tested in a burned-mouse model of infection. motility and glycosylation of the flagellum appear to be important determinants of flagellar-mediated virulence in this model. this is the first report where genetically defined flagellar variants of p. aeruginosa were tested in the b ...	2005	15972536
a rab-e gtpase mutant acts downstream of the rab-d subclass in biosynthetic membrane traffic to the plasma membrane in tobacco leaf epidermis.	the function of the rab-e subclass of plant rab gtpases in membrane traffic was investigated using a dominant-inhibitory mutant (rab-e1(d)[ni]) of arabidopsis thaliana rab-e1(d) and in vivo imaging approaches that have been used to characterize similar mutants in the plant rab-d2 and rab-f2 subclasses. rab-e1(d)[ni] inhibited the transport of a secreted green fluorescent protein marker, secgfp, but in contrast with dominant-inhibitory rab-d2 or rab-f2 mutants, it did not affect the transport of ...	2005	15972698
a chaperone-like hrpg protein acts as a suppressor of hrpv in regulation of the pseudomonas syringae pv. syringae type iii secretion system.	the cloned hrp/hrc cluster of pseudomonas syringae pv. syringae 61 (pss61) contains 28 proteins, and many of those are assembled into a type iii secretion system (ttss) that is responsible for eliciting the hypersensitive response (hr) in non-host plants and causing diseases on host plants (huang et al., 1995). hrpg, the second gene in the hrpc operon, encodes a 15.4 kda cytoplasmic protein whose predicted structure is similar to sicp (e-value: 0.19), a ttss chaperone of salmonella typhimurium. ...	2005	15978082
nitrite as the major source of nitric oxide production by arabidopsis thaliana in response to pseudomonas syringae.	the origin of nitric oxide (no) in plants is unclear and an no synthase (nos)-like enzyme and nitrate reductase (nr) are claimed as potential sources. here we used wild-type and nr-defective double mutant plants to investigate no production in arabidopsis thaliana in response to pseudomonas syringae pv maculicola. nos activity increased substantially in leaves inoculated with p. syringae. however, electron paramagnetic resonance experiments showed a much higher no formation that was dependen ...	2005	15978583
fatty acid hydroperoxides and h2o2 in the execution of hypersensitive cell death in tobacco leaves.	we initially compared lipid peroxidation profiles in tobacco (nicotiana tabacum) leaves during different cell death events. an upstream oxylipin assay was used to discriminate reactive oxygen species (ros)-mediated lipid peroxidation from 9- and 13-lipoxygenase (lox)-dependent lipid peroxidation. free radical-mediated membrane peroxidation was measured during h(2)o(2)-dependent cell death in leaves of catalase-deficient plants. taking advantage of these transgenic plants, we demonstrate that, un ...	2005	15980200
recent additions and improvements to the onto-tools.	the onto-tools suite is composed of an annotation database and six seamlessly integrated, web-accessible data mining tools: onto-express, onto-compare, onto-design, onto-translate, onto-miner and pathway-express. the onto-tools database has been expanded to include various types of data from 12 new databases. our database now integrates different types of genomic data from 19 sequence, gene, protein and annotation databases. additionally, our database is also expanded to include complete gene on ...	2005	15980579
identification of arabidopsis loci required for susceptibility to the downy mildew pathogen hyaloperonospora parasitica.	plants are susceptible to a limited number of pathogens. most infections fail due to active defense or absence of compatibility. many components of the plant's surveillance system and defense arsenal have been identified in the last decades. however, knowledge is limited on compatibility; in particular, the role of plant factors in the infection process. to gain insight into these processes, we have initiated an arabidopsis thaliana mutant screen for reduced susceptibility to the downy mildew pa ...	2005	15986928