Publications

identification and functional expression of the pepper pathogen-induced gene, capip2, involved in disease resistance and drought and salt stress tolerance.	a novel pathogen-induced gene, designated capip2, was isolated from pepper leaves infected with xanthomonas campestris pv. vesicatoria. capip2:gfp fusion proteins were primarily localized in the cytoplasm. the capip2 transcripts were constitutively expressed in the pepper leaves, flowers, and fruits, but were not detected in the stems and roots. capip2 gene expression was induced strongly in the pepper leaves during pathogen infection, and also after exposure to abiotic elicitors and environment ...	2006	16900319
random mutagenesis in corynebacterium glutamicum atcc 13032 using an is6100-based transposon vector identified the last unknown gene in the histidine biosynthesis pathway.	corynebacterium glutamicum, a gram-positive bacterium of the class actinobacteria, is an industrially relevant producer of amino acids. several methods for the targeted genetic manipulation of this organism and rational strain improvement have been developed. an efficient transposon mutagenesis system for the completely sequenced type strain atcc 13032 would significantly advance functional genome analysis in this bacterium.	2006	16901339
genome comparison using gene ontology (go) with statistical testing.	automated comparison of complete sets of genes encoded in two genomes can provide insight on the genetic basis of differences in biological traits between species. gene ontology (go) is used as a common vocabulary to annotate genes for comparison. current approaches calculate the fold of unweighted or weighted differences between two species at the high-level go functional categories. however, to ensure the reliability of the differences detected, it is important to evaluate their statistical si ...	2006	16901353
gacs-dependent production of 2r, 3r-butanediol by pseudomonas chlororaphis o6 is a major determinant for eliciting systemic resistance against erwinia carotovora but not against pseudomonas syringae pv. tabaci in tobacco.	root colonization by a plant-beneficial rhizobacterium, pseudomonas chlororaphis o6, induces disease resistance in tobacco against leaf pathogens erwinia carotovora subsp. carotovora scc1, causing soft-rot, and pseudomonas syringae pv. tabaci, causing wildfire. in order to identify the bacterial determinants involved in induced systemic resistance against plant diseases, extracellular components produced by the bacterium were fractionated and purified. factors in the culture filtrate inducing sy ...	2006	16903358
the structural basis for promoter -35 element recognition by the group iv sigma factors.	the control of bacterial transcription initiation depends on a primary sigma factor for housekeeping functions, as well as alternative sigma factors that control regulons in response to environmental stresses. the largest and most diverse subgroup of alternative sigma factors, the group iv extracytoplasmic function sigma factors, directs the transcription of genes that regulate a wide variety of responses, including envelope stress and pathogenesis. we determined the 2.3-a resolution crystal str ...	2006	16903784
multiple avirulence paralogues in cereal powdery mildew fungi may contribute to parasite fitness and defeat of plant resistance.	powdery mildews, obligate biotrophic fungal parasites on a wide range of important crops, can be controlled by plant resistance (r) genes, but these are rapidly overcome by parasite mutants evading recognition. it is unknown how this rapid evolution occurs without apparent loss of parasite fitness. r proteins recognize avirulence (avr) molecules from parasites in a gene-for-gene manner and trigger defense responses. we identify avr(a10) and avr(k1) of barley powdery mildew fungus, blumeria grami ...	2006	16905653
characterization of outer membrane vesicles released by the psychrotolerant bacterium pseudoalteromonas antarctica nf3.	pseudoalteromonas antarctica nf3 is an antarctic psychrotolerant gram-negative bacterium that accumulates large amounts of an extracellular polymeric substance (eps) with high protein content. transmission electron microscopy analysis after high-pressure freezing and freeze substitution (hpf-fs) shows that the eps is composed of a capsular polymer and large numbers of outer membrane vesicles (omvs). these vesicles are bilayered structures and predominantly spherical in shape, with an average dia ...	2006	16913913
oxylipin profiling of the hypersensitive response in arabidopsis thaliana. formation of a novel oxo-phytodienoic acid-containing galactolipid, arabidopside e.	oxidation products of unsaturated fatty acids, collectively known as oxylipins, function as signaling molecules in plants during development, wounding, and insect and pathogen attack. certain oxylipins are also known to have direct cytotoxic effects on pathogens. we used inducible expression of bacterial avirulence proteins in planta to study the involvement of oxylipins in race-specific defense against bacterial pathogens. we demonstrate that recognition of the pseudomonas syringae avirulence p ...	2006	16923817
pseudomonas syringae hrpj is a type iii secreted protein that is required for plant pathogenesis, injection of effectors, and secretion of the hrpz1 harpin.	the bacterial plant pathogen pseudomonas syringae requires a type iii protein secretion system (ttss) to cause disease. the p. syringae ttss is encoded by the hrp-hrc gene cluster. one of the genes within this cluster, hrpj, encodes a protein with weak similarity to yopn, a type iii secreted protein from the animal pathogenic yersinia species. here, we show that hrpj is secreted in culture and translocated into plant cells by the p. syringae pv. tomato dc3000 ttss. a dc3000 hrpj mutant, unl140, ...	2006	16923873
evolution of vitamin b2 biosynthesis: 6,7-dimethyl-8-ribityllumazine synthases of brucella.	the penultimate step in the biosynthesis of riboflavin (vitamin b2) involves the condensation of 3,4-dihydroxy-2-butanone 4-phosphate with 5-amino-6-ribitylamino-2,4(1h,3h)-pyrimidinedione, which is catalyzed by 6,7-dimethyl-8-ribityllumazine synthase (lumazine synthase). pathogenic brucella species adapted to an intracellular lifestyle have two genes involved in riboflavin synthesis, ribh1 and ribh2, which are located on different chromosomes. the ribh2 gene was shown previously to specify a lu ...	2006	16923880
phospholipase-dependent signalling during the avrrpm1- and avrrpt2-induced disease resistance responses in arabidopsis thaliana.	bacterial pathogens deliver type iii effector proteins into plant cells during infection. on susceptible host plants, type iii effectors contribute to virulence, but on resistant hosts they betray the pathogen to the plant's immune system and are functionally termed avirulence (avr) proteins. recognition induces a complex suite of cellular and molecular events comprising the plant's inducible defence response. as recognition of type iii effector proteins occurs inside host cells, defence respons ...	2006	16925603
extensive genomic plasticity in pseudomonas aeruginosa revealed by identification and distribution studies of novel genes among clinical isolates.	the distributed genome hypothesis (dgh) states that each strain within a bacterial species receives a unique distribution of genes from a population-based supragenome that is many times larger than the genome of any given strain. the observations that natural infecting populations are often polyclonal and that most chronic bacterial pathogens have highly developed mechanisms for horizontal gene transfer suggested the dgh and provided the means and the mechanisms to explain how chronic infections ...	2006	16926421
comparative analysis of argk-tox clusters and their flanking regions in phaseolotoxin-producing pseudomonas syringae pathovars.	dna fragments containing argk-tox clusters and their flanking regions were cloned from the chromosomes of pseudomonas syringae pathovar (pv.) actinidiae strain kw-11 (act) and p. syringae pv. phaseolicola strain maff 302282 (pha), and then their sequences were determined. comparative analysis of these sequences and the sequences of p. syringae pv. tomato dc3000 (tom) (buell et al., proc natl acad sci usa 100:10181-10186, 2003) and pv. syringae b728a (syr) (feil et al., proc natl acad sci usa 102 ...	2006	16927007
expression and functional roles of the pepper pathogen-induced transcription factor rav1 in bacterial disease resistance, and drought and salt stress tolerance.	a novel pathogen-induced gene encoding the rav (related to abi3/vp1) transcription factor, carav1, was isolated from pepper leaves infected with xanthomonas campestris pv. vesicatoria. carav1 contains two distinct dna-binding domains ap2 and b3 uniquely found in higher plants. transient expression analysis of the smgfp:carav1 fusion construct in arabidopsis protoplasts and pepper epidermal cells revealed the carav1 protein to be localized in the nucleus. the n-terminal region of carav1 fused to ...	2006	16927203
exopolysaccharide-associated protein sorting in environmental organisms: the pep-cterm/epsh system. application of a novel phylogenetic profiling heuristic.	protein translocation to the proper cellular destination may be guided by various classes of sorting signals recognizable in the primary sequence. detection in some genomes, but not others, may reveal sorting system components by comparison of the phylogenetic profile of the class of sorting signal to that of various protein families.	2006	16930487
integrated regulation of the type iii secretion system and other virulence determinants in ralstonia solanacearum.	in many plant and animal bacterial pathogens, the type iii secretion system (ttss) that directly translocates effector proteins into the eukaryotic host cells is essential for the development of disease. in all species studied, the transcription of the ttss and most of its effector substrates is tightly regulated by a succession of consecutively activated regulators. however, the whole genetic programme driven by these regulatory cascades is still unknown, especially in bacterial plant pathogens ...	2006	16933989
dead-box rna helicases in escherichia coli.	in spite of their importance in rna metabolism, the function of dexd/h-box proteins (including dead-box proteins) is poorly understood at the molecular level. here, we present recent progress achieved with the five dead-box proteins from escherichia coli, which have been particularly well studied. these proteins, which have orthologues in many bacteria, participate, in particular, in specific steps of mrna decay and ribosome assembly. in vitro, they behave as poorly processive rna helicases, pre ...	2006	16935881
hormonal and stress induction of the gene encoding common bean acetyl-coenzyme a carboxylase.	regulation of the cytosolic acetyl-coenzyme a carboxylase (accase) gene promoter from common bean (phaseolus vulgaris) was studied in transgenic arabidopsis (arabidopsis thaliana) plants using a beta-glucuronidase (gus) reporter gene fusion (pvaccase::gus). under normal growth conditions, gus was expressed in hydathodes, stipules, trichome bases, flowers, pollen, and embryos. in roots, expression was observed in the tip, elongation zone, hypocotyl-root transition zone, and lateral root primordia ...	2006	16935989
role of ptsp, orft, and sss recombinase genes in root colonization by pseudomonas fluorescens q8r1-96.	pseudomonas fluorescens q8r1-96 produces 2,4-diacetylphloroglucinol (2,4-dapg), a polyketide antibiotic that suppresses a wide variety of soilborne fungal pathogens, including gaeumannomyces graminis var. tritici, which causes take-all disease of wheat. strain q8r1-96 is representative of the d-genotype of 2,4-dapg producers, which are exceptional because of their ability to aggressively colonize and maintain large populations on the roots of host plants, including wheat, pea, and sugar beet. in ...	2006	16936061
transcriptional changes in powdery mildew infected wheat and arabidopsis leaves undergoing syringolin-triggered hypersensitive cell death at infection sites.	blumeria graminis f.sp. tritici, the causal agent of powdery mildew in wheat, is an obligate biotrophic fungus that exclusively invades epidermal cells. as previously shown, spraying of a solution of syringolin a, a circular peptide derivative secreted by the phytopathogenic bacterium pseudomonas syringae pv. syringae, triggers hypersensitive cell death at infection sites in powdery mildew infected wheat. thus, the fungus is essentially eradicated. here we show that syringolin a also triggers hy ...	2006	16941219
genome-wide gene expression analysis of pseudomonas syringae pv. tomato dc3000 reveals overlapping and distinct pathways regulated by hrpl and hrprs.	pseudomonas syringae pv. tomato dc3000 is a model pathogen infecting tomato and arabidopsis plants. genes encoding the type iii secretion system and substrate proteins (collectively called ttss genes) of this bacterium are induced in plants and in minimal medium (mm). the induction of ttss genes is mediated by hrpl, an alternative sigma factor recognizing the hrp box in the promoter of ttss genes. the transcription of hrpl is activated by hrpr and hrps, two homologous dna-binding proteins encode ...	2006	16941902
the type iii effector repertoire of pseudomonas syringae pv. syringae b728a and its role in survival and disease on host and non-host plants.	the bacterial plant pathogen pseudomonas syringae injects a large repertoire of effector proteins into plant cells using a type iii secretion apparatus. effectors can trigger or suppress defences in a host-dependent fashion. host defences are often accompanied by programmed cell death, while interference with defences is sometimes associated with cell death suppression. we previously predicted the effector repertoire of the sequenced bean pathogen p. syringae pv. syringae (psy) b728a using bioin ...	2006	16942603
diversifying selection drives the evolution of the type iii secretion system pilus of pseudomonas syringae.	the plant pathogenic bacterium pseudomonas syringae uses a type iii secretion system to inject virulence proteins directly into the cytoplasm of its hosts. the p. syringae type iii secretion apparatus is encoded, in part, by the hrpz operon, which carries the hrpa gene encoding the pilin subunit of the pilus, various components of the structural apparatus, and the hrpz harpin protein that is believed to produce pores in the host cell membrane. the pilus of the type iii system comes into direct c ...	2006	16950758
characterization of a mitogen-activated protein kinase gene from cucumber required for trichoderma-conferred plant resistance.	the fungal biocontrol agent trichoderma asperellum has been recently shown to induce systemic resistance in plants through a mechanism that employs jasmonic acid and ethylene signal transduction pathways. mitogen-activated protein kinase (mapk) proteins have been implicated in the signal transduction of a wide variety of plant stress responses. here we report the identification and characterization of a trichoderma-induced mapk (tipk) gene function in cucumber (cucumis sativus). similar to its h ...	2006	16950863
comparative genomics of host-specific virulence in pseudomonas syringae.	while much study has gone into characterizing virulence factors that play a general role in disease, less work has been directed at identifying pathogen factors that act in a host-specific manner. understanding these factors will help reveal the variety of mechanisms used by pathogens to suppress or avoid host defenses. we identified candidate pseudomonas syringae host-specific virulence genes by searching for genes whose distribution among natural p. syringae isolates was statistically associat ...	2006	16951068
cawrky2, a chili pepper transcription factor, is rapidly induced by incompatible plant pathogens.	wrky family proteins are a class of plant-specific transcription factors involved in stress response signaling pathways. in this study a gene encoding a putative wrky protein was isolated from a pepper est database (http://genepool.kribb.re.kr). the cdna, named capsicum annuum wrky2 (cawrky2), encodes a putative polypeptide of 548 amino acids, containing two wrky domains with zinc finger motifs and two potential nuclear localization signals. northern blot analyses showed that cawrky2 mrna was pr ...	2006	16951551
identification, typing, and insecticidal activity of xenorhabdus isolates from entomopathogenic nematodes in united kingdom soil and characterization of the xpt toxin loci.	xenorhabdus strains from entomopathogenic nematodes isolated from united kingdom soils by using the insect bait entrapment method were characterized by partial sequencing of the 16s rrna gene, four housekeeping genes (asd, ompr, reca, and serc) and the flagellin gene (flic). most strains (191/197) were found to have genes with greatest similarity to those of xenorhabdus bovienii, and the remaining six strains had genes most similar to those of xenorhabdus nematophila. generally, 16s rrna sequenc ...	2006	16957209
microbial communities in the surface mucopolysaccharide layer and the black band microbial mat of black band-diseased siderastrea siderea.	microbial community profiles and species composition associated with two black band-diseased colonies of the coral siderastrea siderea were studied by 16s rrna-targeted gene cloning, sequencing, and amplicon-length heterogeneity pcr (lh-pcr). bacterial communities associated with the surface mucopolysaccharide layer (sml) of apparently healthy tissues of the infected colonies, together with samples of the black band disease (bbd) infections, were analyzed using the same techniques for comparison ...	2006	16957217
an oxidoreductase is involved in cercosporin degradation by the bacterium xanthomonas campestris pv. zinniae.	the polyketide toxin cercosporin plays a key role in pathogenesis by fungal species of the genus cercospora. the bacterium xanthomonas campestris pv. zinniae is able to rapidly degrade this toxin. growth of x. campestris pv. zinniae strains in cercosporin-containing medium leads to the breakdown of cercosporin and to the formation of xanosporic acid, a nontoxic breakdown product. five non-cercosporin-degrading mutants of a strain that rapidly degrades cercosporin (xcz-3) were generated by ethyl ...	2006	16957231
elucidation of the hrp clusters of xanthomonas oryzae pv. oryzicola that control the hypersensitive response in nonhost tobacco and pathogenicity in susceptible host rice.	xanthomonas oryzae pv. oryzicola, the cause of bacterial leaf streak in rice, possesses clusters of hrp genes that determine its ability to elicit a hypersensitive response (hr) in nonhost tobacco and pathogenicity in host rice. a 27-kb region of the genome of x. oryzae pv. oryzicola (rs105) was identified and sequenced, revealing 10 hrp, 9 hrc (hrp conserved), and 8 hpa (hrp-associated) genes and 7 regulatory plant-inducible promoter boxes. while the region from hpa2 to hpab and the hrpf operon ...	2006	16957248
complete genome sequence of the marine, chemolithoautotrophic, ammonia-oxidizing bacterium nitrosococcus oceani atcc 19707.	the gammaproteobacterium nitrosococcus oceani (atcc 19707) is a gram-negative obligate chemolithoautotroph capable of extracting energy and reducing power from the oxidation of ammonia to nitrite. sequencing and annotation of the genome revealed a single circular chromosome (3,481,691 bp; g+c content of 50.4%) and a plasmid (40,420 bp) that contain 3,052 and 41 candidate protein-encoding genes, respectively. the genes encoding proteins necessary for the function of known modes of lithotrophy and ...	2006	16957257
pathogen-induced arabidopsis wrky7 is a transcriptional repressor and enhances plant susceptibility to pseudomonas syringae.	the arabidopsis (arabidopsis thaliana) wrky7 gene is induced by pathogen infection and salicylic acid (sa) treatment and may therefore play a role in plant defense responses. here, we show that wrky7 is localized in the nucleus, recognizes dna molecules with the w-box (ttgac) elements, and functions as a transcriptional repressor in plant cells. to study its biological functions directly, we have characterized both loss-of-function t-dna insertion and rnai mutants and gain-of-function transgenic ...	2006	16963526
genetic differences between blight-causing erwinia species with differing host specificities, identified by suppression subtractive hybridization.	pcr-based subtractive hybridization was used to isolate sequences from erwinia amylovora strain ea110, which is pathogenic on apples and pears, that were not present in three closely related strains with differing host specificities: e. amylovora mr1, which is pathogenic only on rubus spp.; erwinia pyrifoliae ep1/96, the causal agent of shoot blight of asian pears; and erwinia sp. strain ejp556, the causal agent of bacterial shoot blight of pear in japan. in total, six subtractive libraries were ...	2006	16963554
complete nucleotide sequence of an exogenously isolated plasmid, plb1, involved in gamma-hexachlorocyclohexane degradation.	the alpha-proteobacterial strain sphingobium japonicum ut26 utilizes a highly chlorinated pesticide, gamma-hexachlorocyclohexane (gamma-hch), as a sole source of carbon and energy, and haloalkane dehalogenase linb catalyzes the second step of gamma-hch degradation in ut26. functional complementation of a linb mutant of ut26, ut26db, was performed by the exogenous plasmid isolation technique using hch-contaminated soil, leading to our successful identification of a plasmid, plb1, carrying the lin ...	2006	16963556
eukaryotic cyclophilin as a molecular switch for effector activation.	gram-negative phytopathogenic bacteria, such as pseudomonas syringae, deliver multiple effector proteins into plant cells during infection. it is hypothesized that certain plant and mammalian effector proteins need to traverse the type iii secretion system unfolded and are delivered into host cells as inactive enzymes. we have previously identified cyclophilin as the arabidopsis eukaryotic activator of avrrpt2, a p. syringae effector that is a cysteine protease. cyclophilins are general folding ...	2006	16968222
enhancement of chilling resistance of inoculated grapevine plantlets with a plant growth-promoting rhizobacterium, burkholderia phytofirmans strain psjn.	in vitro inoculation of vitis vinifera l. cv. chardonnay explants with a plant growth-promoting rhizobacterium, burkholderia phytofirmans strain psjn, increased grapevine growth and physiological activity at a low temperature. there was a relationship between endophytic bacterial colonization of the grapevine plantlets and their growth at both ambient (26 degrees c) and low (4 degrees c) temperatures and their sensitivities to chilling. the major benefits of bacterization were observed on root g ...	2006	16980419
colocation of genes encoding a trna-mrna hybrid and a putative signaling peptide on complementary strands in the genome of the hyperthermophilic bacterium thermotoga maritima.	in the genome of the hyperthermophilic bacterium thermotoga maritima, tm0504 encodes a putative signaling peptide implicated in population density-dependent exopolysaccharide formation. although not noted in the original genome annotation, tm0504 was found to colocate, on the opposite strand, with the gene encoding ssra, a hybrid of trna and mrna (tmrna), which is involved in a trans-translation process related to ribosome rescue and is ubiquitous in bacteria. specific dna probes were designed a ...	2006	16980482
ospf and ospc1 are shigella flexneri type iii secretion system effectors that are required for postinvasion aspects of virulence.	shigella flexneri is the causative agent of dysentery, and its pathogenesis is mediated by a type iii secretion system (t3ss). s. flexneri secretes effector proteins into the eukaryotic cell via the t3ss, and these proteins usurp host cellular functions to the benefit of the bacteria. ospf and ospc1 are known to be secreted by s. flexneri, but their functions are unknown. we transformed s. flexneri with a plasmid that expresses a two-hemagglutinin tag (2ha) in frame with ospf or ospc1 and verifi ...	2006	16988276
antimicrobial activity of extracts of chemical races of the lichen pseudevernia furfuracea and their physodic acid, chloroatranorin, atranorin, and olivetoric acid constituents.	the antimicrobial activity and the mic values of the ethanol, chloroform, diethyl ether, and acetone extracts of the chemical races of pseudevernia furfuracea (var. furfuracea and var. ceratea) and their physodic acid, chloroatranorin, atranorin, and olivetoric acid constituents have been investigated against some microorganisms. nearly all extracts of both chemical races showed antimicrobial activity against aeromonas hydrophila, bacillus cereus, bacillus subtilis, listeria monocytogenes, prote ...	2006	16989308
disruption of n-acyl homoserine lactone-mediated cell signaling and iron acquisition in epiphytic bacteria by leaf surface compounds.	since n-acyl homoserine lactones (ahls) are key mediators of cell density-dependent regulation of traits involved in virulence and epiphytic fitness in gram-negative bacteria such as pseudomonas syringae, a variety of plant species were examined to determine their production of leaf surface compounds that could interact with these signaling systems. leaf washings of 17 of 52 plant species tested stimulated or inhibited ahl-dependent traits in at least one of the bacterial reporter strains used. ...	2006	16997987
the crystal structure of the e. coli stress protein ycif.	ycif is a protein that is up-regulated when bacteria experience stress conditions, and is highly conserved in a range of bacterial species. ycif has no known structure or biochemical function. to learn more about its potential molecular function and its role in the bacterial stress response, we solved the crystal structure of ycif at 2.0 angstrom resolution by the multiple wavelength anomalous diffraction (mad) technique. ycif is a dimer in solution, and forms a homodimer in the crystal asymmetr ...	2006	17001035
resistance of yersinia pestis to antimicrobial agents.		2006	17005799
contribution of alginate and levan production to biofilm formation by pseudomonas syringae.	exopolysaccharides (epss) play important roles in the attachment of bacterial cells to a surface and/or in building and maintaining the three-dimensional, complex structure of bacterial biofilms. to elucidate the spatial distribution and function of the epss levan and alginate during biofilm formation, biofilms of pseudomonas syringae strains with different eps patterns were compared. the mucoid strain pg4180.muc, which produces levan and alginate, and its levan- and/or alginate-deficient deriva ...	2006	17005972
plant mpss databases: signature-based transcriptional resources for analyses of mrna and small rna.	mpss (massively parallel signature sequencing) is a sequencing-based technology that uses a unique method to quantify gene expression level, generating millions of short sequence tags per library. we have created a series of databases for four species (arabidopsis, rice, grape and magnaporthe grisea, the rice blast fungus). our mpss databases measure the expression level of most genes under defined conditions and provide information about potentially novel transcripts (antisense transcripts, alt ...	2006	16381968
plant mpss databases: signature-based transcriptional resources for analyses of mrna and small rna.	mpss (massively parallel signature sequencing) is a sequencing-based technology that uses a unique method to quantify gene expression level, generating millions of short sequence tags per library. we have created a series of databases for four species (arabidopsis, rice, grape and magnaporthe grisea, the rice blast fungus). our mpss databases measure the expression level of most genes under defined conditions and provide information about potentially novel transcripts (antisense transcripts, alt ...	2006	16381968
polar flagellum biogenesis in aeromonas hydrophila.	mesophilic aeromonas spp. constitutively express a single polar flagellum that helps the bacteria move to more favorable environments and is an important virulence and colonization factor. certain strains can also produce multiple lateral flagella in semisolid media or over surfaces. we have previously reported 16 genes (flgn to flgl) that constitute region 1 of the aeromonas hydrophila ah-3 polar flagellum biogenesis gene clusters. we identified 39 new polar flagellum genes distributed in four ...	2006	16385045
dna sequence of a colv plasmid and prevalence of selected plasmid-encoded virulence genes among avian escherichia coli strains.	colv plasmids have long been associated with the virulence of escherichia coli, despite the fact that their namesake trait, colv production, does not appear to contribute to virulence. such plasmids or their associated sequences appear to be quite common among avian pathogenic e. coli (apec) and are strongly linked to the virulence of these organisms. in the present study, a 180-kb colv plasmid was sequenced and analyzed. this plasmid, papec-o2-colv, possesses a 93-kb region containing several p ...	2006	16385064
molecular basis for g protein control of the prokaryotic atp sulfurylase.	sulfate assimilation is a critical component of both primary and secondary metabolism. an essential step in this pathway is the activation of sulfate through adenylation by the enzyme atp sulfurylase (atps), forming adenosine 5'-phosphosulfate (aps). proteobacterial atps overcomes this energetically unfavorable reaction by associating with a regulatory g protein, coupling the energy of gtp hydrolysis to aps formation. to discover the molecular basis of this unusual role for a g protein, we bioch ...	2006	16387658
elicitor-mediated oligomerization of the tobacco n disease resistance protein.	plant nucleotide binding site-leucine-rich repeat (nbs-lrr) proteins are similar to the nucleotide binding oligomerization domain (nod) protein family in their domain structure. it has been suggested that most nod proteins rely on ligand-mediated oligomerization for function, and we have tested this possibility with the n protein of tobacco (nicotiana tabacum). the n gene for resistance to tobacco mosaic virus (tmv) is a member of the toll-interleukin receptor (tir)-nbs-lrr class of plant diseas ...	2006	16387833
arabidopsis accelerated cell death2 modulates programmed cell death.	the arabidopsis thaliana chloroplast protein accelerated cell death2 (acd2) modulates the amount of programmed cell death (pcd) triggered by pseudomonas syringae and protoporphyrin ix (ppix) treatment. in vitro, acd2 can reduce red chlorophyll catabolite, a chlorophyll derivative. we find that acd2 shields root protoplasts that lack chlorophyll from light- and ppix-induced pcd. thus, chlorophyll catabolism is not obligatory for acd2 anti-pcd function. upon p. syringae infection, acd2 levels and ...	2006	16387834
a lithium-sensitive and sodium-tolerant 3'-phosphoadenosine-5'-phosphatase encoded by hala from the cyanobacterium arthrospira platensis is closely related to its counterparts from yeasts and plants.	3'-phosphoadenosine-5'-phosphatase (papase) is required for the removal of toxic 3'-phosphoadenosine-5'-phosphate (pap) produced during sulfur assimilation in various eukaryotic organisms. this enzyme is a well-known target of lithium and sodium toxicity and has been used for the production of salt-resistant transgenic plants. in addition, papase has also been proposed as a target in the treatment of manic-depressive patients. one gene, hala, which could encode a protein closely related to the p ...	2006	16391050
diverse avrptob homologs from several pseudomonas syringae pathovars elicit pto-dependent resistance and have similar virulence activities.	avrptob is a type iii effector protein from pseudomonas syringae pv. tomato that physically interacts with the tomato pto kinase and, depending on the host genotype, either elicits or suppresses programmed cell death associated with plant immunity. we reported previously that avrptob-related sequences are present in diverse gram-negative phytopathogenic bacteria. here we describe characterization of avrptob homologs from p. syringae pv. tomato t1, pt23, and jl1065, p. syringae pv. syringae b728a ...	2006	16391110
identification and deletion analysis of the promoter of the pepper sar8.2 gene activated by bacterial infection and abiotic stresses.	the pepper sar8.2 gene, casar82a, was locally and systemically induced in pepper plants which had been infected by xanthomonas campestris pv. vesicatoria or by pseudomonas fluorescens. the dna 1,283 bp sequence upstream of the casar82a gene was assessed with regard to the activity of the casar82a promoter fused to the beta-glucuronidase (gus) reporter gene, via an agrobacterium-mediated transient expression assay. in tobacco leaves which transiently expressed the -831 bp casar82a promoter, gus a ...	2006	16395580
expression analysis of the fpr (ferredoxin-nadp+ reductase) gene in pseudomonas putida kt2440.	the ferredoxin-nadp+ reductase (fpr) participates in cellular defense against oxidative damage. the fpr expression in pseudomonas putida kt2440 is induced by oxidative and osmotic stresses. finr, a lysr-type transcriptional factor near the fpr gene in the p. putida kt2440 genome, is required for induction of the fpr under both conditions. we have shown that the fpr and finr gene products can counteract the effects of oxidative and osmotic stresses. interestingly, finr-independent expression occu ...	2006	16360643
pleiotropic costs of niche expansion in the rna bacteriophage phi 6.	natural and experimental systems have failed to universally demonstrate a trade-off between generalism and specialism. when a trade-off does occur it is difficult to attribute its cause to antagonistic pleiotropy without dissecting the genetic basis of adaptation, and few previous experiments provide these genetic data. here we investigate the evolution of expanded host range (generalism) in the rna virus phi6, an experimental model system allowing adaptive mutations to be readily identified. we ...	2006	16299384
host-mediated phosphorylation of type iii effector avrpto promotes pseudomonas virulence and avirulence in tomato.	the avrpto protein from pseudomonas syringae pv tomato is delivered into plant cells by the bacterial type iii secretion system, where it either promotes host susceptibility or, in tomato plants expressing the pto kinase, elicits disease resistance. using two-dimensional gel electrophoresis, we obtained evidence that avrpto is phosphorylated when expressed in plant leaves. in vitro phosphorylation of avrpto by plant extracts occurs independently of pto and is due to a kinase activity that is con ...	2006	16399801
antimicrobial activity of glycosidase inhibitory protein isolated from cyphomandra betacea sendt. fruit.	broad-spectrum antimicrobial activity of an invertase inhibitory protein (iip) isolated from cyphomandra betacea ripe fruits is documented. minimal inhibitory concentration (mic) values were determined by agar macrodilution and broth microdilution assays. this iip inhibited the growth of xylophagous and phytopatogenic fungi (ganoderma applanatum, schizophyllum commune, lenzites elegans, pycnoporus sanguineous, penicillium notatum, aspergillus niger, phomopsis sojae and fusarium mango) and phytop ...	2006	16406143
identification of a ubiquinone-binding site that affects autophosphorylation of the sensor kinase regb.	rhodobacter capsulatus regulates many metabolic processes in response to the level of environmental oxygen and the energy state of the cell. one of the key global redox regulators of the cell's metabolic physiology is the sensor kinase regb that controls the synthesis of numerous energy generation and utilization processes. in this study, we have succeeded in purifying full-length regb containing six transmembrane-spanning elements. exogenous addition of excess oxidized coenzyme q1 is capable of ...	2006	16407278
rewiring mitogen-activated protein kinase cascade by positive feedback confers potato blight resistance.	late blight, caused by the notorious pathogen phytophthora infestans, is a devastating disease of potato (solanum tuberosum) and tomato (solanum lycopersicum), and during the 1840s caused the irish potato famine and over one million fatalities. currently, grown potato cultivars lack adequate blight tolerance. earlier cultivars bred for resistance used disease resistance genes that confer immunity only to some strains of the pathogen harboring corresponding avirulence gene. specific resistance ge ...	2006	16407438
loss of atpdr8, a plasma membrane abc transporter of arabidopsis thaliana, causes hypersensitive cell death upon pathogen infection.	plants contain a large number of atp-binding cassette (abc) transporters belonging to different subclasses. atpdr8 is the only member of the pleiotropic drug resistance (pdr) abc transporter subclass in arabidopsis that is constitutively highly expressed. in transgenic arabidopsis plants harboring the atpdr8 promoter fused to beta-glucuronidase (gus), reporter expression was shown to be strong in the stomata and hydathode. in the stomata, transcripts of atpdr8 were particularly frequent in the c ...	2006	16415066
characterization of a nonspecific phosphopantetheinyl transferase from pseudomonas syringae pv. syringae ff5.	the 4'-phosphopantetheinyl transferases (pptases) catalyze the transfer of a 4'-phosphopantetheine moiety from coenzyme a to phosphopantetheine-dependent carrier proteins. the carrier proteins (cps) are required for the biosynthesis of peptides synthesized by nonribosomal peptide synthases and the biosynthesis of fatty acids and polyketides. a single pptase (pcps) is present in the pathogenic bacterium pseudomonas aeruginosa. several pathovars of pseudomonas syringae produce the chlorosis-induci ...	2006	16423321
blast screening of chlamydial genomes to identify signature proteins that are unique for the chlamydiales, chlamydiaceae, chlamydophila and chlamydia groups of species.	chlamydiae species are of much importance from a clinical viewpoint. their diversity both in terms of their numbers as well as clinical involvement are presently believed to be significantly underestimated. the obligate intracellular nature of chlamydiae has also limited their genetic and biochemical studies. thus, it is of importance to develop additional means for their identification and characterization.	2006	16436211
pyruvate:quinone oxidoreductase in corynebacterium glutamicum: molecular analysis of the pqo gene, significance of the enzyme, and phylogenetic aspects.	corynebacterium glutamicum recently has been shown to possess pyruvate:quinone oxidoreductase (pqo), catalyzing the oxidative decarboxylation of pyruvate to acetate and co2 with a quinone as the electron acceptor. here, we analyze the expression of the c. glutamicum pqo gene, investigate the relevance of the pqo enzyme for growth and amino acid production, and perform phylogenetic studies. expression analyses revealed that transcription of pqo is initiated 45 bp upstream of the translational sta ...	2006	16452416
positive selection of the hrp pilin hrpe of the plant pathogen xanthomonas.	the plant-pathogenic bacterium xanthomonas campestris pv. vesicatoria possesses a type iii secretion (tts) system which is encoded by the 23-kb hrp (hypersensitive response and pathogenicity) gene cluster. the tts system is necessary for pathogenicity in susceptible hosts and induction of the hypersensitive response in resistant plants. at the cell surface, the tts system is associated with an extracellular filamentous structure, the hrp pilus, which serves as a conduit for the transfer of bacte ...	2006	16452423
quorum sensing in yersinia enterocolitica controls swimming and swarming motility.	the yersinia enterocolitica luxi homologue yeni directs the synthesis of n-3-(oxohexanoyl)homoserine lactone (3-oxo-c6-hsl) and n-hexanoylhomoserine lactone (c6-hsl). in a y. enterocolitica yeni mutant, swimming motility is temporally delayed while swarming motility is abolished. since both swimming and swarming are flagellum dependent, we purified the flagellin protein from the parent and yeni mutant. electrophoresis revealed that in contrast to the parent strain, the yeni mutant grown for 17 h ...	2006	16452428
genetic and transcriptional analysis of the siderophore malleobactin biosynthesis and transport genes in the human pathogen burkholderia pseudomallei k96243.	burkholderia pseudomallei is a gram-negative facultative intracellular pathogen that causes melioidosis, an invasive disease of humans and animals. to address the response of this bacterium to iron-limiting conditions, we first performed a global transcriptional analysis of rna extracted from bacteria grown under iron-limiting and iron-rich conditions by microarrays. we focused our study on those open reading frames (orfs) induced under iron limitation, which encoded predicted proteins that coul ...	2006	16452439
tetrapyrrole biosynthesis in rhodobacter capsulatus is transcriptionally regulated by the heme-binding regulatory protein, hbrl.	we demonstrate that the expression of hem genes in rhodobacter capsulatus is transcriptionally repressed in response to the exogenous addition of heme. a high-copy suppressor screen for regulators of hem gene expression resulted in the identification of an lysr-type transcriptional regulator, called hbrl, that regulates hem promoters in response to the availability of heme. hbrl is shown to activate the expression of hema and hemz in the absence of exogenous hemin and repress hemb expression in ...	2006	16452440
characterisation of basal resistance (br) by expression patterns of newly isolated representative genes in tobacco.	increasing evidence indicates that plants, like animals, use basal resistance (br), a component of the innate immune system, to defend themselves against foreign organisms. contrary to the hypersensitive reaction (hr)-type cell death, recognition in the case of br is unspecific, as intruders are recognised based on their common molecular patterns. induction of br is not associated with visible symptoms, in contrast to the hr-type cell death. to analyse the early events of br in tobacco plants we ...	2006	16456648
the chimeric arabidopsis cyclic nucleotide-gated ion channel11/12 activates multiple pathogen resistance responses.	to investigate the resistance signaling pathways activated by pathogen infection, we previously identified the arabidopsis thaliana mutant constitutive expresser of pr genes22 (cpr22), which displays constitutive activation of multiple defense responses. here, we identify the cpr22 mutation as a 3-kb deletion that fuses two cyclic nucleotide-gated ion channel (atcngc)-encoding genes, atcngc11 and atcngc12, to generate a novel chimeric gene, atcngc11/12. genetic, molecular, and complementation an ...	2006	16461580
within-species flagellin polymorphism in xanthomonas campestris pv campestris and its impact on elicitation of arabidopsis flagellin sensing2-dependent defenses.	bacterial flagellins have been portrayed as a relatively invariant pathogen-associated molecular pattern. we have found within-species, within-pathovar variation for defense-eliciting activity of flagellins among xanthomonas campestris pv campestris (xcc) strains. arabidopsis thaliana flagellin sensing2 (fls2), a transmembrane leucine-rich repeat kinase, confers flagellin responsiveness. the flg22 region was the only xcc flagellin region responsible for detectable elicitation of arabidopsis defe ...	2006	16461584
identification of quip, the product of gene pa1032, as the second acyl-homoserine lactone acylase of pseudomonas aeruginosa pao1.	the relevance of the acyl homoserine lactone (acyl-hsl) quorum signals n-3-oxododecanoyl-homoserine lactone (3oc12hsl) and n-butanoyl-homoserine lactone to the biology and virulence of pseudomonas aeruginosa is well investigated. previously, p. aeruginosa was shown to degrade long-chain, but not short-chain, acyl-hsls as sole carbon and energy sources (j. j. huang, j.-i. han, l.-h. zhang, and j. r. leadbetter, appl. environ. microbiol. 69:5941-5949, 2003). a gene encoding an enzyme with acyl-hsl ...	2006	16461666
isolation and characterization of a cyanophage infecting the toxic cyanobacterium microcystis aeruginosa.	we isolated a cyanophage (ma-lmm01) that specifically infects a toxic strain of the bloom-forming cyanobacterium microcystis aeruginosa. transmission electron microscopy showed that the virion is composed of anisometric head and a tail complex consisting of a central tube and a contractile sheath with helical symmetry. the morphological features and the host specificity suggest that ma-lmm01 is a member of the cyanomyovirus group. using semi-one-step growth experiments, the latent period and bur ...	2006	16461672
engineering the genotype of acinetobacter sp. strain adp1 to enhance biosynthesis of cyanophycin.	to study the importance of arginine provision and phosphate limitation for synthesis and accumulation of cyanophycin (cgp) in acinetobacter sp. strain adp1, genes encoding the putative arginine regulatory protein (argr) and the arginine succinyltransferase (asta) were inactivated, and the effects of these mutations on cgp synthesis were analyzed. the inactivation of these genes resulted in a 3.5- or 7-fold increase in cgp content, respectively, when the cells were grown on glutamate. knockout mu ...	2006	16461694
arabidopsis pen3/pdr8, an atp binding cassette transporter, contributes to nonhost resistance to inappropriate pathogens that enter by direct penetration.	arabidopsis thaliana is a host to the powdery mildew erysiphe cichoracearum and nonhost to blumeria graminis f. sp hordei, the powdery mildew pathogenic on barley (hordeum vulgare). screening for arabidopsis mutants deficient in resistance to barley powdery mildew identified penetration3 (pen3). pen3 plants permitted both increased invasion into epidermal cells and initiation of hyphae by b. g. hordei, suggesting that pen3 contributes to defenses at the cell wall and intracellularly. pen3 mutant ...	2006	16473969
type iii effector avrptob requires intrinsic e3 ubiquitin ligase activity to suppress plant cell death and immunity.	microbial pathogens of both plants and animals employ virulence factors that suppress the host immune response. the tomato pathogen pseudomonas syringae injects the avrptob type iii effector protein into the plant cell to suppress programmed cell death (pcd) associated with plant immunity. avrptob also inhibits pcd in yeast, indicating that avrptob manipulates a conserved component of eukaryotic pcd. to identify host targets of avrptob, we performed a yeast two-hybrid screen and identified tomat ...	2006	16477026
crystallization and preliminary x-ray diffraction analysis of a cold-adapted catalase from vibrio salmonicida.	catalase (ec 1.11.1.6) catalyses the breakdown of hydrogen peroxide to water and molecular oxygen. recombinant vibrio salmonicida catalase (vsc) possesses typical cold-adapted features, with higher catalytic efficiency, lower thermal stability and a lower temperature optimum than its mesophilic counterpart from proteus mirabilis. crystals of vsc were produced by the hanging-drop vapour-diffusion method using ammonium sulfate as precipitant. the crystals belong to the monoclinic space group p2(1) ...	2006	16511268
crystallization and preliminary x-ray diffraction analysis of a cold-adapted catalase from vibrio salmonicida.	catalase (ec 1.11.1.6) catalyses the breakdown of hydrogen peroxide to water and molecular oxygen. recombinant vibrio salmonicida catalase (vsc) possesses typical cold-adapted features, with higher catalytic efficiency, lower thermal stability and a lower temperature optimum than its mesophilic counterpart from proteus mirabilis. crystals of vsc were produced by the hanging-drop vapour-diffusion method using ammonium sulfate as precipitant. the crystals belong to the monoclinic space group p2(1) ...	2006	16511268
structure of lmaj006129aaa, a hypothetical protein from leishmania major.	the gene product of structural genomics target lmaj006129 from leishmania major codes for a 164-residue protein of unknown function. when semet expression of the full-length gene product failed, several truncation variants were created with the aid of ginzu, a domain-prediction method. 11 truncations were selected for expression, purification and crystallization based upon secondary-structure elements and disorder. the structure of one of these variants, lmaj006129aah, was solved by multiple-wav ...	2006	16511295
identification of new flagellar genes of salmonella enterica serovar typhimurium.	rna levels of flagellar genes in eight different genetic backgrounds were compared to that of the wild type by dna microarray analysis. cluster analysis identified new, potential flagellar genes, three putative methyl-accepting chemotaxis proteins, stm3138 (mcpa), stm3152 (mcpb), and stm3216(mcpc), and a chev homolog, stm2314, in salmonella, that are not found in escherichia coli. isolation and characterization of mud-lac insertions in chev, mcpb, mcpc, and the previously uncharacterized aer loc ...	2006	16513753
harpin mediates cell aggregation in erwinia chrysanthemi 3937.	the hypersensitive response elicitor harpin (hrpn) of soft rot pathogen erwinia chrysanthemi strains 3937 and ec16 is secreted via the type iii secretion system and remains cell surface bound. strain 3937 hrpn is essential for cell aggregation, but the c-terminal one-third of the protein is not required for aggregative activity.	2006	16513758
conservation of the pho regulon in pseudomonas fluorescens pf0-1.	the pho regulon integrates the sensing of environmental inorganic phosphate (pi) availability with coregulation of gene expression, mediating an adaptive response to pi limitation. many aspects of the pho regulon have been addressed in studies of escherichia coli; however, it is unclear how transferable this knowledge is to other bacterial systems. here, we report work to discern the conservation of the pho regulon in pseudomonas fluorescens pf0-1. we demonstrate by mutational studies that phob/ ...	2006	16517638
the phytopathogen dickeya dadantii (erwinia chrysanthemi 3937) is a pathogen of the pea aphid.	dickeya dadantii (erwinia chrysanthemi) is a phytopathogenic bacterium causing soft rot diseases on many crops. the sequencing of its genome identified four genes encoding homologues of the cyt family of insecticidal toxins from bacillus thuringiensis, which are not present in the close relative pectobacterium carotovorum subsp. atrosepticum. the pathogenicity of d. dadantii was tested on the pea aphid acyrthosiphon pisum, and the bacterium was shown to be highly virulent for this insect, either ...	2006	16517643
bacteriophage migration via nematode vectors: host-parasite-consumer interactions in laboratory microcosms.	pathogens vectored by nematodes pose serious agricultural, economic, and health threats; however, little is known of the ecological and evolutionary aspects of pathogen transmission by nematodes. here we describe a novel model system with two trophic levels, bacteriophages and nematodes, each of which competes for bacteria. we demonstrate for the first time that nematodes are capable of transmitting phages between spatially distinct patches of bacteria. this model system has considerable advanta ...	2006	16517645
the atu and liu clusters are involved in the catabolic pathways for acyclic monoterpenes and leucine in pseudomonas aeruginosa.	evidence suggests that the pseudomonas aeruginosa pao1 gnyrdbhal cluster, which is involved in acyclic isoprenoid degradation (a. l. díaz-pérez, n. a. zavala-hernández, c. cervantes, and j. campos-garcía, appl. environ. microbiol. 70:5102-5110, 2004), corresponds to the liurabcde cluster (b. hoschle, v. gnau, and d. jendrossek, microbiology 151:3649-3656, 2005). a liu (leucine and isovalerate utilization) homolog cluster was found in the pao1 genome and is related to the catabolism of acyclic mo ...	2006	16517656
sequencing of the rpob gene and flanking spacers for molecular identification of acinetobacter species.	acinetobacter species are defined on the basis of several phenotypic characters, results of dna-dna homology, and more recently, similarities or dissimilarities in 16s rrna gene sequences. however, the 16s rrna gene is not polymorphic enough to clearly distinguish all acinetobacter species. we used an rna polymerase beta-subunit gene (rpob)-based identification scheme for the delineation of species within the genus acinetobacter, and towards that end, we determined the complete rpob gene and fla ...	2006	16517861
a pseudomonas syringae pv. tomato avre1/hopm1 mutant is severely reduced in growth and lesion formation in tomato.	the model plant pathogen pseudomonas syringae pv. tomato dc3000 grows and produces necrotic lesions in the leaves of its host, tomato. both abilities are dependent upon the hypersensitive response and pathogenicity (hrp) type iii secretion system (ttss), which translocates multiple effector proteins into plant cells. a previously constructed dc3000 mutant with a 9.3-kb deletion in the hrp pathogenicity island conserved effector locus (cel) was strongly reduced in growth and lesion formation in t ...	2006	16529372
the pseudomonas syringae pv. tomato dc3000 type iii effector hopf2 has a putative myristoylation site required for its avirulence and virulence functions.	the hopptof locus in pseudomonas syringae pv. tomato dc3000 harbors two genes, shcf and hopf2 (previously named shcf(pto) and hopf(pto)), that encode a type iii chaperone and a cognate effector protein, respectively. the hopf2 gene has a rare initiation codon, ata that was reported to be functional only in mitochondrial genes. here, we report that the native hopptof locus of dc3000 confers an avirulence function in tobacco w38 plants, indicating that the ata start codon directs the synthesis of ...	2006	16529375
novel extracellular chitinases rapidly and specifically induced by general bacterial elicitors and suppressed by virulent bacteria as a marker of early basal resistance in tobacco.	early basal resistance (ebr, formerly known as early induced resistance) is triggered by general bacterial elicitors. ebr has been suggested to inhibit or retard expression of the type iii secretion system of pathogenic bacteria and may also prevent nonpathogenic bacteria from colonizing the plant tissue. the quickness of ebr here plays a crucial role, compensating for a low bactericidal efficacy. this inhibitory activity should take place in the cell wall, as bacteria do not enter living plant ...	2006	16529378
the tat pathway of the plant pathogen pseudomonas syringae is required for optimal virulence.	pseudomonas syringae is a gram-negative bacterium that infects a number of agriculturally important plant species. the ability of the organism to deliver virulence factors across the plant cell wall is a key to its pathogenicity. deletion mutants in the twin arginine translocation (tat) pathway of two pathovars of p. syringae, pvs. tomato dc3000 and maculicola es4326, displayed a range of pleiotropic phenotypic changes, such as defects in fluorescent siderophore production, a decrease in sodium ...	2006	16529382
xanthan induces plant susceptibility by suppressing callose deposition.	xanthan is the major exopolysaccharide secreted by xanthomonas spp. despite its diverse roles in bacterial pathogenesis of plants, little is known about the real implication of this molecule in xanthomonas pathogenesis. in this study we show that in contrast to xanthomonas campestris pv campestris strain 8004 (wild type), the xanthan minus mutant (strain 8397) and the mutant strain 8396, which is producing truncated xanthan, fail to cause disease in both nicotiana benthamiana and arabidopsis (ar ...	2006	16531487
the u-box protein cmpg1 is required for efficient activation of defense mechanisms triggered by multiple resistance genes in tobacco and tomato.	we previously identified three avr9/cf-9 rapidly elicited (acre) genes essential for cf-9- and cf-4-dependent hypersensitive response (hr) production in nicotiana benthamiana. two of them encode putative e3 ubiquitin ligase components. this led us to investigate other acre genes associated with the ubiquitination pathway. acre74 encodes a u-box e3 ligase homolog, highly related to parsley (petroselinum crispum) cmpg1 and arabidopsis thaliana plant u-box20 (pub20) and pub21 proteins, and was call ...	2006	16531490
the e3 ubiquitin ligase activity of arabidopsis plant u-box17 and its functional tobacco homolog acre276 are required for cell death and defense.	previous analysis of transcriptional changes after elicitation of cf-9 transgenic tobacco (nicotiana tabacum) by avr9 peptide revealed a rapidly upregulated gene, acre276. we show that acre276 is transiently induced in wounded leaves within 15 min, but upon avr9 elicitor treatment, this upregulation is enhanced and maintained until cell death onset in cf-9 tobacco. acre276 rna interference (rnai) silencing in tobacco results in loss of hypersensitive response (hr) specified by cf resistance gene ...	2006	16531496
indoleacetic acid, a product of transferred dna, inhibits vir gene expression and growth of agrobacterium tumefaciens c58.	agrobacterium tumefaciens induces crown gall tumors by transferring a piece of its tumor-inducing plasmid into plant cells. this transferred dna encodes the synthesis of indole acetic acid (iaa) and cytokinin, and their overproduction results in tumor formation. the transfer is initiated by a two-component regulatory system, vira/g recognizing plant signal molecules in the plant rhizosphere and activating a regulon on the tumor-inducing plasmid, which is required for the processing and transfer ...	2006	16537403
structural investigation of syringomycin-e using molecular dynamics simulation and nmr.	syringomycin-e (sr-e) is a cyclic lipodepsinonapeptide produced by certain strains of the bacterium pseudomonas syringae pv. syringae. it shows inhibitory effects against many fungal species, including human pathogens. its primary biological target is the plasma membrane, where it forms channels comprised of at least six sr-e molecules. the high-resolution structure of sr-e and the structure of the channels are currently not known. in this paper, we investigate in atomic detail the molecular fea ...	2006	16544138
a new class of [2fe-2s]-cluster-containing protoporphyrin (ix) ferrochelatases.	protoporphyrin (ix) ferrochelatase catalyses the insertion of ferrous iron into protoporphyrin ix to form haem. these ferrochelatases exist as monomers and dimers, both with and without [2fe-2s] clusters. the motifs for [2fe-2s] cluster co-ordination are varied, but in all cases previously reported, three of the four cysteine ligands are present in the 30 c-terminal residues and the fourth ligand is internal. in the present study, we demonstrate that a group of micro-organisms exist which posses ...	2006	16548850
type iii effectors orchestrate a complex interplay between transcriptional networks to modify basal defence responses during pathogenesis and resistance.	to successfully infect a plant, bacterial pathogens inject a collection of type iii effector proteins (ttes) directly into the plant cell that function to overcome basal defences and redirect host metabolism for nutrition and growth. we examined (i) the transcriptional dynamics of basal defence responses between arabidopsis thaliana and pseudomonas syringae and (ii) how basal defence is subsequently modulated by virulence factors during compatible interactions. a set of 96 genes displaying an ea ...	2006	16553893
genome-wide transcriptional analysis of the arabidopsis thaliana interaction with the plant pathogen pseudomonas syringae pv. tomato dc3000 and the human pathogen escherichia coli o157:h7.	pseudomonas syringae pv. tomato dc3000 (pst) is a virulent pathogen that causes disease on tomato and arabidopsis. the type iii secretion system (ttss) plays a key role in pathogenesis by translocating virulence effectors from the bacteria into the plant host cell, while the phytotoxin coronatine (cor) contributes to virulence and disease symptom development. recent studies suggest that both the ttss and cor are involved in the suppression of host basal defenses. however, little is known about t ...	2006	16553894
gem system: automatic prototyping of cell-wide metabolic pathway models from genomes.	successful realization of a "systems biology" approach to analyzing cells is a grand challenge for our understanding of life. however, current modeling approaches to cell simulation are labor-intensive, manual affairs, and therefore constitute a major bottleneck in the evolution of computational cell biology.	2006	16553966
bacterial repetitive extragenic palindromic sequences are dna targets for insertion sequence elements.	mobile elements are involved in genomic rearrangements and virulence acquisition, and hence, are important elements in bacterial genome evolution. the insertion of some specific insertion sequences had been associated with repetitive extragenic palindromic (rep) elements. considering that there are a sufficient number of available genomes with described reps, and exploiting the advantage of the traceability of transposition events in genomes, we decided to exhaustively analyze the relationship b ...	2006	16563168
costs and benefits of priming for defense in arabidopsis.	induced resistance protects plants against a wide spectrum of diseases; however, it can also entail costs due to the allocation of resources or toxicity of defensive products. the cellular defense responses involved in induced resistance are either activated directly or primed for augmented expression upon pathogen attack. priming for defense may combine the advantages of enhanced disease protection and low costs. in this study, we have compared the costs and benefits of priming to those of indu ...	2006	16565218