Publications

a conserved carboxylesterase is a suppressor of avrbst-elicited resistance in arabidopsis.	avrbst is a type iii effector from xanthomonas campestris pv vesicatoria that is translocated into plant cells during infection. avrbst is predicted to encode a cys protease that targets intracellular host proteins. to dissect avrbst function and recognition in arabidopsis thaliana, 71 ecotypes were screened to identify lines that elicit an avrbst-dependent hypersensitive response (hr) after xanthomonas campestris pv campestris (xcc) infection. the hr was observed only in the pi-0 ecotype infect ...	2007	17293566
kinome profiling of arabidopsis using arrays of kinase consensus substrates.	kinome profiling aims at the parallel analysis of kinase activities in a cell. novel developed arrays containing consensus substrates for kinases are used to assess those kinase activities. the arrays described in this paper were already used to determine kinase activities in mammalian systems, but since substrates from many organisms are present we decided to test these arrays for the determination of kinase activities in the model plant species arabidopsis thaliana.	2007	17295910
a novel role for the tir domain in association with pathogen-derived elicitors.	plant innate immunity is mediated by resistance (r) proteins, which bear a striking resemblance to animal molecules of similar function. tobacco n is a tir-nb-lrr r gene that confers resistance to tobacco mosaic virus, specifically the p50 helicase domain. an intriguing question is how plant r proteins recognize the presence of pathogen-derived avirulence (avr) elicitor proteins. we have used biochemical cell fraction and immunoprecipitation in addition to confocal fluorescence microscopy of liv ...	2007	17298188
pseudomonas syringae pv. tomato hijacks the arabidopsis abscisic acid signalling pathway to cause disease.	we have found that a major target for effectors secreted by pseudomonas syringae is the abscisic acid (aba) signalling pathway. microarray data identified a prominent group of effector-induced genes that were associated with aba biosynthesis and also responses to this plant hormone. genes upregulated by effector delivery share a 42% overlap with aba-responsive genes and are also components of networks induced by osmotic stress and drought. strongly induced were nced3, encoding a key enzyme of ab ...	2007	17304219
yeast functional genomic screens lead to identification of a role for a bacterial effector in innate immunity regulation.	numerous bacterial pathogens manipulate host cell processes to promote infection and ultimately cause disease through the action of proteins that they directly inject into host cells. identification of the targets and molecular mechanisms of action used by these bacterial effector proteins is critical to understanding pathogenesis. we have developed a systems biological approach using the yeast saccharomyces cerevisiae that can expedite the identification of cellular processes targeted by bacter ...	2007	17305427
plant carbohydrate scavenging through tonb-dependent receptors: a feature shared by phytopathogenic and aquatic bacteria.	tonb-dependent receptors (tbdrs) are outer membrane proteins mainly known for the active transport of iron siderophore complexes in gram-negative bacteria. analysis of the genome of the phytopathogenic bacterium xanthomonas campestris pv. campestris (xcc), predicts 72 tbdrs. such an overrepresentation is common in xanthomonas species but is limited to only a small number of bacteria. here, we show that one xcc tbdr transports sucrose with a very high affinity, suggesting that it might be a sucro ...	2007	17311090
amyloidogenesis of type iii-dependent harpins from plant pathogenic bacteria.	harpins are heat-stable, glycine-rich type iii-secreted proteins produced by plant pathogenic bacteria, which cause a hypersensitive response (hr) when infiltrated into the intercellular space of tobacco leaves; however, the biochemical mechanisms by which harpins cause plant cell death remain unclear. in this study, we determined the biochemical characteristics of hpag, the first harpin identified from a xanthomonas species, under plant apoplast-like conditions using electron microscopy and cir ...	2007	17314101
over-expression gberf2 transcription factor in tobacco enhances brown spots disease resistance by activating expression of downstream genes.	erf transcription factors can bind gcc boxes or non-gcc cis elements to regulate biotic and abiotic stress responses. here, we report that an erf transcription factor gene (gberf2) was cloned by suppression subtraction hybridization from sea-island cotton after verticillium dahliae attack. the gberf2 cdna has a total length of 1143 bp with an open reading frame of 597 bp. the genomic sequence of gberf2 contains an intron of 515 bp. the gene encodes a predicated polypeptide of 198 amino acids wit ...	2007	17321073
proteomic analysis of a non-virulent mutant of the phytopathogenic bacterium erwinia chrysanthemi deficient in osmoregulated periplasmic glucans: change in protein expression is not restricted to the envelope, but affects general metabolism.	osmoregulated periplasmic glucans (opgs) are general constituents of the envelope of gram-negative bacteria. they are required for full virulence of bacterial phytopathogens such as pseudomonas syringae, xanthomonas campestris and erwinia chrysanthemi. e. chrysanthemi is a pectinolytic gamma-proteobacterium that causes soft rot disease on a wide range of plant species. in addition to the loss of virulence, opg mutants exhibit a pleiotropic phenotype that affects motility, bile-salt resistance, e ...	2007	17322196
role of soil rhizobacteria in phytoremediation of heavy metal contaminated soils.	heavy metal pollution of soil is a significant environmental problem and has its negative impact on human health and agriculture. rhizosphere, as an important interface of soil and plant, plays a significant role in phytoremediation of contaminated soil by heavy metals, in which, microbial populations are known to affect heavy metal mobility and availability to the plant through release of chelating agents, acidification, phosphate solubilization and redox changes, and therefore, have potential ...	2007	17323432
an alpha-amylase (at4g25000) in arabidopsis leaves is secreted and induced by biotic and abiotic stress.	leaves are reported to contain a secreted alpha-amylase that accumulates during senescence or after biotic or abiotic stress; however, a gene encoding this enzyme has not been described. because a secreted amylase is isolated from plastidic starch, the function of this enzyme is difficult to predict, but circumstantial evidence suggests that it may degrade starch after cell death. the arabidopsis thaliana genome contains three alpha-amylase genes, one of which, amy1 (at4g25000), has a putative s ...	2007	17324226
conformational stability and differential structural analysis of lcrv, pcrv, bipd, and sipd from type iii secretion systems.	diverse gram-negative bacteria use type iii secretion systems (t3ss) to translocate effector proteins into the cytoplasm of eukaryotic cells. the type iii secretion apparatus (t3sa) consists of a basal body spanning both bacterial membranes and an external needle. a sensor protein lies at the needle tip to detect environmental signals that trigger type iii secretion. the shigella flexneri t3sa needle tip protein, invasion plasmid antigen d (ipad), possesses two independently folding domains in v ...	2007	17327391
the genetic basis of quantitative variation in susceptibility of arabidopsis thaliana to pseudomonas syringae (pst dc3000): evidence for a new genetic factor of large effect.	* pathogens represent an important threat to plant communities and agriculture, and can shape many aspects of plant evolution. natural variation in plant disease susceptibility is typically quantitative, yet studies on the molecular basis of disease resistance have focused mainly on qualitative variation. * here we investigated the genetic architecture of quantitative susceptibility to the bacterium pseudomonas syringae by performing a quantitative trait locus (qtl) analysis on the f2 progeny of ...	2007	17335507
two host-induced ralstonia solanacearum genes, acra and dinf, encode multidrug efflux pumps and contribute to bacterial wilt virulence.	multidrug efflux pumps (mdrs) are hypothesized to protect pathogenic bacteria from toxic host defense compounds. we created mutations in the ralstonia solanacearum acra and dinf genes, which encode putative mdrs in the broad-host-range plant pathogen. both mutations reduced the ability of r. solanacearum to grow in the presence of various toxic compounds, including antibiotics, phytoalexins, and detergents. both acrab and dinf mutants were significantly less virulent on the tomato plant than the ...	2007	17337552
plasmids and rickettsial evolution: insight from rickettsia felis.	the genome sequence of rickettsia felis revealed a number of rickettsial genetic anomalies that likely contribute not only to a large genome size relative to other rickettsiae, but also to phenotypic oddities that have confounded the categorization of r. felis as either typhus group (tg) or spotted fever group (sfg) rickettsiae. most intriguing was the first report from rickettsiae of a conjugative plasmid (prf) that contains 68 putative open reading frames, several of which are predicted to enc ...	2007	17342200
surprising arginine biosynthesis: a reappraisal of the enzymology and evolution of the pathway in microorganisms.	major aspects of the pathway of de novo arginine biosynthesis via acetylated intermediates in microorganisms must be revised in light of recent enzymatic and genomic investigations. the enzyme n-acetylglutamate synthase (nags), which used to be considered responsible for the first committed step of the pathway, is present in a limited number of bacterial phyla only and is absent from archaea. in many bacteria, shorter proteins related to the gcn5-related n-acetyltransferase family appear to acet ...	2007	17347518
a j domain virulence effector of pseudomonas syringae remodels host chloroplasts and suppresses defenses.	the plant pathogen pseudomonas syringae injects 20-40 different proteins called effectors into host plant cells, yet the functions and sites of action of these effectors in promoting pathogenesis are largely unknown. plants in turn defend themselves against p. syringae by activating the salicylic acid (sa)-mediated signaling pathway. the p. syringae-specific hopi1 effector has a putative chloroplast-targeting sequence and a j domain. j domains function by activating 70 kda heat-shock proteins (h ...	2007	17350264
error-prone dna repair system in enteroaggregative escherichia coli identified by subtractive hybridization.	enteroaggregative escherichia coli (eaec) are etiologic agents of diarrhea. the eaec category is heterogeneous, but most in-depth experimentation has focused on prototypical strain, 042. we hypothesized that 60a, another eaec strain, might posses virulence or fitness genes that 042 does not have. through subtractive hybridization we identified 60a-specific sequences, including loci present in other e. coli and phage dna. one locus thus identified was impb, a lexa repressed error-prone dna repair ...	2007	17351038
the mi-1-mediated pest resistance requires hsp90 and sgt1.	the tomato (solanum lycopersicum) mi-1 gene encodes a protein with putative coiled-coil nucleotide-binding site and leucine-rich repeat motifs. mi-1 confers resistance to root-knot nematodes (meloidogyne spp.), potato aphids (macrosiphum euphorbiae), and sweet potato whitefly (bemisia tabaci). to identify genes required in the mi-1-mediated resistance to nematodes and aphids, we used tobacco rattle virus (trv)-based virus-induced gene silencing (vigs) to repress candidate genes and assay for nem ...	2007	17351050
impairment of cellulose synthases required for arabidopsis secondary cell wall formation enhances disease resistance.	cellulose is synthesized by cellulose synthases (cesas) contained in plasma membrane-localized complexes. in arabidopsis thaliana, three types of cesa subunits (cesa4/irregular xylem5 [irx5], cesa7/irx3, and cesa8/irx1) are required for secondary cell wall formation. we report that mutations in these proteins conferred enhanced resistance to the soil-borne bacterium ralstonia solanacearum and the necrotrophic fungus plectosphaerella cucumerina. by contrast, susceptibility to these pathogens was ...	2007	17351116
infection of tobacco with different pseudomonas syringae pathovars leads to distinct morphotypes of programmed cell death.	tobacco plants (nicotiana tabacum cv. xanthi-nc) infiltrated with either of two pathovars of pseudomonas syringae- an avirulent strain of p. syringae pv. tabaci (pst) or the non-host pathogen p. syringae pv. maculicola m2 (psm) - developed a hypersensitive response (hr). there were considerable differences in hr phenotype, timing and sequence of cell dismantling between the two pathosystems. following psm infiltration, the first macroscopic signs were visible at 4.5 h post-infiltration (hpi). si ...	2007	17355437
signal transduction-related responses to phytohormones and environmental challenges in sugarcane.	sugarcane is an increasingly economically and environmentally important c4 grass, used for the production of sugar and bioethanol, a low-carbon emission fuel. sugarcane originated from crosses of saccharum species and is noted for its unique capacity to accumulate high amounts of sucrose in its stems. environmental stresses limit enormously sugarcane productivity worldwide. to investigate transcriptome changes in response to environmental inputs that alter yield we used cdna microarrays to profi ...	2007	17355627
crystal structures of the pilus retraction motor pilt suggest large domain movements and subunit cooperation drive motility.	pilt is a hexameric atpase required for bacterial type iv pilus retraction and surface motility. crystal structures of adp- and atp-bound aquifex aeolicus pilt at 2.8 and 3.2 a resolution show n-terminal pas-like and c-terminal reca-like atpase domains followed by a set of short c-terminal helices. the hexamer is formed by extensive polar subunit interactions between the atpase core of one monomer and the n-terminal domain of the next. an additional structure captures a nonsymmetric pilt hexamer ...	2007	17355871
crystal structures reveal a thiol protease-like catalytic triad in the c-terminal region of pasteurella multocida toxin.	pasteurella multocida toxin (pmt), one of the virulence factors produced by the bacteria, exerts its toxicity by up-regulating various signaling cascades downstream of the heterotrimeric gtpases gq and g12/13 in an unknown fashion. here, we present the crystal structure of the c-terminal region (residues 575-1,285) of pmt, which carries an intracellularly active moiety. the overall structure of c-terminal region of pmt displays a trojan horse-like shape, composed of three domains with a "feet"-, ...	2007	17360394
arabidopsis sni1 and rad51d regulate both gene transcription and dna recombination during the defense response.	the plant immune response known as systemic acquired resistance (sar) is a general defense mechanism that confers long-lasting resistance against a broad spectrum of pathogens. sar triggers many molecular changes including accumulation of antimicrobial pathogenesis-related (pr) proteins. transcription of pr genes in arabidopsis is regulated by the coactivator npr1 and the repressor sni1. pathogen infection also triggers an increase in somatic dna recombination, which results in transmission of c ...	2007	17360504
overexpression of salicylic acid carboxyl methyltransferase reduces salicylic acid-mediated pathogen resistance in arabidopsis thaliana.	we cloned a salicylic acid/benzoic acid carboxyl methyltransferase gene, osbsmt1, from oryza sativa. a recombinant osbsmt1 protein obtained by expressing the gene in escherichia coli exhibited carboxyl methyltransferase activity in reactions with salicylic acid (sa), benzoic acid (ba), and de-s-methyl benzo(1,2,3)thiadiazole-7-carbothioic acid (dsm-bth), producing methyl salicylate (mesa), methyl benzoate (meba), and methyl dsm-bth (mebth), respectively. compared to wild-type plants, transgenic ...	2007	17364223
oxylipins produced by the 9-lipoxygenase pathway in arabidopsis regulate lateral root development and defense responses through a specific signaling cascade.	arabidopsis thaliana seedling growth with pure oxylipins resulted in root waving, loss of root apical dominance, and decreased root elongation. 9-hydroxyoctadecatrienoic acid (9-hot) was a potent inducer of root waving. studies with noxy2 (for nonresponding to oxylipins2), a new 9-hot-insensitive mutant, and coronatine insensitive1-1 (jasmonate-insensitive) revealed at least three signaling cascades mediating the oxylipin actions. treatment with 9-hot resulted in a reduction in lateral roots and ...	2007	17369372
the antagonist function of arabidopsis wrky53 and esr/esp in leaf senescence is modulated by the jasmonic and salicylic acid equilibrium.	crosstalk between salicylic acid (sa) and jasmonic acid (ja) signaling is well-studied but not during leaf senescence. we found that the senescence-specific wrky53 transcription factor interacts with the ja-inducible protein epithiospecifying senescence regulator (esr/esp). the expression of these genes is antagonistically regulated in response to ja and sa, respectively, and each negatively influences the other. leaf senescence is accelerated in esr knockout plants (esr-ko) but retarded in esr ...	2007	17369373
cowpea chloroplastic atp synthase is the source of multiple plant defense elicitors during insect herbivory.	in cowpea (vigna unguiculata), fall armyworm (spodoptera frugiperda) herbivory and oral secretions (os) elicit phytohormone production and volatile emission due to inceptin [vu-in; (+)icdingvcvda(-)], a peptide derived from chloroplastic atp synthase gamma-subunit (catpc) proteins. elicitor-induced plant volatiles can function as attractants for natural enemies of insect herbivores. we hypothesized that inceptins are gut proteolysis products and that larval os should contain a mixture of related ...	2007	17369425
two-component sensor rhps promotes induction of pseudomonas syringae type iii secretion system by repressing negative regulator rhpr.	the pseudomonas syringae type iii secretion system (t3ss) is induced during interaction with the plant or culture in minimal medium (mm). how the bacterium senses these environments to activate the t3ss is poorly understood. here, we report the identification of a novel two-component system (tcs), rhprs, that regulates the induction of p. syringae t3ss genes. the rhpr and rhps genes are organized in an operon with rhpr encoding a putative tcs response regulator and rhps encoding a putative bipha ...	2007	17378425
the lov domain: a chromophore module servicing multiple photoreceptors.	three different families of blue-light receptors have been characterized from higher plants: three cryptochromes, two phototropins, and the three members of the ztl/ado family. phototropins and the ztl/ado proteins have chromophore modules, designated lov domains, that bind flavin mononucleotide and undergo formation of a c(4a) flavin-cysteinyl adduct. all contain the highly conserved amino acid motif gxncrflq. over 90 prokaryote proteins also contain lov domains with this motif upstream from on ...	2007	17380429
resistance to botrytis cinerea induced in arabidopsis by elicitors is independent of salicylic acid, ethylene, or jasmonate signaling but requires phytoalexin deficient3.	oligogalacturonides (ogs) released from plant cell walls by pathogen polygalacturonases induce a variety of host defense responses. here we show that in arabidopsis (arabidopsis thaliana), ogs increase resistance to the necrotrophic fungal pathogen botrytis cinerea independently of jasmonate (ja)-, salicylic acid (sa)-, and ethylene (et)-mediated signaling. microarray analysis showed that about 50% of the genes regulated by ogs, including genes encoding enzymes involved in secondary metabolism, ...	2007	17384165
death don't have no mercy and neither does calcium: arabidopsis cyclic nucleotide gated channel2 and innate immunity.	plant innate immune response to pathogen infection includes an elegant signaling pathway leading to reactive oxygen species generation and resulting hypersensitive response (hr); localized programmed cell death in tissue surrounding the initial infection site limits pathogen spread. a veritable symphony of cytosolic signaling molecules (including ca(2+), nitric oxide [no], cyclic nucleotides, and calmodulin) have been suggested as early components of hr signaling. however, specific interactions ...	2007	17384171
a permeable cuticle in arabidopsis leads to a strong resistance to botrytis cinerea.	the plant cuticle composed of cutin, a lipid-derived polyester, and cuticular waxes covers the aerial portions of plants and constitutes a hydrophobic extracellular matrix layer that protects plants against environmental stresses. the botrytis-resistant 1 (bre1) mutant of arabidopsis reveals that a permeable cuticle does not facilitate the entry of fungal pathogens in general, but surprisingly causes an arrest of invasion by botrytis. bre1 was identified to be long-chain acyl-coa synthetase2 (la ...	2007	17396154
type iii effector activation via nucleotide binding, phosphorylation, and host target interaction.	the pseudomonas syringae type iii effector protein avirulence protein b (avrb) is delivered into plant cells, where it targets the arabidopsis rin4 protein (resistance to pseudomonas maculicula protein 1 [rpm1]-interacting protein). rin4 is a regulator of basal host defense responses. targeting of rin4 by avrb is recognized by the host rpm1 nucleotide-binding leucine-rich repeat disease resistance protein, leading to accelerated defense responses, cessation of pathogen growth, and hypersensitive ...	2007	17397263
psra, the pseudomonas sigma regulator, controls regulators of epiphytic fitness, quorum-sensing signals, and plant interactions in pseudomonas syringae pv. tomato strain dc3000.	pseudomonas syringae pv. tomato strain dc3000, a pathogen of tomato and arabidopsis, occurs as an epiphyte. it produces n-acyl homoserine lactones (ahls) which apparently function as quorum-sensing signals. a tn5 insertion mutant of dc3000, designated psra(-) (psr is for pseudomonas sigma regulator), overexpresses psyr (a luxr-type regulator of psyi) and psyi (the gene for ahl synthase), and it produces a ca. 8-fold-higher level of ahl than does dc3000. the mutant is impaired in its ability to e ...	2007	17400767
exoribonuclease r in pseudomonas syringae is essential for growth at low temperature and plays a novel role in the 3' end processing of 16 and 5 s ribosomal rna.	the (3'-->5') exoribonuclease rnase r interacts with the endoribonuclease rnase e in the degradosome of the cold-adapted bacterium pseudomonas syringae lz4w. we now present evidence that the rnase r is essential for growth of the organism at low temperature (4 degrees c). mutants of p. syringae with inactivated rnr gene (encoding rnase r) are cold-sensitive and die upon incubation at 4 degrees c, a phenotype that can be complemented by expressing rnase r in trans. overexpressing polyribonucleoti ...	2007	17405875
high frequency of mutations that expand the host range of an rna virus.	the ability of a virus population to colonize a novel host is predicted to depend on the equilibrium frequency of potential colonists (i.e., genotypes capable of infecting the novel host) in the source population. in this study, we investigated the determinants of the equilibrium frequency of potential colonists in the rna bacteriophage 6. we isolated 40 spontaneous mutants capable of infecting a novel pseudomonas syringae host and sequenced their host attachment genes to identify the responsibl ...	2007	17409090
structural properties of periplasmic sodci that correlate with virulence in salmonella enterica serovar typhimurium.	salmonella enterica strains survive and propagate in macrophages by both circumventing and resisting the antibacterial effectors normally delivered to the phagosome. an important aspect of salmonella resistance is the production of periplasmic superoxide dismutase to combat phagocytic superoxide. s. enterica serovar typhimurium strain 14028 produces two periplasmic superoxide dismutases: sodci and sodcii. both enzymes are produced during infection, but only sodci contributes to virulence in the ...	2007	17416645
aconitase plays a role in regulating resistance to oxidative stress and cell death in arabidopsis and nicotiana benthamiana.	in animals, aconitase is a bifunctional protein. when an iron-sulfur cluster is present in its catalytic center, aconitase displays enzymatic activity; when this cluster is lost, it switches to an rna-binding protein that regulates the translatability or stability of certain transcripts. to investigate the role of aconitase in plants, we assessed its ability to bind mrna. recombinant aconitase failed to bind an iron responsive element (ire) from the human ferritin gene. however, it bound the 5' ...	2007	17013749
the rpot regulon of pseudomonas putida dot-t1e and its role in stress endurance against solvents.	pseudomonas putida encodes 20 extracytoplasmic sigma factors (ecfs). in this study, we show that one of these ecfs, known as ecf-pp12 (pp3006), plays a role in tolerance of toluene and other organic solvents. based on this finding, we have called the gene that encodes this new ecf rpot. the rpot gene forms an operon with the preceding gene and with the gene located downstream. the translated gene product of the open reading frame pp3005 is an inner membrane protein, whereas the pp3007 protein is ...	2007	17071759
the rpot regulon of pseudomonas putida dot-t1e and its role in stress endurance against solvents.	pseudomonas putida encodes 20 extracytoplasmic sigma factors (ecfs). in this study, we show that one of these ecfs, known as ecf-pp12 (pp3006), plays a role in tolerance of toluene and other organic solvents. based on this finding, we have called the gene that encodes this new ecf rpot. the rpot gene forms an operon with the preceding gene and with the gene located downstream. the translated gene product of the open reading frame pp3005 is an inner membrane protein, whereas the pp3007 protein is ...	2007	17071759
ntgras1, a novel stress-induced member of the gras family in tobacco, localizes to the nucleus.	we report the isolation and initial characterization of a new member of the gras gene family from tobacco, ntgras1. analysis of the predicted amino acid sequence shows that ntgras1 shares the highly conserved carboxy-terminal motifs common to all members of the gras family. ntgras1 expression was strongly induced in tobacco (by-2) suspension cells by antimycin a, h(2)o(2), salicylic acid, and l-cysteine which were all found to raise intracellular reactive oxygen levels. an increase in ntgras1 ex ...	2007	17007961
a phytophthora infestans cystatin-like protein targets a novel tomato papain-like apoplastic protease.	there is emerging evidence that the proteolytic machinery of plants plays important roles in defense against pathogens. the oomycete pathogen phytophthora infestans, the agent of the devastating late blight disease of tomato (lycopersicon esculentum) and potato (solanum tuberosum), has evolved an arsenal of protease inhibitors to overcome the action of host proteases. previously, we described a family of 14 kazal-like extracellular serine protease inhibitors from p. infestans. among these, epi1 ...	2007	17085509
characterization of a divinyl ether biosynthetic pathway specifically associated with pathogenesis in tobacco.	in tobacco (nicotiana tabacum), an elicitor- and pathogen-induced 9-lipoxygenase (lox) gene, ntlox1, is essential for full resistance to pathogens, notably to an incompatible race of phytophthora parasitica var. nicotianae (ppn race 0). in this work, we aimed to identify those oxylipins induced during attempted infection by ppn race 0 and down-regulated in ntlox1 antisense plants. here we show that colneleic and colnelenic acids, which significantly inhibit germination of ppn zoospores, are prod ...	2007	17085514
genomic structure and phylogeny of the plant pathogen ralstonia solanacearum inferred from gene distribution analysis.	in the present study, we investigated the gene distribution among strains of the highly polymorphic plant pathogenic beta-proteobacterium ralstonia solanacearum, paying particular attention to the status of known or candidate pathogenicity genes. based on the use of comparative genomic hybridization on a pangenomic microarray for the gmi1000 reference strain, we have defined the conditions that allowed comparison of the repertoires of genes among a collection of 18 strains that are representativ ...	2007	17085551
genomic structure and phylogeny of the plant pathogen ralstonia solanacearum inferred from gene distribution analysis.	in the present study, we investigated the gene distribution among strains of the highly polymorphic plant pathogenic beta-proteobacterium ralstonia solanacearum, paying particular attention to the status of known or candidate pathogenicity genes. based on the use of comparative genomic hybridization on a pangenomic microarray for the gmi1000 reference strain, we have defined the conditions that allowed comparison of the repertoires of genes among a collection of 18 strains that are representativ ...	2007	17085551
autoinducer-2 of the fire blight pathogen erwinia amylovora and other plant-associated bacteria.	autoinducers are important for cellular communication of bacteria. the luxs gene has a central role in the synthesis of autoinducer-2 (ai-2). the gene was identified in a shotgun library of erwinia amylovora and primers designed for pcr amplification from bacterial dna. supernatants of several erwinia amylovora strains were assayed for ai-2 activity with a vibrio harveyi mutant and were positive. many other plant-associated bacteria also showed ai-2 activity such as erwinia pyrifoliae and erwini ...	2007	17092294
the single extracytoplasmic-function sigma factor of xylella fastidiosa is involved in the heat shock response and presents an unusual regulatory mechanism.	genome sequence analysis of the bacterium xylella fastidiosa revealed the presence of two genes, named rpoe and rsea, predicted to encode an extracytoplasmic function (ecf) sigma factor and an anti-sigma factor, respectively. in this work, an rpoe null mutant was constructed in the citrus strain j1a12 and shown to be sensitive to exposure to heat shock and ethanol. to identify the x. fastidiosa sigma(e) regulon, global gene expression profiles were obtained by dna microarray analysis of bacteria ...	2007	17098905
the single extracytoplasmic-function sigma factor of xylella fastidiosa is involved in the heat shock response and presents an unusual regulatory mechanism.	genome sequence analysis of the bacterium xylella fastidiosa revealed the presence of two genes, named rpoe and rsea, predicted to encode an extracytoplasmic function (ecf) sigma factor and an anti-sigma factor, respectively. in this work, an rpoe null mutant was constructed in the citrus strain j1a12 and shown to be sensitive to exposure to heat shock and ethanol. to identify the x. fastidiosa sigma(e) regulon, global gene expression profiles were obtained by dna microarray analysis of bacteria ...	2007	17098905
vulnerability of pathogenic biofilms to micavibrio aeruginosavorus.	the host specificity of the gram-negative exoparasitic predatory bacterium micavibrio aeruginosavorus was examined. m. aeruginosavorus preyed on pseudomonas aeruginosa, as previously reported, as well as burkholderia cepacia, klebsiella pneumoniae, and numerous clinical isolates of these species. in a static assay, a reduction in biofilm biomass was observed as early as 3 hours after exposure to m. aeruginosavorus, and an approximately 100-fold reduction in biofilm cell viability was detected fo ...	2007	17098913
vulnerability of pathogenic biofilms to micavibrio aeruginosavorus.	the host specificity of the gram-negative exoparasitic predatory bacterium micavibrio aeruginosavorus was examined. m. aeruginosavorus preyed on pseudomonas aeruginosa, as previously reported, as well as burkholderia cepacia, klebsiella pneumoniae, and numerous clinical isolates of these species. in a static assay, a reduction in biofilm biomass was observed as early as 3 hours after exposure to m. aeruginosavorus, and an approximately 100-fold reduction in biofilm cell viability was detected fo ...	2007	17098913
tobacco nectaries express a novel nadph oxidase implicated in the defense of floral reproductive tissues against microorganisms.	hydrogen peroxide produced from the nectar redox cycle was shown to be a major factor contributing to inhibition of most microbial growth in floral nectar; however, this obstacle can be overcome by the floral pathogen erwinia amylovora. to identify the source of superoxide that leads to hydrogen peroxide accumulation in nectary tissues, nectaries were stained with nitroblue tetrazolium. superoxide production was localized near nectary pores and inhibited by diphenylene iodonium but not by cyanid ...	2007	17114277
aterf14, a member of the erf family of transcription factors, plays a nonredundant role in plant defense.	we had previously shown that several transcription factors of the ethylene (et) response factor (erf) family were induced with different but overlapping kinetics following challenge of arabidopsis (arabidopsis thaliana) with pseudomonas syringae pv tomato dc3000 (avrrpt2). one of these genes, a transcriptional activator, aterf14, was induced at the same time as erf-target genes (chib, basic chitinase). to unravel the potential function of aterf14 in regulating the plant defense response, we have ...	2007	17114278
phylogenetic analysis of the ppt23a plasmid family of pseudomonas syringae.	the ppt23a plasmid family of pseudomonas syringae contains members that contribute to the ecological and pathogenic fitness of their p. syringae hosts. in an effort to understand the evolution of these plasmids and their hosts, we undertook a comparative analysis of the phylogeny of plasmid genes and that of conserved chromosomal genes from p. syringae. in total, comparative sequence and phylogenetic analyses were done utilizing 47 ppt23a family plasmids (pfps) from 16 pathovars belonging to six ...	2007	17114318
phylogenetic analysis of the ppt23a plasmid family of pseudomonas syringae.	the ppt23a plasmid family of pseudomonas syringae contains members that contribute to the ecological and pathogenic fitness of their p. syringae hosts. in an effort to understand the evolution of these plasmids and their hosts, we undertook a comparative analysis of the phylogeny of plasmid genes and that of conserved chromosomal genes from p. syringae. in total, comparative sequence and phylogenetic analyses were done utilizing 47 ppt23a family plasmids (pfps) from 16 pathovars belonging to six ...	2007	17114318
novel type iv secretion system involved in propagation of genomic islands.	type iv secretion systems (t4sss) mediate horizontal gene transfer, thus contributing to genome plasticity, evolution of infectious pathogens, and dissemination of antibiotic resistance and other virulence traits. a gene cluster of the haemophilus influenzae genomic island icehin1056 has been identified as a t4ss involved in the propagation of genomic islands. this t4ss is novel and evolutionarily distant from the previously described systems. mutation analysis showed that inactivation of key ge ...	2007	17122343
novel type iv secretion system involved in propagation of genomic islands.	type iv secretion systems (t4sss) mediate horizontal gene transfer, thus contributing to genome plasticity, evolution of infectious pathogens, and dissemination of antibiotic resistance and other virulence traits. a gene cluster of the haemophilus influenzae genomic island icehin1056 has been identified as a t4ss involved in the propagation of genomic islands. this t4ss is novel and evolutionarily distant from the previously described systems. mutation analysis showed that inactivation of key ge ...	2007	17122343
transcript stabilization by mrna sequences from hrpa of pseudomonas syringae.	production of heterologous proteins in bacteria is one of the main applications of biotechnology. although several high-efficiency expression systems have been developed, different steps in protein production may become rate-limiting depending on the production system and the protein being produced. one bottle neck can be the instability of the mrna. we have used fragments of the unusually long-living mrna hrpa from the plant pathogenic bacteria pseudomonas syringae pathovars tomato and phaseoli ...	2007	17125870
visualization of dynamics of plant-pathogen interaction by novel combination of chlorophyll fluorescence imaging and statistical analysis: differential effects of virulent and avirulent strains of p. syringae and of oxylipins on a. thaliana.	pathogen infection leads to defence induction as well as to changes in carbohydrate metabolism of plants. salicylic acid and oxylipins are involved in the induction of defence, but it is not known if these signalling molecules also mediate changes in carbohydrate metabolism. in this study, the effect of application of salicylic acid and the oxylipins 12-oxo-phytodienoic acid (opda) and jasmonic acid on photosynthesis was investigated by kinetic chlorophyll fluorescence imaging and compared with ...	2007	17138624
mekk1 is required for flg22-induced mpk4 activation in arabidopsis plants.	the arabidopsis (arabidopsis thaliana) gene mekk1 encodes a mitogen-activated protein kinase kinase kinase that has been implicated in the activation of the map kinases mpk3 and mpk6 in response to the flagellin elicitor peptide flg22. in this study, analysis of plants carrying t-dna knockout alleles indicated that mekk1 is required for flg22-induced activation of mpk4 but not mpk3 or mpk6. experiments performed using a kinase-impaired version of mekk1 (k361m) showed that the kinase activity of ...	2007	17142480
atptr3, a wound-induced peptide transporter needed for defence against virulent bacterial pathogens in arabidopsis.	mutation in the wound-induced peptide transporter gene atptr3 (at5g46050) of arabidopsis thaliana has been shown to affect germination on media containing a high salt concentration. the heterologous expression in yeast was utilized to verify that the atptr3 protein transports di-and tripeptides. the t-dna insert in the atptr3-1 mutant in the arabidopsis ecotype c24 revealed two t-dna copies, the whole vector sequence, and the gus marker gene inserted in the second intron of the atptr3 gene. an a ...	2007	17143616
identification of pad2 as a gamma-glutamylcysteine synthetase highlights the importance of glutathione in disease resistance of arabidopsis.	the arabidopsis pad2-1 mutant belongs to a series of non-allelic camalexin-deficient mutants. it was originally described as showing enhanced susceptibility to virulent strains of pseudomonas syringae and was later shown to be hyper-susceptible to the oomycete pathogen phytophthora brassicae (formerly p. porri). surprisingly, in both pathosystems, the disease susceptibility of pad2-1 was not caused by the camalexin deficiency, suggesting additional roles of pad2 in disease resistance. the suscep ...	2007	17144898
suppression by aba of salicylic acid and lignin accumulation and the expression of multiple genes, in arabidopsis infected with pseudomonas syringae pv. tomato.	abscisic acid (aba) has been implicated in determining the outcome of interactions between many plants and their pathogens. we had previously shown that increased concentrations of aba within leaves of arabidopsis induced susceptibility towards an avirulent strain of pseudomonas syringae pathovar (pv.) tomato. we now show that aba induces susceptibility via suppression of the accumulation of components crucial for a resistance response. lignin and salicylic acid concentrations in leaves were inc ...	2007	17149585
role of a novel pathogen-induced pepper c3-h-c4 type ring-finger protein gene, carfpi, in disease susceptibility and osmotic stress tolerance.	limited information is available about the roles of ring-finger proteins in plant defense. a pepper carfp1 encoding the c3-h-c4 type ring-finger protein that physically interacted with the basic pr-1 protein cabpr1 was isolated from pepper leaves infected by xanthomonas campestris pv. vesicatoria. the carfp1 protein has vwfa domain, and n-terminal serine-rich and c-terminal cysteine-rich regions. the carfp1 transcripts accumulated earlier than did those of the basic pr-1 gene cabpr1 during the i ...	2007	17149652
vitamin b1-induced priming is dependent on hydrogen peroxide and the npr1 gene in arabidopsis.	thiamine confers systemic acquired resistance (sar) on susceptible plants through priming, leading to rapid counterattack against pathogen invasion and perturbation of disease progress. priming reduces the metabolic cost required for constitutive expression of acquired resistance. to investigate the effects of priming by thiamine on defense-related responses, arabidopsis (arabidopsis thaliana) was treated with thiamine and effects of pathogen challenge on the production of active oxygen species, ...	2007	17158583
whole-genome analysis of the methyl tert-butyl ether-degrading beta-proteobacterium methylibium petroleiphilum pm1.	methylibium petroleiphilum pm1 is a methylotroph distinguished by its ability to completely metabolize the fuel oxygenate methyl tert-butyl ether (mtbe). strain pm1 also degrades aromatic (benzene, toluene, and xylene) and straight-chain (c(5) to c(12)) hydrocarbons present in petroleum products. whole-genome analysis of pm1 revealed an approximately 4-mb circular chromosome and an approximately 600-kb megaplasmid, containing 3,831 and 646 genes, respectively. aromatic hydrocarbon and alkane deg ...	2007	17158667
whole-genome analysis of the methyl tert-butyl ether-degrading beta-proteobacterium methylibium petroleiphilum pm1.	methylibium petroleiphilum pm1 is a methylotroph distinguished by its ability to completely metabolize the fuel oxygenate methyl tert-butyl ether (mtbe). strain pm1 also degrades aromatic (benzene, toluene, and xylene) and straight-chain (c(5) to c(12)) hydrocarbons present in petroleum products. whole-genome analysis of pm1 revealed an approximately 4-mb circular chromosome and an approximately 600-kb megaplasmid, containing 3,831 and 646 genes, respectively. aromatic hydrocarbon and alkane deg ...	2007	17158667
the sxt conjugative element and linear prophage n15 encode toxin-antitoxin-stabilizing systems homologous to the tad-ata module of the paracoccus aminophilus plasmid pami2.	a group of proteic toxin-antitoxin (ta) cassettes whose representatives are widely distributed among bacterial genomes has been identified. these cassettes occur in chromosomes, plasmids, bacteriophages, and noncomposite transposons, as well as in the sxt conjugative element of vibrio cholerae. the following four homologous loci were subjected to detailed comparative studies: (i) tad-ata from plasmid pami2 of paracoccus aminophilus (the prototype of this group), (ii) gp49-gp48 from the linear ba ...	2007	17158670
the sxt conjugative element and linear prophage n15 encode toxin-antitoxin-stabilizing systems homologous to the tad-ata module of the paracoccus aminophilus plasmid pami2.	a group of proteic toxin-antitoxin (ta) cassettes whose representatives are widely distributed among bacterial genomes has been identified. these cassettes occur in chromosomes, plasmids, bacteriophages, and noncomposite transposons, as well as in the sxt conjugative element of vibrio cholerae. the following four homologous loci were subjected to detailed comparative studies: (i) tad-ata from plasmid pami2 of paracoccus aminophilus (the prototype of this group), (ii) gp49-gp48 from the linear ba ...	2007	17158670
biochemical and genetic analysis of the gamma-resorcylate (2,6-dihydroxybenzoate) catabolic pathway in rhizobium sp. strain mtp-10005: identification and functional analysis of its gene cluster.	we identified a gene cluster that is involved in the gamma-resorcylate (2,6-dihydroxybenzoate) catabolism of the aerobic bacterium rhizobium sp. strain mtp-10005. the cluster consists of the grardafcbek genes, and graa, grab, grac, and grad were heterologously expressed in escherichia coli. enzymological studies showed that grad, graa, grac, and grab encode the reductase (grad) and oxygenase (graa) components of a resorcinol hydroxylase (ec 1.14.13.x), a maleylacetate reductase (grac) (ec 1.3.1. ...	2007	17158677
biochemical and genetic analysis of the gamma-resorcylate (2,6-dihydroxybenzoate) catabolic pathway in rhizobium sp. strain mtp-10005: identification and functional analysis of its gene cluster.	we identified a gene cluster that is involved in the gamma-resorcylate (2,6-dihydroxybenzoate) catabolism of the aerobic bacterium rhizobium sp. strain mtp-10005. the cluster consists of the grardafcbek genes, and graa, grab, grac, and grad were heterologously expressed in escherichia coli. enzymological studies showed that grad, graa, grac, and grab encode the reductase (grad) and oxygenase (graa) components of a resorcinol hydroxylase (ec 1.14.13.x), a maleylacetate reductase (grac) (ec 1.3.1. ...	2007	17158677
a suppressor of cell death caused by the loss of sigmae downregulates extracytoplasmic stress responses and outer membrane vesicle production in escherichia coli.	when envelope biogenesis is compromised or damage to envelope components occurs, bacteria trigger signaling cascades, which lead to the production of proteins that combat such extracytoplasmic stresses. in escherichia coli, there are three pathways known to deal with envelope stresses: the bae, cpx, and sigma(e) responses. although the effectors of the bae and cpx responses are not essential in e. coli, the effector of the sigma(e) response, the sigma factor rpoe (sigma(e)), is essential for via ...	2007	17172327
a suppressor of cell death caused by the loss of sigmae downregulates extracytoplasmic stress responses and outer membrane vesicle production in escherichia coli.	when envelope biogenesis is compromised or damage to envelope components occurs, bacteria trigger signaling cascades, which lead to the production of proteins that combat such extracytoplasmic stresses. in escherichia coli, there are three pathways known to deal with envelope stresses: the bae, cpx, and sigma(e) responses. although the effectors of the bae and cpx responses are not essential in e. coli, the effector of the sigma(e) response, the sigma factor rpoe (sigma(e)), is essential for via ...	2007	17172327
natural variation in the pto disease resistance gene within species of wild tomato (lycopersicon). ii. population genetics of pto.	disease resistance to the bacterial pathogen pseudomonas syringae pv. tomato (pst) in the host species lycopersicon esculentum, the cultivated tomato, and the closely related l. pimpinellifolium is triggered by the physical interaction between the protein products of the host resistance (r) gene pto and the pathogen avirulence genes avrpto and avrptob. sequence variation at the pto locus was surveyed in natural populations of seven species of lycopersicon to test hypotheses of host-parasite coev ...	2007	17179076
a proteasome-regulated glycogen synthase kinase-3 modulates disease response in plants.	glycogen synthase kinase-3 (gsk-3) is a key player in various important signaling pathways in animals. the activity of gsk-3 is known to be modulated by protein phosphorylation and differential complex formation. however, little information is available regarding the function and regulation of plant gsk-3/shaggy-like kinases (gsks). analysis of the in vivo kinase activity of msk1, a gsk from medicago sativa, revealed that msk1 is active in healthy plants and that msk1 activity is down-regulated ...	2007	17179144
a high-performance, small-scale microarray for expression profiling of many samples in arabidopsis-pathogen studies.	studies of the behavior of biological systems often require monitoring of the expression of many genes in a large number of samples. while whole-genome arrays provide high-quality gene-expression profiles, their high cost generally limits the number of samples that can be studied. although inexpensive small-scale arrays representing genes of interest could be used for many applications, it is challenging to obtain accurate measurements with conventional small-scale microarrays. we have developed ...	2007	17181774
exclusion of glucosyl-hydroxymethylcytosine dna containing bacteriophages is overcome by the injected protein inhibitor ipi*.	the escherichia coli isolate ct596 excludes infection by the myoviridae t4 ip1(-) phage that lacks the encapsidated ipi* protein normally injected into the host with the phage dna. screening of a ct596 genomic library identified adjacent genes responsible for this exclusion, gmrs (942 bp) and gmrd (708 bp) that are encoded by a cryptic prophage dna. the two genes are necessary and sufficient to confer upon a host the ability to exclude infection by t4 ip1(-) phage and other glucosyl-hydroxymethy ...	2007	17188711
exclusion of glucosyl-hydroxymethylcytosine dna containing bacteriophages is overcome by the injected protein inhibitor ipi*.	the escherichia coli isolate ct596 excludes infection by the myoviridae t4 ip1(-) phage that lacks the encapsidated ipi* protein normally injected into the host with the phage dna. screening of a ct596 genomic library identified adjacent genes responsible for this exclusion, gmrs (942 bp) and gmrd (708 bp) that are encoded by a cryptic prophage dna. the two genes are necessary and sufficient to confer upon a host the ability to exclude infection by t4 ip1(-) phage and other glucosyl-hydroxymethy ...	2007	17188711
the alternative sigma factor sigmah is required for toxin gene expression by bacillus anthracis.	expression of the structural genes for the anthrax toxin proteins is coordinately controlled by host-related signals, such as elevated co(2), and the trans-acting positive regulator atxa. in addition to these requirements, toxin gene expression is under growth phase regulation. the transition state regulator abrb represses atxa expression to influence toxin synthesis. during the late exponential phase of growth, when abrb levels begin to decrease, toxin synthesis increases. here we report that t ...	2007	17189374
the alternative sigma factor sigmah is required for toxin gene expression by bacillus anthracis.	expression of the structural genes for the anthrax toxin proteins is coordinately controlled by host-related signals, such as elevated co(2), and the trans-acting positive regulator atxa. in addition to these requirements, toxin gene expression is under growth phase regulation. the transition state regulator abrb represses atxa expression to influence toxin synthesis. during the late exponential phase of growth, when abrb levels begin to decrease, toxin synthesis increases. here we report that t ...	2007	17189374
global effect of indole-3-acetic acid biosynthesis on multiple virulence factors of erwinia chrysanthemi 3937.	production of the plant hormone indole-3-acetic acid (iaa) is widespread among plant-associated microorganisms. the non-gall-forming phytopathogen erwinia chrysanthemi 3937 (strain ech3937) possesses iaam (asap16562) and iaah (asap16563) gene homologues. in this work, the null knockout iaam mutant strain ech138 was constructed. the iaa production by ech138 was reduced in m9 minimal medium supplemented with l-tryptophan. compared with wild-type ech3937, ech138 exhibited reduced ability to produce ...	2007	17189441
global effect of indole-3-acetic acid biosynthesis on multiple virulence factors of erwinia chrysanthemi 3937.	production of the plant hormone indole-3-acetic acid (iaa) is widespread among plant-associated microorganisms. the non-gall-forming phytopathogen erwinia chrysanthemi 3937 (strain ech3937) possesses iaam (asap16562) and iaah (asap16563) gene homologues. in this work, the null knockout iaam mutant strain ech138 was constructed. the iaa production by ech138 was reduced in m9 minimal medium supplemented with l-tryptophan. compared with wild-type ech3937, ech138 exhibited reduced ability to produce ...	2007	17189441
regulatory variability of camalexin biosynthesis.	the anthranilate synthase asa1, cyp79b2 and cyp71b15 (pad3) are biosynthetic genes of the arabidopsis phytoalexin camalexin, which are induced after pathogen infection and abiotic treatments like silver nitrate spraying. the natural variation of camalexin biosynthesis in response to pseudomonas syringae infection was determined in several ecotypes, and differential cyp71b15 regulation as a potential basis for this variation was investigated. the expression of camalexin biosynthetic genes was res ...	2007	16769150
surprising niche for the plant pathogen pseudomonas syringae.	the biology and ecology of plant pathogenic bacteria have been studied almost exclusively in agricultural contexts. in contrast, for numerous human pathogens their biological activity in niches outside of medical contexts is well-known. whereas there is increasing evidence that traits fostering survival in 'environmental' niches can be the basis for virulence factors of human pathogens, niches for plant pathogenic bacteria outside of plants or of agricultural settings have not been elucidated. m ...	2007	16807133
insertion sequence diversity in archaea.	insertion sequences (iss) can constitute an important component of prokaryotic (bacterial and archaeal) genomes. over 1,500 individual iss are included at present in the isfinder database (www-is.biotoul.fr), and these represent only a small portion of those in the available prokaryotic genome sequences and those that are being discovered in ongoing sequencing projects. in spite of this diversity, the transposition mechanisms of only a few of these ubiquitous mobile genetic elements are known, a ...	2007	17347521
chloroplast vector systems for biotechnology applications.		2007	18056863
what's new in enzymatic halogenations.	the halogenation of thousands of natural products occurs during biosynthesis and often confers important functional properties. while haloperoxidases had been the default paradigm for enzymatic incorporation of halogens, via x+ equivalents into organic scaffolds, a combination of microbial genome sequencing, enzymatic studies and structural biology have provided deep new insights into enzymatic transfer of halide equivalents in three oxidation states. these are (1) the halide ions (x-) abundant ...	2007	17881282
biotic interactions, ecological knowledge and agriculture.	this paper discusses biotic interactions in agroecosystems and how they may be manipulated to support crop productivity and environmental health by provision of ecosystem services such as weed, pest and disease management, nutrient cycling and biodiversity conservation. important elements for understanding biotic interactions include consideration of the effects of diversity, species composition and food web structure on ecosystem processes; the impacts of timing, frequency and intensity of dist ...	2007	17761466
biotic interactions, ecological knowledge and agriculture.	this paper discusses biotic interactions in agroecosystems and how they may be manipulated to support crop productivity and environmental health by provision of ecosystem services such as weed, pest and disease management, nutrient cycling and biodiversity conservation. important elements for understanding biotic interactions include consideration of the effects of diversity, species composition and food web structure on ecosystem processes; the impacts of timing, frequency and intensity of dist ...	2007	17761466
a survey of orphan enzyme activities.	using computational database searches, we have demonstrated previously that no gene sequences could be found for at least 36% of enzyme activities that have been assigned an enzyme commission number. here we present a follow-up literature-based survey involving a statistically significant sample of such "orphan" activities. the survey was intended to determine whether sequences for these enzyme activities are truly unknown, or whether these sequences are absent from the public sequence databases ...	2007	17623104
darkhorse: a method for genome-wide prediction of horizontal gene transfer.	a new approach to rapid, genome-wide identification and ranking of horizontal transfer candidate proteins is presented. the method is quantitative, reproducible, and computationally undemanding. it can be combined with genomic signature and/or phylogenetic tree-building procedures to improve accuracy and efficiency. the method is also useful for retrospective assessments of horizontal transfer prediction reliability, recognizing orthologous sequences that may have been previously overlooked or u ...	2007	17274820
predicting prokaryotic ecological niches using genome sequence analysis.	automated dna sequencing technology is so rapid that analysis has become the rate-limiting step. hundreds of prokaryotic genome sequences are publicly available, with new genomes uploaded at the rate of approximately 20 per month. as a result, this growing body of genome sequences will include microorganisms not previously identified, isolated, or observed. we hypothesize that evolutionary pressure exerted by an ecological niche selects for a similar genetic repertoire in those prokaryotes that ...	2007	17710143
transcriptional regulatory network discovery via multiple method integration: application to e. coli k12.	transcriptional regulatory network (trn) discovery from one method (e.g. microarray analysis, gene ontology, phylogenic similarity) does not seem feasible due to lack of sufficient information, resulting in the construction of spurious or incomplete trns. we develop a methodology, trnd, that integrates a preliminary trn, microarray data, gene ontology and phylogenic similarity to accurately discover trns and apply the method to e. coli k12. the approach can easily be extended to include other me ...	2007	17397539
the flik protein and flagellar hook-length control.	the bacterial flagellum is a highly complex prokaryotic organelle. it is the motor that drives bacterial motility, and despite the large amount of energy required to make and operate flagella, motile organisms have a strong adaptive advantage. flagellar biogenesis is both complex and highly coordinated and it typically involves at least three two-component systems. part of the flagellum is a type iii secretion system, and it is via this structure that flagellar components are exported. the assem ...	2007	17456739
evolution of the chaperone/usher assembly pathway: fimbrial classification goes greek.	many proteobacteria use the chaperone/usher pathway to assemble proteinaceous filaments on the bacterial surface. these filaments can curl into fimbrial or nonfimbrial surface structures (e.g., a capsule or spore coat). this article reviews the phylogeny of operons belonging to the chaperone/usher assembly class to explore the utility of establishing a scheme for subdividing them into clades of phylogenetically related gene clusters. based on usher amino acid sequence comparisons, our analysis s ...	2007	18063717
a novel superfamily containing the beta-grasp fold involved in binding diverse soluble ligands.	domains containing the beta-grasp fold are utilized in a great diversity of physiological functions but their role, if any, in soluble or small molecule ligand recognition is poorly studied.	2007	17250770
linear array of conserved sequence motifs to discriminate protein subfamilies: study on pyridine nucleotide-disulfide reductases.	the pyridine nucleotide disulfide reductase (pndr) is a large and heterogeneous protein family divided into two classes (i and ii), which reflect the divergent evolution of its characteristic disulfide redox active site. however, not all the pndr members fit into these categories and this suggests the need of further studies to achieve a more comprehensive classification of this complex family.	2007	17367536
global expression analysis of nucleotide binding site-leucine rich repeat-encoding and related genes in arabidopsis.	nucleotide binding site-leucine rich repeat (nbs-lrr)-encoding genes comprise the largest class of plant disease resistance genes. the 149 nbs-lrr-encoding genes and the 58 related genes that do not encode lrrs represent approximately 0.8% of all orfs so far annotated in arabidopsis ecotype col-0. despite their prevalence in the genome and functional importance, there was little information regarding expression of these genes.	2007	17956627
the role and regulation of receptor-like kinases in plant defense.	receptor-like kinases (rlks) in plants are a large superfamily of proteins that are structurally similar. rlks are involved in a diverse array of plant responses including development, growth, hormone perception and the response to pathogens. current studies have focused attention on plant receptor-like kinases as an important class of sentinels acting in plant defense responses. rlks have been identified that act in both broad-spectrum, elicitor-initiated defense responses and as dominant resis ...	2007	19936086