Publications

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jaz8 lacks a canonical degron and has an ear motif that mediates transcriptional repression of jasmonate responses in arabidopsis.the lipid-derived hormone jasmonoyl-l-ile (ja-ile) initiates large-scale changes in gene expression by stabilizing the interaction of jasmonate zim domain (jaz) repressors with the f-box protein coronatine insensitive1 (coi1), which results in jaz degradation by the ubiquitin-proteasome pathway. recent structural studies show that the jaz1 degradation signal (degron) includes a short conserved lpiar motif that seals ja-ile in its binding pocket at the coi1-jaz interface. here, we show that arabi ...201222327740
identification of innate immunity elicitors using molecular signatures of natural selection.the innate immune system is an ancient and broad-spectrum defense system found in all eukaryotes. the detection of microbial elicitors results in the up-regulation of defense-related genes and the elicitation of inflammatory and apoptotic responses. these innate immune responses are the front-line barrier against disease because they collectively suppress the growth of the vast majority of invading microbes. despite their critical role, we know remarkably little about the diversity of immune eli ...201222323605
the arabidopsis lectin receptor kinase lecrk-v.5 represses stomatal immunity induced by pseudomonas syringae pv. tomato dc3000.stomata play an important role in plant innate immunity by limiting pathogen entry into leaves but molecular mechanisms regulating stomatal closure upon pathogen perception are not well understood. here we show that the arabidopsis thaliana l-type lectin receptor kinase-v.5 (lecrk-v.5) negatively regulates stomatal immunity. loss of lecrk-v.5 function increased resistance to surface inoculation with virulent bacteria pseudomonas syringae pv tomato dc3000. levels of resistance were not affected a ...201222346749
biochemical and molecular-genetic characterization of sfd1's involvement in lipid metabolism and defense signaling.the arabidopsis thaliana sfd1 (suppressor of fatty acid desaturase deficiency1) gene (also known as gly1) is required for accumulation of 34:6 (i.e., 18:3-16:3) monogalactosyldiacylglycerol (mgdg) and for the activation of systemic acquired resistance (sar), an inducible defense mechanism that confers resistance against a broad spectrum of pathogens. sfd1, which has been suggested to be involved in lipid-based signaling in sar, contains a putative chloroplast transit peptide and has glycerol-3-p ...201222645576
catabolism and deactivation of the lipid-derived hormone jasmonoyl-isoleucine.the oxylipin hormone jasmonate controls myriad processes involved in plant growth, development, and immune function. the discovery of jasmonoyl-l-isoleucine (ja-ile) as the major bioactive form of the hormone highlights the need to understand biochemical and cell biological processes underlying ja-ile homeostasis. among the major metabolic control points governing the accumulation of ja-ile in plant tissues are the availability of jasmonic acid, the immediate precursor of ja-ile, and oxidative e ...201222639640
mda5 cooperatively forms dimers and atp-sensitive filaments upon binding double-stranded rna.melanoma differentiation-associated gene-5 (mda5) detects viral double-stranded rna in the cytoplasm. rna binding induces mda5 to activate the signalling adaptor mavs through interactions between the caspase recruitment domains (cards) of the two proteins. the molecular mechanism of mda5 signalling is not well understood. here, we show that mda5 cooperatively binds short rna ligands as a dimer with a 16-18-basepair footprint. a crystal structure of the mda5 helicase-insert domain demonstrates an ...201222314235
a peroxidase-dependent apoplastic oxidative burst in cultured arabidopsis cells functions in mamp-elicited defense.perception by plants of so-called microbe-associated molecular patterns (mamps) such as bacterial flagellin, referred to as pattern-triggered immunity, triggers a rapid transient accumulation of reactive oxygen species (ros). we previously identified two cell wall peroxidases, prx33 and prx34, involved in apoplastic hydrogen peroxide (h2o2) production in arabidopsis (arabidopsis thaliana). here, we describe the generation of arabidopsis tissue culture lines in which the expression of prx33 and p ...201222319074
type iii secretion and effectors shape the survival and growth pattern of pseudomonas syringae on leaf surfaces.the bacterium pseudomonas syringae pv syringae b728a (psyb728a) uses a type iii secretion system (t3ss) to inject effector proteins into plant cells, a process that modulates the susceptibility of different plants to infection. analysis of green fluorescent protein-expressing psyb728a after spray inoculation without additives under moderate relative humidity conditions permitted (1) a detailed analysis of this strain's survival and growth pattern on host (nicotiana benthamiana) and nonhost (toma ...201222319072
rna silencing as a tool to uncover gene function and engineer novel traits in soybean.rna silencing refers collectively to diverse rna-mediated pathways of nucleotide-sequence-specific inhibition of gene expression. it has been used to analyze gene function and engineer novel traits in various organisms. here, we review the application of rna silencing in soybean. to produce soybean lines, in which a particular gene is stably silenced, researchers have frequently used a transgene that transcribes inverted repeats of a target gene segment. suppression of gene expression in develop ...201223136487
arabidopsis growth and defense are modulated by bacterial quorum sensing molecules.n-acyl-homoserine lactones (ahls) play an important role in the communication within the rhizosphere; they serve as a chemical base for interactions within and between different species of gram-negative bacteria. not only bacteria, also plants perceive and react to ahls with diverse responses. here we describe a negative correlation between the length of ahls' lipid chains and the observed growth promotion in arabidopsis thaliana. moreover, we speculate on a positive correlation between the rein ...201222307043
role of glutathione in plant signaling under biotic stress.glutathione (gsh) is a non-protein thiol compound which has been repeatedly reported to play an important role in plant responses during biotic stresses. however, our knowledge of glutathione-related molecular mechanisms underlying plant defense responses still remains limited. we first discovered that the arabidopsis thaliana phytoalexin deficient 2-1 (pad2-1) mutant was linked to glutathione deficiency since the mutation was identified in the gsh1 gene encoding the first enzyme of glutathione ...201222353869
role of phytohormones in insect-specific plant reactions.the capacity to perceive and respond is integral to biological immune systems, but to what extent can plants specifically recognize and respond to insects? recent findings suggest that plants possess surveillance systems that are able to detect general patterns of cellular damage as well as highly specific herbivore-associated cues. the jasmonate (ja) pathway has emerged as the major signaling cassette that integrates information perceived at the plant-insect interface into broad-spectrum defens ...201222305233
prime time for transgenerational defense. 201222308198
novel transporter required for biogenesis of cbb3-type cytochrome c oxidase in rhodobacter capsulatus.the acquisition, delivery, and incorporation of metals into their respective metalloproteins are important cellular processes. these processes are tightly controlled in order to prevent exposure of cells to free-metal concentrations that could yield oxidative damage. copper (cu) is one such metal that is required as a cofactor in a variety of proteins. however, when present in excessive amounts, cu is toxic due to its oxidative capability. cytochrome c oxidases (coxs) are among the metalloprotei ...201222294680
loss of function of fatty acid desaturase7 in tomato enhances basal aphid resistance in a salicylate-dependent manner.we report here that disruption of function of the ω-3 fatty acid desaturase7 (fad7) enhances plant defenses against aphids. the suppressor of prosystemin-mediated responses2 (spr2) mutation in tomato (solanum lycopersicum), which eliminates the function of fad7, reduces the settling behavior, survival, and fecundity of the potato aphid (macrosiphum euphorbiae). likewise, the antisense suppression of lefad7 expression in wild-type tomato plants reduces aphid infestations. aphid resistance in the ...201222291202
plant stress surveillance monitored by aba and disease signaling interactions.abiotic and biotic stresses are the major factors that negatively impact plant growth. in response to abiotic environmental stresses such as drought, plants generate resistance responses through abscisic acid (aba) signal transduction. in addition to the major role of aba in abiotic stress signaling, aba signaling was reported to downregulate biotic stress signaling. conversely recent findings provide evidence that initial activation of plant immune signaling inhibits subsequent aba signal trans ...201222314325
proteasome inhibitors: an expanding army attacking a unique target.proteasomes are large, multisubunit proteolytic complexes presenting multiple targets for therapeutic intervention. the 26s proteasome consists of a 20s proteolytic core and one or two 19s regulatory particles. the 20s core contains three types of active sites. many structurally diverse inhibitors of these active sites, both natural product and synthetic, have been discovered in the last two decades. one, bortezomib, is used clinically for treatment of multiple myeloma, mantle cell lymphoma, and ...201222284358
glycolate oxidase modulates reactive oxygen species-mediated signal transduction during nonhost resistance in nicotiana benthamiana and arabidopsis.in contrast to gene-for-gene disease resistance, nonhost resistance governs defense responses to a broad range of potential pathogen species. to identify specific genes involved in the signal transduction cascade associated with nonhost disease resistance, we used a virus-induced gene-silencing screen in nicotiana benthamiana, and identified the peroxisomal enzyme glycolate oxidase (gox) as an essential component of nonhost resistance. gox-silenced n. benthamiana and arabidopsis thaliana gox t-d ...201222286136
non-host defense response in a novel arabidopsis-xanthomonas citri subsp. citri pathosystem.citrus canker, caused by xanthomonas citri subsp. citri (xcc), is one of the most destructive diseases of citrus. progress of breeding citrus canker-resistant varieties is modest due to limited resistant germplasm resources and lack of candidate genes for genetic manipulation. the objective of this study is to establish a novel heterologous pathosystem between xcc and the well-established model plant arabidopsis thaliana for defense mechanism dissection and resistance gene identification. our re ...201222299054
the spliceosome-activating complex: molecular mechanisms underlying the function of a pleiotropic regulator.correct interpretation of the coding capacity of rna polymerase ii transcribed eukaryotic genes is determined by the recognition and removal of intronic sequences of pre-mrnas by the spliceosome. our current knowledge on dynamic assembly and subunit interactions of the spliceosome mostly derived from the characterization of yeast, drosophila, and human spliceosomal complexes formed on model pre-mrna templates in cell extracts. in addition to sequential structural rearrangements catalyzed by atp- ...201222639636
two-component elements mediate interactions between cytokinin and salicylic acid in plant immunity.recent studies have revealed an important role for hormones in plant immunity. we are now beginning to understand the contribution of crosstalk among different hormone signaling networks to the outcome of plant-pathogen interactions. cytokinins are plant hormones that regulate development and responses to the environment. cytokinin signaling involves a phosphorelay circuitry similar to two-component systems used by bacteria and fungi to perceive and react to various environmental stimuli. in thi ...201222291601
identification of genes required for cf-dependent hypersensitive cell death by combined proteomic and rna interfering analyses.identification of hypersensitive cell death (hcd) regulators is essential to dissect the molecular mechanisms underlying plant disease resistance. in this study, combined proteomic and rna interfering (rnai) analyses were employed to identify genes required for the hcd conferred by the tomato resistance gene cf-4 and the cladosporium fulvum avirulence gene avr4. forty-nine proteins differentially expressed in the tomato seedlings mounting and those not mounting cf-4/avr4-dependent hcd were ident ...201222275387
the rolb gene suppresses reactive oxygen species in transformed plant cells through the sustained activation of antioxidant defense.the rolb (for rooting locus of agrobacterium rhizogenes) oncogene has previously been identified as a key player in the formation of hairy roots during the plant-a. rhizogenes interaction. in this study, using single-cell assays based on confocal microscopy, we demonstrated reduced levels of reactive oxygen species (ros) in rolb-expressing rubia cordifolia, panax ginseng, and arabidopsis (arabidopsis thaliana) cells. the expression of rolb was sufficient to inhibit excessive elevations of ros in ...201222271748
the progeny of arabidopsis thaliana plants exposed to salt exhibit changes in dna methylation, histone modifications and gene expression.plants are able to acclimate to new growth conditions on a relatively short time-scale. recently, we showed that the progeny of plants exposed to various abiotic stresses exhibited changes in genome stability, methylation patterns and stress tolerance. here, we performed a more detailed analysis of methylation patterns in the progeny of arabidopsis thaliana (arabidopsis) plants exposed to 25 and 75 mm sodium chloride. we found that the majority of gene promoters exhibiting changes in methylation ...201222291972
wrky54 and wrky70 co-operate as negative regulators of leaf senescence in arabidopsis thaliana.the plant-specific wrky transcription factor (tf) family with 74 members in arabidopsis thaliana appears to be involved in the regulation of various physiological processes including plant defence and senescence. wrky53 and wrky70 were previously implicated as positive and negative regulators of senescence, respectively. here the putative function of other wrky group iii proteins in arabidopsis leaf senescence has been explored and the results suggest the involvement of two additional wrky tfs, ...201222268143
overexpression of the aspartic protease aspg1 gene confers drought avoidance in arabidopsis.drought is one of the most severe environmental stresses affecting plant growth and limiting crop production. although many genes involved in adaptation to drought stress have been disclosed, the relevant molecular mechanisms are far from understood. this study describes an arabidopsis gene, aspg1 (aspartic protease in guard cell 1), that may function in drought avoidance through abscisic acid (aba) signalling in guard cells. overexpression of the aspg1 gene enhanced aba sensitivity in guard cel ...201222268147
microrna response to listeria monocytogenes infection in epithelial cells.micrornas represent a family of very small non-coding rnas that control several physiologic and pathologic processes, including host immune response and cancer by antagonizing a number of target mrnas. there is limited knowledge about cell expression and the regulatory role of micrornas following bacterial infections. we investigated whether infection with a gram-positive bacterium leads to altered expression of micrornas involved in the host cell response in epithelial cells. caco-2 cells were ...201222312311
shade avoidance.the presence of neighboring vegetation modifies the light environment experienced by plants, generating signals that are perceived by phytochromes and cryptochromes. these signals cause large changes in plant body form and function, including enhanced growth of the hypocotyl and petioles, a more erect position of the leaves and early flowering in arabidopsis thaliana. collectively, these so-called shade-avoidance responses tend to reduce the degree of current or future shade by neighbors. shade ...201222582029
the apoplastic oxidative burst peroxidase in arabidopsis is a major component of pattern-triggered immunity.in plants, reactive oxygen species (ros) associated with the response to pathogen attack are generated by nadph oxidases or apoplastic peroxidases. antisense expression of a heterologous french bean (phaseolus vulgaris) peroxidase (fbp1) cdna in arabidopsis thaliana was previously shown to diminish the expression of two arabidopsis peroxidases (peroxidase 33 [prx33] and prx34), block the oxidative burst in response to a fungal elicitor, and cause enhanced susceptibility to a broad range of funga ...201222247251
pseudomonas syringae naturally lacking the canonical type iii secretion system are ubiquitous in nonagricultural habitats, are phylogenetically diverse and can be pathogenic.the type iii secretion system (t3ss) is an important virulence factor of pathogenic bacteria, but the natural occurrence of variants of bacterial plant pathogens with deficiencies in their t3ss raises questions about the significance of the t3ss for fitness. previous work on t3ss-deficient plant pathogenic bacteria has focused on strains from plants or plant debris. here we have characterized t3ss-deficient strains of pseudomonas syringae from plant and nonplant substrates in pristine nonagricul ...201222237542
the hsf-like transcription factor tbf1 is a major molecular switch for plant growth-to-defense transition.induction of plant immune responses involves significant transcription reprogramming that prioritizes defense over growth-related cellular functions. despite intensive forward genetic screens and genome-wide expression-profiling studies, a limited number of transcription factors have been found that regulate this transition.201222244999
quantitative interactor screening with next-generation sequencing (qis-seq) identifies arabidopsis thaliana mlo2 as a target of the pseudomonas syringae type iii effector hopz2.identification of protein-protein interactions is a fundamental aspect of understanding protein function. a commonly used method for identifying protein interactions is the yeast two-hybrid system.201222230763
rootstock-regulated gene expression patterns associated with fire blight resistance in apple.desirable apple varieties are clonally propagated by grafting vegetative scions onto rootstocks. rootstocks influence many phenotypic traits of the scion, including resistance to pathogens such as erwinia amylovora, which causes fire blight, the most serious bacterial disease of apple. the purpose of the present study was to quantify rootstock-mediated differences in scion fire blight susceptibility and to identify transcripts in the scion whose expression levels correlated with this response.201222229964
determining degradation and synthesis rates of arabidopsis proteins using the kinetics of progressive 15n labeling of two-dimensional gel-separated protein spots.the growth and development of plant tissues is associated with an ordered succession of cellular processes that are reflected in the appearance and disappearance of proteins. the control of the kinetics of protein turnover is central to how plants can rapidly and specifically alter protein abundance and thus molecular function in response to environmental or developmental cues. however, the processes of turnover are largely hidden during periods of apparent steady-state protein abundance, and ev ...201222215636
quantitative proteomics reveals dynamic changes in the plasma membrane during arabidopsis immune signaling.the plant plasma membrane is a crucial mediator of the interaction between plants and microbes. understanding how the plasma membrane proteome responds to diverse immune signaling events will lead to a greater understanding of plant immunity and uncover novel targets for crop improvement. here we report the results from a large scale quantitative proteomics study of plasma membrane-enriched fractions upon activation of the arabidopsis thaliana immune receptor rps2. more than 2300 proteins were i ...201222215637
first description of natural and experimental conjugation between mycobacteria mediated by a linear plasmid.in a previous study, we detected the presence of a mycobacterium avium species-specific insertion sequence, is1245, in mycobacterium kansasii. both species were isolated from a mixed m. avium-m. kansasii bone marrow culture from an hiv-positive patient. the transfer mechanism of this insertion sequence to m. kansasii was investigated here.201222235347
low antioxidant concentrations impact on multiple signalling pathways in arabidopsis thaliana partly through npr1.production of reactive oxygen species (ros) is linked to signalling in both developmental and stress responses. the level of ros is controlled by both production and removal through various scavengers including ascorbic acid and glutathione. here, the role of low ascorbic acid or glutathione concentrations was investigated on ozone-induced cell death, defence signalling, and developmental responses. low ascorbic acid concentrations in vtc1 activated expression of salicylic acid (sa)-regulated ge ...201222213815
isolation and profiling of protein-associated small rnas.small rnas are short noncoding rnas with important regulatory roles in many cellular processes. small rnas are generated by dicer or dicer-like proteins and then incorporated into rnai effector -proteins argonautes (agos) for silencing of their targets. in plants, small rnas regulate host innate immunity against various pathogens, but their mode of action and associated protein factors that facilitate their function remain to be elucidated. here, we describe an efficient method to isolate -ago-a ...201222589133
recombineering: a powerful tool for modification of bacteriophage genomes.recombineering, a recently developed technique for efficient genetic manipulation of bacteria, is facilitated by phage-derived recombination proteins and has the advantage of using dna substrates with short regions of homology. this system was first developed in e. coli but has since been adapted for use in other bacteria. it is now widely used in a number of different systems for a variety of purposes, and the construction of chromosomal gene knockouts, deletions, insertions, point mutations, a ...201222666652
characterization of the membrane-associated harxl17 hpa effector candidate.we examined changes to subcellular architecture during the compatible interaction between the biotroph pathogen hyaloperonospora arabidopsidis (hpa) and its host arabidopsis. live-cell imaging highlighted rearrangements in plant cell membranes upon infection. in particular, the tonoplast appeared close to the extrahaustorial membrane surrounding the haustorium. we investigated the subcellular localization patterns of hpa rxlr effector candidates (harxls) in planta. this subcellular localization ...201222301983
student internships at the university hawai'i cancer center. 201222413103
a novel extracellular metallopeptidase domain shared by animal host-associated mutualistic and pathogenic microbes.the mucosal microbiota is recognised as an important factor for our health, with many disease states linked to imbalances in the normal community structure. hence, there is considerable interest in identifying the molecular basis of human-microbe interactions. in this work we investigated the capacity of microbes to thrive on mucosal surfaces, either as mutualists, commensals or pathogens, using comparative genomics to identify co-occurring molecular traits. we identified a novel domain we named ...201222299034
importance of rare taxa for bacterial diversity in the rhizosphere of bt- and conventional maize varieties.ribosomal 16s rrna gene pyrosequencing was used to explore whether the genetically modified (gm) bt-maize hybrid mon 89034 × mon 88017, expressing three insecticidal recombinant cry proteins of bacillus thuringiensis, would alter the rhizosphere bacterial community. fine roots of field cultivated bt-maize and three conventional maize varieties were analyzed together with coarse roots of the bt-maize. a total of 547,000 sequences were obtained. library coverage was 100% at the phylum and 99.8% at ...201222791236
importance of rare taxa for bacterial diversity in the rhizosphere of bt- and conventional maize varieties.ribosomal 16s rrna gene pyrosequencing was used to explore whether the genetically modified (gm) bt-maize hybrid mon 89034 × mon 88017, expressing three insecticidal recombinant cry proteins of bacillus thuringiensis, would alter the rhizosphere bacterial community. fine roots of field cultivated bt-maize and three conventional maize varieties were analyzed together with coarse roots of the bt-maize. a total of 547,000 sequences were obtained. library coverage was 100% at the phylum and 99.8% at ...201222791236
multiple mechanisms contribute to lateral transfer of an organophosphate degradation (opd) island in sphingobium fuliginis atcc 27551.the complete sequence of ppdl2 (37,317 bp), an indigenous plasmid of sphingobium fuliginis atcc 27551 that encodes genes for organophosphate degradation (opd), revealed the existence of a site-specific integrase (int) gene with an attachment site attp, typically seen in integrative mobilizable elements (ime). in agreement with this sequence information, site-specific recombination was observed between ppdl2 and an artificial plasmid having a temperature-sensitive replicon and a cloned attb site ...201223275877
the chemical composition of endotoxin isolated from intestinal strain of desulfovibrio desulfuricans.desulfovibrio desulfuricans anaerobes are constituents of human alimentary tract microflora. there are suggestions that they take part in the pathogenesis of periodontitis and some gastrointestinal inflammatory disorders, such as ulcerative colitis or crohn's disease. endotoxin is one of gram-negative bacteria cellular components that influence these microorganisms pathogenicity. endotoxin is a lipid-polisaccharide heteropolymer consisting of three elements: lipid a, core oligosaccharide, and o- ...201222629175
development of an engineered bioluminescent reporter phage for detection of bacterial blight of crucifers.bacterial blight, caused by the phytopathogen pseudomonas cannabina pv. alisalensis, is an emerging disease afflicting important members of the brassicaceae family. the disease is often misdiagnosed as pepper spot, a much less severe disease caused by the related pathogen pseudomonas syringae pv. maculicola. we have developed a phage-based diagnostic that can both identify and detect the causative agent of bacterial blight and differentiate the two pathogens. a recombinant "light"-tagged reporte ...201222427491
induction of drought tolerance in cucumber plants by a consortium of three plant growth-promoting rhizobacterium strains.our previous work showed that a consortium of three plant growth-promoting rhizobacterium (pgpr) strains (bacillus cereus ar156, bacillus subtilis sm21, and serratia sp. xy21), termed as bbs for short, was a promising biocontrol agent. the present study investigated its effect on drought tolerance in cucumber plants. after withholding watering for 13 days, bbs-treated cucumber plants had much darker green leaves and substantially lighter wilt symptoms than control plants. compared to the control ...201223285089
Cysteine homeostasis plays an essential role in plant immunity.• Cysteine is the metabolic precursor of essential biomolecules such as vitamins, cofactors, antioxidants and many defense compounds. The last step of cysteine metabolism is catalysed by O-acetylserine(thiol)lyase (OASTL), which incorporates reduced sulfur into O-acetylserine to produce cysteine. In Arabidopsis thaliana, the main OASTL isoform OAS-A1 and the cytosolic desulfhydrase DES1, which degrades cysteine, contribute to the cytosolic cysteine homeostasis. • Meta-analysis of the transcripto ...201221988475
identification and evaluation of twin-arginine translocase inhibitors.the twin-arginine translocase (tat) in some bacterial pathogens, including pseudomonas aeruginosa, burkholderia pseudomallei, and mycobacterium tuberculosis, contributes to pathogenesis by translocating extracellular virulence determinants across the inner membrane into the periplasm, thereby allowing access to the xcp (type ii) secretory system for further export in gram-negative organisms, or directly to the outside surface of the cell, as in m. tuberculosis. tat-mediated secretion appreciably ...201223006747
genomic insights into strategies used by xanthomonas albilineans with its reduced artillery to spread within sugarcane xylem vessels.xanthomonas albilineans causes leaf scald, a lethal disease of sugarcane. x. albilineans exhibits distinctive pathogenic mechanisms, ecology and taxonomy compared to other species of xanthomonas. for example, this species produces a potent dna gyrase inhibitor called albicidin that is largely responsible for inducing disease symptoms; its habitat is limited to xylem; and the species exhibits large variability. a first manuscript on the complete genome sequence of the highly pathogenic x. albilin ...201223171051
the large universal pantoea plasmid lpp-1 plays a major role in biological and ecological diversification.pantoea spp. are frequently isolated from a wide range of ecological niches and have various biological roles, as plant epi- or endophytes, biocontrol agents, plant-growth promoters or as pathogens of both plant and animal hosts. this suggests that members of this genus have undergone extensive genotypic diversification. one means by which this occurs among bacteria is through the acquisition and maintenance of plasmids. here, we have analyzed and compared the sequences of a large plasmid common ...201223151240
cellular choline and glycine betaine pools impact osmoprotection and phospholipase c production in pseudomonas aeruginosa.choline is abundantly produced by eukaryotes and plays an important role as a precursor of the osmoprotectant glycine betaine. in pseudomonas aeruginosa, glycine betaine has additional roles as a nutrient source and an inducer of the hemolytic phospholipase c, plch. the multiple functions for glycine betaine suggested that the cytoplasmic pool of glycine betaine is regulated in p. aeruginosa. we used (13)c nuclear magnetic resonance ((13)c-nmr) to demonstrate that p. aeruginosa maintains both ch ...201222753069
bacterial contamination of dental unit waterlines.safety of patients and dental personnel requires the appropriate microbiological water quality in dental units. during treatment, patients and dental workers are exposed both to direct contact with bacteria-contaminated water in the form of splatter and with contaminated water aerosol emitted during work by unit handpieces, including rotating and ultrasonic instruments. the aim of the study was to determine the qualitative and quantitative contamination of water in dental unit reservoirs with ae ...201222899458
bacterial contamination of dental unit waterlines.safety of patients and dental personnel requires the appropriate microbiological water quality in dental units. during treatment, patients and dental workers are exposed both to direct contact with bacteria-contaminated water in the form of splatter and with contaminated water aerosol emitted during work by unit handpieces, including rotating and ultrasonic instruments. the aim of the study was to determine the qualitative and quantitative contamination of water in dental unit reservoirs with ae ...201222899458
dna polymorphisms and biocontrol of bacillus antagonistic to citrus bacterial canker with indication of the interference of phyllosphere biofilms.citrus bacterial canker caused by xanthomonas axonopodis pv. citri is a devastating disease resulting in significant crop losses in various citrus cultivars worldwide. a biocontrol agent has not been recommended for this disease. to explore the potential of bacilli native to taiwan to control this disease, bacillus species with a broad spectrum of antagonistic activity against various phytopathogens were isolated from plant potting mixes, organic compost and the rhizosphere soil. seven strains t ...201222848728
an image classification approach to analyze the suppression of plant immunity by the human pathogen salmonella typhimurium.the enteric pathogen salmonella is the causative agent of the majority of food-borne bacterial poisonings. resent research revealed that colonization of plants by salmonella is an active infection process. salmonella changes the metabolism and adjust the plant host by suppressing the defense mechanisms. in this report we developed an automatic algorithm to quantify the symptoms caused by salmonella infection on arabidopsis.201222812426
quorum quenching revisited--from signal decays to signalling confusion.in a polymicrobial community, while some bacteria are communicating with neighboring cells (quorum sensing), others are interrupting the communication (quorum quenching), thus creating a constant arms race between intercellular communication. in the past decade, numerous quorum quenching enzymes have been found and initially thought to inactivate the signalling molecules. though this is widely accepted, the actual roles of these quorum quenching enzymes are now being uncovered. recent evidence e ...201222666051
distribution and properties of the genes encoding the biosynthesis of the bacterial cofactor, pyrroloquinoline quinone.pyrroloquinoline quinone (pqq) is a small, redox active molecule that serves as a cofactor for several bacterial dehydrogenases, introducing pathways for carbon utilization that confer a growth advantage. early studies had implicated a ribosomally translated peptide as the substrate for pqq production. this study presents a sequence- and structure-based analysis of the components of the pqq operon. we find the necessary components for pqq production are present in 126 prokaryotes, most of which ...201222324760
leveraging proteomics to understand plant-microbe interactions.understanding the interactions of plants with beneficial and pathogenic microbes is a promising avenue to improve crop productivity and agriculture sustainability. proteomic techniques provide a unique angle to describe these intricate interactions and test hypotheses. the various approaches for proteomic analysis generally include protein/peptide separation and identification, but can also provide quantification and the characterization of post-translational modifications. in this review, we di ...201222645586
the multiple signaling systems regulating virulence in pseudomonas aeruginosa.cell-to-cell communication is a major process that allows bacteria to sense and coordinately react to the fluctuating conditions of the surrounding environment. in several pathogens, this process triggers the production of virulence factors and/or a switch in bacterial lifestyle that is a major determining factor in the outcome and severity of the infection. understanding how bacteria control these signaling systems is crucial to the development of novel antimicrobial agents capable of reducing ...201222390972
glioblastoma multiforme: novel therapeutic approaches.the current therapy for glioblastoma multiforme involves total surgical resection followed by combination of radiation therapy and temozolomide. unfortunately, the efficacy for such current therapy is limited, and newer approaches are sorely needed to treat this deadly disease. we have recently described the isolation of bacterial proteins and peptides with anticancer activity. in phase i human clinical trials, one such peptide, p28, derived from a bacterial protein azurin, showed partial and co ...201222462021
structural and functional insights into (s)-ureidoglycolate dehydrogenase, a metabolic branch point enzyme in nitrogen utilization.nitrogen metabolism is one of essential processes in living organisms. the catabolic pathways of nitrogenous compounds play a pivotal role in the storage and recovery of nitrogen. in escherichia coli, two different, interconnecting metabolic routes drive nitrogen utilization through purine degradation metabolites. the enzyme (s)-ureidoglycolate dehydrogenase (alld), which is a member of l-sulfolactate dehydrogenase-like family, converts (s)-ureidoglycolate, a key intermediate in the purine degra ...201223284870
thermal control of microbial development and virulence: molecular mechanisms of microbial temperature sensing.temperature is a critical and ubiquitous environmental signal that governs the development and virulence of diverse microbial species, including viruses, archaea, bacteria, fungi, and parasites. microbial survival is contingent upon initiating appropriate responses to the cellular stress induced by severe environmental temperature change. in the case of microbial pathogens, development and virulence are often coupled to sensing host physiological temperatures. as such, microbes have developed di ...201223033469
small molecules aimed at type iii secretion systems to inhibit bacterial virulence. 201223930198
small molecules aimed at type iii secretion systems to inhibit bacterial virulence. 201223930198
hidden evolutionary complexity of nucleo-cytoplasmic large dna viruses of eukaryotes.the nucleo-cytoplasmic large dna viruses (ncldv) constitute an apparently monophyletic group that consists of at least 6 families of viruses infecting a broad variety of eukaryotic hosts. a comprehensive genome comparison and maximum-likelihood reconstruction of the ncldv evolution revealed a set of approximately 50 conserved, core genes that could be mapped to the genome of the common ancestor of this class of eukaryotic viruses.201222891861
copper starvation-inducible protein for cytochrome oxidase biogenesis in bradyrhizobium japonicum.microarray analysis of bradyrhizobium japonicum grown under copper limitation uncovered five genes named pcuabcde, which are co-transcribed and co-regulated as an operon. the predicted gene products are periplasmic proteins (pcua, pcuc, and pcud), a tonb-dependent outer membrane receptor (pcub), and a cytoplasmic membrane-integral protein (pcue). homologs of pcuc and pcue had been discovered in other bacteria, namely pcu(a)c and ycnj, where they play a role in cytochrome oxidase biogenesis and c ...201223012364
bacterial tyrosine kinases: evolution, biological function and structural insights.reversible protein phosphorylation is a major mechanism in the regulation of fundamental signalling events in all living organisms. bacteria have been shown to possess a versatile repertoire of protein kinases, including histidine and aspartic acid kinases, serine/threonine kinases, and more recently tyrosine and arginine kinases. tyrosine phosphorylation is today recognized as a key regulatory device of bacterial physiology, linked to exopolysaccharide production, virulence, stress response and ...201222889913
pseudomonas syringae catalases are collectively required for plant pathogenesis.the bacterial pathogen pseudomonas syringae pv. tomato dc3000 must detoxify plant-produced hydrogen peroxide (h(2)o(2)) in order to survive in its host plant. candidate enzymes for this detoxification include the monofunctional catalases katb and kate and the bifunctional catalase-peroxidase katg of dc3000. this study shows that katg is the major housekeeping catalase of dc3000 and provides protection against menadione-generated endogenous h(2)o(2). in contrast, katb rapidly and substantially ac ...201222797762
forward genetic in planta screen for identification of plant-protective traits of sphingomonas sp. strain fr1 against pseudomonas syringae dc3000.sphingomonas sp. strain fr1 has recently been shown to protect arabidopsis thaliana against the bacterial leaf pathogen pseudomonas syringae dc3000. here, we describe a forward genetic in planta screen to identify genes in sphingomonas sp. fr1 necessary for this effect. about 5,000 sphingomonas sp. fr1 mini-tn5 mutants were assayed for a defect in plant protection against a luxcdabe-tagged p. syringae dc3000 derivative in a space-saving 24-well plate system. the bioluminescence of the pathogen w ...201222660707
transcriptomic profiling of bacillus amyloliquefaciens fzb42 in response to maize root exudates.plant root exudates have been shown to play an important role in mediating interactions between plant growth-promoting rhizobacteria (pgpr) and their host plants. most investigations were performed on gram-negative rhizobacteria, while much less is known about gram-positive rhizobacteria. to elucidate early responses of pgpr to root exudates, we investigated changes in the transcriptome of a gram-positive pgpr to plant root exudates.201222720735
decolorization of industrial synthetic dyes using engineered pseudomonas putida cells with surface-immobilized bacterial laccase.microbial laccases are highly useful in textile effluent dye biodegradation. however, the bioavailability of cellularly expressed or purified laccases in continuous operations is usually limited by mass transfer impediment or enzyme regeneration difficulty. therefore, this study develops a regenerable bacterial surface-displaying system for industrial synthetic dye decolorization, and evaluates its effects on independent and continuous operations.201222686507
plasmid pp62bp1 isolated from an arctic psychrobacter sp. strain carries two highly homologous type ii restriction-modification systems and a putative organic sulfate metabolism operon.the complete nucleotide sequence of plasmid pp62bp1 (34,467 bp), isolated from arctic psychrobacter sp. dab_al62b, was determined and annotated. the conserved plasmid backbone is composed of several genetic modules, including a replication system (rep) with similarities to the rep region of the iteron-containing plasmid pps10 of pseudomonas syringae. the additional genetic load of pp62bp1 includes two highly related type ii restriction-modification systems and a set of genes (slfrchsl) encoding ...201222392282
ros production during symbiotic infection suppresses pathogenesis-related gene expression.leguminous plants have exclusive ability to form symbiotic relationship with soil bacteria of the genus rhizobium. symbiosis is a complex process that involves multiple molecular signaling activities, such as calcium fluxes, production of reactive oxygen species (ros) and synthesis of nodulation genes. we analyzed the role of ros in defense gene expression in medicago truncatula during symbiosis and pathogenesis. studies in arabidopsis thaliana showed that the induction of pathogenesis-related ( ...201222499208
hemoglobin: a nitric-oxide dioxygenase.members of the hemoglobin superfamily efficiently catalyze nitric-oxide dioxygenation, and when paired with native electron donors, function as no dioxygenases (nods). indeed, the nod function has emerged as a more common and ancient function than the well-known role in o2 transport-storage. novel hemoglobins possessing a nod function continue to be discovered in diverse life forms. unique hemoglobin structures evolved, in part, for catalysis with different electron donors. the mechanism of nod ...201224278729
experimental evidence validating the computational inference of functional associations from gene fusion events: a critical survey.more than a decade ago, a number of methods were proposed for the inference of protein interactions, using whole-genome information from gene clusters, gene fusions and phylogenetic profiles. this structural and evolutionary view of entire genomes has provided a valuable approach for the functional characterization of proteins, especially those without sequence similarity to proteins of known function. furthermore, this view has raised the real possibility to detect functional associations of ge ...201223220349
experimental evidence validating the computational inference of functional associations from gene fusion events: a critical survey.more than a decade ago, a number of methods were proposed for the inference of protein interactions, using whole-genome information from gene clusters, gene fusions and phylogenetic profiles. this structural and evolutionary view of entire genomes has provided a valuable approach for the functional characterization of proteins, especially those without sequence similarity to proteins of known function. furthermore, this view has raised the real possibility to detect functional associations of ge ...201223220349
the non-flagellar type iii secretion system evolved from the bacterial flagellum and diversified into host-cell adapted systems.type 3 secretion systems (t3sss) are essential components of two complex bacterial machineries: the flagellum, which drives cell motility, and the non-flagellar t3ss (nf-t3ss), which delivers effectors into eukaryotic cells. yet the origin, specialization, and diversification of these machineries remained unclear. we developed computational tools to identify homologous components of the two systems and to discriminate between them. our analysis of >1,000 genomes identified 921 t3sss, including 2 ...201223028376
the role of bacterial enhancer binding proteins as specialized activators of σ54-dependent transcription.bacterial enhancer binding proteins (bebps) are transcriptional activators that assemble as hexameric rings in their active forms and utilize atp hydrolysis to remodel the conformation of rna polymerase containing the alternative sigma factor σ(54). we present a comprehensive and detailed summary of recent advances in our understanding of how these specialized molecular machines function. the review is structured by introducing each of the three domains in turn: the central catalytic domain, the ...201222933558
why do bacteria use so many enzymes to scavenge hydrogen peroxide?hydrogen peroxide (h(2)o(2)) is continuously formed by the autoxidation of redox enzymes in aerobic cells, and it also enters from the environment, where it can be generated both by chemical processes and by the deliberate actions of competing organisms. because h(2)o(2) is acutely toxic, bacteria elaborate scavenging enzymes to keep its intracellular concentration at nanomolar levels. mutants that lack such enzymes grow poorly, suffer from high rates of mutagenesis, or even die. in order to und ...201222609271
prediction and comparison of salmonella-human and salmonella-arabidopsis interactomes.salmonellosis caused by salmonella bacteria is a food-borne disease and a worldwide health threat causing millions of infections and thousands of deaths every year. this pathogen infects an unusually broad range of host organisms including human and plants. a better understanding of the mechanisms of communication between salmonella and its hosts requires identifying the interactions between salmonella and host proteins. protein-protein interactions (ppis) are the fundamental building blocks of ...201222589098
antimicrobial activities of isothiocyanates against campylobacter jejuni isolates.food-borne human infection with campylobacter jejuni is a medical concern in both industrialized and developing countries. efficient eradication of c. jejuni reservoirs within live animals and processed foods is limited by the development of antimicrobial resistances and by practical problems related to the use of conventional antibiotics in food processes. we have investigated the bacteriostatic and bactericidal activities of two phytochemicals, allyl-isothiocyanate (aitc), and benzyl isothiocy ...201222919644
separating significant matches from spurious matches in dna sequences.word matches are widely used to compare genomic sequences. complete genome alignment methods often rely on the use of matches as anchors for building their alignments, and various alignment-free approaches that characterize similarities between large sequences are based on word matches. among matches that are retrieved from the comparison of two genomic sequences, a part of them may correspond to spurious matches (sms), which are matches obtained by chance rather than by homologous relationships ...201222149632
ethanolamine utilization in vibrio alginolyticus.ethanolamine is used as an energy source by phylogenetically diverse bacteria including pathogens, by the concerted action of proteins from the eut-operon. previous studies have revealed the presence of eutbc genes encoding ethanolamine-ammonia lyase, a key enzyme that breaks ethanolamine into acetaldehyde and ammonia, in about 100 bacterial genomes including members of gamma-proteobacteria. however, ethanolamine utilization has not been reported for any member of the vibrio genus. our comparati ...201223234435
immunological characterization of a gida mutant strain of salmonella for potential use in a live-attenuated vaccine.salmonella is often associated with gastrointestinal disease outbreaks in humans throughout the world due to the consumption of contaminated food. our previous studies have shown that deletion of glucose-inhibited division gene (gida) significantly attenuated salmonella enterica serovar typhimurium (stm) virulence in both in vitro and in vivo models of infection. most importantly, immunization with the gida mutant protected mice from a lethal dose challenge of wild-type stm. in this study, we fu ...201223194372
genome analysis of a simultaneously predatory and prey-independent, novel bdellovibrio bacteriovorus from the river tiber, supports in silico predictions of both ancient and recent lateral gene transfer from diverse bacteria.evolution equipped bdellovibrio bacteriovorus predatory bacteria to invade other bacteria, digesting and replicating, sealed within them thus preventing nutrient-sharing with organisms in the surrounding environment. bdellovibrio were previously described as "obligate predators" because only by mutations, often in gene bd0108, are 1 in ~1x10(7) of predatory lab strains of bdellovibrio converted to prey-independent growth. a previous genomic analysis of b. bacteriovorus strain hd100 suggested tha ...201223181807
prokaryotic caspase homologs: phylogenetic patterns and functional characteristics reveal considerable diversity.caspases accomplish initiation and execution of apoptosis, a programmed cell death process specific to metazoans. the existence of prokaryotic caspase homologs, termed metacaspases, has been known for slightly more than a decade. despite their potential connection to the evolution of programmed cell death in eukaryotes, the phylogenetic distribution and functions of these prokaryotic metacaspase sequences are largely uncharted, while a few experiments imply involvement in programmed cell death. ...201223185476
revised phylogeny and novel horizontally acquired virulence determinants of the model soft rot phytopathogen pectobacterium wasabiae scc3193.soft rot disease is economically one of the most devastating bacterial diseases affecting plants worldwide. in this study, we present novel insights into the phylogeny and virulence of the soft rot model pectobacterium sp. scc3193, which was isolated from a diseased potato stem in finland in the early 1980s. genomic approaches, including proteome and genome comparisons of all sequenced soft rot bacteria, revealed that scc3193, previously included in the species pectobacterium carotovorum, can no ...201223133391
kinome profiling.the use of arrays in genomics has led to a fast and reliable way to screen the transcriptome of an organism. it can be automated and analysis tools have become available and hence the technique has become widely used within the past few years. signal-transduction routes rely mainly on the phosphorylation status of already available proteins; therefore kinases are central players in signal-transduction routes. the array technology can now also be used for the analysis of the kinome. to enable arr ...201224278683
protein export according to schedule: architecture, assembly, and regulation of type iii secretion systems from plant- and animal-pathogenic bacteria.flagellar and translocation-associated type iii secretion (t3s) systems are present in most gram-negative plant- and animal-pathogenic bacteria and are often essential for bacterial motility or pathogenicity. the architectures of the complex membrane-spanning secretion apparatuses of both systems are similar, but they are associated with different extracellular appendages, including the flagellar hook and filament or the needle/pilus structures of translocation-associated t3s systems. the needle ...201222688814
development of proteasome inhibitors as therapeutic drugs.the proteasome is a multi-unit enzyme complex found in the cytoplasm and nucleus of all eukaryotic cells and is responsible for degradation of unneeded or damaged intracellular proteins by proteolysis, a chemical reaction that breaks peptide bonds. proteasome inhibition presents a promising approach to cancer therapy by targeting the proteasome function in tumor cells. delineating the success of bortezomib in the treatment of multiple myeloma and mantle cell lymphoma, this review explores variou ...201223338480
whole genome analysis of leptospira licerasiae provides insight into leptospiral evolution and pathogenicity.the whole genome analysis of two strains of the first intermediately pathogenic leptospiral species to be sequenced (leptospira licerasiae strains var010 and mmd0835) provides insight into their pathogenic potential and deepens our understanding of leptospiral evolution. comparative analysis of eight leptospiral genomes shows the existence of a core leptospiral genome comprising 1547 genes and 452 conserved genes restricted to infectious species (including l. licerasiae) that are likely to be pa ...201223145189
lon protease of azorhizobium caulinodans ors571 is required for suppression of reb gene expression.bacterial lon proteases play important roles in a variety of biological processes in addition to housekeeping functions. in this study, we focused on the lon protease of azorhizobium caulinodans, which can fix nitrogen both during free-living growth and in stem nodules of the legume sesbania rostrata. the nitrogen fixation activity of an a. caulinodans lon mutant in the free-living state was not significantly different from that of the wild-type strain. however, the stem nodules formed by the lo ...201222752172
dickeya dadantii, a plant pathogenic bacterium producing cyt-like entomotoxins, causes septicemia in the pea aphid acyrthosiphon pisum.dickeya dadantii (syn. erwinia chrysanthemi) is a plant pathogenic bacteria that harbours a cluster of four horizontally-transferred, insect-specific toxin genes. it was recently shown to be capable of causing an acute infection in the pea aphid acyrthosiphon pisum (insecta: hemiptera). the infection route of the pathogen, and the role and in vivo expression pattern of these toxins, remain unknown. using bacterial numeration and immunolocalization, we investigated the kinetics and the pattern of ...201222292023
regulation of the histidine utilization (hut) system in bacteria.the ability to degrade the amino acid histidine to ammonia, glutamate, and a one-carbon compound (formate or formamide) is a property that is widely distributed among bacteria. the four or five enzymatic steps of the pathway are highly conserved, and the chemistry of the reactions displays several unusual features, including the rearrangement of a portion of the histidase polypeptide chain to yield an unusual imidazole structure at the active site and the use of a tightly bound nad molecule as a ...201222933560
a lov protein modulates the physiological attributes of xanthomonas axonopodis pv. citri relevant for host plant colonization.recent studies have demonstrated that an appropriate light environment is required for the establishment of efficient vegetal resistance responses in several plant-pathogen interactions. the photoreceptors implicated in such responses are mainly those belonging to the phytochrome family. data obtained from bacterial genome sequences revealed the presence of photosensory proteins of the bluf (blue light sensing using fad), lov (light, oxygen, voltage) and phytochrome families with no known functi ...201222675525
characterization of a trypanosoma brucei alkb homolog capable of repairing alkylated dna.trypanosoma brucei encodes a protein (denoted tbabh) that is homologous to alkb of escherichia coli and alkb homolog (abh) proteins in other organisms, raising the possibility that trypanosomes catalyze oxidative repair of alkylation-damaged dna. tbabh was cloned and expressed in e. coli, and the recombinant protein was purified and characterized. incubation of anaerobic tbabh with fe(ii) and α-ketoglutarate (αkg) produces a characteristic metal-to-ligand charge-transfer chromophore, confirming ...201222465611
the potential of effector-target genes in breeding for plant innate immunity.increasing numbers of infectious crop diseases that are caused by fungi and oomycetes urge the need to develop alternative strategies for resistance breeding. as an alternative for the use of resistance (r) genes, the application of mutant susceptibility (s) genes has been proposed as a potentially more durable type of resistance. identification of s genes is hampered by their recessive nature. here we explore the use of pathogen-derived effectors as molecular probes to identify s genes. effecto ...201223279965
the potential of effector-target genes in breeding for plant innate immunity.increasing numbers of infectious crop diseases that are caused by fungi and oomycetes urge the need to develop alternative strategies for resistance breeding. as an alternative for the use of resistance (r) genes, the application of mutant susceptibility (s) genes has been proposed as a potentially more durable type of resistance. identification of s genes is hampered by their recessive nature. here we explore the use of pathogen-derived effectors as molecular probes to identify s genes. effecto ...201223279965
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