Publications

pathogen virulence factors as molecular probes of basic plant cellular functions.	to successfully colonize plants, pathogens have evolved a myriad of virulence factors that allow them to manipulate host cellular pathways in order to gain entry into, multiply and move within, and eventually exit the host for a new infection cycle. in the past few years, substantial progress has been made in characterizing the host targets of viral and bacterial virulence factors, providing unique insights into basic plant cellular processes such as gene silencing, vesicle trafficking, hormone ...	2007	17884715
rumble in the nuclear jungle: compartmentalization, trafficking, and nuclear action of plant immune receptors.	plants and animals have evolved structurally related innate immune sensors inside cells to detect the presence of microbial molecules. an evolutionary ancient folding machinery becomes engaged for the synthesis of autorepressed receptor forms in both kingdoms. the receptors act as regulatory signal transduction switches and are activated upon direct or indirect perception of non-self structures. recent findings indicate that nucleo-cytoplasmic partitioning and nuclear activity is critical for th ...	2007	17853890
specific elements of the glyoxylate pathway play a significant role in the functional transition of the soybean cotyledon during seedling development.	the soybean (glycine max) cotyledon is a specialized tissue whose main function is to serve as a nutrient reserve that supplies the needs of the young plant throughout seedling development. during this process the cotyledons experience a functional transition to a mainly photosynthetic tissue. to identify at the genetic level the specific active elements that participate in the natural transition of the cotyledon from storage to photosynthetic activity, we studied the transcript abundance profil ...	2007	18093333
intraspecific variation in a generalist herbivore accounts for differential induction and impact of host plant defences.	plants and herbivores are thought to be engaged in a coevolutionary arms race: rising frequencies of plants with anti-herbivore defences exert pressure on herbivores to resist or circumvent these defences and vice versa. owing to its frequency-dependent character, the arms race hypothesis predicts that herbivores exhibit genetic variation for traits that determine how they deal with the defences of a given host plant phenotype. here, we show the existence of distinct variation within a single he ...	2007	18055390
intraspecific variation in a generalist herbivore accounts for differential induction and impact of host plant defences.	plants and herbivores are thought to be engaged in a coevolutionary arms race: rising frequencies of plants with anti-herbivore defences exert pressure on herbivores to resist or circumvent these defences and vice versa. owing to its frequency-dependent character, the arms race hypothesis predicts that herbivores exhibit genetic variation for traits that determine how they deal with the defences of a given host plant phenotype. here, we show the existence of distinct variation within a single he ...	2007	18055390
rna recognition by 3'-to-5' exonucleases: the substrate perspective.	the 3'-to-5' exonucleolytic decay and processing of a variety of rnas is an essential feature of rna metabolism in all cells. the 3'-5' exonucleases, and in particular the exosome, are involved in a large number of pathways from 3' processing of rrna, snrna and snorna, to decay of mrnas and mrna surveillance. the potent enzymes performing these reactions are regulated to prevent processing of inappropriate substrates whilst mature rna molecules exhibit several attributes that enable them to evad ...	2007	18078842
rna recognition by 3'-to-5' exonucleases: the substrate perspective.	the 3'-to-5' exonucleolytic decay and processing of a variety of rnas is an essential feature of rna metabolism in all cells. the 3'-5' exonucleases, and in particular the exosome, are involved in a large number of pathways from 3' processing of rrna, snrna and snorna, to decay of mrnas and mrna surveillance. the potent enzymes performing these reactions are regulated to prevent processing of inappropriate substrates whilst mature rna molecules exhibit several attributes that enable them to evad ...	2007	18078842
s-nitrosylation of peroxiredoxin ii e promotes peroxynitrite-mediated tyrosine nitration.	nitric oxide (no) is a free radical product of cell metabolism that plays diverse and important roles in the regulation of cellular function. s-nitrosylation is emerging as a specific and fundamental posttranslational protein modification for the transduction of no bioactivity, but very little is known about its physiological functions in plants. we investigated the molecular mechanism for s-nitrosylation of peroxiredoxin ii e (prxii e) from arabidopsis thaliana and found that this posttranslati ...	2007	18165327
systemic and intracellular responses to photooxidative stress in arabidopsis.	as the sun tracks daily through the sky from east to west, different parts of the canopy are exposed to high light (hl). the extent of and mechanisms by which a systemic acquired acclimation (saa) response might preacclimate shaded leaves that will be subsequently exposed to full sunlight is largely undefined. we investigated the role of an arabidopsis thaliana zinc finger transcription factor, zat10, in saa. zat10 overexpression resulted in enhanced tolerance to photoinhibitory light and exogen ...	2007	18156220
two distinct forms of m-locus protein kinase localize to the plasma membrane and interact directly with s-locus receptor kinase to transduce self-incompatibility signaling in brassica rapa.	many flowering plants possess systems of self-incompatibility (si) to prevent inbreeding. in brassica, si recognition is controlled by the multiallelic gene complex (s-haplotypes) at the s-locus, which encodes both the male determinant s-locus protein 11 (sp11/scr) and the female determinant s-receptor kinase (srk). upon self-pollination, the s-haplotype-specific interaction between the pollen-borne sp11 and the cognate stigmatic srk receptor induces si signaling in the stigmatic papilla cell an ...	2007	18065692
the jaz proteins link jasmonate perception with transcriptional changes.		2007	18165326
structural basis for regulation of bifunctional roles in replication initiator protein.	dna replication initiator protein repe stringently regulates f plasmid replication by its two distinct molecular association states. a predominant dimer functions as an autogenous repressor, whereas monomers act as replication initiators, and the dimer requires actions of the dnak molecular chaperone system for monomerization. the structure of the monomeric form is known, whereas the dimeric structure and structural details of the dimer-to-monomer conversion have been unclear. here we present th ...	2007	18000058
network inference, analysis, and modeling in systems biology.		2007	18055607
genome-wide annotation of remorins, a plant-specific protein family: evolutionary and functional perspectives.		2007	17984200
determination of the substrate binding mode to the active site iron of (s)-2-hydroxypropylphosphonic acid epoxidase using 17o-enriched substrates and substrate analogues.	(s)-2-hydroxypropylphosphonic acid epoxidase (hppe) is an o2-dependent, nonheme fe(ii)-containing oxidase that converts (s)-2-hydroxypropylphosphonic acid ((s)-hpp) to the regio- and enantiomerically specific epoxide, fosfomycin. use of (r)-2-hydroxypropylphosphonic acid ((r)-hpp) yields the 2-keto-adduct rather than the epoxide. here we report the chemical synthesis of a range of hpp analogues designed to probe the basis for this specificity. in past studies, no has been used as an o2 surrogate ...	2007	17927218
identification and mutational analysis of arabidopsis fls2 leucine-rich repeat domain residues that contribute to flagellin perception.	mutational, phylogenetic, and structural modeling approaches were combined to develop a general method to study leucine-rich repeat (lrr) domains and were used to identify residues within the arabidopsis thaliana flagellin-sensing2 (fls2) lrr that contribute to flagellin perception. fls2 is a transmembrane receptor kinase that binds bacterial flagellin or a flagellin-based flg22 peptide through a presumed physical interaction within the fls2 extracellular domain. double-ala scanning mutagenesis ...	2007	17933906
beta-1,3-glucanases: plasmodesmal gate keepers for intercellular communication.	plasmodesmata (pd), coaxial membranous channels that connect adjacent plant cells, are not static, but show a dynamic nature and can be opened or closed. these controlled changes in pd conductivity regulate plant symplasmic permeability and play a role both in development and defense processes. one of the mechanisms shown to produce these changes is the deposition and hydrolysis of callose by beta-1-3-synthase and glucanase, respectively. recently we have identified the first beta-1,3-glucanase ...	2007	19704615
genome mapping and molecular breeding of tomato.	the cultivated tomato, lycopersicon esculentum, is the second most consumed vegetable worldwide and a well-studied crop species in terms of genetics, genomics, and breeding. it is one of the earliest crop plants for which a genetic linkage map was constructed, and currently there are several molecular maps based on crosses between the cultivated and various wild species of tomato. the high-density molecular map, developed based on an l. esculentum x l. pennellii cross, includes more than 2200 ma ...	2007	18364989
a downstream mediator in the growth repression limb of the jasmonate pathway.	wounding plant tissues initiates large-scale changes in transcription coupled to growth arrest, allowing resource diversion for defense. these processes are mediated in large part by the potent lipid regulator jasmonic acid (ja). genes selected from a list of wound-inducible transcripts regulated by the jasmonate pathway were overexpressed in arabidopsis thaliana, and the transgenic plants were then assayed for sensitivity to methyl jasmonate (meja). when grown in the presence of meja, the roots ...	2007	17675405
functional associations by response overlap (faro), a functional genomics approach matching gene expression phenotypes.	the systematic comparison of transcriptional responses of organisms is a powerful tool in functional genomics. for example, mutants may be characterized by comparing their transcript profiles to those obtained in other experiments querying the effects on gene expression of many experimental factors including treatments, mutations and pathogen infections. similarly, drugs may be discovered by the relationship between the transcript profiles effectuated or impacted by a candidate drug and by the t ...	2007	17668056
phenotypic diversity and altered environmental plasticity in arabidopsis thaliana with reduced hsp90 levels.	the molecular chaperone hsp90 aids the maturation of a diverse but select set of metastable protein clients, many of which are key to a variety of signal transduction pathways. hsp90 function has been best investigated in animal and fungal systems, where inhibition of the chaperone has exceptionally diverse effects, ranging from reversing oncogenic transformation to preventing the acquisition of drug resistance. inhibition of hsp90 in the model plant arabidopsis thaliana uncovers novel morpholog ...	2007	17653275
the future for plants and plants for the future.		2007	17626611
the receptor-like kinase serk3/bak1 is a central regulator of innate immunity in plants.	in pathogen-associated molecular pattern (pamp)-triggered immunity (pti), plant cell surface receptors sense potential microbial pathogens by recognizing elicitors called pamps. although diverse pamps trigger pti through distinct receptors, the resulting intracellular responses overlap extensively. despite this, a common component(s) linking signal perception with transduction remains unknown. in this study, we identify somatic embryogenesis receptor kinase (serk)3/brassinosteroid-associated kin ...	2007	17626179
roles of iron in plant defence and fungal virulence.	iron is an essential component of various proteins and pigments for both plants and pathogenic fungi. however, redox cycling between the ferric and ferrous forms of iron can also catalyse the production of dangerous free radicals and iron homeostasis is therefore tightly regulated. our work has indicated that monocot plants challenged by pathogenic fungi redistribute cellular iron to the apoplast in a controlled manner to activate both intracellular and extracellular defences. in the apoplast, t ...	2007	19704628
regulation of plant innate immunity by sumo e3 ligase.	reversible posttranslational modification of proteins by the action of small ubiquitin-like modifier (sumo) peptide (sumoylation) has been known to participate in various biological processes in eukaryotes. however, much less is known about the role of sumoylation in plants. in our recent paper to which we write this addendum, we show that loss of siz1, a sumo e3 ligase, results in a highly increased sa-mediated defense signaling through a pad4-dependent pathway. this signaling leads to constitu ...	2007	19704670
natural variation among arabidopsis thaliana accessions for transcriptome response to exogenous salicylic acid.	little is known about how gene expression variation within a given species controls phenotypic variation under different treatments or environments. here, we surveyed the transcriptome response of seven diverse arabidopsis thaliana accessions in response to two treatments: the presence and absence of exogenously applied salicylic acid (sa), an important signaling molecule in plant defense. a factorial experiment was conducted with three biological replicates per accession with and without applic ...	2007	17630278
myc2 differentially modulates diverse jasmonate-dependent functions in arabidopsis.	the arabidopsis thaliana basic helix-loop-helix leu zipper transcription factor (tf) myc2/jin1 differentially regulates jasmonate (ja)-responsive pathogen defense (e.g., pdf1.2) and wound response (e.g., vsp) genes. in this study, genome-wide transcriptional profiling of wild type and mutant myc2/jin1 plants followed by functional analyses has revealed new roles for myc2 in the modulation of diverse ja functions. we found that myc2 negatively regulates trp and trp-derived secondary metabolism su ...	2007	17616737
genes misregulated in c. elegans deficient in dicer, rde-4, or rde-1 are enriched for innate immunity genes.	we describe the first microarray analysis of a whole animal containing a mutation in the dicer gene. we used adult caenorhabditis elegans and, to distinguish among different roles of dicer, we also performed microarray analyses of animals with mutations in rde-4 and rde-1, which are involved in silencing by sirna, but not mirna. surprisingly, we find that the x chromosome is greatly enriched for genes regulated by dicer. comparison of all three microarray data sets indicates the majority of dice ...	2007	17526642
rice wrky45 plays a crucial role in benzothiadiazole-inducible blast resistance.	benzothiadiazole (bth) is a so-called plant activator and protects plants from diseases by activating the salicylic acid (sa) signaling pathway. by microarray screening, we identified bth- and sa-inducible wrky transcription factor (tf) genes that were upregulated within 3 h after bth treatment. overexpression of one of them, wrky45, in rice (oryza sativa) markedly enhanced resistance to rice blast fungus. rna interference-mediated knockdown of wrky45 compromised bth-inducible resistance to blas ...	2007	17601827
inactivation of thioredoxin reductases reveals a complex interplay between thioredoxin and glutathione pathways in arabidopsis development.	nadph-dependent thioredoxin reductases (ntrs) are key regulatory enzymes determining the redox state of the thioredoxin system. the arabidopsis thaliana genome has two genes coding for ntrs (ntra and ntrb), both of which encode mitochondrial and cytosolic isoforms. surprisingly, plants of the ntra ntrb knockout mutant are viable and fertile, although with a wrinkled seed phenotype, slower plant growth, and pollen with reduced fitness. thus, in contrast with mammals, our data demonstrate that nei ...	2007	17586656
comprehensive transcriptome profiling in tomato reveals a role for glycosyltransferase in mi-mediated nematode resistance.	root-knot nematode (rkn; meloidogyne spp.) is a major crop pathogen worldwide. effective resistance exists for a few plant species, including that conditioned by mi in tomato (solanum lycopersicum). we interrogated the root transcriptome of the resistant (mi+) and susceptible (mi-) cultivars 'motelle' and 'moneymaker,' respectively, during a time-course infection by the mi-susceptible rkn species meloidogyne incognita and the mi-resistant species meloidogyne hapla. in the absence of rkn infectio ...	2007	17434994
recent advances in legume-microbe interactions: recognition, defense response, and symbiosis from a genomic perspective.		2007	17556521
a sub-proteome of arabidopsis thaliana mature stems trapped on concanavalin a is enriched in cell wall glycoside hydrolases.	n-glycosylated proteins were isolated from arabidopsis thaliana mature stems using affinity chromatography on concanavalin a sepharose, separated by 2d-electrophoresis and identified using nanohplc-ms/ms and maldi-tof ms. 102 glycoproteins were identified. 94% of these proteins were predicted by bioinformatics to be targeted to the secretory pathway and 87% of them were predicted to be localized in the cell wall or at the plasma membrane. 30% of these proteins belong to glycoside hydrolase (gh) ...	2007	17526915
jasmonates: an update on biosynthesis, signal transduction and action in plant stress response, growth and development.	jasmonates are ubiquitously occurring lipid-derived compounds with signal functions in plant responses to abiotic and biotic stresses, as well as in plant growth and development. jasmonic acid and its various metabolites are members of the oxylipin family. many of them alter gene expression positively or negatively in a regulatory network with synergistic and antagonistic effects in relation to other plant hormones such as salicylate, auxin, ethylene and abscisic acid.	2007	17513307
oviposition-induced changes in arabidopsis genome expression: anticipating your enemy?	plants have evolved exquisite ways to detect their enemies and are able to induce defenses responses tailored to their specific aggressors. insect eggs deposited on a leaf represent a future threat as larvae hatching from the egg will ultimately feed on the plant. although direct and indirect defenses towards oviposition have been documented, our knowledge of the molecular changes triggered by egg deposition is limited. using a whole-genome microarray, we recently analyzed the expression profile ...	2007	19704745
genetic interactions of tga transcription factors in the regulation of pathogenesis-related genes and disease resistance in arabidopsis.	tga transcription factors are implicated as regulators of pathogenesis-related (pr) genes because of their physical interaction with the known positive regulator, nonexpresser of pr gene1 (npr1). a triple-knockout mutant tga2-1 tga5-1 tga6-1 was shown previously to be defective in the induction of pr genes and systemic acquired resistance, confirming their role in disease resistance. however, the contributions of individual tga factors have been difficult to discern because of functional redunda ...	2007	17369431
experimental estimate of the abundance and effects of nearly neutral mutations in the rna virus phi 6.	although the frequency and effects of neutral and nearly neutral mutations are critical to evolutionary patterns and processes governed by genetic drift, the small effects of such mutations make them difficult to study empirically. here we present the results of a mutation-accumulation experiment designed to assess the frequencies of deleterious mutations with undetectable effects. we promoted the accumulation of spontaneous mutations by subjecting independent lineages of the rna virus 6 to repe ...	2007	17339206
integration of arabidopsis thaliana stress-related transcript profiles, promoter structures, and cell-specific expression.	arabidopsis thaliana transcript profiles indicate effects of abiotic and biotic stresses and tissue-specific and cell-specific gene expression. organizing these datasets could reveal the structure and mechanisms of responses and crosstalk between pathways, and in which cells the plants perceive, signal, respond to, and integrate environmental inputs.	2007	17408486
gap junctional proteins of animals: the innexin/pannexin superfamily.	there has been some controversy as to whether vertebrate pannexins are related to invertebrate innexins. using statistical, topological and conserved sequence motif analyses, we establish that these proteins belong to a single superfamily. we also demonstrate the occurrence of large homologues with c-terminal proline-rich domains that may have arisen by gene fusion events. phylogenetic analyses reveal the orthologous and paralogous relationships of these homologues to each other. we show that di ...	2007	17507077
the complete nucleotide sequence of the coffee (coffea arabica l.) chloroplast genome: organization and implications for biotechnology and phylogenetic relationships amongst angiosperms.	the chloroplast genome sequence of coffea arabica l., the first sequenced member of the fourth largest family of angiosperms, rubiaceae, is reported. the genome is 155 189 bp in length, including a pair of inverted repeats of 25,943 bp. of the 130 genes present, 112 are distinct and 18 are duplicated in the inverted repeat. the coding region comprises 79 protein genes, 29 transfer rna genes, four ribosomal rna genes and 18 genes containing introns (three with three exons). repeat analysis reveal ...	2007	17309688
calcium-dependent protein kinases regulate the production of reactive oxygen species by potato nadph oxidase.	reactive oxygen species (ros) are implicated in plant innate immunity. nadph oxidase (rboh; for respiratory burst oxidase homolog) plays a central role in the oxidative burst, and ef-hand motifs in the n terminus of this protein suggest possible regulation by ca(2+). however, regulatory mechanisms are largely unknown. we identified ser-82 and ser-97 in the n terminus of potato (solanum tuberosum) st rbohb as potential phosphorylation sites. an anti-phosphopeptide antibody (pser82) indicated that ...	2007	17400895
large-scale production of dsrna and sirna pools for rna interference utilizing bacteriophage phi6 rna-dependent rna polymerase.	the discovery of rna interference (rnai) has revolutionized biological research and has a huge potential for therapy. since small double-stranded rnas (dsrnas) are required for various rnai applications, there is a need for cost-effective methods for producing large quantities of high-quality dsrna. we present two novel, flexible virus-based systems for the efficient production of dsrna: (1) an in vitro system utilizing the combination of t7 rna polymerase and rna-dependent rna polymerase (rdrp) ...	2007	17237359
arabidopsis-insect interactions.		2007	22303231
the protein phosphatases and protein kinases of arabidopsis thaliana.		2007	22303230
high-throughput sequencing of arabidopsis micrornas: evidence for frequent birth and death of mirna genes.	in plants, micrornas (mirnas) comprise one of two classes of small rnas that function primarily as negative regulators at the posttranscriptional level. several mirna genes in the plant kingdom are ancient, with conservation extending between angiosperms and the mosses, whereas many others are more recently evolved. here, we use deep sequencing and computational methods to identify, profile and analyze non-conserved mirna genes in arabidopsis thaliana. 48 non-conserved mirna families, nearly all ...	2007	17299599
thioredoxin h5 is required for victorin sensitivity mediated by a cc-nbs-lrr gene in arabidopsis.	the fungus cochliobolus victoriae causes victoria blight of oats (avena sativa) and is pathogenic due to its production of victorin, which induces programmed cell death in sensitive plants. victorin sensitivity has been identified in arabidopsis thaliana and is conferred by the dominant gene locus orchestrating victorin effects1 (lov1), which encodes a coiled-coil-nucleotide binding site-leucine-rich repeat protein. we isolated 63 victorin-insensitive mutants, including 59 lov1 mutants and four ...	2007	17322408
oviposition by pierid butterflies triggers defense responses in arabidopsis.	insect eggs represent a threat for the plant as hatching larvae rapidly start with their feeding activity. using a whole-genome microarray, we studied the expression profile of arabidopsis (arabidopsis thaliana) leaves after oviposition by two pierid butterflies. for pieris brassicae, the deposition of egg batches changed the expression of hundreds of genes over a period of 3 d after oviposition. the transcript signature was similar to that observed during a hypersensitive response or in lesion- ...	2007	17142483
arabidopsis transcriptome changes in response to phloem-feeding silverleaf whitefly nymphs. similarities and distinctions in responses to aphids.	phloem-feeding pests cause extensive crop damage throughout the world, yet little is understood about how plants perceive and defend themselves from these threats. the silverleaf whitefly (slwf; bemisia tabaci type b) is a good model for studying phloem-feeding insect-plant interactions, as slwf nymphs cause little wounding and have a long, continuous interaction with the plant. using the affymetrix ath1 genechip to monitor the arabidopsis (arabidopsis thaliana) transcriptome, 700 transcripts we ...	2007	17189325
silverleaf whitefly induces salicylic acid defenses and suppresses effectual jasmonic acid defenses.	the basal defenses important in curtailing the development of the phloem-feeding silverleaf whitefly (bemisia tabaci type b; slwf) on arabidopsis (arabidopsis thaliana) were investigated. sentinel defense gene rnas were monitored in slwf-infested and control plants. salicylic acid (sa)-responsive gene transcripts accumulated locally (pr1, bgl2, pr5, sid2, eds5, pad4) and systemically (pr1, bgl2, pr5) during slwf nymph feeding. in contrast, jasmonic acid (ja)- and ethylene-dependent rnas (pdf1.2, ...	2007	17189328
natural genetic variation in arabidopsis: tools, traits and prospects for evolutionary ecology.	the model plant arabidopsis thaliana (arabidopsis) shows a wide range of genetic and trait variation among wild accessions. because of its unparalleled biological and genomic resources, the potential of arabidopsis for molecular genetic analysis of this natural variation has increased dramatically in recent years.	2007	17259228
ubiquitin, hormones and biotic stress in plants.	the covalent attachment of ubiquitin to a substrate protein changes its fate. notably, proteins typically tagged with a lysine48-linked polyubiquitin chain become substrates for degradation by the 26s proteasome. in recent years many experiments have been performed to characterize the proteins involved in the ubiquitylation process and to identify their substrates, in order to understand better the mechanisms that link specific protein degradation events to regulation of plant growth and develop ...	2007	17220175
in vivo participation of red chlorophyll catabolite reductase in chlorophyll breakdown.	a central reaction of chlorophyll breakdown, porphyrin ring opening of pheophorbide a to the primary fluorescent chlorophyll catabolite (pfcc), requires pheophorbide a oxygenase (pao) and red chlorophyll catabolite reductase (rccr), with red chlorophyll catabolite (rcc) as a presumably pao-bound intermediate. in subsequent steps, pfcc is converted to different fluorescent chlorophyll catabolites (fccs) and nonfluorescent chlorophyll catabolites (nccs). here, we show that rccr-deficient arabidops ...	2007	17237353
effects of freezing on membranes and proteins in lncap prostate tumor cells.	fourier transform infrared spectroscopy (ftir) and cryomicroscopy were used to define the process of cellular injury during freezing in lncap prostate tumor cells, at the molecular level. cell pellets were monitored during cooling at 2 degrees c/min while the ice nucleation temperature was varied between -3 and -10 degrees c. we show that the cells tend to dehydrate precipitously after nucleation unless intracellular ice formation occurs. the predicted incidence of intracellular ice formation ra ...	2006	17239814
effects of freezing on membranes and proteins in lncap prostate tumor cells.	fourier transform infrared spectroscopy (ftir) and cryomicroscopy were used to define the process of cellular injury during freezing in lncap prostate tumor cells, at the molecular level. cell pellets were monitored during cooling at 2 degrees c/min while the ice nucleation temperature was varied between -3 and -10 degrees c. we show that the cells tend to dehydrate precipitously after nucleation unless intracellular ice formation occurs. the predicted incidence of intracellular ice formation ra ...	2006	17239814
a genomic approach to identify regulatory nodes in the transcriptional network of systemic acquired resistance in plants.	many biological processes are controlled by intricate networks of transcriptional regulators. with the development of microarray technology, transcriptional changes can be examined at the whole-genome level. however, such analysis often lacks information on the hierarchical relationship between components of a given system. systemic acquired resistance (sar) is an inducible plant defense response involving a cascade of transcriptional events induced by salicylic acid through the transcription co ...	2006	17096590
a novel function for the cathepsin d inhibitor in tomato.	proteinaceous aspartic proteinase inhibitors are rare in nature and are described in only a few plant species. one of them corresponds to a family of cathepsin d inhibitors (cdis) described in potato (solanum tuberosum), involving up to 15 isoforms with a high sequence similarity. in this work, we describe a tomato (solanum lycopersicum) wound-inducible protein called jasmonic-induced protein 21 (jip21). sequence analysis of its cdna predicted a putative function as a cdi. the jip21 gene, whose ...	2006	17012408
plant response to bacterial pathogens. overlap between innate and gene-for-gene defense response.		2006	17093133
biosynthesis of fosfomycin, re-examination and re-confirmation of a unique fe(ii)- and nad(p)h-dependent epoxidation reaction.	(s)-2-hydroxypropylphosphonic acid epoxidase (hppe) catalyzes the epoxide ring closure of (s)-hpp to form fosfomycin, a clinically useful antibiotic. early investigation showed that its activity can be reconstituted with fe(ii), fmn, nadh, and o2 and identified hppe as a new type of mononuclear non-heme iron-dependent oxygenase involving high-valent iron-oxo species in the catalysis. however, a recent study showed that the zn(ii)-reconstituted hppe is active, and hppe exhibits modest affinity fo ...	2006	16981707
a high-resolution map of arabidopsis recombinant inbred lines by whole-genome exon array hybridization.	recombinant populations were the basis for mendel's first genetic experiments and continue to be key to the study of genes, heredity, and genetic variation today. genotyping several hundred thousand loci in a single assay by hybridizing genomic dna to oligonucleotide arrays provides a powerful technique to improve precision linkage mapping. the genotypes of two accessions of arabidopsis were compared by using a 400,000 feature exon-specific oligonucleotide array. around 16,000 single feature pol ...	2006	17044735
protein structure database search and evolutionary classification.	as more protein structures become available and structural genomics efforts provide structural models in a genome-wide strategy, there is a growing need for fast and accurate methods for discovering homologous proteins and evolutionary classifications of newly determined structures. we have developed 3d-blast, in part, to address these issues. 3d-blast is as fast as blast and calculates the statistical significance (e-value) of an alignment to indicate the reliability of the prediction. using th ...	2006	16885238
proteomic analysis of the eyespot of chlamydomonas reinhardtii provides novel insights into its components and tactic movements.	flagellate green algae have developed a visual system, the eyespot apparatus, which allows the cell to phototax. to further understand the molecular organization of the eyespot apparatus and the phototactic movement that is controlled by light and the circadian clock, a detailed understanding of all components of the eyespot apparatus is needed. we developed a procedure to purify the eyespot apparatus from the green model alga chlamydomonas reinhardtii. its proteomic analysis resulted in the ide ...	2006	16798888
a genome-wide survey of r gene polymorphisms in arabidopsis.	we used polymorphism analysis to study the evolutionary dynamics of 27 disease resistance (r) genes by resequencing the leucine-rich repeat (lrr) region in 96 arabidopsis thaliana accessions. we compared single nucleotide polymorphisms (snps) in these r genes to an empirical distribution of snp in the same sample based on 876 fragments selected to sample the entire genome. lrr regions are highly polymorphic for protein variants but not for synonymous changes, suggesting that they generate many a ...	2006	16798885
enigma variations for peptides and their transporters in higher plants.	two families of proteins that transport small peptides, the oligopeptide transporters (opts) and the peptide transporters (ptrs), have been recognized in eukaryotes. higher plants contain a far greater number of genes for these transporters than do other eukaryotes. this may be indicative of the relative importance of (oligo)peptides and their transport to plant growth and metabolism.	2006	16735405
systemic acquired resistance.	upon infection with necrotizing pathogens many plants develop an enhanced resistance to further pathogen attack also in the uninoculated organs. this type of enhanced resistance is referred to as systemic acquired resistance (sar). in the sar state, plants are primed (sensitized) to more quickly and more effectively activate defense responses the second time they encounter pathogen attack. since sar depends on the ability to access past experience, acquired disease resistance is a paradigm for t ...	2006	19521483
redox regulation of a novel plastid-targeted beta-amylase of arabidopsis.	nine genes of arabidopsis (arabidopsis thaliana) encode for beta-amylase isozymes. six members of the family are predicted to be extrachloroplastic isozymes and three contain predicted plastid transit peptides. among the latter, chloroplast-targeted beta-amylase (at4g17090) and thioredoxin-regulated beta-amylase (tr-bamy; at3g23920; this work) are experimentally demonstrated to be targeted to plastids. recombinant tr-bamy was catalytically active only when expressed as a mature protein, i.e. wit ...	2006	16698902
rna helicases and abiotic stress.	rna helicases function as molecular motors that rearrange rna secondary structure, potentially performing roles in any cellular process involving rna metabolism. although rna helicase association with a range of cellular functions is well documented, their importance in response to abiotic stress is only beginning to emerge. this review summarizes the available data on the expression, biochemistry and physiological function(s) of rna helicases regulated by abiotic stress. examples originate prim ...	2006	16790567
production of reactive oxygen species by plant nadph oxidases.		2006	16760484
metabolic and proteomic markers for oxidative stress. new tools for reactive oxygen species research.		2006	16760489
mitogen-activated protein kinases and reactive oxygen species signaling in plants.		2006	16760487
simple sequence repeat-based comparative genomics between brassica rapa and arabidopsis thaliana: the genetic origin of clubroot resistance.	an ssr-based linkage map was constructed in brassica rapa. it includes 113 ssr, 87 rflp, and 62 rapd markers. it consists of 10 linkage groups with a total distance of 1005.5 cm and an average distance of 3.7 cm. ssrs are distributed throughout the linkage groups at an average of 8.7 cm. synteny between b. rapa and a model plant, arabidopsis thaliana, was analyzed. a number of small genomic segments of a. thaliana were scattered throughout an entire b. rapa linkage map. this points out the compl ...	2006	16723420
conservation of intrinsic disorder in protein domains and families: ii. functions of conserved disorder.	regions of conserved disorder prediction (cdp) were found in protein domains from all available interpro member databases, although with varying frequency. these cdp regions were found in proteins from all kingdoms of life, including viruses. however, eukaryotes had 1 order of magnitude more proteins containing long disordered regions than did archaea and bacteria. sequence conservation in cdp regions varied, but was on average slightly lower than in regions of conserved order. in some cases, di ...	2006	16602696
mutations in the nb-arc domain of i-2 that impair atp hydrolysis cause autoactivation.	resistance (r) proteins in plants confer specificity to the innate immune system. most r proteins have a centrally located nb-arc (nucleotide-binding adaptor shared by apaf-1, r proteins, and ced-4) domain. for two tomato (lycopersicon esculentum) r proteins, i-2 and mi-1, we have previously shown that this domain acts as an atpase module that can hydrolyze atp in vitro. to investigate the role of nucleotide binding and hydrolysis for the function of i-2 in planta, specific mutations were introd ...	2006	16489136
extracellular atp induces the accumulation of superoxide via nadph oxidases in arabidopsis.	extracellular atp can serve as a signaling agent in animal cells, and, as suggested by recent reports, may also do so in plant cells. in animal cells it induces the production of reactive oxygen species through the mediation of nadph oxidase. similarly, here we report that in leaves of arabidopsis (arabidopsis thaliana), applied atp, but not amp or phosphate, induces the accumulation of superoxide (o2-) in a biphasic, dose-dependent manner, with a threshold at 500 nm atp. this effect did not req ...	2006	16428598
salicylic acid-independent enhanced disease susceptibility1 signaling in arabidopsis immunity and cell death is regulated by the monooxygenase fmo1 and the nudix hydrolase nudt7.	arabidopsis thaliana enhanced disease susceptibility1 (eds1) controls defense activation and programmed cell death conditioned by intracellular toll-related immune receptors that recognize specific pathogen effectors. eds1 is also needed for basal resistance to invasive pathogens by restricting the progression of disease. in both responses, eds1, assisted by its interacting partner, phytoalexin-deficient4 (pad4), regulates accumulation of the phenolic defense molecule salicylic acid (sa) and oth ...	2006	16531493
extratrain: a database of extragenic regions and transcriptional information in prokaryotic organisms.	transcriptional regulation processes are the principal mechanisms of adaptation in prokaryotes. in these processes, the regulatory proteins and the regulatory dna signals located in extragenic regions are the key elements involved. as all extragenic spaces are putative regulatory regions, extratrain covers all extragenic regions of available genomes and regulatory proteins from bacteria and archaea included in the uniprot database.	2006	16539733
natural products from plant-associated microorganisms: distribution, structural diversity, bioactivity, and implications of their occurrence.	a growing body of evidence suggests that plant-associated microorganisms, especially endophytic and rhizosphere bacteria and fungi, represent a huge and largely untapped resource of natural products with chemical structures that have been optimized by evolution for biological and ecological relevance. a diverse array of bioactive small molecule natural products has been encountered in these microorganisms. the structures of over 230 metabolites isolated and characterized from over 70 plant-assoc ...	2006	16562864
nitric oxide production in plants: facts and fictions.	there is now general agreement that nitric oxide (no) is an important and almost universal signal in plants. nevertheless, there are still many controversial observations and opinions on the importance and function of no in plants. partly, this may be due to the difficulties in detecting and even more in quantifying no. here, we summarize major pathways of no production in plants, and briefly discuss some methodical problems.	2006	19521475
ligand-induced endocytosis of the pattern recognition receptor fls2 in arabidopsis.	pattern-recognition receptors (prrs) trigger innate immune responses in animals and plants. one such prr is the flagellin receptor fls2 in arabidopsis. here, we demonstrate that a functional fusion of fls2 to the green fluorescent protein (gfp) resides in cell membranes of most tissues. stimulation with the flagellin epitope flg22 induces its transfer into intracellular mobile vesicles, followed by degradation. fls2 internalization depends on cytoskeleton and proteasome functions, and receptor a ...	2006	16510871
chemoenzymatic and template-directed synthesis of bioactive macrocyclic peptides.	non-ribosomally synthesized peptides have compelling biological activities ranging from antimicrobial to immunosuppressive and from cytostatic to antitumor. the broad spectrum of applications in modern medicine is reflected in the great structural diversity of these natural products. they contain unique building blocks, such as d-amino acids, fatty acids, sugar moieties, and heterocyclic elements, as well as halogenated, methylated, and formylated residues. in the past decades, significant progr ...	2006	16524919
transcriptome analysis of a cnidarian-dinoflagellate mutualism reveals complex modulation of host gene expression.	cnidarian-dinoflagellate intracellular symbioses are one of the most important mutualisms in the marine environment. they form the trophic and structural foundation of coral reef ecosystems, and have played a key role in the evolutionary radiation and biodiversity of cnidarian species. despite the prevalence of these symbioses, we still know very little about the molecular modulators that initiate, regulate, and maintain the interaction between these two different biological entities. in this st ...	2006	16472376
degradation of rna in bacteria: comparison of mrna and stable rna.	degradation of rna plays a central role in rna metabolism. in recent years, our knowledge of the mechanisms of rna degradation has increased considerably with discovery of the participating rnases and analysis of mutants affected in the various degradative pathways. among these processes, mrna decay and stable rna degradation generally have been considered distinct, and also separate from rna maturation. in this review, each of these processes is described, as it is currently understood in bacte ...	2006	16452296
plant nbs-lrr proteins in pathogen sensing and host defense.	plant proteins belonging to the nucleotide-binding site-leucine-rich repeat (nbs-lrr) family are used for pathogen detection. like the mammalian nod-lrr protein 'sensors' that detect intracellular conserved pathogen-associated molecular patterns, plant nbs-lrr proteins detect pathogen-associated proteins, most often the effector molecules of pathogens responsible for virulence. many virulence proteins are detected indirectly by plant nbs-lrr proteins from modifications the virulence proteins inf ...	2006	17110940
dissecting the wrky web of plant defense regulators.		2006	17121464
bacterial elicitation and evasion of plant innate immunity.	recent research on plant responses to bacterial attack has identified extracellular and intracellular host receptors that recognize conserved pathogen-associated molecular patterns and more specialized virulence proteins, respectively. these findings have shed light on our understanding of the molecular mechanisms by which bacteria elicit host defences and how pathogens have evolved to evade or suppress these defences.	2006	16936700
amplification generates modular diversity at an avirulence locus in the pathogen phytophthora.	the destructive late blight pathogen phytophthora infestans is notorious for its rapid adaptation to circumvent detection mediated by plant resistance (r) genes. we performed comparative genomic hybridization on microarrays (array-cgh) in a near genome-wide survey to identify genome rearrangements related to changes in virulence. six loci with copy number variation were found, one of which involves an amplification colocalizing with a previously identified locus that confers avirulence in combin ...	2006	16818726
plant nbs-lrr proteins: adaptable guards.	the majority of disease resistance genes in plants encode nucleotide-binding site leucine-rich repeat (nbs-lrr) proteins. this large family is encoded by hundreds of diverse genes per genome and can be subdivided into the functionally distinct tir-domain-containing (tnl) and cc-domain-containing (cnl) subfamilies. their precise role in recognition is unknown; however, they are thought to monitor the status of plant proteins that are targeted by pathogen effectors.	2006	16677430
the prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains.	ubiquitin (ub)-mediated signaling is one of the hallmarks of all eukaryotes. prokaryotic homologs of ub (this and moad) and e1 ligases have been studied in relation to sulfur incorporation reactions in thiamine and molybdenum/tungsten cofactor biosynthesis. however, there is no evidence for entire protein modification systems with ub-like proteins and deconjugation by deubiquitinating enzymes in prokaryotes. hence, the evolutionary assembly of the eukaryotic ub-signaling apparatus remains unclea ...	2006	16859499
evolutionary links between flih/yscl-like proteins from bacterial type iii secretion systems and second-stalk components of the fof1 and vacuolar atpases.	bacterial type iii secretion drives flagellar biosynthesis and mediates bacterial-eukaryotic interactions. type iii secretion is driven by an atpase that is homologous to the catalytic subunits of proton-translocating atpases, such as the f(o)f(1) atpase. here we use psi-blast searches to show that some noncalatytic components are also conserved between type iii secretion systems and proton-translocating atpases. in particular, we show that the flih/yscl-like proteins and the e subunits of vacuo ...	2006	16522800
coverage of whole proteome by structural genomics observed through protein homology modeling database.	we have been developing famsbase, a protein homology-modeling database of whole orfs predicted from genome sequences. the latest update of famsbase ( http://daisy.nagahama-i-bio.ac.jp/famsbase/ ), which is based on the protein three-dimensional (3d) structures released by november 2003, contains modeled 3d structures for 368,724 open reading frames (orfs) derived from genomes of 276 species, namely 17 archaebacterial, 130 eubacterial, 18 eukaryotic and 111 phage genomes. those 276 genomes are pr ...	2006	17146617
comparative genomics and evolution of the hsp90 family of genes across all kingdoms of organisms.	hsp90 proteins are essential molecular chaperones involved in signal transduction, cell cycle control, stress management, and folding, degradation, and transport of proteins. hsp90 proteins have been found in a variety of organisms suggesting that they are ancient and conserved. in this study we investigate the nuclear genomes of 32 species across all kingdoms of organisms, and all sequences available in genbank, and address the diversity, evolution, gene structure, conservation and nomenclature ...	2006	16780600
a database of bacterial lipoproteins (dolop) with functional assignments to predicted lipoproteins.	lipid modification of the n-terminal cys residue (n-acyl-s-diacylglyceryl-cys) has been found to be an essential, ubiquitous, and unique bacterial posttranslational modification. such a modification allows anchoring of even highly hydrophilic proteins to the membrane which carry out a variety of functions important for bacteria, including pathogenesis. hence, being able to identify such proteins is of great value. to this end, we have created a comprehensive database of bacterial lipoproteins, c ...	2006	16585737
psychrophilic microorganisms: challenges for life.	the ability of psychrophiles to survive and proliferate at low temperatures implies that they have overcome key barriers inherent to permanently cold environments. these challenges include: reduced enzyme activity; decreased membrane fluidity; altered transport of nutrients and waste products; decreased rates of transcription, translation and cell division; protein cold-denaturation; inappropriate protein folding; and intracellular ice formation. cold-adapted organisms have successfully evolved ...	2006	16585939
stimulus perception in bacterial signal-transducing histidine kinases.	two-component signal-transducing systems are ubiquitously distributed communication interfaces in bacteria. they consist of a histidine kinase that senses a specific environmental stimulus and a cognate response regulator that mediates the cellular response, mostly through differential expression of target genes. histidine kinases are typically transmembrane proteins harboring at least two domains: an input (or sensor) domain and a cytoplasmic transmitter (or kinase) domain. they can be identifi ...	2006	17158704
the evolution of two-component systems in bacteria reveals different strategies for niche adaptation.	two-component systems including histidine protein kinases represent the primary signal transduction paradigm in prokaryotic organisms. to understand how these systems adapt to allow organisms to detect niche-specific signals, we analyzed the phylogenetic distribution of nearly 5,000 histidine protein kinases from 207 sequenced prokaryotic genomes. we found that many genomes carry a large repertoire of recently evolved signaling genes, which may reflect selective pressure to adapt to new environm ...	2006	17083272
dispersal and regulation of an adaptive mutagenesis cassette in the bacteria domain.	recently, a multiple gene cassette with mutagenic translation synthesis activity was identified and shown to be under lexa regulation in several proteobacteria species. in this work, we have traced down instances of this multiple gene cassette across the bacteria domain. phylogenetic analyses show that this cassette has undergone several reorganizations since its inception in the actinobacteria, and that it has dispersed across the bacterial domain through a combination of vertical inheritance, ...	2006	16407325
surface display of proteins by gram-negative bacterial autotransporters.	expressing proteins of interest as fusions to proteins of the bacterial envelope is a powerful technique with many biotechnological and medical applications. autotransporters have recently emerged as a good tool for bacterial surface display. these proteins are composed of an n-terminal signal peptide, followed by a passenger domain and a translocator domain that mediates the outer membrane translocation of the passenger. the natural passenger domain of autotransporters can be replaced by hetero ...	2006	16787545
terminal reassortment drives the quantum evolution of type iii effectors in bacterial pathogens.	many bacterial pathogens employ a type iii secretion system to deliver type iii secreted effectors (t3ses) into host cells, where they interact directly with host substrates to modulate defense pathways and promote disease. this interaction creates intense selective pressures on these secreted effectors, necessitating rapid evolution to overcome host surveillance systems and defenses. using computational and evolutionary approaches, we have identified numerous mosaic and truncated t3ses among an ...	2006	17040127
cytological and other aspects of pathogenesis-related gene expression in tomato plants grown on a suppressive compost.	recent studies have shown that certain composts may trigger indirect defence mechanisms by sensitizing the plant to create an increased state of resistance, similar to systemic acquired resistance. in this study, the capacity of a disease-suppressive compost to alter the expression pattern of certain pathogenesis-related (pr) genes in the root system of tomato plants (solanum lycopersicum) provided the opportunity to study their cellular expression pattern and to investigate putative roles of th ...	2006	16877456
isolation and characterization of a novel lipase from a metagenomic library of tidal flat sediments: evidence for a new family of bacterial lipases.	we cloned lipg, which encoded a lipolytic enzyme, from a korean tidal flat metagenomic library. lipg was related to six putative lipases previously identified only in bacterial genome sequences. these enzymes comprise a new family. we partially characterized lipg, providing the first experimental data for a member of this family.	2006	16950897
overexpression of gberf confers alteration of ethylene-responsive gene expression and enhanced resistance to pseudomonas syringae in transgenic tobacco.	gberf belongs to the erf (ethylene responsive factor) family of transcription factors and regulates the gcc-box containing pathogen-related (pr) genes in the ethylene signal transduction pathway. to study the function of gberf in the process of biotic stress, transgenic tobacco plants expressing gberf were generated. overexpression of gberf did not change transgenic plant's phenotype and endogenous ethylene level. however, the expression profile of some ethylene-inducible gcc-box and non-gcc-box ...	2006	16809858