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Search Results: 1 - 10 of 30960 matches for " Thomas Eulgem "
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Dissecting the WRKY Web of Plant Defense Regulators
Thomas Eulgem
PLOS Pathogens , 2006, DOI: 10.1371/journal.ppat.0020126
Microarray analysis of plant defenses
Thomas Eulgem
Genome Biology , 2001, DOI: 10.1186/gb-2000-2-1-reports0001
Abstract: Gene expression changes were monitored using a cDNA microarray with 2,375 Arabidopsis thaliana ESTs predominantly representing putative defense-associated and regulatory genes. Arabidopsis plants were either treated with SA, ET or MJ or infected with the fungal pathogen Alternaria brassicola, which is recognized by the plant and triggers defense reactions. Significant changes in expression were detected for 705 genes in response to one or more of the treatments. Some genes responding to the treatments encode potential defense regulators such as transcription factors or protein kinases. Other functional classes of responsive genes comprise previously described antimicrobial genes or genes potentially involved in the oxidative burst and hypersensitive programmed cell death - two early defense reactions. Many genes affected have unknown functions.Whereas a substantial fraction of the gene expression changes were specific for individual treatments, many genes were up- or downregulated in response to more than one defense condition. Strikingly, 55 genes were co-induced by SA and MJ, which were previously shown to act antagonistically. Expression of 28 genes was co-repressed by both treatments. Similar overlaps were observed between the responses to all four treatments. These results suggest a high degree of cross-talk between the signaling pathways specified by the individual treatments.Arabidopsis defense gene regulation cluster analysis data for this study can be downloaded and Supplementary data to PNAS 2000, 97:11655-11660 is available.The data presented appear reliable, as only genes that showed consistent expression behavior between two independent replicate array experiments for each treatment were included in the final data set. The identification of genes that are co-induced or co-repressed by more than one treatment is significant and may serve as a starting point to study interactions between different defense signaling pathways. Given the strong emphasis in t
Eukaryotic transcription factors
Thomas Eulgem
Genome Biology , 2001, DOI: 10.1186/gb-2001-2-2-reports0004
Abstract: Within the Arabidopsis genome, 1,533 genes were found to encode members of known transcription factor families, 45% of which are from families specific for plants. The fraction of transcription factor genes among all genes is slightly higher in Arabidopsis (5.9%) compared with Drosophila, C. elegans and yeast (4.5, 3.5 and 3.5%, respectively). A variety of prominent transcription factor families are present in all four species, including Myb, basic helix-loop-helix, basic leucine zipper, C2H2 zinc finger and homeodomain transcription factors. Except for the conserved DNA-binding domains, however, there are no significant similarities between members of the same transcription factor family from different kingdoms.Three types of evolutionary process appear to be mainly responsible for the observed differences in transcription factor complements: the generation of completely novel families; the specific amplification of families common to all three eukaryotic kingdoms; and domain shuffling, leading to new combinations of common transcription factor domains. As well as several small families, the large families of AP2/EREBP, NAC and WRKY transcription factors, consisting of 144, 109 and 72 members, respectively, are found exclusively in plants. In contrast, nuclear hormone receptors and GAL4-like C6 zinc finger proteins, which are strongly represented in animals and yeast, respectively, appear to be absent from plants. In plants, the Myb superfamily is strongly amplified, comprising 190 members. These regulators, which constitute the largest class of plant transcription factors, are only weakly represented in the other eukaryotic kingdoms. Exon shuffling has led to transcription factors unique to plants that contain both homeodomains and leucine zippers. In addition to these HD-ZIP proteins, leucine zippers can be found in the plant-specific WRKY factors as well as in basic leucine zippers, which are present in all three eukaryotic kingdoms.Supplementary data to Science
Clock-controlled genes in Arabidopsis
Thomas Eulgem
Genome Biology , 2001, DOI: 10.1186/gb-2001-2-2-reports0005
Abstract: Of roughly 8,200 different Arabidopsis genes on the chip that was used, 453 were found to be clock-regulated. These cycling genes were grouped into phase clusters according to their peak expression time. Many simultaneously cycling genes could be assigned to functional groups on the basis of their known or predicted function. For instance, 22 genes encoding proteins implicated in various photosynthetic reactions were found to be co-regulated. Their expressionpeaks around midday, when photosynthetic activity is highest. Furthermore, 23 genes, encoding enzymes of the phenylpropanoid biosynthetic pathway, simultaneously peak before dawn. The gene encoding the Myb transcription factor PAP1 is co-regulated with this cluster. Overexpression of this transcription factor had previously been shown to upregulate several phenylpropanoid biosynthetic genes. The authors suggest that PAP1 may act as a master regulator of clock-controlled transcription of these genes. Other interesting clusters comprise co-regulated genes potentially involved in chilling resistance, sugar catabolism, sugar transport, sugar storage, starch mobilization, and nitrogen and sulfur assimilation, as well as developmental processes such as flowering and cell elongation.Using the AlignACE program, a nine-nucleotide motif, called 'evening element', was found to be strictly conserved within promoters of genes peaking towards the end of the subjective day. The promoter of the 'evening-specific' gene CCR2 contains four copies of this motif. The CCR2 promoter was functionally dissected in transgenic Arabidopsis plants containing luciferase reporter constructs. By deletion and mutational analysis the evening element was shown to be required for phase-specific reporter gene expression.Supplementary data to Science 2000, 290:2110-2113 are freely available.Harmer et al. present a comprehensive description of the circadian clock-controlled transcriptome in Arabidopsis and relate their findings to a variety of known
Plant-pathogen interactions
Thomas Eulgem
Genome Biology , 2000, DOI: 10.1186/gb-2000-1-2-reports0062
Abstract: Using cDNA amplified fragment length polymorphism (AFLP), Durrant et al. have for the first time comprehensively examined early gene expression changes, which are independent of the oxidative burst, induced during a race-specific plant pathogen interaction. By choosing a time window that covers the first 30 minutes after pathogen recognition, they focused exclusively on early response genes, some of which may encode regulators of successive defense responses, including the oxidative burst.The tomato R gene Cf9 confers resistance to races of the fungal pathogen Cladosporium fulvum expressing the Avr9 avirulence gene. A cDNA-AFLP-based RNA fingerprinting analysis was applied to cultured tobacco cells that contain Cf9 as a transgene, 30 minutes after treatment with recombinant Avr9 protein. Based on non-selective amplification of cDNA fragments representing cellular mRNAs, this method allows gene expression profiling which requires, in contrast to cDNA microarrays, no prior assumptions about the set of genes that might be affected.Using 512 primer combinations, approximately 30,000 AFLP fragments were visualized. The authors estimate that this may represent more than 75% of all tobacco transcript species. Differential expression in response to Avr9 could be observed for 290 of these fragments (in 273 cases expression was upregulated). The genes represented by these fragments were named ACRE (Avr9/Cf9 rapidly elicited) genes. Application of a specific inhibitor of the oxidative burst, diphenyleneiodonium, showed that only 4% of the early expression changes are dependent on AOS. Furthermore, Avr9-induced expression seems, at least in some cases, to be independent of de novo protein biosynthesis, as determined by experiments with the translation inhibitor cycloheximide. Only 42 ACREs show similarity to known genes. A subset of these encodes potential regulatory proteins, such as protein kinases, protein phosphatases and transcription factors including EREBPs (ethylene res
Plant wound responses
Thomas Eulgem
Genome Biology , 2000, DOI: 10.1186/gb-2000-1-2-reports0061
Abstract: A time-course study of mechanically wounded Arabidopsis leaves revealed groups of genes with similar expression behavior. Among the earliest responses was the activation of various genes implicated in pathogen resistance, including PR-1, PR-2 and PR-5, as well as two genes encoding mitogen-activated protein kinases (MPK3 and MEKK1). The early activation of a set of genes with a potential function in defense could reflect the need to prevent opportunistic pathogen infections at open wounds. Another group of co-regulated genes includes two genes encoding enzymes involved in JA biosynthesis (LOX2 and AOS). Interestingly, the temporal expression pattern of these genes coincides with the kinetics of JA accumulation after wounding, suggesting a causal relationship between LOX2 and AOS transcript accumulation and JA biosynthesis.Using the JA-insensitive Arabidopsis mutant coi1, the authors could categorize wound-responsive genes into two basic classes: a class of COI1-dependent genes for which activation, or repression, by wounding appears to be mediated by JA; and a class of COI1-independent genes whose wound-responsiveness appears not to be mediated by JA. To identify a potential signal involved in the regulation of the COI1-independent group of genes, ethylene was investigated. Surprisingly, expression of none of the wound-responsive genes analyzed in this study was substantially altered in the ethylene-insensitive ein2-1 mutant as compared to wild-type plants. Thus, ethylene plays no essential role in the regulation of the large number of wound-responsive genes examined in this study.Dehydration of the leaves was found to induce expression of many wound-inducible genes, including 13 COI1-independent genes. Hence, water stress as a result of tissue damage might constitute a distinct stimulus responsible for the activation of some genes after wounding. Only a subset of genes activated by artificial wounding was activated in response to insect feeding by larvae of the cab
Co-option of EDM2 to distinct regulatory modules in Arabidopsis thaliana development
Tokuji Tsuchiya, Thomas Eulgem
BMC Plant Biology , 2010, DOI: 10.1186/1471-2229-10-203
Abstract: Here we report that EDM2 affects additional developmental processes which include the formation of leaf pavement cells and leaf expansion as well as the development of morphological features related to vegetative phase change. EDM2 has a promoting effect of each of these processes. While WNK8 seems not to exhibit any vegetative phase change-related function, it has a promoting effect on the development of leaf pavement cells and leaf expansion. Microarray data further support regulatory interactions between WNK8 and EDM2. The fact that the effects of EDM2 and WNK8 on leaf pavement cell formation and leaf expansion are co-directional, while WNK8 counteracts the promoting effect of EDM2 on floral transition, is surprising and suggests that WNK8 can modulate the activity of EDM2.We propose that EDM2 has been co-opted to distinct regulatory modules controlling a set of different processes in plant immunity and development. WNK8 appears to modulate some functions of EDM2.The defense regulator EDM (Enhanced Downy Mildew) 2 was previously shown in Col (Columbia) accessions of Arabidopsis thaliana (Arabidopsis) to be specifically required for immunity mediated by the disease resistance (R)-gene RPP (Resistance to Peronospora parasitica) 7 against the Hiks1 isolate of the pathogenic oomycete Hyaloperonospora arabidopsidis (formerly Peronospora parasitica; Hpa) [1]. Unlike many other plant defense mechanisms RPP7-mediated immunity is independent from the defense hormone salicylic acid. Furthermore, RPP7-mediated immunity appears thus far to be the only defense mechanism that EDM2 is involved in, as no other EDM2-dependent R-gene functions have been reported yet. EDM2 also does not contribute to basal defense, a weaker non-specific plant immune response [2]. Thus, the role of EDM2 in plant defense seems to be restricted to a single or a limited number of defense pathways. The EDM2 protein is nuclear-localized and bears typical features of transcription factors and epigenetic r
FORCA, a promoter element that responds to crosstalk between defense and light signaling
Alexandre Evrard, Theogene Ndatimana, Thomas Eulgem
BMC Plant Biology , 2009, DOI: 10.1186/1471-2229-9-2
Abstract: FORCA is a hexameric promoter motif that is conserved in clusters of Arabidopsis genes co-expressed in response to fungal or oomycete pathogens as well as defined light treatments. FORCA is generally more frequently present in Arabidopsis promoter regions than statistically expected. It constitutively interacts in a DNA-sequence specific manner with nuclear Arabidopsis proteins. These interactions are suppressed by defense-related stimuli and enhanced by prolonged exposure to constant light. Furthermore FORCA mediates constitutive reporter gene expression in transiently transformed Nicotiana benthamiana leaves as well as in stably transformed Arabidopsis plants. Its responsiveness to defense-stimuli is modulated by the duration of light exposure. In plants grown under normal light conditions or constant darkness defense-related stimuli result in suppression of FORCA-mediated reporter gene expression, while in plants grown under constant light exposure, defense-induction results in enhanced FORCA-mediated expression. In addition, we found plants subjected to constant light exposure to exhibit reduced susceptibility to virulent H. parasitica.We propose that FORCA is a regulatory cis-element that is present in a wide variety of Arabidopsis promoters. It integrates light- and defense-related signals and participates in adjusting the transcriptome to changes in environmental conditions.Molecular recognition of pathogenic microorganisms triggers in plants comprehensive transcriptional reprogramming. A network of defense-regulators transduces information about the attacking microbe into appropriate transcriptional responses. Two functionally distinct classes of pathogen molecules are known to elicit plant immune responses [1-3]. Receptor-mediated recognition of pathogen/microbe associated molecular patterns (PAMPs/MAMPs) activates PAMP-triggered immunity (PTI), while recognition of pathogen effectors by plant disease resistance (R) proteins leads to effector-triggered immu
NSD1 Mitigates Caspase-1 Activation by Listeriolysin O in Macrophages
Olivia S. Sakhon, Kaitlin A. Victor, Anthony Choy, Tokuji Tsuchiya, Thomas Eulgem, Joao H. F. Pedra
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0075911
Abstract: Mammals and plants share pathogen-sensing systems named nod-like receptors (NLRs). Some NLRs form the inflammasome, a protein scaffold that regulates the secretion of interleukin (IL)-1β and IL-18 by cleaving catalytically inactive substrates into mature cytokines. Here, we show an immune conservation between plant and mammalian NLRs and demonstrate that the murine nuclear receptor binding SET domain protein 1 (NSD1), a protein that bears similarity to the NLR regulator enhanced downy mildew 2 (EDM2) in Arabidopsis, diminishes caspase-1 activity during extracellular stimulation with Listeria monocytogenes listeriolysin O (LLO). EDM2 is known to regulate plant developmental processes, whereas NSD1 is associated with developmental disorders. We observed that NSD1 neither affects nuclear factor (NF)-κB signaling nor regulates NLRP3 inflammasome gene expression at the chromatin, transcriptional or translational level during LLO stimulation of macrophages. Silencing of Nsd1 followed by LLO stimulation led to increased caspase-1 activation, enhanced post-translational maturation of IL-1β and IL-18 and elevated pyroptosis, a form of cell death associated with inflammation. Furthermore, treatment of macrophages with LLOW492A, which lacks hemolytic activity due to a tryptophan to alanine substitution in the undecapeptide motif, indicates the importance of functional LLO for NSD1 regulation of the NLRP3 inflammasome. Taken together, our results indicate that NLR signaling in plants may be used for gene discovery in mammals.
Global Chemical Leasing Award 2010  [PDF]
Thomas Jakl
Technology and Investment (TI) , 2011, DOI: 10.4236/ti.2011.21003
Abstract: The Global Chemical Leasing Award was presented for the first time in March 2010 to organizations, companies and individuals for their outstanding efforts to enhance the visibility of Chemical Leasing around the world and reward successful Chemical Leasing initiatives and implementation. Chemical Leasing is the new business model in the field of sound use of chemicals, initiated and subsidized by the Austrian Federal Ministry for Agriculture, Forestry, the Environment and Water Management and jointly promoted with UNIDO. The decisive new aspect of this business model, which distinguishes itself from the traditional supplier-user relation, is to make the service performed by the chemical substance the basis of payment for the business operation, e.g. according to cleaned area, treated number of pieces, or performed hours of operation (= unit of payment). In this way an efficient use of chemicals is in the interest of all parties involved. The award was jointly organized by UNIDO and the Austrian Federal Ministry for Agriculture, Forestry, the Environment and Water Management. Organizations, companies and individuals worldwide were able to take part in the competition. The cases of the winners are described in detail and show the applicability of Chemical Leasing to the different industrial processes. Among these are water clarification and oil dehydration in Colombia, mineral water and beverage production in Serbia, oil & gas exploration and production and specifically deep gas field development projects in different places, industrial cleaning with solvents in Austria and textile dyeing in India.
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