Faculty
Thomas Eulgem
Assistant Professor of Plant Cell Biology (Ph.D., 1999, Max-Planck Institute)
Office: 3234A Genomics Building
Phone: (951) 827-7740
Fax: (951) 827-5155
Email: thomas.eulgem@ucr.edu
Areas of Expertise
- Plant Immune Biology
- Defense Signaling
- Gene Regulation
- Transcriptomics
- Functional Genomics
Background
Transcriptional Re-programming During Plant Immune Responses
Current Projects
- Identification of new regulatory elements controlling defense gene clusters
- Identification of synthetic elicitors of plant defense responses and their targets by chemical genomics
- Identification of defense promoter elements by enhancer trapping
- Functional characterization of EDM2, a novel transcriptional regulator mediating disease resistance in Arabidopsis thaliana
Current Lab Members
Selected Publications (Bibliography page)
Background
In 1999, I received a doctoral degree for research I did on the roles of WRKY transcription factors during plant immune responses in Imre Somssich’s lab (Klaus Hahlbrock’s department; Max-Planck-Institut fuer Zuechtungsforschung; Cologne, Germany). Funded by the Deutsche-Forschungsgemeinschaft and Max-Planck-Society, I continued from 2000 to 2003 as a Post-Doc in Jeff Dangl’s lab (University of North Carolina; Chapel Hill, USA) with research on the plant immune system. Using microarrays I performed a comprehensive study of global gene expression changes associated with disease resistance in Arabidopsis thaliana (Arabidopsis). In addition, I characterized and cloned the EDM2 locus of Arabidopsis, which encodes a novel immune regulator operating at an early step in defense signaling. In September 2003 I started as an Assistant Professor for Plant Cell Biology at UCR. My lab focuses on mechanisms controlling transcriptional reprogramming during plant immune responses.
Transcriptional Reprogramming During Plant Immune Responses
Plant immune responses are associated with extensive transcriptional reprogramming (Figure 1). However, molecular mechanisms that translate recognition of pathogens into defined transcriptional outputs are still poorly understood. The plant defense transcriptome is controlled by a complex signaling network consisting of two interconnected branches termed PTI (PAMP-triggered Immunity) and ETI (Effector-triggered Immunity). PTI is activated by receptor-mediated recognition of pathogen-associated molecular patterns (PAMPs), molecular signatures which are ubiquitously present in certain types of pathogens. Multiple pathogens transfer effector proteins into host cells that intercept PAMP triggered signals and thereby attenuate PTI. The remaining weak immune response, often called basal defense, is typically insufficient to prevent disease. Co-evolution of virulent pathogens with their hosts frequently resulted in the establishment of effector-triggered immunity (ETI). Of key importance for ETI are plant disease resistance (R) genes that mediate specific recognition of pathogen effectors and trigger strong disease resistance by boosting basal defense reactions and activation of programmed death of plant cells at pathogen infection sites (hypersensitive reaction, HR).
Current Projects
1) Identification of new regulatory elements controlling defense gene clusters
We are using microarray data to define clusters of genes coordinately responding to Peronospora recognition and, hence, likely to be controlled by common regulatory mechanisms (Fig. 2A). Conserved sequence motifs we identified in the promoters of such co-regulated genes may constitute cis-elements responsible for their coordinated activity. We proved that some of these motifs interact with nuclear-localized proteins and act as defense-associated cis-elements in reporter gene assays (Fig. 2B). Furthermore, we identified putative transcription factors (TFs) interacting with these elements by a proteomics-based approach. Their functional connection to plant immune responses is currently being studied. In addition, we are dissecting the promoters of members of the LURP cluster, a set of tightly co-regulated defense genes, by 5’ deletion analyses using promoter reporter fusions. Short regions within these promoters that bear strong pathogen-response elements have been identified and are currently being further examined (Fig. 2C & D). Moreover, we found that the transcription factor AtWRKY70 contributes to the re gu lation of LURP genes (Knoth et al., 2007). Defense promoter elements and their cognate TFs identified in this study will serve as starting points to design new strategies to improve disease resistance in crops.
2) Identification of synthetic elicitors of plant defense responses and their targets by chemical genomics
Using chemical genomics resources of the CEPCEB we are screening for drug-like organic compounds that activate LURP-promoter/reporter fusions in transgenic Arabidopsis seedlings. The CEPCEB is equipped for high throughput chemical screens, providing libraries representing ~50,000 diverse organic compounds and robotic equipment to deliver them to screening plates. Chemical genomics offers several advantages over classical genetics and can facilitate the discovery of biological pathway components that cannot be identified by conventional approaches. For example, due to functional redundancy the in vivo roles of many structurally-related proteins are difficult to study by loss-of-function mutations. Chemical genomics can lead to the identification of compounds that target multiple members of protein families and trigger clear phenotypes by simultaneously altering their function. In addition, loss-of-function mutations in genes required for plant development or other essential physiological processes may be lethal, while many gain-of-function mutations have detrimental pleiotropic effects. Bioactive chemicals, however, can be administered in a highly controlled manner (e.g. timing, concentration) minimizing undesired effects. Finally, such compounds can be applied to a wide variety of plant species to examine and manipulate homologous biological mechanisms.
Specific “inducers” of LURP genes are likely to interfere with defense signaling components and can be used instead of pathogens to activate plant immune responses. Our goal is to identify a suite of molecular probes that can be used to target defined nodes and branches of the defense network controlling transcriptional reprogramming. Such synthetic elicitors will be powerful tools for the fine dissection of defense mechanisms, as they are likely to trigger strong, uniform and synchronous defense responses in plants and cell cultures. Protein targets of these synthetic elicitors will be identified by genetic screens for mutants with altered sensitivity to the respective chemical as well as biochemical approaches. In addition, synthetic defense elicitors may allow the development of novel types of pesticides specifically tailored to fight plant diseases by enhancing the plant’s inherent defense capabilities. This project is partially performed in collaboration with the labs of Dr. Thomas Girke and Dr. Isgouhi Kaloshian (both UCR).
3) Identification of defense promoter elements by enhancer trapping
Enhancer trapping is based on random insertions of core-promoter-reporter fusions into genomes. Core promoters are insufficient to mediate gene expression. Only enhancer traps inserted in the vicinity of active enhancers can exhibit reporter gene activity (Fig. 4A). Screening ~11,000 Arabidopsis enhancer trap lines (Campisi et al., 1999, Plant Journal, 17: 699) we identified multiple individuals that exhibit highly localized GUS reporter gene activity in response to Peronospora infections (Fig. 4B). These lines are being analyzed to identify and characterize the respective enhancers. One goal of this project is to identify strictly pathogen-responsive enhancers and to use them to drive defense gene expression in crop plants to improve disease resistance. In addition, we will perform experiments to identify transcription factors interacting with such enhancers and to elucidate their roles in plant defense.
4) Functional characterization of EDM2, a novel transcriptional regulator mediating disease resistance in Arabidopsis thaliana
EDM2(enhanced downy mildew 2) was identified in a mutant screen for loci required for RPP7 function and isolated by map-based cloning (Eulgem et al., 2007). EDM2 mutations are recessive, block an early defense signaling step, fully abolish RPP7-resistance, and reduce RPP7 transcript levels, strongly suggesting that EDM2 is a positive regulator of RPP7 expression. EDM2 is structurally unrelated to known components of the plant immune system, and bears typical features of transcriptional regulators, but does not belong to any previously characterized classes of TFs. Motifs conserved between EDM2 and EDM2-like proteins (ELPs) from Arabidopsis and rice define a novel plant specific protein family (Fig. 5A) . Our main goal is to understand the molecular roles of EDM2 in disease resistance and its causal connection to RPP7 function. We found that EDM2 is nuclear-localized and activates transcription. Furthermore, we identified by yeast two-hybrid screening multiple chromatin associated proteins and transcriptional regulators that specifically interact with EDM2, suggesting that EDM2 is a component of a transcriptional co-regulator complex. As we found by microarray and RT-PCR analyses, several other R-like genes (besides RPP7) are EDM2-dependent, indicating that EDM2 has additional roles in the plant immune system. Moreover, we identified a putative binding site of EDM2 complexes in the promoters of RPP7 and other EDM2 target genes. Mechanistic details of EDM2-dependent R gene activation, their connection to defense signaling and their significance in disease resistance are being examined. EDM2 appears to be the first TF implicated in controlling R gene activity. We propose that this novel regulator mediates disease resistance by fine-tuning the transcription of RPP7 and additional R genes (Fig. 5B).
Current Lab Members:
YU-HUNG (LINDA) WEI
Junior Specialist
M.Sc. University of Cape Town, South Africa (2002)
Analysis of EDM2/R-promoter interactions and roles of EDM2 in RPP7-resistance.
E-mail: lindaw@ucr.edu
DR. ALEX EVRARD
Post-Doc
M.S. Agro Montpellier, France (1999)
Ph.D.: Agro Montpellier, France (2003)
Analysis of conserved promoter motifs of EURP and LURP genes and cloning of their cognate TFs.
E-mail: aevrard@ucr.edu
DR. TOKUJI TSUCHIYA
Post-Doc
MS Chiba University University, Japan (2000)
Ph.D.: Chiba University, Japan (2003)
Identification of EDM2 complex components. Analysis of molecular functions and regulation of EDM2.
E-mail: tokujit@ucr.edu
COLLEEN KNOTH
Graduate student
B.S. Cal Poly Pomona (2003)
Functional analysis of LURP genes and their regulation by molecular genetics and chemical genomics. Supported by a pre-doctoral fellowship from the NSF-funded ChemGen IGERT program (DGE 0504249). Co-supervised by Dr. Thomas Girke (CEPCEB, UCR)
E-mail: colleen.knoth@email.ucr.edu
Web: http://cepceb.ucr.edu/IGERT/IGERT_
Students2007.htm#knoth
MELINDA SALUS
Graduate student
B.S. University of Wisconsin at Madison (2000)
Identification of synthetic defense elicitors by chemical genomics.
E-mail: msalu001@ucr.edu
MERCEDES SCHROEDER
Graduate student
B.S. Tulane University (2001)
Enhancer trap screens to identify pathogen-responsive enhancers
E-mail: msch001@ucr.edu
Ndatimana
THEO NDATIMANA
Undergraduate Student
Statistical analyses of conserved promoter motifs; microarray analyses
E-mail: tndat001@student.ucr.edu
MINDY NGYEN
Undergraduate student
Enhancer trap screens to identify pathogen-responsive enhancers
E-mail: mnguy039@student.ucr.edu
Selected Publications (Bibliography page)