Arabidopsis 2010: Expression Profiling of Plant Disease Resistance Pathways

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The goal of this project is to determine the function of key transcription factors (TFs) in the plant Arabidopsis defense-response signaling network (see http://ausubellab. mgh.harvard.edu/nsf2010/ for the current list of transcription factors under study). TFs are key switches that control plant defense responses against pathogens, and expression profiling using Gene Chips (microarrays) is the most powerful genomics approach available for high through-put analysis of transcriptional events. Profiling will identify candidate TFs in understudied defense pathways, including those induced by so-called "PAMP" molecules that are commonly associated with pathogens of plants as well as animals. We will evaluate the TF mutants for their impact on disease resistance to find whether disrupting the genes and their functions will affect any defense response. The TFs identified in this way will be linked to green fluorescent protein to mark and sort the cells expressing the TF genes . Transcriptional profiling will be conducted in these cells to identify genes whose expression patterns mirror those of the TFs (i.e., cohort transcriptomes). The TFs will also be modified so their transport into the nucleus, where they function, can be controlled experimentally and their target genes will be identified. Collectively, these experiments will provide the spatial, temporal, and hierarchical information about defense-related transcriptional events which is currently lacking, but needed to build a model of the transcriptional network of interacting defense pathways. Data obtained in this project will be deposited in IMDS (integrated microarray data system) (http://ausubellab.mgh.harvard.edu/imds) and made available to the public in a timely manner. IMDS is a public web-accessible microarray database created by this project to facilitate storage, retrieval and analysis of microarray data sets. It stores experimental descriptions, raw microarray data and sets of normalized data. The data in IMDS will be maintained beyond the lifetime of the 2010 award by exporting it to the NCBI Gene Expression Omnibus and the Arabidopsis Information Resource. The significance of this multi-investigator effort to the overall 2010 project objectives is several-fold. Defense responses in plants involve global changes in gene expression (10% of the genome). Therefore, identifying TFs holds the key for understanding the mechanism of defense. Also, an in-depth analysis of large gene sets requires the efforts of several laboratories and coordination afforded by this project avoids duplication of efforts and cuts costs. Finally, each new profiling experiment added to IMDS will enhance the ability of researchers in the scientific community to design experiments that will further elucidate key features of the plant defense response. This project provides a training environment for undergraduates, doctoral students, and postdocs. Participants will learn not only classical genetic and phytopathology methods, but also cutting-edge genomics and bioinformatics technologies. A key training component is the project's annual workshop, where students and postdocs present their research in a semi-formal setting. Undergraduate training in genomics and bioinformatics is also a significant aspect of this project.