Title: "Computational Exploration of the Plant Kinome"
Speaker: Dr. Michael Gribskov, San Diego Supercomputer Center & Dept. of Biology, University of California, San Diego, CA
Place: SMITH 108; Tuesday, 4:30pm


Protein phosphorylation and dephosphorylation are fundamental to cellular regulation. These post-translational modifications, which are catalyzed by protein kinases and phosphatases, constitute a reversible molecular switch. In plants protein phosphorylation has been implicated in the control of most developmental events and environmental responses including governance of the cell cycle, transcriptional and translational regulation, control of carbon and nitrogen metabolism, regulation of growth and differentiation, and responses to abiotic and biotic environmental cues. The breadth of cellular processes regulated by protein kinases is reflected in the genomes of plants. Currently it is estimated that about 1000 genes encode proteins belonging to the eukaryotic protein kinase superfamily in the model organism Arabidopsis thaliana, and even more are found in rice. An additional 300 genes encode protein phosphatases. Furthermore, at least 50 members of two-component systems are predicted to be present in Arabidopsis (e.g., histidine kinases and response regulators). Because protein kinases and phosphatases control so many processes in plants, and occur in networks that unite different cellular processes, a genome wide approach is needed to make significant advances in discovering the roles of these enzymes in the regulation of plant function.

I will discuss computational methods used to identify the complete suite of protein kinases and phosphatases in Arabidopsis thaliana based on the complete genomic sequence, several approaches to inferring the function of protein kinases, and the creation of a data laboratory, PlantsP, for studying the functional genomics of phosphorylation in plants. We have been able to assign probable functions to many protein kinases based on intergenomic and motif based comparisons. Future challenges include incorporation of diverse experimental datatypes (such as microarray and protein-protein interaction data) into the database and the integration of the PlantsP database with other databases. A key issue in the development of the PlantsP is the question of how to obtain expert annotation of the various molecules. A prototype system allowing scientists to directly enter information into the database itself using computer assisted tools is online.

PlantsP is available at http://plantsP.sdsc.edu, and would not be possible without the participation of the members of the Functional Genomics of Plant Phosphorylation Project (NSF DBI-9975808 and DBI-0217312).

(This is a candidate for the Bioinformatics COALESCE hires in the School of Science. To meet with the candidate, please contact RW Doerge at doerge@purdue.edu)

See http://www.stat.purdue.edu/~doerge/BIOINFORM.D/SPRING04/sem.html for a full scheule of BIOINFORMATICS SEMINARS.