Arabidopsis 2010: Metabolomics: A Functional Genomics Tool for Deciphering Functions of Arabidopsis Genes in the Context of Metabolic and Regulatory Networks

Iowa State University, Ames IA

Investigators

Abstract

The functions of over 1/3 of the annotated protein-coding genes of the Arabidopsis genome are still unknown, and the annotation of an even larger portion of the genome is not sufficiently accurate for unambiguous assignment of function at the biochemical and physiological levels. This project will bring together a consortium of multidisciplinary collaborators to establish pipelines for generating metabolomics data-streams and to provide statistical and computational interpretation of the resulting integrated datasets. The goal is to develop metabolite-profiling capabilities that will enhance the research community's ability to formulate testable hypotheses concerning Arabidopsis gene functions. The consortium has developed metabolomic platforms that together detect approximately 1,800 metabolites, of which 900 are chemically defined. The aim of the project is to apply these established metabolite-profiling platforms to reveal changes in the metabolome associated with knockout mutations in up to 200 Arabidopsis genes of unknown function and compare these to similar mutants in 50 genes of known function. The consortium will disseminate these data via the existing multi-functional metabolomics database: www.plantmetabolomics.org. Enhancement of this database and associated statistical and visualization toolsets will enable researchers to formulate testable computational models of the metabolic network of Arabidopsis. The successful completion of these goals and integration with other NSF-sponsored functional genomics and cyber infrastructure developments will generate transformational resources for ultimately modeling the complex metabolism of Arabidopsis. Broader Impacts The project will develop new resources for the research community that will enhance the capability to globally profile genome expression at the metabolite level. These metabolite resources, in collaboration with other NSF-funded resource development projects, will enable researchers in the community to formulate credible, testable hypotheses concerning gene function. The project will foster the development of the science of metabolomics as a functional genomics tool through workshops, internships and organization of national and international meetings. The project will also develop new activities to enhance the impact of science education and training in the community, by conducting workshops for researchers at consortium labs and at international biological meetings. In addition, research internships will be offered to undergraduate students, eight of whom will have the opportunity to experience international science training in a European genomics laboratory. These research-based training internships will illustrate to the students the synergy that accompanies the integrated applications of chemistry, biochemistry, genetics, bioinformatics and computational sciences to solving complex biological problems.