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RESEARCH PAPERS ON SYSTEMS BIOLOGY/GENOMICS/BIOINFORMATICS

Arabidopsis Genes Involved in Acyl Lipid Metabolism. A 2003 Census of the Candidates, a Study of the Distribution of Expressed Sequence Tags in Organs, and a Web-Based Database¹

Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824

The genome of Arabidopsis has been searched for sequences of genes involved in acyl lipid metabolism. Over 600 encoded proteins have been identified, cataloged, and classified according to predicted function, subcellular location, and alternative splicing. At least one-third of these proteins were previously annotated as "unknown function" or with functions unrelated to acyl lipid metabolism; therefore, this study has improved the annotation of over 200 genes. In particular, annotation of the lipolytic enzyme group (at least 110 members total) has been improved by the critical examination of the biochemical literature and the sequences of the numerous proteins annotated as "lipases." In addition, expressed sequence tag (EST) data have been surveyed, and more than 3,700 ESTs associated with the genes were cataloged. Statistical analysis of the number of ESTs associated with specific cDNA libraries has allowed calculation of probabilities of differential expression between different organs. More than 130 genes have been identified with a statistical probability > 0.95 of preferential expression in seed, leaf, root, or flower. All the data are available as a Web-based database, the Arabidopsis Lipid Gene database (http://www.plantbiology.msu.edu/lipids/genesurvey/index.htm). The combination of the data of the Lipid Gene Catalog and the EST analysis can be used to gain insights into differential expression of gene family members and sets of pathway-specific genes, which in turn will guide studies to understand specific functions of individual genes.

¹ This work was supported by the Department of Energy (grant no. DE–FG02–87ER13729), by the National Science Foundation (grant no. MCB 98–17882), and by the Michigan Agricultural Experiment Station.

² Present address: Department of Biological Sciences, Proteomics Center, University of Missouri, Columbia MO 65211.

³ Present address: Department of Plant Biology, Ohio State University, Columbus OH 43210.

⁴ Present address: Instituto de la Grasa, Consejo Superior de Investigaciones Científicas, 41012 Sevilla, Spain.

⁵ Present address: Institute for Environment and Sustainability, European Union Joint Research Center, 21020 Ispra, Italy.

⁶ Present address: Department of Genetics, Harvard Medical School and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114.

^* Corresponding author; e-mail ohlrogge{at}msu.edu; fax 517–353–1926.

Received March 4, 2003; returned for revision March 25, 2003; accepted March 28, 2003.

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