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 Database

Abstract

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 Ͼ 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.Acyl lipids can be defined as fatty acids and their naturally occurring ester, ether, or amide derivatives. In plants, these include acylglycerols such as triacylglycerols (TAGs), phospholipids, galactolipids, and sulfolipids, plus sphingolipids, acylated steryl glycosides, oxylipins, cutins, suberins, estolides and wax, and sterol esters. The list may be extended if we consider molecules immediately derived from acyl groups, such as the epicuticular wax components (hydrocarbons, alcohols, ketones, and so on) or natural products such as anacardic acids that impart protection to predation. Polar lipids are amphipathic and as such self-associate in water to produce a variety of structures. Therefore, they provide the building blocks for biological membranes. There is substantial evidence indicating that the composition of acyl lipids in membranes influences the targeting, distribution, and functional properties of both integral and membrane-associated proteins (Sprong et al., 2001;Wallis and Browse, 2002). Furthermore, many polar lipids and the intermediates in their synthesis and degradation serve as signaling molecules. In summary, acyl lipids function in a wide range of biological processes, such as carbon and free energy storage, cell signaling, modulation of enzyme activity and protein localization, vesicle budding and fusion, waterproofing, and surface protection (Browse and Somerville, 1994).Some acyl lipids such as TAGs, the major constituent of vegetable oils, are ...

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