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 > 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.

Figure 1.

An overview of the Lipid Gene Catalog: construction and global final content. The complete content of the Lipid Gene Catalog is available in the ALG database (http://www.plantbiology.msu.edu/lipids/genesurvey/index.htm). For a summary of the type of information contained in the catalog, see Figure 2. For a summary of the candidates, see Table I.

Figure 2.

Structure and content of the Web-based ALG database. Each box represents a different Web page. Arrows indicate links between pages. For each enzyme, there is a link to the corresponding Web page of the International Union of Biochemistry and Molecular Biology (http://www.chem.qmw.ac.uk/iubmb) when available. The International Union of Biochemistry and Molecular Biology Web pages have links to many other databases. TIGR and MIPS databases: see “Materials and Methods” for abbreviations and Web addresses.

Figure 3.

EST frequencies in organs (synthetic libraries) for the three proteins of acyl lipid metabolism showing the highest number of total ESTs. Synthetic libraries group cDNA libraries made from the same organ. Total numbers of ESTs in the synthetic libraries are: seed, 11,155; leaf, 3,944; root, 21,515; flower, 7,935; silique, 13,382; and seedling, 7,050. The proteins are: lipoxygenase At3g45140 (147 total ESTs), LTP1 At2g38540a (146 total ESTs), and endoplasmic oleate desaturase At3g12120 (131 total ESTs).

Figure 4.

Possible preferential organ expressions in the KCS family based on EST data. Each of the 19 KCS genes was classified in one category only based on the probabilities of differential expression between organs (see Tables IV and V for an example of the data used).