Functional Genomics from a Plant Biochemist's Perspective

Abstract

The lipids derived from plant seeds provide approximately 20% of dietary calories in developed nations. The fatty acid composition of these dietary oils can influence several components of long-term health. Almost all the genes involved in producing dietary oils are now isolated, allowing rational modifications in saturated and polyunsaturated fatty acid content in foods. Several of these genes have been identified using genomic approaches. However, many questions about the regulation of plant lipid metabolism seem difficult to solve using conventional biochemical or molecular approaches. For example, we have little understanding of why or how some seeds produce >50% oil whereas other seeds store largely carbohydrate or protein. Major control over complex plant biochemical pathways may only become possible by understanding regulatory networks which provide ‘global’ control over these pathways. To begin to discover such networks and provide a broad analysis of gene expression in developing oilseeds, we have taken two genomic approaches: 1) We have sequenced 10,500 expressed sequence tags (EST) from developing Arabidopsis seeds and analyzed these using different bioinformatics tools. Approximately 30% of the ESTs have no match in dbEST, suggesting many represent mRNAs derived from genes that are specifically expressed in seeds. ‘Electronic northern’ analysis of EST abundance data has provided insights into the import of photosynthate into developing embryos, its conversion into seed oil and the regulation of this pathway. 2) We have produced microarrays which display ca. 4000 seed-expressed Arabidopsis genes. Sensitivity of the arrays is estimated at 1–2 copies mRNA/cell. The arrays have been hybridized with probes derived from seeds, leaves, and roots and analysis of expression ratios between the different tissues has allowed the tissue-specific expression patterns of many hundreds of genes to be described for the first time. Approximately 10% of the genes were expressed at ratios ≥10-fold higher in seeds than leaves or roots. We also identified several transcription factors, as well as kinases and phosphatases, whose expression changed during the seed development, and which may be involved in the regulation of the storage compound synthesis. Moreover, cluster analysis of the expression profiles established distinct groups of co-regulated genes.