Research Focus: Functional Genomics of Plant Secondary Metabolism

Plants have evolved various strategies for survival and reproduction during the long evolutionary course, one of which is the production of a myriad of small molecular weight compounds, also known as secondary metabolites or natural products. With at least 50,000 so far identified, the total number of such compounds in the plant kingdom is estimated to be much higher. Secondary metabolites are believed to play vital roles in the physiology and ecology of the plants that produce them, particularly as defense elements against pests and pathogens. The potent biological activity of some secondary metabolites has also led to their exploitation as pharmaceuticals and insecticides. Although much progress has been made, particularly in the past few decades, a lot more still need to be learned about the mechanisms responsible for the formation of most plant secondary metabolites.

Our research aims at improving the understanding of plant secondary metabolism. In particular, we are interested in investigating the biochemistry, regulation and function of secondary metabolism in model plant species rice and Arabidopsis, using an integrated functional genomic approach. The study of secondary metabolism in rice and Arabidopsis is expected to heighten our appreciation for the complexity and importance of plant secondary metabolites. The knowledge gained from this study will also build a platform for comparative analysis of secondary metabolism in rice and Arabidopsis at the genome level, which will shed important new light on the evolution of plant secondary metabolism. In addition, once the tools are fully developed in rice and Arabidopsis, they can be applied to explore secondary metabolism in less genetically tractable plant species, such as medicinal plants.

Currently, we are pursuing two major areas of interest. One project is to study the biochemical mechanism for the formation of volatile secondary metabolites that are involved in tri-trophic interactions in rice. When attacked by insects, rice plants release a blend of volatiles, which act as a cue for attracting the predators/parasitoids of the insects. We are using Gas Chromatography/Mass Spectrometry (GC/MS) to identify the volatiles, using bioinformatics and microarray analysis to identify candidate genes, and using in vitro biochemical assays to determine the function of individual genes that are responsible for the production of certain herbivory induced volatiles in rice. The identification of such genes will provide tools for the elucidation of the function of individual volatile components in rice tri-trophic interactions. The study of the biochemical mechanism of tri-trophic interactions in rice serves as a proof-of-concept project for a long term goal of systemically investigating the whole spectrum of secondary metabolism in rice. Additionally, because of the strong synteny between the rice genome and the genomes of other cereal species, the knowledge gained from rice will facilitate cloning and functional determination of the genes of secondary metabolism in other cereals, such as maize and wheat.

A second project, in collaboration with Dr. Eran Pichersky at University of Michigan, focuses on a cluster of three methyl transferase genes in Arabidopsis. One member of the three genes shows activity with farnesoic acid for the formation of methyl farnesoate. Methyl farnesoate is the immediate precursor of insect juvenile hormone III (JH III). This finding opens up intriguing questions regarding the biological and ecological functions of methyl farnesoate, which itself was shown to have insect juvenile hormonal activity, and JH III if present, in Arabidopsis. The questions will be addressed through enzymatic characterization, gene expression analysis, metabolite analysis and bioassays of transgenic plants, which will have altered expression of this particular methyl transferase gene, with insects. In addition, we are interested in determining the functions of the other two methyl transferase genes in the cluster, and understanding how these three genes have been evolved.