RESEARCH-PGR: How do plants produce so many diverse metabolites: A computational and experimental comparative genomics investigation in the Solanaceae

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Part 1: Non-technical abstractPlants are master chemists, producing thousands of small molecules of varied structures and activities. Some of these specialized metabolites have well established roles, including protection from diseases and insects and attraction of beneficial partner organisms. Some are used by humans as medicines and environmentally safe pesticides. The metabolic pathways for only a small fraction of these compounds are well understood, leaving much to learn about how plants produce this enormous diversity of products. This research will focus on specialized metabolism in the Solanaceae (nightshade) family, which includes the important crops tomato, potato, peppers and eggplant and in which a great diversity of natural products is documented. The overarching goal is to develop computational and experimental approaches to discover new plant chemicals and to find the genes that plants use to make small molecules that are valuable for agriculture and human wellbeing. The project outcomes will expand the understanding of the biochemical and genetic mechanisms by which plants produce different classes of specialized metabolites. This research will support breeding and transgenic approaches to improve specialized metabolite synthesis in crop plants to increase resistance to disease and insects and enhance crop value; it will also develop new methods for combining computational and experimental approaches in the study of metabolism. The project outreach activities include summer research for undergraduates from under-represented groups, training of faculty for primarily undergraduate institutions with substantial minority enrollments, and a summer program for science outreach to adults.Part 2: Technical abstractThe identification of genes involved in specialized metabolism is of great importance, since changes in these genes provide a basis for lineage-specific chemical diversity. This project will provide quantitative assessments of the differences between specialized metabolism genes and other genes. The predicted portion of the genome devoted to specialized metabolism within the Solanaceae will be tested using hypothesis-driven experimental approaches. This analysis of the Solanaceae family, which includes important crops as well as models in plant ecology and evolution, will establish a paradigm for computationally predicting and experimentally validating specialized metabolism-related genes across the plant kingdom. The project will take advantage of the rapidly increasing plant genome and transcriptome resources in the Solanaceae to define computationally the characteristics of genes encoding specialized metabolic enzymes. The computational approaches will be coupled with analytical chemical methods, including mass spectrometry and nuclear magnetic resonance spectroscopy, to discover specialized metabolites and to guide the identification of candidate genes encoding enzymes that produce novel metabolites. In vitro protein biochemistry and functional genomics methods will be employed to validate gene candidate functions, and to improve the accuracy of the computational methods. The project outreach activities include summer research for undergraduates from under-represented groups, training of faculty for primarily undergraduate institutions with substantial minority enrollments, and a summer program for science outreach to adults.