Our group uses genetic, genomic and biochemical approaches to understand the regulation of biosynthetic pathways of importance to flowering plants and the animals that depend on plants for sustenance. Plants synthesize an enormous number and variety of primary and specialized (‘secondary’) metabolites. Many have documented or proposed roles in homeostasis (hormones, for example), interaction with other organisms (pathogens, symbionts, and herbivores), and defense against harmful non-biological stress agents (cold, drought, light, oxidizing chemicals, etc). In addition, plants are primary sources of nutrients essential to humans and other animals (for examples: vitamins, essential amino acids, and minerals), pharmaceuticals, and phytochemicals with proposed health-promoting value (antioxidants, phytosterols, glucosinolates, etc). Recent quantum leaps in structural and functional genomics coupled with breakthroughs in mass spectrometry-based analytical chemistry have created unprecedented opportunities to rapidly increase our understanding of how plants synthesize these diverse and important compounds.
While classical ‘forward’ genetics continues to play an important role in increasing our understanding of plant biochemistry, the one pathway at a time approaches taken in the past are not well suited for systems biology approaches, which aim to describe the roles and interactions of all gene products. Two of our major projects aim to rapidly increase our understanding of plant biochemistry using genomics technologies.
In the NSF-funded Chloroplast Phenomics project being done collaboratively with faculty in the Departments of Biochemistry and Molecular Biology and Plant Biology at MSU, we are focusing on functional analysis of several thousand nuclear genes that encode chloroplast-targeted proteins. Recent progress in creating collections of 'sequence indexed' mutants of Arabidopsis, where each line contains a characterized T-DNA insertion in a specific gene, greatly increases the power of reverse genetics in large-scale gene function discovery. Using these resources we can efficiently obtain information about the roles of thousands of Arabidopsis genes of interest. Because many of these have no known physiological function, knock-out mutants are being run through a battery of phenotypic assays related to plastid biology. These range from metabolite analyses (for amino acids, fatty acids and starch) to studies of plastid structure and photosynthetic function. The results of these studies will provide information about functions of individual genes and their relationships to each other. They will also enable a systems level understanding of the networks controlling chloroplast function.
Our laboratory is using secretory and glandular trichomes of tomato (Solanum lycopersicum) and related species as a system for analysis of specialized metabolism (aka secondary metabolism) in flowering plants. These biochemical factories are found on the surfaces of above-ground plant tissues of approximately one third of all vascular plant species. Humans are familiar with these structures because they contain the essential oils that give cooking herbs their distinctive smell and taste. In addition to making foods taste better, these uni- and multi-cellular appendages are proposed to have roles in plant protection against various environmental stresses including herbivore attack, pathogen infection, extreme temperature, and excessive light.
This National Science Foundation-funded project is in collaboration with laboratories at MSU, University of Arizona and University of Michigan. We are using metabolomic, genetic, genomic and biochemical approaches to discover the pathways that operate in these fascinating organs. We are taking an integrated approach to lay the foundation for a longer-term ‘systems biology’ understanding of the entire network of genes and proteins involved in the development of each of the different types of SGT found in Solanum plants and the genes and enzymes responsible for their biosynthetic capacity.
The approaches being used include:
- Characterization of the chemical composition of secretory glandular trichomes from cultivated tomato and wild Solanum species. This has required the development of new mass spectrometry-based analytical chemistry assays of mass isolated and individual glands.
- Screening for differences in chemistry in introgression lines from crosses between S. lycopersicum and S. pennellii and EMS mutants of tomato. Phenotypic analysis of these mutants and introgression lines will help create models for how these metabolic pathways are regulated, and identify key genes responsible for these biochemical differences.
- Analysis of cDNA and protein sequences from specific trichome types in each of five different Solanum species. These sequences will identify the highly expressed genes and proteins in each gland type and across species. Comparison of these sequences and chemistry in each gland type will lead to discovery of enzymes and regulators that influence the production of these specialized metabolites.