Characterization of the Tomato Secretome Using Integrated Functional and Computational Strategies

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The plant cell wall plays a central role in many diverse aspects of plant biology, including organ growth and differentiation, defence against microbial pathogens, metabolism and transport of nutrients and responses to environmental stresses. In addition, the plant cell wall can be thought of as a vital compartment that acts as the interface with the environment and so substantial molecular signaling occurs in and across the wall environment. In accordance with its multifunctional nature, the plant cell wall houses a large and complex protein population, or proteome, including enzymes with a broad range of catalytic functions as well as structural proteins. However, it is increasingly evident that there is still a very limited understanding of the extent, composition and dynamic properties of the cell wall proteome, also termed the 'secretome'. This project will use an integrated approach to catalog the tomato secretome, coupling a suite of newly developed functional screens with sequencing of highly purified wall protein extracts, bioinfomatic tools and computational prediction. This infrastructure will be used to evaluate the qualitative and quantitative dynamics of the cell wall proteome during two biological processes that are intimately associated with wall biology: fruit ripening and plant defence responses. To this end, protein and mRNA expression will be studied in a standard experimental tomato genotype and contrasted with those in several non-softening tomato mutants.This research will generate a comprehensive catalog of the plant secretome in a range of tomato tissues and importantly, provide insights into the extracellular proteins that appear to contribute to, and play a role in, signaling during fruit ripening and in response to pathogen attack. The resulting information should allow important insights into how to improve fruit quality and agricultural productivity. A publicly accessible tomato secretome database (SecreTom) will be developed to house the project data, to provide access to all associated computational tools, and to act as a hub for plant wall proteome research. SecreTom will be accessible through the Solanaceous Genomes Database (SGN: http://www.sgn.cornell.edu/), which will also serve as the long-term repository for the project data. In addition, an annual summer Proteomics Workshop will be held, comprising a seminar series, poster presentations, and lab-based practical training. The participation of under-represented groups at the undergraduate and graduate levels will be ensured through the support of a network of existing Cornell programs.