Discovery, Revision and Validation of Maize Genes by Proteogenomics

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PI: Steven P. Briggs (University of California - San Diego)CoPI: Vineet Bafna and Laurie G. Smith (University of California - San Diego)Collaborators: W. Joan Chen (San Diego State University), Laura J. Olsen (University of Michigan - Ann Arbor), Steven Rodermel and Patrick Schnable (Iowa State University), and Frank Hochholdinger (Universität Tübingen, Tübingen, Germany)The most fundamental goal of genome science is to discover all of the protein-coding genes, and then to discern the abundance, location, and exact chemical composition of every protein made during the life cycle of an organism; this is called the proteome. A complete and accurately annotated proteome provides the foundation for studies of systems biology and molecular evolution, as well as for hypothesis-driven research. Recent progress in proteogenomics (using proteomic information to annotate the genome) has established it as a data-driven method that complements nucleotide (DNA and RNA)-based annotation strategies. Genome-wide, quantitative proteomics also makes possible the creation of a protein atlas that reveals the anatomical distribution of the proteome and protein sub-cellular locations. This project has two research aims. Aim 1 is to create an Atlas of Maize Proteins. The atlas includes the identity and relative amount of 40,000-50,000 proteins in each of 37 different tissues and stages of maize development. The atlas also includes the protein composition of the plasma membrane, chloroplast, mitochondrion, and peroxisome along with information about the protein changes caused by abiotic and biotic stress. Aim 2 provides proteogenomic discovery, revision, and confirmation of 40,000-50,000 maize gene models, including the identification of exons, the definition of translation start sites and exon borders, and the determination of the correct exon reading frames. This project enhances genome-enabled maize research and breeding by increasing the completeness and accuracy of maize genome annotation. Furthermore, investigations of maize physiology, development, cell functions, and breeding benefit from knowledge of the anatomical and sub-cellular distribution of maize proteins provided by the Atlas of Maize Proteins. Interdisciplinary educational and outreach opportunities are provided to post-docs, graduate students, undergraduates, high school students and Cal State researchers, with an emphasis on involvement of under-represented minorities.This project will provide interdisciplinary educational and outreach opportunities for post-docs, graduate students, undergraduates, high school students and San Diego State University researchers, with an emphasis on involvement of under-represented minorities. All project participants in San Diego including post-docs, graduate students and undergraduates are receiving unique, interdisciplinary training made possible by the collaboration this project involves between investigators with expertise in mass spectrometry, bioinformatics, maize developmental and cell biology, and plant responses to stress. High school students are participating in the research via a module developed for BioBridge, a UC San Diego outreach program that brings hands-on learning activities into San Diego public schools. Researchers at San Diego State University will receive training and education in proteomics and bioinformatics through workshops. Access to the biological materials used in the project is provided by the Germplasm Resources Information Network (GRIN, http://www.ars-grin.gov/). Access to the project results, including data and software, is provided by websites and publications by the investigators (http://briggs.ucsd.edu/; http://www-cse.ucsd.edu/~vbafna/). The long-term repository for project data is Tranche (https://proteomecommons.org/index.jsp) and Gramene (http://www.gramene.org).