Developing a Bioinformatics Database for Stoichioproteomics

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PI: William Fagan, University of MarylandCoPI: James Elser, Arizona State University Sudhir Kumar, Arizona State University Fast growing DNA and protein sequence databases, knowledge of the basic biological function of individual proteins, and availability of information characterizing relative gene expression intensities provide unique and exciting opportunities to construct eco-genomic hypotheses and test their predictions. One fundamental question involves how environmental constraints (such as nutrient limitation) shape protein sequences. In particular, this award explores how the availability of nutrients in the environment affects proteins by modulating their amino acid composition. This issue can be addressed because ecologists have demonstrated extensive interspecific variation in the elemental compositions and protein content of organisms and their tissues (e.g., plants are nitrogen-poor relative to insect herbivores; grasshoppers are nitrogen-rich relative to butterflies)., Amino acids, which are the building blocks of all proteins, can differ in their atomic compositions (e.g., carbon [C], nitrogen [N], sulfur [S], and oxygen [O]) because of differences in the "R-groups" (side-chains), which contribute to the unique chemical reactivity of individual amino acids and allow them to play individual structural and functional roles within protein sequences. Combining ecological and genomic perspectives allows examining directly whether the proteomes of N-rich and N-poor species differ with regard to the standardized N-content of the side chains of their proteins. These problems in "stoichio-proteomics" require the exploration of interspecific and intergenic variation in the elemental composition of proteins. To facilitate these explorations, this project will create a bioinformatics knowledgebase at the interface of ecology, evolution, and genomics. This database, the Genomics Resource Access for Stoichio-Proteomics (GRASP), will be implemented as a multi-tiered, data-driven web application. It will be a flexible and scalable system that will contain an integrated ecological dataset (characterizing key life history traits of insect species) and a database of protein composition. Some of the stoichioproteomic research hypotheses will be tested using these data. The Broader Impacts from this research extend beyond the immediate scientific interests in three ways. First, the GRASP-database and its query/retrieval system will provide an extensive, easy-to-use tool for the exploration and analysis of stoichiometric characteristics of proteins that will be freely available to the research community. GRASP will facilitate diverse stoichio-proteomic analyses far beyond our own research interests. The database technology will be made available to anyone who is interested in developing similar resources. Second, the proposed computing platform will be a useful teaching tool for undergraduate and graduate students at universities worldwide. Third, research and development conducted under the auspices of this proposal will make a significant, but focused, contribution to human resources development in interdisciplinary biology, especially at the interface of computational genomics and ecological evolution.