FatPlants: A Comprehensive Information System for Lipid-Related Genes and Metabolic Pathways in Plants
Chunhui Xu1, Trey Shaw1, Sai Akhil Choppararu1, Yiwei Lu1, Matt Hudson1, Brock Weekley1, Michael Fisher1, Fei He1, Nicholas Wergeles1, Philip D. Bates2, Abraham J. Koo1, Doug K. Allen3,4, Timothy P. Durrett5* (firstname.lastname@example.org), Edgar B. Cahoon6* (email@example.com), Jay J. Thelen1, and Dong Xu1
1University of Missouri; 2Washington State University; 3Agricultural Research Service, U.S. Department of Agriculture; 4Donald Danforth Plant Science Center; 5Kansas State University; and 6University of Nebraska
The team will develop a dedicated web resource that provides a “one-stop” solution for plant acyl-lipid metabolism so that the research community can use it to study lipid science, model lipid networks, and pursue their own hypotheses.
Increasing seed oil content for biofuels and bioproducts by breeding and biotechnology has resulted in trade-offs or penalties with respect to protein content, seed size, or seed fitness. The molecular basis for this impasse is mostly speculative. Use of current global profiling approaches to better understand both the metabolic consequences of altered oil content and composition and the basis for reduced yield must also deal with off-target genetic mutations, ultimately confounding cause-effect interpretations. The team proposes a diverse, integrated strategy to study the consequences of higher and tailored lipid production by studying transgenic plants specifically engineered to produce altered seed oil content and composition. As a continuation of a prior project, researchers are developing a “one-stop-shop” community web resource for all data pertaining to modifying oil composition and increasing oil content in plants, and to leverage data generated from this project with curated forms of public data from other funded websites and the literature. The FatPlants framework and tools currently exist for a number of crop and model oilseeds, including camelina (Camelina sativa). As part of the B5 project, the team is expanding these resources to include pennycress (Thlaspi arvense) and Cuphea viscosissima, an “extreme” producer of seeds with medium-chain fatty-rich oils. Researchers will present all the known fatty acid related proteins and genes in these species and overlay these data with lipidomic measurements from seeds of B5 target species. As a comparative analysis tool, FatPlants includes pathway viewer, protein structure viewer, Basic Local Alignment Search Tool, protein-protein interaction viewer, and Gene Ontology enrichment viewer. To strengthen interactions among B5 investigators, a user authentication internal data-sharing space has been provided to all collaborative labs. The website is publicly available as a community tool at www.fatplants.net.
This research was supported by the DOE Office of Science, Biological and Environmental Research (BER) Program, grant no. DE-SC0023142.