Mapping local proteomic environments for lipid biosynthesis, trafficking, and compartmentation in plants

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Acyl lipids are the most abundant lipids in plants and have highly valuable applications in food, feed and oleochemical industries. For example, seed storage lipids or seed oils are primarily used as edible oils and are among the most important agricultural commodities in the world. In Canada, canola alone generates $29.9 billion in economic value each year. Moreover, acyl lipids play essential roles in plant development, from forming cell membranes and storing energy to signaling, and are crucial for plant adaptation to adverse environments (e.g., cold stress, pathogen infection). In plants, the lipid biosynthetic network is highly compartmentalized: de novo fatty acids are synthesized in chloroplasts, and acyl lipid assembly occurs in the endoplasmic reticulum (ER) and chloroplasts. Thus, lipid biosynthesis relies on extensive lipid trafficking among subcellular compartments. Spatial organization of lipid biosynthetic players is also crucial for the process. As our recent findings suggest, lipid biosynthetic proteins may form interactomes in the ER and chloroplasts. However, how lipids are trafficked among organelles and channeled within spatially distinct interactomes remains a key question in biology. The proposed research aims to address fundamental gaps in our knowledge of plant lipid trafficking and channeling using the tools of molecular biology, genetics, biochemistry and proteomics. Given the rapidly changing climate and an ever-growing population, answers to these basic questions will be critical to the future rational design of plants and other photosynthetic organisms (e.g., microalgae) to enhance oil production and meet the growing demand for food, fuel and renewable materials. Over the next 5 years, I propose to determine, for the first time, the full proteomes of sub-organellar compartments that are important for plant lipid biosynthesis using proximity labeling and the model plant Arabidopsis, and to identify novel protein players in lipid trafficking and channeling. Specifically, the three main goals of this proposal include: 1) map local proteomes of organellar subdomains that are involved in lipid biosynthesis, including the ER-chloroplast membrane contact sites and chloroplast intermembrane spaces; 2) map local proteomes of lipid biosynthetic interactomes in the ER and chloroplasts; 3) mine proteomic data to identify novel protein players in lipid biosynthesis and characterize the function of top candidates. This research will make a significant contribution to our mechanistic understanding of lipid trafficking and channeling in photosynthetic organisms, establish valuable publicly-available proteomic databases, and lay the foundation for future efforts to rationally design crops to enhance agricultural production. It will also provide an outstanding training opportunity for 10 HQP who will gain valuable technical and professional skills that will prepare them for their future careers.