Systems-to-structure approaches for defining mitochondrial protein function

PROJECT SUMMARY Mitochondria are centers of metabolism and signaling, and their functions are essential for all but a few eukaryotic cell types. Despite the widespread importance of these organelles, many aspects of mitochondrial biology remain remarkably obscure. This fact contributes to our poor ability to diagnose mitochondrial diseases and our near complete inability to rectify mitochondrial dysfunction therapeutically. This dysfunction is associated with ~350 rare inborn errors of metabolism and an increasing number of common diseases—including Parkinson’s, Alzheimer’s, various cancers, and type 2 diabetes—often through distinct, yet unclear means. A major bottleneck to further understanding mitochondrial processes and addressing their dysfunction in human disease is that the proteins driving them have often not been identified. Concurrently, the basic biochemical functions of many mitochondrial proteins that may fulfill these roles are undefined, or at best are poorly understood. This reality was made manifest by my efforts to generate MitoCarta, which doubled the number of known mammalian mitochondrial proteins and revealed a striking ~300 lacking any annotated function. Thus, an overarching goal of my research program is to achieve a more comprehensive understanding of mitochondrial biology by systematically establishing the functions of orphan mitochondrial proteins and their roles within disease-related processes. We do so by first devising novel, multi-dimensional analyses designed to make new connections between these proteins and established pathways and processes. These include customized, multiomic analyses of yeast and human cell gene knockouts, deep mutational scanning approaches, large-scale genetic screens, and other mass spectrometry-based investigations. We then employ mechanistic and structural approaches to define the functions of select proteins at biochemical depth, and chemical biology approaches to design small molecules to manipulate their functions in vitro and in vivo. This strategy leads us into diverse and unanticipated new directions; however, we also maintain a persistent focus on the biochemistry, biosynthesis, and transport of coenzyme Q (CoQ). We are driven to define how this remarkable, redox-active, extremely hydrophobic molecule is produced in mitochondria, distributed throughout the cell, and how its cofactor and antioxidant functions empower an ever-growing list of diverse biochemical processes. Overall, these “systems biochemistry” efforts promise to help establish a deep, mechanistic understanding of mitochondrial biochemistry that will motivate novel therapeutic strategies for the vast array of human disorders rooted in mitochondrial dysfunction.