High-Resolution Complexome-Profiling of Mitochondria Reveals Quality Control Pathways of Protein Import

Mitochondria contain ~1,000 different proteins that may assemble into larger entities such as respiratory (super)complexes and preprotein translocases. The molecular/structural organization of major parts of the mitochondrial proteome, however, has not yet been resolved. We report a quantitative mapping of mitochondrial protein assemblies by high-resolution complexome-profiling of >90% of the yeast mitochondrial proteome, termed MitCOM. Analysis of MitCOM unraveled an unexpected complexity of protein assemblies with each protein found in an average of at least six assemblies. Organization of proteins was distinct between the major classes of mitochondrial function, but independent of their biochemical properties. We detected interactions of the mitochondrial receptor for cytosolic ribosomes, of prohibitin scaffolds and respiratory complexes. Identification of quality control factors operating at the mitochondrial protein entry gate uncovered pathways for preprotein ubiquitylation, deubiquitylation and degradation. MitCOM, made accessible through an interactive viewer on the CEDAR database, may serve as a comprehensive resource for analyzing functional organization and interaction of mitochondrial protein machineries and pathways.