Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory Chain Function

Mitochondria are essential for numerous cellular processes, yet hundreds of their proteins lack robust functional annotation. To reveal functions for these proteins (termed MXPs), we assessed condition-specific protein-protein interactions for 50 select MXPs using affinity enrichment mass spectrometry. Our data connect MXPs to diverse mitochondrial processes, including multiple aspects of respiratory chain function. Building upon these observations, we validated C17orf89 as a complex I (CI) assembly factor. Disruption of C17orf89 markedly reduced CI activity, and its depletion is found in an unresolved case of CI deficiency. We likewise discovered that LYRM5 interacts with and deflavinates the electron-transferring flavoprotein that shuttles electrons to coenzyme Q (CoQ). Finally, we identified a dynamic human CoQ biosynthetic complex involving multiple MXPs whose topology we map using purified components. Collectively, our data lend mechanistic insight into respiratory chain-related activities and prioritize hundreds of additional interactions for further exploration of mitochondrial protein function. [Display omitted] •PPI mapping of 50 MXPs reveals mitochondrial protein functions•C17orf89 is a CI assembly factor depleted in a case of CI deficiency•LYRM5 interacts with and deflavinates the electron transferring flavoprotein•Proteins involved in coenzyme Q biosynthesis form a dynamic “complex Q” Mitochondria are essential organelles, yet hundreds of their proteins lack robust functional characterization. Floyd et al. (2016) define interaction partners for 50 such proteins, providing hypotheses about their roles in mitochondria. In particular, their work lends mechanistic insight into respiratory chain activities related to complex I, the electron transferring flavoprotein, and coenzyme Q.