Pathogenic variants of the mitochondrial copper chaperones SCO1 and SCO2 reshape their respective interactomes and disrupt cellular phospholipid metabolism

SCO1 and SCO2 are required for copper delivery to COX2, a copper-containing subunit of cytochrome c oxidase (COX), yet how mutations in these genes cause distinct, tissue-specific forms of human disease remains poorly understood. To gain further insight into the molecular underpinnings of this clinical heterogeneity, we used BioID to map the interactomes of four pathogenic SCO variants (SCO1 G132S, SCO1 P174L, SCO1 M294V and SCO2 E140K) and the wild-type proteins. While this approach identified many proteins common to both wild-type neighbourhoods, several potential interacting partners unique to each SCO protein were also observed that were consistent with their known roles in COX assembly. Follow-up analyses revealed that SCO1 interacts with COX16 and that this interaction is stabilized within the membrane by a coiled-coil helix-helix interface, with the soluble C-terminal region of COX16 physically bridging SCO1 and COX2 within a ternary complex to facilitate copper delivery. We further observed that COX16 abundance is relatively low in the brain and its association with SCO1 is most severely impaired by the M294V substitution associated with a fatal encephalopathy. Intriguingly, our BioID analyses also detected significant enrichment in each SCO neighbourhood for biosynthetic enzymes and lipases critical to phospholipid metabolism and found that the affinity for these candidate interactors was uniquely perturbed by various pathogenic variants of SCO1 and SCO2. Collectively, our data emphasize the potential of proximity labelling to further define the molecular roles of disease-causing variants that perturb mitochondrial function and suggest that SCO proteins impinge upon phospholipid metabolism.