OMA1-mediated cleavage of AIFM1 upon mitochondrial stress and suppression of cell growth through the control of OXPHOS activity

Mitochondrial proteases regulate the dynamic properties of the organelle morphology and ensure functional plasticity at the cellular level. The metalloprotease OMA1 mediates constitutive and stress-inducible processing of its substrates in mitochondria, but the number of functionally characterized substrates remains limited. Using multiproteomic and biochemical approaches, we show that the membrane-anchored inner membrane space (IMS) protein AIFM1 serves as a mitochondrial stress-responsive substrate of OMA1. We define that OMA1 cleaves AIFM1 in the IMS under stress conditions, which is a kinetically slower reaction than that of the conventional substrate, the dynamin-like GTPase OPA1. Membrane dislocation of the cleaved AIFM1 in mitochondria leads to reduced binding to subunits of the oxidative phosphorylation machinery. This leads to a decrease in the respiratory activity and ultimately impairs cell growth. Mechanistically, we show that AIFM1 broadly safeguards the mitochondrial proteome at steady state by participating in the protein import, in particular respiratory complex I subunits, via the Tim23 complex. These results reveal an unrecognized role of OMA1 for integrating mitochondrial stress sensing and cellular energetics by altering the topology of AIFM1. Overall design: RNA-seq profilling of AIFM1 variants cells