AIFM1 KO and AIFM1del mutant HEK cell proteomics

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 cleaved AIFM1 in mitochondria reduces its 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 for OMA1 in integrating mitochondrial stress sensing and cellular energetics by altering the topology of AIFM1.The internal identifier was: m4m1hgAENCThe repository contains AIFM1 wildtype and KO TREx cells (samples 1-8), which were not used in the associated publication. The file names contain pp for +/+ and mm for -/-.File names 09-12 (file names: R98ENLYFG) correspond to TCS. The file names 13-16 (M1_R98del) correspond to TCS/TEV.Raw fileSample Name01_AIFM1_KO_pp_fyxK.rawFlp-In-T REx-293-mock#102_AIFM1_KO_pp_wxP9.rawFlp-In-T REx-293-mock#203_AIFM1_KO_pp_Djpr.rawFlp-In-T REx-293-mock#304_AIFM1_KO_pp_txOk.rawFlp-In-T REx-293-mock#405_AIFM1_KO_mm_moaT.rawFlp-In-T REx-293 AIFM1 KO-mock#106_AIFM1_KO_mm_W5lK.rawFlp-In-T REx-293 AIFM1 KO-mock#207_AIFM1_KO_mm_XIc0.rawFlp-In-T REx-293 AIFM1 KO-mock#308_AIFM1_KO_mm_pdxt.rawFlp-In-T REx-293 AIFM1 KO-mock#409_AIFM1_C_MycAIFM1_R98ENLYFG_I2x8.rawFlp-In-T REx-293 AIFM1 KO-AIFM1TCS#110_AIFM1_C_MycAIFM1_R98ENLYFG_Hzqq.rawFlp-In-T REx-293 AIFM1 KO-AIFM1TCS#211_AIFM1_C_MycAIFM1_R98ENLYFG_4P4M.rawFlp-In-T REx-293 AIFM1 KO-AIFM1TCS#312_AIFM1_C_MycAIFM1_R98ENLYFG_MktX.rawFlp-In-T REx-293 AIFM1 KO-AIFM1TCS#413_AIFM1_C_MycAIFM1_M1_R98del_7NiF.rawFlp-In-T REx-293 AIFM1 KO-AIFM1TCS/TEV#114_AIFM1_C_MycAIFM1_M1_R98del_yf68.rawFlp-In-T REx-293 AIFM1 KO-AIFM1TCS/TEV#215_AIFM1_C_MycAIFM1_M1_R98del_hmKM.rawFlp-In-T REx-293 AIFM1 KO-AIFM1TCS/TEV#316_AIFM1_C_MycAIFM1_M1_R98del_qXgO.rawFlp-In-T REx-293 AIFM1 KO-AIFM1TCS/TEV#4