Rigoni, GiovanniCalvo, EnriqueGlytsou, ChristinaCarro-Alvarellos, MartaNoguchi, MasafumiSemenzato, MartinaQuirin, CharlotteCaicci, FedericoMeneghetti, NatasciaSturlese, MattiaIshihara, TakayaMoro, StefanoRampazzo, ChiaraIshihara, NaotadaBezzo, FabrizioSalviati, LeonardoVazquez, JesùsSales, GabrieleRomualdi, ChiaraEnriquez, Jose AntonioScorrano, LucaSoriano, Maria Eugenia2025-07-092025-07-092025-04-01Cell Metab. 2025 Apr 1;37(4):1024-1038.e8.https://hdl.handle.net/20.500.12105/26814Mitochondrial proteins assemble dynamically in high molecular weight complexes essential for their functions. We generated and validated two searchable compendia of these mitochondrial complexes. Following identification by mass spectrometry of proteins in complexes separated using blue-native gel electrophoresis from unperturbed, cristae-remodeled, and outer membrane-permeabilized mitochondria, we created MARIGOLD, a mitochondrial apoptotic remodeling complexome database of 627 proteins. MARIGOLD elucidates how dynamically proteins distribute in complexes upon mitochondrial membrane remodeling. From MARIGOLD, we developed MitoCIAO, a mitochondrial complexes interactome tool that, by statistical correlation, calculates the likelihood of protein cooccurrence in complexes. MitoCIAO correctly predicted biologically validated interactions among components of the mitochondrial cristae organization system (MICOS) and optic atrophy 1 (OPA1) complexes. We used MitoCIAO to functionalize two ATPase family AAA domain-containing 3A (ATAD3A) complexes: one with OPA1 that regulates mitochondrial ultrastructure and the second containing ribosomal proteins that is essential for mitoribosome stability. These compendia reveal the dynamic nature of mitochondrial complexes and enable their functionalization.This work was supported by Associazione Italiana per la Ricerca sul Cancro (AIRC) IG19991; European Research Council (ERC) FP7-282280 and European Union FP7 CIG PCIG13-GA-2013-618697; Fondazione Cariparo Progetto d’eccellenza SIGMI; Ministero dell’Universita` e della Ricerca (MUR) FIRB RBAP11Z3YA_005, PRIN 2017BF3PXZ; the National Recovery and Resilience Plan (NRRP), Mission 4, Component 2, Investment 1.4, funded by the European Union—NextGenerationEU; and Telethon GGP15091 (to L. Scorrano). Additional support was provided by Telethon GJC22073, M.U.R. PRIN 2022PLZP9T and 2022XL4TE9, and University of Padua DiBio PRID 2018 (to M.E.S.); AMED-CREST (grant number JP22gm1110006 to N.I.); Fondazione IRP Citta` della Speranza (to L. Salviati); and the Spanish Ministry of Science, Innovation, and Universities (PGC2018-097019-B-I00), the Instituto de Salud Carlos III (Fondo de Investigacio´ n Sanitaria grant PRB3) (PT17/0019/0003-ISCIII-SGEFI/ERDF, ProteoRed), and Foundation ‘‘La Caixa’’ (HR17-00247) (to J.V.). M.C.A. and C.G. were supported by a PhD fellowship for international PhD students from Fondazione Cariparo. M.N. was supported by a JSPS Postdoctoral Fellowship for abroad.engVoRhttp://creativecommons.org/licenses/by/4.0/ATAD3AOPA1cristae remodelinginteractomemitochondriamitochondrial complexesmitoribosome stabilityAttribution 4.0 International39999845Cell Metabolismopen access