Mitochondrial SUMOylation of NDUFA9 drives ClpP-dependent degradation and complex I dysfunction in a Leigh syndrome–associated mutation

Mitochondrial complex I (CI) dysfunction causes many inherited mitochondrial diseases, including Leigh syndrome, yet how post-translational modifications control CI subunit proteostasis remains unclear. Here we identify NDUFA9 as a mitochondrial SUMOylation substrate. SUMO1 conjugation at Lys370 promotes NDUFA9 binding to ClpP through the SIM motifs of ClpP and accelerates ClpP-dependent degradation. This destabilizes NDUFA9, reduces fully assembled CI and CI activity, and impairs mitochondrial bioenergetics. Mitochondrial SENP2 counteracts this process, defining a SUMO–SENP2–ClpP axis that preserves NDUFA9 and CI integrity. The Leigh syndrome–associated NDUFA9R321P mutation enhances Ubc9 binding, increases Lys370 SUMOylation, and drives excessive ClpP-dependent degradation. Preventing SUMOylation with the K370R substitution restores NDUFA9 abundance, CI integrity, and mitochondrial function. In systemic and brain-specific AAV replacement models, blocking SUMOylation also alleviates R321P-induced CI deficiency and motor dysfunction. These findings reveal aberrant NDUFA9 SUMOylation as a pathogenic mechanism in mitochondrial disease. The Leigh syndrome–associated R321P mutation drives excessive SUMOylation of NDUFA9, promoting ClpP-dependent degradation, weakening mitochondrial complex I, and causing mitochondrial and motor dysfunction.