Cells employ mitophagy, a specialised form of autophagy, to selectively remove damaged or excess mitochondria. Different conditions like hypoxia, cellular differentiation, and mitochondrial damage can induce mitophagy. However, the mechanisms governing the selective removal of dysfunctional mitochondria under basal conditions are poorly understood.
We have shown that the SCFFBXL4 ubiquitin ligase complex localizes to the mitochondrial outer membrane in unstressed cells to mediate the ubiquitylation and degradation of the mitophagy receptors NIX and BNIP3, thereby suppressing basal mitophagy. Furthermore, we found that pathogenic variants of FBXL4 associated with encephalopathic mtDNA depletion syndrome (MTDPS13) fail to interact efficiently with the core SCF ubiquitin ligase machinery or facilitate the degradation of NIX and BNIP3, leading to excessive basal mitophagy due to the accumulation of these receptors.
Additionally, we identified the mitochondrial phosphatase PPTC7 as an essential cofactor for SCFFBXL4-mediated degradation of BNIP3 and NIX. Notably, the phosphatase activity of PPTC7 is not required for this turnover. Instead, a specific pool of PPTC7 on the mitochondrial outer membrane functions as an adaptor, linking BNIP3 and NIX to FBXL4. We mapped critical residues necessary for PPTC7 interactions with NIX/BNIP3 and FBXL4, and found that disrupting these interactions impairs the degradation of NIX/BNIP3 and mitophagy suppression.
Together, our findings define a cooperative FBXL4–PPTC7 pathway that maintains mitochondrial homeostasis by restraining inappropriate mitophagy. These results offer mechanistic insight into MTDPS13 pathogenesis and suggest potential therapeutic targets for restoring mitophagy balance in mitochondrial disease. The underlying molecular mechanisms and implications for targeted intervention will be discussed.