A mitochondrial SCF‐FBXL4 ubiquitin E3 ligase complex degrades BNIP3 and NIX to restrain mitophagy and prevent mitochondrial disease

• Published in: The EMBO journal 2023-07, Vol.42 (13), p.e113033-n/a
• Main Authors: Cao, Yu, Zheng, Jing, Wan, Huayun, Sun, Yuqiu, Fu, Song, Liu, Shanshan, He, Baiyu, Cai, Gaihong, Cao, Yang, Huang, Huanwei, Li, Qi, Ma, Yan, Chen, She, Wang, Fengchao, Jiang, Hui
• Format: Article
• Language: English
• Subjects: Animals; BNIP3 protein; BNIP3/NIX; Degradation; EMBO07; EMBO31; EMBO57; FBXL4; Genetic screening; Lethality; Life Sciences; Membrane proteins; Mice; Mitochondria; Mitochondria - metabolism; mitochondrial disease; Mitochondrial Diseases - metabolism; Mitochondrial DNA; Mitochondrial Proteins - genetics; Mitochondrial Proteins - metabolism; Mitophagy; Mitophagy - physiology; Mutation; Proteins; Quality control; Receptors; Regulatory mechanisms (biology); Substrates; Ubiquitin; Ubiquitin-protein ligase; Ubiquitin-Protein Ligases - genetics; Ubiquitin-Protein Ligases - metabolism; Ubiquitins - metabolism; ubiquitin‐proteasome pathway
• ISSN: 0261-4189; 1460-2075
• DOI: 10.15252/embj.2022113033

Mitophagy is a fundamental quality control mechanism of mitochondria. Its regulatory mechanisms and pathological implications remain poorly understood. Here, via a mitochondria‐targeted genetic screen, we found that knockout (KO) of FBXL4, a mitochondrial disease gene, hyperactivates mitophagy at basal conditions. Subsequent counter screen revealed that FBXL4‐KO hyperactivates mitophagy via two mitophagy receptors BNIP3 and NIX. We determined that FBXL4 functions as an integral outer‐membrane protein that forms an SCF‐FBXL4 ubiquitin E3 ligase complex. SCF‐FBXL4 ubiquitinates BNIP3 and NIX to target them for degradation. Pathogenic FBXL4 mutations disrupt SCF‐FBXL4 assembly and impair substrate degradation. Fbxl4 −/− mice exhibit elevated BNIP3 and NIX proteins, hyperactive mitophagy, and perinatal lethality. Importantly, knockout of either Bnip3 or Nix rescues metabolic derangements and viability of the Fbxl4 −/− mice. Together, beyond identifying SCF‐FBXL4 as a novel mitochondrial ubiquitin E3 ligase restraining basal mitophagy, our results reveal hyperactivated mitophagy as a cause of mitochondrial disease and suggest therapeutic strategies. Synopsis FBXL4 mutations result in encephalomyopathic mtDNA depletion syndrome 13 (MTDPS13). This study shows that FBXL4 forms a mitochondrial SCF‐FBXL4 ubiquitin E3 ligase complex that degrades mitophagy receptors BNIP3 and NIX to prevent excessive mitochondria loss and perinatal lethality in mice. A mitochondria‐targeted genetic screen identifies FBXL4 as a mitophagy suppressor. A counter screen reveals mitophagy receptors BNIP3 and NIX as required for hyperactivated mitophagy in the absence of FBXL4. FBXL4 forms a mitochondria‐localized SCF‐FBXL4 ubiquitin E3 ligase complex to degrade BNIP3 and NIX. Fbxl4 knockout mice exhibit excessive mitophagy, mitochondria loss, and perinatal lethality, which can be rescued by either Bnip3 or Nix deletion. Graphical Abstract Mice lacking disease‐mutated FBXL4 exhibit loss of mitochondria and perinatal lethality due to excessive basal mitophagy.