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

Abstract

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 À/À 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 À/À 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.

The ER membrane protein complex governs lysosomal turnover of a mitochondrial tail-anchored protein, BNIP3, to restrict mitophagy

“…Early studies identified transcriptional regulation by hypoxia-inducible factor 1 (HIF-1) as a key facet of BNIP3 and NIX regulation 4 . Consistent with this model, both BNIP3 and NIX expression and associated mitophagy are potently induced upon hypoxia onset 14 . Recently, multiple groups have extended this model, reporting that the ubiquitin-proteasome system (UPS) potently restricts BNIP3 and NIX levels to further curb mitophagy [12][13][14][15][16][17] .…”

“…Consistent with this model, both BNIP3 and NIX expression and associated mitophagy are potently induced upon hypoxia onset 14 . Recently, multiple groups have extended this model, reporting that the ubiquitin-proteasome system (UPS) potently restricts BNIP3 and NIX levels to further curb mitophagy [12][13][14][15][16][17] . In light of these concepts, it is important to develop a unified understanding of how steady-state levels of these mitophagy receptors are established and maintained, and how this regulation governs underlying cell physiology.…”

“…Early models for BNIP3-mediated mitophagy centered on its transcriptional control, particularly in response to hypoxic stress 4,71 . Recently, these models have been appended to account for post-translational control by the ubiquitin-proteasome system [12][13][14][15][16]56,72 . Using an unbiased, genome-wide CRISPR screen, we similarly identified a role for the ubiquitin-proteasome system in regulating BNIP3, providing independent support for these models.…”

“…Post-translational control of BNIP3 stability was previously reported to depend on the ubiquitin-proteasome system [12][13][14][15][16][54][55][56] . Consistent with these reports, our list of genetic effectors recovered numerous UPS factors previously implicated in the regulation of BNIP3, including proteasomal subunits, the NEDD8 conjugation machinery, and the membrane protein extratase valosin-containing protein (VCP).…”

Eating your mitochondria—when too much of a good thing turns bad

“…It is this latter scenario that appears to underlie a rare form of mitochondrial disease characterised by a mutation in FBXL4, the substrate binding component of a particular cullin‐RING E3 ubiquitin ligase (CRL) (Alsina et al , 2020). Three new EMBO Journal publications have now elucidated the mechanism behind how FBXL4 regulates mitophagy, shedding light on the pathology of this debilitating disease and opening potential therapeutic opportunities (Cao et al , 2023; Elcocks et al , 2023; Nguyen‐Dien et al , 2023).…”