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FBXL4 mutations cause excessive mitophagy via BNIP3/BNIP3L accumulation leading to mitochondrial DNA depletion syndrome

Cell Death & Differentiation volume 30, pages 2351–2363 (2023)Cite this article

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Abstract

Mitochondria are essential organelles found in eukaryotic cells that play a crucial role in ATP production through oxidative phosphorylation (OXPHOS). Mitochondrial DNA depletion syndrome (MTDPS) is a group of genetic disorders characterized by the reduction of mtDNA copy number, leading to deficiencies in OXPHOS and mitochondrial functions. Mutations in FBXL4, a substrate-binding adaptor of Cullin 1-RING ubiquitin ligase complex (CRL1), are associated with MTDPS, type 13 (MTDPS13). Here, we demonstrate that, FBXL4 directly interacts with the mitophagy cargo receptors BNIP3 and BNIP3L, promoting their degradation through the ubiquitin-proteasome pathway via the assembly of an active CRL1FBXL4 complex. However, MTDPS13-associated FBXL4 mutations impair the assembly of an active CRL1FBXL4 complex. This results in a notable accumulation of BNIP3/3L proteins and robust mitophagy even at basal levels. Excessive mitophagy was observed in Knockin (KI) mice carrying a patient-derived FBXL4 mutation and cortical neurons (CNs)-induced from MTDPS13 patient human induced pluripotent stem cells (hiPSCs). In summary, our findings suggest that abnormal activation of BNIP3/BNIP3L-dependent mitophagy impairs mitochondrial homeostasis and underlies FBXL4-mutated MTDPS13.

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Fig. 1: Identification of BNIP3 and BNIP3L proteins as FBXL4 interacting proteins.
Fig. 2: FBXL4 mediates ubiquitination and degradation of BNIP3 and BNIP3L.
Fig. 3: MTDPS13 patient-associated FBXL4 mutants are defective in promoting ubiquitination and degradation of BNIP3/BNIP3L.
Fig. 4: FBXL4 deficiency activates mitophagy in a BNIP3/BNIP3L-dependent manner.
Fig. 5: BNIP3/BNIP3L-dependent mitophagy was abnormally activated in Fbxl4 mutation KI mouse model.
Fig. 6: Mitophagy is abnormally activated in CNs induced from MTDPS13 patient hiPSCs.
Fig. 7: A working model proposed in this study.

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Data availability

The mass spectrometry proteomics data have been deposited to the via the PRIDE partner repository with the dataset identifier PXD040601. All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials.

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Acknowledgements

The image in graphical model is produced by online program FigDraw (https://www.figdraw.com).

Funding

Funding

This work was in part supported by the National Natural Science Foundation of China (No. 91957125, 81972396 to CW; 31821002, 31930062 to SZ; 82071269 to LM; 82272992, 91954106 to KG), the State Key Development Programs of China (No. 2022YFA1104200 to CW; 2018YFA0800300 to SZ; 2021YFA1101302 to LM), the Natural Science Foundation of Shanghai (No. 22ZR1406600 to CW; 22ZR1449200 to KG), and the Open Research Fund of State Key Laboratory of Genetic Engineering, Fudan University (No. SKLGE-2111 to KG). Science and Technology Research Program of Shanghai (No. 9DZ2282100), Shanghai key clinical specialty project (No. shslczdzk05705 to YC), National Fund Cultivation Special Project of Shanghai Children’s Hospital (No. 2021YGZQ05 to XL).

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Author notes

  1. These authors contributed equally: Yingji Chen, Dongyue Jiao, Yang Liu.

Authors and Affiliations

  1. Obstetrics & Gynecology Hospital of Fudan University, Institutes of Metabolism and Integrative Biology, State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, PR China

    Yingji Chen, Dongyue Jiao, Xiayun Xu, Yao Li, Shi-Min Zhao & Chenji Wang

  2. Department of Anatomy, Histology & Embryology, School of Basic Medical Science, Fudan University, Shanghai, PR China

    Yang Liu & Lixiang Ma

  3. Department of Neurology, Shanghai Children’s Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, PR China

    Yilin Wang, Xiaona Luo & Yucai Chen

  4. State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, PR China

    Hexige Saiyin

  5. Department of Clinical Laboratory, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, PR China

    Kun Gao

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  1. Yingji Chen
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Contributions

CW conceived the study. YC, DJ, YL, XX, YW, and XL performed the experiments and data analyses. CW, LM, SZ, YC, YL, HS, and KG analyzed and interpreted the data. CW wrote the manuscript.

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Correspondence to Yucai Chen, Shi-Min Zhao, Lixiang Ma or Chenji Wang.

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Chen, Y., Jiao, D., Liu, Y. et al. FBXL4 mutations cause excessive mitophagy via BNIP3/BNIP3L accumulation leading to mitochondrial DNA depletion syndrome. Cell Death Differ 30, 2351–2363 (2023). https://doi.org/10.1038/s41418-023-01205-1

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