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RUNDC1 inhibits autolysosome formation and survival of zebrafish via clasping ATG14-STX17-SNAP29 complex

Cell Death & Differentiation volume 30, pages 2231–2248 (2023)Cite this article

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Abstract

Autophagy serves as a pro-survival mechanism for a cell or a whole organism to cope with nutrient stress. Our understanding of the molecular regulation of this fusion event remains incomplete. Here, we identified RUNDC1 as a novel ATG14-interacting protein, which is highly conserved across vertebrates, including zebrafish and humans. By gain and loss of function studies, we demonstrate that RUNDC1 negatively modulates autophagy by blocking fusion between autophagosomes and lysosomes via inhibiting the assembly of the STX17-SNAP29-VAMP8 complex both in human cells and the zebrafish model. Moreover, RUNDC1 clasps the ATG14-STX17-SNAP29 complex via stimulating ATG14 homo-oligomerization to inhibit ATG14 dissociation. This also prevents VAMP8 from binding to STX17-SNAP29. We further identified that phosphorylation of RUNDC1 Ser379 is crucial to inhibit the assembly of the STX17-SNAP29-VAMP8 complex via promoting ATG14 homo-oligomerization. In line with our findings, RunDC1 is crucial for zebrafish in their response to nutrient-deficient conditions. Taken together, our findings demonstrate that RUNDC1 is a negative regulator of autophagy that restricts autophagosome fusion with lysosomes by clasping the ATG14-STX17-SNAP29 complex to hinder VAMP8 binding.

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Fig. 1: RUNDC1 is a protein partner of ATG14, but is not involved in the assembly of the PtdIns3K-C1 complex.
Fig. 2: RunDC1 negatively affects autophagy in zebrafish.
Fig. 3: RUNDC1 inhibits fusion between autophagosomes and lysosomes in cell and zebrafish models.
Fig. 4: RUNDC1 interacts with the ATG14-STX17-SNAP29 complex.
Fig. 5: RUNDC1 inhibits assembly of the VAMP8 -STX17-SNAP29 complex.
Fig. 6: RUNDC1 promotes ATG14 homo-oligomerization resulted in clasping of the ATG14-STX17-SNAP29 complex.
Fig. 7: RUNDC1 Ser379 phosphorylation inhibits ATG14 dissociation from the ATG14-STX17-SNAP29 complex.
Fig. 8: RunDC1 affects the survival of zebrafish larvae and adults in response to starvation.

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Data availability

The data analyzed during this study are included in this published article and the supplemental data files. Additional supporting data are available from the corresponding authors upon reasonable request.

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Acknowledgements

We are grateful to Prof. Daniel Klionsky and Prof. Annemarie Meijer for sharing the GFP-Lc3 transgenic zebrafish line. We also thank the Hubei University of Technology for financial and equipment support for this research.

Funding

This work was supported by the National Natural Science Foundation of China (32000523 to RZ, 82273970 and 32070726 to JFT, 31871176 to XZC, 32270768 to CFZ), International Science and Technology Cooperation Project of Hubei Province (2022EHB038 to CFZ), Wuhan Science and Technology Project (2022020801020272 to C.F.Z) and Innovation Group Project of Hubei Province (2023AFA026).

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  1. These authors contributed equally: Rui Zhang, Yuyan Yang, Chao He.

Authors and Affiliations

  1. National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan, China

    Rui Zhang, Yuyan Yang, Chao He, Xin Zhang, Nan Liu, Jiaren Yang, Shicheng Liu, Jinglei Yuan, Shi Li, Xueying Dong, Hua Bai, Mengyu Hu, Zhiquan Liao, Yuan Huang, Hao Lyu, Shuai Xiao, Dong Guo, Jingfeng Tang & Cefan Zhou

  2. Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK

    Vincenzo Torraca

  3. School of Life Sciences, University of Westminster, London, UK

    Vincenzo Torraca

  4. Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology and the Collaborative Innovation Center for Brain Science, Huazhong University of Science and Technology, Wuhan, China

    Shen Wang & Cong Ma

  5. School of Public Health, Chongqing Medical University, Chongqing, China

    Dongzhi Gou

  6. School of food science and bioengineering, Changsha University of Science & Technology, Changsha, China

    Yufei Xie

  7. Department of Nephrology, Daping hospital, Army Medical Center, Army Medical University, Chongqing, China

    Junling He

  8. Department of Biochemistry, University of Alberta, Edmonton, AB, Canada

    Declan William Ali & Xing-Zhen Chen

  9. Membrane Protein Disease Research Group, Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada

    Marek Michalak

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Contributions

RZ, YY, CH, XZ and SW performed molecular biology and zebrafish experiments and write the main manuscript. JT and CZ designed the whole project and supervised all experiments. RZ, YY, CH, XZ conducted all experiments and analyzed the data. VC, NL, YR, LC, LY, GZ, LS, DY, XF, HY, LH, SX, GD, DA, MM, XC, and CM contributed with critical feedback on the presented work. All authors read and approved the final manuscript.

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Correspondence to Jingfeng Tang or Cefan Zhou.

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The experimental protocol for animal studies was reviewed and approved by the institutional animal care and use committee of the Hubei University of Technology.

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Zhang, R., Yang, Y., He, C. et al. RUNDC1 inhibits autolysosome formation and survival of zebrafish via clasping ATG14-STX17-SNAP29 complex. Cell Death Differ 30, 2231–2248 (2023). https://doi.org/10.1038/s41418-023-01215-z

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