Preprint / Version 1

A stress-sensing C9ORF72-SMCR8 switch licenses FIP200 condensates for rapid mitophagy

This article is a preprint and has not been certified by peer review.

Authors

    Dan Tang,  
    Dan Tang
    Hui Bao,  
    Hui Bao
    Shijian Feng,  
    Shijian Feng
    Wei Chen,  
    Wei Chen
    Hang Ci,   Haiying Zhang,   Xi Jin,   Liangting Xu,   Xinjun Zhao,   Yu Liu,   Qiuxiao Shi,   Xiaofang Huang,   Liping Su,   Lunzhi Dai,   Wei Cheng,   Lei Gao,  
    Lei Gao
    • Sichuan Real & Best Biotech Co., Ltd
    Biao Dong,   Xiaohe Tian,   Jing Chen,   Haoyang Cai,  
    Haoyang Cai
    Kunjie Wang,  
    Kunjie Wang
    Zhonghan Li,  
    Zhonghan Li
    Shiqian Qi
    Shiqian Qi
Categories
Keywords
C9orf72; SMCR8; ALS; mitophagy; ischemic injury

Abstract

Acute mitochondrial damage demands rapid and spatially restricted quality control, yet how cells convert such stress into immediate mitophagic responses remains elusive. Here, we identify the C9ORF72-SMCR8 complex as a phosphorylation-gated molecular switch that couples mitochondrial damage to rapid mitophagy through regulated protein condensation. Ischemic stress induces transient upregulation of C9ORF72, which stabilizes SMCR8 and licenses its effector function. Upon mitochondrial damage, ULK1 phosphorylates SMCR8 at Ser471, enabling engagement with the FIP200 Claw domain and licensing FIP200 condensation at damaged mitochondria. These condensates nucleate mitophagosome biogenesis, thereby promoting rapid and spatially restricted mitochondrial clearance. Disruption of this switch impairs FIP200 condensation and exacerbates ischemic injury in vivo. Conversely, a minimal SMCR8-derived peptide is sufficient to reconstitute FIP200 condensate formation, restore mitophagy, and support tissue protection in vivo. Together, these findings define a phosphorylation-controlled condensate mechanism in which an intrinsically disordered region in SMCR8 couples mitochondrial stress to rapid mitophagy.

 

References

1. Collaborators, G.B.D.L.R.o.S. et al. Global, Regional, and Country-Specific Lifetime Risks of Stroke, 1990 and 2016. N Engl J Med 379, 2429-2437 (2018).

2. Diseases, G.B.D. & Injuries, C. Global burden of 369 diseases and injuries in 204 countries and territories, 1990-2019: a systematic analysis for the Global Burden of Disease Study 2019. Lancet 396, 1204-1222 (2020).

3. Virani, S.S. et al. Heart Disease and Stroke Statistics-2021 Update: A Report From the American Heart Association. Circulation 143, e254-e743 (2021).

4. Collaborators, G.B.D.S.R.F. Global, regional, and national burden of stroke and its risk factors, 1990-2021: a systematic analysis for the Global Burden of Disease Study 2021. Lancet Neurol 23, 973-1003 (2024).

5. Francis, A. et al. Chronic kidney disease and the global public health agenda: an international consensus. Nat Rev Nephrol 20, 473-485 (2024).

6. Sun, J. et al. Mitochondria in Sepsis-Induced AKI. J Am Soc Nephrol 30, 1151-1161 (2019).

7. Granger, D.N. & Kvietys, P.R. Reperfusion injury and reactive oxygen species: The evolution of a concept. Redox Biol 6, 524-551 (2015).

8. Chouchani, E.T. et al. Ischaemic accumulation of succinate controls reperfusion injury through mitochondrial ROS. Nature 515, 431-435 (2014).

9. Brookes, P.S., Yoon, Y., Robotham, J.L., Anders, M.W. & Sheu, S.S. Calcium, ATP, and ROS: a mitochondrial love-hate triangle. Am J Physiol Cell Physiol 287, C817-833 (2004).

10. Lesnefsky, E.J., Moghaddas, S., Tandler, B., Kerner, J. & Hoppel, C.L. Mitochondrial dysfunction in cardiac disease: ischemia--reperfusion, aging, and heart failure. J Mol Cell Cardiol 33, 1065-1089 (2001).

11. Ramachandra, C.J.A., Hernandez-Resendiz, S., Crespo-Avilan, G.E., Lin, Y.H. & Hausenloy, D.J. Mitochondria in acute myocardial infarction and cardioprotection. EBioMedicine 57, 102884 (2020).

12. Yao, C. et al. Mitochondrial dysfunction in acute kidney injury. Ren Fail 46, 2393262 (2024).

13. Vargas, J.N.S., Hamasaki, M., Kawabata, T., Youle, R.J. & Yoshimori, T. The mechanisms and roles of selective autophagy in mammals. Nat Rev Mol Cell Biol 24, 167-185 (2023).

14. Wang, S. et al. The mitophagy pathway and its implications in human diseases. Signal Transduct Target Ther 8, 304 (2023).

15. Zhang, L., Dai, L. & Li, D. Mitophagy in neurological disorders. J Neuroinflammation 18, 297 (2021).

16. Baek, S.H. et al. Modulation of mitochondrial function and autophagy mediates carnosine neuroprotection against ischemic brain damage. Stroke 45, 2438-2443 (2014).

17. Antico, O., Thompson, P.W., Hertz, N.T., Muqit, M.M.K. & Parton, L.E. Targeting mitophagy in neurodegenerative diseases. Nat Rev Drug Discov (2025).

18. Denk, D. et al. Effect of the mitophagy inducer urolithin A on age-related immune decline: a randomized, placebo-controlled trial. Nat Aging 5, 2309-2322 (2025).

19. Qader, M.A. et al. A systematic review of the therapeutic potential of nicotinamide adenine dinucleotide precursors for cognitive diseases in preclinical rodent models. BMC Neurosci 26, 17 (2025).

20. DeJesus-Hernandez, M. et al. Expanded GGGGCC hexanucleotide repeat in noncoding region of C9ORF72 causes chromosome 9p-linked FTD and ALS. Neuron 72, 245-256 (2011).

21. Renton, A.E. et al. A hexanucleotide repeat expansion in C9ORF72 is the cause of chromosome 9p21-linked ALS-FTD. Neuron 72, 257-268 (2011).

22. Pang, W. & Hu, F. Cellular and physiological functions of C9ORF72 and implications for ALS/FTD. J Neurochem 157, 334-350 (2021).

23. Mizielinska, S. et al. Amyotrophic lateral sclerosis caused by hexanucleotide repeat expansions in C9orf72: from genetics to therapeutics. Lancet Neurol 24, 261-274 (2025).

24. Jiang, L., Zhang, T., Lu, K. & Qi, S. The progress in C9orf72 research: ALS/FTD pathogenesis, functions and structure. Small GTPases 13, 56-76 (2022).

25. Lan, Y., Sullivan, P.M. & Hu, F. SMCR8 negatively regulates AKT and MTORC1 signaling to modulate lysosome biogenesis and tissue homeostasis. Autophagy 15, 871-885 (2019).

26. Zhang, Y. et al. The C9orf72-interacting protein Smcr8 is a negative regulator of autoimmunity and lysosomal exocytosis. Genes Dev 32, 929-943 (2018).

27. Yang, M. et al. A C9ORF72/SMCR8-containing complex regulates ULK1 and plays a dual role in autophagy. Sci Adv 2, e1601167 (2016).

28. Sullivan, P.M. et al. The ALS/FTLD associated protein C9orf72 associates with SMCR8 and WDR41 to regulate the autophagy-lysosome pathway. Acta Neuropathol Commun 4, 51 (2016).

29. Ugolino, J. et al. Loss of C9orf72 Enhances Autophagic Activity via Deregulated mTOR and TFEB Signaling. PLoS Genet 12, e1006443 (2016).

30. Zucha, D. et al. Spatiotemporal transcriptomic map of glial cell response in a mouse model of acute brain ischemia. Proc Natl Acad Sci U S A 121, e2404203121 (2024).

31. Bormann, D. et al. Single-nucleus RNA sequencing reveals glial cell type-specific responses to ischemic stroke in male rodents. Nat Commun 15, 6232 (2024).

32. Cui, M. et al. Dynamic Transcriptional Responses to Injury of Regenerative and Non-regenerative Cardiomyocytes Revealed by Single-Nucleus RNA Sequencing. Dev Cell 53, 102-116 e108 (2020).

33. Balzer, M.S. et al. Single-cell analysis highlights differences in druggable pathways underlying adaptive or fibrotic kidney regeneration. Nat Commun 13, 4018 (2022).

34. Malone, A.F. et al. Harnessing Expressed Single Nucleotide Variation and Single Cell RNA Sequencing To Define Immune Cell Chimerism in the Rejecting Kidney Transplant. J Am Soc Nephrol 31, 1977-1986 (2020).

35. Xu, X. et al. Tet2 acts in the lateral habenula to regulate social preference in mice. Cell Rep 42, 112695 (2023).

36. Zhang, Y. et al. HDAC9-mediated epithelial cell cycle arrest in G2/M contributes to kidney fibrosis in male mice. Nat Commun 14, 3007 (2023).

37. Tang, D. et al. ALS-linked C9orf72-SMCR8 complex is a negative regulator of primary ciliogenesis. Proc Natl Acad Sci U S A 120, e2220496120 (2023).

38. Tang, D. et al. Cryo-EM structure of C9ORF72-SMCR8-WDR41 reveals the role as a GAP for Rab8a and Rab11a. Proc Natl Acad Sci U S A 117, 9876-9883 (2020).

39. Wang, C. A Sensitive and Quantitative mKeima Assay for Mitophagy via FACS. Curr Protoc Cell Biol 86, e99 (2020).

40. Jung, J. et al. Multiplex image-based autophagy RNAi screening identifies SMCR8 as ULK1 kinase activity and gene expression regulator. Elife 6 (2017).

41. Zhang, M. et al. Mechanistic insights into the interactions of TAX1BP1 with RB1CC1 and mammalian ATG8 family proteins. Proceedings of the National Academy of Sciences 121, e2315550121 (2024).

42. Eickhorst, C. et al. FIP200 Phosphorylation Regulates Late Steps in Mitophagy. J Mol Biol, 168631 (2024).

43. Wu, S. et al. Structural basis for TNIP1 binding to FIP200 during mitophagy. J Biol Chem 300, 107605 (2024).

44. Zheng, Q. et al. Calcium transients on the ER surface trigger liquid-liquid phase separation of FIP200 to specify autophagosome initiation sites. Cell 185, 4082-4098 e4022 (2022).

45. Turco, E. et al. FIP200 Claw Domain Binding to p62 Promotes Autophagosome Formation at Ubiquitin Condensates. Mol Cell 74, 330-346 e311 (2019).

46. Zhou, Z. et al. Phosphorylation regulates the binding of autophagy receptors to FIP200 Claw domain for selective autophagy initiation. Nat Commun 12, 1570 (2021).

47. Sellier, C. et al. Loss of C9ORF72 impairs autophagy and synergizes with polyQ Ataxin-2 to induce motor neuron dysfunction and cell death. EMBO J 35, 1276-1297 (2016).

48. Majounie, E. et al. Frequency of the C9orf72 hexanucleotide repeat expansion in patients with amyotrophic lateral sclerosis and frontotemporal dementia: a cross-sectional study. Lancet Neurol 11, 323-330 (2012).

49. Webster, C.P. et al. The C9orf72 protein interacts with Rab1a and the ULK1 complex to regulate initiation of autophagy. EMBO J 35, 1656-1676 (2016).

50. Tang, D., Bao, H. & Qi, S. The C9orf72-SMCR8 complex suppresses primary ciliogenesis as a RAB8A GAP. Autophagy 20, 1205-1207 (2024).

51. Zhang, S. et al. C9orf72-catalyzed GTP loading of Rab39A enables HOPS-mediated membrane tethering and fusion in mammalian autophagy. Nat Commun 14, 6360 (2023).

52. Su, M.Y., Fromm, S.A., Zoncu, R. & Hurley, J.H. Structure of the C9orf72 ARF GAP complex that is haploinsufficient in ALS and FTD. Nature 585, 251-255 (2020).

53. Tang, D. et al. Cryo-EM structure of C9ORF72–SMCR8–WDR41 reveals the role as a GAP for Rab8a and Rab11a. Proceedings of the National Academy of Sciences 117, 9876-9883 (2020).

54. Licheva, M. et al. Phase separation of initiation hubs on cargo is a trigger switch for selective autophagy. Nat Cell Biol (2025).

55. Shi, X. et al. ULK complex organization in autophagy by a C-shaped FIP200 N-terminal domain dimer. J Cell Biol 219 (2020).

56. Jung, J. & Behrends, C. Multifaceted role of SMCR8 as autophagy regulator. Small GTPases 11, 53-61 (2020).

57. Vargas, J.N.S. et al. Spatiotemporal Control of ULK1 Activation by NDP52 and TBK1 during Selective Autophagy. Mol Cell 74, 347-362 e346 (2019).

58. Tang, D., Sheng, J., Xu, L., Yan, C. & Qi, S. The C9orf72-SMCR8-WDR41 complex is a GAP for small GTPases. Autophagy 16, 1542-1543 (2020).

59. Goodier, J.L. et al. C9orf72-associated SMCR8 protein binds in the ubiquitin pathway and with proteins linked with neurological disease. Acta Neuropathol Commun 8, 110 (2020).

60. Amick, J., Tharkeshwar, A.K., Talaia, G. & Ferguson, S.M. PQLC2 recruits the C9orf72 complex to lysosomes in response to cationic amino acid starvation. J Cell Biol 219 (2020).

61. Talaia, G., Amick, J. & Ferguson, S.M. Receptor-like role for PQLC2 amino acid transporter in the lysosomal sensing of cationic amino acids. bioRxiv (2020).

62. Zhu, Q. et al. Reduced C9ORF72 function exacerbates gain of toxicity from ALS/FTD-causing repeat expansion in C9orf72. Nat Neurosci 23, 615-624 (2020).

63. Butti, Z., Pan, Y.E., Giacomotto, J. & Patten, S.A. Reduced C9orf72 function leads to defective synaptic vesicle release and neuromuscular dysfunction in zebrafish. Commun Biol 4, 792 (2021).

64. Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573-3587 e3529 (2021).

65. Yan, L., Edn. 0.1.19 An easy-to-use way to draw pretty Venn diagrams using 'ggplot2'. This package provides functions to create Venn diagrams with customizable colors, labels, and styling options. (2025).

66. Gene Ontology, C. The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Res 49, D325-D334 (2021).

67. Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25, 25-29 (2000).

68. Kanehisa, M. & Goto, S. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28, 27-30 (2000).

69. Kanehisa, M., Furumichi, M., Sato, Y., Matsuura, Y. & Ishiguro-Watanabe, M. KEGG: biological systems database as a model of the real world. Nucleic Acids Res 53, D672-D677 (2025).

70. Wu, T. et al. clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. Innovation (Camb) 2, 100141 (2021).

71. Benjamini, Y. & Hochberg, Y. Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society: Series B (Methodological) 57, 289-300 (1995).

72. Lazarou, M. et al. The ubiquitin kinase PINK1 recruits autophagy receptors to induce mitophagy. Nature 524, 309-314 (2015).

73. Cong, L. et al. Multiplex Genome Engineering Using CRISPR/Cas Systems. Science 339, 819-823 (2013).

74. Tai, R.-Z. & Zhao, Z.-T. Overview of SSRF phase-II beamlines. Nuclear Science and Techniques 35, 137 (2024).

75. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276, 307-326 (1997).

76. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60, 2126-2132 (2004).

77. Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr D Struct Biol 75, 861-877 (2019).

78. Schrodinger, LLC (2015).

79. Jin, X. et al. Membraneless organelles formed by liquid-liquid phase separation increase bacterial fitness. Sci Adv 7, eabh2929 (2021).

80. Muzzopappa, F. et al. Detecting and quantifying liquid-liquid phase separation in living cells by model-free calibrated half-bleaching. Nat Commun 13, 7787 (2022).

81. Takaori, K. et al. Severity and Frequency of Proximal Tubule Injury Determines Renal Prognosis. J Am Soc Nephrol 27, 2393-2406 (2016).

82. Chiang, T., Messing, R.O. & Chou, W.H. Mouse model of middle cerebral artery occlusion. J Vis Exp (2011).

83. Wang, Q. et al. Efficient production of dual recombinant adeno-associated viral vectors for factor VIII delivery. Hum Gene Ther Methods 25, 261-268 (2014).

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2026-05-13

How to Cite

Tang, D., Bao, H., Feng, S., Chen, W., Ci, H., Zhang, H., Jin, X., Xu, L., Zhao, X., Liu, Y., Shi, Q., Huang, X., Su, L., Dai, L., Cheng, W., Gao, L., Dong, B., Tian, X., Chen, J., … Qi, S. (2026). A stress-sensing C9ORF72-SMCR8 switch licenses FIP200 condensates for rapid mitophagy. LangTaoSha Preprint Server. https://doi.org/10.65215/LTSpreprints.2026.05.13.000241

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Declaration of Competing Interests

The authors declare no competing interests to disclose.