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Oxidation of retromer complex controls mitochondrial translation

Zhang, Junbing, Ali, Md Yousuf, Chong, Harrison Byron, Tien, Pei-Chieh, Woods, James, Noble, Carolina, Vornbäumen, Tristan, Ordulu, Zehra, Possemato, Anthony P., Harry, Stefan, Fonticella, Jay Miguel, Fellah, Lina, Harrison, Drew, Ge, Maolin, Khandelwal, Neha, Huang, Yingfei, Chauvin, Maëva, Bischof, Anica Tamara, Hambelton, Grace Marie, Gohar, Magdy Farag, Zhang, Siwen, Choi, MinGyu, Bouberhan, Sara, Oliva, Esther, Mino-Kenudson, Mari, Pavlova, Natalya N., Lawrence, Michael, Gainor, Justin F., Beausoleil, Sean A., Bardeesy, Nabeel, Mostoslavsky, Raul, Pépin, David, Ott, Christopher J., Liau, Brian, Bar-Peled, Liron·2025·Nature
DOI 10.1038/s41586-025-08756-yPMC PMC13005050
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  1. Chio, I. I. C. & Tuveson, D. A. ROS in cancer: the burning question. Trends Mol. Med. 23, 411–429 (2017). · DOI · Paper page
  2. Williams, E. T., Chen, X. & Moore, D. J. VPS35, the retromer complex and Parkinson’s disease. J. Parkinsons Dis. 7, 219–233 (2017). · DOI
  3. Liu, Y. & Birsoy, K. Metabolic sensing and control in mitochondria. Mol. Cell 83, 877–889 (2023). · DOI
  4. Bar-Peled, L. & Kory, N. Principles and functions of metabolic compartmentalization. Nat. Metab. 4, 1232–1244 (2022). · DOI
  5. Cheung, E. C. & Vousden, K. H. The role of ROS in tumour development and progression. Nat. Rev. Cancer 22, 280–297 (2022). · DOI
  6. Reczek, C. R. & Chandel, N. S. ROS-dependent signal transduction. Curr. Opin. Cell Biol. 33, 8–13 (2015). · DOI
  7. Chouchani, E. T., Kazak, L. & Spiegelman, B. M. Mitochondrial reactive oxygen species and adipose tissue thermogenesis: bridging physiology and mechanisms. J. Biol. Chem. 292, 16810–16816 (2017). · DOI
  8. Collins, Y. et al. Mitochondrial redox signalling at a glance. J. Cell Sci. 125, 801–806 (2012). · DOI
  9. Xiao, H. et al. A quantitative tissue-specific landscape of protein redox regulation during aging. Cell 180, 968–983.e924 (2020). · DOI
  10. Takahashi, M. et al. DrugMap: a quantitative pan-cancer analysis of cysteine ligandability. Cell 187, 2536–2556 e2530 (2024). · DOI
  11. Zhang, J. & Bar-Peled, L. Chemical biology approaches to uncovering nuclear ROS control. Curr. Opin. Chem. Biol. 76, 102352 (2023). · DOI
  12. Harris, I. S. & DeNicola, G. M. The complex interplay between antioxidants and ROS in cancer. Trends Cell Biol. 30, 440–451 (2020). · DOI
  13. Ge, M., Papagiannakopoulos, T. & Bar-Peled, L. Reductive stress in cancer: coming out of the shadows. Trends Cancer 10, 103–112 (2024). · DOI
  14. Murphy, M. P. How mitochondria produce reactive oxygen species. Biochem. J 417, 1–13 (2009). · DOI · Paper page
  15. Li, H. et al. Assigning functionality to cysteines by base editing of cancer dependency genes. Nat. Chem. Biol. 19, 1320–1330 (2023). · DOI · Paper page
  16. Lue, N. Z. et al. Base editor scanning charts the DNMT3A activity landscape. Nat. Chem. Biol. 19, 176–186 (2023). · DOI
  17. Gallon, M. & Cullen, P. J. Retromer and sorting nexins in endosomal sorting. Biochem. Soc. Trans. 43, 33–47 (2015). · DOI
  18. Chandel, N. S. Evolution of mitochondria as signaling organelles. Cell Metab. 22, 204–206 (2015). · DOI · Paper page
  19. Fu, Y. et al. The role of mitochondria in the chemoresistance of pancreatic cancer cells. Cells 10, 497 (2021). · DOI
  20. Zhang, J. et al. Systematic identification of anticancer drug targets reveals a nucleus-to-mitochondria ROS-sensing pathway. Cell 186, 2361–2379 e2325 (2023). · DOI
  21. Saeed, M. et al. Low-dose doxycycline inhibits hydrogen peroxide-induced oxidative stress, MMP-2 up-regulation and contractile dysfunction in human saphenous vein grafts. Drug Des. Devel. Ther. 13, 1791–1801 (2019). · DOI
  22. Luger, A. L. et al. Doxycycline impairs mitochondrial function and protects human glioma cells from hypoxia-induced cell death: implications of using Tet-inducible systems. Int. J. Mol. Sci. 19, 1504 (2018). · DOI
  23. Suhm, T. et al. Mitochondrial translation efficiency controls cytoplasmic protein homeostasis. Cell Metab. 27, 1309–1322.e1306 (2018). · DOI
  24. Steinhorn, B. et al. Chemogenetic generation of hydrogen peroxide in the heart induces severe cardiac dysfunction. Nat. Commun. 9, 4044 (2018). · DOI
  25. Nakagawa, T. et al. Doxycycline attenuates cisplatin-induced acute kidney injury through pleiotropic effects. Am. J. Physiol. Renal Physiol. 315, F1347–f1357 (2018). · DOI
  26. Bak, D. W. & Weerapana, E. Cysteine-mediated redox signalling in the mitochondria. Mol. Biosyst. 11, 678–697 (2015). · DOI
  27. Lue, N. Z. & Liau, B. B. Base editor screens for in situ mutational scanning at scale. Mol. Cell 83, 2167–2187 (2023). · DOI
  28. Komor, A. C., Kim, Y. B., Packer, M. S., Zuris, J. A. & Liu, D. R. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533, 420–424 (2016). · DOI · Paper page
  29. Anantharaman, V., Aravind, L. & Koonin, E. V. Emergence of diverse biochemical activities in evolutionarily conserved structural scaffolds of proteins. Curr. Opin. Chem. Biol. 7, 12–20 (2003). · DOI
  30. Boatner, L. M., Palafox, M. F., Schweppe, D. K. & Backus, K. M. CysDB: a human cysteine database based on experimental quantitative chemoproteomics. Cell. Chem. Biol. 30, 683–698 e683 (2023). · DOI
  31. Li, C. et al. Spermine synthase deficiency causes lysosomal dysfunction and oxidative stress in models of Snyder–Robinson syndrome. Nat. Commun. 8, 1257 (2017). · DOI
  32. Kovtun, O. et al. Structure of the membrane-assembled retromer coat determined by cryo-electron tomography. Nature 561, 561–564 (2018). · DOI · Paper page
  33. Hierro, A. et al. Functional architecture of the retromer cargo-recognition complex. Nature 449, 1063–1067 (2007). · DOI · Paper page
  34. Haft, C. R. et al. Human orthologs of yeast vacuolar protein sorting proteins Vps26, 29, and 35: assembly into multimeric complexes. Mol. Biol. Cell 11, 4105–4116 (2000). · DOI · Paper page
  35. Arighi, C. N., Hartnell, L. M., Aguilar, R. C., Haft, C. R. & Bonifacino, J. S. Role of the mammalian retromer in sorting of the cation-independent mannose 6-phosphate receptor. J. Cell Biol. 165, 123–133 (2004). · DOI · Paper page
  36. Tabuchi, M., Yanatori, I., Kawai, Y. & Kishi, F. Retromer-mediated direct sorting is required for proper endosomal recycling of the mammalian iron transporter DMT1. J. Cell Sci. 123, 756–766 (2010). · DOI
  37. Lo Conte, M. & Carroll, K. S. Chemoselective ligation of sulfinic acids with aryl-nitroso compounds. Angew. Chem. 51, 6502–6505 (2012). · DOI
  38. Yin, Z. et al. Structural basis for a complex I mutation that blocks pathological ROS production. Nat. Commun. 12, 707 (2021). · DOI
  39. Pak, V. V. et al. Ultrasensitive genetically encoded indicator for hydrogen peroxide identifies roles for the oxidant in cell migration and mitochondrial function. Cell Metab. 31, 642–653.e646 (2020). · DOI
  40. Gai, X. et al. Oncogenic KRAS induces arginine auxotrophy and confers a therapeutic vulnerability to SLC7A1 inhibition in non-small cell lung cancer. Cancer Res. 84, 1963–1977 (2024). · DOI
  41. Jungnickel, K. E. J., Parker, J. L. & Newstead, S. Structural basis for amino acid transport by the CAT family of SLC7 transporters. Nat. Commun. 9, 550 (2018). · DOI
  42. Atwal, S. et al. Clickable methionine as a universal probe for labelling intracellular bacteria. J. Microbiol. Methods 169, 105812 (2020). · DOI
  43. Kimura, Y. et al. Mito-FUNCAT-FACS reveals cellular heterogeneity in mitochondrial translation. RNA 28, 895–904 (2022). · DOI
  44. Hällberg, B. M. & Larsson, N. G. Making proteins in the powerhouse. Cell Metab. 20, 226–240 (2014). · DOI
  45. Rottenberg, S., Disler, C. & Perego, P. The rediscovery of platinum-based cancer therapy. Nat. Rev. Cancer 21, 37–50 (2021). · DOI
  46. Vasan, N. & Cantley, L. C. At a crossroads: how to translate the roles of PI3K in oncogenic and metabolic signalling into improvements in cancer therapy. Nat. Rev. Clin. Oncol. 19, 471–485 (2022). · DOI
  47. Cheng, J. et al. Accurate proteome-wide missense variant effect prediction with AlphaMissense. Science 381, eadg7492 (2023). · DOI · Paper page
  48. Cutillo, G., Simon, D. K. & Eleuteri, S. VPS35 and the mitochondria: connecting the dots in Parkinson’s disease pathophysiology. Neurobiol. Dis. 145, 105056 (2020). · DOI
  49. Tang, F.-L. et al. VPS35 deficiency or mutation causes dopaminergic neuronal loss by impairing mitochondrial fusion and function. Cell Rep. 12, 1631–1643 (2015). · DOI
  50. Wider, C. et al. Autosomal dominant dopa-responsive parkinsonism in a multigenerational Swiss family. Parkinsonism Relat. Disord. 14, 465–470 (2008). · DOI
  51. Sanmamed, M. F. & Chen, L. A paradigm shift in cancer immunotherapy: from enhancement to normalization. Cell 175, 313–326 (2018). · DOI
  52. Lee, M. Y., Jeon, J. W., Sievers, C. & Allen, C. T. Antigen processing and presentation in cancer immunotherapy. J. Immunother. Cancer 8, e001111 (2020). · DOI
  53. Blanc-Durand, F., Clemence Wei Xian, L. & Tan, D. S. P. Targeting the immune microenvironment for ovarian cancer therapy. Front. Immunol. 14, 1328651 (2023). · DOI
  54. Canver, M. C. et al. Integrated design, execution, and analysis of arrayed and pooled CRISPR genome-editing experiments. Nat. Protoc. 13, 946–986 (2018). · DOI
  55. Concordet, J. P. & Haeussler, M. CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens. Nucleic Acids Res. 46, W242–w245 (2018). · DOI
  56. Adelmann, C. H., Wang, T., Sabatini, D. M. & Lander, E. S. Genome-wide CRISPR/Cas9 screening for identification of cancer genes in cell lines. Methods Mol. Biol. 1907, 125–136 (2019). · DOI
  57. Bordier, C. Phase separation of integral membrane proteins in Triton X-114 solution. J. Biol. Chem. 256, 1604–1607 (1981). · DOI
  58. Weiss-Sadan, T. et al. NRF2 activation induces NADH-reductive stress, providing a metabolic vulnerability in lung cancer. Cell Metab. 35, 722 (2023). · DOI
  59. Pavlova, N. N. et al. Translation in amino-acid-poor environments is limited by tRNAGln charging. eLife 9, e62307 (2020). · DOI
  60. Elia, I. et al. Proline metabolism supports metastasis formation and could be inhibited to selectively target metastasizing cancer cells. Nat. Commun. 8, 15267 (2017). · DOI
  61. Oliva, C. R., Ali, M. Y., Flor, S. & Griguer, C. E. COX4-1 promotes mitochondrial supercomplex assembly and limits reactive oxide species production in radioresistant GBM. Cell Stress 6, 45–60 (2022). · DOI
  62. Timón-Gómez, A. et al. Protocol for the analysis of yeast and human mitochondrial respiratory chain complexes and supercomplexes by blue native electrophoresis. STAR Protoc. 1, 100089 (2020). · DOI
  63. Nassar, L. R. et al. The UCSC Genome Browser database: 2023 update. Nucleic Acids Res. 51, D1188–d1195 (2023). · DOI
  64. Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015). · DOI · Paper page
  65. Marino, S. M. & Gladyshev, V, N. Cysteine function governs its conservation and degeneration and restricts its utilization on protein surfaces. J. Mol. Biol. 404, 902–916 (2010). · DOI
  66. Van Der Spoel, D. et al. GROMACS: fast, flexible, and free. J. Comput. Chem. 26, 1701–1718 (2005). · DOI
  67. Brooks, B. R. et al. CHARMM: the biomolecular simulation program. J. Comput. Chem. 30, 1545–1614 (2009). · DOI
  68. Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004). · DOI

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Metadata

Authors
Zhang, J., Ali, M. Y., Chong, H. B., Tien, P.-C., Woods, J., Noble, C., Vornbäumen, T., Ordulu, Z., Possemato, A. P., Harry, S., Fonticella, J. M., Fellah, L., Harrison, D., Ge, M., Khandelwal, N., Huang, Y., Chauvin, M., Bischof, A. T., Hambelton, G. M., Gohar, M. F., Zhang, S., Choi, M., Bouberhan, S., Oliva, E., Mino-Kenudson, M., Pavlova, N. N., Lawrence, M., Gainor, J. F., Beausoleil, S. A., Bardeesy, N., Mostoslavsky, R., Pépin, D., Ott, C. J., Liau, B., & Bar-Peled, L.
Venue
Nature
Publisher
Springer Science and Business Media LLC
Published
2025-03-26
Volume
641
Issue
8064
Pages
1048-1058
ISSN
  • 0028-0836
  • 1476-4687
DOI
10.1038/s41586-025-08756-y
PMC
PMC13005050
Cited by
38
References
10
Language
en
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