Oxidation of retromer complex controls mitochondrial translation – Nature
Chio, I. I. C. & Tuveson, D. A. ROS in cancer: the burning question. Trends Mol. Med. 23, 411–429 (2017).
Google Scholar
Weinberg, F. et al. Mitochondrial metabolism and ROS generation are essential for Kras-mediated tumorigenicity. Proc. Natl Acad. Sci. USA 107, 8788–8793 (2010).
Google Scholar
Williams, E. T., Chen, X. & Moore, D. J. VPS35, the retromer complex and Parkinson’s disease. J. Parkinsons Dis. 7, 219–233 (2017).
Google Scholar
Liu, Y. & Birsoy, K. Metabolic sensing and control in mitochondria. Mol. Cell 83, 877–889 (2023).
Google Scholar
Bar-Peled, L. & Kory, N. Principles and functions of metabolic compartmentalization. Nat. Metab. 4, 1232–1244 (2022).
Google Scholar
Cheung, E. C. & Vousden, K. H. The role of ROS in tumour development and progression. Nat. Rev. Cancer 22, 280–297 (2022).
Google Scholar
Reczek, C. R. & Chandel, N. S. ROS-dependent signal transduction. Curr. Opin. Cell Biol. 33, 8–13 (2015).
Google Scholar
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).
Google Scholar
Collins, Y. et al. Mitochondrial redox signalling at a glance. J. Cell Sci. 125, 801–806 (2012).
Google Scholar
Xiao, H. et al. A quantitative tissue-specific landscape of protein redox regulation during aging. Cell 180, 968–983.e924 (2020).
Google Scholar
Takahashi, M. et al. DrugMap: a quantitative pan-cancer analysis of cysteine ligandability. Cell 187, 2536–2556 e2530 (2024).
Google Scholar
Zhang, J. & Bar-Peled, L. Chemical biology approaches to uncovering nuclear ROS control. Curr. Opin. Chem. Biol. 76, 102352 (2023).
Google Scholar
Harris, I. S. & DeNicola, G. M. The complex interplay between antioxidants and ROS in cancer. Trends Cell Biol. 30, 440–451 (2020).
Google Scholar
Ge, M., Papagiannakopoulos, T. & Bar-Peled, L. Reductive stress in cancer: coming out of the shadows. Trends Cancer 10, 103–112 (2024).
Google Scholar
Murphy, M. P. How mitochondria produce reactive oxygen species. Biochem. J 417, 1–13 (2009).
Google Scholar
Brand, M. D. et al. Suppressors of superoxide-H2O2 production at site IQ of mitochondrial complex I protect against stem cell hyperplasia and ischemia-reperfusion injury. Cell Metab. 24, 582–592 (2016).
Google Scholar
Ashrafi, G., Schlehe, J. S., LaVoie, M. J. & Schwarz, T. L. Mitophagy of damaged mitochondria occurs locally in distal neuronal axons and requires PINK1 and Parkin. J. Cell Biol. 206, 655–670 (2014).
Google Scholar
Li, H. et al. Assigning functionality to cysteines by base editing of cancer dependency genes. Nat. Chem. Biol. 19, 1320–1330 (2023).
Google Scholar
Lue, N. Z. et al. Base editor scanning charts the DNMT3A activity landscape. Nat. Chem. Biol. 19, 176–186 (2023).
Google Scholar
Gallon, M. & Cullen, P. J. Retromer and sorting nexins in endosomal sorting. Biochem. Soc. Trans. 43, 33–47 (2015).
Google Scholar
Chandel, N. S. Evolution of mitochondria as signaling organelles. Cell Metab. 22, 204–206 (2015).
Google Scholar
Yang, H. et al. The role of cellular reactive oxygen species in cancer chemotherapy. J. Exp. Clin. Cancer Res. 37, 266 (2018).
Google Scholar
Fu, Y. et al. The role of mitochondria in the chemoresistance of pancreatic cancer cells. Cells 10, 497 (2021).
Google Scholar
Zhang, J. et al. Systematic identification of anticancer drug targets reveals a nucleus-to-mitochondria ROS-sensing pathway. Cell 186, 2361–2379 e2325 (2023).
Google Scholar
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).
Google Scholar
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).
Google Scholar
Suhm, T. et al. Mitochondrial translation efficiency controls cytoplasmic protein homeostasis. Cell Metab. 27, 1309–1322.e1306 (2018).
Google Scholar
Steinhorn, B. et al. Chemogenetic generation of hydrogen peroxide in the heart induces severe cardiac dysfunction. Nat. Commun. 9, 4044 (2018).
Google Scholar
Nakagawa, T. et al. Doxycycline attenuates cisplatin-induced acute kidney injury through pleiotropic effects. Am. J. Physiol. Renal Physiol. 315, F1347–f1357 (2018).
Google Scholar
Bak, D. W. & Weerapana, E. Cysteine-mediated redox signalling in the mitochondria. Mol. Biosyst. 11, 678–697 (2015).
Google Scholar
Lue, N. Z. & Liau, B. B. Base editor screens for in situ mutational scanning at scale. Mol. Cell 83, 2167–2187 (2023).
Google Scholar
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).
Google Scholar
Gabaldón, T. & Koonin, E. V. Functional and evolutionary implications of gene orthology. Nat. Rev. Genet. 14, 360–366 (2013).
Google Scholar
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).
Google Scholar
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).
Google Scholar
Li, C. et al. Spermine synthase deficiency causes lysosomal dysfunction and oxidative stress in models of Snyder–Robinson syndrome. Nat. Commun. 8, 1257 (2017).
Google Scholar
Kovtun, O. et al. Structure of the membrane-assembled retromer coat determined by cryo-electron tomography. Nature 561, 561–564 (2018).
Google Scholar
Hierro, A. et al. Functional architecture of the retromer cargo-recognition complex. Nature 449, 1063–1067 (2007).
Google Scholar
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).
Google Scholar
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).
Google Scholar
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).
Google Scholar
Lo Conte, M. & Carroll, K. S. Chemoselective ligation of sulfinic acids with aryl-nitroso compounds. Angew. Chem. 51, 6502–6505 (2012).
Google Scholar
Yin, Z. et al. Structural basis for a complex I mutation that blocks pathological ROS production. Nat. Commun. 12, 707 (2021).
Google Scholar
Liu, G. Y. & Sabatini, D. M. mTOR at the nexus of nutrition, growth, ageing and disease. Nat. Rev. Mol. Cell Biol. 21, 183–203 (2020).
Google Scholar
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).
Google Scholar
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).
Google Scholar
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).
Google Scholar
Atwal, S. et al. Clickable methionine as a universal probe for labelling intracellular bacteria. J. Microbiol. Methods 169, 105812 (2020).
Google Scholar
Kimura, Y. et al. Mito-FUNCAT-FACS reveals cellular heterogeneity in mitochondrial translation. RNA 28, 895–904 (2022).
Google Scholar
Hällberg, B. M. & Larsson, N. G. Making proteins in the powerhouse. Cell Metab. 20, 226–240 (2014).
Google Scholar
Rottenberg, S., Disler, C. & Perego, P. The rediscovery of platinum-based cancer therapy. Nat. Rev. Cancer 21, 37–50 (2021).
Google Scholar
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).
Google Scholar
Shaw, R. J. & Cantley, L. C. Ras, PI(3)K and mTOR signalling controls tumour cell growth. Nature 441, 424–430 (2006).
Google Scholar
Cheng, J. et al. Accurate proteome-wide missense variant effect prediction with AlphaMissense. Science 381, eadg7492 (2023).
Google Scholar
Cutillo, G., Simon, D. K. & Eleuteri, S. VPS35 and the mitochondria: connecting the dots in Parkinson’s disease pathophysiology. Neurobiol. Dis. 145, 105056 (2020).
Google Scholar
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).
Google Scholar
Wider, C. et al. Autosomal dominant dopa-responsive parkinsonism in a multigenerational Swiss family. Parkinsonism Relat. Disord. 14, 465–470 (2008).
Google Scholar
Sanmamed, M. F. & Chen, L. A paradigm shift in cancer immunotherapy: from enhancement to normalization. Cell 175, 313–326 (2018).
Google Scholar
Lee, M. Y., Jeon, J. W., Sievers, C. & Allen, C. T. Antigen processing and presentation in cancer immunotherapy. J. Immunother. Cancer 8, e001111 (2020).
Google Scholar
Blanc-Durand, F., Clemence Wei Xian, L. & Tan, D. S. P. Targeting the immune microenvironment for ovarian cancer therapy. Front. Immunol. 14, 1328651 (2023).
Google Scholar
Canver, M. C. et al. Integrated design, execution, and analysis of arrayed and pooled CRISPR genome-editing experiments. Nat. Protoc. 13, 946–986 (2018).
Google Scholar
Hanna, R. E. et al. Massively parallel assessment of human variants with base editor screens. Cell 184, 1064–1080.e1020 (2021).
Google Scholar
Concordet, J. P. & Haeussler, M. CRISPOR: intuitive guide selection for CRISPR/Cas9 genome editing experiments and screens. Nucleic Acids Res. 46, W242–w245 (2018).
Google Scholar
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).
Google Scholar
Bar-Peled, L. et al. Chemical proteomics identifies druggable vulnerabilities in a genetically defined cancer. Cell 171, 696–709.e623 (2017).
Google Scholar
Bordier, C. Phase separation of integral membrane proteins in Triton X-114 solution. J. Biol. Chem. 256, 1604–1607 (1981).
Google Scholar
Weiss-Sadan, T. et al. NRF2 activation induces NADH-reductive stress, providing a metabolic vulnerability in lung cancer. Cell Metab. 35, 722 (2023).
Google Scholar
Pavlova, N. N. et al. Translation in amino-acid-poor environments is limited by tRNAGln charging. eLife 9, e62307 (2020).
Google Scholar
Elia, I. et al. Proline metabolism supports metastasis formation and could be inhibited to selectively target metastasizing cancer cells. Nat. Commun. 8, 15267 (2017).
Google Scholar
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).
Google Scholar
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).
Google Scholar
Nassar, L. R. et al. The UCSC Genome Browser database: 2023 update. Nucleic Acids Res. 51, D1188–d1195 (2023).
Google Scholar
Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2015).
Google Scholar
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).
Van Der Spoel, D. et al. GROMACS: fast, flexible, and free. J. Comput. Chem. 26, 1701–1718 (2005).
Google Scholar
Brooks, B. R. et al. CHARMM: the biomolecular simulation program. J. Comput. Chem. 30, 1545–1614 (2009).
Google Scholar
Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
Google Scholar
