Kondadi, A. K., Anand, R. & Reichert, A. S. Cristae membrane dynamics â a paradigm change. Trends Cell Biol. 30, 923â936 (2020).
Soubannier, V. et al. A vesicular transport pathway shuttles cargo from mitochondria to lysosomes. Curr. Biol. 22, 135â141 (2012).
Li, X. et al. Mitochondria shed their outer membrane in response to infection-induced stress. Science 375, eabi4343 (2022).
Jiao, H. et al. Mitocytosis, a migrasome-mediated mitochondrial quality-control process. Cell 184, 2896â2910 (2021).
Ma, X. Mitochondria-lysosome-related organelles mediate mitochondrial clearance during cellular dedifferentiation. Cell Rep. 42, 113291 (2023).
Hughes, A. L., Hughes, C. E., Henderson, K. A., Yazvenko, N. & Gottschling, D. E. Selective sorting and destruction of mitochondrial membrane proteins in aged yeast. eLife 5, e13943 (2016).
Wolf, D. M. et al. Individual cristae within the same mitochondrion display different membrane potentials and are functionally independent. EMBO J. 38, e101056 (2019).
Kondadi, A. K. et al. Cristae undergo continuous cycles of membrane remodelling in a MICOSâdependent manner. EMBO Rep. 21, e49776 (2020).
Cogliati, S., Enriquez, J. A. & Scorrano, L. Mitochondrial cristae: where beauty meets functionality. Trends Biochem. Sci. 41, 261â273 (2016).
Correia-Melo, C., Ichim, G., G Tait, S. W. & Passos, F. Depletion of mitochondria in mammalian cells through enforced mitophagy. Nat. Protoc. 12, 183â194 (2016).
Stephan, T. et al. MICOS assembly controls mitochondrial inner membrane remodeling and crista junction redistribution to mediate cristae formation. EMBO J. 39, e104105 (2020).
Sugiura, A., McLelland, G., Fon, E. A. & McBride, H. M. A new pathway for mitochondrial quality control: mitochondrialâderived vesicles. EMBO J. 33, 2142â2156 (2014).
König, T. et al. MIROs and DRP1 drive mitochondrial-derived vesicle biogenesis and promote quality control. Nat. Cell Biol. 23, 1271â1286 (2021).
Matheoud, D. et al. Parkinsonâs disease-related proteins PINK1 and Parkin repress mitochondrial antigen presentation. Cell 166, 314â327 (2016).
Schuler, M. H. et al. Mitochondrial-derived compartments facilitate cellular adaptation to amino acid stress. Mol. Cell 81, 3786â3802 (2021).
Lyamzaev, K. G. et al. MitoCLox: a novel mitochondria-targeted fluorescent probe for tracing lipid peroxidation. Oxid. Med. Cell. Longev. 2019, 9710208 (2019).
Lyamzaev, K. G. et al. Novel fluorescent mitochondria-targeted probe MitoCLox reports lipid peroxidation in response to oxidative stress in vivo. Oxid. Med. Cell. Longev. 2020, 3631272 (2020).
McArthur, K. et al. BAK/BAX macropores facilitate mitochondrial herniation and mtDNA efflux during apoptosis. Science 359, eaao6047 (2018).
Xian, H. et al. Oxidized DNA fragments exit mitochondria via mPTP- and VDAC-dependent channels to activate NLRP3 inflammasome and interferon signaling. Immunity 55, 1370â1385 (2022).
Kim, J. et al. VDAC oligomers form mitochondrial pores to release mtDNA fragments and promote lupus-like disease. Science 366, 1531â1536 (2019).
Zecchini, V. et al. Fumarate induces vesicular release of mtDNA to drive innate immunity. Nature 615, 499â506 (2023).
Newman, L. E. et al. Mitochondrial DNA replication stress triggers a pro-inflammatory endosomal pathway of nucleoid disposal. Nat. Cell Biol. 26, 194â206 (2024).
DâAco, K. E. et al. Mitochondrial tRNA(Phe) mutation as a cause of end-stage renal disease in childhood. Pediatr. Nephrol. 28, 515â519 (2013).
Piper, R. C. & Katzmann, D. J. Biogenesis and function of multivesicular bodies. Annu. Rev. Cell Dev. Biol. 23, 519â547 (2007).
Shelke, G. V., Williamson, C. D., Jarnik, M. & Bonifacino, J. S. Inhibition of endolysosome fusion increases exosome secretion. J. Cell Biol. 222, e202209084 (2023).
Kleele, T. et al. Distinct fission signatures predict mitochondrial degradation or biogenesis. Nature 593, 435â439 (2021).
Hoogenboom, B. W., Suda, K., Engel, A. & Fotiadis, D. The supramolecular assemblies of voltage-dependent anion channels in the native membrane. J. Mol. Biol. 370, 246â255 (2007).
Gonçalves, R. P., Buzhynskyy, N., Prima, V., Sturgis, J. N. & Scheuring, S. Supramolecular assembly of VDAC in native mitochondrial outer membranes. J. Mol. Biol. 369, 413â418 (2007).
Keinan, N., Tyomkin, D. & Shoshan-Barmatz, V. Oligomerization of the mitochondrial protein voltage-dependent anion channel is coupled to the induction of apoptosis. Mol. Cell. Biol. 30, 5698â5709 (2010).
Shteinfer-Kuzmine, A. et al. Targeting the mitochondrial protein VDAC1 as a potential therapeutic strategy in ALS. Int. J. Mol. Sci. 23, 9946 (2022).
Peng, W., Wong, Y. C. & Krainc, D. Mitochondria-lysosome contacts regulate mitochondrial Ca2+ dynamics via lysosomal TRPML1. Proc. Natl Acad. Sci. USA 117, 19266â19275 (2020).
Zhang, X. et al. MCOLN1 is a ROS sensor in lysosomes that regulates autophagy. Nat. Commun. 7, 12109 (2016).
Rossi, A., Pizzo, P. & Filadi, R. Calcium, mitochondria and cell metabolism: a functional triangle in bioenergetics. Biochim. Biophys. Acta Mol. Cell. Res. 1866, 1068â1078 (2019).
Dayam, R. M., Saric, A., Shilliday, R. E. & Botelho, R. J. The phosphoinositide-gated lysosomal Ca2+ channel, TRPML1, is required for phagosome maturation. Traffic 16, 1010â1026 (2015).
Chen, C. C. et al. A small molecule restores function to TRPML1 mutant isoforms responsible for mucolipidosis type IV. Nat. Commun. 5, 4681 (2014).
Dikic, I. & Elazar, Z. Mechanism and medical implications of mammalian autophagy. Nat. Rev. Mol. Cell Biol. 19, 349â364 (2018).
Kaushik, S. & Cuervo, A. M. The coming of age of chaperone-mediated autophagy. Nat. Rev. Mol. Cell Biol. 19, 365â381 (2018).
Wang, L., Klionsky, D. J. & Shen, H. M. The emerging mechanisms and functions of microautophagy. Nat. Rev. Mol. Cell Biol. 24, 186â203 (2023).
Müller, O. et al. Autophagic tubes: vacuolar invaginations involved in lateral membrane sorting and inverse vesicle budding. J. Cell Biol. 151, 519â528 (2000).
Oku, M. et al. Evidence for ESC RT- and clathrin-dependent microautophagy. J. Cell Biol. 216, 3263â3274 (2017).
Omari, S. et al. Noncanonical autophagy at ER exit sites regulates procollagen turnover. Proc. Natl Acad. Sci. USA 115, E10099âE10108 (2018).
Lee, C., Lamech, L., Johns, E. & Overholtzer, M. Selective lysosome membrane turnover is induced by nutrient starvation. Dev. Cell 55, 289â297 (2020).
Bento, C. F. et al. Mammalian autophagy: how does it work? Annu. Rev. Biochem. 85, 685â713 (2016).
Pickles, S., Vigi, P. & Youle, R. J. Current biology review mitophagy and quality control mechanisms in mitochondrial maintenance. Curr. Biol. 28, R170âR185 (2018).
Kuchitsu, Y. & Taguchi, T. Lysosomal microautophagy: an emerging dimension in mammalian autophagy. Trends Cell Biol. 34, 606â616 (2023).
Palikaras, K., Lionaki, E. & Tavernarakis, N. Mechanisms of mitophagy in cellular homeostasis, physiology and pathology. Nat. Cell Biol. 20, 1013â1022 (2018).
Vietri, M., Radulovic, M. & Stenmark, H. The many functions of ESCRTs. Nat. Rev. Mol. Cell Biol. 21, 25â42 (2020).
Scheffer, L. L. et al. Mechanism of Ca2+-triggered ESCRT assembly and regulation of cell membrane repair. Nat. Commun. 5, 5646 (2014).
Huang, C., Deng, K. & Wu, M. Mitochondrial cristae in health and disease. Int. J. Biol. Macromol. 235, 123755 (2023).
Tábara, L. C. et al. MTFP1 controls mitochondrial fusion to regulate inner membrane quality control and maintain mtDNA levels. Cell 187, 3619â3637 (2024).
Elia, N., Sougrat, R., Spurlin, T. A., Hurley, J. H. & Lippincott-Schwartz, J. Dynamics of endosomal sorting complex required for transport (ESCRT) machinery during cytokinesis and its role in abscission. Proc Natl Acad. Sci. USA 108, 4846â4851 (2011).
Bagshaw, R. D., Callahan, J. W. & Mahuran, D. J. The Arf-family protein, Arl8b, is involved in the spatial distribution of lysosomes. Biochem. Biophys. Res. Commun. 344, 1186â1191 (2006).
Cemma, M., Kim, P. K. & Brumell, J. H. The ubiquitin-binding adaptor proteins p62/SQSTM1 and NDP52 are recruited independently to bacteria-associated microdomains to target Salmonella to the autophagy pathway. Autophagy 7, 341â345 (2011).
Boutry, M. & Kim, P. K. ORP1L mediated PI(4)P signaling at ER-lysosome-mitochondrion three-way contact contributes to mitochondrial division. Nat. Commun. 12, 5354 (2021).
Law, K. B. et al. The peroxisomal AAA ATPase complex prevents pexophagy and development of peroxisome biogenesis disorders. Autophagy 13, 868â884 (2017).
Sargent, G. et al. PEX2 is the E3 ubiquitin ligase required for pexophagy during starvation. J. Cell Biol. 214, 677â690 (2016).
Wang, Y., Nartiss, Y., Steipe, B., McQuibban, G. A. & Kim, P. K. ROS-induced mitochondrial depolarization initiates PARK2/PARKIN-dependent mitochondrial degradation by autophagy. Autophagy 8, 1462â1476 (2012).
Roy, M., Itoh, K., Iijima, M. & Sesaki, H. Parkin suppresses Drp1-independent mitochondrial division. Biochem. Biophys. Res. Commun. 475, 283â288 (2016).
Kageyama, Y. et al. Parkinâindependent mitophagy requires Drp1 and maintains the integrity of mammalian heart and brain. EMBO J. 33, 2798â2813 (2014).
Fujita, N. et al. Recruitment of the autophagic machinery to endosomes during infection is mediated by ubiquitin. J. Cell Biol. 203, 115â128 (2013).
Yan, B. R. et al. C5orf51 is a component of the MON1-CCZ1 complex and controls RAB7A localization and stability during mitophagy. Autophagy 18, 829â840 (2022).
Durkin, M., Qian, X., Popescu, N. & Lowy, D. Isolation of mouse embryo fibroblasts. Bio Protoc. 3, e908 (2013).
Paul-Gilloteaux, P. et al. eC-CLEM: flexible multidimensional registration software for correlative microscopies. Nat. Methods 14, 102â103 (2017).
