Nakatogawa, H. Mechanisms governing autophagosome biogenesis. Nat. Rev. Mol. Cell Biol. 21, 439–458 (2020).

Article  CAS  Google Scholar 

Schuck, S. Microautophagy — distinct molecular mechanisms handle cargoes of many sizes. J. Cell Sci. 133, jcs246322 (2020).

Article  CAS  Google Scholar 

Mizushima, N. & Komatsu, M. Autophagy: renovation of cells and tissues. Cell 147, 728–741 (2011).

Article  CAS  Google Scholar 

Levine, B. & Kroemer, G. Biological functions of autophagy genes: a disease perspective. Cell 176, 11–42 (2019).

Article  CAS  Google Scholar 

Mejlvang, J. et al. Starvation induces rapid degradation of selective autophagy receptors by endosomal microautophagy. J. Cell Biol. 217, 3640–3655 (2018).

Article  CAS  Google Scholar 

Müller, M. et al. The coordinated action of the MVB pathway and autophagy ensures cell survival during starvation. eLife 4, e07736 (2015).

Article  Google Scholar 

Lynch-Day, M. A. & Klionsky, D. J. The Cvt pathway as a model for selective autophagy. FEBS Lett. 584, 1359–1366 (2010).

Article  CAS  Google Scholar 

Liu, X. M. et al. ESCRTs cooperate with a selective autophagy receptor to mediate vacuolar targeting of soluble cargos. Mol. Cell 59, 1035–1042 (2015).

Article  CAS  Google Scholar 

Leidal, A. M. & Debnath, J. Emerging roles for the autophagy machinery in extracellular vesicle biogenesis and secretion. FASEB Bioadv. 3, 377–386 (2021).

Article  Google Scholar 

Mizushima, N. & Levine, B. Autophagy in human diseases. N. Engl. J. Med. 383, 1564–1576 (2020).

Article  CAS  Google Scholar 

Kaushik, S. & Cuervo, A. M. The coming of age of chaperone-mediated autophagy. Nat. Rev. Mol. Cell Biol. 19, 365–381 (2018).

Article  CAS  Google Scholar 

Fujioka, Y. et al. Structural basis of starvation-induced assembly of the autophagy initiation complex. Nat. Struct. Mol. Biol. 21, 513–521 (2014).

Article  CAS  Google Scholar 

Yamamoto, H. et al. The intrinsically disordered protein Atg13 mediates supramolecular assembly of autophagy initiation complexes. Dev. Cell 38, 86–99 (2016).

Article  CAS  Google Scholar 

Fujioka, Y. et al. Phase separation organizes the site of autophagosome formation. Nature 578, 301–305 (2020). This paper reports liquid–liquid phase separation of the Atg1 complex that initiates autophagosome formation in yeast.

Article  CAS  Google Scholar 

Turco, E. et al. FIP200 claw domain binding to p62 promotes autophagosome formation at ubiquitin condensates. Mol. Cell 74, 330–346.e311 (2019).

Article  CAS  Google Scholar 

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).

Article  CAS  Google Scholar 

Ravenhill, B. J. et al. The cargo receptor NDP52 initiates selective autophagy by recruiting the ULK complex to cytosol-invading bacteria. Mol. Cell 74, 320–329.e326 (2019). The 2019 papers by Turco et al., Vargas et al. and Ravenhill et al. report the recruitment of the ULK complex by selective autophagy adaptors.

Article  CAS  Google Scholar 

Turco, E. et al. Reconstitution defines the roles of p62, NBR1 and TAX1BP1 in ubiquitin condensate formation and autophagy initiation. Nat. Commun. 12, 5212 (2021).

Article  CAS  Google Scholar 

Smith, M. D. et al. CCPG1 is a non-canonical autophagy cargo receptor essential for ER-phagy and pancreatic ER proteostasis. Dev. Cell 44, 217–232 (2018).

Article  CAS  Google Scholar 

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

Article  CAS  Google Scholar 

Sawa-Makarska, J. et al. Reconstitution of autophagosome nucleation defines Atg9 vesicles as seeds for membrane formation. Science 369, eaaz7714 (2020).

Article  CAS  Google Scholar 

Ren, X. et al. Structural basis for ATG9A recruitment to the ULK1 complex in mitophagy initiation. Preprint at bioRxiv https://doi.org/10.1101/2022.07.12.499634 (2022).

Yamano, K. et al. Critical role of mitochondrial ubiquitination and the OPTN–ATG9A axis in mitophagy. J. Cell Biol. 219, e201912144 (2020).

Article  CAS  Google Scholar 

Coudevylle, N. et al. Mechanism of Atg9 recruitment by Atg11 in the cytoplasm-to-vacuole targeting pathway. J. Biol. Chem. 298, 101573 (2022).

Article  CAS  Google Scholar 

Baskaran, S. et al. Architecture and dynamics of the autophagic phosphatidylinositol 3-kinase complex. eLife 3, e05115 (2014).

Article  Google Scholar 

Hurley, J. H. & Young, L. N. Mechanisms of autophagy initiation. Annu. Rev. Biochem. 86, 225–244 (2017).

Article  CAS  Google Scholar 

Zheng, J. X. et al. Architecture of the ATG2B-WDR45 complex and an aromatic Y/HF motif crucial for complex formation. Autophagy 13, 1870–1883 (2017).

Article  CAS  Google Scholar 

Chowdhury, S. et al. Insights into autophagosome biogenesis from structural and biochemical analyses of the ATG2A–WIPI4 complex. Proc. Natl. Acad. Sci. USA 115, E9792–E9801 (2018).

Article  CAS  Google Scholar 

Maeda, S., Otomo, C. & Otomo, T. The autophagic membrane tether ATG2A transfers lipids between membranes. eLife 8, e45777 (2019).

Article  Google Scholar 

Osawa, T. et al. Atg2 mediates direct lipid transfer between membranes for autophagosome formation. Nat. Struct. Mol. Biol. 26, 281–288 (2019).

Article  CAS  Google Scholar 

Valverde, D. P. et al. ATG2 transports lipids to promote autophagosome biogenesis. J. Cell Biol. 218, 1787–1798 (2019). The 2019 papers by Maeda et al., Osawa et al. and Valverde et al. report that mammalian ATG2A and yeast Atg2 have lipid transfer activity.

Article  CAS  Google Scholar 

Ren, J. et al. Multi-site-mediated entwining of the linear WIR-motif around WIPI β-propellers for autophagy. Nat. Commun. 11, 2702 (2020).

Article  CAS  Google Scholar 

Dooley, H. C. et al. WIPI2 links LC3 conjugation with PI3P, autophagosome formation, and pathogen clearance by recruiting Atg12-5-16L1. Mol. Cell 55, 238–252 (2014).

Article  CAS  Google Scholar 

Bakula, D. et al. WIPI3 and WIPI4 beta-propellers are scaffolds for LKB1–AMPK–TSC signalling circuits in the control of autophagy. Nat. Commun. 8, 15637 (2017).

Article  CAS  Google Scholar 

Bozic, M. et al. A conserved ATG2–GABARAP family interaction is critical for phagophore formation. EMBO Rep. 21, e201948412 (2020).

Article  Google Scholar 

Maeda, S. et al. Structure, lipid scrambling activity and role in autophagosome formation of ATG9A. Nat. Struct. Mol. Biol. 27, 1194–1201 (2020).

Article  CAS  Google Scholar 

Matoba, K. et al. Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion. Nat. Struct. Mol. Biol. 27, 1185–1193 (2020). The 2020 papers by Maeda et al. and Matoba et al. demonstrate that mammalian ATG9A and yeast Atg9 have lipid scramblase activity.

Article  CAS  Google Scholar 

Ghanbarpour, A., Valverde, D. P., Melia, T. J. & Reinisch, K. M. A model for a partnership of lipid transfer proteins and scramblases in membrane expansion and organelle biogenesis. Proc. Natl. Acad. Sci. USA 118, e2101562118 (2021).

Article  CAS  Google Scholar 

Li, Y. E. et al. TMEM41B and VMP1 are scramblases and regulate the distribution of cholesterol and phosphatidylserine. J. Cell Biol. 220, e202103105 (2021).

Article  CAS  Google Scholar 

Huang, D. et al. TMEM41B acts as an ER scramblase required for lipoprotein biogenesis and lipid homeostasis. Cell Metab. 33, 1655–1670.e1658 (2021). The 2021 papers by Ghanbarpour et al., Li et al. and Huang et al. demonstrate that the ER membrane proteins TMEM41B and VMP1 have lipid scramblase activity.

Article  CAS  Google Scholar 

Okawa, F. et al. Evolution and insights into the structure and function of the DedA superfamily containing TMEM41B and VMP1. J. Cell Sci. 134, jcs255877 (2021).

Article  CAS  Google Scholar 

Mesdaghi, S., Murphy, D. L., Sanchez Rodriguez, F., Burgos-Marmol, J. J. & Rigden, D. J. In silico prediction of structure and function for a large family of transmembrane proteins that includes human Tmem41b. F1000Res 9, 1395 (2020).

Article  CAS  Google Scholar 

Hama, Y., Morishita, H. & Mizushima, N. Regulation of ER-derived membrane dynamics by the DedA domain-containing proteins VMP1 and TMEM41B. EMBO Rep. 23, e53894 (2022).

Article  CAS  Google Scholar 

Fujita, N. et al. An Atg4B mutant hampers the lipidation of LC3 paralogues and causes defects in autophagosome closure. Mol. Biol. Cell 19, 4651–4659 (2008).

Article  CAS  Google Scholar 

Sou, Y. S. et al. The Atg8 conjugation system is indispensable for proper development of autophagic isolation membranes in mice. Mol. Biol. Cell 19, 4762–4775 (2008).

Article  CAS  Google Scholar 

Uemura, T. et al. A cluster of thin tubular structures mediates transformation of the ER to autophagic isolation membrane. Mol. Cell. Biol. 34, 1695–1706 (2014).

Article  Google Scholar 

Tsuboyama, K. et al. The ATG conjugation systems are important for degradation of the inner autophagosomal membrane. Science 354, 1036–1041 (2016).

Article  CAS