Fig. 1. A simplified scheme of the autophagy process.

(1) mTORC1 negatively regulates ULK1/2 by phosphorylating Ser 317 and Ser 777, whereas AMPK positively regulates ULK1/2 by phosphorylating S637 and S757 of ULK1/2. Nucleation of the pre-autophagosome structure requires both the ULK complex and the PtdIns3K complex. Activated ULK1/2 phosphorylates Beclin-1, leading to VPS34 activation and phagophore formation. (2) Elongation and autophagosome formation are mediated by two “ubiquitin-like conjugation systems”. In general, the protease ATG4 first processes nascent LC3 to the cytosolic form LC3-I, and then ATG7 and ATG3 act as E1-, E2-like enzymes to further process LC3-I to the lipid-conjugated form LC3-II. Meanwhile, ATG7 (E1) and ATG10 (E2) promote the ATG12-ATG5 conjugation with ATG16L1 to form the ATG12-ATG5-ATG16L1 complex, which works as an E3 ligase to promote the formation of phosphatidylethanolamine (PE)-conjugated LC3-II. The phagophore transmembrane protein ATG9, with ATG2 and WIPI1/2 (ATG18) participates in the expanding phagophore by delivering membrane and lipids from donor sources such as ER and Golgi complex. The closure of autophagosome membranes requires ESCRT, including VPS37A, CHMP2A, and VPS4, as well as ER transmembrane proteins VMP1 and TMEM41B. (3) The autophagosome-lysosome fusion process is regulated by the fusion machinery NSF and SNARE family proteins, such as VAMP7, VAMP8, VAMP9, SNAP29 and STX17. STX17 interacts with SNAP29 and lysosomal VAMP8, which leads to autophagosome-lysosome fusion. In addition, LAMP-1 and LAMP-2, two lysosomal membrane proteins, and RAB7, a small GTPase, are required for the fusion of autophagosomes with lysosomes. Finally, the autophagosome content is degraded by acidic hydrolases within the lysosome.