FIGURE 2.

The processes of autophagy. Autophagy processes include autophagy induction, phagophore nucleation, elongation and closure, autophagosome maturation, and fusion with lysosomes to form autolysosomes, which are mediated by multiple ATG proteins and a variety of kinases or partners with complex mechanisms. Autophagy initiation requires the activation of the uncoordinated-51-like kinase (ULK) complex, which is regulated by two kinases, AMP-activated protein kinase (AMPK) and mammalian target of rapamycin (mTOR) complex 1 (mTORC1). ULK1 activation causes phosphorylation of BECLIN1 and ATG14, thus promoting the formation of the PI3KC3 complex, which enhances the activity of VPS34 to generate phosphatidylinositol 3-phosphate (PI3P) (Russell et al., 2013; Nascimbeni et al., 2017). The enrichment of PI3P recruits double FYVE domain-containing protein 1 (DFCP1), downstream ATG proteins, and WD repeat proteins interacting with phosphoinositides 1 and 2 (WIPI1/2) for phagophore nucleation (Young and Wang, 2018). Phagophore elongation is mediated by two ubiquitin-like conjugation systems, ATG12-ATG5-ATG16L and the ATG8 (light chain 3, LC3) conjugation system (Noda and Inagaki, 2015). Phagophore closure is most likely accomplished by endosomal sorting complex required for transport (ESCRT) machinery-mediated membrane abscission (Tsuboyama et al., 2016; Takahashi et al., 2018, 2019). Additionally, the γ-aminobutyric acid receptor-associated protein (GABARAP) and ATG2 family are also critical for phagophore closure (Weidberg et al., 2010; Bozic et al., 2020). The ER-localized transmembrane protein vacuole membrane protein 1 (VMP1) mediates ER-phagophore dissociation via activating ER Ca²⁺ channel sarcoplasmic Ca²⁺-ATPase (SERCA) and perturbing the local Ca²⁺ concentration (Zhao et al., 2017). Mature autophagosomes migrate to lysosomes involves the participation of proteins such as RAB7, FYVE coiled-coil domain-containing protein 1 (FYCO1), RAB-interacting lysosomal protein (RILP), Oxysterol-binding protein-related protein 1L (ORP1L), histone deacetylase 6 (HDAC6), kinesin or dynein (Nakamura and Yoshimori, 2017). RAB GTPases, soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs), PI3K complex, and multiple tethering factors are involved in the fusion of autophagosomes with lysosomes to form autolysosomes, in which the autophagosomal contents are degraded by lysosomal acid hydrolases (Martini-Stoica et al., 2016; Zhao and Zhang, 2019). Transcription factor EB (TFEB) is a major regulator for autophagosome formation, lysosomal biogenesis, and lysosomal function (Martini-Stoica et al., 2016; Cortes and La Spada, 2019).