br Introduction The term autophagy

Introduction The term “autophagy” was coined by Christian de Duve in 1963 to describe the process of removing and degrading intracellular components such as unused proteins and damaged organelles through lysosomes [1,2]. Autophagy has been divided into three main types, namely, macroautophagy, microautophagy, and chaperone-mediated autophagy. Microautophagy is mediated by direct lysosomal engulfment of cytoplasmic cargo [3]. Chaperone-mediated autophagy (CMA) involves having heat shock proteins (HSPs; e.g., HSPA8/HSC70 [HSP family A Hsp70 member 8]) that recognize proteins with the amino 17-aag motif KFERQ, which are then degraded in lysosomes [4]. Macroautophagy (hereafter referred to as autophagy) involves the sequestration of autophagic cargo in phagophores that close to form autophagosomes, which later fuse with lysosomes to generated autolysosomes. Macroautophagy can be further divided into bulk and selective autophagy. This process has been most extensively investigated in mammalian models and regulates cellular homeostasis in human health and disease [[5], [6], [7]]. Research on autophagy has developed rapidly since the discovery of autophagy-related (ATG) genes in the yeast Saccharomyces cerevisiae, which was used as a model system to study autophagy starting in the 1990s [[8], [9], [10]]. Today, over 40 ATG genes have been identified in yeast by genetic screening, and approximately half of the Atg proteins have clear homologs in mammalian cells [11,12]. These Atg/ATG (yeast/mammalian) proteins can form complexes with other molecular regulators to control the formation and maturation of autophagy-associated membrane structures, including phagophores, autophagosomes and autolysosomes (Fig. 1). Phagophores are newly formed membranes from various resources (e.g., the endoplasmic reticulum, trans-Golgi network, and plasma membrane) to enclose and isolate the cytoplasmic components during autophagy. The induction of autophagy and phagophore formation require the activation of two protein complexes, namely the ULK complex (containing ULK1 [unc-51 like autophagy activating kinase 1, an ortholog of yeast Atg1], ATG13, and the scaffold protein RB1CC1/FIP200 [RB1 inducible coiled-coil 1, an ortholog of yeast Atg17]) and the class III phosphatidylinositol 3-kinase complex (containing PIK3C3 [phosphatidylinositol 3-kinase catalytic subunit type 3, an ortholog of yeast Vps34], BECN1 [a mammalian homolog of yeast Vps30/Atg6], and PIK3R4 [phosphoinositide 3-kinase regulatory subunit 4, a mammalian homolog of yeast Vps15]). The elongation of the phagophore requires two ubiquitin-like conjugation systems, namely ATG12 and MAP1LC3 (microtubule-associated protein 1 light chain 3, an ortholog of yeast Atg8), which results in the formation of autophagosomes, the characteristic double-membrane structures during autophagy. Conjugation reactions of ATG12 and MAP1LC3 are catalyzed by the E1-like enzyme ATG7, and the E2-like enzymes ATG10 (for conjugation of ATG12) and ATG3 (for MAP1LC3), and result in the formation of either a multimeric complex with ATG5 (involving ATG12) or a phosphatidylethanolamine (PE) conjugate (with MAP1LC3). The ATG12–ATG5 conjugate further forms a complex with ATG16L1 (autophagy related 16-like 1 [S. cerevisiae]) during autophagosome formation. ATG4 is a cysteine protease and plays an important role in the redox regulation of autophagy by the lipidation and delipidation of MAP1LC3. The oxidization of ATG4 at Cys81 by hydrogen peroxide inhibits ATG4′s catalytic activity and promotes subsequent lipidation of MAP1LC3, which is required for autophagosome formation [13]. Lipidated MAP1LC3 marks the phagophore assembly site, thus generating a critical signal and a marker of the biogenesis of these vesicles. Furthermore, the formation of autolysosomes by autophagosome-lysosome fusion requires the lysosomal membrane protein LAMP2 (lysosomal-associated membrane protein 2) and other regulator proteins such as SNARE (soluble NSF attachment protein receptor), GTPase-activating protein RAB7, and the HOPS (homotypic fusion and protein sorting) complex [14]. Ultimately, after fusion, a series of lysosomal enzymes such as proteases, acid phosphatases, lipases and nucleases are implicated in the degradation of the lumenal content.