Advances in Autophagy Regulatory Mechanisms

Abstract

Autophagy plays a critical role in cell metabolism by degrading and recycling internal components when challenged with limited nutrients. This fundamental and conserved mechanism is based on a membrane trafficking pathway in which nascent autophagosomes engulf cytoplasmic cargo to form vesicles that transport their content to the lysosome for degradation. Based on this simple scheme, autophagy modulates cellular metabolism and cytoplasmic quality control to influence an unexpectedly wide range of normal mammalian physiology and pathophysiology. In this review, we summarise recent advancements in three broad areas of autophagy regulation. We discuss current models on how autophagosomes are initiated from endogenous membranes. We detail how the uncoordinated 51-like kinase (ULK) complex becomes activated downstream of mechanistic target of rapamycin complex 1 (MTORC1). Finally, we summarise the upstream signalling mechanisms that can sense amino acid availability leading to activation of MTORC1.

Keywords: ATG14L; Beclin 1; MTOR; ULK; VPS34; amino acids; autophagosome; autophagy; isolation membrane.

Figure 1

Assembly of autophagy isolation membranes. Starvation of nutrients leads to suppression of MTOR complex 1 resulting in downstream activation of the ULK1 autophagy initiation complex. The activated ULK1 complex translocates to an ER-based early autophagy membrane assembly zone associated with mitochondria contact sites, maintained in part via mitofusin 2 (Mfn2) and phosphofurin acidic cluster sorting protein-2 (PACS2). This assembly zone corresponds to early autophagy initiation puncta visualised by light microscopy. Activated ULK1 signals downstream by phosphorylating and activating the Beclin 1–VPS34–ATG14L–VPS15 complex, driving the generation of isolation membrane associated tubules (IMAT) and the omegasome. PI3P-enriched microdomains recruit markers like DFCP1 and machinery like WIPI2b along with further associated factors such as the ATG16L1–ATG5–ATG12 complex. After initial stages of membrane assembly, Golgi-derived vesicles containing ATG9A- and ERGIC-derived vesicles contribute further membranes and assembly machinery.

Figure 2

Summary of the ULK1 interactome. A subset of ULK1 protein interactions collated by the BioGRID server was selected for representation. Proteins characterised to also serve as ULK1 substrates are highlighted pink. Thickness of connectors corresponds to numbers of experimental entries supporting interaction. Note: this interaction database does not capture all known ULK1-binding partners including, for example, ATG9, ATG14L1 or FUNDC1.

Figure 3

Circuitry of amino acid signalling to MTORC1. Extracellular amino acids are first transported into the cell. Regulatory amino acids such as Leu and Arg are further transported into the lysosome. Lysosomal Arg is sensed via SLC38A9.1, leading to activation of the vATPase-Ragulator complex and MTORC1. Leu is sensed via Sesn2 to regulate the GATOR1 pathway. Gln activates MTORC1 via an Arf1-mediated pathway. Amino acids also activate MTORC1 at the Golgi via Rab1A. Growth factor signalling leads to activation of PI3K and AKT, which controls the TSC1/2 complex and Rheb.