Autophagy: a critical regulator of cellular metabolism and homeostasis

Abstract

Autophagy is a dynamic process by which cytosolic material, including organelles, proteins, and pathogens, are sequestered into membrane vesicles called autophagosomes, and then delivered to the lysosome for degradation. By recycling cellular components, this process provides a mechanism for adaptation to starvation. The regulation of autophagy by nutrient signals involves a complex network of proteins that include mammalian target of rapamycin, the class III phosphatidylinositol-3 kinase/Beclin 1 complex, and two ubiquitin-like conjugation systems. Additionally, autophagy, which can be induced by multiple forms of chemical and physical stress, including endoplasmic reticulum stress, and hypoxia, plays an integral role in the mammalian stress response. Recent studies indicate that, in addition to bulk assimilation of cytosol, autophagy may proceed through selective pathways that target distinct cargoes to autophagosomes. The principle homeostatic functions of autophagy include the selective clearance of aggregated protein to preserve proteostasis, and the selective removal of dysfunctional mitochondria (mitophagy). Additionally, autophagy plays a central role in innate and adaptive immunity, with diverse functions such as regulation of inflammatory responses, antigen presentation, and pathogen clearance. Autophagy can preserve cellular function in a wide variety of tissue injury and disease states, however, maladaptive or pro-pathogenic outcomes have also been described. Among the many diseases where autophagy may play a role include proteopathies which involve aberrant accumulation of proteins (e.g., neurodegenerative disorders), infectious diseases, and metabolic disorders such as diabetes and metabolic syndrome. Targeting the autophagy pathway and its regulatory components may eventually lead to the development of therapeutics.

Fig. 1.

Autophagy pathway. The autophagic pathway procedes through a series of sequential steps. These begin with the initiation of the pathway and autophagosome nucleation (formation of a pre-autophagosomal structure leading to an isolation membrane or phagophore). This is followed by autophagosomal elongation, a step mediated by two ubiquitin-like conjugation systems (i.e., ATG8, and the ATG5/ATG12 systems). The next steps involve autophagosome maturation, including the sequestration of cytosol or specific substrates, and autophagosome/lysosome fusion. In the final stage, autophagosomal cargoes are digested by lysosomal enzymes, and the contents released for metabolic recycling.

Fig. 2.

Regulation of autophagy by nutrient signals. Autophagy responds to regulation by nutrient signals, which operate a signaling pathway involving mammalian (or mechanistic) target of rapamycin (mTOR). Autophagy is negatively regulated by the Class I phosphatidylinositol 3-kinase (PI3K)/Akt signaling pathway, which activates mTOR in response to insulin and other growth factors. Akt may also negatively regulate autophagy by phosphorylating Beclin 1. The adenosine 5′-monophosphate-activated protein kinase (AMPK) which is regulated by AMP levels, negatively regulates mTOR, and also phosphorylates ULK1, thereby acting as a positive regulator of autophagy in response to energy exhaustion. mTOR is a major component of the mTOR signaling complex (mTORC1), which regulates the ULK1 complex, consisting of the mammalian uncoordinated-51-like protein kinase ULK1, ATG13, ATG101, and FIP200. Under nutrient rich conditions, mTORC1 inhibits ULK1 kinase activity, thereby inhibiting the activation of autophagy. Autophagy is also regulated by the Beclin 1 interactive complex, consisting of Beclin 1, class III phosphatidylinositol-3-kinase (VPS34 or PI3KC3) and ATG14L. Stimulation of this complex generates phosphatidylinositol-3-phosphate (PI3P), which triggers autophagosomal membrane nucleation. Several interacting factors may participate in this regulation, including UVRAG and Bif-1, which substitute for ATG14L, Ambra1, the negative regulator Rubicon, and Bcl-2 family proteins.

Fig. 3.

Regulation of autophagosome elongation. Autophagosome membrane elongation is regulated by two ubiquitin-like conjugation systems. The ubiquitin-like protein ATG12 is conjugated to ATG5 by ATG7 (E1-like) and ATG10 (E2-like) enzymes. The resulting ATG5–ATG12 forms a complex with ATG16L1, which participates in elongation of the autophagic membrane. A second conjugation system requires the ubiquitin-like protein microtubule-associated protein-1 light chain 3 (LC3, ATG8). LC3 and its homologues are modified with the cellular lipid phosphatidylethanolamine (PE). The precursor form of LC3 is cleaved by the protease ATG4B to generate the LC3-I form, with an exposed lipid conjugation site at the C-terminal glycine residue. Conjugation of PE with LC3-I occurs from the sequential action of ATG7 (E1-like) and ATG3 (E2-like) activities. In mammals, the conversion of LC3-I (free form) to LC3-II (PE-conjugated form) is a key regulatory step in autophagosome formation.