Autophagy
Autophagy is a highly regulated self-degradative process that facilitates the removal of unnecessary or dysfunctional cellular components. This lysosome-dependent pathway is evolutionarily conserved and orchestrates the engulfment, degradation, and recycling of cellular contents, including long-lived proteins and organelles, thereby supporting cellular homeostasis and survival. Autophagy is induced under conditions of nutrient deprivation, as well as in various physiological and pathological processes, including development, differentiation, neurodegenerative diseases, stress, infection, obesity, and cancer.
Three major forms of autophagy are commonly described: Macroautophagy, microautophagy, and mitophagy, along with chaperone-mediated autophagy (CMA). Macroautophagy is the primary pathway and involves the sequestration of cytoplasmic targets within a double-membraned vesicle—the autophagosome. The autophagosome is transported through the cytoplasm and subsequently fuses with a lysosome. Within the resulting autolysosome, the autophagosome’s contents are degraded by acidic lysosomal hydrolases.
Macroautophagy is regulated by more than 30 autophagy-related (Atg) genes. In mammals, amino acids, growth factors, and reactive oxygen species (ROS) regulate the activity of the key protein kinases mechanistic target of rapamycin (mTOR) and AMP-activated protein kinase (AMPK). These kinases are pivotal in autophagy regulation through the phosphorylation-mediated inhibition of the Unc-51-like kinases ULK1 and ULK2. ULK forms a protein complex with Atg13, Atg101, and RB1CC1 (FIP200), which subsequently phosphorylates and activates Beclin-1 (BECN1). The active ULK and Beclin-1 complexes localize to the site of autophagosome initiation, the phagophore, where they facilitate the activation of downstream autophagy components. The class III phosphatidylinositol 3-kinase (PI3K) complex mediates the nucleation of autophagosomes, with VPS34 phosphorylating PI to generate PI(3)P on the phagophore surface.
Further downstream, WIPI2B links PI(3)P signaling to LC3 lipidation via the ATG12–ATG5-ATG16L1 complex, which acts as an E3-like ligase to facilitate phagophore membrane elongation. The ATG3/ATG7/LC3 conjugation system drives the expansion of the phagophore membrane, with lipidated LC3 (LC3-II) playing a critical role in autophagosome maturation by enabling cargo recognition through adaptor proteins such as sequestosome-1 (SQSTM1/p62). The completed autophagosome fuses with a lysosome via SNARE complexes and UVRAG, which results in the degradation of its contents. Lysosomal permeases facilitate the release of degradation products back into the cytoplasm for reuse.
Mitophagy is the selective degradation of mitochondria via autophagy, which is triggered in response to mitochondrial damage or oxidative stress. Mitophagy plays a crucial role in preventing cellular degeneration caused by the accumulation of dysfunctional mitochondria. In mammals, mitophagy is primarily mediated by the PINK1-parkin pathway, where PINK1 accumulation on damaged mitochondria recruits parkin, leading to ubiquitination and recruitment of autophagy receptors such as OPTN and CALCOCO2 (NDP52). CALCOCO2 makes multiple contributions to selective autophagy. By interacting with cargos and LC3, it directs autophagy targets to autophagosomes. In addition, CALCOCO2 promotes autophagosomes fusion with endolysosomes by connecting autophagosomes to MYOSIN VI. Additionally, BNIP3 and NIX serve as alternative mitophagy regulators under specific physiological conditions, such as erythrocyte maturation. Recent studies have also identified FUNDC1 as a key mitophagy receptor in hypoxic conditions. Mitophagy not only targets dysfunctional mitochondria but also contributes to the turnover of functional mitochondria to maintain mitochondrial quality control.
Microautophagy involves the direct engulfment of cytoplasmic material, including organelles such as peroxisomes and portions of the nucleus, by lysosomes. ATG8-Phosphatidylethanolamine(PE) conjugates are incorporated into vacuolar and lysosomal membranes. They promote membrane curvature, enabling invagination and tubulation necessary for cargo engulfment. ATG8 also functions as a receptor for selective cargo sequestration. Dysregulation of ATG8-PE-mediated processes is linked to neurodegenerative diseases, metabolic disorders, and aging-related pathologies, highlighting their significance in cellular quality control.
Chaperone-mediated autophagy (CMA) differs from other autophagic pathways as it does not involve vesicle formation but instead relies on the direct translocation of specific proteins across the lysosomal membrane. The cytosolic chaperone heat shock cognate protein 70 (HSC70) plays a major role in substrate recognition and transport to the lysosome. Targeted proteins must contain a pentapeptide motif related to KFERQ, which enables binding to HSC70. Once recognized, substrates are transported to the lysosomal membrane, where they interact with lysosome-associated membrane protein type 2A (LAMP2A), which facilitates their translocation into the lysosomal lumen for degradation. Recent studies suggest that dysregulation of CMA contributes to age-related diseases, including neurodegeneration and cancer, highlighting its role beyond protein turnover.
Related Pathways and Resources
References:
- : "Autophagy: cellular and molecular mechanisms." in: The Journal of pathology, Vol. 221, Issue 1, pp. 3-12, (2010) (PubMed).
- : "Autophagy--a key player in cellular and body metabolism." in: Nature reviews. Endocrinology, Vol. 10, Issue 6, pp. 322-37, (2014) (PubMed).
- : "Oxidative stress and autophagy: the clash between damage and metabolic needs." in: Cell death and differentiation, Vol. 22, Issue 3, pp. 377-88, (2015) (PubMed).
- : "Biological Functions of Autophagy Genes: A Disease Perspective." in: Cell, Vol. 176, Issue 1-2, pp. 11-42, (2019) (PubMed).
- : "Novel Insights into NDP52 Autophagy Receptor Functioning." in: Trends in cell biology, Vol. 28, Issue 4, pp. 255-257, (2019) (PubMed).
- : "An update on autophagy disorders." in: Journal of inherited metabolic disease, Vol. 48, Issue 1, pp. e12798, (2024) (PubMed).
- : "Phase separation of initiation hubs on cargo is a trigger switch for selective autophagy." in: Nature cell biology, Vol. 27, Issue 2, pp. 283-297, (2025) (PubMed).
