The term “autophagy” introduced by the biochemist Christian de Duve in 1963 is derived from the Greek meaning “self-eating” and is a fundamental process for the degradation and recycling of cytoplasmic components.
Types of Autophagy
The broad term autophagy has been classified into different types, which include the following:
- Macroautophagy: The primary pathway in which cellular contents and organelles are engulfed by double-membrane autophagosomes that fuse to lysosomes for degradation.
- Microautophagy: A process in which the lysosome directly fuses with cytoplasmic cargo.
- Chaperone-mediated autophagy: A process in which cytoplasmic chaperones assist in bringing targets to the lysosome.
Macroautophagy, frequently just referred to as autophagy, is the best characterized of these processes. It is highly regulated by nutrient conditions and cellular stress and plays important roles in normal physiological homeostasis. It is frequently regulated in pathological conditions including cancer, metabolic disorders, inflammatory diseases, host defense, and neurodegeneration.
In 2016, the Nobel Prize in Physiology or Medicine was awarded Yoshinori Ohsumi for the initial identification of genes in yeast required for autophagy. Genes discovered in yeast paved the way for the discovery and characterization of over 20 autophagy-related genes (ATG) with critical roles in autophagy. General features of the autophagic pathway include:
- Initiation of autophagy with sequestration of cargo to a phagophore;
- Elongation and maturation of the autophagosome to a fully enclosed structure; and
- Fusion of the autophagosome with the lysosome.
Initiation of autophagy is frequently controlled by sensors of cellular energy and nutrients, AMPK and mTORC1. These master kinases have a yin and yang relationship in the initiation of autophagy. Among the targets for these kinases is the autophagy kinase ULK1. Phosphorylation of ULK1 by AMPK at multiple sites, including Ser317 and Ser555, activates the kinase; whereas phosphorylation of ULK1 by mTORC1 at Ser757 inhibits its activity. Maturation of the autophagosome requires activation ULK1 and the recruitment of a multiprotein complex activating the lipid kinase class III phosphatidylinositol 3‐kinase (VSP34). Substrates of ULK1 that are part of this complex and required for autophagosome maturation include ATG13, Beclin-1, ATG14, and VSP34. Also required for autophagosome maturation are two ubiquitin-like conjugation systems that function in a stepwise manner.
In the first step, ATG12 is conjugated to ATG5. This is followed by the lipid conjugation of phosphatidylethanolamine (PE) to LC3 or GABARAP family members. This second conjugation step, generally referred to as the type II form, permits incorporation into the autophagosome membrane and is frequently used as a marker for autophagy. Finally, the contents of the autophagosome are degraded by the pH-sensitive hydrolases within the lysosome. Drugs such as chloroquine and bafilomycin A1, which inhibit lysosomal acidification, are often used to inhibit late stages of autophagy.
Autophagy Pathways for Organelle Degradation
Autophagy is more than just the bulk degradation of intracellular components. Rather, it can also be a highly selective process orchestrated to degrade specific organelles, pathogens, and proteins. Specific pathways for organelle degradation have been described for mitochondria (mitophagy), ER (reticulophagy or ER-phagy), ribosomes (ribophagy), peroxisomes (pexophagy), lysosome (lysophagy) and the nucleus (nucleophagy), as well protein aggregates (aggrephagy), lipid droplets (lipophagy), and intracellular pathogens (xenophagy).
Autophagy can also target selective proteins, like ferritin (ferritophagy), important in the regulation of iron metabolism and controls iron-dependent cell death via ferroptosis. Cellular components are frequently targeted to the autophagosome by cargo receptors, such as those in the SQSTM1/p62 family, which bind their targeted contents to the autophagosome through interactions with LC3 family members. Selective autophagy is generally associated with a growing number of specific cargo receptors that target select components.
Authophagy and Disease
The last decade has seen tremendous advances in our understanding of both non-selective and selective autophagy in the context of health and disease. Numerous studies have described both positive and negative roles of autophagy with respect to cancer. While the clearance of damage organelles through autophagy can prevent tumor initiation, cancer cells frequently have an increased rate of autophagy, required for survival in nutrient-poor environments. Inhibition of autophagy, either genetically through knockout of key autophagy genes, or pharmacologically with drugs like chloroquine and its derivatives, can lead to decreased tumor burden.
Blog: Unravelling Parkinson’s Disease: The Role of Mitophagy, Autophagy & Lysosomal Processing
More recently, specific autophagy inhibitors, such as compounds that inhibit ULK1 have been have provided new therapeutic opportunities. Conversely, inducing autophagy, such as by inhibition of mTORC1, may also prove to have a clinical impact for other conditions. Selective autophagy of pathogens via xenophagy is an important factor in host defense. Microbial virulence may be impacted by their ability to subvert autophagy defense mechanisms. Proteins like the kinase TBK1 play dual roles in innate immune pathways and enhancing autophagy.
The protective role of autophagy is also a common feature in neurogenerative diseases. Selective degradation of damaged mitochondria through mitophagy has been recognized as an important factor in energy homeostasis and is frequently disrupted in neurodegeneration. Proteins involved in mitophagy like PINK1 and Parkin may be mutated in Parkinson’s and other diseases. In this pathway, PINK1 phosphorylation of ubiquitin at Ser65 leads to activation and recruitment of the ubiquitin E3 ligase Parkin to the mitochondria, leading to ubiquitination of mitochondrial targets for recognition by autophagy cargo receptors. Identification of activators of mitophagy are being investigated to treat these diseases.
Antibodies for Autophagy Research
Cell Signaling Technology has developed fully validated antibodies and kits driven to meet the needs of autophagy researchers and progress therapeutic development. Autophagy may be analyzed using our highly cited antibodies against LC3 family members, cargo receptors, and phospho-specific targets of key autophagy kinases of including AMPK, mTORC1, TBK1, PINK1, and ULK1.
Select References
- Yang Y, Klionsky DJ. Autophagy and disease: unanswered questions. Cell Death Differ. 2020 Mar;27(3):858-871. doi: 10.1038/s41418-019-0480-9. Epub 2020 Jan 3. PMID: 31900427; PMCID: PMC7206137.
- Mizushima N, Levine B. Autophagy in Human Diseases. N Engl J Med. 2020 Oct 15;383(16):1564-1576. doi: 10.1056/NEJMra2022774. PMID: 33053285.
- Miller DR, Thorburn A. Autophagy and organelle homeostasis in cancer. Dev Cell. 2021 Apr 5;56(7):906-918. doi: 10.1016/j.devcel.2021.02.010. Epub 2021 Mar 8. PMID: 33689692; PMCID: PMC8026727.
- Giorgi C, Bouhamida E, Danese A, Previati M, Pinton P, Patergnani S. Relevance of Autophagy and Mitophagy Dynamics and Markers in Neurodegenerative Diseases. Biomedicines. 2021 Feb 4;9(2):149. doi: 10.3390/biomedicines9020149. PMID: 33557057; PMCID: PMC7913851.
- Poillet-Perez L, White E. Role of tumor and host autophagy in cancer metabolism. Genes Dev. 2019 Jun 1;33(11-12):610-619. doi: 10.1101/gad.325514.119. PMID: 31160394; PMCID: PMC6546058.
- Deretic V. Autophagy in inflammation, infection, and immunometabolism. Immunity. 2021 Mar 9;54(3):437-453. doi: 10.1016/j.immuni.2021.01.018. PMID: 33691134; PMCID: PMC8026106.
- Egan DF, Chun MG, Vamos M, Zou H, Rong J, Miller CJ, Lou HJ, Raveendra-Panickar D, Yang CC, Sheffler DJ, Teriete P, Asara JM, Turk BE, Cosford ND, Shaw RJ. Small Molecule Inhibition of the Autophagy Kinase ULK1 and Identification of ULK1 Substrates. Mol Cell. 2015 Jul 16;59(2):285-97. doi: 10.1016/j.molcel.2015.05.031. Epub 2015 Jun 25. PMID: 26118643; PMCID: PMC4530630.
