Autophagy: Molecular mechanisms and overview

​​​​​Autophagy is a complex process by which dysfunctional cellular components are degraded inside the cell through the action of lysosomes. Here, we review the key stages and processes involved in this pathway, as well as the role of autophagy in different diseases.   

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Contents

• Overview of autophagy
• Molecular mechanisms of autophagy - interactive pathway 
• Types of autophagy
• ​Autophagy in disease
  • Cancer
  • Neurodegenerative disease
  • Cardiovascular disease
  • Infectious disease
• References

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​​​​Overview of autophagy

Components of the cytoplasm are broken down into basic components and returned to the cytosol for reuse. Autophagy is a dynamic process present in all cells at low levels under basal conditions, but stimuli such as nutrient starvation or hypoxia can lead to its upregulation.

​​Autophagy is a tightly regulated pathway with an important housekeeping role, allowing cells to eliminate damaged or harmful components through catabolism and recycle them to maintain nutrient and energy homeostasis. Autophagy is also a major protective mechanism, which allows cell survival in response to multiple stress conditions, such as nutrient or growth factor deprivation, hypoxia, reactive oxygen species (ROS), DNA damage, or intracellular pathogens1. 

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​​Figure 1. Overview of the autophagy process. An expanding membrane structure (phagophore) enwraps portions of the cytoplasm, followed by the formation of a double-membrane sequestering vesicle (autophagosome). The autophagosome fuses with the lysosome and releases its inner compartment into the lysosomal lumen. The inner membrane part of the autophagosome is degraded together with the enclosed cargo. The resulting macromolecules are released into the cytosol for recycling through lysosomal membrane permeases2.

Initiation and phagophore formation

The molecular mechanism of autophagy involves several conserved Atg (autophagy-related) proteins. Various stimuli, such as nutrient starvation, lead to the formation of the phagophore, a step that involves two protein complexes:

• A Vps34 complex that contains Vps34 (the class III PI3K), Beclin1 (Atg6 in yeast), Atg14, and Vps15 (p150).
• A ULK1 complex that includes the serine/threonine kinase ULK1 (Atg1 in yeast), an essential positive regulator of autophagosome formation.

Phagophore elongation and autophagosome formation (or nucleation, expansion, and maturation)

The elongation of the phagophore results in the formation of the characteristic double-membrane autophagosome. This step requires two ubiquitin-like conjugation pathways, both catalyzed by Atg7.

• The first ubiquitin-like system leads to the conjugation of Atg5-Atg12, which then forms a multimeric complex with Atg16L. The Atg5-Atg12-Atg16L complex associates with the outer membrane of the extending phagophore3,4.
• The second system results in the processing of LC3, encoded by the mammalian homolog of the yeast Atg8. Upon autophagy induction, LC3B is proteolytically cleaved by Atg4 to generate LC3-I. LC3-I is activated by Atg7 and then conjugated to phosphatidylethanolamine (PE) in the membrane to generate processed LC3-II.

Processed LC3-II is recruited onto the growing phagophore and its integration is dependent on Atg5-Atg12. Unlike Atg5-Atg12-Atg16L, LC3-II is found on both the inner and outer surfaces of the autophagosome, where it is required for the expansion and completion of the autophagic membrane. After the closure of the autophagosomal membrane, the Atg16-Atg5-Atg12 complex dissociates from the vesicle, whereas a portion of LC3-II remains covalently bound to the membrane (Figure 1). Therefore, LC3-II can be used as a marker to monitor the level of autophagy in cells.

It has been postulated that various organelles, including mitochondria, the Golgi complex, and the endoplasmic reticulum (ER), can be the origin of the autophagosomal membrane5. Recent studies demonstrate that the self-multimerization of Atg9 may facilitate membrane tethering and/or fusion6.

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Fusion, degradation, and recycling

When the autophagosome formation is completed, LC3-II attached to the outer membrane is cleaved from PE by Atg4 and released back to the cytosol. The fusion between the autophagosome and the lysosome is thought to require the lysosomal membrane protein LAMP-1 and the small GTPase Rab7. 

After fusion, a series of acid hydrolases are involved in the degradation of the sequestered cytoplasmic cargo. The small molecules resulting from the degradation, particularly amino acids, are transported back to the cytosol for protein synthesis and maintenance of cellular functions under starvation conditions. The identification of Atg22 together with other vacuolar permeases (such as Avt3 and Avt4) as vacuolar amino acid effluxers during yeast autophagy has helped in the understanding of the mechanisms of nutrient recycling7. These permeases represent the last step in the degradation and recycling process7.

Types of autophagy

There are currently three types of autophagy in mammalian cells³:

• Macroautophagy

Macroautophagy is the main autophagic pathway and it is characterized by the delivery of cytoplasmic cargo to the lysosome through an intermediary double membrane-bound vesicle, known as an autophagosome, which fuses with the lysosome to form an autolysosome.

• Microautophagy

Microautophagy involves the direct engulfment of cytoplasmic cargo into the lysosome through the invagination of the lysosomal membrane. Microautophagy is important in the maintenance of organellar size, membrane homeostasis, and cell survival under nitrogen restriction⁸.   

• Chaperone-mediated autophagy (CMA)

Chaperone-mediated autophagy (CMA) involves the direct translocation of cytoplasmic proteins across the lysosomal membrane in a complex with chaperone proteins that are recognized by the lysosomal membrane receptor LAMP-2A (lysosomal-associated membrane protein 2A), resulting in their unfolding and degradation.​

Autophagy in disease

Autophagy has been widely implicated in many pathophysiological processes, including cancer, metabolic and neurodegenerative disorders, cardiovascular and pulmonary diseases. It also has an important role in aging and exercise⁹.

Autophagy in cancer

Autophagy was first linked to cancer through the role of Beclin 1, which is essential for the autophagy pathway and has been mapped to tumor susceptibility¹⁰. Since then, multiple tumor-suppressor proteins have been identified that are involved in the control of the autophagy pathway (eg p53, Bcl2, PTEN, etc).

​​​The tumor cells exploit the autophagic mechanism to provide a way for them to overcome nutrient-limiting conditions and facilitate tumor growth. Studies show that autophagy can modulate the tumor microenvironment by promoting angiogenesis, supply nutrients, and modulate inflammatory response¹¹.

Autophagy in neurodegenerative diseases

Neurodegenerative diseases are characterized by the accumulation of mutant or toxic proteins^12,13. It has been shown that the autophagic pathway helps in cell survival by removing unwanted cellular organelle and protein aggregates. Disruption of autophagy-specific genes in neural cells leads to neurodegeneration^14,15.

Autophagy in cardiovascular diseases

The autophagic pathway is essential for normal maintenance, repair, and adaptation of the heart tissue. Unsurprisingly, therefore, autophagic deficiencies have been associated with a variety of cardiac pathologies¹⁶.

Check out our Autophagy in heart disease pathway.

Autophagy in infectious disease

Autophagy plays a key role in immune defense against invading bacteria and pathogens. Upon infection, autophagy regulates inflammation, antigen presentation, and micro-organism capture and degradation¹⁷.

References

1. Levine, B. & Kroemer, G. Autophagy in the pathogenesis of disease. Cell, 11, 27-42 (2008).
2. Mizushima, N. Autophagy: process and function. Genes Dev, 21, 2861-2873 (2007).
3. Glick, D., Barth, S., Macleod, K.F. Autophagy: cellular and molecular mechanisms. J. Pathol. 221, 3-12 (2010).
4. Kaur, J. & Debnath, J. Autophagy at the crossroads of catabolism and anabolism. Nat. Rev. Mol. Cell Biol. 16, 461-472 (2015).
5. Wei, Y., Liu, M., Li, X., Liu, J., Li, H. Origin of the autophagosome membrane in mammals. Biomed Res Int. 2018:1012789 (2018).
6. He, C., Baba, M., Cao, Y., Klionsky, D.J. Self-interaction is critical for Atg9 transport and function at the phagophore assembly site during autophagy. Mol. Biol. Cell. 19, 5506-5516 (2008).
7. Yang, Z., Huang, J., Geng, J., Nair, U., Klionsky, D.J. Atg22 recycles amino acids to link the degradative and recycling functions of autophagy. Mol Biol Cell. 17, 5094-5104 (2006). 
8. Li, W.W., Li, J, Bao, J.K. Microautophagy: lesser-known self-eating. Cell Mol. Life Sci., 69, 1125-1136 (2012).
9. Choi, A.M., Ryter, S.W., Levine, B. Autophagy in human health and disease. N. Engl. J. Med., 368, 1845-1846 (2013).
10. Liang, X.H., et al. Induction of autophagy and inhibition of tumorigenesis by Beclin 1. Nature, 402, 672-676 (1999). 
11. Yang, X., et al. The role of autophagy induced by tumor microenvironment in different cells and stages of cancer. Cell Biosci., 5: 14 (2015). 
12. Ravikumar, B., Duden, R., Rubinsztein, D.C. Aggregate-prone proteins with polyglutamine and polyalanine expansions are degraded by autophagy. Hum. Mol. Genet., 11, 1107-1117 (2002).
13. Ravikumar, B., et al. Inhibition of mTOR induces autophagy and reduces toxicity of polyglutamine expansions in fly and mouse models of Huntington disease. Nat. Genet., 36, 585-595 (2004). 
14. Komatsu, M., et al. Loss of autophagy in the central nervous system causes neurodegeneration in mice. Nature, 441, 880-884 (2006). 
15. Hara, T., et al. Suppression of basal autophagy in neural cells causes neurodegenerative disease in mice. Nature, 441, 885-889 (2006).
16. Cuervo, A.M. Autophagy: in sickness and in health. Trends Cell Bio., 14, 70-77 (2004). 
17. Levine, B., Mizushima, N., Virgin, H.W. Autophagy in immunity and inflammation. Nature, 469, 323-335 (2011).