Autophagosomes are double-membrane vesicles newly formed during autophagy to engulf a wide range of intracellular material and transport this autophagic cargo to lysosomes (or vacuoles in yeasts and plants) for subsequent degradation. Autophagosome biogenesis responds to a plethora of signals and involves unique and dynamic membrane processes. Autophagy is an important cellular mechanism allowing the cell to meet various demands, and its disruption compromises homeostasis and leads to various diseases, including metabolic disorders, neurodegeneration and cancer. Thus, not surprisingly, the elucidation of the molecular mechanisms governing autophagosome biogenesis has attracted considerable interest. Key molecules and organelles involved in autophagosome biogenesis, including autophagy-related (ATG) proteins and the endoplasmic reticulum, have been discovered, and their roles and relationships have been investigated intensely. However, several fundamental questions, such as what supplies membranes/lipids to build the autophagosome and how the membrane nucleates, expands, bends into a spherical shape and finally closes, have proven difficult to address. Nonetheless, owing to recent studies with new approaches and technologies, we have begun to unveil the mechanisms underlying these processes on a molecular level. We now know that autophagosome biogenesis is a highly complex process, in which multiple proteins and lipids from various membrane sources, supported by the formation of membrane contact sites, cooperate with biophysical phenomena, including membrane shaping and liquid–liquid phase separation, to ensure seamless segregation of the autophagic cargo. Together, these studies pave the way to obtaining a holistic view of autophagosome biogenesis.
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The author thanks several colleagues for helpful comments and apologizes to those whose work could not be cited due to lack of space. Research in the author’s group is supported in part by KAKENHI Grants-in-Aid for Scientific Research 17H01430 and 19H05708 from the Ministry of Education, Culture, Sports, Science and Technology of Japan, JST CREST grant number JPMJCR13M7 and a STAR grant funded by the Tokyo Institute of Technology Foundation.
The author declares no competing interests.
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- Target of rapamycin complex 1
(TORC1). A serine/threonine kinase complex that controls various cellular activities, including autophagy, according to nutrient availability.
- Recycling endosomes
Organelles that receive proteins from early endosomes and mediate their recycling to the plasma membrane.
- Ubiquitin-like protein
Small protein similar to ubiquitin that is conjugated to the amino group of target molecules at their C termini.
- E1 enzyme
Enzyme that activates the C-terminal carboxyl group of ubiquitin or ubiquitin-like proteins using ATP.
- E2 enzyme
Enzyme that receives ubiquitin/ubiquitin-like proteins from E1 enzymes and conjugates them to target molecules directly or via E3 enzymes.
- E3 enzyme
Enzyme that determines target specificity and stimulates or mediates the conjugation reaction by E2 enzymes.
- cAMP-dependent protein kinase A
A protein kinase that is activated on increase in cAMP levels and regulates various metabolic enzymes.
- AMP-activated protein kinase
(AMPK). A protein kinase that is activated in response to low ATP levels and acts to maintain cellular energy homeostasis.
- Contact sites
Sites where two different organelles contact with each other for interorganellar communication, including transfer of molecules such as lipids.
- Intrinsically disordered region
Protein region that does not adopt a defined 3D structure even under physiological conditions.
- Exocyst complex
A multimeric protein complex that tethers secretory vesicles to the plasma membrane in exocytosis.
- Early endosomes
Organelles that serve as a sorting platform for proteins endocytosed from the plasma membrane or transported from the Golgi apparatus.
A family of proteins that mediate most membrane fusion events within cells. For fusion, SNAREs on two opposed membranes tightly associate with each other, bring the membranes in close proximity and induce their fusion.
- Sorting nexin
A group of proteins that contain the PX and BAR domains and function in membrane trafficking.
- ER exit sites
(ERES). A domain in the endoplasmic reticulum where COPII proteins are assembled to form COPII vesicles.
- ER–Golgi intermediate compartment
(ERGIC). A membrane compartment that mediates vesicle transport between the endoplasmic reticulum and the Golgi apparatus.
Coenzyme that functions in fatty acid metabolism; it serves as an acyl chain donor in phospholipid synthesis.
- Giant unilamellar vesicles
(GUVs). Artificial micrometre-sized vesicles bound by a single membrane that are used as a model for analysis of cellular membranes.
- Actin-capping protein
Protein that binds to the end of actin filaments and blocks the polymerization and depolymerization of the filaments at the end.
- Multivesicular bodies
Endosome-related organelles that contain lumenal vesicles that mediate lysosomal degradation of membrane proteins or secrete these vesicles as exosomes.
(Endosomal sorting complexes required for transport). Protein complexes (ESCRT-0, ESCRT-I, ESCRT-II and ESCRT-III) that mediate protein sorting and intralumenal vesicle formation in the endosome and are also responsible for different membrane fission events. Their main activity is driving membrane constriction, and hence they can be involved in different processes requiring membrane shaping in the cell.
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Nakatogawa, H. Mechanisms governing autophagosome biogenesis. Nat Rev Mol Cell Biol 21, 439–458 (2020). https://doi.org/10.1038/s41580-020-0241-0
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