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The autophagosome: origins unknown, biogenesis complex

Key Points

  • Autophagy is an evolutionarily conserved lysosome-mediated degradation process that involves membrane-bound organelles called autophagosomes. Macroautophagy, commonly referred to as autophagy, is induced by amino acid starvation.

  • Autophagosome formation is mediated by autophagy-related (ATG) proteins. There are more than 34 ATG proteins in yeast, of which almost half are conserved in mammals.

  • Amino acid starvation inactivates mammalian target of rapamycin complex 1 (mTORC1), which leads to the induction of autophagy and increased autophagsome formation. Both the UNC51-like kinase (ULK) complex and the autophagy-specific class III PI3K complex are activated downstream of mTORC1 inactivation.

  • Autophagosome formation after amino acid starvation occurs at contact sites between the endoplasmic reticulum (ER) and mitochondria. Expansion of the site occurs on omegasomes, which are platforms that are enriched in phosphatidylinositol 3-phosphate produced by the autophagy-specific PI3K complex.

  • Omegasomes give rise to isolation membranes (also known as phagophores), which recruit ATG proteins, including the ULK complex, the PI3K complex, WD-repeat domain phosphoinositide-interacting 2 (WIPI2), ATG12, ATG5, ATG16L1 and LC3.

  • Expansion of the isolation membrane is driven by vesicular traffic from several cellular compartments, including the ER–Golgi intermediate compartment (ERGIC), the Golgi and recycling endosomes. Expansion of the isolation membrane is followed by detachment from the omegasome and closure of the vesicle around the cytosolic proteins and membranes.

Abstract

Healthy cells use autophagy as a general 'housekeeping' mechanism and to survive stress, including stress induced by nutrient deprivation. Autophagy is initiated at the isolation membrane (originally termed the phagophore), and the coordinated action of ATG (autophagy-related) proteins results in the expansion of this membrane to form the autophagosome. Although the biogenesis of the isolation membrane and the autophagosome is complex and incompletely understood, insight has been gained into the molecular processes involved in initiating the isolation membrane, the source from which this originates (for example, it was recently proposed that the isolation membrane forms from the mitochondria-associated endoplasmic reticulum (ER) membrane (MAM)) and the role of ATG proteins and the vesicular trafficking machinery in autophagosome formation.

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Figure 1: Overview of the autophagic pathway and organelles that might contribute to autophagosome biogenesis.
Figure 2: Formation and expansion of the isolation membrane.
Figure 3: A model of autophagosome formation at the ER–mitochondria contact site.
Figure 4: Endocytic contributions to the growing autophagosome.

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Acknowledgements

C.A.L. and S.A.T. are supported by Cancer Research UK. T.Y is supported by the Japanese Ministry of Education, Culture, Sports, Science, and Technology.

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Correspondence to Sharon A. Tooze.

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Glossary

Osmium

The transition metal compound osmium tetroxide (OsO4) is widely used as a fixative and to stain lipids to provide contrast in transmission electron micrographs.

Bin–amphiphysin–Rvs domains

(BAR domains). Crescent-shaped protein domains that bind to membranes through their concave face and may sense membrane curvature by preferentially binding curved membranes.

PX domains

P40/P47phox domains. Bind phosphoinositides and are found in proteins including sorting nexins.

PH domains

(pleckstrin homology domains). These domains bind phosphoinositides to target PH domain-containing proteins to specific subcellular compartments.

HORMA domain

(HOP1, REV7 and MAD2 protein domains). May recognize DNA damage-related chromatin structures, although the HORMA domain in ATG13 may be involved in phosphoinositide binding.

Guanine nucleotide exchange factor

(GEF). Promotes exchange of bound GDP for GTP on RAB proteins, which activates RAB and enables it to bind effectors.

GTPase-activating protein

(GAP). A protein family that enhances the GTP hydrolysis activity of RAB GTPase proteins. GAPs contain a TBC (TRE2–BUB2–CDC16) domain, effectively switching RAB off.

Unfolded protein response

(UPR). A stress response induced in response to the accumulation of misfolded proteins in the endoplasmic reticulum lumen. Broadly, this process involves stopping the translation of new proteins and increasing the production of molecular chaperones to refold the peptide chains.

LC3-interacting region

(LIR). A short peptide sequence (Ψ-Xaa-Xaa-Lys/Ile; where Ψ is an aromatic residue and Xaa is any amino acid), frequently found carboxy-terminal to acidic residues, which confers the ability to bind to members of the autophagy-related 8 (ATG8) protein family such as LC3.

Percoll

A silica colloid used to perform density gradient centrifugation to isolate subcellular particles of interest.

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Lamb, C., Yoshimori, T. & Tooze, S. The autophagosome: origins unknown, biogenesis complex. Nat Rev Mol Cell Biol 14, 759–774 (2013). https://doi.org/10.1038/nrm3696

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