Autophagosome lifecycle

The autophagosome is a transient organelle. It is assembled from a phagophore that nucleates at a phagophore assembly site, expands around cytoplasmic cargo with membrane supplied by Atg9 vesicles and lipid transfer from the ER, closes into a double-membrane vesicle, and then fuses with a lysosome or vacuole, where its inner membrane and cargo are degraded. This umbrella module composes the modules for those stages by reference. The core autophagy machinery is required in every eukaryote; the lineage-specific descriptions of assembly are optional.

Organelle lifecycle umbrella (see projects/ORGANELLE_LIFECYCLES.md); stage roles follow the shared skeleton. Read as a satisfiability rule, the umbrella is satisfied when the core biogenesis module is. The metazoan_autophagosome_biogenesis and phagophore_assembly_site modules are optional references, because they describe the pathway in animals and at the yeast assembly site and are not written as eukaryote-wide rules. Not yet modelled, because no eukaryote-wide module exists: phagophore closure (ESCRT-III), autophagosome-lysosome fusion (the syntaxin-17 or Ykt6 SNAREs with HOPS), and selective autophagy receptors other than those in the mitophagy module.