Lysosome and lytic vacuole lifecycle

Lysosomes in animals and lytic vacuoles in fungi and plants are the acidic, hydrolase-filled compartments where the endocytic, autophagic and biosynthetic routes end. They form by maturation of endosomes, which turn membrane cargo into intralumenal vesicles and fuse with existing lysosomes; they receive hydrolases from the Golgi; they degrade macromolecules in an acidified lumen; and damaged lysosomes are repaired or removed by lysophagy. This umbrella module composes the modules for those stages by reference. Lumen acidification and ESCRT-III membrane scission are required in every eukaryote; hydrolase delivery and the degradative pathways are optional because the modelled routes are animal-specific.

Organelle lifecycle umbrella (see projects/ORGANELLE_LIFECYCLES.md); stage roles follow the shared skeleton. Read as a satisfiability rule, the umbrella is satisfied when its required stages are: intralumenal vesicle formation and lumen acidification. Hydrolase delivery is optional because the modelled route, mannose 6-phosphate tagging, is metazoan; fungi and plants sort hydrolases with Vps10/VSR receptors, not yet modelled. The degradative pathways are optional because they are substrate-specific and mostly scoped to animals. Not yet modelled, because no eukaryote-wide module exists to reference: endosome maturation and fusion (Rab5-to-Rab7 conversion by Mon1-Ccz1, CORVET and HOPS tethering, which phagosome_maturation covers in a metazoan context), lysosomal ion channels, lysosome repair and lysophagy, and lysosome-related organelles.