Endoplasmic reticulum lifecycle

The endoplasmic reticulum is never made de novo: it grows from existing membrane, is shaped into sheets and tubules, imports the proteins of the secretory pathway as they are made, folds and modifies them, removes those that fail to fold, adjusts its capacity through the unfolded protein response, and is turned over by ER-phagy. This umbrella module composes the modules for those stages by reference. Co-translational protein import and oxidative folding are required in every eukaryote; the other stages are optional because the modelled pathways are lineage-specific or are not yet written as eukaryote-wide rules.

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: co-translational translocation and oxidative folding. N-glycosylation by the oligosaccharyltransferase is optional until its module is written as a eukaryote-wide rule. The unfolded protein response is optional because the referenced module is metazoan (IRE1 is the eukaryote-wide branch). Not yet modelled, because no eukaryote-wide module exists: ER-associated degradation, whose eukaryote-wide grounding is blocked locally (Hrd1's PANTHER family has no entries table, and Cdc48 and Hrd3/Sel1 fall into lineage-specific subfamilies); ER shaping by reticulons, Yop1/DP1 and atlastin/Sey1; ER export by COPII; lipid synthesis; and ER-phagy.