Peroxisomal protein import machinery

Peroxisomal proteins are made in the cytosol and imported post-translationally, membrane proteins by the Pex19/Pex3 route and folded matrix proteins by a receptor cycle: the PTS1 receptor Pex5 carries cargo to the Pex14/Pex13 docking machinery, releases it into the matrix, and is then monoubiquitinated by the Pex2/Pex10/Pex12 RING peroxins and extracted for reuse by the Pex1/Pex6 AAA ATPase. This module is the eukaryote-wide core of that machinery, written so that it can be evaluated in any genome; lineage-specific peroxins are optional parts.

Split out of MODULE:peroxisome_lifecycle, whose curated annotons and evidence it carries. Two rule semantics changed in the split: the old one-of choices between insertion routes and between PTS1 and PTS2 receptors became a required core (the Pex19/Pex3 route; the PTS1 receptor Pex5) plus optional parts (Pex16, RRBP1; Pex7), so a genome with only Pex7 no longer satisfies matrix targeting. Eukaryote-wide scope: PAINT places the IBD nodes for Pex19, Pex3, Pex5, Pex7, Pex14, Pex13, Pex10, Pex12 and the Pex1 and Pex6 clades at Eukaryota (taxon:2759); Pex2's only node is at Amniota, so its step rests on subfamily membership spanning animals, fungi, Dictyostelium and Arabidopsis; Pex26 is placed at Eumetazoa and is optional. Read as a satisfiability rule, every non-optional part is expected in any eukaryote with peroxisomes. Peroxisome-derived organelles such as kinetoplastid glycosomes are a test case, not an assumption: PEX3 (required here) and PEX16 have been reported as hard to identify by sequence in trypanosomatids, so those genomes should be checked before the PEX3 step is treated as universal. Optional, as lineage-specific: Pex16 (some fungi lack it), the PTS2 receptor Pex7 (some lineages have lost PTS2), the mammalian RNF146-TNKS/2 input to PEX14, the human RRBP1 route, and the PEX1/PEX6 membrane anchor (PEX26 in animals, Pex15 in fungi). These lineage statements come from the curated module and the general literature and have not yet been checked against data in this repository. Not yet modelled: the receptor-ubiquitinating E2 (Pex4/Pex22 in fungi and plants; other E2s in animals) and receptor deubiquitination. This module treats matrix import as a coupled import-export cycle. The docking/translocation importomer is modeled separately from the receptor ubiquitination and ATP-dependent extraction machinery, even though some literature uses "importomer" more broadly. Pexophagy and organelle contact sites are represented as interfaces to the lifecycle, not as part of the core matrix import mechanism. GO release 2026-06-15 obsoleted the three substrate-specific receptor terms GO:0033328 (mPTS binding, PEX19), GO:0005052 (PTS1 binding, PEX5) and GO:0005053 (PTS2 binding, PEX7), each with replaced_by GO:0000268 (peroxisome signal sequence receptor activity), so the three receptor annotons now share one molecular-function id. The mPTS/PTS1/PTS2 distinction is kept in each annoton's preferred_term and cargo. The three PAINT ancestral-node descriptors were re-transcribed from the current PAINT rows, whose F:GO:0000268 IBD assertions are dated 20260828.