identifier: traitmech:000640 label: pexophagy definition: An autophagy phenotype in which a microbial cell selectively degrades its peroxisomes by delivering them to lysosomal or vacuolar compartments. definition_source: DOI:10.1038/emboj.2012.151 trait_category: PHYSIOLOGY term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000638 evidence: - reference: DOI:10.1038/emboj.2012.151 snippet: Peroxisomes undergo rapid, selective autophagic degradation (pexophagy) when the metabolic pathways they contain are no longer required for cellular metabolism. notes: PMID:22643220, PMC3395097. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. Results sec3/sec4 and Methods sec16/sec20/sec23 were also directly read in https://www.ebi.ac.uk/europepmc/webservices/rest/PMC3395097/fullTextXML. In Saccharomyces cerevisiae, Pex11-GFP processing and peroxisomal reporters, with Atg1 and vacuolar-protease controls, support degradation rather than puncta alone. Atg36 perturbation distinguishes peroxisome turnover from mitophagy, Cvt and bulk autophagy in the tested conditions. Post-log turnover also occurs in glucose, glycerol and oleate media; starvation is not a universal requirement. Pex14 deletion retains pexophagy in this species. The abstract's mitochondrial Pex3 redirection is engineered, not native Atg36 mitophagy evidence. Figure 1/2 captions were read, but actual figures, supplements, complete Methods and natural strain provenance were not inspected. - reference: DOI:10.1016/j.devcel.2007.12.011 snippet: It is necessary for pexophagy, but not for other selective and nonselective autophagy-related processes. notes: PMID:18331717, PMC3763908. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. The quoted protein is PpAtg30 in historically named Pichia pastoris. The abstract explicitly uses pexophagy for selective peroxisome turnover through micropexophagy and macropexophagy, and reports cargo selection and delivery. This supports route-inclusive terminology and selectivity in the tested yeast, not a universal Atg30 requirement or a gene-presence trait. The opening nonselective description of autophagy is not imposed on the broader local parent, which includes selective turnover. Full-text retrieval failed; methods, actual figures and strain-specific modern taxonomy were not inspected. - reference: DOI:10.1242/jcs.108.1.25 snippet: there exist in P. pastoris at least two pathways for the sequestration of peroxisomes into the vacuole for degradation. notes: PMID:7738102. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. Methanol-to-ethanol adaptation elicits individual wrapping and vacuolar fusion; glucose adaptation elicits vacuolar engulfment of peroxisome clusters and also turnover of a cytosolic enzyme. Morphology, enzyme measurements and mutant controls support distinct routes; vacuolar-proteinase mutants accumulate undegraded peroxisomes. Enzyme loss or delivery alone is not completed organelle degradation. These conditions are not universal trait requirements. Full methods, actual figures and natural strain provenance were not inspected. - reference: DOI:10.1080/15548627.2019.1603546 snippet: the cytosolic pools of PTS receptors and their cargoes are degraded via a pexophagy-independent, selective autophagy pathway under pexophagy conditions. notes: 'PMID:31007124, PMC6984484. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. This is boundary evidence, not a positive whole-peroxisome turnover experiment: cytosolic Pex5/Pex7 and cargo pools undergo Atg30-independent selective autophagy in Pichia pastoris. Peroxisomal-protein turnover outside the organelle must not be equated with pexophagy. The background''s damaged-or-redundant wording does not make damage obligatory. Full text, actual figures and strain provenance were not inspected.' discussions: - discussion_id: pexophagy-selectivity-and-route-scope prompt: Review route-inclusive phenotype against narrower GO terminology. kind: CURATION_TODO status: OPEN rationale: Use autophagy traitmech:000638 as the direct broader phenotype. The 2008 PpAtg30 scientific abstract uses pexophagy for both micropexophagy and macropexophagy. In contrast, issuing GO:0000425 names pexophagy specifically for selective macroautophagy and lists macropexophagy as exact; GO:0000426 micropexophagy is its sibling under GO:0030242 autophagy of peroxisome, which lists pexophagy as related. These nonobsolete biological-process records were resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0000425,GO%3A0000426,GO%3A0030242. Retain the source-attributed route-inclusive interpretation for human review and omit exact phenotype xrefs and synonyms. Bulk incidental capture, peroxisome presence, import defects, puncta, protein abundance and delivery without degradation alone are insufficient. Cytosolic peroxisomal-protein autophagy is a separate endpoint. The microbial cell doing the degradation carries the trait, not an organism merely inducing an animal host response. posed_by: codex posed_date: '2026-10-06' - discussion_id: pexophagy-exemplars-and-native-mechanisms prompt: Resolve strain provenance and taxon-paired mechanisms before expansion. kind: KNOWLEDGE_GAP status: OPEN rationale: The evidence uses reporter and perturbation strains; natural strain provenance is not independently established. Keep canonical examples unset rather than presenting deficient mutants as positive exemplars. Historical Pichia names also need strain-specific taxonomic review. Atg36 in budding yeast and PpAtg30 do not define a universal receptor inventory; putative BLAST orthologues are not functional protein examples. Require native taxon-paired protein accession checks and direct functional evidence before a causal graph. Neither an ATG locus nor a detector profile is the phenotype, and neither starvation nor damaged cargo is universally required. posed_by: codex posed_date: '2026-10-06' curation_history: - timestamp: '2026-10-06T11:04:55Z' curator: codex action: MINTED_TRAITMECH_ID changes: Added pexophagy as selective peroxisome degradation under autophagy, with four DOI-backed snippets and explicit route, flux and cytosolic-protein boundaries. Ignored-and-hidden searches and pinned METPO review found no exact record. Reserved METPO:1059300 in v516, carrying v514's unchanged parent row as context. Deferred unverified examples, mappings and protein graphs. llm_assisted: true