identifier: traitmech:000642 label: ER-phagy definition: An autophagy phenotype in which a microbial cell selectively degrades portions of its endoplasmic reticulum by delivering them to lysosomal or vacuolar compartments. definition_source: DOI:10.15252/embj.2019102586 trait_category: PHYSIOLOGY term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000638 evidence: - reference: DOI:10.1242/jcs.154716 snippet: Finally, we provide evidence that ER-phagy degrades excess ER membrane, suggesting that it contributes to cell homeostasis by controlling organelle size. notes: PMID:25052096, PMC4163648. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. XML Results s2c/s2e and Methods s4b/s4f were read. In Saccharomyces cerevisiae, ER-targeted Pho8 reporters distinguish selective turnover from cytosolic and mitochondrial cargo; Atg7 and vacuolar-protease controls distinguish routes and reporter activation. ER whorls enter the vacuole by microautophagy. DTT and tunicamycin interfere with vacuolar proteolysis, so stress-induced whorl accumulation alone is not completed degradation. Untreated opi1 mutants show partly disintegrated vacuolar whorls, unlike opi1 pep4 prb1 mutants; membrane expansion can elicit this response without misfolded-protein stress. The strains derive from W303, but independent natural provenance was not verified. Figure 5/7 captions were read; actual figures, supplements and complete Methods were not inspected. - reference: DOI:10.1038/nature14506 snippet: Atg40 is enriched in the cortical and cytoplasmic ER, and loads these ER subdomains into autophagosomes. notes: PMID:26040717. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. This Saccharomyces cerevisiae study explicitly restricts its use of autophagy to macroautophagy. Atg40 targets cortical/cytoplasmic ER, whereas Atg39 targets perinuclear ER and nuclear material. These source-specific subdomain assignments do not make ER-phagy and nucleophagy synonyms or restrict all ER-phagy to the macro route. The proposed mammalian FAM134B functional counterpart is qualified as probable, not experimentally universal. Full text, actual figures, supplements and strain provenance were not inspected. - reference: DOI:10.15252/embj.2019102586 snippet: Third, we demonstrate that macro- and micro-ER-phagy are parallel pathways with distinct molecular requirements. notes: PMID:31802527, PMC6960443. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. XML Results embj2019102586-sec-0005 and Methods sec-0011/sec-0018/sec-0019 were read. This yeast study explicitly includes macro- and microautophagic ER turnover. Their contributions depend on the trigger; do not universalize measured proportions. Nem1-Spo7 and ESCRTs contribute to micro-ER-phagy, but ESCRT mutants also impair nonselective autophagy and vacuolar function, so their defects are not micro-ER-phagy-specific absence tests. Atg40 is dispensable for the Atg7-independent micro route. Pho8 assays require background correction; the Sec63-GFP assay quantifies Pep4-dependent, Atg7-independent cleavage products using unsaturated exposures. Uptake or membrane scission alone does not prove complete degradation. Actual figures, supplements, complete Methods and independent strain provenance were not inspected. discussions: - discussion_id: er-phagy-route-scope-and-flux prompt: Review route-inclusive scope and cargo-selective degradative flux. kind: CURATION_TODO status: OPEN rationale: Use autophagy traitmech:000638 as parent. The 2014 microautophagy study and the 2019 online/2020 issue ESCRT paper support a route-inclusive phenotype, whereas Mochida et al. 2015 use autophagy specifically for macroautophagy. GO:0061709 reticulophagy, resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0061709, is a nonobsolete biological process whose definition specifies autophagosomes and whose exact synonyms include ER-phagy. That route restriction and the process-to-phenotype shift prevent an exact xref here; retain the source-attributed difference for human review without silently narrowing the microbial phenotype. No synonyms or SSSOM mapping are asserted. ER stress, unfolded-protein responses, ER-associated protein degradation outside the lysosome/vacuole, bulk cytoplasmic turnover, gene presence, puncta or accumulated whorls alone are insufficient. Nuclear-envelope cargo can overlap nucleophagy without making the two traits equivalent. posed_by: codex posed_date: '2026-10-06' - discussion_id: er-phagy-exemplars-and-route-mechanisms prompt: Resolve natural exemplars and route-specific protein mechanisms. kind: KNOWLEDGE_GAP status: OPEN rationale: Canonical examples remain unset because natural strain provenance has not been independently verified for the laboratory reporter and perturbation strains. Do not infer natural or engineered origin from a mutant label. The yeast doing the degradation carries this phenotype; a bacterium eliciting an animal-host response does not. Resolve native taxon-paired protein accessions and direct functional evidence before adding a causal graph. Neither Atg39/Atg40 nor Nem1-Spo7/ESCRT dependence is an unconditional definition of ER-phagy across all routes and microbial taxa. Keep reduced rates, residual turnover and complete absence distinct, and do not equate impaired vacuolar function with selective loss of this phenotype. posed_by: codex posed_date: '2026-10-06' curation_history: - timestamp: '2026-10-06T12:48:38Z' curator: codex action: MINTED_TRAITMECH_ID changes: Added route-inclusive ER-phagy under autophagy with three DOI-backed scientific-abstract snippets and explicit selectivity, flux and source-access limits. Ignored-and-hidden searches and pinned METPO review found no exact record. Reserved METPO:1059500 in v518 with v514's unchanged parent context. Deferred unverified examples, mappings and protein graphs. llm_assisted: true