TraitMech

TraitMech › PHYSIOLOGY

ER-phagy

traitmech:000642 · CLASS · PROPOSED

An autophagy phenotype in which a microbial cell selectively degrades portions of its endoplasmic reticulum by delivering them to lysosomal or vacuolar compartments.

Trait evidence (3)

  • DOI:10.1242/jcs.154716
    Finally, we provide evidence that ER-phagy degrades excess ER membrane, suggesting that it contributes to cell homeostasis by controlling organelle size.

    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.

  • DOI:10.1038/nature14506
    Atg40 is enriched in the cortical and cytoplasmic ER, and loads these ER subdomains into autophagosomes.

    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.

  • DOI:10.15252/embj.2019102586
    Third, we demonstrate that macro- and micro-ER-phagy are parallel pathways with distinct molecular requirements.

    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.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.15252/embj.2019102586

Parent traits (1)

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Discussions and Knowledge Gaps (2)

Open questions attached to this trait. Seeded by just knowledge-gap-scan and curated; see the corpus-wide index.

Review route-inclusive scope and cargo-selective degradative flux.

CURATION TODO OPEN er-phagy-route-scope-and-flux · raised by codex · 2026-10-06

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

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.

Resolve natural exemplars and route-specific protein mechanisms.

KNOWLEDGE GAP OPEN er-phagy-exemplars-and-route-mechanisms · raised by codex · 2026-10-06

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

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.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    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.