TraitMech

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ribophagy

traitmech:000641 · CLASS · PROPOSED

An autophagy phenotype in which a microbial cell selectively degrades mature ribosomes or their subunits through macroautophagic delivery to lysosomal or vacuolar compartments.

Trait evidence (4)

  • DOI:10.1038/ncb1723
    A genetic screen revealed that selective degradation of ribosomes requires catalytic activity of the Ubp3p/Bre5p ubiquitin protease.

    PMID:18391941. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. Saccharomyces cerevisiae degrades mature ribosomes during nutrient starvation by both nonselective autophagy and a selective component named ribophagy. The deletion phenotype concerns 60S particles despite retained starvation sensing and general autophagy; do not transfer the same dependence to 40S subunits. Enriched ubiquitination suggests direct regulation rather than proving every substrate or step. Full text, actual figures and natural strain provenance were not inspected.

  • DOI:10.1083/jcb.201308139
    Its ubiquitylation is Ltn1 dependent and Ubp3 reversed, and mutation of its ubiquitylation site rendered ribophagy less dependent on Ubp3.

    PMID:24616224, PMC3998797. Scientific Abstract directly read in Europe PMC core metadata and XML, distinct from the precis. The quoted substrate is Rpl25. Introduction, the LTN1-deletion Results and strain/culture Methods were also read. This yeast study explicitly treats 60S subunit turnover as ribophagy; Rpl5/Rpl25-GFP processing and vacuolar localization support degradation. LTN1 deletion rescues the delayed reporter cleavage in ubp3 mutants, so Ubp3 is not an unconditional presence criterion. Table 1 identifies the reference as BY4741 with auxotrophic deletions, not an independently verified natural exemplar. Figure 1 caption was read; actual figures, supplements, complete Methods and independent strain provenance were not inspected.

  • DOI:10.15252/embj.201489083
    Under nutrient starvation, a portion of the cytoplasm is non-selectively sequestered into autophagosomes.

    PMID:25468960, PMC4337068. Scientific Abstract directly read in Europe PMC core metadata with matching DOI. This is boundary evidence, not a positive selective-ribophagy observation: the study frames yeast vacuolar RNA catabolism as bulk nonselective autophagy. Rny1-mediated RNA cleavage, downstream nucleotide metabolism or ribosome delivery alone does not establish cargo selectivity. Full-text retrieval returned HTTP 500; full Methods and actual figures were not inspected.

  • DOI:10.1016/j.jbc.2025.108554
    We discovered that most ribosomes are selectively degraded, whose mechanism differs from the previously reported selective degradation process called "ribophagy."

    PMID:40294649, PMC12152620. Scientific Abstract directly read in Europe PMC core metadata and XML. Results sec1.1-sec1.3, Discussion sec2 and Methods sec3.1/sec3.7-sec3.11/sec3.13 were read. The authors distinguish Rsa1-dependent turnover from previously named Ubp3/Ufd3/Cdc48-dependent ribophagy; this is terminology/mechanism boundary evidence, not an unqualified canonical ribophagy assignment. Rpl25-GFP processing, Atg2 controls and rRNA measurements support degradation; RNA accumulation in rny1 mutants alone does not. Residual turnover in rsa1 mutants is retained. The Results support mature rRNA turnover, while the Discussion also hypothesizes nascent nuclear cargo; that cargo choice is not established. Rpl8 contact and Atg8-binding motifs are modeled, not experimentally mapped. Captions were read, but actual figures, supplements, complete Methods and independent natural strain provenance were not inspected.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1038/ncb1723

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 cargo selectivity and mechanism-dependent terminology.

CURATION TODO OPEN ribophagy-selectivity-and-terminology · 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 the broader phenotype. The 2008 paper names selective mature-ribosome turnover ribophagy; the 2014 paper explicitly includes 60S subunits. Neither ribosome protection in dormancy nor bulk RNA decay, free ribosomal-protein degradation, ribosome biogenesis, gene presence or puncta alone establishes this phenotype. The 2025 Rsa1 paper distinguishes its pathway from known ribophagy and notes differing mammalian usage. Retain that source-attributed distinction for human review; do not silently equate Rsa1-dependent turnover with the historically named pathway or make Ubp3 universal. GO:0034517, resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0034517, is a nonobsolete biological process for selective mature ribosome degradation by macroautophagy, not an exact organismal phenotype. Preserve that route qualifier and omit exact xrefs and synonyms.

Resolve natural exemplars and subunit-specific mechanisms.

KNOWLEDGE GAP OPEN ribophagy-exemplars-and-native-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: the experiments use laboratory reporter and perturbation strains, and natural strain provenance has not been independently verified. The microbial cell doing the degradation carries the phenotype, not bacteria expressing purified yeast proteins or organisms eliciting an animal host response. Require native taxon-paired protein accessions and functional evidence before a causal graph; do not impose the 60S Ubp3/Bre5 mechanism on 40S turnover or all microbial taxa. Preserve the difference between normal rates, residual activity and complete absence of degradation. A predicted binding motif is not a separate trait or a proven causal contact.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Added ribophagy as selective mature ribosome or subunit degradation under autophagy, with four DOI-backed snippets and explicit bulk-turnover, source-access and terminology limits. Ignored-and-hidden searches and pinned METPO review found no exact record. Reserved METPO:1059400 in v517 with v514's unchanged parent context. Deferred unverified examples, mappings and protein graphs.