YTM1 encodes the conserved WD40-repeat/UBL ribosome biogenesis factor Ytm1. Ytm1 acts in the nucleolus as part of the Nop7-Erb1-Ytm1, PeBoW-like subcomplex on 66S/pre-60S particles, where its WD40 propeller binds Erb1 and helps assemble and stabilize the Nop7 subcomplex for 25S and 5.8S rRNA maturation. Its N-terminal MIDO/UBL region is later recognized by the AAA-ATPase Rea1, enabling ATP-dependent release of Ytm1-Erb1-Nop7 as nucleolar large-subunit precursors are remodeled and progress toward the nucleoplasm.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000463 maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) | IEA GO_REF:0000104 | ACCEPT | Summary: Ytm1/WDR12-family proteins support 60S-subunit pre-rRNA maturation. Reason: The UniRule annotation matches the conserved Nop7-Erb1-Ytm1/WDR12 role: the budding-yeast protein is required for efficient processing of 27S pre-rRNA intermediates during 25S/5.8S rRNA and large-subunit maturation. Supporting Evidence: PMID:16287855 Mutations in the WD40 motifs of Ytm1 disrupt binding to Erb1, destabilize the heterotrimer, and delay pre-rRNA processing and nuclear export of preribosomes. PMID:18448671 assembly of Nop7, Erb1, and Ytm1 into preribosomes is interdependent. |
| GO:0000466 maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) | IEA GO_REF:0000104 | ACCEPT | Summary: Ytm1/WDR12-family proteins support the 5.8S branch of pre-60S rRNA maturation. Reason: Ytm1 acts in 66S/pre-60S particles containing 27S and 7S pre-rRNAs, so the UniRule 5.8S rRNA maturation annotation is consistent with the direct yeast perturbation and Nop7-subcomplex assembly evidence. Supporting Evidence: PMID:16287855 Ytm1 binds directly to Erb1 and is present in a heterotrimeric subcomplex together with Erb1 and Nop7, both within preribosomes and independently of preribosomes. PMID:16287855 Mutations in the WD40 motifs of Ytm1 disrupt binding to Erb1, destabilize the heterotrimer, and delay pre-rRNA processing and nuclear export of preribosomes. |
| GO:0003674 molecular_function | ND GO_REF:0000015 | ACCEPT | Summary: Root molecular function ND annotation: when it was made, no molecular function had been curated for this gene product from literature. Reason: ACCEPT under the ND acceptance rule (projects/NO_DATA.md). The evidence this review cites for the molecular function is inferred (from orthologs, family membership or sequence features) or comes from other species; none of it is literature on this gene product in this species. This was judged from the review's own content during the NO_DATA re-action pass, not from a new literature search. Earlier action: REMOVE. Re-checked 2026-10-31: the yeast Ytm1 papers cited in core_functions show complex membership with Nop7 and Erb1; an interaction identifies no activity. Possibly stale: the 2026-11-06 ND citation pass found literature on this gene in this species that may identify a molecular function; see YTM1-notes.md, section "ND literature-search citations (2026-11-06)". A curator should check it before this ACCEPT stands. |
| GO:0005515 protein binding | IPI PMID:11805837 Systematic identification of protein complexes in Saccharomy... | REMOVE | Summary: The Erb1 interaction is real, but generic protein binding is not an informative Ytm1 molecular-function annotation. Reason: The existing PeBoW-complex, pre-60S, and ribonucleoprotein-complex-binding rows capture the supported biology more usefully. Removing this row does not dispute the observed Erb1 physical interaction. |
| GO:0005515 protein binding | IPI PMID:16429126 Proteome survey reveals modularity of the yeast cell machine... | REMOVE | Summary: The Erb1 interaction is real, but generic protein binding is not an informative Ytm1 molecular-function annotation. Reason: The existing PeBoW-complex, pre-60S, and ribonucleoprotein-complex-binding rows capture the supported biology more usefully. Removing this row does not dispute the observed Erb1 physical interaction. |
| GO:0005515 protein binding | IPI PMID:18448671 Interactions among Ytm1, Erb1, and Nop7 required for assembl... | REMOVE | Summary: The Erb1 interaction is real, but generic protein binding is not an informative Ytm1 molecular-function annotation. Reason: The existing PeBoW-complex, pre-60S, and ribonucleoprotein-complex-binding rows capture the supported biology more usefully. Removing this row does not dispute the observed Erb1 physical interaction. |
| GO:0005515 protein binding | IPI PMID:25877921 A protein interaction map of the LSU processome. | REMOVE | Summary: The Erb1 interaction is real, but generic protein binding is not an informative Ytm1 molecular-function annotation. Reason: The existing PeBoW-complex, pre-60S, and ribonucleoprotein-complex-binding rows capture the supported biology more usefully. Removing this row does not dispute the observed Erb1 physical interaction. |
| GO:0005515 protein binding | IPI PMID:37968396 The social and structural architecture of the yeast protein ... | REMOVE | Summary: The Erb1 interaction is real, but generic protein binding is not an informative Ytm1 molecular-function annotation. Reason: The existing PeBoW-complex, pre-60S, and ribonucleoprotein-complex-binding rows capture the supported biology more usefully. Removing this row does not dispute the observed Erb1 physical interaction. |
| GO:0005634 nucleus | HDA PMID:11914276 Subcellular localization of the yeast proteome. | ACCEPT | Summary: The broad nuclear localization is true for a nucleolar/nuclear pre-60S factor. Reason: This high-throughput nuclear localization is broad but compatible with the more specific nucleolus and nucleoplasm annotations for Ytm1. Supporting Evidence: PMID:16287855 Ytm1 binds directly to Erb1 and is present in a heterotrimeric subcomplex together with Erb1 and Nop7, both within preribosomes and independently of preribosomes. |
| GO:0005634 nucleus | IEA GO_REF:0000104 | ACCEPT | Summary: The UniRule nuclear localization is broad but correct. Reason: Ytm1 is a nucleolar/nuclear pre-60S assembly factor, and the broad nuclear row is compatible with the direct yeast literature. Supporting Evidence: PMID:16287855 Ytm1 binds directly to Erb1 and is present in a heterotrimeric subcomplex together with Erb1 and Nop7, both within preribosomes and independently of preribosomes. |
| GO:0005654 nucleoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: The nucleoplasm annotation is plausible for a factor released during nucleolar-to-nucleoplasmic pre-60S maturation. Reason: Ytm1 mainly acts in nucleolar pre-60S particles and is removed during exit toward the nucleoplasm; the broad UniProt subcellular-location transfer is not misleading. Supporting Evidence: PMID:20542003 Rea1 induces the release of the Ytm1-Erb1-Nop7 subcomplex from the nascent 60S subunit and consequently enables this early pre-60S intermediate to exit from the nucleolus. |
| GO:0005730 nucleolus | IDA PMID:11583614 Composition and functional characterization of yeast 66S rib... | ACCEPT | Summary: Ytm1 is a nucleolar pre-60S biogenesis factor. Reason: The nucleolar localization is consistent with Ytm1 entry into early 66S/pre-60S particles and with its Rea1/Mdn1-triggered removal at the nucleolar-to-nucleoplasmic transition. Supporting Evidence: PMID:16287855 Ytm1 binds directly to Erb1 and is present in a heterotrimeric subcomplex together with Erb1 and Nop7, both within preribosomes and independently of preribosomes. PMID:20542003 Rea1 induces the release of the Ytm1-Erb1-Nop7 subcomplex from the nascent 60S subunit and consequently enables this early pre-60S intermediate to exit from the nucleolus. |
| GO:0005730 nucleolus | IEA GO_REF:0000120 | ACCEPT | Summary: Ytm1 is a nucleolar pre-60S biogenesis factor. Reason: The nucleolar localization is consistent with Ytm1 entry into early 66S/pre-60S particles and with its Rea1/Mdn1-triggered removal at the nucleolar-to-nucleoplasmic transition. Supporting Evidence: PMID:16287855 Ytm1 binds directly to Erb1 and is present in a heterotrimeric subcomplex together with Erb1 and Nop7, both within preribosomes and independently of preribosomes. PMID:20542003 Rea1 induces the release of the Ytm1-Erb1-Nop7 subcomplex from the nascent 60S subunit and consequently enables this early pre-60S intermediate to exit from the nucleolus. |
| GO:0006364 rRNA processing | IDA PMID:18448671 Interactions among Ytm1, Erb1, and Nop7 required for assembl... | MODIFY | Summary: rRNA processing is correct but less specific than the 25S/5.8S maturation branch that Ytm1 supports. Reason: The direct paper examined 60S pre-rRNA maturation through the Nop7-Erb1-Ytm1 subcomplex. Replace the broad parent with the two specific tricistronic-transcript maturation terms already present by UniRule. Proposed replacements: maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Supporting Evidence: PMID:18448671 assembly of Nop7, Erb1, and Ytm1 into preribosomes is interdependent. |
| GO:0030687 preribosome, large subunit precursor | HDA PMID:17443350 In vivo functional characterization of the Saccharomyces cer... | ACCEPT | Summary: Ytm1 is a component of large-subunit preribosomes. Reason: The large-subunit-precursor term captures the preribosomal particle in which Ytm1 acts with Nop7/Erb1 during 60S maturation. Supporting Evidence: PMID:16287855 Ytm1 binds directly to Erb1 and is present in a heterotrimeric subcomplex together with Erb1 and Nop7, both within preribosomes and independently of preribosomes. PMID:36423630 the biogenesis complex Ytm1-Erb1-Ppp1 (Ytm1-Erb1-Nop7 in S. cerevisiae) is incorporated |
| GO:0030687 preribosome, large subunit precursor | IBA GO_REF:0000033 | ACCEPT | Summary: The PAINT large-subunit-preribosome IBA is correctly placed on the fungal YTM1/WDR12 ancestor. Reason: PANTHER:PTN000458086 is the fungal Ytm1 node, and its short SGD-seeded donor list is not a weakness: the budding-yeast protein is directly observed in 66S preribosomes and the fission-yeast ortholog is observed in nascent 60S particles. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000458086 · fungal WDR12/YTM1 node SUPPORTS TRANSFER PTN000458086 places GO:0030687 on the Ascomycota Ytm1/WDR12 ancestor, seeded by curated S. cerevisiae YTM1 evidence. Supporting Evidence: PMID:16287855 Ytm1 binds directly to Erb1 and is present in a heterotrimeric subcomplex together with Erb1 and Nop7, both within preribosomes and independently of preribosomes. PMID:36423630 the biogenesis complex Ytm1-Erb1-Ppp1 (Ytm1-Erb1-Nop7 in S. cerevisiae) is incorporated |
| GO:0030687 preribosome, large subunit precursor | IDA PMID:11583614 Composition and functional characterization of yeast 66S rib... | ACCEPT | Summary: Ytm1 is a component of large-subunit preribosomes. Reason: The large-subunit-precursor term captures the preribosomal particle in which Ytm1 acts with Nop7/Erb1 during 60S maturation. Supporting Evidence: PMID:16287855 Ytm1 binds directly to Erb1 and is present in a heterotrimeric subcomplex together with Erb1 and Nop7, both within preribosomes and independently of preribosomes. PMID:36423630 the biogenesis complex Ytm1-Erb1-Ppp1 (Ytm1-Erb1-Nop7 in S. cerevisiae) is incorporated |
| GO:0030687 preribosome, large subunit precursor | IEA GO_REF:0000104 | ACCEPT | Summary: Ytm1 is a component of large-subunit preribosomes. Reason: The large-subunit-precursor term captures the preribosomal particle in which Ytm1 acts with Nop7/Erb1 during 60S maturation. Supporting Evidence: PMID:16287855 Ytm1 binds directly to Erb1 and is present in a heterotrimeric subcomplex together with Erb1 and Nop7, both within preribosomes and independently of preribosomes. PMID:36423630 the biogenesis complex Ytm1-Erb1-Ppp1 (Ytm1-Erb1-Nop7 in S. cerevisiae) is incorporated |
| GO:0042254 ribosome biogenesis | IEA GO_REF:0000002 | TOO GENERAL | Summary: Ribosome biogenesis is true but less precise than the 60S branch. Reason: The WDR12/Ytm1 InterPro mapping points at ribosome assembly, but this review already accepts GO:0042273 for the specific conserved ribosomal large subunit biogenesis branch. Supporting Evidence: PMID:16287855 Mutations in the WD40 motifs of Ytm1 disrupt binding to Erb1, destabilize the heterotrimer, and delay pre-rRNA processing and nuclear export of preribosomes. |
| GO:0042273 ribosomal large subunit biogenesis | IBA GO_REF:0000033 | ACCEPT | Summary: The PAINT large-subunit-biogenesis IBA is the central conserved fungal Ytm1 process. Reason: PANTHER:PTN000458086 carries the 2024 GO:0042273 IBD from both SGD and PomBase seeds. The target belongs to the fungal WDR12/Ytm1 subfamily and there is no target-specific loss signal. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000458086 · fungal WDR12/YTM1 node SUPPORTS TRANSFER PTN000458086 places GO:0042273 on the Ascomycota Ytm1/WDR12 ancestor with both S. cerevisiae and S. pombe curated seeds. Supporting Evidence: PMID:16287855 Mutations in the WD40 motifs of Ytm1 disrupt binding to Erb1, destabilize the heterotrimer, and delay pre-rRNA processing and nuclear export of preribosomes. PMID:36423630 the biogenesis complex Ytm1-Erb1-Ppp1 (Ytm1-Erb1-Nop7 in S. cerevisiae) is incorporated |
| GO:0042273 ribosomal large subunit biogenesis | IDA PMID:18448671 Interactions among Ytm1, Erb1, and Nop7 required for assembl... | ACCEPT | Summary: Ytm1 acts in ribosomal large subunit biogenesis. Reason: Ytm1 is a conserved Nop7/Erb1/Ppp1 partner on pre-60S particles, contributes to 25S/5.8S maturation, and is released by Rea1/Mdn1 as large-subunit precursors mature. Supporting Evidence: PMID:16287855 Mutations in the WD40 motifs of Ytm1 disrupt binding to Erb1, destabilize the heterotrimer, and delay pre-rRNA processing and nuclear export of preribosomes. PMID:18448671 assembly of Nop7, Erb1, and Ytm1 into preribosomes is interdependent. PMID:20542003 Rea1 induces the release of the Ytm1-Erb1-Nop7 subcomplex from the nascent 60S subunit and consequently enables this early pre-60S intermediate to exit from the nucleolus. |
| GO:0042273 ribosomal large subunit biogenesis | IEA GO_REF:0000104 | ACCEPT | Summary: Ytm1 acts in ribosomal large subunit biogenesis. Reason: Ytm1 is a conserved Nop7/Erb1/Ppp1 partner on pre-60S particles, contributes to 25S/5.8S maturation, and is released by Rea1/Mdn1 as large-subunit precursors mature. Supporting Evidence: PMID:16287855 Mutations in the WD40 motifs of Ytm1 disrupt binding to Erb1, destabilize the heterotrimer, and delay pre-rRNA processing and nuclear export of preribosomes. PMID:18448671 assembly of Nop7, Erb1, and Ytm1 into preribosomes is interdependent. PMID:20542003 Rea1 induces the release of the Ytm1-Erb1-Nop7 subcomplex from the nascent 60S subunit and consequently enables this early pre-60S intermediate to exit from the nucleolus. |
| GO:0042273 ribosomal large subunit biogenesis | IMP PMID:11583614 Composition and functional characterization of yeast 66S rib... | ACCEPT | Summary: Ytm1 acts in ribosomal large subunit biogenesis. Reason: Ytm1 is a conserved Nop7/Erb1/Ppp1 partner on pre-60S particles, contributes to 25S/5.8S maturation, and is released by Rea1/Mdn1 as large-subunit precursors mature. Supporting Evidence: PMID:16287855 Mutations in the WD40 motifs of Ytm1 disrupt binding to Erb1, destabilize the heterotrimer, and delay pre-rRNA processing and nuclear export of preribosomes. PMID:18448671 assembly of Nop7, Erb1, and Ytm1 into preribosomes is interdependent. PMID:20542003 Rea1 induces the release of the Ytm1-Erb1-Nop7 subcomplex from the nascent 60S subunit and consequently enables this early pre-60S intermediate to exit from the nucleolus. |
| GO:0043021 ribonucleoprotein complex binding | IEA GO_REF:0000104 | ACCEPT | Summary: Ribonucleoprotein complex binding is a defensible molecular-function abstraction for the WD-repeat pre-60S assembly factor. Reason: Ytm1 uses its WD40 beta propeller to bind Erb1 and thereby associate the Nop7 subcomplex with preribosomal RNPs; no established GO molecular-function term captures that scaffold/adaptor activity more exactly. Supporting Evidence: PMID:18448671 Once in preribosomes, Erb1 recruits Ytm1 by the interaction between amino acids 383 and 419 within the amino-terminal conserved region of Erb1 and the carboxyl-terminal seven WD40 domains of Ytm1 |
| GO:0051276 chromosome organization | IMP PMID:10454593 New yeast genes important for chromosome integrity and segre... | MARK AS OVER ANNOTATED | Summary: The chromosome-organization row is an over-annotation from a dosage chromosome-stability screen. Reason: The 1999 screen supports a perturbation link between YTM1 dosage and chromosome-stability phenotypes, but the mature evidence places Ytm1 in pre-60S biogenesis rather than as a normal executor of chromosome organization. Supporting Evidence: PMID:10454593 we have performed a search for genes that affect chromo-some stability when overexpressed in the budding yeast Saccharomyces cerevisiae. |
| GO:0070545 PeBoW complex | IBA GO_REF:0000033 | ACCEPT | Summary: The PAINT PeBoW-complex IBA is correctly placed on the fungal YTM1/WDR12 ancestor. Reason: PTN000458086 transfers the yeast Nop7-Erb1-Ytm1, PeBoW-like complex to fungal Ytm1/WDR12 proteins at the right specificity. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000458086 · fungal WDR12/YTM1 node SUPPORTS TRANSFER PTN000458086 places GO:0070545 on the Ascomycota Ytm1/WDR12 ancestor, seeded by curated S. cerevisiae YTM1 evidence. Supporting Evidence: PMID:16287855 Ytm1 binds directly to Erb1 and is present in a heterotrimeric subcomplex together with Erb1 and Nop7, both within preribosomes and independently of preribosomes. PMID:18448671 assembly of Nop7, Erb1, and Ytm1 into preribosomes is interdependent. |
| GO:0070545 PeBoW complex | IDA PMID:16287855 Ytm1, Nop7, and Erb1 form a complex necessary for maturation... | ACCEPT | Summary: Ytm1 is part of the fungal Nop7-Erb1-Ytm1, PeBoW-like pre-60S subcomplex. Reason: Direct yeast work shows that Ytm1 binds Erb1 and forms a heterotrimeric subcomplex with Erb1 and Nop7 in and outside preribosomes. Supporting Evidence: PMID:16287855 Ytm1 binds directly to Erb1 and is present in a heterotrimeric subcomplex together with Erb1 and Nop7, both within preribosomes and independently of preribosomes. PMID:18448671 assembly of Nop7, Erb1, and Ytm1 into preribosomes is interdependent. |
| GO:0070545 PeBoW complex | IPI PMID:16287855 Ytm1, Nop7, and Erb1 form a complex necessary for maturation... | ACCEPT | Summary: Ytm1 is part of the fungal Nop7-Erb1-Ytm1, PeBoW-like pre-60S subcomplex. Reason: Direct yeast work shows that Ytm1 binds Erb1 and forms a heterotrimeric subcomplex with Erb1 and Nop7 in and outside preribosomes. Supporting Evidence: PMID:16287855 Ytm1 binds directly to Erb1 and is present in a heterotrimeric subcomplex together with Erb1 and Nop7, both within preribosomes and independently of preribosomes. PMID:18448671 assembly of Nop7, Erb1, and Ytm1 into preribosomes is interdependent. |
| GO:0070545 PeBoW complex | IPI PMID:18448671 Interactions among Ytm1, Erb1, and Nop7 required for assembl... | ACCEPT | Summary: Ytm1 is part of the fungal Nop7-Erb1-Ytm1, PeBoW-like pre-60S subcomplex. Reason: Direct yeast work shows that Ytm1 binds Erb1 and forms a heterotrimeric subcomplex with Erb1 and Nop7 in and outside preribosomes. Supporting Evidence: PMID:16287855 Ytm1 binds directly to Erb1 and is present in a heterotrimeric subcomplex together with Erb1 and Nop7, both within preribosomes and independently of preribosomes. PMID:18448671 assembly of Nop7, Erb1, and Ytm1 into preribosomes is interdependent. |
| GO:0110136 protein-RNA complex remodeling | IDA PMID:20542003 The AAA-ATPase Rea1 drives removal of biogenesis factors dur... | ACCEPT | Summary: Ytm1 participates in the Rea1/Mdn1-dependent remodeling step that removes Ytm1-Erb1-Nop7 from pre-60S particles. Reason: Ytm1 is the Rea1-recognized MIDO/UBL ligand in this remodeling event. The ATPase does the mechanical work, but the Ytm1 interaction is the conserved handle required for ATP-dependent release of the subcomplex. Supporting Evidence: PMID:20542003 Rea1 induces the release of the Ytm1-Erb1-Nop7 subcomplex from the nascent 60S subunit and consequently enables this early pre-60S intermediate to exit from the nucleolus. PMID:36929751 The AAA+-ATPase Rea1 participates in the nucleolar exit by releasing the Ytm1-Erb1 heterodimer from the evolving pre-60S particle. |
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Download this section (compressed HTML)Q: Should GO add a more specific molecular-function term for the Ytm1/WDR12 MIDO-UBL adaptor activity that recruits or presents the Rea1/Mdn1 MIDAS domain for ATP-dependent pre-60S remodeling, rather than relying on the broad GO:0043021 ribonucleoprotein complex binding term?
Ribosomal assembly factor and 66S pre-ribosomal particle constituent; subunit of the Nop7-subcomplex (PeBoW complex), required for an early nucleolar step in pre-60S ribosomal particle maturation; interaction of its ubiquitin-like (UBL) domain with the MIDAS domain in the Rea1p tail triggers release of the subcomplex and possibly other biogenesis factors via cycles of ATP hydrolysis; involved in the processing of 27S pre-rRNA; contains an N-terminal UBL domain and seven C-terminal WD repeats
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