YTM1 notes

2026-10-17

• Deep research did not complete: the Falcon wrapper fell back to the lightweight
  provider but the fresh provider environment had no agentapi credentials on
  PATH. I therefore used cached primary literature and manual PubMed follow-up.
• PANTHER:PTN000458086 is the relevant fungal WDR12/YTM1 PAINT node. The
  2024 IBDs place GO:0030687, GO:0070545, and GO:0042273 on the fungal
  Ytm1 ancestor; the short donor list and the SGD self-source are expected for
  a PAINT placement grounded by SGD YTM1 evidence.
• The core mechanism is the Nop7-Erb1-Ytm1 subcomplex on 66S/pre-60S
  preribosomes. Miles et al. show that "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.
• WD40 mutations impair the Erb1 interaction and large-subunit maturation:
  "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:16287855. Tang et al. refine the interaction map:
  "assembly of Nop7, Erb1, and Ytm1 into preribosomes is interdependent"
  PMID:18448671.
• Bassler et al. establish the direct Rea1 remodeling step: "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:20542003. The newer Mitterer et al. structure/function
  paper integrates Spb4 and Rrp17 into the same late-nucleolar transition:
  "The AAA+-ATPase Rea1 participates in the nucleolar exit by releasing the
  Ytm1-Erb1 heterodimer from the evolving pre-60S particle"
  PMID:36929751.
• I retained GO:0110136 protein-RNA complex remodeling: Ytm1 is not the
  ATPase or helicase, but its MIDO/UBL region is the conserved Rea1 handle that
  enables ATP-dependent release of the subcomplex.
• The old GO:0051276 chromosome organization IMP row comes from a dosage
  chromosome-stability screen rather than normal Ytm1 mechanism. I marked it
  over-annotated and did not propagate it to the core function.

ND literature-search citations (2026-11-06)

• existing_annotations[2], GO:0003674 molecular_function (ND, GO_REF:0000015), ACCEPT: the ND may be stale. These notes cite yeast Ytm1 papers showing that Ytm1 binds directly to Erb1 in the Nop7-Erb1-Ytm1 subcomplex (PMID:16287855) and that Rea1 releases the Ytm1-Erb1-Nop7 subcomplex from the nascent 60S particle (PMID:20542003, PMID:36929751); the notes also describe the Ytm1 MIDO/UBL region as the conserved Rea1 handle. Those are direct molecular studies of this gene product in S. cerevisiae, so a curator should decide whether they support an informative MF, such as a structural or adaptor activity within the pre-60S particle, instead of ND. The review's 2026-10-31 re-check judged that an interaction alone identifies no activity. The review action was left unchanged.