Rrp36 (SPAC823.04) is a 279-residue nucleolar ribosome-biogenesis factor of the eukaryote-specific RRP36 family (Pfam PF06102), with long disordered, charged N- and C-terminal regions flanking a central coiled-coil segment. Its budding yeast and human orthologs associate with the 90S preribosome (small-subunit processome) and, more weakly, with pre-40S particles, and are required for the early cleavages of the primary pre-rRNA transcript that release the 18S rRNA precursor, and hence for 40S ribosomal subunit production; large-subunit rRNA production is not affected. In yeast, Rrp36 joins the preribosome after the UTP-A and UTP-B modules and interacts with the U3 snoRNP protein Rrp9. In fission yeast, Rrp36 localizes to the nucleolus. No catalytic activity or catalytic motif is known; Rrp36 is regarded as a non-enzymatic assembly factor, and its position within the 90S particle has not been resolved structurally.
Existing Annotations Review
GO Term
Evidence
Action
Reason
GO:0000462 maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
IBA GO_REF:0000033
ACCEPT
Summary: Early SSU-rRNA maturation, inherited from the PAINT node seeded by budding yeast Rrp36; this is the core process of the gene.
Reason: PTHR21738 has a single subfamily (SF0) that contains S. pombe rrp36 (Q9P6P2), S. cerevisiae RRP36 (Q12481) and human RRP36 (Q96EU6), so the target sits inside the clade from which PAINT propagated the donor's experimental process term. In budding yeast, Rrp36 depletion blocks the early A0-A2 cleavages of the 35S pre-rRNA and depletes 18S rRNA, and the human ortholog has the same requirement, so the function predates the fungal/animal split. Rrp36 itself joins the 90S particle that performs these steps, so this is participation rather than mere necessity, even though the endonucleolytic chemistry belongs to other subunits. There is no S. pombe-specific evidence of loss, and the target is nucleolar. The single-donor seed is not a weakness.
We show that the Rrp36p protein is nucleolar and interacts with 90S and pre-40S preribosomal particles. Its depletion affects early cleavages of the 35S pre-rRNA and results in a rapid decrease in mature 18S rRNA levels.
In parallel, we studied the human orthologue of Rrp36p in HeLa cells, and we show that the function of this protein in early cleavages of the pre-rRNA has been conserved through evolution in eukaryotes.
Summary: No molecular function is established for Rrp36 in any species; the ND root is correct.
Reason: The characterised orthologs show only that Rrp36 is part of the preribosome and is required for cleavage. Rrp36 has no recognisable catalytic motif and has not been placed in any 90S cryo-EM structure. Its one documented binary contact is a yeast two-hybrid interaction with the U3 snoRNP protein Rrp9. That is not enough for an informative binding or structural-molecule term, and GO:0005515 protein binding would be uninformative anyway. Both the literature summary and the deep research found no biochemical activity, so the ND root should stay until there is direct evidence.
Supporting Evidence:
file:SCHPO/rrp36/rrp36-deep-research-falcon.md
No nuclease, helicase, ATPase, GTPase, transferase, or other catalytic activity has been reported for Rrp36.
HDA PMID:16823372 ORFeome cloning and global analysis of protein localization ...
MODIFY
Summary: Nuclear localization from the ORFeome YFP screen is correct but less specific than the nucleolar localization reported in the same screen.
Reason: The same high-throughput study gives a nucleolar localization for rrp36, and UniProt records this as curated, publication-backed evidence. Nucleolus is part_of nucleus and is where early 90S assembly happens, so it is the more specific supported term. The gene already carries it from the same reference.
We show that the Rrp36p protein is nucleolar and interacts with 90S and pre-40S preribosomal particles. Its depletion affects early cleavages of the 35S pre-rRNA and results in a rapid decrease in mature 18S rRNA levels.
HDA PMID:16823372 ORFeome cloning and global analysis of protein localization ...
ACCEPT
Summary: Direct (high-throughput) fission yeast evidence that Rrp36 is nucleolar, the site of 90S preribosome assembly.
Reason: The YFP-tagged ORFeome screen placed rrp36 in the nucleolus, and UniProt has curated this with experimental evidence code ECO:0000269. Budding yeast Rrp36 and human RRP36 are also nucleolar, so the observation agrees with orthologs in the same PANTHER subfamily. The cached publication is abstract only, but the curator read the full dataset, so we defer to them.
Next, we determined the localization of 4,431 proteins, corresponding to approximately 90% of the fission yeast proteome, by tagging each ORF with the yellow fluorescent protein.
We show that the Rrp36p protein is nucleolar and interacts with 90S and pre-40S preribosomal particles. Its depletion affects early cleavages of the 35S pre-rRNA and results in a rapid decrease in mature 18S rRNA levels.
Summary: Nucleolar localization inherited from the RRP36 ancestral node, with yeast and human donors; it agrees with the direct fission yeast observation.
Reason: The donors (budding yeast Rrp36 and human RRP36) and the target all belong to PTHR21738:SF0. The function is placed at an ancestral eukaryotic node, and fission yeast HDA data independently confirm it for this protein.
We show that the Rrp36p protein is nucleolar and interacts with 90S and pre-40S preribosomal particles. Its depletion affects early cleavages of the 35S pre-rRNA and results in a rapid decrease in mature 18S rRNA levels.
Summary: UniProt subcellular-location mapping to nucleolus. It agrees with the curated, experimentally backed UniProt location.
Reason: The mapping comes from a UniProt location annotation that is itself backed by experimental evidence (ECO:0000269, PMID:16823372). It is consistent with the HDA and IBA rows for the same term.
Summary: Membership of the 90S preribosome (SSU processome), inherited from the RRP36 node seeded by budding yeast Rrp36.
Reason: Budding yeast Rrp36 co-purifies with 35S/33S/32S pre-rRNAs, U3 snoRNA and 90S proteins. Its recruitment depends on UTP-A and UTP-B, and it interacts with the U3 snoRNP protein Rrp9 by two-hybrid assay. The target is in the same single-subfamily PANTHER family and is nucleolar, so inheritance is sound. The 90S particle is the complex in which Rrp36 does its work. Weaker pre-40S association exists in yeast, but PAINT did not propagate a pre-40S term, and this review does not add one.
We show that the Rrp36p protein is nucleolar and interacts with 90S and pre-40S preribosomal particles. Its depletion affects early cleavages of the 35S pre-rRNA and results in a rapid decrease in mature 18S rRNA levels.
strong positive interactions were observed for Rrp9 with Rrp36 and Sgd1
Core Functions
Non-enzymatic component of the nucleolar 90S preribosome (SSU processome) required for the early cleavages of the primary pre-rRNA transcript that lead to 18S rRNA and 40S subunit production. The function is inherited within PANTHER PTHR21738:SF0 from experimentally characterised budding yeast and human orthologs; nucleolar localization is observed directly in fission yeast.
We show that the Rrp36p protein is nucleolar and interacts with 90S and pre-40S preribosomal particles. Its depletion affects early cleavages of the 35S pre-rRNA and results in a rapid decrease in mature 18S rRNA levels.
In parallel, we studied the human orthologue of Rrp36p in HeLa cells, and we show that the function of this protein in early cleavages of the pre-rRNA has been conserved through evolution in eukaryotes.
Q: Where does Rrp36 sit in the 90S preribosome? Does its conserved coiled-coil segment contact pre-rRNA, the U3 snoRNP (Rrp9), or UTP-C subunits?
Q: Is S. pombe rrp36 essential, and does its depletion block the early pre-rRNA cleavages that separate the SSU precursor from the 5.8S/LSU precursor, as in budding yeast?
Suggested Experiments
Experiment: Make a conditional (degron or nmt1-repressible) rrp36 allele in S. pombe. Map pre-rRNA intermediates by Northern blotting and primer extension, and measure 40S/60S ratios by polysome profiling, to test directly the requirement for early SSU processing that is inferred from orthologs.
Type: genetic depletion with RNA processing analysis
Experiment: Affinity-purify tagged S. pombe Rrp36 and identify co-purifying pre-rRNAs and proteins (RNA-seq/CRAC and mass spectrometry) to confirm 90S membership and find direct RNA contacts.
Type: affinity purification and crosslinking
External Prediction Reviews
These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.
Rrp36 is a conserved 90S preribosome factor supporting small-subunit rRNA maturation. Both predictions are supported but less precise than the established process and complex assignments.
Review rationale: The specific RRP36 domain and target nucleolar localization support the conserved preribosome role inferred by PAINT. Purification and depletion in budding yeast establish 90S/pre-40S association and early small-subunit rRNA maturation; human depletion supports conservation across eukaryotes. GOA already records maturation of SSU-rRNA from tricistronic rRNA transcript (GO:0000462). The broad rRNA-processing prediction is supported but loses small-subunit specificity; no intrinsic RNase chemistry is implied.
Supporting Evidence:
PMID:20038530: "We show that the Rrp36p protein is nucleolar and interacts with 90S and pre-40S preribosomal particles. Its depletion affects early cleavages of the 35S pre-rRNA and results in a rapid decrease in mature 18S rRNA levels."
Review rationale: Rrp36 belongs to a specifically identified ribosome-biogenesis family; characterized ortholog copurification with RNA-containing 90S and pre-40S particles establishes the relevant complex type. Curated ancestral inference already places fission yeast Rrp36 in the 90S preribosome (GO:0030686), consistent with its nucleolar localization. A ribonucleoprotein complex is a broader description of that supported complex membership. The prediction is correct but less precise than the existing 90S assignment.
Supporting Evidence:
PMID:20038530: "We show that the Rrp36p protein is nucleolar and interacts with 90S and pre-40S preribosomal particles. Its depletion affects early cleavages of the 35S pre-rRNA and results in a rapid decrease in mature 18S rRNA levels."