Conserved, non-essential nuclear protein of the CMS1/CMSS1 family (Pfam PF14617; PANTHER PTHR24030), with single-copy orthologs from fungi to vertebrates including Saccharomyces cerevisiae CMS1 and human CMSS1. Based on orthology to the strongly characterized budding-yeast factor, Cms1 is an accessory assembly factor of the nucleolar 90S pre-ribosome (small subunit processome) that acts in ribosomal small subunit (18S rRNA) biogenesis, where the budding-yeast ortholog associates with the 18S rRNA 3' major domain of an early 90S carrying the H/ACA snoRNA snR83 and coordinates stepwise local assembly with timely snR83 release. The protein carries a degenerate, catalytically inactive helicase-like fold and a basic disordered patch, but no molecular activity has been experimentally demonstrated in any species. In Schizosaccharomyces pombe the protein itself is uncharacterized (UniProt evidence level: inferred from homology; PomBase characterisation status: biological role inferred): all functional annotations are orthology transfers and deletion is viable.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005634 nucleus | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Electronic (IEA) subcellular-location annotation derived from the UniProt Swiss-Prot "Nucleus" keyword mapping (GO_REF:0000044). It is consistent with, but redundant to, the ISO nuclear annotation (is_active_in nucleus) transferred from the S. cerevisiae ortholog. The nuclear localization is itself a by-similarity inference (UniProt SUBCELLULAR LOCATION: Nucleus, ECO:0000250); no direct localization has been reported for the S. pombe protein. Reason: A defensible location call but not a core function, and redundant with the ISO nucleus annotation. The physiologically relevant compartment is more precisely the nucleolus (site of 90S pre-ribosome assembly), but nucleus is a correct, conservative parent. Retained as a non-core localization annotation. |
| GO:0003674 molecular_function | ND GO_REF:0000015 | ACCEPT | Summary: Root molecular_function term with ND (No Data) evidence, used by PomBase as a placeholder because no specific molecular function is known for cms1. This accurately reflects the current state of knowledge: cms1 encodes a degenerate, catalytically inactive helicase-like fold and no molecular activity has been demonstrated. Even for the well-studied S. cerevisiae ortholog, a possible RNA-binding activity is explicitly hypothetical rather than measured. Reason: The ND molecular_function annotation is appropriate and honest. No specific MF should be asserted: the only proposed activity (RNA binding via an inactive helicase domain) is speculative even for the budding-yeast ortholog and has not been biochemically demonstrated in any species. This is a genuine molecular- function knowledge gap (see knowledge_gaps). Supporting Evidence: PMID:36417864 little is known about how the many different snoRNAs that modify the |
| GO:0030686 90S preribosome | ISO GO_REF:0000024 | ACCEPT | Summary: Part_of the 90S preribosome (small subunit processome), transferred by orthology (ISO) from S. cerevisiae CMS1 (SGD:S000003993). This is well supported for the ortholog: budding-yeast Cms1 co-precipitates with many 90S factors and is detected on early 90S particles at the 18S rRNA 3' major domain. cms1 is a single-copy member of a family conserved from fungi to human (human CMSS1), so the orthology transfer is reliable. PomBase names the product "U3-containing 90S preribosome complex subunit Cms1". Reason: A well-founded core annotation. Unlike a spurious ortholog transfer, this ISO is supported by strong experimental evidence in the closely related S. cerevisiae ortholog and by robust single-copy conservation across the CMS1/CMSS1 family. The 90S preribosome is the defining complex for this protein's inferred role. Supporting Evidence: PMID:36417864 Cms1 co-precipitates with many 90S PMID:36417864 detected Cms1 at the 18S rRNA 3 |
| GO:0042274 ribosomal small subunit biogenesis | ISO GO_REF:0000024 | ACCEPT | Summary: Involved_in ribosomal small subunit biogenesis, transferred by orthology (ISO) from S. cerevisiae CMS1 (SGD:S000003993). The ortholog is a non-essential early 90S / small-subunit-processome assembly factor that acts at the 18S rRNA 3' major domain and coordinates local assembly with timely release of the H/ACA snoRNA snR83. This process assignment is the best-supported functional statement for cms1. Reason: The core biological process. Strongly supported for the S. cerevisiae ortholog and reliable to transfer given single-copy family conservation. The role is accessory/regulatory within 90S assembly rather than a distinct catalytic step, consistent with the protein's degenerate helicase-like fold and non-essentiality. Supporting Evidence: PMID:36417864 Ribosome synthesis begins in the nucleolus with 90S pre-ribosome construction, PMID:36417864 restrict premature Rrp12-Enp1 binding but allows snR83 to |
| GO:0005634 nucleus | ISO GO_REF:0000024 | KEEP AS NON CORE | Summary: Is_active_in nucleus, transferred by orthology (ISO) from S. cerevisiae CMS1 (SGD:S000003993), consistent with UniProt's by-similarity Nucleus localization. The functionally relevant sub-compartment is the nucleolus, where 90S pre- ribosome assembly occurs, but nucleus is a correct conservative parent. Reason: The nuclear localization is consistent with the protein's inferred role as a nucleolar 90S assembly factor and with the ortholog, and is retained as a supporting location rather than a core function. A nucleolus (GO:0005730) annotation would be more precise but is not asserted here in the absence of direct S. pombe localization data. Supporting Evidence: PMID:36417864 Ribosome synthesis begins in the nucleolus with 90S pre-ribosome construction, |
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Download this section (compressed HTML)Q: Does the degenerate helicase-like CMS1/CMSS1 fold have any real RNA-binding (or other) biochemical activity, or is cms1 a purely structural/placeholder subunit of the early 90S?
Q: Does S. pombe cms1 localize to the nucleolus and associate with the 90S pre- ribosome as predicted from the S. cerevisiae ortholog, and does cms1 deletion impair 18S rRNA / small-subunit maturation in fission yeast?
Q: Is the snR83-coordination role of the budding-yeast ortholog conserved in S. pombe (i.e. does cms1 act with the fission-yeast H/ACA snoRNA that pseudouridylates the 18S 3' major domain)?
Experiment: Affinity purification of tagged S. pombe Cms1 followed by mass spectrometry and RNA identification (RIP/CLIP) to define its 90S partners and any bound rRNA/snoRNA.
Experiment: GFP/fluorescent tagging of cms1 to determine subcellular (nucleolar) localization in S. pombe.
Experiment: Northern/primer-extension analysis of pre-rRNA processing intermediates and polysome/40S profiling in a cms1 deletion strain to test the small-subunit- biogenesis role directly.
Experiment: In vitro RNA-binding assays on recombinant Cms1 (and structure-guided mutants of the inactive helicase fold and the basic disordered patch) to test the proposed RNA-binding activity.
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