sen15 (SPAC959.10) encodes a 143-residue fission yeast member of the fungal Sen15 family, the predicted noncatalytic subunit of the heterotetrameric tRNA-splicing endonuclease (Sen2-Sen15-Sen34-Sen54). This complex recognizes intron-containing precursor tRNAs and cleaves them at the 5' and 3' splice sites, releasing the intron and two tRNA half-molecules that are subsequently joined by tRNA ligase. The two splice-site active sites lie in Sen2 and Sen34; Sen15 has a degenerate, catalytically inactive version of the archaeal endonuclease C-terminal fold and, by analogy with the budding-yeast and human orthologous complexes, pairs with Sen34 to form the 3'-splice-site half of the enzyme. In the human complex the substrate tRNA body is recognized by the other three subunits, so Sen15 is best regarded as an architectural/assembly subunit rather than an RNA-binding or catalytic one. Function in fission yeast is inferred from family membership; the protein has not been studied directly. A genome-wide YFP-tagging screen detected the protein in both nucleus and cytosol.
Summary: Membership of the tRNA-splicing endonuclease complex, propagated by PAINT from budding-yeast Sen15 within the fungal Sen15 family.
Reason: Q7LKV3 is in PANTHER PTHR28518:SF1 together with the experimentally characterized S. cerevisiae SEN15 (Q04675, SGD:S000004663), the donor of this IBA; budding-yeast SEN15 was purified as one of the four subunits of the endonuclease (PMID:9200603). The fungal Sen15 signature (IPR042777) is present, the protein is full-length relative to its family members, and UniProt curators describe sen15 as a subunit of the sen2/sen15/sen34/sen54 heterotetramer by similarity. Human TSEN15 (a different PANTHER family, PTHR28582, but the same Pfam Sen15 family PF09631) is likewise an obligatory subunit of the reconstituted tetramer (PMID:34584079). Complex membership is the core, best-supported claim for this protein.
Summary: InterPro2GO mapping from the fungal Sen15 signature; agrees with the IBA.
Reason: IPR042777 (Sen15_fungi) is a family-level signature for fungal Sen15 proteins, all of which are predicted endonuclease subunits; the mapping to the complex is appropriate and consistent with the PAINT-based IBA row for the same term.
We have cloned the genes encoding all four protein subunits of endonuclease.
GO:0000379 tRNA-type intron splice site recognition and cleavage
IBA GO_REF:0000033
ACCEPT
Summary: Participation in the endonucleolytic step of tRNA splicing, propagated from budding-yeast SEN15.
Reason: GO:0000379 covers recognition of the tRNA-type intron and cleavage at both splice sites, which is exactly what the endonuclease complex does. Sen15 does not carry either active site (those are in Sen2 and Sen34; PMID:9200603), but as an obligatory structural subunit it contributes the structure on which the 3'-splice-site half of the enzyme depends (it pairs with Sen34; Sen15-Sen34 interaction in yeast two-hybrid, PMID:17166513; human TSEN15-34 heterodimer crystal structure, PMID:34584079), so involved_in passes the participation test. The PAINT donor is in the same PANTHER subfamily (PTHR28518:SF1). PAINT propagated this BP and the complex CC but not the donor's contributes_to tRNA-intron endonuclease activity (GO:0000213, SGD IDA); that omission is respected here and no MF is added.
Our results demonstrate that the eucaryal tRNA splicing endonuclease contains two functionally independent active sites for cleavage of the 5' and 3' splice sites, encoded by SEN2 and SEN34, respectively.
Yeast two-hybrid analysis further showed strong interactions between Sen2 and Sen54 and between Sen34 and Sen15
GO:0000379 tRNA-type intron splice site recognition and cleavage
IEA GO_REF:0000002
ACCEPT
Summary: InterPro2GO mapping from the fungal Sen15 signature; agrees with the IBA.
Reason: Same claim as the IBA row; the family-level fungal Sen15 signature supports participation of this structural subunit in splice-site recognition and cleavage by the endonuclease complex.
Our results demonstrate that the eucaryal tRNA splicing endonuclease contains two functionally independent active sites for cleavage of the 5' and 3' splice sites, encoded by SEN2 and SEN34, respectively.
Summary: Generic nucleic acid binding inferred from the tRNA endonuclease-like domain superfamily; not supported for the Sen15 subunit.
Reason: IPR011856 is a structural superfamily covering the archaeal endonuclease fold shared by the catalytic subunits (Sen2, Sen34) and the structural subunits (Sen15, Sen54). Sen15 retains only the C-terminal part of that fold and lacks the catalytic triad (PMID:17166513). In the cryo-EM structures of the human TSEN complex bound to pre-tRNA, substrate recognition is attributed to TSEN34, TSEN54 and TSEN2, not TSEN15 (PMID:37028420). Human TSEN15 is in a separate PANTHER family (PTHR28582) from fungal Sen15 (PTHR28518), but both share the Pfam Sen15 family and the same position in the complex, and nothing indicates RNA contacts by the fungal protein. The superfamily-to-GO mapping therefore transfers a property of the RNA-contacting subunits to a subunit that is not known to bind RNA. Not marked REMOVE because absence of contacts in human structures is negative evidence from a related family, not a direct test on the fission yeast protein.
Sen15 and Sen54, which are otherwise non-homologous, contain C-terminal sequences similar to the stretch of MJ_endo that spans the last two Ξ² -strands
HDA PMID:16823372 ORFeome cloning and global analysis of protein localization ...
KEEP AS NON CORE
Summary: Nuclear signal from the PomBase genome-wide YFP-ORFeome localization screen.
Reason: The high-throughput screen (PMID:16823372; abstract only in cache) is the only localization evidence for the fission yeast protein and is consistent with tRNA splicing being nuclear in many eukaryotes. In S. cerevisiae the endonuclease is on the mitochondrial outer surface, so localization is lineage-variable and should not be transferred between yeasts. Kept, but not core, because a single HDA observation does not establish where the complex acts.
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.
HDA PMID:16823372 ORFeome cloning and global analysis of protein localization ...
KEEP AS NON CORE
Summary: Cytosolic signal from the PomBase genome-wide YFP-ORFeome localization screen.
Reason: Same high-throughput screen as the nucleus row. A cytosolic pool is plausible for a small subunit (and cytoplasmic tRNA splicing occurs in budding yeast), but the screen alone does not show that the cytosolic pool is the functional one. Retained as non-core.
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.
GO:0006388 tRNA splicing, via endonucleolytic cleavage and ligation
IEA GO_REF:0000002
MODIFY
Summary: Correct but broader than the step Sen15 contributes to.
Reason: The overall tRNA splicing process includes exon ligation and 2'-phosphate removal, performed by tRNA ligase and phosphotransferase, not by the endonuclease. Sen15 contributes only to the first step, which GO represents as GO:0000379 tRNA-type intron splice site recognition and cleavage, a part_of child of GO:0006388 that the gene already carries (IBA and IEA, accepted above). The annotation is derived from IPR036167, a fold-level superfamily, so the more specific, phylogenetically supported term is preferred.
In yeast, the tRNA splicing endonuclease is responsible for identification and cleavage of the splice sites in pre-tRNA.
Core Functions
Noncatalytic structural subunit of the tRNA-splicing endonuclease complex; partners Sen34 in the 3'-splice-site half of the enzyme and supports recognition and cleavage of intron-containing pre-tRNAs, with catalysis supplied by Sen2 and Sen34.
Our results demonstrate that the eucaryal tRNA splicing endonuclease contains two functionally independent active sites for cleavage of the 5' and 3' splice sites, encoded by SEN2 and SEN34, respectively.
Q: Should Sen15 orthologs carry contributes_to GO:0000213 tRNA-intron endonuclease activity (as S. cerevisiae SEN15 does by IDA), given that PAINT propagated only the complex and process terms from that node?
Q: Does the S. pombe tRNA-splicing endonuclease act in the nucleus, as in vertebrates, or on the mitochondrial surface/cytoplasm, as in S. cerevisiae?
Suggested Experiments
Experiment: Endogenously tag sen15 and a catalytic subunit (sen2 or sen34) and image them at low copy number, together with pre-tRNA northern blots after sen15 depletion, to establish where fission yeast tRNA splicing occurs and confirm sen15 is required for intron cleavage.
Type: localization and RNA processing assay
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.
Sen15 is the predicted noncatalytic structural subunit of the tRNA-splicing endonuclease complex, pairing with the 3'-splice-site catalytic subunit Sen34. The predicted tRNA-splicing process is correct but broader than the endonucleolytic step that Sen15 contributes to, which the gene already carries as GO:0000379 tRNA-type intron splice site recognition and cleavage.
Review rationale: Sen15 belongs to the fungal Sen15 family (IPR042777) of noncatalytic endonuclease subunits; the cleavage active sites lie in Sen2 and Sen34, and Sen15 pairs with Sen34 as a structural partner. Participation in tRNA splicing is therefore correct. However, Sen15 contributes only to the endonucleolytic step, not to exon ligation or 2'-phosphate removal, and the gene already carries the more specific GO:0000379 tRNA-type intron splice site recognition and cleavage (IBA from the same PANTHER subfamily and InterPro2GO), a descendant of the predicted GO:0006388 (OLS4 hierarchical ancestors). The prediction is broadly correct but less specific than the supported existing annotation. No fission-yeast experimental study of sen15 was found in PubMed.
Supporting Evidence:
PMID:9200603: "Our results demonstrate that the eucaryal tRNA splicing endonuclease contains two functionally independent active sites for cleavage of the 5' and 3' splice sites, encoded by SEN2 and SEN34, respectively."
PMID:17166513: "Yeast two-hybrid analysis further showed strong interactions between Sen2 and Sen54 and between Sen34 and Sen15"