Pta1 is the fission yeast member of the symplekin/Pta1 family of HEAT/ARM-like helical scaffold proteins. It is a noncatalytic subunit of the ten-protein core of the nuclear cleavage and polyadenylation factor (CPF), the assembly that cleaves RNA polymerase II pre-mRNAs at the poly(A) site, adds the poly(A) tail and couples 3'-end processing to transcription termination. The cleavage endonuclease (Ysh1) and poly(A) polymerase (Pla1) are separate CPF subunits; by analogy with its budding yeast ortholog, which uses distinct regions to bind Ssu72, Pti1 and Ysh1, Pta1 is thought to organize the processing machinery and connect it to the Ssu72 CTD-phosphatase that acts in termination.
Summary: PomBase records the molecular function of pta1 as unknown (ND).
Reason: No molecular activity of pombe Pta1 itself has been measured. The CPF composition study assigns the catalytic activities of the complex to other subunits and gives Pta1 no catalytic descriptor. In the budding yeast ortholog (same PANTHER subfamily PTHR15245:SF20), domain-deletion and interaction mapping support a scaffolding role, but the only MF terms SGD curators have assigned are generic protein binding and a complex-level contributes_to RNA binding, and PAINT propagated only the CPF complex term to this node. No specific MF term is established for this subfamily, so the ND statement remains the accurate description; a scaffold/adaptor MF is raised as a question instead.
Holo-CPF consists of two component complexes (Fig 1): a 10-subunit CPF core composed of proteins Ysh1 (the cleavage endonuclease), Pla1 (the poly(A) polymerase), Pta1, Yth1 (a zinc finger protein), Pfs2 (a WD repeat protein), Iss1, Cft1 (a WD repeat protein), Cft2 (a metallo-Ξ²-lactamase/Ξ²-CASP protein), Ctf1, and Ssu72 (a phosphoprotein phosphatase); and a 3-subunit DPS complex comprising Dis2 (a phosphoprotein phosphatase), Ppn1, and Swd22 (a WD repeat protein).
Furthermore, different regions of Pta1 interact with the CPF subunits Ssu72, Pti1, and Ysh1, supporting the idea that Pta1 acts as a scaffold to organize CPF.
HDA PMID:16823372 ORFeome cloning and global analysis of protein localization ...
ACCEPT
Summary: Nuclear localization from the genome-wide YFP-tagging localization screen.
Reason: The ORFeome screen (abstract-only in cache; PomBase and UniProt both cite it for nuclear localization of Pta1) is consistent with Pta1 being a constituent of the nuclear cotranscriptional 3'-processing machinery. Nucleus is the appropriate level for a high-throughput imaging result.
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.
Summary: Electronic nucleus annotation, agreeing with the experimental localization.
Reason: The electronic pipeline output agrees with the curated experimental localization and with Pta1 membership of the nuclear CPF complex; the ARBA component is not itself treated as evidence.
Fission yeast Schizosaccharomyces pombe Cleavage and Polyadenylation Factor (CPF) is a 13-subunit protein assembly responsible for the cotranscriptional 3β processing of RNA polymerase II (Pol2) transcripts that precedes Pol2 transcription termination
NAS PMID:33711009 Structure-function analysis of fission yeast cleavage and po...
ACCEPT
Summary: ComplexPortal-style statement of nuclear location for the CPF subunit.
Reason: CPF processes nascent Pol II transcripts cotranscriptionally, which places its core subunits, including Pta1, in the nucleus; consistent with the experimental HDA row.
Fission yeast Schizosaccharomyces pombe Cleavage and Polyadenylation Factor (CPF) is a 13-subunit protein assembly responsible for the cotranscriptional 3β processing of RNA polymerase II (Pol2) transcripts that precedes Pol2 transcription termination
GO:0005847 mRNA cleavage and polyadenylation specificity factor complex
IBA GO_REF:0000033
ACCEPT
Summary: PAINT propagation of CPF/CPSF complex membership across the symplekin/Pta1 subfamily.
Reason: Pta1, budding yeast Pta1 (Q01329), and animal symplekins (human Q92797, mouse Q80X82) are all classified in PANTHER subfamily PTHR15245:SF20, and the IBA descends from node PTN000391745, whose experimental donors include S. cerevisiae Pta1, human symplekin and pombe pta1 itself (the target's own experimental annotation is expected among the donors). Membership of the cleavage and polyadenylation complex is the conserved, best-supported property of the family, and pombe Pta1 is directly listed as a CPF core subunit.
Holo-CPF consists of two component complexes (Fig 1): a 10-subunit CPF core composed of proteins Ysh1 (the cleavage endonuclease), Pla1 (the poly(A) polymerase), Pta1, Yth1 (a zinc finger protein), Pfs2 (a WD repeat protein), Iss1, Cft1 (a WD repeat protein), Cft2 (a metallo-Ξ²-lactamase/Ξ²-CASP protein), Ctf1, and Ssu72 (a phosphoprotein phosphatase); and a 3-subunit DPS complex comprising Dis2 (a phosphoprotein phosphatase), Ppn1, and Swd22 (a WD repeat protein).
In this report, we show by protein sequencing and immunoreactivity that the fourth subunit of CF II is Pta1, an essential 90-kDa protein originally implicated in tRNA splicing.
GO:0005847 mRNA cleavage and polyadenylation specificity factor complex
IDA PMID:14617822 A comparative analysis of an orthologous proteomic environme...
ACCEPT
Summary: Pta1 identified in affinity-purified pombe CPF.
Reason: The cached record of PMID:14617822 is abstract-only and the abstract foregrounds Set1 complexes; the CPF identification is in the full text (UniProt records "IDENTIFICATION IN THE CPF COMPLEX" from this paper, with Pta1 in the subunit list). Per project policy the curator's reading of the full text is accepted, and the later pombe CPF literature independently lists Pta1 among the CPF core subunits.
Supporting Evidence:
file:SCHPO/pta1/pta1-uniprot.txt
SUBUNIT: Component of the cleavage and polyadenylation factor (CPF) complex, which is composed of cft1, cft2, ysh1, pta1, swd2, pfs2, dis2, yth1, ssu72, and fip1. {ECO:0000269|PubMed:14617822}.
Holo-CPF consists of two component complexes (Fig 1): a 10-subunit CPF core composed of proteins Ysh1 (the cleavage endonuclease), Pla1 (the poly(A) polymerase), Pta1, Yth1 (a zinc finger protein), Pfs2 (a WD repeat protein), Iss1, Cft1 (a WD repeat protein), Cft2 (a metallo-Ξ²-lactamase/Ξ²-CASP protein), Ctf1, and Ssu72 (a phosphoprotein phosphatase); and a 3-subunit DPS complex comprising Dis2 (a phosphoprotein phosphatase), Ppn1, and Swd22 (a WD repeat protein).
GO:0005847 mRNA cleavage and polyadenylation specificity factor complex
NAS PMID:33711009 Structure-function analysis of fission yeast cleavage and po...
ACCEPT
Summary: Pta1 named as a CPF core subunit in the pombe CPF literature.
Reason: The cited paper explicitly lists Pta1 among the ten CPF core subunits of S. pombe; this agrees with the IDA and IBA rows.
Holo-CPF consists of two component complexes (Fig 1): a 10-subunit CPF core composed of proteins Ysh1 (the cleavage endonuclease), Pla1 (the poly(A) polymerase), Pta1, Yth1 (a zinc finger protein), Pfs2 (a WD repeat protein), Iss1, Cft1 (a WD repeat protein), Cft2 (a metallo-Ξ²-lactamase/Ξ²-CASP protein), Ctf1, and Ssu72 (a phosphoprotein phosphatase); and a 3-subunit DPS complex comprising Dis2 (a phosphoprotein phosphatase), Ppn1, and Swd22 (a WD repeat protein).
Summary: Orthology transfer of the budding yeast pta1-1 pre-tRNA accumulation phenotype.
Reason: The only basis is the 1992 observation that the S. cerevisiae pta1-1 nonsense allele accumulates end-trimmed, intron-containing pre-tRNAs. The same study found normal pre-tRNA splicing endonuclease activity in mutant extracts, and the paper that later identified Pta1 as a CF II/CPF subunit states that the cause of the tRNA defect is unknown. There is no evidence that Pta1 performs or structurally supports any step of tRNA processing; the phenotype is a necessity observation from a mutant that also cripples mRNA 3'-end formation and is likely indirect. PAINT curators, who propagated CPF membership from the same SGD donor to node PTN000391745, did not propagate tRNA processing, and no tRNA-related phenotype or activity has been reported for pombe Pta1. The term is therefore kept out of the core description and flagged as an over-annotation rather than removed, because the ortholog phenotype itself is real.
Propagation Review
Root cause:SOURCE WEAK OR INFERRED
Failure modes:SOURCE EVIDENCE WEAK
Sources checked:
SGD:S000000041 Β· PTA1 SOURCE WEAK OR INFERRED
The SGD donor is an IMP from the pta1-1 nonsense allele (PMID:1508188); the pre-tRNA accumulation has no identified mechanism, splicing endonuclease activity is normal, and the phenotype is plausibly indirect, so it supports necessity rather than participation.
The cause of the tRNA splicing defect in yeast is not known.
GO:0030846 termination of RNA polymerase II transcription, poly(A)-coupled
NAS PMID:33711009 Structure-function analysis of fission yeast cleavage and po...
ACCEPT
Summary: Participation of CPF, including its Pta1 scaffold, in poly(A)-coupled Pol II termination.
Reason: In S. pombe, CPF-mediated 3' processing precedes and is coupled to Pol II termination, and the CPF core contains the Ssu72 CTD phosphatase. In budding yeast Pta1 (same PANTHER subfamily), the Pta1 N-terminus is the Ssu72-binding region and is required for snoRNA termination and CTD Ser5-P dephosphorylation, giving the scaffold a structural part in the termination step rather than a mere requirement. Direct termination assays on pombe Pta1 are lacking, so this rests on complex-level evidence plus conserved subfamily mechanism.
Fission yeast Schizosaccharomyces pombe Cleavage and Polyadenylation Factor (CPF) is a 13-subunit protein assembly responsible for the cotranscriptional 3β processing of RNA polymerase II (Pol2) transcripts that precedes Pol2 transcription termination
The pta1-Delta75 mutant is defective for snoRNA termination, RNA polymerase II C-terminal domain Ser5-P dephosphorylation, and gene looping but is fully functional for mRNA 3'-end processing.
GO:0180010 co-transcriptional mRNA 3'-end processing, cleavage and polyadenylation pathway
IC GO_REF:0000111
ACCEPT
Summary: Curator inference from CPF membership to mRNA cleavage and polyadenylation.
Reason: This is the core process of the CPF core to which Pta1 belongs. Ortholog evidence within subfamily PTHR15245:SF20 shows that Pta1 is required for both cleavage and poly(A) addition in extracts and that defective extracts are rescued by the Pta1-containing CF II, and that Pta1 contacts Ysh1 and other CPF subunits, so the scaffold contributes structure on which the processing steps depend. Pta1 does not catalyse either chemical step.
Extracts prepared from pta1 mutant strains are impaired in the cleavage and the poly(A) addition of both GAL7 and CYC1 substrates and exhibit little processing activity even after prolonged incubation. However, activity is efficiently rescued by the addition of purified CF II to the defective extracts.
Furthermore, different regions of Pta1 interact with the CPF subunits Ssu72, Pti1, and Ysh1, supporting the idea that Pta1 acts as a scaffold to organize CPF.
Core Functions
Noncatalytic symplekin/Pta1-family scaffold subunit of the CPF core that supports pre-mRNA cleavage and polyadenylation at the 3' end of RNA polymerase II transcripts and the coupled termination of transcription.
Holo-CPF consists of two component complexes (Fig 1): a 10-subunit CPF core composed of proteins Ysh1 (the cleavage endonuclease), Pla1 (the poly(A) polymerase), Pta1, Yth1 (a zinc finger protein), Pfs2 (a WD repeat protein), Iss1, Cft1 (a WD repeat protein), Cft2 (a metallo-Ξ²-lactamase/Ξ²-CASP protein), Ctf1, and Ssu72 (a phosphoprotein phosphatase); and a 3-subunit DPS complex comprising Dis2 (a phosphoprotein phosphatase), Ppn1, and Swd22 (a WD repeat protein).
Extracts prepared from pta1 mutant strains are impaired in the cleavage and the poly(A) addition of both GAL7 and CYC1 substrates and exhibit little processing activity even after prolonged incubation. However, activity is efficiently rescued by the addition of purified CF II to the defective extracts.
Furthermore, different regions of Pta1 interact with the CPF subunits Ssu72, Pti1, and Ysh1, supporting the idea that Pta1 acts as a scaffold to organize CPF.
Q: Does pombe Pta1 use its N-terminal region to bind and position Ssu72 within CPF, as in budding yeast, and would a scaffold MF term such as protein-macromolecule adaptor activity be justified for the symplekin/Pta1 subfamily as a whole?
Q: Is the budding yeast pta1-1 pre-tRNA accumulation an indirect consequence of impaired mRNA 3'-end formation or transcription termination, and is any tRNA phenotype seen for pombe pta1 alleles?
Suggested Experiments
Experiment: Map pombe Pta1 binding surfaces for Ssu72, Ysh1 and Cft2 by deletion analysis and crosslinking mass spectrometry of purified CPF, and test N-terminal truncations for termination versus cleavage defects with RNA-seq readthrough analysis.
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.
Pta1 participates in CPF-mediated mRNA 3β²-end formation; the predicted mRNA-processing role is supported but less precise than this established function.
Review rationale: Pta1 is a component of the experimentally characterized fission yeast CPF core. Purified-factor rescue of budding yeast pta1 mutant extracts establishes its conserved participation in mRNA cleavage and poly(A) addition. GOA already records co-transcriptional mRNA 3β²-end processing, cleavage and polyadenylation pathway (GO:0180010). The broad mRNA-processing prediction is correct but loses the established mechanistic specificity and does not assign intrinsic nuclease activity.
Supporting Evidence:
PMID:33711009: "Holo-CPF consists of two component complexes (Fig 1): a 10-subunit CPF core composed of proteins Ysh1 (the cleavage endonuclease), Pla1 (the poly(A) polymerase), Pta1, Yth1 (a zinc finger protein), Pfs2 (a WD repeat protein), Iss1, Cft1 (a WD repeat protein), Cft2 (a metallo-Ξ²-lactamase/Ξ²-CASP protein), Ctf1, and Ssu72 (a phosphoprotein phosphatase); and a 3-subunit DPS complex comprising Dis2 (a phosphoprotein phosphatase), Ppn1, and Swd22 (a WD repeat protein)."
PMID:10523662: "Extracts prepared from pta1 mutant strains are impaired in the cleavage and the poly(A) addition of both GAL7 and CYC1 substrates and exhibit little processing activity even after prolonged incubation. However, activity is efficiently rescued by the addition of purified CF II to the defective extracts."