The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
The requested identity is internally consistent: Q10222 is the fission-yeast Pta1 protein encoded by pta1 (SPAC1071.01c; alternate ORF SPAC4H3.15c) in Schizosaccharomyces pombe strain 972/ATCC 24843. In the organism-specific literature, Pta1 is explicitly included among the ten proteins of the core cleavage and polyadenylation factor (CPF), which combines with the Dis2–Ppn1–Swd22 module to form the 13-subunit holo-CPF. This matches the supplied Pta1/symplekin-family and ARM-like domain annotations; no conflicting same-symbol protein was used in this report. (benjamin2021structurefunctionanalysisof pages 1-3)
The most defensible primary annotation is:
Pta1 is a non-catalytic, Pta1/symplekin-family architectural subunit of nuclear CPF that helps organize cotranscriptional RNA polymerase II transcript 3′-end cleavage, poly(A)-tail synthesis, and transcription termination.
This conclusion is strong at the level of complex membership and conserved family function, but direct biochemical, structural, localization, and genetic characterization of Q10222 itself is limited. Several mechanistic details therefore derive from the behavior of S. pombe CPF as a whole or from budding-yeast Pta1/metazoan symplekin and are labeled accordingly.
| Annotation question | Best-supported conclusion | Evidence type | Confidence | Key caveat |
|---|---|---|---|---|
| Identity | Q10222 corresponds to Schizosaccharomyces pombe Pta1 (SPAC1071.01c/SPAC4H3.15c), named as a core component of fission-yeast CPF (benjamin2021structurefunctionanalysisof pages 1-3) | Direct Pta1-specific | High | Literature rarely identifies the protein by UniProt accession; identity relies partly on curated locus mapping supplied by UniProt. |
| Molecular role | Pta1 is best annotated as a conserved architectural/scaffold subunit that helps organize the cleavage and polyadenylation machinery, rather than as the cleavage or polymerization enzyme (xiang2013structuralandbiochemical pages 41-45, benjamin2021structurefunctionanalysisof pages 1-3) | S. pombe CPF-level plus comparative inference | Moderate–high | Direct interaction mapping has largely been performed on budding-yeast Pta1 or metazoan symplekin, not Q10222. |
| Catalytic status | No catalytic reaction or substrate specificity is established for Pta1 itself. Within CPF, Ysh1 is the RNA-cleavage endonuclease and Pla1 is the poly(A) polymerase; Pta1 is therefore non-catalytic (benjamin2021structurefunctionanalysisof pages 1-3) | S. pombe CPF-level | High | Absence of a demonstrated catalytic activity is not proof that Pta1 has no regulatory effect on catalysis. |
| Cellular localization | Function is expected in the nucleus, at nascent RNA polymerase II transcripts and their 3′ ends, because fission-yeast CPF performs cotranscriptional 3′ processing before termination (benjamin2021structurefunctionanalysisof pages 1-3, mata2013genomewidemappingof pages 1-2) | S. pombe CPF-level | Moderate–high | No retrieved study directly imaged or fractionated Q10222; “nuclear” is a strong functional inference rather than a Pta1-specific localization measurement. |
| Principal pathway | Pta1 participates as a CPF-core subunit in pre-mRNA cleavage, polyadenylation, and the transition to RNA polymerase II transcription termination (benjamin2021structurefunctionanalysisof pages 1-3) | S. pombe CPF-level | High | Direct loss-of-function assays isolating Pta1’s individual contribution were not found. |
| Regulatory pathway extensions | CPF also terminates regulatory lncRNAs and can promote MTREC-dependent RNA degradation, RNAi-independent heterochromatin assembly, and gene silencing in S. pombe (vo2019cpfrecruitmentto pages 13-14, vo2019cpfrecruitmentto pages 1-3) | S. pombe CPF-level | Moderate | These functions are established for CPF recruitment or other CPF subunits, not specifically for Pta1. |
| Physiological substrate landscape | CPF acts on a broad transcript population: 8,883 cleavage sites were mapped from 2,021,000 individual S. pombe mRNAs; 41% of detected coding genes and 45% of detected noncoding genes used multiple sites (mata2013genomewidemappingof pages 3-5, mata2013genomewidemappingof pages 1-2) | S. pombe CPF-level | High for pathway; low for Pta1 specificity | The mapping study measured RNA 3′ ends, not Pta1 occupancy or dependence. |
| Domains and structure | The supplied ARM-like, Symplekin/Pta1, and Symplekin/Pta1_N annotations fit a helical Pta1/symplekin-family scaffold, including a conserved N-terminal regulatory/interaction region (xiang2013structuralandbiochemical pages 41-45) | Comparative inference | Moderate | No experimental structure of Q10222 was retrieved, and ARM-like assignment does not by itself identify specific binding partners. |
| Recent research | A 2023 S. pombe study connected canonical poly(A) polymerase Pla1 to the 11-subunit MTREC surveillance complex: Red1 binds Pla1 through a 58-residue segment, and disruption shortened PROMPT poly(A) tails from a median 54 nt to 35–37 nt (soni2023mechanisticinsightsinto pages 7-8, soni2023mechanisticinsightsinto pages 1-2) | S. pombe pathway-level | High for Pla1–MTREC; low for Pta1 | Pta1 was not tested; this development refines the network surrounding CPF rather than Q10222’s individual mechanism. |
| Overall annotation confidence | “Non-catalytic Pta1/symplekin-family core scaffold of nuclear CPF, supporting cotranscriptional RNA 3′-end cleavage/polyadenylation and termination” is the most defensible functional annotation (xiang2013structuralandbiochemical pages 41-45, benjamin2021structurefunctionanalysisof pages 1-3) | Integrated evidence | Moderate–high | Direct Q10222-specific biochemical, structural, localization, and genetic evidence remains limited. |
Table: Evidence-ranked functional annotation of S. pombe Pta1 (Q10222), separating direct protein evidence from CPF-level findings and comparative inference. The table highlights strong pathway placement but limited Q10222-specific mechanistic characterization.
The organism-specific CPF inventory names Pta1 as a core CPF protein in S. pombe, alongside the catalytic cleavage endonuclease Ysh1 and poly(A) polymerase Pla1. Holo-CPF comprises this ten-protein core plus the three-subunit DPS module—Dis2, Ppn1, and Swd22. This validates the supplied description “mRNA cleavage and polyadenylation specificity factor complex subunit Pta1” rather than a same-symbol protein from another species. (benjamin2021structurefunctionanalysisof pages 1-3)
The symbol remains potentially confusing across databases and organisms, because much of the detailed Pta1 literature concerns Saccharomyces cerevisiae rather than S. pombe. Claims from that literature should not be treated as direct experiments on Q10222.
The supplied InterPro/Pfam annotations—ARM-like, Symplekin/Pta1, Symplekin/Pta1_N, and PF11935/SYMPK_PTA1_N—fit the conserved Pta1/symplekin class. Structural work on related proteins supports an elongated, helical, multidomain scaffold with an N-terminal regulatory/interaction region. Budding-yeast Pta1 has been reported to contact multiple 3′-processing factors, including Ysh1, Ydh1/Cft2, Fip1, Pcf11, Clp1, Pap1, and Ssu72, consistent with an organizing rather than catalytic function. These interactions are comparative evidence, not direct Q10222 interaction measurements. (xiang2013structuralandbiochemical pages 41-45)
The ARM-like assignment is also mechanistically compatible with protein–protein interaction scaffolding. However, no experimental structure of Q10222 was retrieved, so individual ARM-like repeats, binding surfaces, and partner stoichiometries should not be asserted for this protein without further work.
No cleavage, polymerization, phosphatase, or other catalytic reaction has been demonstrated for Pta1 itself. In S. pombe CPF, the biochemical labor is partitioned among other subunits: Ysh1 is the pre-mRNA cleavage endonuclease and Pla1 is the canonical poly(A) polymerase. Pta1 is therefore best classified as a non-catalytic core organizer that supports assembly, positioning, and regulation of these activities. (benjamin2021structurefunctionanalysisof pages 1-3)
Accordingly, an enzyme-style substrate-specificity statement does not apply to Pta1. Its functional “substrates” are better understood as protein partners and CPF-bound nascent RNAs, while the RNA cleavage and adenosine-addition reactions are executed by Ysh1 and Pla1, respectively. Conserved Pta1/symplekin evidence suggests that the scaffold coordinates cleavage/polyadenylation proteins and connects processing to transcription-associated factors, but this precise interaction map remains to be established for Q10222. (xiang2013structuralandbiochemical pages 41-45)
The pathway is:
The direct S. pombe evidence establishes that holo-CPF is a 13-subunit complex that executes cotranscriptional 3′ processing before Pol II termination; assignment of an indispensable organizing step specifically to Pta1 is a conserved-family inference rather than a Q10222-specific perturbation result. (benjamin2021structurefunctionanalysisof pages 1-3, mata2013genomewidemappingof pages 1-2)
Pta1’s principal pathway is canonical Pol II transcript 3′-end processing. This process determines mature mRNA 3′ ends and poly(A)-tail acquisition and contributes to transcript stability, export, and translation competence. The broad physiological scale of this pathway is demonstrated by an S. pombe map based on 2,021,000 individual mRNA molecules, which identified 8,883 cleavage sites, covering 90% of coding genes and 50% of noncoding RNAs. (mata2013genomewidemappingof pages 1-2)
The same study resolved 7,253 3′-UTR, 1,277 ncRNA, and 353 coding-sequence cleavage-site clusters. Median and mean 3′-UTR lengths were 203 and 284 nucleotides. AAUAAA was found at 20.1% of all sites and peaked 24 nucleotides upstream; for ncRNAs it occurred at 25.1% and peaked at −22 nucleotides. These measurements describe the RNA substrate landscape of the processing machinery, not Pta1-dependent site recognition specifically. (mata2013genomewidemappingof pages 3-5)
Alternative cleavage/polyadenylation is common in vegetatively growing fission yeast: 41% of detected coding genes and 45% of detected noncoding genes used more than one cleavage site. Coding-gene 3′ UTRs averaged 1.54 clusters per gene, while ncRNAs averaged 1.63. Thus, Pta1-containing CPF operates in a transcript environment with substantial site choice and 3′-UTR heterogeneity, although no evidence shows that Pta1 independently selects among sites. (mata2013genomewidemappingof pages 3-5, mata2013genomewidemappingof pages 1-2)
CPF activity is coupled to Pol II termination. Studies of the DPS arm show that CPF integrates RNA processing with the phosphorylation state of the Pol II CTD and elongation machinery. Loss of DPS components changes expression of genes controlled by upstream lncRNA termination, and genetic interactions connect CPF to the termination factor Rhn1 and core phosphatase Ssu72. These are strong CPF-pathway observations but do not isolate Pta1’s individual contribution. (benjamin2021structurefunctionanalysisof pages 21-23, benjamin2021structurefunctionanalysisof pages 3-4, benjamin2021structurefunctionanalysisof pages 11-13)
In a quantitative RNA-seq analysis, ppn1Δ, swd22Δ, and dis2Δ produced 38, 36, and 60 upregulated coding genes and 67, 57, and 26 downregulated genes, respectively, under a twofold and corrected-p<0.05 threshold. Approximately 2% of 5,118 coding transcripts were affected in ppn1Δ and swd22Δ. This demonstrates selective regulatory consequences of CPF-associated phosphatase-module defects, not a genome-wide Pta1-loss phenotype. (benjamin2021structurefunctionanalysisof pages 4-7, benjamin2021structurefunctionanalysisof pages 21-23)
Fission-yeast phosphate genes such as pho1 and pho84 are controlled by upstream lncRNA transcriptional interference. CPF-associated mutations that impair lncRNA 3′ processing or termination can extend lncRNA transcription into the downstream promoter and repress these genes. This provides a concrete biological implementation of CPF as a coupling system between RNA processing and metabolic gene regulation, although Pta1-specific mutant evidence was not retrieved. (benjamin2021structurefunctionanalysisof pages 4-7, benjamin2021structurefunctionanalysisof pages 21-23)
CPF also acts at noncanonical termination sites. Mmi1 can recruit CPF cotranscriptionally to regulatory lncRNAs; cleavage and termination then facilitate MTREC/exosome-dependent RNA disposal and can promote Clr4/SUV39H-dependent, RNAi-independent facultative heterochromatin and gene silencing. Again, these experiments establish a property of recruited CPF, not a unique Pta1 activity. (vo2019cpfrecruitmentto pages 13-14, vo2019cpfrecruitmentto pages 1-3)
The functional site is best assigned as the nucleus, on nascent Pol II transcription complexes and particularly around transcript 3′ ends/polyadenylation signals. The evidence is that S. pombe CPF performs cotranscriptional pre-mRNA processing before transcription termination and is recruited to nascent regulatory RNAs. (benjamin2021structurefunctionanalysisof pages 1-3, vo2019cpfrecruitmentto pages 1-3, mata2013genomewidemappingof pages 1-2)
This should be recorded as a high-confidence functional localization but not a direct Q10222 imaging result. No retrieved study demonstrated Pta1-Q10222 localization by fluorescence microscopy, immuno-electron microscopy, or biochemical fractionation. There is no evidence that it is secreted, membrane-associated, mitochondrial, or cytosolic in its primary role.
Direct 2023–2024 research centered specifically on Q10222 was not found. The most relevant recent advance concerns the interface between canonical 3′ processing and nuclear RNA surveillance. Soni and colleagues reported in Nature Communications, February 2023 that S. pombe Pla1 also associates with the eleven-subunit MTREC complex through the scaffold Red1. A 58-residue Red1 segment binds the Pla1 RRM-containing region, and structure-guided disruption selectively depleted Pla1 from MTREC. (soni2023mechanisticinsightsinto pages 1-2)
The mutants reduced median PROMPT poly(A)-tail length from 54 nucleotides to 35–37 nucleotides, while ordinary mRNA tails remained near 31 nucleotides. The results support a model in which MTREC-associated Pla1 extends surveillance-substrate tails to facilitate exosome degradation and contributes to facultative heterochromatin. Pta1 was not tested, so this work refines the functional network surrounding Pta1-containing CPF rather than Pta1’s individual mechanism. [Soni et al., published February 2023, DOI/URL: https://doi.org/10.1038/s41467-023-36402-6]. (soni2023mechanisticinsightsinto pages 7-8, soni2023mechanisticinsightsinto pages 1-2)
The recent expert-level interpretation is therefore that canonical 3′-end processing is not an isolated linear pathway: CPF components and catalytic factors are dynamically shared or connected with termination, nuclear surveillance, exosome targeting, and chromatin regulation. Pta1 is likely an architectural component of this network, but direct evidence that Q10222 mediates the CPF–MTREC interface is absent.
Pta1 is not known as a clinical target, industrial enzyme, transporter, or diagnostic marker. Its practical value is primarily as a research-system component:
These are laboratory and conceptual implementations, not deployed medical or commercial uses.
The literature supports three different confidence levels:
No retrieved study provided a Q10222-specific structure, purified biochemical reconstitution, quantitative interactome, direct localization assay, conditional depletion phenotype, or transcriptome-wide cleavage-site comparison. Consequently, the following remain unresolved:
The highest-value future experiments would be endogenous Pta1 tagging and microscopy; affinity purification–mass spectrometry; conditional depletion followed by long-read 3′-end sequencing and nascent-transcription profiling; and structure-guided mutation of the conserved Symplekin/Pta1_N and ARM-like regions.
Recommended functional statement: S. pombe Pta1/Q10222 is a conserved, non-catalytic Pta1/symplekin-family core scaffold of the nuclear cleavage and polyadenylation factor. It supports cotranscriptional assembly and function of the machinery that cleaves Pol II pre-mRNAs, adds poly(A) tails, and promotes transcription termination. CPF-level evidence additionally places it in pathways governing alternative polyadenylation, regulatory-lncRNA termination, RNA surveillance, phosphate-homeostasis gene control, and heterochromatin-linked silencing, but these extended roles have not been demonstrated individually for Q10222. (xiang2013structuralandbiochemical pages 41-45, benjamin2021structurefunctionanalysisof pages 1-3, vo2019cpfrecruitmentto pages 13-14, vo2019cpfrecruitmentto pages 1-3)
References
(benjamin2021structurefunctionanalysisof pages 1-3): Bradley Benjamin, Ana M. Sanchez, Angad Garg, Beate Schwer, and Stewart Shuman. Structure-function analysis of fission yeast cleavage and polyadenylation factor (cpf) subunit ppn1 and its interactions with dis2 and swd22. PLOS Genetics, 17(3):e1009452, Mar 2021. URL: https://doi.org/10.1371/journal.pgen.1009452, doi:10.1371/journal.pgen.1009452. This article has 17 citations and is from a domain leading peer-reviewed journal.
(xiang2013structuralandbiochemical pages 41-45): Kehui Xiang. Structural and biochemical characterizations of the symplekin-ssu72-ctd complex in pre-mrna 3' end processing. ArXiv, Jan 2013. URL: https://doi.org/10.7916/d8nk3c0g, doi:10.7916/d8nk3c0g. This article has 0 citations.
(mata2013genomewidemappingof pages 1-2): Juan Mata. Genome-wide mapping of polyadenylation sites in fission yeast reveals widespread alternative polyadenylation. Aug 2013. URL: https://doi.org/10.4161/rna.25758, doi:10.4161/rna.25758. This article has 62 citations and is from a peer-reviewed journal.
(vo2019cpfrecruitmentto pages 13-14): Tommy V. Vo, Jothy Dhakshnamoorthy, Madeline Larkin, Martin Zofall, Gobi Thillainadesan, Vanivilasini Balachandran, Sahana Holla, David Wheeler, and Shiv I.S. Grewal. Cpf recruitment to non-canonical transcription termination sites triggers heterochromatin assembly and gene silencing. Jul 2019. URL: https://doi.org/10.1016/j.celrep.2019.05.107, doi:10.1016/j.celrep.2019.05.107. This article has 57 citations and is from a highest quality peer-reviewed journal.
(vo2019cpfrecruitmentto pages 1-3): Tommy V. Vo, Jothy Dhakshnamoorthy, Madeline Larkin, Martin Zofall, Gobi Thillainadesan, Vanivilasini Balachandran, Sahana Holla, David Wheeler, and Shiv I.S. Grewal. Cpf recruitment to non-canonical transcription termination sites triggers heterochromatin assembly and gene silencing. Jul 2019. URL: https://doi.org/10.1016/j.celrep.2019.05.107, doi:10.1016/j.celrep.2019.05.107. This article has 57 citations and is from a highest quality peer-reviewed journal.
(mata2013genomewidemappingof pages 3-5): Juan Mata. Genome-wide mapping of polyadenylation sites in fission yeast reveals widespread alternative polyadenylation. Aug 2013. URL: https://doi.org/10.4161/rna.25758, doi:10.4161/rna.25758. This article has 62 citations and is from a peer-reviewed journal.
(soni2023mechanisticinsightsinto pages 7-8): Komal Soni, Anusree Sivadas, Attila Horvath, Nikolay Dobrev, Rippei Hayashi, Leo Kiss, Bernd Simon, Klemens Wild, Irmgard Sinning, and Tamás Fischer. Mechanistic insights into rna surveillance by the canonical poly(a) polymerase pla1 of the mtrec complex. Nature Communications, Feb 2023. URL: https://doi.org/10.1038/s41467-023-36402-6, doi:10.1038/s41467-023-36402-6. This article has 18 citations and is from a highest quality peer-reviewed journal.
(soni2023mechanisticinsightsinto pages 1-2): Komal Soni, Anusree Sivadas, Attila Horvath, Nikolay Dobrev, Rippei Hayashi, Leo Kiss, Bernd Simon, Klemens Wild, Irmgard Sinning, and Tamás Fischer. Mechanistic insights into rna surveillance by the canonical poly(a) polymerase pla1 of the mtrec complex. Nature Communications, Feb 2023. URL: https://doi.org/10.1038/s41467-023-36402-6, doi:10.1038/s41467-023-36402-6. This article has 18 citations and is from a highest quality peer-reviewed journal.
(benjamin2021structurefunctionanalysisof pages 21-23): Bradley Benjamin, Ana M. Sanchez, Angad Garg, Beate Schwer, and Stewart Shuman. Structure-function analysis of fission yeast cleavage and polyadenylation factor (cpf) subunit ppn1 and its interactions with dis2 and swd22. PLOS Genetics, 17(3):e1009452, Mar 2021. URL: https://doi.org/10.1371/journal.pgen.1009452, doi:10.1371/journal.pgen.1009452. This article has 17 citations and is from a domain leading peer-reviewed journal.
(benjamin2021structurefunctionanalysisof pages 3-4): Bradley Benjamin, Ana M. Sanchez, Angad Garg, Beate Schwer, and Stewart Shuman. Structure-function analysis of fission yeast cleavage and polyadenylation factor (cpf) subunit ppn1 and its interactions with dis2 and swd22. PLOS Genetics, 17(3):e1009452, Mar 2021. URL: https://doi.org/10.1371/journal.pgen.1009452, doi:10.1371/journal.pgen.1009452. This article has 17 citations and is from a domain leading peer-reviewed journal.
(benjamin2021structurefunctionanalysisof pages 11-13): Bradley Benjamin, Ana M. Sanchez, Angad Garg, Beate Schwer, and Stewart Shuman. Structure-function analysis of fission yeast cleavage and polyadenylation factor (cpf) subunit ppn1 and its interactions with dis2 and swd22. PLOS Genetics, 17(3):e1009452, Mar 2021. URL: https://doi.org/10.1371/journal.pgen.1009452, doi:10.1371/journal.pgen.1009452. This article has 17 citations and is from a domain leading peer-reviewed journal.
(benjamin2021structurefunctionanalysisof pages 4-7): Bradley Benjamin, Ana M. Sanchez, Angad Garg, Beate Schwer, and Stewart Shuman. Structure-function analysis of fission yeast cleavage and polyadenylation factor (cpf) subunit ppn1 and its interactions with dis2 and swd22. PLOS Genetics, 17(3):e1009452, Mar 2021. URL: https://doi.org/10.1371/journal.pgen.1009452, doi:10.1371/journal.pgen.1009452. This article has 17 citations and is from a domain leading peer-reviewed journal.