PAP2 (also known as TRF4) encodes the catalytic poly(A) RNA polymerase subunit of the TRAMP complex (Trf4/Air2/Mtr4 polyadenylation complex) in S. cerevisiae. It adds short adenosine tails to aberrant and specialized nuclear RNAs, marking them for degradation by the nuclear exosome. Substrates include hypomodified tRNAs, pre-rRNAs, snoRNA precursors, cryptic unstable transcripts (CUTs), histone mRNAs, and snRNA processing intermediates. PAP2 was originally identified as a topoisomerase I-related function gene and was erroneously thought to be a DNA polymerase; it was definitively shown to lack DNA polymerase activity and to function exclusively as a poly(A) RNA polymerase. PAP2 also possesses an intrinsic 5'-deoxyribose-5-phosphate lyase activity with a possible role in base excision DNA repair. Indirectly, through its RNA surveillance function, PAP2 contributes to genome integrity by preventing R-loop accumulation and by maintaining nuclear cap-binding complex availability during meiosis.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005730 nucleolus | IBA GO_REF:0000033 | ACCEPT | Summary: IBA annotation for nucleolus is consistent with direct experimental evidence showing Trf4p localizes to a subnucleolar region for surveillance of nuclear-restricted pre-ribosomes. Supporting Evidence: PMID:16541108 Surveillance of nuclear-restricted pre-ribosomes within a subnucleolar region of Saccharomyces cerevisiae |
| GO:0031123 RNA 3'-end processing | IBA GO_REF:0000033 | ACCEPT | Summary: PAP2/Trf4 participates in RNA 3'-end processing through polyadenylation that targets RNAs for exosome-mediated trimming or degradation. This is a core function supported by extensive evidence. Supporting Evidence: PMID:15935758 TRAMP is required for polyadenylation and degradation of rRNA and snoRNA precursors PMID:16373491 Contributions of Trf4p- and Trf5p-dependent polyadenylation to the processing and degradative functions of the yeast nuclear exosome file:yeast/PAP2/PAP2-deep-research-falcon.md oligoadenylation serving as an exosome-engagement handle rather than a stabilizing poly(A) tail |
| GO:1990817 poly(A) RNA polymerase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Poly(A) RNA polymerase activity is the defining molecular function of PAP2/Trf4. The IBA annotation correctly reflects the conserved catalytic activity across orthologs. Supporting Evidence: PMID:16260630 both proteins exhibit a robust poly(A) polymerase activity file:yeast/PAP2/PAP2-deep-research-bioreason-sft.md [BioReason] The catalytic core uses a metal-dependent nucleotidyltransferase palm to extend 3' termini file:yeast/PAP2/PAP2-deep-research-falcon.md Trf4 is a **non-templated poly(A) RNA polymerase** that adds adenosines to the **free 3′-OH** of RNA substrates |
| GO:0043634 polyadenylation-dependent ncRNA catabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: PAP2/Trf4 polyadenylates diverse ncRNAs (tRNAs, rRNAs, snoRNAs, CUTs) to target them for exosome-mediated degradation. This is a core function. Supporting Evidence: PMID:15935759 RNAs originating from these regions are rapidly degraded by the combined action of the exosome and a new poly(A) polymerase activity |
| GO:0031499 TRAMP complex | IBA GO_REF:0000033 | ACCEPT | Summary: PAP2/Trf4 is the catalytic subunit of the TRAMP complex. IBA annotation is consistent with extensive direct experimental evidence. Supporting Evidence: PMID:15935758 identifies a nuclear polyadenylation complex containing a known exosome cofactor, the RNA helicase Mtr4p; a poly(A) polymerase, Trf4p; and a zinc knuckle protein, Air2p file:yeast/PAP2/PAP2-deep-research-falcon.md the minimal active surveillance polymerase is a **heteromer** of **Trf4 + Air1 or Air2**, consistent with Trf4 lacking an intrinsic RNA-binding domain and relying on Air proteins for substrate engagement |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: Nuclear localization of PAP2/Trf4 is well established by direct experimental evidence. The IEA annotation is correct but redundant with IDA evidence. Supporting Evidence: PMID:10066793 We show that Trf4 is a nuclear protein |
| GO:0031499 TRAMP complex | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA-inferred TRAMP complex membership is correct and supported by multiple IDA annotations. Supporting Evidence: PMID:15828860 Trf4p is the catalytic subunit of a new poly(A) polymerase complex |
| GO:0034475 U4 snRNA 3'-end processing | IEA GO_REF:0000117 | ACCEPT | Summary: Supported by experimental evidence showing 3'-extended forms of U4 snRNA accumulate in trf4-delta mutants. Supporting Evidence: PMID:16373491 in the absence of Trf4p, we observed 3'-extended forms of the U4 snRNA |
| GO:0071035 nuclear polyadenylation-dependent rRNA catabolic process | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA inference is correct. Trf4-dependent polyadenylation of rRNA precursors for exosome degradation is well documented. Supporting Evidence: PMID:15935758 TRAMP is required for polyadenylation and degradation of rRNA and snoRNA precursors |
| GO:0071036 nuclear polyadenylation-dependent snoRNA catabolic process | IEA GO_REF:0000117 | ACCEPT | Summary: Correct. snoRNA precursors are polyadenylated by Trf4 for exosome-mediated processing and degradation. Supporting Evidence: PMID:15935758 TRAMP is required for polyadenylation and degradation of rRNA and snoRNA precursors |
| GO:0071037 nuclear polyadenylation-dependent snRNA catabolic process | IEA GO_REF:0000117 | ACCEPT | Summary: Consistent with evidence that snRNA processing intermediates accumulate in trf4-delta and rrp6-delta mutants with polyadenylated forms. Supporting Evidence: PMID:16373491 polyadenylation of cleavage intermediates was inhibited when Trf4p was absent |
| GO:0071038 TRAMP-dependent tRNA surveillance pathway | IEA GO_REF:0000117 | ACCEPT | Summary: Core function. Trf4 polyadenylates hypomodified tRNAi-Met for exosome degradation, the founding discovery of TRAMP-mediated RNA surveillance. Supporting Evidence: PMID:15145828 Nuclear surveillance and degradation of hypomodified initiator tRNAMet file:yeast/PAP2/PAP2-deep-research-falcon.md Trf4-containing complexes preferentially polyadenylate **aberrant/unmodified** tRNAs over correctly folded native tRNAs, indicating recognition of **structural defects** rather than a simple “unmodified vs modified” rule |
| GO:0071039 nuclear polyadenylation-dependent CUT catabolic process | IEA GO_REF:0000117 | ACCEPT | Summary: Core function. CUT degradation by Trf4/TRAMP-mediated polyadenylation is one of the defining activities of this pathway. Supporting Evidence: PMID:15935759 Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase file:yeast/PAP2/PAP2-deep-research-falcon.md TRAMP is a major cofactor for degrading pervasive nuclear transcripts and many ncRNAs generated by widespread RNA polymerase II transcription. Trf4–Air2 is particularly connected to NNS-terminated ncRNA decay |
| GO:0071042 nuclear polyadenylation-dependent mRNA catabolic process | IEA GO_REF:0000117 | ACCEPT | Summary: Supported by evidence that TRAMP participates in polyadenylation-dependent mRNA degradation pathways including NAB2 mRNA regulation. Supporting Evidence: PMID:19369424 Regulation of NAB2 mRNA 3'-end formation requires the core exosome and the Trf4p component of the TRAMP complex |
| GO:0071044 histone mRNA catabolic process | IEA GO_REF:0000117 | ACCEPT | Summary: Supported. Trf4/5 regulate histone mRNA levels through the nuclear exosome. Supporting Evidence: PMID:17179095 Contribution of Trf4/5 and the nuclear exosome to genome stability through regulation of histone mRNA levels |
| GO:0071051 poly(A)-dependent snoRNA 3'-end processing | IEA GO_REF:0000117 | ACCEPT | Summary: Supported by experimental evidence that polyadenylation linked to transcription termination directs snoRNA precursor processing. Supporting Evidence: PMID:18951092 Polyadenylation linked to transcription termination directs the processing of snoRNA precursors in yeast |
| GO:1990817 poly(A) RNA polymerase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Combined automated annotation correctly identifies the defining molecular function of PAP2/Trf4. Supporting Evidence: PMID:16260630 both proteins exhibit a robust poly(A) polymerase activity |
| GO:0005515 protein binding | IPI PMID:11805837 Systematic identification of protein complexes in Saccharomy... | MARK AS OVER ANNOTATED | Summary: Large-scale mass spectrometry identification of protein complexes. While the interaction data is valid, GO:0005515 is uninformative per curation guidelines. Reason: Protein binding is too generic. The relevant specific annotation is TRAMP complex membership (GO:0031499), which captures the biologically meaningful interaction. Supporting Evidence: PMID:11805837 Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry |
| GO:0005515 protein binding | IPI PMID:15828860 A new yeast poly(A) polymerase complex involved in RNA quali... | MARK AS OVER ANNOTATED | Summary: Demonstrates Trf4p interaction with Air1p/Air2p and Mtr4p in TRAMP complex. The specific complex annotation (GO:0031499) is more informative. Reason: Protein binding is too generic. TRAMP complex membership (GO:0031499) already captures the biologically meaningful interaction. Supporting Evidence: PMID:15828860 Trf4p is the catalytic subunit of a new poly(A) polymerase complex that contains Air1p or Air2p as potential RNA-binding subunits, as well as the putative RNA helicase Mtr4p |
| GO:0005515 protein binding | IPI PMID:15935758 RNA degradation by the exosome is promoted by a nuclear poly... | MARK AS OVER ANNOTATED | Summary: TRAMP complex identification paper. Specific complex annotation is more appropriate. Reason: Protein binding is too generic. TRAMP complex (GO:0031499) captures this interaction. Supporting Evidence: PMID:15935758 a nuclear polyadenylation complex containing a known exosome cofactor, the RNA helicase Mtr4p; a poly(A) polymerase, Trf4p; and a zinc knuckle protein, Air2p |
| GO:0005515 protein binding | IPI PMID:15935759 Cryptic pol II transcripts are degraded by a nuclear quality... | MARK AS OVER ANNOTATED | Summary: Trf4 complex identification. TRAMP complex annotation is more informative. Reason: Protein binding is too generic. TRAMP complex (GO:0031499) captures this interaction. Supporting Evidence: PMID:15935759 a new poly(A) polymerase activity that is defined by the Trf4 protein and one of two RNA binding proteins, Air1p or Air2p |
| GO:0005515 protein binding | IPI PMID:16429126 Proteome survey reveals modularity of the yeast cell machine... | MARK AS OVER ANNOTATED | Summary: Large-scale proteome survey. Protein binding is too generic. Reason: Protein binding is uninformative per curation guidelines. More specific complex or function annotations should be used. Supporting Evidence: PMID:16429126 Proteome survey reveals modularity of the yeast cell machinery |
| GO:0005515 protein binding | IPI PMID:20566885 Structural analysis reveals the characteristic features of M... | MARK AS OVER ANNOTATED | Summary: Structural analysis of Mtr4 interaction with TRAMP. The specific complex annotation and helicase contribution annotation are more informative. Reason: Protein binding is too generic. TRAMP complex (GO:0031499) and contributes_to helicase activity capture the biology. Supporting Evidence: PMID:20566885 Structural analysis reveals the characteristic features of Mtr4, a DExH helicase involved in nuclear RNA processing and surveillance |
| GO:0005515 protein binding | IPI PMID:20696927 Structure and function of the polymerase core of TRAMP, a RN... | MARK AS OVER ANNOTATED | Summary: Crystal structure of Trf4p/Air2p complex. Specific structural and functional annotations are more informative. Reason: Protein binding is too generic. TRAMP complex (GO:0031499) captures the biology. Supporting Evidence: PMID:20696927 Air2p, and in particular sequences encompassing a zinc knuckle motif near its N terminus, modulate Trf4p activity |
| GO:0005515 protein binding | IPI PMID:21663793 The RNA helicase Mtr4p modulates polyadenylation in the TRAM... | MARK AS OVER ANNOTATED | Summary: Mtr4p modulates polyadenylation in TRAMP. Specific complex and function annotations are more informative. Reason: Protein binding is too generic. Supporting Evidence: PMID:21663793 The RNA helicase Mtr4p modulates polyadenylation in the TRAMP complex |
| GO:0005515 protein binding | IPI PMID:37070168 RNA-dependent interactome allows network-based assignment of... | MARK AS OVER ANNOTATED | Summary: RNA-dependent interactome study. Protein binding is too generic. Reason: Protein binding is uninformative per curation guidelines. Supporting Evidence: PMID:37070168 RNA-dependent interactome allows network-based assignment of RNA-binding protein function |
| GO:0005515 protein binding | IPI PMID:37968396 The social and structural architecture of the yeast protein ... | MARK AS OVER ANNOTATED | Summary: Large-scale yeast interactome study. Protein binding is too generic. Reason: Protein binding is uninformative per curation guidelines. Supporting Evidence: PMID:37968396 The social and structural architecture of the yeast protein interactome |
| GO:0005515 protein binding | IPI PMID:27076633 Exosome Cofactors Connect Transcription Termination to RNA P... | MARK AS OVER ANNOTATED | Summary: Exosome cofactor study showing how terminated transcripts are guided to exonucleases. The specific functional annotations are more informative. Reason: Protein binding is too generic per curation guidelines. Supporting Evidence: PMID:27076633 Exosome Cofactors Connect Transcription Termination to RNA Processing by Guiding Terminated Transcripts to the Appropriate Exonuclease within the Nuclear Exosome |
| GO:0000292 RNA fragment catabolic process | NAS PMID:32561742 Substrate specificity of the TRAMP nuclear surveillance comp... | KEEP AS NON CORE | Summary: TRAMP complexes participate in degradation of RNA fragments as part of nuclear RNA surveillance. Supported by substrate specificity analysis of TRAMP complexes. Reason: RNA fragment degradation is a consequence of the core TRAMP surveillance function rather than a distinct evolved function. The more specific polyadenylation-dependent degradation terms are more appropriate for capturing the core biology. Supporting Evidence: PMID:32561742 Substrate specificity of the TRAMP nuclear surveillance complexes |
| GO:0071051 poly(A)-dependent snoRNA 3'-end processing | IGI PMID:18951092 Polyadenylation linked to transcription termination directs ... | ACCEPT | Summary: Genetic interaction evidence supports role in poly(A)-dependent snoRNA 3'-end processing. Polyadenylation linked to transcription termination directs snoRNA precursor processing. Supporting Evidence: PMID:18951092 Polyadenylation linked to transcription termination directs the processing of snoRNA precursors in yeast |
| GO:1990817 poly(A) RNA polymerase activity | IDA PMID:12062100 Cid13 is a cytoplasmic poly(A) polymerase that regulates rib... | ACCEPT | Summary: Saitoh et al. demonstrated that Trf4/Trf5 family members have poly(A) polymerase activity. This paper primarily characterized S. pombe Cid13 but confirmed Trf4 activity. Supporting Evidence: PMID:12062100 Fission yeast Cid13 and budding yeast Trf4/5 are members of a newly identified nucleotidyltransferase family |
| GO:1990817 poly(A) RNA polymerase activity | IMP PMID:15828860 A new yeast poly(A) polymerase complex involved in RNA quali... | ACCEPT | Summary: Vanacova et al. demonstrated Trf4 complex has poly(A) polymerase activity that preferentially polyadenylates unmodified tRNAi-Met over native tRNA. Supporting Evidence: PMID:15828860 the unmodified RNA was preferentially polyadenylated by affinity-purified Trf4 complex from yeast |
| GO:1990817 poly(A) RNA polymerase activity | IDA PMID:15935758 RNA degradation by the exosome is promoted by a nuclear poly... | ACCEPT | Summary: LaCava et al. showed TRAMP complex has distributive RNA polyadenylation activity in vitro. Supporting Evidence: PMID:15935758 the Trf4p/Air2p/Mtr4p polyadenylation complex (TRAMP) showed distributive RNA polyadenylation activity |
| GO:1990817 poly(A) RNA polymerase activity | IDA PMID:15935759 Cryptic pol II transcripts are degraded by a nuclear quality... | ACCEPT | Summary: Wyers et al. demonstrated a new poly(A) polymerase activity defined by Trf4 protein. Supporting Evidence: PMID:15935759 a new poly(A) polymerase activity that is defined by the Trf4 protein |
| GO:1990817 poly(A) RNA polymerase activity | IMP PMID:15935759 Cryptic pol II transcripts are degraded by a nuclear quality... | ACCEPT | Summary: Mutant phenotype evidence supports poly(A) polymerase activity in vivo. Supporting Evidence: PMID:15935759 a polyadenylation-assisted degradation mechanism |
| GO:1990817 poly(A) RNA polymerase activity | IDA PMID:16260630 Trf4 and Trf5 proteins of Saccharomyces cerevisiae exhibit p... | ACCEPT | Summary: Definitive demonstration that purified Trf4 and Trf5 proteins exhibit robust poly(A) polymerase activity but no DNA polymerase activity. Strictly Mn2+-dependent, highly ATP-specific. Supporting Evidence: PMID:16260630 both proteins exhibit a robust poly(A) polymerase activity, neither of them shows any evidence of a DNA polymerase activity file:yeast/PAP2/PAP2-deep-research-falcon.md Catalytic Asp residues are essential; activity has been reported to prefer Mn²⁺ in biochemical assays |
| GO:1990817 poly(A) RNA polymerase activity | IMP PMID:16260630 Trf4 and Trf5 proteins of Saccharomyces cerevisiae exhibit p... | ACCEPT | Summary: In vivo mutant phenotype evidence supports poly(A) polymerase activity. Supporting Evidence: PMID:16260630 Trf4 and Trf5 proteins of Saccharomyces cerevisiae exhibit poly(A) RNA polymerase activity |
| GO:1990817 poly(A) RNA polymerase activity | IDA PMID:16374505 Yeast Trf5p is a nuclear poly(A) polymerase. | ACCEPT | Summary: Houseley and Tollervey showed Trf5p (the Trf4 homolog) has polyadenylation activity. This paper is about Trf5, not Trf4/PAP2, but confirms the activity in the family. Supporting Evidence: PMID:16374505 Trf5p showed polyadenylation activity in vitro |
| GO:1990817 poly(A) RNA polymerase activity | IGI PMID:16374505 Yeast Trf5p is a nuclear poly(A) polymerase. | ACCEPT | Summary: Genetic interaction evidence showing Trf5p polyadenylation is reduced in strains lacking Trf4p, indicating partially overlapping functions. Supporting Evidence: PMID:16374505 polyadenylation is reduced in strains lacking either the poly(A) polymerase Trf4p or its close homologue Trf5p |
| GO:1990817 poly(A) RNA polymerase activity | IDA PMID:20696927 Structure and function of the polymerase core of TRAMP, a RN... | ACCEPT | Summary: Crystal structure-based functional analysis confirmed Trf4p catalytic activity and showed Air2p modulates Trf4p activity. Supporting Evidence: PMID:20696927 Air2p, and in particular sequences encompassing a zinc knuckle motif near its N terminus, modulate Trf4p activity |
| GO:0034458 3'-5' RNA helicase activity | IDA PMID:22532666 RNA unwinding by the Trf4/Air2/Mtr4 polyadenylation (TRAMP) ... | ACCEPT | Summary: Trf4p/Air2p stimulate Mtr4p RNA helicase activity within the TRAMP complex. The contributes_to qualifier is appropriate because Trf4 does not independently have helicase activity; Mtr4p provides the helicase function. Supporting Evidence: PMID:22532666 The unwinding activity of Mtr4p is significantly stimulated by Trf4p/Air2p file:yeast/PAP2/PAP2-deep-research-falcon.md Mtr4 is the essential nuclear 3′→5′ DExH-box RNA helicase within TRAMP and also acts with the nuclear exosome beyond TRAMP |
| GO:0003729 mRNA binding | HDA PMID:23222640 Global analysis of yeast mRNPs. | ACCEPT | Summary: High-throughput direct assay identified PAP2/Trf4 as an mRNA-binding protein. Consistent with its role in mRNA surveillance and polyadenylation. Supporting Evidence: PMID:23222640 Global analysis of yeast mRNPs |
| GO:0005829 cytosol | IDA PMID:22932476 The nuclear localization of SWI/SNF proteins is subjected to... | KEEP AS NON CORE | Summary: Large-scale GFP localization study detected PAP2/Trf4 in the cytosol. This is likely a minor pool; the primary functional localization is nuclear/nucleolar. Reason: Cytosolic localization is real but minor. The core functional localization is nuclear and nucleolar where TRAMP-mediated RNA surveillance occurs. Supporting Evidence: PMID:22932476 The nuclear localization of SWI/SNF proteins is subjected to oxygen regulation |
| GO:0005634 nucleus | IDA PMID:10066793 The topoisomerase-related function gene TRF4 affects cellula... | ACCEPT | Summary: Direct experimental evidence showing Trf4 is a nuclear protein. Core localization. Supporting Evidence: PMID:10066793 We show that Trf4 is a nuclear protein |
| GO:0005634 nucleus | IDA PMID:22932476 The nuclear localization of SWI/SNF proteins is subjected to... | ACCEPT | Summary: Large-scale localization study confirms nuclear localization. Redundant with PMID:10066793 but provides independent evidence. Supporting Evidence: PMID:22932476 The nuclear localization of SWI/SNF proteins is subjected to oxygen regulation |
| GO:0005730 nucleolus | IDA PMID:16541108 Surveillance of nuclear-restricted pre-ribosomes within a su... | ACCEPT | Summary: Trf4 localizes to a subnucleolar region where it participates in surveillance of nuclear-restricted pre-ribosomes. Core localization for rRNA quality control. Supporting Evidence: PMID:16541108 Surveillance of nuclear-restricted pre-ribosomes within a subnucleolar region of Saccharomyces cerevisiae file:yeast/PAP2/PAP2-deep-research-falcon.md GFP-fusion evidence indicates **slight nucleolar enrichment** for some TRAMP components (Trf5-GFP, Air1-GFP) compared to Trf4-GFP/Air2-GFP, and Trf4-GFP can accumulate in the nucleolus under conditions that cause nucleolar rRNA accumulation |
| GO:0042138 meiotic DNA double-strand break formation | IMP PMID:25210768 The nuclear exosome is active and important during budding y... | KEEP AS NON CORE | Summary: TRAMP mutants (trf4-delta) show defects in meiotic DSB formation. However, this is an indirect effect: TRAMP loss stabilizes ~1600 CUTs that saturate 40% of nuclear cap-binding complex (CBC) capacity, and CBC mutants show DSB defects. This is not a direct role in DSB formation. Reason: The DSB formation defect is an indirect consequence of CUT accumulation saturating the CBC complex, not a direct role of Trf4 in meiotic recombination machinery. Supporting Evidence: PMID:25210768 CBC mutants display defects in the formation of meiotic double strand breaks (DSBs), and we see similar defects in TRAMP mutants, suggesting that a key function of the nuclear exosome is to prevent saturation of the CBC complex by CUTs |
| GO:0045910 negative regulation of DNA recombination | IMP PMID:23762389 R-loop mediated transcription-associated recombination in tr... | KEEP AS NON CORE | Summary: trf4-delta mutants show R-loop-mediated transcription-associated hyperrecombination. Trf4 prevents R-loop accumulation by degrading aberrant RNAs, thereby indirectly suppressing recombination. Reason: This is an indirect effect of impaired RNA surveillance leading to R-loop accumulation, not a direct role in regulating recombination machinery. Supporting Evidence: PMID:23762389 in the absence of Trf4 R-loops accumulate co-transcriptionally increasing the recombination and mutation frequencies |
| GO:0006284 base-excision repair | IMP PMID:17983848 Intrinsic 5'-deoxyribose-5-phosphate lyase activity in Sacch... | KEEP AS NON CORE | Summary: trf4-delta mutants are hypersensitive to MMS and show genetic interaction with RAD27, suggesting a role in BER parallel to Rad27-dependent long-patch BER. Reason: While the dRP lyase activity is intrinsic to Trf4, the BER role appears to be a secondary function. The core evolved function is RNA surveillance. The BER contribution is supported but is not the primary biological role. Supporting Evidence: PMID:17983848 The data strongly suggest a role for Trf4 in a pathway parallel to the Rad27-dependent LP-BER in yeast |
| GO:0006284 base-excision repair | IGI PMID:17983848 Intrinsic 5'-deoxyribose-5-phosphate lyase activity in Sacch... | KEEP AS NON CORE | Summary: Genetic interaction between TRF4 and RAD27 supports BER role. Higher MMS sensitivity in double mutant than either single mutant. Reason: Secondary function. Core function is RNA surveillance. Supporting Evidence: PMID:17983848 there was higher sensitivity for strains mutated in both TRF4 and RAD27 than either single mutant |
| GO:0006400 tRNA modification | IMP PMID:22319136 The TRAMP complex shows tRNA editing activity in S. cerevisi... | KEEP AS NON CORE | Summary: Dickinson et al. showed the TRAMP complex can perform tRNA editing -- adding nucleotides at internal positions. However, this was demonstrated with an introduced artificial tRNA substrate and likely represents enzymatic promiscuity rather than an evolved function. Reason: The tRNA editing activity was demonstrated with an artificial substrate and represents enzymatic promiscuity of the distributive polymerase. Not a primary evolved function. Supporting Evidence: PMID:22319136 the noncanonical poly(A) polymerase Trf4p in the TRAMP complex can be recruited for such an editing reaction at an introduced tRNA transcript |
| GO:0031499 TRAMP complex | IDA PMID:15828860 A new yeast poly(A) polymerase complex involved in RNA quali... | ACCEPT | Summary: Vanacova et al. affinity-purified the Trf4 complex and identified Air1p/Air2p and Mtr4p as components. Direct evidence for TRAMP complex membership. Supporting Evidence: PMID:15828860 Trf4p is the catalytic subunit of a new poly(A) polymerase complex that contains Air1p or Air2p as potential RNA-binding subunits, as well as the putative RNA helicase Mtr4p |
| GO:0031499 TRAMP complex | IDA PMID:15935758 RNA degradation by the exosome is promoted by a nuclear poly... | ACCEPT | Summary: LaCava et al. identified the TRAMP complex containing Trf4p, Air2p, and Mtr4p. Supporting Evidence: PMID:15935758 a nuclear polyadenylation complex containing a known exosome cofactor, the RNA helicase Mtr4p; a poly(A) polymerase, Trf4p; and a zinc knuckle protein, Air2p |
| GO:0031499 TRAMP complex | IDA PMID:15935759 Cryptic pol II transcripts are degraded by a nuclear quality... | ACCEPT | Summary: Wyers et al. identified Trf4 in complex with Air1/Air2 by mass spectrometry. Supporting Evidence: PMID:15935759 a new poly(A) polymerase activity that is defined by the Trf4 protein and one of two RNA binding proteins, Air1p or Air2p |
| GO:0034475 U4 snRNA 3'-end processing | IMP PMID:16373491 Contributions of Trf4p- and Trf5p-dependent polyadenylation ... | ACCEPT | Summary: In the absence of Trf4p, 3'-extended forms of U4 snRNA accumulate, similar to rrp6-delta. Polyadenylation by Trf4 is required for proper U4 snRNA 3'-end processing. Supporting Evidence: PMID:16373491 in the absence of Trf4p, we observed 3'-extended forms of the U4 snRNA that are similar to those observed in the absence of Rrp6p |
| GO:0034475 U4 snRNA 3'-end processing | IGI PMID:16373491 Contributions of Trf4p- and Trf5p-dependent polyadenylation ... | ACCEPT | Summary: Genetic interaction evidence supports role in U4 snRNA processing. Supporting Evidence: PMID:16373491 polyadenylation of RNA processing intermediates plays a functional role in RNA processing pathways |
| GO:0051575 5'-deoxyribose-5-phosphate lyase activity | IDA PMID:17983848 Intrinsic 5'-deoxyribose-5-phosphate lyase activity in Sacch... | KEEP AS NON CORE | Summary: Trf4 has intrinsic dRP lyase activity demonstrated by Schiff base intermediate formation with 5'-deoxyribose-5-phosphate substrates, similar to mammalian Pol-beta. Reason: While this is a genuine intrinsic enzymatic activity, the primary evolved function of PAP2/Trf4 is poly(A) RNA polymerase activity. The dRP lyase is likely a secondary activity of the nucleotidyltransferase fold. Supporting Evidence: PMID:17983848 Trf4 is able to form a Schiff base intermediate with a 5'-deoxyribose-5-phosphate substrate and to excise the abasic residue through a dRP lyase activity |
| GO:0051575 5'-deoxyribose-5-phosphate lyase activity | IMP PMID:17983848 Intrinsic 5'-deoxyribose-5-phosphate lyase activity in Sacch... | KEEP AS NON CORE | Summary: In vivo evidence supports dRP lyase activity through genetic interaction with RAD27. Reason: Secondary function. Core function is poly(A) RNA polymerase activity. Supporting Evidence: PMID:17983848 overexpression of Trf4 in a rad27Delta background partially suppressed MMS sensitivity |
| GO:0071031 nuclear mRNA surveillance of mRNA 3'-end processing | IGI PMID:17410208 Dissecting mechanisms of nuclear mRNA surveillance in THO/su... | ACCEPT | Summary: Trf4 participates in nuclear mRNA surveillance, demonstrated through genetic interactions in THO/sub2 complex mutants. Supporting Evidence: PMID:17410208 Dissecting mechanisms of nuclear mRNA surveillance in THO/sub2 complex mutants |
| GO:0071035 nuclear polyadenylation-dependent rRNA catabolic process | IMP PMID:15935758 RNA degradation by the exosome is promoted by a nuclear poly... | ACCEPT | Summary: TRAMP is required for polyadenylation and degradation of rRNA precursors. Supporting Evidence: PMID:15935758 TRAMP is required for polyadenylation and degradation of rRNA and snoRNA precursors |
| GO:0071035 nuclear polyadenylation-dependent rRNA catabolic process | IGI PMID:15935758 RNA degradation by the exosome is promoted by a nuclear poly... | ACCEPT | Summary: Genetic interaction evidence supports rRNA surveillance function. Supporting Evidence: PMID:15935758 TRAMP is required for polyadenylation and degradation of rRNA and snoRNA precursors |
| GO:0071035 nuclear polyadenylation-dependent rRNA catabolic process | IMP PMID:16431988 Nuclear RNA surveillance in Saccharomyces cerevisiae: Trf4p-... | ACCEPT | Summary: Trf4p-dependent polyadenylation of aberrant 5S rRNA demonstrated. Supporting Evidence: PMID:16431988 Trf4p-dependent polyadenylation of nascent hypomethylated tRNA and an aberrant form of 5S rRNA |
| GO:0071035 nuclear polyadenylation-dependent rRNA catabolic process | IGI PMID:16541108 Surveillance of nuclear-restricted pre-ribosomes within a su... | ACCEPT | Summary: Genetic interaction evidence for rRNA surveillance in subnucleolar region. Supporting Evidence: PMID:16541108 Surveillance of nuclear-restricted pre-ribosomes within a subnucleolar region |
| GO:0071035 nuclear polyadenylation-dependent rRNA catabolic process | IMP PMID:18007593 Trf4 targets ncRNAs from telomeric and rDNA spacer regions a... | ACCEPT | Summary: Trf4 targets ncRNAs from rDNA spacer regions and functions in rDNA copy number control. Supporting Evidence: PMID:18007593 Trf4 targets ncRNAs from telomeric and rDNA spacer regions and functions in rDNA copy number control |
| GO:0071036 nuclear polyadenylation-dependent snoRNA catabolic process | IMP PMID:15935758 RNA degradation by the exosome is promoted by a nuclear poly... | ACCEPT | Summary: TRAMP is required for polyadenylation and degradation of snoRNA precursors. Supporting Evidence: PMID:15935758 TRAMP is required for polyadenylation and degradation of rRNA and snoRNA precursors |
| GO:0071036 nuclear polyadenylation-dependent snoRNA catabolic process | IGI PMID:15935758 RNA degradation by the exosome is promoted by a nuclear poly... | ACCEPT | Summary: Genetic interaction evidence supports snoRNA surveillance. Supporting Evidence: PMID:15935758 TRAMP is required for polyadenylation and degradation of rRNA and snoRNA precursors |
| GO:0071036 nuclear polyadenylation-dependent snoRNA catabolic process | IGI PMID:16373491 Contributions of Trf4p- and Trf5p-dependent polyadenylation ... | ACCEPT | Summary: Trf4p and Trf5p contribute to snoRNA processing and degradation by the nuclear exosome. Supporting Evidence: PMID:16373491 Contributions of Trf4p- and Trf5p-dependent polyadenylation to the processing and degradative functions of the yeast nuclear exosome |
| GO:0071037 nuclear polyadenylation-dependent snRNA catabolic process | IMP PMID:15935758 RNA degradation by the exosome is promoted by a nuclear poly... | ACCEPT | Summary: snRNA processing intermediates are polyadenylated by TRAMP for exosome degradation. Supporting Evidence: PMID:15935758 the Trf4p/Air2p/Mtr4p polyadenylation complex (TRAMP) showed distributive RNA polyadenylation activity |
| GO:0071037 nuclear polyadenylation-dependent snRNA catabolic process | IMP PMID:16431988 Nuclear RNA surveillance in Saccharomyces cerevisiae: Trf4p-... | ACCEPT | Summary: Trf4-dependent polyadenylation of snRNA species demonstrated. Supporting Evidence: PMID:16431988 Nuclear RNA surveillance in Saccharomyces cerevisiae: Trf4p-dependent polyadenylation |
| GO:0071038 TRAMP-dependent tRNA surveillance pathway | IGI PMID:15145828 Nuclear surveillance and degradation of hypomodified initiat... | ACCEPT | Summary: Founding paper for TRAMP-dependent tRNA surveillance. Hypomodified initiator tRNAi-Met is degraded through Trf4-dependent polyadenylation and exosome degradation. Supporting Evidence: PMID:15145828 Nuclear surveillance and degradation of hypomodified initiator tRNAMet in S. cerevisiae |
| GO:0071038 TRAMP-dependent tRNA surveillance pathway | IDA PMID:15828860 A new yeast poly(A) polymerase complex involved in RNA quali... | ACCEPT | Summary: Direct biochemical demonstration that Trf4 complex discriminates between correctly and incorrectly folded tRNAs and polyadenylates aberrant species. Supporting Evidence: PMID:15828860 the Trf4 complex can discriminate between native tRNAs and molecules that are incorrectly folded |
| GO:0071038 TRAMP-dependent tRNA surveillance pathway | IDA PMID:15935758 RNA degradation by the exosome is promoted by a nuclear poly... | ACCEPT | Summary: TRAMP complex identification and functional characterization in tRNA surveillance. Supporting Evidence: PMID:15935758 In vitro, the Trf4p/Air2p/Mtr4p polyadenylation complex (TRAMP) showed distributive RNA polyadenylation activity |
| GO:0071038 TRAMP-dependent tRNA surveillance pathway | IMP PMID:16431988 Nuclear RNA surveillance in Saccharomyces cerevisiae: Trf4p-... | ACCEPT | Summary: Trf4-dependent polyadenylation of nascent hypomethylated tRNA established in vivo. Supporting Evidence: PMID:16431988 Trf4p-dependent polyadenylation of nascent hypomethylated tRNA |
| GO:0071038 TRAMP-dependent tRNA surveillance pathway | IDA PMID:17643380 The exosome subunit Rrp44 plays a direct role in RNA substra... | ACCEPT | Summary: Rrp44 directly recognizes RNA substrates including those polyadenylated by TRAMP for tRNA surveillance. Supporting Evidence: PMID:17643380 The exosome subunit Rrp44 plays a direct role in RNA substrate recognition |
| GO:0071038 TRAMP-dependent tRNA surveillance pathway | IMP PMID:18456844 Competition between the Rex1 exonuclease and the La protein ... | ACCEPT | Summary: Competition between Rex1 exonuclease and La protein affects Trf4-mediated RNA quality control and pre-tRNA maturation. Supporting Evidence: PMID:18456844 Competition between the Rex1 exonuclease and the La protein affects both Trf4p-mediated RNA quality control and pre-tRNA maturation |
| GO:0071039 nuclear polyadenylation-dependent CUT catabolic process | IMP PMID:15935759 Cryptic pol II transcripts are degraded by a nuclear quality... | ACCEPT | Summary: Landmark paper showing CUTs are degraded by Trf4-dependent polyadenylation pathway. Supporting Evidence: PMID:15935759 Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase |
| GO:0071039 nuclear polyadenylation-dependent CUT catabolic process | IGI PMID:15935759 Cryptic pol II transcripts are degraded by a nuclear quality... | ACCEPT | Summary: Genetic interaction evidence supports CUT degradation by Trf4/exosome pathway. Supporting Evidence: PMID:15935759 a polyadenylation-assisted degradation mechanism is also responsible for the degradation of several Pol I and Pol III transcripts |
| GO:0071039 nuclear polyadenylation-dependent CUT catabolic process | IMP PMID:16973436 Termination of cryptic unstable transcripts is directed by y... | ACCEPT | Summary: Nrd1 and Nab3 RNA-binding proteins direct termination of CUTs for TRAMP-mediated degradation. Supporting Evidence: PMID:16973436 Termination of cryptic unstable transcripts is directed by yeast RNA-binding proteins Nrd1 and Nab3 |
| GO:0071039 nuclear polyadenylation-dependent CUT catabolic process | IMP PMID:18007593 Trf4 targets ncRNAs from telomeric and rDNA spacer regions a... | ACCEPT | Summary: Trf4 targets ncRNAs from telomeric and rDNA spacer regions. Supporting Evidence: PMID:18007593 Trf4 targets ncRNAs from telomeric and rDNA spacer regions |
| GO:0071039 nuclear polyadenylation-dependent CUT catabolic process | IMP PMID:18591258 A yeast exosome cofactor, Mpp6, functions in RNA surveillanc... | ACCEPT | Summary: Mpp6 cooperates with TRAMP in CUT degradation as an exosome cofactor. Supporting Evidence: PMID:18591258 Mpp6, functions in RNA surveillance and in the degradation of noncoding RNA transcripts |
| GO:0071040 nuclear polyadenylation-dependent antisense transcript catabolic process | IMP PMID:18022365 Antisense RNA stabilization induces transcriptional gene sil... | ACCEPT | Summary: Antisense RNA stabilization in trf4-delta mutants induces transcriptional gene silencing via histone deacetylation. Trf4 normally degrades antisense transcripts. Supporting Evidence: PMID:18022365 Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in S. cerevisiae |
| GO:0071042 nuclear polyadenylation-dependent mRNA catabolic process | IGI PMID:16373491 Contributions of Trf4p- and Trf5p-dependent polyadenylation ... | ACCEPT | Summary: Trf4 and Trf5 contribute to mRNA degradation by the nuclear exosome through polyadenylation. Supporting Evidence: PMID:16373491 Contributions of Trf4p- and Trf5p-dependent polyadenylation to the processing and degradative functions of the yeast nuclear exosome |
| GO:0071044 histone mRNA catabolic process | IGI PMID:17179095 Contribution of Trf4/5 and the nuclear exosome to genome sta... | ACCEPT | Summary: Trf4/5 and the nuclear exosome regulate histone mRNA levels, contributing to genome stability. Supporting Evidence: PMID:17179095 Contribution of Trf4/5 and the nuclear exosome to genome stability through regulation of histone mRNA levels |
| GO:0071047 polyadenylation-dependent mRNA catabolic process | IMP PMID:19369424 Regulation of NAB2 mRNA 3'-end formation requires the core e... | ACCEPT | Summary: NAB2 mRNA 3'-end formation requires Trf4 TRAMP component, demonstrating role in polyadenylation-dependent mRNA catabolism. Supporting Evidence: PMID:19369424 Regulation of NAB2 mRNA 3'-end formation requires the core exosome and the Trf4p component of the TRAMP complex |
| GO:0071051 poly(A)-dependent snoRNA 3'-end processing | IGI PMID:16373491 Contributions of Trf4p- and Trf5p-dependent polyadenylation ... | ACCEPT | Summary: Trf4/Trf5-dependent polyadenylation contributes to snoRNA 3'-end processing by the nuclear exosome. Supporting Evidence: PMID:16373491 polyadenylation of RNA processing intermediates plays a functional role in RNA processing pathways |
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