PAP2 non-canonical poly(A) polymerase PAP2 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Gene symbol: PAP2
Gene description: non-canonical poly(A) polymerase PAP2
Primary source: FungiDB:YOL115W
Locus tag: YOL115W
See related: SGD:S000005475; AllianceGenome:SGD:S000005475; VEuPathDB:YOL115W
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Also known as: TRF4
Summary: Enables 5'-deoxyribose-5-phosphate lyase activity and polynucleotide adenylyltransferase activity. Contributes to 3'-5' RNA helicase activity. Involved in negative regulation of DNA recombination and nucleic acid metabolic process. Located in cytosol and nucleolus. Part of TRAMP complex. Orthologous to human TENT4A (terminal nucleotidyltransferase 4A) and TENT4B (terminal nucleotidyltransferase 4B). [provided by Alliance of Genome Resources, Apr 2022]
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Genomic context

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See PAP2 in Genome Data Viewer

Location:: chromosome: XV

Exon count:: 1

Sequence:: Chromosome: XV; NC_001147.6 (101475..103229)

Chromosome XV - NC_001147.6 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001147.6

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Results show that the Nrd1-Trf4 interaction is required for optimal exosome activity in vivo and for the stimulation of polyadenylation of NNS targets by TRAMP in vitro.
Title: Molecular basis for coordinating transcription termination with noncoding RNA degradation.
Cotranscriptional recruitment of RNA exosome cofactors Rrp47p and Mpp6p and two distinct Trf-Air-Mtr4 polyadenylation (TRAMP) complexes assists the exonuclease Rrp6p in the targeting and degradation of an aberrant messenger
Title: Cotranscriptional recruitment of RNA exosome cofactors Rrp47p and Mpp6p and two distinct Trf-Air-Mtr4 polyadenylation (TRAMP) complexes assists the exonuclease Rrp6p in the targeting and degradation of an aberrant messenger ribonucleoprotein particle (mRNP) in yeast.
Data show that the unwinding activity of Mtr4p is significantly stimulated by Trf4p/Air2p, but the stimulation of Mtr4p does not depend on ongoing polyadenylation.
Title: RNA unwinding by the Trf4/Air2/Mtr4 polyadenylation (TRAMP) complex.
Air1 zinc knuckles 4 and 5 and a conserved IWRXY motif are critical for the function and integrity of the Trf4/5-Air1/2-Mtr4 polyadenylation (TRAMP) RNA quality control complex.
Title: Air1 zinc knuckles 4 and 5 and a conserved IWRXY motif are critical for the function and integrity of the Trf4/5-Air1/2-Mtr4 polyadenylation (TRAMP) RNA quality control complex.
Data suggest that neither the poly(A) polymerase activity of Trf4 nor the helicase activity of Mtr4 plays a role in the enhancement of RNA degradation by the nuclear exosome component Rrp6.
Title: TRAMP complex enhances RNA degradation by the nuclear exosome component Rrp6.
These experiments reveal that one consequence of Rex1p-dependent 3' trimming is the generation of aberrant RNAs that are targeted for decay by Trf4p.
Title: Competition between the Rex1 exonuclease and the La protein affects both Trf4p-mediated RNA quality control and pre-tRNA maturation.
Trf4 protein has intrinsic 5'-deoxyribose-5-phosphate lyase activity and a possible role in base excision DNA repair.
Title: Intrinsic 5'-deoxyribose-5-phosphate lyase activity in Saccharomyces cerevisiae Trf4 protein with a possible role in base excision DNA repair.
Results report that in Saccharomyces cerevisiae strains lacking Trf4, cryptic transcripts are detected from regions of repressed chromatin at telomeres and the rDNA intergenic spacer region (IGS1-R), and at CEN3.
Title: Trf4 targets ncRNAs from telomeric and rDNA spacer regions and functions in rDNA copy number control.
TRF4, TRF5, and RRP6 play a role in the regulation of histone mRNA levels in yeast.
Title: Contribution of Trf4/5 and the nuclear exosome to genome stability through regulation of histone mRNA levels in Saccharomyces cerevisiae.
RNA processing and degradation intermediates are polyadenylated, and that their polyadenylation is dependent on the activity of Trf4p and Trf5p, two variant poly(A) polymerases.
Title: Contributions of Trf4p- and Trf5p-dependent polyadenylation to the processing and degradative functions of the yeast nuclear exosome.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

Gene Ontology Provided by SGD

Function	Evidence Code	Pubs
contributes_to 3'-5' RNA helicase activity	IDA Inferred from Direct Assay more info	PubMed
enables 5'-deoxyribose-5-phosphate lyase activity	IDA Inferred from Direct Assay more info	PubMed
enables 5'-deoxyribose-5-phosphate lyase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables mRNA binding	HDA more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables nucleotidyltransferase activity	IEA Inferred from Electronic Annotation more info
enables poly(A) RNA polymerase activity	IBA Inferred from Biological aspect of Ancestor more info
enables poly(A) RNA polymerase activity	IDA Inferred from Direct Assay more info	PubMed
enables poly(A) RNA polymerase activity	IEA Inferred from Electronic Annotation more info
enables poly(A) RNA polymerase activity	IGI Inferred from Genetic Interaction more info	PubMed
enables poly(A) RNA polymerase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA 3'-end processing	IBA Inferred from Biological aspect of Ancestor more info
involved_in RNA metabolic process	IEA Inferred from Electronic Annotation more info
involved_in TRAMP-dependent tRNA surveillance pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in TRAMP-dependent tRNA surveillance pathway	IGI Inferred from Genetic Interaction more info	PubMed
involved_in TRAMP-dependent tRNA surveillance pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in U4 snRNA 3'-end processing	IGI Inferred from Genetic Interaction more info	PubMed
involved_in U4 snRNA 3'-end processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in base-excision repair	IGI Inferred from Genetic Interaction more info	PubMed
involved_in base-excision repair	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cell division	IEA Inferred from Electronic Annotation more info
involved_in histone mRNA catabolic process	IGI Inferred from Genetic Interaction more info	PubMed
involved_in meiotic DNA double-strand break formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of DNA recombination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear mRNA surveillance of mRNA 3'-end processing	IGI Inferred from Genetic Interaction more info	PubMed
involved_in nuclear polyadenylation-dependent CUT catabolic process	IGI Inferred from Genetic Interaction more info	PubMed
involved_in nuclear polyadenylation-dependent CUT catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear polyadenylation-dependent antisense transcript catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear polyadenylation-dependent mRNA catabolic process	IGI Inferred from Genetic Interaction more info	PubMed
involved_in nuclear polyadenylation-dependent rRNA catabolic process	IGI Inferred from Genetic Interaction more info	PubMed
involved_in nuclear polyadenylation-dependent rRNA catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear polyadenylation-dependent snRNA catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear polyadenylation-dependent snoRNA catabolic process	IGI Inferred from Genetic Interaction more info	PubMed
involved_in nuclear polyadenylation-dependent snoRNA catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in poly(A)-dependent snoRNA 3'-end processing	IGI Inferred from Genetic Interaction more info	PubMed
involved_in polyadenylation-dependent mRNA catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in polyadenylation-dependent ncRNA catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in tRNA modification	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of TRAMP complex	IBA Inferred from Biological aspect of Ancestor more info
part_of TRAMP complex	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
is_active_in nucleolus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: non-canonical poly(A) polymerase PAP2

NP_014526.1

EC 2.7.7.19

Non-canonical poly(A) polymerase; involved in nuclear RNA degradation as a component of TRAMP; catalyzes polyadenylation of hypomodified tRNAs, and snoRNA and rRNA precursors; required for mRNA surveillance and maintenance of genome integrity, serving as a link between RNA and DNA metabolism; overlapping but non-redundant functions with Trf5p; relocalizes to cytosol in response to hypoxia

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_001147.6 Reference assembly

Range

101475..103229

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001183369.1 → NP_014526.1 TPA: non-canonical poly(A) polymerase PAP2 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_014526.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D6W1V2, P53632

UniProtKB/TrEMBL

A0A8H4BUG2, G2WMC1, N1NYZ5

Conserved Domains (1) summary

COG5260
Location:116 → 584

TRF4; DNA polymerase sigma [Replication, recombination and repair]