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Gene Review

PAP1  -  polynucleotide adenylyltransferase PAP1

Saccharomyces cerevisiae S288c

Synonyms: PAP, Poly(A) polymerase, Polynucleotide adenylyltransferase, YKR002W
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Disease relevance of PAP1

  • The antibodies show species specificity and cannot recognize mammalian, Xenopus, or vaccinia PAP [1].
  • Salt toxicity in yeast results from Hal2 inhibition and accumulation of PAP, which inhibits sulphate assimilation and RNA processing [2].
  • Structural modeling of ME1 showed that it has folding patterns similar to other RIPs, indicating that ME1 and PAP, which share a similar folding pattern, can show different substrate specificity towards E. coli ribosomes [3].
  • We demonstrate the principle of the assay using influenza virus RNA polymerase and yeast PAP as examples [4].

High impact information on PAP1

  • Recombinant FIP1 protein forms a 1:1 complex with PAP1 in vitro [5].
  • Like other nucleic acid polymerases, Pap1 is composed of three domains that encircle the active site [6].
  • The crystal structure of the PAP from Saccharomyces cerevisiae (Pap1) has been solved to 2.6 angstroms, both alone and in complex with 3'-deoxyadenosine triphosphate (3'-dATP) [6].
  • Here, mutations in the PAP1 gene were shown to be synergistically lethal with previously identified mutations in the RNA14 and RNA15 genes, which suggests that their encoded proteins participate in 3'-end processing [7].
  • In yeast, four factors (CF I, CF II, PF I, and PAP) are required for accurate pre-mRNA cleavage and polyadenylation in vitro [8].

Biological context of PAP1


Associations of PAP1 with chemical compounds

  • Further analysis revealed that the specificity of PAP for adenosine is not simply a function of the ATP binding site but also reflects interactions with bases at the 3' end of the primer and at another contact site 14 nucleotides upstream of the 3' end [13].
  • These results suggest that the unique specificity of PAP for ribose and base, and thus the extent and type of activity with different substrates, depends on interactions at multiple nucleotide binding sites [13].
  • To further probe this model we examined the growth inhibitory effects of lithium under conditions in which PAP biosynthetic machinery was concomitantly down-regulated [14].
  • This novel RNA binding site was further localized using additional deletions, cyanogen bromide cleavage of PAP cross-linked with RNA or 8-azido-ATP, and a monoclonal antibody against a COOH-terminal PAP epitope [15].
  • Epitope mapping using truncated forms of PAP and cyanogen bromide cleavage products revealed two classes of antibodies [1].

Physical interactions of PAP1

  • Both Uba2 and Ufd1 can be co-immunoprecipitated from extracts with Pap1, confirming in vitro the interaction identified by two-hybrid analysis [16].

Other interactions of PAP1

  • In addition, sequence analysis revealed three recently functionally characterized genes (MET14, VPS/SPO15, PAP1), which could be joined to the earlier published CEN11 region [17].
  • Specific polyadenylation of a precleaved GAL7 RNA requires CF I, PF I, and a crude fraction containing PAP activity [18].
  • In S. cerevisiae, the poly(A)+ fraction quickly disappeared when a conditional pap1 or rna15 mutant was shifted to the nonpermissive temperature, indicating that polyadenylation is accomplished by the same machinery that polyadenylates mRNAs [19].
  • The last 115 amino acids of Uba2, which contains an 82-amino acid region not present in previously characterized E1 enzymes, is sufficient for the interaction with Pap1 [16].

Analytical, diagnostic and therapeutic context of PAP1


  1. Monoclonal antibodies to yeast poly(A) polymerase (PAP) provide evidence for association of PAP with cleavage factor I. Kessler, M.M., Zhelkovsky, A.M., Skvorak, A., Moore, C.L. Biochemistry (1995) [Pubmed]
  2. The Arabidopsis HAL2-like gene family includes a novel sodium-sensitive phosphatase. Gil-Mascarell, R., López-Coronado, J.M., Bellés, J.M., Serrano, R., Rodríguez, P.L. Plant J. (1999) [Pubmed]
  3. Bacterial expression and enzymatic activity analysis of ME1, a ribosome-inactivating protein from Mirabilis expansa. Vepachedu, R., Park, S.W., Sharma, N., Vivanco, J.M. Protein Expr. Purif. (2005) [Pubmed]
  4. A sensitive, single-tube assay to measure the enzymatic activities of influenza RNA polymerase and other poly(A) polymerases: application to kinetic and inhibitor analysis. Hooker, L., Strong, R., Adams, R., Handa, B., Merrett, J.H., Martin, J.A., Klumpp, K. Nucleic Acids Res. (2001) [Pubmed]
  5. The FIP1 gene encodes a component of a yeast pre-mRNA polyadenylation factor that directly interacts with poly(A) polymerase. Preker, P.J., Lingner, J., Minvielle-Sebastia, L., Keller, W. Cell (1995) [Pubmed]
  6. Structure of yeast poly(A) polymerase alone and in complex with 3'-dATP. Bard, J., Zhelkovsky, A.M., Helmling, S., Earnest, T.N., Moore, C.L., Bohm, A. Science (2000) [Pubmed]
  7. RNA14 and RNA15 proteins as components of a yeast pre-mRNA 3'-end processing factor. Minvielle-Sebastia, L., Preker, P.J., Keller, W. Science (1994) [Pubmed]
  8. Hrp1, a sequence-specific RNA-binding protein that shuttles between the nucleus and the cytoplasm, is required for mRNA 3'-end formation in yeast. Kessler, M.M., Henry, M.F., Shen, E., Zhao, J., Gross, S., Silver, P.A., Moore, C.L. Genes Dev. (1997) [Pubmed]
  9. Conditional defect in mRNA 3' end processing caused by a mutation in the gene for poly(A) polymerase. Patel, D., Butler, J.S. Mol. Cell. Biol. (1992) [Pubmed]
  10. The yeast HAL2 nucleotidase is an in vivo target of salt toxicity. Murguía, J.R., Bellés, J.M., Serrano, R. J. Biol. Chem. (1996) [Pubmed]
  11. Isolation, expression, and regulation of the pgr1(+) gene encoding glutathione reductase absolutely required for the growth of Schizosaccharomyces pombe. Lee, J., Dawes, I.W., Roe, J.H. J. Biol. Chem. (1997) [Pubmed]
  12. The gene encoding gamma-glutamyl transpeptidase II in the fission yeast is regulated by oxidative and metabolic stress. Kang, H.J., Kim, B.C., Park, E.H., Ahn, K., Lim, C.J. J. Biochem. Mol. Biol. (2005) [Pubmed]
  13. Processivity of the Saccharomyces cerevisiae poly(A) polymerase requires interactions at the carboxyl-terminal RNA binding domain. Zhelkovsky, A., Helmling, S., Moore, C. Mol. Cell. Biol. (1998) [Pubmed]
  14. Alteration of lithium pharmacology through manipulation of phosphoadenosine phosphate metabolism. Spiegelberg, B.D., Dela Cruz, J., Law, T.H., York, J.D. J. Biol. Chem. (2005) [Pubmed]
  15. Structure-function relationships in the Saccharomyces cerevisiae poly(A) polymerase. Identification of a novel RNA binding site and a domain that interacts with specificity factor(s). Zhelkovsky, A.M., Kessler, M.M., Moore, C.L. J. Biol. Chem. (1995) [Pubmed]
  16. The Uba2 and Ufd1 proteins of Saccharomyces cerevisiae interact with poly(A) polymerase and affect the polyadenylation activity of cell extracts. del Olmo, M., Mizrahi, N., Gross, S., Moore, C.L. Mol. Gen. Genet. (1997) [Pubmed]
  17. DNA sequencing and analysis of a 24.7 kb segment encompassing centromere CEN11 of Saccharomyces cerevisiae reveals nine previously unknown open reading frames. Düsterhöft, A., Philippsen, P. Yeast (1992) [Pubmed]
  18. Separation of factors required for cleavage and polyadenylation of yeast pre-mRNA. Chen, J., Moore, C. Mol. Cell. Biol. (1992) [Pubmed]
  19. Polyadenylation of telomerase RNA in budding yeast. Chapon, C., Cech, T.R., Zaug, A.J. RNA (1997) [Pubmed]
  20. The Schizosaccharomyces pombe pla1 gene encodes a poly(A) polymerase and can functionally replace its Saccharomyces cerevisiae homologue. Ohnacker, M., Minvielle-Sebastia, L., Keller, W. Nucleic Acids Res. (1996) [Pubmed]
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