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Low fidelity DNA synthesis by human DNA polymerase-η

Abstract

A superfamily of DNA polymerases that bypass lesions in DNA has been described1,2,3,4. Some family members are described as error-prone because mutations that inactivate the polymerase reduce damage-induced mutagenesis. In contrast, mutations in the skin cancer susceptibility gene XPV5,6, which encodes DNA polymerase (pol)-η, lead to increased ultraviolet-induced mutagenesis7,8,9,10,11. This, and the fact that pol-η primarily inserts adenines during efficient bypass of thymine–thymine dimers in vitro8,12,13, has led to the description of pol-η as error-free. However, here we show that human pol-η copies undamaged DNA with much lower fidelity than any other template-dependent DNA polymerase studied. Pol-η lacks an intrinsic proofreading exonuclease activity and, depending on the mismatch, makes one base substitution error for every 18 to 380 nucleotides synthesized. This very low fidelity indicates a relaxed requirement for correct base pairing geometry and indicates that the function of pol-η may be tightly controlled to prevent potentially mutagenic DNA synthesis.

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Figure 1: Exonuclease activities and gap-filling synthesis by pol-η.

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References

  1. Friedberg,E. C. & Gerlach,V. L. Novel DNA polymerases offer clues to the molecular basis of mutagenesis. Cell 98, 413–416 (1999).

    Article  CAS  Google Scholar 

  2. Woodgate,R. A plethora of lesion-replicating DNA polymerases. Genes Dev. 13, 2191–2195 (1999).

    Article  CAS  Google Scholar 

  3. Johnson,R. E., Washington,M. T., Prakash, S. & Prakash,L. Bridging the gap: A family of novel DNA polymerases that replicate faulty DNA. Proc. Natl Acad. Sci. USA 96, 12224 –12226 (1999).

    Article  ADS  CAS  Google Scholar 

  4. Ogi,T., Kato,T. Jr, Kato, T. & Ohmori,H. Mutation enhancement by DINB1, a mammalian homologue of the Escherichia coli mutagenesis protein DinB. Genes Cells 4, 607–618 (1999).

    Article  CAS  Google Scholar 

  5. Masutani,C. et al. The XPV (xeroderma pigmentosum variant) gene encodes human DNA polymerase η. Nature 399, 700–704 (1999).

    Article  ADS  CAS  Google Scholar 

  6. Johnson,R. E., Kondratick,C. M., Prakash, S. & Prakash,L. hRAD30 mutations in the variant form of xeroderma pigmentosum. Science 285, 263–265 ( 1999).

    Article  CAS  Google Scholar 

  7. Maher,V. M., Ouellette,L. M., Curren,R. D. & McCormick,J. J. Frequency of ultraviolet light-induced mutations is higher in xeroderma pigmentosum variant cells than in normal human cells. Nature 261 , 593–595 (1976).

    Article  ADS  CAS  Google Scholar 

  8. Myhr,B. C., Turnbull,D. & DiPaolo, J. A. Ultraviolet mutagenesis of normal and xeroderma pigmentosum variant human fibroblasts. Mutat. Res. 62, 341–353 (1979).

    Article  CAS  Google Scholar 

  9. Wang,Y. C., Maher,V. M. & McCormick, J. J. Xeroderma pigmentosum variant cells are less likely than normal cells to incorporate dAMP opposite photoproducts during replication of UV-irradiated plasmids. Proc. Natl Acad. Sci. USA 88, 7810–7814 (1991).

    Article  ADS  CAS  Google Scholar 

  10. Wang,Y. C., Maher,V. M., Mitchell,D. L. & McCormick,J. J. Evidence from mutation spectra that the UV hypermutability of xeroderma pigmentosum variant cell reflects abnormal, error-prone replication on a template containing photoproducts. Mol. Cell. Biol. 13, 4276 –4283 (1993).

    Article  CAS  Google Scholar 

  11. Waters,H. L., Seetharam,S., Seidman,M. M. & Kraemer,K. H. Ultraviolet hypermutability of a shuttle vector propagated in xeroderma pigmentosum variant cells. J. Invest. Dermatol. 101, 744–748 (1993).

    Article  CAS  Google Scholar 

  12. Masutani,C. et al. Xeroderma pigmentosum variant (XP-V) correcting protein from HeLa cells has a thymine dimer bypass DNA polymerase activity. EMBO J. 18, 3491–3501 ( 1999).

    Article  CAS  Google Scholar 

  13. Johnson,R. E., Prakash,S. & Prakash, L. Efficient bypass of a thymine-thymine dimer by yeast DNA polymerase, Pol η. Science 283, 1001–1004 (1999).

    Article  ADS  CAS  Google Scholar 

  14. Roberts,J. D., Bebenek,K. & Kunkel,T. A. The accuracy of reverse transcriptase from HIV-1. Science 242, 1171–1173 ( 1988).

    Article  ADS  CAS  Google Scholar 

  15. Osheroff,W. P. et al. The fidelity of DNA polymerase beta during distributive and processive DNA synthesis. J. Biol. Chem. 274, 3642–3650 (1999).

    Article  CAS  Google Scholar 

  16. Bebenek,K. & Kunkel,T. A. Analyzing the fidelity of DNA polymerases. Methods Enzymol. 262, 217– 232 (1995).

    Article  CAS  Google Scholar 

  17. Washington,M. T., Johnson,R. E., Prakash,S. & Prakash,L. Fidelity and processivity of Saccharomyces cereivisiae DNA polymerase η. J. Biol. Chem. 274, 36835– 36838 (1999).

    Article  CAS  Google Scholar 

  18. Perrino,F. W. & Loeb,L. A. Differential extension of 3′ mispairs is a major contribution to the high fidelity of calf thymus DNA polymerase-α. J. Biol. Chem. 264, 2898– 2905 (1989).

    CAS  PubMed  Google Scholar 

  19. Wang,H., Lawrence,C. W., Li,G. M. & Hays,J. B. Specific binding of human MSH2·MSH6 mismatch-repair protein heterodimers to DNA incorporating thymine- or uracil-containing UV light photoproducts opposite mismatched bases. J. Biol. Chem. 274, 16894– 16900 (1999).

    Article  CAS  Google Scholar 

  20. McDonald,J. P., Levine,A. S. & Woodgate, R. The Saccharomyces cerevisiae RAD30 gene, a homologue of Escherichia coli dinB and umuC, is damage inducible and functions in a novel error-free postreplication repair mechanism. Genetics 147, 1557–1568 ( 1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Kang,X. L., Yadao,F., Gietz,R. D. & Kunz,B. A. Elimination of the yeast RAD6 ubiquitin conjugase enhances base-pair transitions and G.C to T.A transversions as well as transposition of the Ty element: implications for the control of spontaneous mutation. Genetics 130 , 285–294 (1992).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Clairmont,C. A. et al. The Tyr-265-to-Cys mutator mutant of DNA polymerase beta induces a mutator phenotype in mouse LN12 cells. Proc. Natl Acad. Sci. USA 96, 9580–9585 ( 1999).

    Article  ADS  CAS  Google Scholar 

  23. Kim,S. R. et al. Multiple pathways for SOS-induced mutagenesis in Escherichia coli: an overexpression of dinB/dinP results in strongly enhancing mutagenesis in the absence of any exogenous treatment to damage DNA. Proc. Natl Acad. Sci. USA 94, 13792–13797 (1997).

    Article  ADS  CAS  Google Scholar 

  24. Kunkel,T. A. & Bebenek,K. DNA replication fidelity. Annu. Rev. Biochem. 69, (in the press).

  25. Nelson,J. R., Lawrence,C. W. & Hinkle, D. C. Thymine-thymine dimer bypass by yeast DNA polymerase ζ. Science 272, 1646–1649 (1996).

    Article  ADS  CAS  Google Scholar 

  26. Lewis,D. A. et al. Uniquely altered DNA replication fidelity conferred by an amino acid change in the nucleotide binding pocket of human immunodeficiency virus type 1 reverse transcriptase. J. Biol. Chem. 274, 32924–32930 (1999).

    Article  CAS  Google Scholar 

  27. Bebenek,K., Joyce,C. M., Fitzgerald,M. P. & Kunkel,T. A. The fidelity of DNA synthesis catalyzed by derivatives of Escherichia coli DNA polymerase I. J. Biol. Chem. 265, 13878 –13887 (1990).

    CAS  PubMed  Google Scholar 

  28. Roberts,J. D. & Kunkel,T. A. in DNA Replication in Eukaryotic Cells: Concepts, Enzymes and Systems (ed. Pamphilis, M. D.) 217 –247 (Cold Spring Harbor Laboratory Press, New York, 1996).

    Google Scholar 

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Acknowledgements

We thank W. A. Beard and Y. Pavlov for critical evaluation of the manuscript.

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Correspondence to Thomas A. Kunkel.

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Matsuda, T., Bebenek, K., Masutani, C. et al. Low fidelity DNA synthesis by human DNA polymerase-η. Nature 404, 1011–1013 (2000). https://doi.org/10.1038/35010014

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