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Hoogsteen base pair formation promotes synthesis opposite the 1,N6-ethenodeoxyadenosine lesion by human DNA polymerase ι

Nature Structural & Molecular Biology volume 13, pages 619–625 (2006)Cite this article

Abstract

The 1,N6-ethenodeoxyadenosine (εdA) lesion is promutagenic and has been implicated in carcinogenesis. We show here that human Polι, a Y-family DNA polymerase, can promote replication through this lesion by proficiently incorporating a nucleotide opposite it. The structural basis of this action is rotation of the εdA adduct to the syn conformation in the Polι active site and presentation of its 'Hoogsteen edge' for hydrogen-bonding with incoming dTTP or dCTP. We also show that Polζ carries out the subsequent extension reaction and that efficiency of extension from εdA·T is notably higher than from εdA·C. Together, our studies reveal for the first time how the exocyclic εdA adduct is accommodated in a DNA polymerase active site, and they show that the combined action of Polι and Polζ provides for efficient and error-free synthesis through this potentially carcinogenic DNA lesion.

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Figure 1: Hoogsteen pairing of εdA with T or C.
Figure 2: Nucleotide incorporation opposite an undamaged A or an εdA by Polι and Polζ.
Figure 3: Polι–εdA·dTTP ternary complex.
Figure 4: Polι–εdA·dCTP ternary complex.
Figure 5: Primer extension by Polι and Polζ from T or C opposite the εdA adduct.

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References

  1. Bartsch, H., Barbin, A., Marion, M.J., Nair, J. & Guichard, Y. Formation, detection, and role in carcinogenesis of ethenobases in DNA. Drug Metab. Rev. 26, 349–371 (1994).

    Article  CAS  PubMed  Google Scholar 

  2. Chung, F.L., Zhang, L., Ocando, J.E. & Nath, R.G. Role of 1,N2-propanodeoxyguanosine adducts as endogenous DNA lesions in rodents and humans. IARC Sci. Publ. 150, 45–54 (1999).

    CAS  Google Scholar 

  3. Luczaj, W. & Skrzydlewska, E. DNA damage caused by lipid peroxidation products. Cell. Mol. Biol. Lett. 8, 391–413 (2003).

    CAS  PubMed  Google Scholar 

  4. Levine, R.L. et al. Translesion DNA synthesis catalyzed by human pol eta and pol kappa across 1,N6-ethenodeoxyadenosine. J. Biol. Chem. 276, 18717–18721 (2001).

    Article  CAS  PubMed  Google Scholar 

  5. Prakash, S., Johnson, R.E. & Prakash, L. Eukaryotic translesion synthesis DNA polymerases: specificity of structure and function. Annu. Rev. Biochem. 74, 317–353 (2005).

    Article  CAS  PubMed  Google Scholar 

  6. Haracska, L. et al. Targeting of human DNA polymerase iota to the replication machinery via interaction with PCNA. Proc. Natl. Acad. Sci. USA 98, 14256–14261 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Johnson, R.E., Washington, M.T., Haracska, L., Prakash, S. & Prakash, L. Eukaryotic polymerases iota and zeta act sequentially to bypass DNA lesions. Nature 406, 1015–1019 (2000).

    Article  CAS  PubMed  Google Scholar 

  8. Tissier, A., McDonald, J.P., Frank, E.G. & Woodgate, R. poliota, a remarkably error-prone human DNA polymerase. Genes Dev. 14, 1642–1650 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. Washington, M.T., Johnson, R.E., Prakash, L. & Prakash, S. Human DNA polymerase iota utilizes different nucleotide incorporation mechanisms dependent upon the template base. Mol. Cell. Biol. 24, 936–943 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Zhang, Y., Yuan, F., Wu, X. & Wang, Z. Preferential incorporation of G opposite template T by the low-fidelity human DNA polymerase iota. Mol. Cell. Biol. 20, 7099–7108 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Nair, D.T., Johnson, R.E., Prakash, S., Prakash, L. & Aggarwal, A.K. Replication by human DNA polymerase-iota occurs by Hoogsteen base-pairing. Nature 430, 377–380 (2004).

    Article  CAS  PubMed  Google Scholar 

  12. Nair, D.T., Johnson, R.E., Prakash, L., Prakash, S. & Aggarwal, A.K. Human DNA polymerase iota incorporates dCTP opposite template G via a G.C+ Hoogsteen base pair. Structure 13, 1569–1577 (2005).

    Article  CAS  PubMed  Google Scholar 

  13. Trincao, J. et al. Structure of the catalytic core of S. cerevisiae DNA polymerase eta: implications for translesion DNA synthesis. Mol. Cell 8, 417–426 (2001).

    Article  CAS  PubMed  Google Scholar 

  14. Zhou, B.L., Pata, J.D. & Steitz, T.A. Crystal structure of a DinB lesion bypass DNA polymerase catalytic fragment reveals a classic polymerase catalytic domain. Mol. Cell 8, 427–437 (2001).

    Article  CAS  PubMed  Google Scholar 

  15. Silvian, L.F., Toth, E.A., Pham, P., Goodman, M.F. & Ellenberger, T. Crystal structure of a DinB family error-prone DNA polymerase from Sulfolobus solfataricus. Nat. Struct. Biol. 8, 984–989 (2001).

    Article  CAS  PubMed  Google Scholar 

  16. Ling, H., Boudsocq, F., Woodgate, R. & Yang, W. Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication. Cell 107, 91–102 (2001).

    Article  CAS  PubMed  Google Scholar 

  17. Uljon, S.N. et al. Crystal structure of the catalytic core of human DNA polymerase kappa. Structure 12, 1395–1404 (2004).

    Article  CAS  PubMed  Google Scholar 

  18. Nair, D.T., Johnson, R.E., Prakash, L., Prakash, S. & Aggarwal, A.K. Rev1 employs a novel mechanism of DNA synthesis using a protein template. Science 309, 2219–2222 (2005).

    Article  CAS  PubMed  Google Scholar 

  19. de los Santos, C. et al. NMR studies of 1,N6-ethenodeoxyadenosine adduct (epsilon dA) opposite deoxyguanosine in a DNA duplex. Epsilon dA(syn).dG(anti) pairing at the lesion site. Biochemistry 30, 1828–1835 (1991).

    Article  CAS  PubMed  Google Scholar 

  20. Dosanjh, M.K. et al. All four known cyclic adducts formed in DNA by the vinyl chloride metabolite chloroacetaldehyde are released by a human DNA glycosylase. Proc. Natl. Acad. Sci. USA 91, 1024–1028 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Saparbaev, M., Kleibl, K. & Laval, J. Escherichia coli, Saccharomyces cerevisiae, rat and human 3-methyladenine DNA glycosylases repair 1,N6-ethenoadenine when present in DNA. Nucleic Acids Res. 23, 3750–3755 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Eichman, B.F., O'Rourke, E.J., Radicella, J.P. & Ellenberger, T. Crystal structures of 3-methyladenine DNA glycosylase MagIII and the recognition of alkylated bases. EMBO J. 22, 4898–4909 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Johnson, R.E., Prakash, L. & Prakash, S. Biochemical evidence for the requirement of Hoogsteen base pairing for replication by human DNA polymerase iota. Proc. Natl. Acad. Sci. USA 102, 10466–10471 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Nair, D.T., Johnson, R.E., Prakash, S., Prakash, L. & Aggarwal, A.K. An incoming nucleotide imposes an anti to syn conformational change on the templating purine in the human DNA polymerase-iota active site. Structure 14, 749–755 (2006).

    Article  CAS  PubMed  Google Scholar 

  25. Asensio, J.L., Lane, A.N., Dhesi, J., Bergqvist, S. & Brown, T. The contribution of cytosine protonation to the stability of parallel DNA triple helices. J. Mol. Biol. 275, 811–822 (1998).

    Article  CAS  PubMed  Google Scholar 

  26. Plum, G.E. & Breslauer, K.J. Thermodynamics of an intramolecular DNA triple helix: a calorimetric and spectroscopic study of the pH and salt dependence of thermally induced structural transitions. J. Mol. Biol. 248, 679–695 (1995).

    Article  CAS  PubMed  Google Scholar 

  27. Kang, C.H. et al. Crystal structure of intercalated four-stranded d(C3T) at 1.4 A resolution. Proc. Natl. Acad. Sci. USA 91, 11636–11640 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Betts, L., Josey, J.A., Veal, J.M. & Jordan, S.R. A nucleic acid triple helix formed by a peptide nucleic acid-DNA complex. Science 270, 1838–1841 (1995).

    Article  CAS  PubMed  Google Scholar 

  29. Nunn, C.M., Trent, J.O. & Neidle, S. A model for the [C+-GxC]n triple helix derived from observation of the C+-GxC base triplet in a crystal structure. FEBS Lett. 416, 86–89 (1997).

    Article  CAS  PubMed  Google Scholar 

  30. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997).

    Article  CAS  PubMed  Google Scholar 

  31. Navaza, J. AMoRe: an automated package for molecular replacement. Acta Crystallogr. 50, 157–163 (1994).

    Article  Google Scholar 

  32. Brunger, A.T. et al. Crystallography & NMR system: a software suite for macromolecular structure determination. Acta Crystallogr. D Biol.Crystallogr. 54, 905 (1998).

    Article  CAS  PubMed  Google Scholar 

  33. Jones, A.T., Zou, J.Y., Cowan, S.W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991).

    Article  PubMed  Google Scholar 

  34. Murshudov, G.N., Vagin, A.A. & Dodson, E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53, 240–255 (1997).

    Article  CAS  PubMed  Google Scholar 

  35. Winn, M.D., Murshudov, G.N. & Papiz, M.Z. Macromolecular TLS refinement in REFMAC at moderate resolutions. Methods Enzymol. 374, 300–321 (2003).

    Article  CAS  PubMed  Google Scholar 

  36. Laskowski, R.A., MacArthur, M.W., Moss, D.S. & Thornton, J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. A 47, 110–119 (1993).

    Google Scholar 

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Acknowledgements

We thank the staff at the Advanced Photon Source (beamline 19ID) and Brookhaven National Laboratory (beamline X29) for facilitating X-ray data collection. We thank S. Townson and S. Lone for help with data collection and DNA purification. This work was supported by grant CA115856 from the US National Institutes of Health (S.P. and A.K.A.).

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Author notes

  1. Deepak T Nair and Robert E Johnson: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Molecular Physiology and Biophysics, Mount Sinai School of Medicine, Box 1677, 1425 Madison Avenue, New York, 10029, New York, USA

    Deepak T Nair & Aneel K Aggarwal

  2. Sealy Center for Molecular Science, University of Texas Medical Branch, 6.014 Medical Research Building, 11th & Mechanic Streets, Galveston, 77755, Texas, USA

    Robert E Johnson, Louise Prakash & Satya Prakash

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  1. Deepak T Nair
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Contributions

D.T.N. performed the crystallographic experiments, R.E.J. conducted the kinetic experiments and all of the authors contributed to the concepts and to the writing of the paper.

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Correspondence to Satya Prakash or Aneel K Aggarwal.

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Nair, D., Johnson, R., Prakash, L. et al. Hoogsteen base pair formation promotes synthesis opposite the 1,N6-ethenodeoxyadenosine lesion by human DNA polymerase ι. Nat Struct Mol Biol 13, 619–625 (2006). https://doi.org/10.1038/nsmb1118

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