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The DNA-polymerase-X family: controllers of DNA quality?

Abstract

Synthesis of the genetic material of the cell is achieved by a large number of DNA polymerases. Besides replicating the genome, they are involved in DNA-repair processes. Recent studies have indicated that certain DNA-polymerase-X-family members can synthesize unusual DNA structures, and we propose that these DNA structures might serve as 'flag wavers' for the induction of DNA-repair and/or DNA-damage-checkpoint pathways.

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Figure 1: Domain structure of the DNA-polymerase-X-family members.
Figure 2: Unusual DNA structures created by members of the DNA-polymerase-X family.
Figure 3: A 'flag waving' model for Pol λ and Pol μ?

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References

  1. Kolodner, R. D., Putnam, C. D. & Myung, K. Maintenance of genome stability in Saccharomyces cerevisiae. Science 297, 552–557 (2002).

    Article  CAS  Google Scholar 

  2. Motoyama, N. & Naka, K. DNA damage tumor suppressor genes and genomic instability. Curr. Opin. Genet. Dev. 14, 11–16 (2004).

    Article  CAS  Google Scholar 

  3. Hoeijmakers, J. H. Genome maintenance mechanisms for preventing cancer. Nature 411, 366–374 (2001).

    CAS  Google Scholar 

  4. Friedberg, E. C., McDaniel, L. D. & Schultz, R. A. The role of endogenous and exogenous DNA damage and mutagenesis. Curr. Opin. Genet. Dev. 14, 5–10 (2004).

    Article  CAS  Google Scholar 

  5. Friedberg, E. C., Wagner, R. & Radman, M. Specialized DNA polymerases, cellular survival, and the genesis of mutations. Science 296, 1627–1630 (2002).

    Article  CAS  Google Scholar 

  6. Hübscher, U., Maga, G. & Spadari, S. Eukaryotic DNA polymerases. Annu. Rev. Biochem. 71, 133–163 (2002).

    Article  Google Scholar 

  7. Pham, P., Rangarajan, S., Woodgate, R. & Goodman, M. F. Roles of DNA polymerases V and II in SOS-induced error-prone and error-free repair in Escherichia coli. Proc. Natl Acad. Sci. USA 98, 8350–8354 (2001).

    Article  CAS  Google Scholar 

  8. Wang, Z. Translesion synthesis by the UmuC family of DNA polymerases. Mutat. Res. 486, 59–70 (2001).

    Article  CAS  Google Scholar 

  9. Lukas, J., Lukas, C. & Bartek, J. Mammalian cell cycle checkpoints: signalling pathways and their organization in space and time. DNA Repair (Amst.) 3, 997–1007 (2004).

    Article  CAS  Google Scholar 

  10. Sancar, A., Lindsey-Boltz, L. A., Unsal-Kaccmaz, K. & Linn, S. Molecular mechanisms of mammalian DNA repair and the DNA damage checkpoints. Annu. Rev. Biochem. 73, 39–85 (2004).

    Article  CAS  Google Scholar 

  11. Lecointe, F., Shevelev, I. V., Bailone, A., Sommer, S. & Hübscher, U. Involvement of an X family DNA polymerase in double strand break repair in the radioresistant organism Dienococcus radiodurans. Mol. Microbiol. 53, 1721–1730 (2004).

    Article  CAS  Google Scholar 

  12. Ruiz, J. F. et al. Lack of sugar discrimination by human Pol μ requires a single glycine residue. Nucleic Acids Res. 31, 4441–4449 (2003).

    Article  CAS  Google Scholar 

  13. Blasius, M. DNA polymerases from the X Family: Expression in E. coli and Isolation of Two Putative Archaeal DNA Polymerases. Diploma Thesis, Potsdam Univ. (2004).

    Google Scholar 

  14. Oliveros, M. et al. Characterization of an African swine fever virus 20-kDa DNA polymerase involved in DNA repair. J. Biol. Chem. 272, 30899–30910 (1997).

    Article  CAS  Google Scholar 

  15. Bork, P. et al. A superfamily of conserved domains in DNA damage-responsive cell cycle checkpoint proteins. FASEB J. 11, 68–76 (1997).

    Article  CAS  Google Scholar 

  16. Manke, I. A., Lowery, D. M., Nguen, A. & Yaffe, M. B. BRCT repeats as phosphopeptide-binding modules involved in protein targeting. Science 302, 636–639 (2003).

    Article  CAS  Google Scholar 

  17. Rodriguez, M., Yu, X., Chen, J. & Songyang, Z. Phosphopeptide binding specificities of BRCA1 COOH-terminal (BRCT) domains. J. Biol. Chem. 278, 52914–52918 (2003).

    Article  CAS  Google Scholar 

  18. Lee, J. W. et al. Implication of DNA polymeraseλ in alignment-based gap filling for nonhomologous DNA end joining in human nuclear extracts. J. Biol. Chem. 279, 805–811 (2004).

    Article  CAS  Google Scholar 

  19. Beard, W. A. & Wilson, S. H. Structural design of a eukaryotic DNA repair polymerase: DNA polymerase β. Mutat. Res. 460, 231–244 (2000).

    Article  CAS  Google Scholar 

  20. Maciejewski, M. W. et al. Solution structure of a viral DNA repair polymerase. Nature Struct. Biol. 8, 936–941 (2001).

    Article  CAS  Google Scholar 

  21. Showalter, A. K., Byeon, I. J., Su, M. I. & Tsai, M. D. Solution structure of a viral DNA polymerase X and evidence for a mutagenic function. Nature Struct. Biol. 8, 942–946 (2001).

    Article  CAS  Google Scholar 

  22. Delarue, M. et al. Crystal structures of a template-independent DNA polymerase: murine terminal deoxynucleotidyltransferase. EMBO J. 21, 427–439 (2002).

    Article  CAS  Google Scholar 

  23. Garcia-Diaz, M. et al. A structural solution for the DNA polymerase λ-dependent repair of DNA gaps with minimal homology. Mol. Cell 13, 561–572 (2004).

    Article  CAS  Google Scholar 

  24. Pelletier, H., Sawaya, M. R., Kumar, A., Wilson, S. H. & Kraut, J. Structures of ternary complexes of rat DNA polymerase β, a DNA template-primer, and ddCTP. Science 264, 1891–1903 (1994).

    Article  CAS  Google Scholar 

  25. Sawaya, M. R., Pelletier, H., Kumar, A., Wilson, S. H. & Kraut, J. Crystal structure of rat DNA polymerase β: evidence for a common polymerase mechanism. Science 264, 1930–1935 (1994).

    Article  CAS  Google Scholar 

  26. Ramadan, K., Shevelev, I. V., Maga, G. & Hübscher, U. DNA polymerase λ from calf thymus preferentially replicates damaged DNA. J. Biol. Chem. 277, 18454–18458 (2002).

    Article  CAS  Google Scholar 

  27. Bebenek, K., Garcia-Diaz, M., Blanco, L. & Kunkel, T. A. The frameshift infidelity of human DNA polymeraseλ. Implications for function. J. Biol. Chem. 278, 34685–34690 (2003).

    Article  CAS  Google Scholar 

  28. Garcia-Diaz, M., Bebenek, K., Kunkel, T. A. & Blanco, L. Identification of an intrinsic 5′-deoxyribose-5-phosphate lyase activity in human DNA polymerase λ: a possible role in base excision repair. J. Biol. Chem. 276, 34659–34663 (2001).

    Article  CAS  Google Scholar 

  29. Mahajan, K. N., Nick McElhinny, S. A., Mitchell, B. S. & Ramsden, D. A. Association of DNA polymerase μ (pol μ) with Ku and ligase IV: role for pol μ in end-joining double-strand break repair. Mol. Cell. Biol. 22, 5194–5202 (2002).

    Article  CAS  Google Scholar 

  30. Idriss, H. T., Al-Assar, O. & Wilson, S. H. DNA polymerase β. Int. J. Biochem. Cell. Biol. 34, 321–324 (2002).

    Article  CAS  Google Scholar 

  31. Edwards, S. et al. Saccharomyces cerevisiae DNA polymeraseε and polymerase σ interact physically and functionally, suggesting a role for polymerase ε in sister chromatid cohesion. Mol. Cell. Biol. 23, 2733–2748 (2003).

    Article  CAS  Google Scholar 

  32. Zhang, Y. et al. Lesion bypass activities of human DNA polymerase μ. J. Biol. Chem. 277, 44582–44587 (2002).

    Article  CAS  Google Scholar 

  33. Duvauchelle, J. B., Blanco, L., Fuchs, R. P. & Cordonnier, A. M. Human DNA polymerase μ (Pol μ) exhibits an unusual replication slippage ability at AAF lesion. Nucleic Acids Res. 30, 2061–2067 (2002).

    Article  CAS  Google Scholar 

  34. Havener, J. M. et al. Translesion synthesis past platinum DNA adducts by human DNA polymerase μ. Biochemistry 42, 1777–1788 (2003).

    Article  CAS  Google Scholar 

  35. Blanca, G. et al. Human DNA polymerases λ and β show different efficiencies of translesion DNA synthesis past abasic sites and alternative mechanisms for frameshifts generation. Biochemistry 43, 11605–11615 (2004).

    Article  CAS  Google Scholar 

  36. Ramadan, K., Shevelev, I. V., Maga, G. & Hübscher, U. De novo DNA synthesis by human DNA polymerase λ, DNA polymerase μ and terminal deoxyribonucleotidyl transferase. J. Mol. Biol. 339, 395–404 (2004).

    Article  CAS  Google Scholar 

  37. Ramadan, K. et al. Human DNA polymerase λ possesses terminal deoxyribonucleotidyl transferase activity and can elongate RNA primers: implications for novel functions. J. Mol. Biol. 328, 63–72 (2003).

    Article  CAS  Google Scholar 

  38. Wilson, T. E. & Lieber, M. R. Efficient processing of DNA ends during yeast nonhomologous end joining. Evidence for a DNA polymerase β (Pol4)-dependent pathway. J. Biol. Chem. 274, 23599–23609 (1999).

    Article  CAS  Google Scholar 

  39. Ruiz, J. F. et al. DNA polymerase μ, a candidate hypermutase? Philos. Trans. R. Soc. Lond. B. 356, 99–109 (2001).

    Article  CAS  Google Scholar 

  40. Bertocci, B., De Smet, A., Berek, C., Weill, J. C. & Reynaud, C. A. Immunoglobulin κ light chain gene rearrangement is impaired in mice deficient for DNA polymerase μ. Immunity 19, 203–211 (2003).

    Article  CAS  Google Scholar 

  41. Bergoglio, V., Ferrari, E., Hübscher, U., Cazaux, C. & Hoffmann, J. S. DNA polymerase β can incorporate ribonucleotides during DNA synthesis of undamaged and CPD-damaged DNA. J. Mol. Biol. 331, 1017–1023 (2003).

    Article  CAS  Google Scholar 

  42. Nick McElhinny, S. A. & Ramsden, D. A. Polymerase μ is a DNA-directed DNA/RNA polymerase. Mol. Cell. Biol. 23, 2309–2315 (2003).

    Article  CAS  Google Scholar 

  43. Boule, J. B., Rougeon, F. & Papanicolaou, C. Terminal deoxynucleotidyl transferase indiscriminately incorporates ribonucleotides and deoxyribonucleotides. J. Biol. Chem. 276, 31388–31393 (2001).

    Article  CAS  Google Scholar 

  44. Maga, G. & Hübscher, U. Proliferating cell nuclear antigen (PCNA): a dancer with many partners. J. Cell Sci. 116, 3051–3060 (2003).

    Article  CAS  Google Scholar 

  45. Yang, W. Damage repair DNA polymerases Y. Curr. Opin. Struct. Biol. 13, 23–30 (2003).

    Article  CAS  Google Scholar 

  46. Maga, G. et al. Human DNA polymerase λ functionally and physically interacts with proliferating cell nuclear antigen in normal and translesion DNA synthesis. J. Biol. Chem. 277, 48434–48440 (2002).

    Article  CAS  Google Scholar 

  47. Covo, S., Blanco, L. & Livneh, Z. Lesion bypass by human DNA polymerase μ reveals a template-dependent, sequence-independent nucleotidyl transferase activity. J. Biol. Chem. 279, 859–865 (2004).

    Article  CAS  Google Scholar 

  48. Zhang, Y., Wu, X., Yuan, F., Xie, Z. & Wang, Z. Highly frequent frameshift DNA synthesis by human DNA polymerase μ. Mol. Cell. Biol. 21, 7995–8006 (2001).

    Article  CAS  Google Scholar 

  49. Lindahl, T. & Andersson, A. Rate of chain breakage at apurinic sites in double-stranded deoxyribonucleic acid. Biochemistry 11, 3618–3623 (1972).

    Article  CAS  Google Scholar 

  50. Chaudhuri, J., Khuong, C. & Alt, F. W. Replication protein A interacts with AID to promote deamination of somatic hypermutation targets. Nature 430, 992–998 (2004).

    Article  CAS  Google Scholar 

  51. Vasquez, K. M., Christensen, J., Li, L., Finch, R. A. & Glazer, P. M. Human XPA and RPA DNA repair proteins participate in specific recognition of triplex-induced helical distortions. Proc. Natl Acad. Sci. USA 99, 5848–5853 (2002).

    Article  CAS  Google Scholar 

  52. Zou, L. & Elledge, S. J. Sensing DNA damage through ATRIP recognition of RPA–ssDNA complexes. Science 300, 1542–1548 (2003).

    Article  CAS  Google Scholar 

  53. Shechter, D., Costanzo, V. & Gautier, J. ATR and ATM regulate the timing of DNA replication origin firing. Nature Cell. Biol. 6, 648–655 (2004).

    Article  CAS  Google Scholar 

  54. Lisby, M. & Rothstein, R. DNA damage checkpoint and repair centers. Curr. Opin. Cell Biol. 16, 328–334 (2004).

    Article  CAS  Google Scholar 

  55. Dodson, G. E., Shi, Y. & Tibbetts, R. S. DNA replication defects, spontaneous DNA damage, and ATM-dependent checkpoint activation in replication protein A-deficient cells. J. Biol. Chem. 279, 34010–34014 (2004).

    Article  CAS  Google Scholar 

  56. Matsunaga, T., Park, C. H., Bessho, T., Mu, D. & Sancar, A. Replication protein A confers structure-specific endonuclease activities to the XPF-ERCC1 and XPG subunits of human DNA repair excision nuclease. J. Biol. Chem. 271, 11047–11050 (1996).

    Article  CAS  Google Scholar 

  57. Steitz, T. A. DNA polymerases: structural diversity and common mechanisms. J. Biol. Chem. 274, 17395–17398 (1999).

    Article  CAS  Google Scholar 

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Acknowledgements

The authors thank G. Villani and H.-P. Nägeli for their critical comments on the manuscript and U. Hübscher for her help with the figures. The work carried out in the authors' laboratory is supported by the Swiss National Science Foundation, by the Union Bank of Switzerland (UBS) 'im Auftrage eines Kunden', by the Wolfermann-Nägeli Stiftung and by the University of Zürich.

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Correspondence to Ulrich Hübscher.

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Related links

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DATABASES

Interpro

BRCT domain

PHP domain

pol-X family

Pol-β-like domain

OMIM

ATR

ataxia-telangiectasia

Fanconi anaemia

hereditary non-polposis colon cancer

Werner's syndrome

Swiss-Prot

ATM

BRCA1

Pol β

Pol λ

Pol μ

TdT

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Ramadan, K., Shevelev, I. & Hübscher, U. The DNA-polymerase-X family: controllers of DNA quality?. Nat Rev Mol Cell Biol 5, 1038–1043 (2004). https://doi.org/10.1038/nrm1530

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