Molecular Mechanism of Global Genome Nucleotide Excision Repair

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Abstract


Nucleotide excision repair (NER) is a multistep process that recognizes and eliminates a wide spectrum of damage causing significant distortions in the DNA structure, such as UV-induced damage and bulky chemical adducts. The consequences of defective NER are apparent in the clinical symptoms of individuals affected by three disorders associated with reduced NER capacities: xeroderma pigmentosum (XP), Cockayne syndrome (CS), and trichothiodystrophy (TTD). These disorders have in common increased sensitivity to UV irradiation, greatly elevated cancer incidence (XP), and multi-system immunological and neurological disorders. The eucaryotic NER system eliminates DNA damage by the excision of 24-32 nt single-strand oligonucleotides from a damaged strand, followed by restoration of an intact double helix by DNA repair synthesis and DNA ligation. About 30 core polypeptides are involved in the entire repair process. NER consists of two pathways distinct in initial damage sensor proteins: transcription-coupled repair (TC-NER) and global genome repair (GG-NER). The article reviews current knowledge on the molecular mechanisms underlying damage recognition and its elimination from mammalian DNA.


I. O. Petruseva

Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences

Author for correspondence.
Email: lavrik@niboch.nsc.ru

Russian Federation

A. N. Evdokimov

Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences; Altai State University, Ministry of Education and Science of the Russian Federation

Email: lavrik@niboch.nsc.ru

Russian Federation

O. I. Lavrik

Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences; Altai State University, Ministry of Education and Science of the Russian Federation; Novosibirsk State University, Ministry of Education and Science of the Russian Federation

Email: lavrik@niboch.nsc.ru

Russian Federation

  1. Gillet L.C., Schärer O.D. // Chem. Rev. 2006. V. 106. № 2. P. 253-276.
  2. Sugasawa K. // Mutat. Res. 2010. V. 685. № 1. P. 29-37.
  3. Volker M., Mone M.J., Karmakar P., van Hoffen A., Schul W., Vermeulen W., Hoeijmakers J.H., van Driel R., van Zeeland A.A., Mullenders L.H. // Mol. Cell. 2001. V. 8. № 1. P. 213-224.
  4. Lehmann A.R. // Biochimie. 2003. V. 85. P. 1101-1111.
  5. Hanawalt P.C., Spivak G. // Nat. Rev. Mol. Cell Biol. 2008. V. 9. № 11. P. 958-970.
  6. Friedberg E.C. // Nat. Rev. Cancer. 2001. V. 1. P. 22-33.
  7. Hoeijmakers J.H. // Nature. 2001. V. 411. № 6835. P. 366-374.
  8. Kuraoka I., Bender C., Romieu A., Cadet J., Wood R.D., Lindahl T. // Proc. Natl. Acad. Sci. USA. 2000. V. 97. № 8. P. 3832-3837.
  9. D'Errico M., Parlanti E., Teson M., de Jesus B.M., Degan P., Calcagnile A., Jaruga P., Bjoras M., Crescenzi M., Pedrini A.M., et al. // EMBO J. 2006. V. 25. № 18. P. 4305-4315.
  10. Johnson K.A., Fink S.P., Marnett L.J. // J. Biol. Chem. 1997. V. 272. № 17. P. 11434-11438.
  11. Luijsterburg M.S., Bornstaedt G., von Gourdin A.M., Politi A.Z., Moné M.J., Warmerdam D.O., Goedhart J., Vermeulen W., van Driel R., Höfer T. // J. Cell Biol. 2010. V. 189. № 17. P. 445-463.
  12. Svilar D., Goellner E.M., Almeida K.H., Sobol R.W. // Antioxid. Redox Signal. 2011. V. 14. № 12. P. 2491-2507.
  13. Yang W. // Cell Research. 2008. V. 18. № 1. P. 184-197.
  14. Isaacs R.J., Spielmann H.P. // DNA Repair (Amst.). 2004. V. 3. № 5. P. 455-464.
  15. Hess M.T., Schwitter U., Petretta M., Giese B., Naegeli H. // Proc. Natl. Acad. Sci. USA. 1997. V. 94. № 13. P. 6664-6669.
  16. Buterin T., Meyer C., Giese B., Naegeli H. // Chem. Biol. 2005. V. 12. № 8. P. 913-922.
  17. Sugasawa K., Ng J., Masutani C., Iwai S., van der Spek P., Eker A., Hanaoka F., Bootsma D., Hoeijmakers Jan H.J. // Mol. Cell. 1998. V. 2. № 2. P. 223-232.
  18. Rademakers S., Volker M., Hoogstraten D., Nigg A.L., Moné M.J., van Zeeland A.A., Hoeijmakers J.H., Houtsmuller A.B., Vermeulen W. // Mol. Cell Biol. 2003. V. 23. № 16. P. 5755-5767.
  19. Sugasawa K., Shimuzu Y., Shigenori I., Iwai S., Hanaoka F. // DNA Repair. 2002. V. 12. № 1. P. 95-107.
  20. Nocentini S., Coin F., Saijo M., Tanaka K., Egly J.M. // J. Biol. Chem. 1997. V. 272. № 37. P. 22991-22994.
  21. Missura M., Buterin T., Hindges R., Hübscher U., Kaspárková J., Brabec V., Naegeli H. // EMBO J. 2001. V. 20. № 13. P. 3554-3564.
  22. Hermanson-Miller I.L., Turchi J.J. // Biochemistry. 2002. V. 41. № 7. P. 2402-2408.
  23. Thoma B.S., Wakasugi M., Christensen J., Reddy M.C., Vasquez K.M. // Nucl. Acids Res. 2005. V. 33. № 9. P. 2993-3001.
  24. Sugasawa K., Okamoto T., Shimizu Y., Masutani C., Iwai S., Hanaoka F. // Genes Dev. 2001. V. 15. № 5. P. 507-521.
  25. Hoogstraten D., Bergink S., Ng J., Verbiest V.H., Luijsterburg M.S., Geverts B., Raams A., Dinant C., Hoeijmakers J.H., Vermeulen W., Houtsmuller A.B. // J. Cell Sci. 2008. V. 121. № 16. P. 2850-2859.
  26. Reardon J.T., Sancar A. // Genes Dev. 2003. V. 17. № 20. P. 2539-2551.
  27. Fitch M.E., Nakajima S., Yasui A., Ford J.M. // J. Biol. Chem. 2003. V. 278. № 47. P. 46906-46910.
  28. Sugasawa K., Okuda Y., Saijo M., Nishi R., Matsuda N., Chu G., Mori T., Iwai S., Tanaka K., Hanaoka F. // Cell. 2005. V. 121. № 3. P. 387-400.
  29. Scrima A., Konícková R., Czyzewski B.K., Kawasaki Y., Jeffrey P.D., Groisman R., Nakatani Y., Iwai S., Pavletich N.P., Thomä N.H. // Cell. 2008. V. 135. № 7. P. 1213-1223.
  30. Min J.H., Pavletich N.P. // Nature. 2007. V. 449. № 7162. P. 570-575.
  31. Murzin A.G. // EMBO J. 1993. V. 12. № 3. P. 861-867.
  32. Janićijević A., Sugasawa K., Shimizu Y., Hanaoka F., Wijgers N., Djurica M., Hoeijmakers J.H., Wyman C. // DNA Repair (Amst.). 2003. V. 2. № 3. P. 325-336.
  33. Mocquet V., Kropachev K., Kolbanovskiy M., Kolbanovskiy A., Tapias A., Cai Y., Broyde S., Geacintov N.E., Egly J.M. // EMBO J. 2007. V. 26. № 12. P. 2923-2932.
  34. Krasikova Y.S., Rechkunova N.I., Maltseva E.A., Pestryakov P.E., Petruseva I.O., Sugasawa K., Chen X., Min J.H., Lavrik O.I. // J. Biol. Chem. 2013. V. 288. № 15. P. 10936-10947.
  35. Bunick C.G., Miller M.R., Fuller B.E., Fanning E., Chazin W.J. // Biochemistry. 2006. V. 45. № 50. P. 14965-14979.
  36. Maillard O., Solyom S., Naegeli H. // PLoS Biol. 2007. V. 5. № 4. e79.
  37. Camenisch U., Trutlein D., Clement F.C., Fei J., Leitenstorfer A., Ferrando-May E., Naegeli H. // EMBO J. 2009. V. 28. № 16. P. 2387-2399.
  38. Clement F.C., Camenisch U., Fei J., Kaczmarek N., Mathieu N., Naegeli H. // Mutat. Res. 2010. V. 685. № 1. P. 21-28.
  39. Sugasawa K., Akagi J., Nishi R., Iwai S., Hanaoka F. // Mol. Cell. 2009. V. 36. № 4. P. 642-653.
  40. Araki M., Masutani C., Takemura M., Uchida A., Sugasawa K., Kondoh J., Ohkuma Y., Hanaoka F. // J. Biol. Chem. 2001. V. 276. № 22. P. 18665-18672.
  41. Nishi R., Okuda Y., Watanabe E., Mori T., Iwai S., Masutani C., Sugasawa K., Hanaoka F. // Mol. Cell Biol. 2005. V. 25. № 13. P. 5664-5674.
  42. Maltseva E.A., Rechkunova N.I., Gillet L.C., Petruseva I.O., Schärer O.D., Lavrik O.I. // Biochim. Biophys. Acta. 2007. V. 1770. № 5. P. 781-789.
  43. Maltseva E.A., Rechkunova N.I., Petruseva I.O., Vermeulen W., Schärer O.D., Lavrik O.I. // Bioorg. Chem. 2008. V. 36. № 2. P. 77-84.
  44. Evdokimov A.N., Petruseva I.O., Pestryakov P.E., Lavrik O.I. // Biochemistry (Moscow). 2011. V. 76. № 1. P. 188-200.
  45. Neher T.M., Rechkunova N.I., Lavrik O.I., Turchi J.J. // Biochemistry. 2010. V. 49. № 4. P. 669-678.
  46. Bergink S., Toussaint W., Luijsterburg M.S., Dinant C., Alekseev S., Hoeijmakers J.H., Dantuma N.P., Houtsmuller A.B., Vermeulen W. // J. Cell Biol. 2012. V. 196. № 6. P. 681-688.
  47. Schultz P., Fribourg S., Poterszman A., Mallouh V., Moras D., Egly J.M. // Cell. 2000. V. 102. № 5. 599-606.
  48. Araújo S.J., Nigg E.A., Wood R.D. // Mol. Cell Biol. 2001. V. 21. № 7. P. 2281-2291.
  49. Oksenych V., de Jesus B.B., Zhovmer A., Egly J.M., Coin F. // EMBO J. 2009. V. 28. № 19. P. 2971-2980.
  50. Egly J.M., Coin F. // DNA Repair. 2011. V. 10. № 7. P. 714-721.
  51. Compe E., Egly J.M. // Nat. Rev. Mol. Cell Biol. 2012. V. 13. № 6. P. 343-354.
  52. Fan L., Arvai A.S., Cooper P.K., Iwai S., Hanaoka F., Tainer J.A. // Mol. Cell. 2006. V. 22. № 1. P. 27-37.
  53. Hilario E., Li Y., Nobumori Y., Liu X., Fan L. // Acta Crystallogr. D Biol. Crystallogr. 2013. V. 69. № 2. P. 237-246.
  54. Wolski S.C., Kuper J., Hazelmann P., Truglio J.J., Croteau D.L., van Houten B., Kisker C. // PLoS Biol. 2008. V. 6. № 6. e149.
  55. Fan L., Fuss J.O., Cheng Q.J., Arvai A.S., Hammel M., Roberts V.A., Cooper P.K., Tainer J.A. // Cell. 2008. V. 133. № 5. P. 789-800.
  56. Kuper J., Wolski S.C., Michels G., Kisker C. // EMBO J. 2012. V. 31. № 2. P. 494-502.
  57. Naegeli H., Modrich P., Friedberg E.C. // J. Biol. Chem. 1993. V. 268. № 14. P. 10386-10392.
  58. Mathieu N., Kaczmarek N., Naegeli H. // Proc. Natl. Acad. Sci. USA. 2010. V. 107. № 41. P. 17545-17550.
  59. Mathieu N., Kaczmarek N., Rüthemann P., Luch A., Naegeli H. // Curr. Biol. 2013. V. 23. № 3. P. 204-212.
  60. Oksenych V., Coin F. // Cell Cycle. 2010. V. 9. № 1. P. 90-96.
  61. Fan L. How two helicases work together within the TFIIH complex, a perspective from structural studies of XPB and XPD helicases. Berlin-Heidelberg: Higher Education Press and Springer-Verlag, 2013. V. 1. 6 p.
  62. Fanning E., Klimovic V., Nager A.R. // Nucl. Acids Res. 2006. V. 34. № 15. P. 4126-4137.
  63. De Laat W.L., Appeldoorn E., Sugasawa K., Weterings E., Jaspers N.G.J., Hoeijmakers J. // Genes Dev. 1998. V. 12. № 16. P. 2598-2609.
  64. Kolpashchikov D.M., Khodyreva S.N., Khlimankov D.Y., Wold M.S., Favre A., Lavrik O.I. // Nucl. Acids Res. 2001. V. 29. № 2. P. 373-379.
  65. Hey T., Lipps G., Krauss G. // Biochemistry. 2001. V. 40. № 9. P. 2901-2910.
  66. Patrick S.M., Turchi J.J. // J. Biol. Chem. 2002. V. 277. № 18. P. 16096-17101.
  67. Ikegami T., Kuraoka I., Saijo M., Kodo N., Kyogoku Y., Morikawa K., Tanaka K., Shirakawa M. // Nat. Struct. Biol. 1998. V. 5. № 8. P. 701-706.
  68. Buchko G.W., Ni S., Thrall B.D., Kennedy M.A. // Nucl. Acids Res. 1998. V. 26. № 11. P. 2779-2788.
  69. Krasikova Y.S., Rechkunova N.I., Maltseva E.A., Petruseva I.O., Lavrik O.I. // Nucl. Acids Res. 2010. V. 38. № 22. P. 8083-8094.
  70. Camenisch U., Dip R., Vitanescu M., Naegeli H. // DNA Repair (Amst.). 2007. V. 6. № 12. P. 1819-1828.
  71. Missura M., Buterin T., Hindges R., Hübscher U., Kaspárková J., Brabec V., Naegeli H. // EMBO J. 2001. V. 20. № 13. P. 3554-3564.
  72. Thoma B.S., Vasquez K.M. // Mol. Carcinog. 2003. V. 38. № 1. P. 1-13.
  73. Iakoucheva L.M., Walker R.K., van Houten B., Ackerman E.J. // Biochemistry. 2002. V. 41. № 2. P. 131-143.
  74. Park C.H., Sancar A. // Proc. Natl. Acad. Sci. USA. 1994. V. 91. № 11. P. 5017-5021.
  75. Riedl T., Hanaoka F., Egly J.M. // EMBO J. 2003. V. 22. № 19. P. 5293-5303.
  76. Zotter A., Luijsterburg M.S., Warmerdam D.O., Ibrahim S., Nigg A., van Cappellen W.A., Hoeijmakers J.H., van Driel R., Vermeulen W., Houtsmuller A.B. // Mol. Cell Biol. 2006. V. 23. № 23. P. 8868-8879.
  77. Hohl M., Thorel F., Clarkson S.G., Schärer O.D. // J. Biol. Chem. 2003. V. 278. P. 19500-19508.
  78. Hohl M., Dunand-Sauthier I., Staresincic L., Jaquier- Gubler P., Thorel F., Modesti M., Clarkson S.G., Schärer O.D. // Nucl. Acids Res. 2007. V. 35. № 9. P. 3053-3063.
  79. Enzlin J.H., Schärer O.D. // EMBO J. 2002. V. 21. P. 2045-2053.
  80. Tsodikov O.V., Enzlin J.H., Schärer O.D., Ellenberger T. // Proc. Natl. Acad. Sci. USA. 2005. V. 102. № 32. P. 11236- 11241.
  81. Tsodikov O.V., Ivanov D., Orelli B., Staresincic L., Shoshani I., Oberman R., Schärer O.D., Wagner G., Ellenberger T. // EMBO J. 2007. V. 26. № 22. P. 4768-4776.
  82. Tripsianes K., Folkers G., Ab E., Das D., Odijk H., Jaspers N.G., Hoeijmakers J.H., Kaptein R., Boelens R. // Structure. 2005. V. 13. № 12. P. 1849-1858.
  83. Tripsianes K., Folkers G.E., Zheng C., Das D., Grinstead J.S., Kaptein R., Boelens R. // Nucl. Acids Res. 2007. V. 35. № 17. P. 5789-5798.
  84. Das D., Folkers G.E., van Dijk M., Jaspers N.G.J., Hoeijmakers J.H.J., Kaptein R., Boelens R. // Structure. 2012. V. 20. № 4. P. 667-675.
  85. Su Y., Orelli B., Madireddy A., Niedernhofer L.J., Schärer O.D. // J. Biol. Chem. 2012. V. 287. № 26. P. 21846-21855.

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