Skip to main content
SpringerLink
Log in

Pathways of Accumulation and Repair of Deoxyuridine Residues in DNA of Higher and Lower Organisms

  • Published:
Biochemistry (Moscow) Aims and scope Submit manuscript

Abstract

Uracil DNA glycosylase hydrolyzes the N-glycosidic bond between sugar phosphate backbone and uracil residue appearing as the result of spontaneous deamination of cytosine or during wrong incorporation of dU residues during DNA synthesis. Uracil DNA glycosylases are very conservative enzymes. They have been recognized in all pro- and eukaryotic organisms and also in pox and herpes viruses. This review highlights the pathways of accumulation of uracil and its derivatives in DNA, the main physicochemical and biochemical properties of uracil DNA glycosylase, and regulation of its functioning. Special attention is paid to detailed mechanisms of recognition and removing of damaged (or wrong) base by uracil DNA glycosylase. These mechanisms have been validated by the methods of X-ray analysis and kinetic and thermodynamic approaches.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

REFERENCES

  1. Friedberg, E. C. (1985) DNA Repair, W. H. Freeman, S.-F., pp. 433-435.

  2. Friedberg, E. C., Walker, G. C., and Siede, W. (1995) DNA Repair and Mutagenesis, ASM Press, Washington DC, p. 247.

    Google Scholar 

  3. Sancar, A. (1995) J. Biol. Chem., 270, 15915-15918.

    Google Scholar 

  4. Wood, R. D. (1996) Annu. Rev. Biochem., 65, 135-167.

    Google Scholar 

  5. Krokan, H. E., Standal, R., and Sluppaugh, G. (1997) Biochem. J., 325, 1-16.

    Google Scholar 

  6. Krokan, H. E., Standal, R., Bharati, S., Otterllei, M., Haug, T., Slupphaug, G., and Skoren, F. (1997) in The Base Excision Repair of DNA Damage, Landes, Bioscience, pp. 7-30.

  7. Rupert, C. S. in Molecular Mechanisms for the Repair of DNA, Pt. A, New York-London, pp. 73-78.

  8. Pearl, L. H. (2000) Mutat. Res., 460, 165-181.

    Google Scholar 

  9. Mol, C. D., Parikh, S. S., Putnam, C. D., Lo, T. P., and Tainer, J. A. (1999) Annu. Rev. Biophys. Biomol. Struct., 28, 101-128.

    Google Scholar 

  10. He, Z., Henricksen, L. A., Wold, M. S., and Ingles, J. C. (1995) Nature, 374, 566-568.

    Google Scholar 

  11. Shapiro, R., and Klein, R. S. (1966) Biochemistry, 5, 2358-2363.

    Google Scholar 

  12. Shapiro, R. (1981) Chromosome Damage and Repair (E. Seeberg and K. Kleppe, eds.) Plenum, N. Y., pp. 3-10.

    Google Scholar 

  13. Lindahl, T., and Vyberg, B. (1974) Biochemistry, 13, 340-3409.

    Google Scholar 

  14. Beletskii, A., and Bhagwat, A. S. (1996) Proc. Natl. Acad. Sci. USA, 93, 13919-13924.

    Google Scholar 

  15. Frederico, L. A., Kunkel, T. A., and Shaw, B. R. (1990) Biochemistry, 29, 2532-2537.

    Google Scholar 

  16. Shuster, H. (1960) Biochem. Biophys. Res. Commun., 2, 320-329.

    Google Scholar 

  17. Hayatsu, H. (1976) Progr. Nucleic Acids Res., 16, 75-88.

    Google Scholar 

  18. Lindahl, T. (1979) Progr. Nucleic Acids Res. Mol. Biol., 22, 135-145.

    Google Scholar 

  19. Shapiro, R., Dubelman, S., Feinberg, A. M., Grain, P. F., and Closkey, J. A. M. (1977) J. Am. Chem. Soc., 99, 302-311.

    Google Scholar 

  20. Ullman, J. S., and McCarthy, B. J. (1973) Biochim. Biophys. Acta, 294, 396-404.

    Google Scholar 

  21. Lion, M. B. (1968) Biochim. Biophys. Acta, 155, 505-512.

    Google Scholar 

  22. Tate, P. H., and Bird, A. P. (1993) Curr. Opin. Genet. Dev., 3, 226-231.

    Google Scholar 

  23. Shen, J.-C., Rideout, W. M., and Jones, P. A. (1992) Cell, 71, 1073-1080.

    Google Scholar 

  24. Wyszynski, M., Gabbara, S., and Bhagwat, A. S. (1994) Proc. Natl. Acad. Sci. USA, 91, 1574-1578.

    Google Scholar 

  25. Bandaru, B., Gopal, J., and Bhagwat, A. S. (1996) J. Biol. Chem., 271, 7851-7859.

    Google Scholar 

  26. Geider, K. (1972) Eur. J. Biochem., 27, 554-560.

    Google Scholar 

  27. Tye, B.-K., Chien, J., Lehman, J. R., Duncan, B. K., and Warner, H. R. (1978) Proc. Natl. Acad. Sci. USA., 75, 233-243.

    Google Scholar 

  28. Tamnoi, F., and Okazaki, T. (1978) Proc. Natl. Acad. Sci. USA, 75, 2195-2203.

    Google Scholar 

  29. Warner, H. R., and Duncan, B. K (1978) Nature, 272, 32-35.

    Google Scholar 

  30. Kornberg, A. (1980) DNA Replication, Freeman Co., S.-F.

    Google Scholar 

  31. Goulian, M., Bleile, B., and Tseng, B. Y. (1980) Proc. Natl. Acad. Sci. USA, 77, 1956-1965.

    Google Scholar 

  32. Goulian, M., Bleile, B., and Tseng, B. (1980) J. Biol. Chem., 255, 10630-10639.

    Google Scholar 

  33. Myers, C. E., Young, R. C., and Chabener, A. (1975) J. Clin. Invest., 56, 1231-1238.

    Google Scholar 

  34. Takahashi, J., and Marmur, J. (1963) Nature, 197, 794-800.

    Google Scholar 

  35. Tomita, F., and Takahashi, J. (1969) J. Virol., 15, 1073-1080.

    Google Scholar 

  36. Lindahl, T. (1974) Proc. Natl. Acad. Sci. USA, 71, 3649-3654.

    Google Scholar 

  37. Cone, R., Duncan, J., Hamilton, J., and Friedberg, E. C. (1977) Biochemistry, 16, 3194-3201.

    Google Scholar 

  38. Warner, H. (1983) J. Biol. Chem., 258, 1603-1609.

    Google Scholar 

  39. Guyer, R. B., Nonnemarker, J. M., and Deering, R. A. (1986) Biochim. Biophys. Acta, 868, 262-264.

    Google Scholar 

  40. Crosby, B. L., Prakash, H. D., Hinkle, D., and Hinkle, D. C. (1981) Nucleic Acids Res., 9, 5797-5809.

    Google Scholar 

  41. Caradonna, S., Worrad, D., and Lirette, R. (1987) J. Virol., 61, 3040-3047.

    Google Scholar 

  42. Focher, F., Verri, A., and Spadari, S. (1993) Biochem. J., 292, 883-889.

    Google Scholar 

  43. Koilis, A., Cowan, D. A., Pearl, L. H., and Savva, R. (1996) FEMS Microbiol. Lett., 143, 267-271.

    Google Scholar 

  44. Sandigursky, M., and Franklin, W. A. (1999) Curr. Biol., 9, 531-534.

    Google Scholar 

  45. Domena, J. D., Timmer, R. T., Dicharry, S. A., and Mosbaugh, D. W. (1988) Biochemistry, 27, 6742-6751.

    Google Scholar 

  46. Borle, M.-T., Campagnary, F., and Creissen, D. M. (1982) J. Biol. Chem., 257, 1208-1216.

    Google Scholar 

  47. Borle, M.-T., Clerici, L., and Campagnary, F. (1979) J. Biol. Chem., 254, 6387-6395.

    Google Scholar 

  48. Kuhnlein, U., Lee, B., and Linn, S. (1978) Nucleic Acids Res., 5, 117-126.

    Google Scholar 

  49. Myrnes, B., and Wittwer, C. U. (1988) Eur. J. Biochem., 173, 383-387.

    Google Scholar 

  50. Krokan, H., and Wittwer, C. U. (1981) Nucleic Acids Res., 9, 2599-2613.

    Google Scholar 

  51. Sirover, M. A. (1979) Cancer Res., 39, 2090-2095.

    Google Scholar 

  52. Andeson, C. T., and Friedberg, E. C. (1980) Nucleic Acids Res., 8, 875-888.

    Google Scholar 

  53. Caradonna, S. J., and Cheng, Y.-C. (1980) J. Biol. Chem., 255, 2293-2300.

    Google Scholar 

  54. Kuzmin, I. A., Golubovskaya, V. M., and Aprelikova, O. M. (1988) Biokhimiya, 53, 1002-1008.

    Google Scholar 

  55. Savva, R., McAuley-Hecht, K., Brown, T., and Pearl, L. (1995) Nature, 373, 487-493.

    Google Scholar 

  56. Mol, C. D., Arvai, A. S., Slupphaug, G., Kalvi, B., Alseth, H., Krokan, H. E., and Tainer, J. A. (1995) Cell, 80, 869-878.

    Google Scholar 

  57. Svendsen, P. C., Yee, H. A., Winkfein, R. J., and van de Sande, J. H. (1997) Gene, 189, 175-181.

    Google Scholar 

  58. Worrad, D. M., and Caradonna, S. (1988) J. Virol., 12, 4774-4777.

    Google Scholar 

  59. Percival, K. J., Klein, M. B., and Burgers, P. M. J. (1989) J. Biol. Chem., 264, 2593-2598.

    Google Scholar 

  60. Wittwer, C. U., Bauw, G., and Krokan, H. E. (1989) Biochemistry, 28, 780-784.

    Google Scholar 

  61. Haug, T., Skorpen, F., Kvaloy, K., Eftedal, J., Lund, H., and Krokan, H. E. (1996) Genomics, 36, 408-416.

    Google Scholar 

  62. Nilsen, H., Otterlei, M., Haug, T., Solum, K., Nagelhus, T. A., Skorpen, F., and Krokan, H. E. (1997) Nucleic Acids Res., 25, 750-755.

    Google Scholar 

  63. Olsen, L. C., Aasland, R., Wittwer, C. U., Krokan, H. E., and Helland, D. E. (1989) EMBO J., 8, 3121-3125.

    Google Scholar 

  64. Haug, T., Skorpen, F., and Lund, H. (1994) FEBS Lett., 353, 180-184.

    Google Scholar 

  65. Otterlei, M., Nagelhus, T. A., Slupphaug, G., Lindmo, T., and Krokan, H. E. (1998) Nucleic Acids Res., 26, 4611-4617.

    Google Scholar 

  66. Moon, Y. W., Park, W. S., Vortemeyer, A. O., Weil, R. J., Lee, Y. S., Winters, T. A., Zhuang, Z., and Fuller, B. G. (1998) Mutat. Res., 421, 191-196.

    Google Scholar 

  67. Drohat, A. C., Xiao, G., Tordova, M., Jagadeesh, J., Pankiewicz, K. W., Watanabe, K. A., Gilliland, G. L., and Stivers, J. T. (1999) Biochemistry, 38, 11876-11886.

    Google Scholar 

  68. Xiao, G., Tordova, M., Jagadeesh, J., Drohat, A. C., Stivers, J. T., and Gilliland, G. L. (1999) Proteins, 35, 13-24.

    Google Scholar 

  69. Sluppaugh, G., Markussen, F._H., Olsen, L. C., Aasland, R., Aarsaether, N., Barke, O., Krokan, E., and Helland, D. E. (1993) Nucleic Acids Res., 21, 2579-2584.

    Google Scholar 

  70. Domena, J. D., and Mosbaugh, D. W. (1985) Biochemistry, 24, 7320-7328.

    Google Scholar 

  71. Mosbaugh, D. W. (1988) Rev. Biochem. Toxicol., 9, 69-130.

    Google Scholar 

  72. Nilsen, H., Otterlei, M., Haug, T., Solum, K., Nagelhus, T. A., Skorpen, F., and Krokan, H. E. (1997) Nucleic Acids Res., 25, 750-755.

    Google Scholar 

  73. Otterlei, M., Nagelhus, T. A., Slupphaug, G., Lindmo, T., and Krokan, H. E. (1998) Nucleic Acids Res., 26, 4611-4617.

    Google Scholar 

  74. Muller-Weeks, S., Mastran, B., and Caradonna, S. (1998) J. Biol. Chem., 273, 21909-21917.

    Google Scholar 

  75. Seal, G., and Sirover, M. A. (1986) Proc. Natl. Acad. Sci. USA, 83, 7608-7612.

    Google Scholar 

  76. Meyer-Siegler, K., Mauro, D. J., Seal, G., Wuzzer, J., de Riel, J. K., and Sirover, M. A. (1991) Proc. Natl. Acad. Sci. USA, 88, 8460-8464.

    Google Scholar 

  77. Vollberg, T. M., Lee, K. A., and Sirover, M. A. (1984) Cancer Res., 44, 2377-2381.

    Google Scholar 

  78. Cool, B. L., and Sirover, M. A. (1989) Cancer Res., 49, 3029-3036.

    Google Scholar 

  79. Gupta, P. K., and Sirover, M. A. (1980) Mutat. Res., 42, 470-475.

    Google Scholar 

  80. Nagelhus, T. A., Slupphaug, G., Lindmo, T., and Krokan, H. E. (1995) Exp. Cell Res., 220, 292-297.

    Google Scholar 

  81. Slupphaug, G., Olsen, L. C., and Aasland, R. (1991) Nucleic Acids Res., 19, 5131-5137.

    Google Scholar 

  82. Haug, T., Skorpen, F., Aas, Pa., Malm, V., Skjelberd, C., and Krokan, H. E. (1998) Nucleic Acids Res., 26, 1449-1457.

    Google Scholar 

  83. Yamamoto, Y., and Fujiwara, Y. (1987) J. Virol., 42, 470-475.

    Google Scholar 

  84. Myrnes, B., Giercksky, K.-E., and Krokan, H. (1983) Carcinogenesis, 4, 1565-1568.

    Google Scholar 

  85. Krokan, H., Haugen, A., and Myrnes, B. (1983) Carcinogenesis, 4, 1559-1564.

    Google Scholar 

  86. Weng, Y., and Sirover, M. A. (1993) Mutat. Res., 293, 133-141.

    Google Scholar 

  87. Dudley, B., Hammond, A., and Deutsch, W. A. (1992) J. Biol. Chem., 267, 11964-11967.

    Google Scholar 

  88. Tomilin, N. V., and Aprelikova, O. N. (1989) Int. Rev. Cytol., 114, 125-179.

    Google Scholar 

  89. Varshney, U., and van Sande, J. H. (1991) Biochemistry, 30, 4055-4061.

    Google Scholar 

  90. Vinogradova, N. L., Bulychev, N. V., Maksakova, G. A., Johnson, F., and Nevinsky, G. A. (1998) Mol. Biol. (Moscow), 32, 489-499.

    Google Scholar 

  91. Mauro, D. J., Riel, J. K., Tallard, R. J., and Sirover, M. A. (1993) Mol. Pharmacol., 43, 854-857.

    Google Scholar 

  92. Hatahet, Z., Kow, Y. W., Purmal, A. P., Cunningham, R. P., and Wallase, S. S. (1994) J. Biol. Chem., 269, 18814-18820.

    Google Scholar 

  93. Dizdaroglu, M., Karakaya, A., and Jaruga, P. (1996) Nucleic Acids Res., 24, 418-422.

    Google Scholar 

  94. Zastawny, T. H., Doetsch, P. W., and Dizdaroglu, M. (1995) FEBS Lett., 364, 255-258.

    Google Scholar 

  95. Saparbaev, M., and Laval, J. (1998) Proc. Natl. Acad. Sci. USA, 95, 8508-8513.

    Google Scholar 

  96. Slupphaug, G., Eftedal, I., and Kavli, B. (1995) Biochemistry, 34, 128-138.

    Google Scholar 

  97. Verri, A., Mazzarello, P., Spadari, S., and Focher, F. (1992) Biochem. J., 287, 1007-1010.

    Google Scholar 

  98. Nilsen, H., Yazadankhah, S. P., Eftedal, J., and Krokan, H. E. (1995) FEBS Lett., 362, 205-209.

    Google Scholar 

  99. Eftedal, J., Guddal, P. H., Sluppaugh, G., Volden, G., and Krokan, H. E. (1993) Nucleic Acids Res., 21, 2095-2101.

    Google Scholar 

  100. Duncan, B. K. (1981) The Enzyme, 3rd Ed., Academic Press, XIV, Pt. A, p. 575.

  101. Parikh, S. S., Mol, C. D., Slupphaug, G., Krokan, H. E., and Tainer, J. A. (1998) EMBO J., 17, 5214-5226.

    Google Scholar 

  102. Kumar, N. V., and Varshney, U. (1994) Nucleic Acids Res., 22, 3737-3744.

    Google Scholar 

  103. Kumar, N. V., and Varshney, U. (1997) Nucleic Acids Res., 25, 2336-2343.

    Google Scholar 

  104. Nevinsky, G. A. (1995) Mol. Biol. (Moscow), 29, 16-37.

    Google Scholar 

  105. Bugreev, D. V., and Nevinsky, G. A. (1999) Biochemistry (Moscow), 64, 291-305.

    Google Scholar 

  106. Vasilenko, N. L., Bulychev, N. V., Horn, V. V., Levina, A. S., and Nevinsky, G. A. (1994) Mol. Biol. (Moscow), 28, 679-690.

    Google Scholar 

  107. Vinogradova, N. L., Yamkovoi, V. I., Tsvetkov, I. V., and Nevinsky, G. A. (1996) Mol. Biol. (Moscow), 30, 209-219.

    Google Scholar 

  108. Kubareva, E. A., Volkov, E. M., Vinogradova, N. L., Kanevsky, I. A., Oretskaya, T. S., Kuznetsova, S. A., Brevnov, M. G., Gromova, E. S., Nevinsky, G. A., and Shabarova, Z. A. (1995) Gene, 157, 167-171.

    Google Scholar 

  109. Kubareva, E. A., Vasilenko, N. L., Vorobjeva, O. V., Volkov, E. M., Oretskaya, T. S., Korshunova, G. A., and Nevinsky, G. A. (1998) Biochem. Mol. Biol. Int., 46, 597-606.

    Google Scholar 

  110. Nevinsky, G. A., Vinogradova, N. L., Bugreev, D. V., Ishchenko, A. A., Vasyutina, E. L., Ul'yanova, E. P., Zakharova, O. D., and Kolocheva, T. I. (1998) Proc. 1st Int. Conf. on Bioinformatics of Genome Regulation and Structure, 2, 384-387.

    Google Scholar 

  111. Putcham, C. D., Shroyer, M. J., Lundquist, A. J., Mol, C. D., Arvai, A. S., Mosbaugh, D. W., and Tainer, J. A. (1999) J. Mol. Biol., 287, 331-346.

    Google Scholar 

  112. Wang, Z., and Mosbaugh, D. W. (1989) J. Biol. Chem., 264, 1163-1171.

    Google Scholar 

  113. Karran, P., Cone, R., and Friedberg, E. C. (1981) Biochemistry, 20, 6092-6096.

    Google Scholar 

  114. Balasubramanian, S., Beger, R. D., and Benett, S. E. (1995) J. Biol. Chem., 270, 296-303.

    Google Scholar 

  115. Mol, C. D., Arvai, A. S., Sanderson, R. J., Slupphaug, G., Kalvi, B., Krokan, H. E., Mosbaugh, D. W., and Tainer, J. A. (1995) Cell, 82, 701-708.

    Google Scholar 

  116. Higley, M., and Lloyd, R. S. (1993) Mutat. Res., 294, 109-116.

    Google Scholar 

  117. Benett, S. E., Sanderson, R. J., and Mosbaugh, D. W. (1995) Biochemistry, 34, 6109-6119.

    Google Scholar 

  118. Stivers, J. T., Pankiewicz, K. W., and Watanabe, K. A. (1999) Biochemistry, 38, 952-963.

    Google Scholar 

  119. Klimasauskas, S., Kumar, S., Roberts, R. J., and Cheng, X. (1994) Cell, 76, 357-369.

    Google Scholar 

  120. Zimmerman, S. B., and Pheiffer, B. M. (1986) Proc. Natl. Acad. Sci. USA, 78, 78-82.

    Google Scholar 

  121. Viswamitra, M. A., and Seshadri, T. P. (1975) Nature, 258, 542-544.

    Google Scholar 

  122. Luo, N., Mehler, E., and Osman, R. (1999) Biochemistry, 38, 9209-9220.

    Google Scholar 

  123. Fersht A. (1980) Structure and Mechanism of Enzyme Action [Russian translation], Mir, Moscow.

    Google Scholar 

  124. Gallinari, P., and Jirincy, J. (1996) Nature, 383, 735-738.

    Google Scholar 

  125. Kavli, B., Slupphaug, G., Mol, C. D., Arvai, A. S., Petersen, S. B., Tainer, J. A., and Krokan, H. E. (1996) EMBO J., 15, 3442-3447.

    Google Scholar 

  126. Slupphaug, G., Mol, C. D., Kavli, B., Arvai, A. S., Krokan, H. E., and Tainer, J. A. (1996) Nature, 384, 87-92.

    Google Scholar 

  127. Shroyer, M. J. N., Benett, S. E., Putham, C. D., Tainer, J. A., and Mosbaugh, D. W. (1999) Biochemistry, 38, 4834-4845.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Siberian Division of the Russian Academy of Sciences, ul. Lavrentieva 8, Novosibirsk Institute of Bioorganic Chemistry, Novosibirsk, 630090, Russia

    N. L. Vasilenko & G. A. Nevinsky

Authors
  1. N. L. Vasilenko
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. G. A. Nevinsky
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Vasilenko, N.L., Nevinsky, G.A. Pathways of Accumulation and Repair of Deoxyuridine Residues in DNA of Higher and Lower Organisms. Biochemistry (Moscow) 68, 135–151 (2003). https://doi.org/10.1023/A:1022637026155

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1023/A:1022637026155

Search

Navigation