Journal of Microbiology and Biotechnology

The Korean Society for Microbiology and Biotechnology (한국미생물·생명공학회)
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Sensing Domain and Extension Rate of a Family B-Type DNA Polymerase Determine the Stalling at a Deaminated Base

  • Kim, Yun-Jae (Korea Ocean Research and Development Institute) ;
  • Cha, Sun-Shin (Korea Ocean Research and Development Institute) ;
  • Lee, Hyun-Sook (Korea Ocean Research and Development Institute) ;
  • Ryu, Yong-Gu (Korea Ocean Research and Development Institute) ;
  • Bae, Seung-Seob (Korea Ocean Research and Development Institute) ;
  • Cho, Yo-Na (Korea Ocean Research and Development Institute) ;
  • Cho, Hyun-Soo (Department of Biology, College of Science, Yonsei University) ;
  • Kim, Sang-Jin (Korea Ocean Research and Development Institute) ;
  • Kwon, Suk-Tae (Department of Genetic Engineering, Sungkyunkwan University) ;
  • Lee, Jung-Hyun (Korea Ocean Research and Development Institute) ;
  • Kang, Sung-Gyun (Korea Ocean Research and Development Institute)
  • Published : 2008.08.31
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Abstract

The uracil-sensing domain in archaeal family B-type DNA polymerases recognizes pro-mutagenic uracils in the DNA template, leading to stalling of DNA polymerases. Here, we describe our new findings regarding the molecular, mechanism underpinning the stalling of polymerases. We observed that two successive deaminated bases were required to stall TNA1 and KOD1 DNA polymerases, whereas a single deaminated base was enough for stalling Pfu DNA polymerase, in spite of the virtually identical uracil-sensing domains. TNA1 and KOD1 DNA polymerases have a much higher extension rate than Pfu DNA polymerase; decreasing the extension rate resulted in stalling by TNA1 and KOD1 DNA polymerases at a single deaminated base. These results strongly suggest that these polymerases require two factors to stop DNA polymerization at a single deaminated base: the presence of the uracil-sensing domain and a relatively slow extension rate.

Keywords

References

  1. Bae, S. S., Y. J. Kim, S. H. Yang, J. K. Lim, J. H. Jeon, H. S. Lee, S. G. Kang, S.-J. Kim, and J.-H. Lee. 2006. Thermococcus onnurineus sp. nov., a hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent area at the PACMANUS field. J. Microbiol. Biotechnol. 16: 1826-1831
  2. Bradford, M. M. 1976. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72: 248-254 https://doi.org/10.1016/0003-2697(76)90527-3
  3. Cann, I. K. and Y. Ishino. 1999. Archaeal DNA replication: Identifying the pieces to solve a puzzle. Genetics 152: 1249-1267
  4. Cho, Y., H. S. Lee, Y. J. Kim, S. G. Kang, S.-J. Kim, and J.-H. Lee. 2007. Characterization of a dUTPase from the hyperthermophilic archaeon Thermococcus onnurineus NA1 and its application in polymerase chain reaction amplification. Mar. Biotechnol. 9: 450-458 https://doi.org/10.1007/s10126-007-9002-8
  5. Chung, J. H., J. H. Back, Y. I. Park, and Y. S. Han. 2001. Biochemical characterization of a novel hypoxanthine/xanthine dNTP pyrophosphatase from Methanococcus jannaschii. Nucleic Acids Res. 29: 3099-3107 https://doi.org/10.1093/nar/29.14.3099
  6. Fogg, M. J., L. H. Pearl, and B. A. Connolly. 2002. Structural basis for uracil recognition by archaeal family B DNA polymerases. Nature Struct. Biol. 9: 922-927 https://doi.org/10.1038/nsb867
  7. Friedberg, E. C., G. C. Walker, and W. Siede. 1995. DNA Repair and Mutagenesis. American Society of Microbiology Press. Washington, DC
  8. Gill, S., R. O'Neill, R. J. Lewis, and B. A. Connolly. 2007. Interaction of the family-B DNA polymerase from the archaeon Pyrococcus furiosus with deaminated bases. J. Mol. Biol. 372:855-863 https://doi.org/10.1016/j.jmb.2007.07.015
  9. Greagg, M. A., M. J. Fogg, G. Panayootu, S. J. Evans, B. A. Connolly, and L. H. Pearl. 1999. A read-ahead function in archaeal DNA polymerases detects pro-mutagenic templatestrand uracil. Proc. Natl. Acad. Sci. USA 96: 9045-9050
  10. Grogan, D. W. 1998. Hyperthermophiles and the problems of DNA instability. Mol. Microbiol. 28: 1043-1049 https://doi.org/10.1046/j.1365-2958.1998.00853.x
  11. Gruz, P., M. Shimizu, F. M. Pisani, M. De Felice, Y. Kanke, and T. Nohmi. 2003. Processing of DNA lesions by archaeal DNA polymerases from Sulfolobus solfataricus. Nucleic Acids Res. 31: 4024-4030 https://doi.org/10.1093/nar/gkg447
  12. Hill-Perkins, M., M. D. Jones, and P. Karran. 1986. Site-specific mutagenesis in vivo by single methylated or deamintaed purine bases. Mutat. Res. 162: 153-163 https://doi.org/10.1016/0027-5107(86)90081-3
  13. Hogrefe, H. H., C. J. Hansen, B. R. Scott, and K. B. Nelson. 2001. Archaeal dUTPase enhances PCR amplifications with archaeal DNA polymerases by preventing dUTP incorporation. Proc. Natl. Acad. Sci. USA 99: 596-601
  14. Karran, P. and T. Lindahl. 1980. Hypoxanthine in deoxyribonucleic acid: Generation by heat-induced hydrolysis of adenine residues and release in free form by a deoxyribonucleic acid glycosylase from calf thymus. Biochemistry 19: 6005-6011 https://doi.org/10.1021/bi00567a010
  15. Kelman, Z. and J. A. Hurwitz. 2000. A unique organization of the protein subunits of the DNA polymerase clamp loader in the archaeon Methanobacterium thermoautotrophicum H*. J. Biol. Chem. 275: 7327-7336 https://doi.org/10.1074/jbc.275.10.7327
  16. Kim, Y. J., H. S. Lee, S. S. Bae, J. H. Jeon, J. K. Lim, Y. Cho, et al. 2007. Cloning, purification, and characterization of a new DNA polymerase from a hyperthermophilic archaeon, Thermococcus sp. NA1. J. Microbiol. Biotechnol. 17: 1090-1097
  17. Kow, Y. W. 2002. Repair of deaminated bases in DNA. Free Radic. Biol. Med. 33: 886-893 https://doi.org/10.1016/S0891-5849(02)00902-4
  18. Laemmli, U. K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227: 680-685 https://doi.org/10.1038/227680a0
  19. Lim, J. K., H. S. Lee, Y. J. Lim, S. S. Bae, J. H. Jeon, S. G. Kang, and J.-H. Lee. 2007. Critical factors to high thermostability of an alpha-amylase from hyperthermophilic archaeon Thermococcus onnurineus NA1. J. Microbiol. Biotechnol. 17: 1242-1248
  20. Lindahl, T. and B. Nyberg. 1974. Heat-induced deamination of cytosine residues in deoxyribonucleic acid. Biochemistry 13: 3405-3410 https://doi.org/10.1021/bi00713a035
  21. Lindahl, T. 1979. DNA glycosylases, endonucleases for apurinic/apyrimidinic sites and base excision-repair. Prog. Nucleic Acid Res. Mol. Biol. 22: 135-192 https://doi.org/10.1016/S0079-6603(08)60800-4
  22. Lindahl, T. 1993. Instability and decay of the primary structure of DNA. Nature 362: 709-715 https://doi.org/10.1038/362709a0
  23. Motz, M., I. Kober, C. Girardot, E. Loeser, U. Bauer, M. Albers, et al. 2002. Elucidation of an archaeal replication protein network to generate enhanced PCR enzymes. J. Biol. Chem. 277: 16179-16188 https://doi.org/10.1074/jbc.M107793200
  24. Sandigursky, M. and W. A. Franklin. 2000 Uracil-DNA glycosylase in the extreme thermophile Archaeoglobus fulgidus. J. Biol. Chem. 275: 19146-19149 https://doi.org/10.1074/jbc.M001995200
  25. Sartori, A. A., P. Schar, S. Fitz-Gibbon, J. E. Miller, and J. Jiriciny. 2001. Biochemical characterization of uracil processing activities in the hyperthermophilic archaeon Pyrobaculum aerophilum. J. Biol. Chem. 276: 29979-29986 https://doi.org/10.1074/jbc.M102985200
  26. Shapiro, R. and S. H. Pohl. 1968. The reaction of ribonucleosides with nitrous acid. Side products and kinetics. Biochemistry 7: 448-455 https://doi.org/10.1021/bi00841a057
  27. Shuttleworth, G., M. J. Fogg, M. R. Kurpiewski, L. Jen-Jacobson, and B. A. Connolly. 2004. Recognition of the pro-mutagenic base uracil by family B DNA polymerases from archaea. J. Mol. Biol. 337: 621-634 https://doi.org/10.1016/j.jmb.2004.01.021
  28. Takagi, M., M. Nishioka, H. Kakihara, M. Kitabayashi, H. Inoue, B. Kawakami, M. Oka, and T. Imanaka. 1997. Characterization of DNA polymerase from Pyrococcus sp. strain KOD1 and its application to PCR. Appl. Environ. Microbiol. 63: 4504-4510
  29. Yang, H., S. Fitz-Gibbon, E. M. Marcotte, J. H. Tai, E. C. Hyman, and J. H. Miller. 1999. Characterization of a thermostable DNA glycosylase specific for U/G and T/G mismatches from the hyperthermophilic archaeon Pyrobaculum aerophilum. J. Bacteriol. 182: 1272-1279 https://doi.org/10.1128/JB.182.5.1272-1279.2000