Skip to main content
SpringerLink
Log in

Modeling base excision repair in Escherichia coli bacterial cells

  • Radiobiology, Ecology, and Nuclear Medicine
  • Published:
Physics of Particles and Nuclei Letters Aims and scope Submit manuscript

Abstract

A model describing the key processes in Escherichia coli bacterial cells during base excision repair is developed. The mechanism is modeled of damaged base elimination involving formamidopyrimidine DNA glycosylase (the Fpg protein), which possesses several types of activities. The modeling of the transitions between DNA states is based on a stochastic approach to the chemical reaction description.

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. T. Lindahl, “New Class of Enzymes Acting on Damaged DNA,” Nature 259, 64–66 (1976).

    Article  ADS  Google Scholar 

  2. B. A. Sokhansanj et al., “A Quantitative Model of Human DNA Base Excision Repair. I. Mechanistic Insights,” Nucleic Acids Res. 30, 1817–1825 (2002).

    Article  Google Scholar 

  3. D. T. Gillespie, “Exact Stochastic Simulation of Coupled Chemical Reactions,” J. Phys. Chem. 81, 2340–2361 (1977).

    Article  Google Scholar 

  4. B. N. Ames and L. S. Gold, “Endogenous Mutagens and the Causes of Aging and Cancer,” Mutat. Res. 250, 3–16 (1991).

    Article  Google Scholar 

  5. K. C. Cheng et al., “8-Hydroxyguanine, an Abundant Form of Oxidative DNA Damage, Causes G → T and A → C Substitutions,” J. Biol. Chem. 267, 166–172 (1992).

    Google Scholar 

  6. M. Moriya and A. P. Grollman, “Mutations in the mutY Gene of Escherichia coli Enhance the Frequency of Targeted G:C → T:A Transversions Induced by a Single 8-Oxoguanine Residue in Single-Stranded DNA,” Mol. Gen. Genet. 239, 72–76 (1993).

    Google Scholar 

  7. B. Epe, “DNA Damage Profiles Induced by Oxidizing Agents,” Rev. Physiol. Biochem. Pharmacol. 127, 223–249 (1995).

    Article  Google Scholar 

  8. M. Dizdaroglu, J. Laval, and S. Boiteux, “Substrate Specificity of the Escherichia coli Endonuclease III Excision of Thymine- and Cytosine-Derived Lesions in DNA Produced by Radiation-Generated Free Radicals,” Biochemistry 32, 12105–12111 (1993).

    Article  Google Scholar 

  9. A. F. Fuciarelli et al., “Yields of Radiation-Induced Base Products in DNA Effects of DNA Conformation and Gassing Conditions,” Intern. J. Rad. Biol. 58, 397–415 (1990).

    Article  Google Scholar 

  10. J. Cadet et al., “Oxidative Damage to DNA: Formation, Measurement and Biochemical Features,” Mutat. Res. 531, 5–23 (2003).

    Article  ADS  Google Scholar 

  11. O. S. Fedorova et al., “Stopped-flow Kinetic Studies of the Interaction between Escherichia coli Fpg Protein and DNA Substrates,” Biochemistry 41, 1520–1528 (2002).

    Article  Google Scholar 

  12. J. Laval et al., “Antimutagenic Role of Base-Excision Repair Enzymes upon Free Radical-Induced DNA Damage,” Mutat. Res. 402, 93–102 (1998).

    Article  Google Scholar 

  13. T. R. O’Connor and J. Laval, “Physical Association of the 2,6-Diamino-4-Hydroxy-5N-Formamidopyrimidine-DNA Glycosylase of Escherichia coli and an Activity Nicking DNA at Apurinic/Apyrimidinic Sites,” Proc. Nat. Acad. Sci. USA 86, 5222–5226 (1989).

    Article  ADS  Google Scholar 

  14. V. Bailly et al., “Mechanism of DNA Strand Nicking at Apurinic/Apyrimidinic Sites by Escherichia coli [formamidopyrimidine] DNA Glycosylase,” Biochem. J. 262, 581–589 (1989).

    Google Scholar 

  15. R. J. Graves et al., “Excision of 5′-Terminal Deoxyribose Phosphate from Damaged DNA is Catalyzed by the Fpg Protein of Escherichia coli, J. Biol. Chem. 267, 14429–14435 (1992).

    Google Scholar 

  16. N. Krishnamurthy et al., “Efficient Removal of Formamidopyrimidines by 8-Oxoguanine Glycosylases,” Biochemistry 47, 1043–1050 (2008).

    Article  Google Scholar 

  17. B. Castaing et al., “Cleavage and Binding of a DNA Fragment Containing a Single 8-Oxoguanine by Wild Type and Mutant FPG Proteins,” Nucleic Acids Res. 21, 2899–2905 (1993).

    Article  Google Scholar 

  18. N. Gillard et al., “Radiation Affects Binding of Fpg Repair Protein to an Abasic Site Containing DNA,” Rad. Res. 162, 566–571 (2004).

    Article  Google Scholar 

  19. R. L. P. Adams, J. T. Knowler, and D. P. Leader, The Biochemistry of the Nucleic Acids (Chapman and Hall, New York, 1992).

    Google Scholar 

  20. A. Kornberg and T. A. Baker, DNA Replication, 2nd ed. (Freeman, New York, 1992).

    Google Scholar 

  21. A. Chang et al., “BRENDA, AMENDA and FRENDA the Enzyme Information System: New Content and Tools in 2009,” Nucleic Acids Res. 37, D588–D592 (2009).

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Laboratory of Radiation Biology, JINR, Moscow, Russia

    O. V. Belov

Authors
  1. O. V. Belov
    View author publications

    You can also search for this author in PubMed Google Scholar

Additional information

Original Russian Text © O.V. Belov, 2011, published in Pis’ma v Zhurnal Fizika Elementarnykh Chastits i Atomnogo Yadra, 2011, No. 2(165), pp. 241–251.

The article was translated by the authors.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Belov, O.V. Modeling base excision repair in Escherichia coli bacterial cells. Phys. Part. Nuclei Lett. 8, 141–148 (2011). https://doi.org/10.1134/S1547477111020038

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S1547477111020038

Keywords

Search

Navigation