Oxidative demethylation by Escherichia coli AlkB directly reverts DNA base damage (original) (raw)

References

1. Lindahl, T., Sedgwick, B., Sekiguchi, M. & Nakabeppu, Y. Regulation and expression of the adaptive response to alkylating agents. Annu. Rev. Biochem. 57, 133–157 (1988)
   Article CAS PubMed Google Scholar
2. Seeberg, E. & Berdal, K. G. in Base Excision Repair of DNA Damage: Repair of Alkylation Damage to DNA (ed. Hickson, I. D.) 151–168 (Landes Bioscience, Austin, 1999)
   Google Scholar
3. Kataoka, H., Yamamoto, Y. & Sekiguchi, M. A new gene (alkB) of Escherichia coli that controls sensitivity to methyl methane sulfonate. J. Bacteriol. 153, 1301–1307 (1983)
   CAS PubMed PubMed Central Google Scholar
4. Kondo, H. et al. Structure and expression of the alkB gene of Escherichia coli related to the repair of alkylated DNA. J. Biol. Chem. 261, 15772–15777 (1986)
   CAS PubMed Google Scholar
5. Dinglay, S., Trewick, S. C., Lindahl, T. & Sedgwick, B. Defective processing of methylated single-stranded DNA by E. coli alkB mutants. Genes Dev. 14, 2097–2105 (2000)
   CAS PubMed PubMed Central Google Scholar
6. Aravind, L. & Koonin, E. V. The DNA-repair protein AlkB, EGL-9, and leprecan define new families of 2-oxoglutarate- and iron-dependent dioxygenases. Genome Biol. 2 RESEARCH0007 (2001)
7. Prescott, A. G. & Lloyd, M. D. The iron(ii) and 2-oxoacid-dependent dioxygenases and their role in metabolism. Nat. Prod. Rep. 17, 367–383 (2000)
   Article CAS PubMed Google Scholar
8. Ryle, M. J. & Hausinger, R. P. Non-heme iron oxygenases. Curr. Opin. Chem. Biol. 6, 193–201 (2002)
   Article CAS PubMed Google Scholar
9. Rebeck, G. W. & Samson, L. Increased spontaneous mutation and alkylation sensitivity of Escherichia coli strains lacking the ogt O6-methylguanine-DNA methyltransferase. J. Bacteriol. 173, 2068–2076 (1991)
   Article CAS PubMed PubMed Central Google Scholar
10. Vaughan, P., Sedgwick, B., Hall, J., Gannon, J. & Lindahl, T. Environmental mutagens that induce the adaptive response to alkylating agents in Escherichia coli. Carcinogenesis 12, 263–268 (1991)
    Article CAS PubMed Google Scholar
11. Chen, B. J., Carroll, P. & Samson, L. The Escherichia coli AlkB protein protects human cells against alkylation-induced toxicity. J. Bacteriol. 176, 6255–6261 (1994)
    Article CAS PubMed PubMed Central Google Scholar
12. Wei, Y., Carter, K. C., Wang, R. & Shell, B. K. Molecular cloning and functional analysis of a human cDNA encoding an Escherichia coli AlkB homolog, a protein involved in DNA alkylation damage repair. Nucleic Acids Res. 24, 931–937 (1996)
    Article CAS PubMed PubMed Central Google Scholar
13. Bodell, W. J. & Singer, B. Influence of hydrogen bonding in DNA and polynucleotides on reaction of nitrogens and oxygens toward ethylnitrosourea. Biochemistry 18, 2860–2863 (1979)
    Article CAS PubMed Google Scholar
14. Singer, B. & Grunberger, D. Molecular Biology of Mutagens and Carcinogens: Reactions of Directly Acting Agents with Nucleic Acids 45–96 (Plenum, New York, 1983)
    Book Google Scholar
15. Aravind, L., Walker, D. R. & Koonin, E. V. Conserved domains in DNA repair proteins and evolution of repair systems. Nucleic Acids Res. 27, 1223–1242 (1999)
    Article CAS PubMed PubMed Central Google Scholar
16. Hegg, E. L. et al. Herbicide-degrading α-keto acid-dependent enzyme: metal coordination environment and mechanistic insights. Biochemistry 38, 16714–16726 (1999)
    Article CAS PubMed Google Scholar
17. Pavel, E. G. et al. Circular dichroism and magnetic circular dichroism spectroscopic studies of the non-heme ferrous active site in clavaminate synthase and its interaction with α-ketoglutarate co-substrate. J. Am. Chem. Soc. 120, 743–753 (1998)
    Article CAS Google Scholar
18. Ryle, M. J., Padmakumar, R. & Hausinger, R. P. Stopped-flow kinetic analysis of Escherichia coli taurine/α-ketoglutarate dioxygenase: interactions with α-ketoglutarate, taurine, and oxygen. Biochemistry 38, 15278–15286 (1999)
    Article CAS PubMed Google Scholar
19. Heck, H. D. A., White, E. L. & Cassanova-Schmitz, M. Determination of formaldehyde in biological tissues by gas chromatography/mass spectrometry. Biomed. Mass Spectrom. 9, 347–353 (1982)
    Article CAS PubMed Google Scholar
20. Lizcano, M. J., Unzeta, M. & Tipton, K. F. A spectrophotometric method for determining the oxidative deamination of methylamine by amine oxidases. Anal. Biochem. 286, 75–79 (2000)
    Article CAS PubMed Google Scholar
21. de Jong, L., Albracht, S. P. & Kemp, A. Prolyl 4-hydroxylase activity in relation to the oxidation state of enzyme-bound iron. The role of ascorbate in peptidyl proline hydroxylation. Biochim. Biophys. Acta 704, 326–332 (1982)
    Article CAS PubMed Google Scholar
22. Myllyla, R., Majamaa, K., Gunzler, V., Hanauske-Abel, H. M. & Kivirikko, K. I. Ascorbate is consumed stoichiometrically in the uncoupled reactions catalysed by prolyl 4-hydroxylase and lysyl hydroxylase. J. Biol. Chem. 10, 5403–5405 (1984)
    Google Scholar
23. Colombi, D. & Gomes, S. L. An alkB homologue is differentially transcribed during the Caulobacter crescentus cell cycle. J. Bacteriol. 179, 3139–3145 (1997)
    Article CAS PubMed PubMed Central Google Scholar
24. Thornburg, L. D., Lai, M.-T., Wishnok, J. S. & Stubbe, J. A non-heme iron protein with heme tendencies: an investigation of the substrate specificity of thymine hydroxylase. Biochemistry 32, 14023–14033 (1993)
    Article CAS PubMed Google Scholar
25. Mayer, W., Niveleau, A., Walter, J., Fundele, R. & Haaf, T. Demethylation of the zygotic paternal genome. Nature 403, 501–502 (2000)
    Article ADS CAS PubMed Google Scholar
26. Smith, S. S. Gilbert's conjecture: the search for DNA (cytosine-5) demethylases and the emergence of new functions for eukaryotic DNA (cytosine-5) methyltransferases. J. Mol. Biol. 302, 1–7 (2000)
    Article CAS PubMed Google Scholar

Download references