Skip to main content
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1985 Dec;82(24):8354–8358. doi: 10.1073/pnas.82.24.8354

Exonuclease III recognizes urea residues in oxidized DNA.

Y W Kow, S S Wallace
PMCID: PMC390914  PMID: 3001698

Abstract

Escherichia coli exonuclease III was found to be associated with an activity that recognizes urea residues in DNA but not thymine glycol residues from which the urea residues were prepared. This activity was not due to a contaminating activity such as endonuclease III since urea-containing DNA was a competitive inhibitor of exonuclease III when apurinic DNA was used as a substrate and vice versa. The apparent kinetic constants for both the substrate and inhibitor were determined. Like its apurinic activity, exonuclease III activity against urea residues was endonucleolytic, nicking on the 5' side of the damage and having an optimal Mg2+ concentration between 2 and 10 mM. Also, the enzyme recognized alkali-stable damages produced in DNA by H2O2 in vitro. We suggest that it may be this activity of exonuclease III that accounts for its biological role in vivo.

Full text

PDF
8358

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Breimer L. H., Lindahl T. DNA glycosylase activities for thymine residues damaged by ring saturation, fragmentation, or ring contraction are functions of endonuclease III in Escherichia coli. J Biol Chem. 1984 May 10;259(9):5543–5548. [PubMed] [Google Scholar]
  2. Breimer L. H. Urea--DNA glycosylase in mammalian cells. Biochemistry. 1983 Aug 30;22(18):4192–4197. doi: 10.1021/bi00287a005. [DOI] [PubMed] [Google Scholar]
  3. Breimer L., Lindahl T. A DNA glycosylase from Escherichia coli that releases free urea from a polydeoxyribonucleotide containing fragments of base residues. Nucleic Acids Res. 1980 Dec 20;8(24):6199–6211. doi: 10.1093/nar/8.24.6199. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Cathcart R., Schwiers E., Saul R. L., Ames B. N. Thymine glycol and thymidine glycol in human and rat urine: a possible assay for oxidative DNA damage. Proc Natl Acad Sci U S A. 1984 Sep;81(18):5633–5637. doi: 10.1073/pnas.81.18.5633. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Demple B., Halbrook J., Linn S. Escherichia coli xth mutants are hypersensitive to hydrogen peroxide. J Bacteriol. 1983 Feb;153(2):1079–1082. doi: 10.1128/jb.153.2.1079-1082.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Demple B., Linn S. 5,6-Saturated thymine lesions in DNA: production by ultraviolet light or hydrogen peroxide. Nucleic Acids Res. 1982 Jun 25;10(12):3781–3789. doi: 10.1093/nar/10.12.3781. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Gossard F., Verly W. G. Properties of the main endonuclease specific for apurinic sites of Escherichia coli (endonuclease VI). Mechanism of apurinic site excision from DNA. Eur J Biochem. 1978 Jan 16;82(2):321–332. doi: 10.1111/j.1432-1033.1978.tb12026.x. [DOI] [PubMed] [Google Scholar]
  8. Hadi S. M., Goldthwait D. A. Endonuclease II of Escherichia coli. Degradation of partially depurinated deoxyribonucleic acid. Biochemistry. 1971 Dec 21;10(26):4986–4993. doi: 10.1021/bi00802a024. [DOI] [PubMed] [Google Scholar]
  9. Henner W. D., Grunberg S. M., Haseltine W. A. Sites and structure of gamma radiation-induced DNA strand breaks. J Biol Chem. 1982 Oct 10;257(19):11750–11754. [PubMed] [Google Scholar]
  10. Iida S., Hayatsu H. The permanganate oxidation of thymine. Biochim Biophys Acta. 1970 Jul 16;213(1):1–13. doi: 10.1016/0005-2787(70)90002-x. [DOI] [PubMed] [Google Scholar]
  11. Katcher H. L., Wallace S. S. Characterization of the Escherichia coli X-ray endonuclease, endonuclease III. Biochemistry. 1983 Aug 16;22(17):4071–4081. doi: 10.1021/bi00286a013. [DOI] [PubMed] [Google Scholar]
  12. Kowalski D. A procedure for the quantitation of relaxed closed circular DNA in the presence of superhelical DNA: an improved fluorometric assay for nicking-closing enzyme. Anal Biochem. 1979 Mar;93(2):346–354. doi: 10.1016/s0003-2697(79)80161-x. [DOI] [PubMed] [Google Scholar]
  13. Lindahl T., Andersson A. Rate of chain breakage at apurinic sites in double-stranded deoxyribonucleic acid. Biochemistry. 1972 Sep 12;11(19):3618–3623. doi: 10.1021/bi00769a019. [DOI] [PubMed] [Google Scholar]
  14. Ljungquist S., Lindahl T., Howard-Flanders P. Methyl methane sulfonate-sensitive mutant of Escherichia coli deficient in an endonuclease specific for apurinic sites in deoxyribonucleic acid. J Bacteriol. 1976 May;126(2):646–653. doi: 10.1128/jb.126.2.646-653.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Massie H. R., Samis H. V., Baird M. B. The kinetics of degradation of DNA and RNA by H 2 O 2 . Biochim Biophys Acta. 1972 Jul 31;272(4):539–548. doi: 10.1016/0005-2787(72)90509-6. [DOI] [PubMed] [Google Scholar]
  16. Mello Filho A. C., Meneghini R. In vivo formation of single-strand breaks in DNA by hydrogen peroxide is mediated by the Haber-Weiss reaction. Biochim Biophys Acta. 1984 Feb 24;781(1-2):56–63. doi: 10.1016/0167-4781(84)90123-4. [DOI] [PubMed] [Google Scholar]
  17. Milcarek C., Weiss B. Mutants of Escherichia coli with altered deoxyribonucleases. I. Isolation and characterization of mutants for exonuclease 3. J Mol Biol. 1972 Jul 21;68(2):303–318. doi: 10.1016/0022-2836(72)90215-x. [DOI] [PubMed] [Google Scholar]
  18. RICHARDSON C. C., KORNBERG A. A DEOXYRIBONUCLEIC ACID PHOSPHATASE-EXONUCLEASE FROM ESCHERICHIA COLI. I. PURIFICATION OF THE ENZYME AND CHARACTERIZATION OF THE PHOSPHATASE ACTIVITY. J Biol Chem. 1964 Jan;239:242–250. [PubMed] [Google Scholar]
  19. RICHARDSON C. C., LEHMAN I. R., KORNBERG A. A DEOXYRIBONUCLEIC ACID PHOSPHATASE-EXONUCLEASE FROM ESCHERICHIA COLI. II. CHARACTERIZATION OF THE EXONUCLEASE ACTIVITY. J Biol Chem. 1964 Jan;239:251–258. [PubMed] [Google Scholar]
  20. Roti J. L., Cerutti P. A. Letter: Gamma-ray induced thymine damage in mammalian cells. Int J Radiat Biol Relat Stud Phys Chem Med. 1974 Apr;25(4):413–417. doi: 10.1080/09553007414550491. [DOI] [PubMed] [Google Scholar]
  21. Sammartano L. J., Tuveson R. W. Escherichia coli xthA mutants are sensitive to inactivation by broad-spectrum near-UV (300- to 400-nm) radiation. J Bacteriol. 1983 Nov;156(2):904–906. doi: 10.1128/jb.156.2.904-906.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Sammartano L. J., Tuveson R. W. The effects of exogenous catalase on broad-spectrum near-UV (300-400 nm) treated Escherichia coli cells. Photochem Photobiol. 1984 Nov;40(5):607–612. doi: 10.1111/j.1751-1097.1984.tb05348.x. [DOI] [PubMed] [Google Scholar]
  23. Verly W. G., Rassart E. Purification of Escherichia coli endonuclease specific for apurinic sites in DNA. J Biol Chem. 1975 Oct 25;250(20):8214–8219. [PubMed] [Google Scholar]
  24. Wang R. J., Ananthaswamy H. N., Nixon B. T., Hartman P. S., Eisenstark A. Induction of single-strand DNA breaks in human cells by H2O2 formed in near-uv (black light) irradiated medium. Radiat Res. 1980 May;82(2):269–276. [PubMed] [Google Scholar]
  25. Warner H. R., Demple B. F., Deutsch W. A., Kane C. M., Linn S. Apurinic/apyrimidinic endonucleases in repair of pyrimidine dimers and other lesions in DNA. Proc Natl Acad Sci U S A. 1980 Aug;77(8):4602–4606. doi: 10.1073/pnas.77.8.4602. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Weiss B. Endonuclease II of Escherichia coli is exonuclease III. J Biol Chem. 1976 Apr 10;251(7):1896–1901. [PubMed] [Google Scholar]
  27. White B. J., Hochhauser S. J., Cintron N. M., Weiss B. Genetic mapping of xthA, the structural gene for exonuclease III in Escherichia coli K-12. J Bacteriol. 1976 Jun;126(3):1082–1088. doi: 10.1128/jb.126.3.1082-1088.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Yajko D. M., Weiss B. Mutations simultaneously affecting endonuclease II and exonuclease III in Escherichia coli. Proc Natl Acad Sci U S A. 1975 Feb;72(2):688–692. doi: 10.1073/pnas.72.2.688. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES