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. 1998 Jun 1;26(11):2593–2597. doi: 10.1093/nar/26.11.2593

Exonuclease IX of Escherichia coli.

K M Shafritz 1, M Sandigursky 1, W A Franklin 1
PMCID: PMC147613  PMID: 9592142

Abstract

The bacteria Escherichia coli contains several exonucleases acting on both double- and single-stranded DNA and in both a 5'-->3' and 3'-->5' direction. These enzymes are involved in replicative, repair and recombination functions. We have identified a new exonuclease found in E.coli, termed exonuclease IX, that acts preferentially on single-stranded DNA as a 3'-->5' exonuclease and also functions as a 3'-phosphodiesterase on DNA containing 3'-incised apurinic/apyrimidinic (AP) sites to remove the product trans -4-hydroxy-2-pentenal 5-phosphate. The enzyme showed essentially no activity as a deoxyribophosphodiesterase acting on 5'-incised AP sites. The activity was isolated as a glutathione S-transferase fusion protein from a sequence of the E.coli genome that was 60% identical to a 260 bp region of the small fragment of the DNA polymerase I gene. The protein has a molecular weight of 28 kDa and is free of AP endonuclease and phosphatase activities. Exonuclease IX is expressed in E.coli , as demonstrated by reverse transcription-PCR, and it may function in the DNA base excision repair and other pathways.

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Selected References

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  1. Bernelot-Moens C., Demple B. Multiple DNA repair activities for 3'-deoxyribose fragments in Escherichia coli. Nucleic Acids Res. 1989 Jan 25;17(2):587–600. doi: 10.1093/nar/17.2.587. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bradford M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 1976 May 7;72:248–254. doi: 10.1016/0003-2697(76)90527-3. [DOI] [PubMed] [Google Scholar]
  3. Cooper D. L., Lahue R. S., Modrich P. Methyl-directed mismatch repair is bidirectional. J Biol Chem. 1993 Jun 5;268(16):11823–11829. [PubMed] [Google Scholar]
  4. Demple B., Johnson A., Fung D. Exonuclease III and endonuclease IV remove 3' blocks from DNA synthesis primers in H2O2-damaged Escherichia coli. Proc Natl Acad Sci U S A. 1986 Oct;83(20):7731–7735. doi: 10.1073/pnas.83.20.7731. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Dianov G., Sedgwick B., Daly G., Olsson M., Lovett S., Lindahl T. Release of 5'-terminal deoxyribose-phosphate residues from incised abasic sites in DNA by the Escherichia coli RecJ protein. Nucleic Acids Res. 1994 Mar 25;22(6):993–998. doi: 10.1093/nar/22.6.993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Doetsch P. W., Cunningham R. P. The enzymology of apurinic/apyrimidinic endonucleases. Mutat Res. 1990 Sep-Nov;236(2-3):173–201. doi: 10.1016/0921-8777(90)90004-o. [DOI] [PubMed] [Google Scholar]
  7. Feilotter H. E., Hannon G. J., Ruddell C. J., Beach D. Construction of an improved host strain for two hybrid screening. Nucleic Acids Res. 1994 Apr 25;22(8):1502–1503. doi: 10.1093/nar/22.8.1502. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Franklin W. A., Lindahl T. DNA deoxyribophosphodiesterase. EMBO J. 1988 Nov;7(11):3617–3622. doi: 10.1002/j.1460-2075.1988.tb03240.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Gillen J. R., Karu A. E., Nagaishi H., Clark A. J. Characterization of the deoxyribonuclease determined by lambda reverse as exonuclease VIII of Escherichia coli. J Mol Biol. 1977 Jun 15;113(1):27–41. doi: 10.1016/0022-2836(77)90039-0. [DOI] [PubMed] [Google Scholar]
  10. Graves R. J., Felzenszwalb I., Laval J., O'Connor T. R. Excision of 5'-terminal deoxyribose phosphate from damaged DNA is catalyzed by the Fpg protein of Escherichia coli. J Biol Chem. 1992 Jul 15;267(20):14429–14435. [PubMed] [Google Scholar]
  11. Klenow H., Henningsen I. Selective elimination of the exonuclease activity of the deoxyribonucleic acid polymerase from Escherichia coli B by limited proteolysis. Proc Natl Acad Sci U S A. 1970 Jan;65(1):168–175. doi: 10.1073/pnas.65.1.168. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Kornberg A. The private life of DNA polymerase I. Methods Enzymol. 1990;182:783–788. doi: 10.1016/0076-6879(90)82060-f. [DOI] [PubMed] [Google Scholar]
  13. Kushner S. R., Nagaishi H., Clark A. J. Isolation of exonuclease VIII: the enzyme associated with sbcA indirect suppressor. Proc Natl Acad Sci U S A. 1974 Sep;71(9):3593–3597. doi: 10.1073/pnas.71.9.3593. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Ljungquist S. A new endonuclease from Escherichia coli acting at apurinic sites in DNA. J Biol Chem. 1977 May 10;252(9):2808–2814. [PubMed] [Google Scholar]
  15. Lovett S. T., Kolodner R. D. Identification and purification of a single-stranded-DNA-specific exonuclease encoded by the recJ gene of Escherichia coli. Proc Natl Acad Sci U S A. 1989 Apr;86(8):2627–2631. doi: 10.1073/pnas.86.8.2627. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Mazumder A., Gerlt J. A., Absalon M. J., Stubbe J., Cunningham R. P., Withka J., Bolton P. H. Stereochemical studies of the beta-elimination reactions at aldehydic abasic sites in DNA: endonuclease III from Escherichia coli, sodium hydroxide, and Lys-Trp-Lys. Biochemistry. 1991 Jan 29;30(4):1119–1126. doi: 10.1021/bi00218a033. [DOI] [PubMed] [Google Scholar]
  17. Prasher D. C., Conarro L., Kushner S. R. Amplification and purification of exonuclease I from Escherichia coli K12. J Biol Chem. 1983 May 25;258(10):6340–6343. [PubMed] [Google Scholar]
  18. Razavy H., Szigety S. K., Rosenberg S. M. Evidence for both 3' and 5' single-strand DNA ends in intermediates in chi-stimulated recombination in vivo. Genetics. 1996 Feb;142(2):333–339. doi: 10.1093/genetics/142.2.333. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Sandigursky M., Franklin W. A. DNA deoxyribophosphodiesterase of Escherichia coli is associated with exonuclease I. Nucleic Acids Res. 1992 Sep 25;20(18):4699–4703. doi: 10.1093/nar/20.18.4699. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Sandigursky M., Franklin W. A. Exonuclease I of Escherichia coli removes phosphoglycolate 3'-end groups from DNA. Radiat Res. 1993 Aug;135(2):229–233. [PubMed] [Google Scholar]
  21. Sandigursky M., Lalezari I., Franklin W. A. Excision of sugar-phosphate products at apurinic/apyrimidinic sites by DNA deoxyribophosphodiesterase of Escherichia coli. Radiat Res. 1992 Sep;131(3):332–337. [PubMed] [Google Scholar]
  22. Sandigursky M., Mendez F., Bases R. E., Matsumoto T., Franklin W. A. Protein-protein interactions between the Escherichia coli single-stranded DNA-binding protein and exonuclease I. Radiat Res. 1996 May;145(5):619–623. [PubMed] [Google Scholar]
  23. Sandigursky M., Yacoub A., Kelley M. R., Deutsch W. A., Franklin W. A. The Drosophila ribosomal protein S3 contains a DNA deoxyribophosphodiesterase (dRpase) activity. J Biol Chem. 1997 Jul 11;272(28):17480–17484. doi: 10.1074/jbc.272.28.17480. [DOI] [PubMed] [Google Scholar]
  24. Sayers J. R. Computer aided identification of a potential 5'-3' exonuclease gene encoded by Escherichia coli. J Theor Biol. 1994 Oct 21;170(4):415–421. doi: 10.1006/jtbi.1994.1202. [DOI] [PubMed] [Google Scholar]
  25. Wallace S. S. DNA damages processed by base excision repair: biological consequences. Int J Radiat Biol. 1994 Nov;66(5):579–589. doi: 10.1080/09553009414551661. [DOI] [PubMed] [Google Scholar]
  26. Yajko D. M., Valentine M. C., Weiss B. Mutants of Escherichia coli with altered deoxyribonucleases. II. Isolation and characterization of mutants for exonuclease I. J Mol Biol. 1974 May 15;85(2):323–343. doi: 10.1016/0022-2836(74)90367-2. [DOI] [PubMed] [Google Scholar]

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