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Role of the 5´ → 3´ exonuclease and Klenow fragment of Escherichia coli DNA polymerase I in base mismatch repair

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Abstract

We have previously demonstrated that the Escherichia coli strain mutS ΔpolA had a higher rate of transition and minus frameshift mutations than mutS or ΔpolA strains. We argued that DNA polymerase I (PolI) corrects transition mismatches. PolI, encoded by the polA gene, possesses Klenow and 5´ → 3´ exonuclease domains. In the present study, rates of mutation were found to be higher in Klenow-defective mutS strains and 5´ → 3´ exonuclease-defective mutS strains than mutS or polA strains. The Klenow-defective or 5´ → 3´ exonuclease-defective mutS strains showed a marked increase in transition mutations. Sites of transition mutations in mutS, Klenow-defective mutS and 5´ → 3´ exonuclease-defective mutS strains are different. Thus, it is suggested that, in addition to mutS function, both the Klenow and 5´ → 3´ exonuclease domains are involved in the decrease of transition mutations. Transition hot and warm spots in mutS + polA + strains were found to differ from those in mutS and mutS ΔpolA strains. We thus argue that all the spontaneous transition mutations in the wild-type strain do not arise from transition mismatches left unrepaired by the MutS system or MutS PolI system.

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References

  • Agemizu Y, Uematsu N, Yamamoto K (1999) DNA sequence analysis of spontaneous tonB deletion mutations in a polA1 strain of Escherichia coli K12. Biochem Biophys Res Commun 261:584–589

    Article  PubMed  CAS  Google Scholar 

  • Akasaka S, Yamamoto K (1991) Construction of Escherichia coli K12 phr deletion and insertion mutants by gene replacement. Mutat Res 254:27–35

    PubMed  CAS  Google Scholar 

  • Akasaka S, Yamamoto K (1994) Hydrogen peroxide induces G:C to T:A and G:C to C:G transversions in the supF gene of Escherichia coli. Mol Gen Genet 243:500–505

    Article  PubMed  CAS  Google Scholar 

  • Berkower I, Leis J, Hurwitz J (1973) Isolation and characterization of an endonuclease from Escherichia coli specific for ribonucleic acid in ribonucleic acid-deoxyribonucleic acid hybrid structures. J Biol Chem 248:5914–5921

    PubMed  CAS  Google Scholar 

  • Brutlag D, Atkinson MR, Setlow P, Kornberg A (1969) An active fragment of DNA polymerase produced by proteolytic cleavage. Biochem Biophys Res Commun 37:982–989

    Article  PubMed  CAS  Google Scholar 

  • Cheng KC, Cahill DS, Kasai H, Nishimura S, Loeb LA (1992) 8-Hydroxyguanine, an abundant form of oxidative DNA damage, causes G-T and A-C substitutions. J Biol Chem 267:166–172

    PubMed  CAS  Google Scholar 

  • Coukell MB, Yanofsky C (1970) Increased frequency of deletions in DNA polymerase mutants of Escherichia coli. Nature 228:633–635

    Article  PubMed  CAS  Google Scholar 

  • Fijalkowska IJ, Jonczyk P, Tkaczyk MM, Bialoskorska M, Schaaper RM (1998) Unequal fidelity of leading strand and lagging strand DNA replication on the Escherichia coli chromosome. Proc Natl Acad Sci USA 95:10020–10025

    Article  PubMed  CAS  Google Scholar 

  • Fix DF, Burns PA, Glickman BW (1987) DNA sequence analysis of spontaneous mutation in a polA1 strain of Escherichia coli indicates sequence-specific effects. Mol Gen Genet 207:267–272

    Article  PubMed  CAS  Google Scholar 

  • Heijneker HL, Ellens DJ, Tjeerde RH, Glickman BW, van Dorp B, Pouwels PH (1973) A mutant of Escherichia coli K12 deficient in the 5′-3′ exonucleolytic activity of DNA polymerase I. II. Purification and properties of the mutant enzyme. Mol Gen Genet 124:83–96

    Article  PubMed  CAS  Google Scholar 

  • Ishii Y, Kondo S (1972) Spontaneous and radiation-induced deletion mutations in Escherichia coli strains with different DNA repair capacities. Mutat Res 16:13–25

    PubMed  CAS  Google Scholar 

  • Joyce CM, Grindley ND (1984) Method for determining whether a gene of Escherichia coli is essential: application to the polA gene. J Bacteriol 158:636–643

    PubMed  CAS  Google Scholar 

  • Joyce CM, Fujii DM, Laks HS, Hughes CM, Grindley ND (1985) Genetic mapping and DNA sequence analysis of mutations in the polA gene of Escherichia coli. J Mol Biol 186:283–293

    Article  PubMed  CAS  Google Scholar 

  • Kitamura K, Torii Y, Matsuoka C, Yamamoto K (1995) DNA sequence changes in mutations in the tonB gene on the chromosome of Escherichia coli K12: insertion elements dominate the spontaneous spectra. Jpn J Genet 70:35–46

    Article  PubMed  CAS  Google Scholar 

  • Kitamura K, Yamamoto K (1996) Mutagenic specificity of ultraviolet light in the tonB gene on the chromosome of Escherichia coli uvrA cells. Biochem Biophys Res Commun 220:496–501

    Article  PubMed  CAS  Google Scholar 

  • Kornberg A, Baker TA (1992) DNA polymerase I of E. coli. In: DNA replication. 2nd edn. WH Freeman and Company, NY, pp 113–159

  • Lea DE, Coulson CA (1949) The distribution of the numbers of mutants in bacterial populations. J Genet 49:264–285

    Article  Google Scholar 

  • Lehman IR, Chien JR (1973) Persistence of deoxyribonucleic acid polymerase I and its 5’→3’ exonuclease activity in polA mutants of Escherichia coli K12. J Biol Chem 248:7717–7723

    PubMed  CAS  Google Scholar 

  • Lu AL, Chang DY (1988) Repair of single base-pair transversion mismatches of Escherichia coli in vitro: correction of certain A/G mismatches is independent of dam methylation and host mutHLS gene functions. Genetics 118:593–600

    PubMed  CAS  Google Scholar 

  • Mashimo K, Kawata M, Yamamoto K (2003) Roles of the RecJ and RecQ proteins in spontaneous formation of deletion mutations in the Escherichia coli K12 endogenous tonB gene. Mutagenesis 18:355–363

    Article  PubMed  CAS  Google Scholar 

  • Mashimo K, Nagata Y, Kawata M, Iwasaki H, Yamamoto K (2004) Role of the RuvAB protein in avoiding spontaneous formation of deletion mutations in the Escherichia coli K-12 endogenous tonB gene. Biochem Biophys Res Commun 323:197–203

    Article  PubMed  CAS  Google Scholar 

  • Modrich P (1987) DNA mismatch correction. Annu Rev Biochem 56:435–466

    Article  PubMed  CAS  Google Scholar 

  • Nagata Y, Mashimo K, Kawata M, Yamamoto K (2002) The roles of Klenow processing and flap processing activities of DNA polymerase I in chromosome instability in Escherichia coli K12 strains. Genetics 160:13–23

    PubMed  CAS  Google Scholar 

  • Nagata Y, Kawaguchi G, Tago Y, Imai M, Watanabe T, Sakurai S, Ihara M, Kawata M, Yamamoto K (2005) Absence of strand bias for deletion mutagenesis during chromosomal leading and lagging strand replication in Escherichia coli. Genes Genet Syst 80:1–8

    Article  PubMed  CAS  Google Scholar 

  • Radman M, Wagner R (1986) Mismatch repair in Escherichia coli. Annu Rev Genet 20:523–538

    Article  PubMed  CAS  Google Scholar 

  • Schaaper RM (1993) Base selection, proofreading, and mismatch repair during DNA replication in Escherichia coli. J Bio Chem 268:23762–23765

    CAS  Google Scholar 

  • Schaaper RM, Dunn RI (1987) Spectra of spontaneous mutations in Escherichia coli strains defective in mismatch correction: the nature of in vivo DNA replication errors. Proc Natl Acad Sci USA 84:6220–6224

    Article  PubMed  CAS  Google Scholar 

  • Schaaper RM, Dunn RI (1991) Spontaneous mutation in the Escherichia coli lacI gene. Genetics 129:317–326

    PubMed  CAS  Google Scholar 

  • Streisinger G, Okada Y, Emrich YJ, Newton J, Tsugita A, Terzaghi E, Inouye M (1996) Frameshift mutations and the genetic code. Cold Spring Harb Symp Quant Biol 31:77–84

    Google Scholar 

  • Su SS, Lahue RS, Au KG, Modrich P (1988) Mispair specificity of methyl-directed DNA mismatch correction in vitro. J Biol Chem 263:6829–6835

    PubMed  CAS  Google Scholar 

  • Tago YI, Imai M, Ihara M, Atofuji H, Nagata Y, Yamamoto K (2005) Escherichia coli Mutator ΔpolA is defective in base mismatch correction: the nature of in vivo DNA replication errors. J Mol Biol 351:299–308

    Article  PubMed  CAS  Google Scholar 

  • Wang RF, Kushner SR (1991) Construction of versatile low-copy-number vectors for cloning, sequencing and gene expression in Escherichia coli. Gene 100:195–199

    Article  PubMed  CAS  Google Scholar 

  • Wang X, Kitamura K, Yamamoto K (1996) Mutagenic specificity of N-methyl-N’-nitro-N-nitrosoguanidine in the tonB gene on the chromosome of Escherichia coli recA + and recA − cells. Biochem Biophys Res Commun 227:334–339

    Article  PubMed  CAS  Google Scholar 

  • Yamamura E, Nunoshiba T, Kawata M, Yamamoto K (2000) Characterization of spontaneous mutation in the oxyR strain of Escherichia coli. Biochem Biophys Res Commun 279:427–432

    Article  PubMed  CAS  Google Scholar 

  • Yamamura E, Lee EH, Kuzumaki A, Uematsu N, Nunoshiba T, Kawata M, Yamamoto K (2002) Characterization of spontaneous mutation in the ΔsoxR and SoxS overproducing strains of Escherichia coli. J Radiat Res 43:195–203

    Article  PubMed  CAS  Google Scholar 

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Acknowledgements

The research was sponsored by a Grant-in-aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology, Japan

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Authors and Affiliations

  1. Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan

    Masaru Imai, Yu-ichiro Tago, Masakado Kawata & Kazuo Yamamoto

  2. Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-8523, Japan

    Makoto Ihara

  3. Department of Biomolecular Sciences, Graduate School of Life Sciences, Tohoku University, Katahira 2-1-1, Aoba-ku, Sendai, 980-8577, Japan

    Kazuo Yamamoto

Authors
  1. Masaru Imai
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  2. Yu-ichiro Tago
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  3. Makoto Ihara
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  4. Masakado Kawata
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  5. Kazuo Yamamoto
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Corresponding author

Correspondence to Kazuo Yamamoto.

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Communicated by A. Aguilera.

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Imai, M., Tago, Yi., Ihara, M. et al. Role of the 5´ → 3´ exonuclease and Klenow fragment of Escherichia coli DNA polymerase I in base mismatch repair. Mol Genet Genomics 278, 211–220 (2007). https://doi.org/10.1007/s00438-007-0239-8

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  • DOI: https://doi.org/10.1007/s00438-007-0239-8

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