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Molecular mechanisms generating and suppressing spontaneous mutations

Research Project

Project/Area Number 12213082
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionNara Institute of Science and Technology

Principal Investigator

MAKI Hisaji  The Graduate school of Biological Science, Prof, バイオサイエンス研究科, 教授 (20199649)

Co-Investigator(Kenkyū-buntansha) YOSHIYAMA Kaoru  The Graduate school of Biological Science, Asst. Prof, バイオサイエンス研究科, 助手 (10346322)
Project Period (FY) 2000 – 2004
Project Status Completed (Fiscal Year 2004)
Budget Amount *help
¥66,000,000 (Direct Cost: ¥66,000,000)
Fiscal Year 2004: ¥13,300,000 (Direct Cost: ¥13,300,000)
Fiscal Year 2003: ¥13,600,000 (Direct Cost: ¥13,600,000)
Fiscal Year 2002: ¥14,000,000 (Direct Cost: ¥14,000,000)
Fiscal Year 2001: ¥13,100,000 (Direct Cost: ¥13,100,000)
Fiscal Year 2000: ¥12,000,000 (Direct Cost: ¥12,000,000)
Keywordsmutator / DNA replication / DNA repair / KO mouse / DNA damage / DNA polymerase / proofreading / frameshift / DNA報復 / 修復 / 大腸菌
Research Abstract

Spontaneous mutations are derived from various sources, including errors made during replication of undamaged template DNA, mutagenic nucleotide substrates, and endogenous DNA lesions. These sources vary in their frequencies and resultant mutations, and are differently affected by the DNA sequence, DNA transactions, and cellular metabolism. Organisms possess a variety of cellular functions to suppress spontaneous mutagenesis, and the specificity and effectiveness of each function strongly affect the pattern of spontaneous mutations. Base substitutions and single-base frameshifts, two major classes of spontaneous mutations, occur non-randomly throughout the genome. Within target DNA sequences there are hotspots for particular types of spontaneous mutations; outside of the hotspots, spontaneous mutations occur more randomly and much less frequently. Hotspot mutations are attributable more to endogenous DNA lesions than to replication errors. Recently, a novel class of mutagenic pathway t … More hat depends on short inverted repeats was identified as another important source of hotspot mutagenesis. In our project, we focused on molecular mechanisms that induce and suppress the spontaneous mutagenesis. From systematic analyses of spontaneous mutations occurring in wild-type and mismatch-repair deficient mutant of Eschrichia coli as well as mice, we first revealed that almost all of the DNA replication errors are corrected by the mismatch repair system and do not contribute to the generation of spontaneous mutations. Therefore, most of the spontaneous mutations are likely to arise from pre-mutagenic DNA lesions that are resistant to the mismatch-repair correction. As a major source of such pre-mutagenic lesion, we examined relative contribution of spontaneous oxidative DNA lesion and found that hydroxyl radicals are responsible to produce spontaneous base substitutions, especially hot-spot type of mutations. As another source of spontaneous mutations, we identified templete-switching type of DNA replication errors. This involves inverted repeats in geenome DNA, and processing of Okazaki-fragment seemed to play a crucial role. Furthermore, it appeared that exonuclease I sharply suppresses spontaneous mutagenesis caused by the template-switching errors. Using a system of semi-bidirectional DNA replication of an oriC plasmid that employs purified replicative enzymes and a replication-terminating protein of Escherichia coli, we examined the dynamics of the replication fork when it encounters a single abasic DNA lesion on the template DNA. A DNA lesion located on the lagging strand completely blocked the synthesis of the Okazaki fragment extending toward the lesion site but did not affect the progression of the replication fork or leading-strand DNA synthesis. In contrast, a DNA lesion on the leading strand stalled the replication fork in conjunction with strongly inhibiting leading-strand synthesis. However, about two thirds of the replication forks encountering this lesion maintained lagging-strand synthesis for about 1 kb beyond the lesion site, and the velocity with which the replication fork progressed seemed to be significantly reduced. Less

Report

(6 results)
  • 2004 Annual Research Report   Final Research Report Summary
  • 2003 Annual Research Report
  • 2002 Annual Research Report
  • 2001 Annual Research Report
  • 2000 Annual Research Report
  • Research Products

    (53 results)

All 2004 2003 2002 2001 2000 Other

All Journal Article (31 results) Publications (22 results)

  • [Journal Article] Evidence for interplay among yeast replicative DNA polymerases alpha, delta and epsilon from studies of exonuclease and polymerase active site mutations.2004

    • Author(s)
      Pavlov, Y.
    • Journal Title

      BMC Biol 2

      Pages: 11-11

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Distinct roles of DNA polymerases dalta and epsilon at the replication fork in Xenopus egg extracts.2004

    • Author(s)
      Fukui, T.
    • Journal Title

      Genes to Cells 9

      Pages: 179-191

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Evidence for interplay among yeast replicative DNA polymerases alpha, delta and epsilon from studies of exonuclease and polymerase active site mutations.2004

    • Author(s)
      Pavlov, Y., et al.
    • Journal Title

      BMC Biol 2

      Pages: 11-11

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Distinct roles of DNA polymerases dalta and epsilon at the replication fork in Xenopus egg extracts.2004

    • Author(s)
      Fukui, T., et al.
    • Journal Title

      Genes to Cells 9

      Pages: 179-191

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Distinct roles of DNA polymerases dalta and epsilon at the replication fork in Xenopus egg extracts.2004

    • Author(s)
      T.Fukui
    • Journal Title

      Genes to Cells 9

      Pages: 179-191

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Evidence for interplay among yeast replicative DNA polymerases alpha, delta and epsilon from studies of exonuclease and polymerase active site mutations.2004

    • Author(s)
      Y.Pavlov
    • Journal Title

      BMC Biol 2・1

      Pages: 11-11

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Double-stranded DNA binding properties of Saccharomyces cerevisiae DNA polymerase ε and of the Dpb3p-Dpb4p subassembly.2003

    • Author(s)
      Tsubota, T.
    • Journal Title

      Genes to Cells 8

      Pages: 873-888

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Fate of DNA replication fork encountering a single DNA lesion during oriC plasmid DNA replication in vitro.2003

    • Author(s)
      Higuchi, K.
    • Journal Title

      Genes to Cells 8

      Pages: 437-449

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Positive and negative roles of homologous recombination in the maintenance of genome stability in Saccbaromyces cerevisiae2003

    • Author(s)
      Yoshida, J.
    • Journal Title

      Genetics 164

      Pages: 31-46

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Spontaneous hotspot mutations resistant to mismatch correction in Escherichia coli : Transcription-dependent mutagenesis involving template-switching mechanisms.2003

    • Author(s)
      Yoshiyama, K.
    • Journal Title

      J.Mol.Biol. 327

      Pages: 7-18

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Double-stranded DNA binding properties of Saccharomyces cerevisiae DNA polymerase ε and of the Dpb3p-Dpb4p subassembly.2003

    • Author(s)
      Tsubota, T., et al.
    • Journal Title

      Genes to Cells 8

      Pages: 873-888

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Fate of DNA replication fork encountering a single DNA lesion during oriC plasmid DNA replication in vitro.2003

    • Author(s)
      Higuchi, K., et al.
    • Journal Title

      Genes to Cells 8

      Pages: 437-449

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Positive and negative roles of homologous recombination in the maintenance of genome stability in Saccharomyces cerevisiae.2003

    • Author(s)
      Yoshida, J., et al.
    • Journal Title

      Genetics 164

      Pages: 31-46

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Spontaneous hotspot mutations resistant to mismatch correction in Escherichia coli : Transcription-dependent mutagenesis involving template-switching mechanisms.2003

    • Author(s)
      Yoshiyama, K., et al.
    • Journal Title

      J.Mol.Biol. 327

      Pages: 7-18

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Origins of spontaneous mutations : Specificity of base-substitution, frameshift and sequence-substitution mutageneses.2002

    • Author(s)
      Maki, H.
    • Journal Title

      Annu.Rev.Genet. 36

      Pages: 279-303

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Mutational specificity of mice defective in the MTH1 and/or the MSH2 genes.2002

    • Author(s)
      Egashira, A.
    • Journal Title

      DNA Repair 1

      Pages: 881-893

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Eleveted incidence of loss of heterozygosity(LOH) in an sgs1 mutant of Saccharomyces cerevisiae.2002

    • Author(s)
      Ajima, J.
    • Journal Title

      Mutation Research 504

      Pages: 157-172

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Hyper-processive and slower DNA chain elongation catalyzed by DNA polymerase III holoenzyme purified from tha dnaE173 mutator mutant of Escherichia coli.2002

    • Author(s)
      Sugaya, Y.
    • Journal Title

      Genes to Cells 7

      Pages: 385-399

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Involvement of RAD9-dependent damage checkpoint control in arrest of cell cycle, induction of cell death, and chromosome instability caused by defects in origin recognition complex in Saccharomyces cerevisiae2002

    • Author(s)
      Watanabe, K.
    • Journal Title

      Eukaryotic Cell 1

      Pages: 200-212

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Structural analysis of aberrant chromosomes that occur spontaneously in diploid Saccharomyces cerevisiae : Retrotransposon Tyl plays a crucial role in chromosomal rearrangements.2002

    • Author(s)
      Umezu, K.
    • Journal Title

      Genetics 160

      Pages: 97-110

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Mutational specificity of mice defective in the MTH1 and/or the MSH2 genes.2002

    • Author(s)
      Egashira, A., et al.
    • Journal Title

      DNA Repair 1

      Pages: 881-893

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Eleveted incidence of loss of heterozygosity(LOH) in an sgsl mutant of Saccharomyces cerevisiae.2002

    • Author(s)
      Ajima, J., et al.
    • Journal Title

      Mutation Research 504

      Pages: 157-172

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Hyper-processive and slower DNA chain elongation catalyzed by DNA polymerase III holoenzyme purified from tha dnaE173 mutator mutant of Escherichia coli.2002

    • Author(s)
      Sugaya, Y., et al.
    • Journal Title

      Genes to Cells 7

      Pages: 385-399

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Involvement of RAD9-dependent damage checkpoint control in arrest of cell cycle, induction of cell death, and chromosome instability caused by defects in origin recognition complex in Saccharomyces cerevisiae.2002

    • Author(s)
      Watanabe, K., et al.
    • Journal Title

      Eukaryotic Cell 1

      Pages: 200-212

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Structural analysis of aberrant chromosomes that occur spontaneously in diploid Saccharomyces cerevisiae : Retrotransposon Tyl plays a crucial role in chromosomal rearrangements.2002

    • Author(s)
      Umezu, K., et al.
    • Journal Title

      Genetics 160

      Pages: 97-110

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Directionality of DNA replication fork movement strongly affects the generation of spontaneous mutations in Escherichia coli.2001

    • Author(s)
      Yoshiyama, K.
    • Journal Title

      J.Mol.Biol. 307

      Pages: 1195-1206

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Directionality of DNA replication fork movement strongly affects the generation of spontaneous mutations in Escherichia coli.2001

    • Author(s)
      Yoshiyama, K., et al.
    • Journal Title

      J.Mol.Biol. 307

      Pages: 1195-1206

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Spontaneous loss heterozygosity in diploid Saccharomyces cerevisiae.2000

    • Author(s)
      Hiraoka, M.
    • Journal Title

      Genetics 156

      Pages: 1531-1548

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Two DNA polymerases of Escherichia coli display distinct misinsertion specificities for 2-Hydroxy-dATP during DNA synthesis.2000

    • Author(s)
      Kamiya, M.
    • Journal Title

      Biochemistry 39

      Pages: 9508-9513

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Spontaneous loss heterozygosity in diploid Saccharomyces cerevisiae.2000

    • Author(s)
      Hiraoka, M., et al.
    • Journal Title

      Genetics 156

      Pages: 1531-1548

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Journal Article] Two DNA polymerases of Escherichia coli display distinct misinsertion specificities for 2-Hydroxy-dATP during DNA synthesis.2000

    • Author(s)
      Kamiya, M., et al.
    • Journal Title

      Biochemistry 39

      Pages: 9508-9513

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2004 Final Research Report Summary
  • [Publications] Yoshiyama, K.: "Spontaneous hotspot mutations resistant to mismatch correction in Escherichia coli Transcription-dependent mutagenesis involving template-switching mechanisms."J.Mol.Biol.. 327. 7-18 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Yoshida, J.: "Positive and negative roles of homologous recombination in the maintenance of genome stability in Saccharomyces cerevisiae"Genetics. 164. 31-46 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Higuchi, K.: "Fate of DNA replication fork encountering a single DNA lesion during oriC plasmid DNA replication in vitro."Genes to Cells. 8. 437-449 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Tsubota, T.: "Double-stranded DNA binding properties of Saccharomyces cerevisiae DNA polymerase ε and of the Dpb3p-Dpb4p subassembly."Genes to Cells. 8. 837-888 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Umezu, K.: "Structural analysis of aberrant chromosomes that occur spontaneously in diploid Saccharomyces cerevisiae : Retrotransposon Ty1 plays a crucial role in chromosomal rearrangements"Genetics. 160. 97-110 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Watanabe, K.: "Involvement of RAD9-dependent damage checkpoint control in arrest of cell cycle, induction of cell death, and chromsome instability caused by defects in origin recognition complex in Saccharomyces cerevisiae"Eukaryotic Cell. 1. 200-212 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Sugaya, Y.: "Hyper-processive and slower DNA chain elongation catalyzed by DNA polymerase III holoenzyme purified from tha dnaE173 mutator mutant of Escherichia coli"Genes to Cells. 7. 385-399 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Ajima, J.: "Eleveted incidence of loss of heterozygosity (LOH) in an sgs1 mutant of Saccharomyces cerevisiae"Mutation Research. 504. 157-172 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Egashira, A.: "Mutational specificity of mice defective in the MTH1 and/or the MSH2 genes"DNA Repair. 1. 884-893 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Maki, H.: "Origins of spontaneous mutations : Specificity of base-substitution, frameshift and sequence-substitution mutageneses"Annu. Rev. Genet.. 36. 279-303 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] Yoshiyama, K.: "Spontaneous hotspot mutations resistant to mismatch correction in Escherichia coli ; Transcription-dependent mutagenesis involving template-switching mechanisms"J. Mol. Biol.. 327. 7-18 (2003)

    • Related Report
      2002 Annual Research Report
  • [Publications] Yoshida, J.: "Positive and negative roles of homologous recombination in the maintenance of genome stability in Saccharomyces cerevisiae"Genetics. (In Press). (2003)

    • Related Report
      2002 Annual Research Report
  • [Publications] Higuchi, K.: "Fate of DNA replication fork encountering a single DNA lesion during oriC plasmid DNA replication in vitro"Genes to Cells. (In Press). (2003)

    • Related Report
      2002 Annual Research Report
  • [Publications] Yoshiyama, K.: "Directionality of DNA replication fork movement strongly affects the generation of spontaneous mutations in Escherichia coli"J. Mol. Biol.. 307. 1195-1206 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] Umezu, K.: "Structural analysis of aberrant chromosomes that occur spontaneously in diploid Saccharomyces cerevisiae : Retrotransposon Ty1 plays a crucial role in chromosomal rearrangements"Genetics. 160. 97-110 (2002)

    • Related Report
      2001 Annual Research Report
  • [Publications] Watanabe, K.: "Involvement of RAD9-dependent damage checkpoint control in arrest of cell cycle, induction of cell death, and chromosome instability caused by defects in origin recognition complex in Saccharomyces cerevisiae"Eukaryotic Cell. (In press). (2002)

    • Related Report
      2001 Annual Research Report
  • [Publications] Sugaya, Y.: "Hyper-processive and slower DNA chain elongation catalyzed by DNA polymerase III holoenzyme purified from tha dnaE173 mutator mutant of Escherichia coli"Genes to Cells. (In press). (2002)

    • Related Report
      2001 Annual Research Report
  • [Publications] Tsuzuki, T.: "Spontaneous tumorigenesis and mutagenesis in mice defective in the MTH1 gene encoding 8-oxo-dGTPase"Mutation Research. (In Press). (2002)

    • Related Report
      2001 Annual Research Report
  • [Publications] Ajima, J.: "Eleveted incidence of loss of heterozygosity(LOH) in an sgs1 mutant of Saccharomyces cerevisiae"Mutation Research. (In Press). (2002)

    • Related Report
      2001 Annual Research Report
  • [Publications] Yoshiyama,K.: "Directionality of DNA replication fork movement strongly affects the generation of spontaneous mutations in Escherichia coli."J.Mol.Biol.. (印刷中). (2001)

    • Related Report
      2000 Annual Research Report
  • [Publications] Hiraoka,M.: "Spontaneous loss of heterozygosity in diploid Saccharomyces cerevisiae cells."Genetics. 156. 1531-1548 (2000)

    • Related Report
      2000 Annual Research Report
  • [Publications] Kamiya,H.: "Two DNA polymerases of Escherichia coli display distinct misinsertion specificities for 2-Hydroxy-dATP during DNA synthesis."Biochemistry. 39. 9508-9513 (2000)

    • Related Report
      2000 Annual Research Report

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Published: 2000-04-01   Modified: 2018-03-28  

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