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. 2001 Sep;159(1):65–75. doi: 10.1093/genetics/159.1.65

Spontaneous frameshift mutations in Saccharomyces cerevisiae: accumulation during DNA replication and removal by proofreading and mismatch repair activities.

C N Greene 1, S Jinks-Robertson 1
PMCID: PMC1461796  PMID: 11560887

Abstract

The accumulation of frameshift mutations during DNA synthesis is determined by the rate at which frameshift intermediates are generated during DNA polymerization and the efficiency with which frameshift intermediates are removed by DNA polymerase-associated exonucleolytic proofreading activity and/or the postreplicative mismatch repair machinery. To examine the relative contributions of these factors to replication fidelity in Saccharomyces cerevisiae, we determined the reversion rates and spectra of the lys2 Delta Bgl +1 frameshift allele. Wild-type and homozygous mutant diploid strains with all possible combinations of defects in the exonuclease activities of DNA polymerases delta and epsilon (conferred by the pol3-01 and pol2-4 alleles, respectively) and in mismatch repair (deletion of MSH2) were analyzed. Although there was no direct correlation between homopolymer run length and frameshift accumulation in the wild-type strain, such a correlation was evident in the triple mutant strain lacking all repair capacity. Furthermore, examination of strains defective in one or two repair activities revealed distinct biases in the removal of the corresponding frameshift intermediates by exonucleolytic proofreading and/or mismatch repair. Finally, these analyses suggest that the mismatch repair machinery may be important for generating some classes of frameshift mutations in yeast.

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Selected References

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  1. Bebenek K., Kunkel T. A. Frameshift errors initiated by nucleotide misincorporation. Proc Natl Acad Sci U S A. 1990 Jul;87(13):4946–4950. doi: 10.1073/pnas.87.13.4946. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bessman M. J., Reha-Krantz L. J. Studies on the biochemical basis of spontaneous mutation. V. Effect of temperature on mutation frequency. J Mol Biol. 1977 Oct 15;116(1):115–123. doi: 10.1016/0022-2836(77)90122-x. [DOI] [PubMed] [Google Scholar]
  3. Bloom L. B., Chen X., Fygenson D. K., Turner J., O'Donnell M., Goodman M. F. Fidelity of Escherichia coli DNA polymerase III holoenzyme. The effects of beta, gamma complex processivity proteins and epsilon proofreading exonuclease on nucleotide misincorporation efficiencies. J Biol Chem. 1997 Oct 31;272(44):27919–27930. doi: 10.1074/jbc.272.44.27919. [DOI] [PubMed] [Google Scholar]
  4. Boeke J. D., Trueheart J., Natsoulis G., Fink G. R. 5-Fluoroorotic acid as a selective agent in yeast molecular genetics. Methods Enzymol. 1987;154:164–175. doi: 10.1016/0076-6879(87)54076-9. [DOI] [PubMed] [Google Scholar]
  5. Buermeyer A. B., Deschênes S. M., Baker S. M., Liskay R. M. Mammalian DNA mismatch repair. Annu Rev Genet. 1999;33:533–564. doi: 10.1146/annurev.genet.33.1.533. [DOI] [PubMed] [Google Scholar]
  6. Datta A., Schmeits J. L., Amin N. S., Lau P. J., Myung K., Kolodner R. D. Checkpoint-dependent activation of mutagenic repair in Saccharomyces cerevisiae pol3-01 mutants. Mol Cell. 2000 Sep;6(3):593–603. doi: 10.1016/s1097-2765(00)00058-7. [DOI] [PubMed] [Google Scholar]
  7. Drake J. W., Charlesworth B., Charlesworth D., Crow J. F. Rates of spontaneous mutation. Genetics. 1998 Apr;148(4):1667–1686. doi: 10.1093/genetics/148.4.1667. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Fijalkowska I. J., Schaaper R. M. Mutants in the Exo I motif of Escherichia coli dnaQ: defective proofreading and inviability due to error catastrophe. Proc Natl Acad Sci U S A. 1996 Apr 2;93(7):2856–2861. doi: 10.1073/pnas.93.7.2856. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Flores-Rozas H., Kolodner R. D. The Saccharomyces cerevisiae MLH3 gene functions in MSH3-dependent suppression of frameshift mutations. Proc Natl Acad Sci U S A. 1998 Oct 13;95(21):12404–12409. doi: 10.1073/pnas.95.21.12404. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Foiani M., Pellicioli A., Lopes M., Lucca C., Ferrari M., Liberi G., Muzi Falconi M., Plevani1 P. DNA damage checkpoints and DNA replication controls in Saccharomyces cerevisiae. Mutat Res. 2000 Jun 30;451(1-2):187–196. doi: 10.1016/s0027-5107(00)00049-x. [DOI] [PubMed] [Google Scholar]
  11. Gietz D., St Jean A., Woods R. A., Schiestl R. H. Improved method for high efficiency transformation of intact yeast cells. Nucleic Acids Res. 1992 Mar 25;20(6):1425–1425. doi: 10.1093/nar/20.6.1425. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Gong J. G., Costanzo A., Yang H. Q., Melino G., Kaelin W. G., Jr, Levrero M., Wang J. Y. The tyrosine kinase c-Abl regulates p73 in apoptotic response to cisplatin-induced DNA damage. Nature. 1999 Jun 24;399(6738):806–809. doi: 10.1038/21690. [DOI] [PubMed] [Google Scholar]
  13. Goodman M. F., Fygenson K. D. DNA polymerase fidelity: from genetics toward a biochemical understanding. Genetics. 1998 Apr;148(4):1475–1482. doi: 10.1093/genetics/148.4.1475. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Gordenin D. A., Malkova A. L., Peterzen A., Kulikov V. N., Pavlov Y. I., Perkins E., Resnick M. A. Transposon Tn5 excision in yeast: influence of DNA polymerases alpha, delta, and epsilon and repair genes. Proc Natl Acad Sci U S A. 1992 May 1;89(9):3785–3789. doi: 10.1073/pnas.89.9.3785. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Greene C. N., Jinks-Robertson S. Frameshift intermediates in homopolymer runs are removed efficiently by yeast mismatch repair proteins. Mol Cell Biol. 1997 May;17(5):2844–2850. doi: 10.1128/mcb.17.5.2844. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Harfe B. D., Jinks-Robertson S. DNA mismatch repair and genetic instability. Annu Rev Genet. 2000;34:359–399. doi: 10.1146/annurev.genet.34.1.359. [DOI] [PubMed] [Google Scholar]
  17. Johnson R. E., Kovvali G. K., Prakash L., Prakash S. Requirement of the yeast MSH3 and MSH6 genes for MSH2-dependent genomic stability. J Biol Chem. 1996 Mar 29;271(13):7285–7288. doi: 10.1074/jbc.271.13.7285. [DOI] [PubMed] [Google Scholar]
  18. Karthikeyan R., Vonarx E. J., Straffon A. F., Simon M., Faye G., Kunz B. A. Evidence from mutational specificity studies that yeast DNA polymerases delta and epsilon replicate different DNA strands at an intracellular replication fork. J Mol Biol. 2000 Jun 2;299(2):405–419. doi: 10.1006/jmbi.2000.3744. [DOI] [PubMed] [Google Scholar]
  19. Kesti T., Flick K., Keränen S., Syväoja J. E., Wittenberg C. DNA polymerase epsilon catalytic domains are dispensable for DNA replication, DNA repair, and cell viability. Mol Cell. 1999 May;3(5):679–685. doi: 10.1016/s1097-2765(00)80361-5. [DOI] [PubMed] [Google Scholar]
  20. Kroutil L. C., Register K., Bebenek K., Kunkel T. A. Exonucleolytic proofreading during replication of repetitive DNA. Biochemistry. 1996 Jan 23;35(3):1046–1053. doi: 10.1021/bi952178h. [DOI] [PubMed] [Google Scholar]
  21. Kunkel T. A., Bebenek K. DNA replication fidelity. Annu Rev Biochem. 2000;69:497–529. doi: 10.1146/annurev.biochem.69.1.497. [DOI] [PubMed] [Google Scholar]
  22. Kunkel T. A. Biological asymmetries and the fidelity of eukaryotic DNA replication. Bioessays. 1992 May;14(5):303–308. doi: 10.1002/bies.950140503. [DOI] [PubMed] [Google Scholar]
  23. Kunkel T. A., Soni A. Mutagenesis by transient misalignment. J Biol Chem. 1988 Oct 15;263(29):14784–14789. [PubMed] [Google Scholar]
  24. Lichten M., Borts R. H., Haber J. E. Meiotic gene conversion and crossing over between dispersed homologous sequences occurs frequently in Saccharomyces cerevisiae. Genetics. 1987 Feb;115(2):233–246. doi: 10.1093/genetics/115.2.233. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Marsischky G. T., Filosi N., Kane M. F., Kolodner R. Redundancy of Saccharomyces cerevisiae MSH3 and MSH6 in MSH2-dependent mismatch repair. Genes Dev. 1996 Feb 15;10(4):407–420. doi: 10.1101/gad.10.4.407. [DOI] [PubMed] [Google Scholar]
  26. Morrison A., Bell J. B., Kunkel T. A., Sugino A. Eukaryotic DNA polymerase amino acid sequence required for 3'----5' exonuclease activity. Proc Natl Acad Sci U S A. 1991 Nov 1;88(21):9473–9477. doi: 10.1073/pnas.88.21.9473. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Morrison A., Johnson A. L., Johnston L. H., Sugino A. Pathway correcting DNA replication errors in Saccharomyces cerevisiae. EMBO J. 1993 Apr;12(4):1467–1473. doi: 10.1002/j.1460-2075.1993.tb05790.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Morrison A., Sugino A. The 3'-->5' exonucleases of both DNA polymerases delta and epsilon participate in correcting errors of DNA replication in Saccharomyces cerevisiae. Mol Gen Genet. 1994 Feb;242(3):289–296. doi: 10.1007/BF00280418. [DOI] [PubMed] [Google Scholar]
  29. Schaaper R. M. Base selection, proofreading, and mismatch repair during DNA replication in Escherichia coli. J Biol Chem. 1993 Nov 15;268(32):23762–23765. [PubMed] [Google Scholar]
  30. Shcherbakova P. V., Pavlov Y. I. 3'-->5' exonucleases of DNA polymerases epsilon and delta correct base analog induced DNA replication errors on opposite DNA strands in Saccharomyces cerevisiae. Genetics. 1996 Mar;142(3):717–726. doi: 10.1093/genetics/142.3.717. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Streisinger G., Okada Y., Emrich J., Newton J., Tsugita A., Terzaghi E., Inouye M. Frameshift mutations and the genetic code. This paper is dedicated to Professor Theodosius Dobzhansky on the occasion of his 66th birthday. Cold Spring Harb Symp Quant Biol. 1966;31:77–84. doi: 10.1101/sqb.1966.031.01.014. [DOI] [PubMed] [Google Scholar]
  32. Sugino A. Yeast DNA polymerases and their role at the replication fork. Trends Biochem Sci. 1995 Aug;20(8):319–323. doi: 10.1016/s0968-0004(00)89059-3. [DOI] [PubMed] [Google Scholar]
  33. Toft N. J., Winton D. J., Kelly J., Howard L. A., Dekker M., te Riele H., Arends M. J., Wyllie A. H., Margison G. P., Clarke A. R. Msh2 status modulates both apoptosis and mutation frequency in the murine small intestine. Proc Natl Acad Sci U S A. 1999 Mar 30;96(7):3911–3915. doi: 10.1073/pnas.96.7.3911. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Tran H. T., Gordenin D. A., Resnick M. A. The 3'-->5' exonucleases of DNA polymerases delta and epsilon and the 5'-->3' exonuclease Exo1 have major roles in postreplication mutation avoidance in Saccharomyces cerevisiae. Mol Cell Biol. 1999 Mar;19(3):2000–2007. doi: 10.1128/mcb.19.3.2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Tran H. T., Keen J. D., Kricker M., Resnick M. A., Gordenin D. A. Hypermutability of homonucleotide runs in mismatch repair and DNA polymerase proofreading yeast mutants. Mol Cell Biol. 1997 May;17(5):2859–2865. doi: 10.1128/mcb.17.5.2859. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Wang T. F., Kleckner N., Hunter N. Functional specificity of MutL homologs in yeast: evidence for three Mlh1-based heterocomplexes with distinct roles during meiosis in recombination and mismatch correction. Proc Natl Acad Sci U S A. 1999 Nov 23;96(24):13914–13919. doi: 10.1073/pnas.96.24.13914. [DOI] [PMC free article] [PubMed] [Google Scholar]

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