The 3′→5′ Exonucleases of DNA Polymerases δ and ɛ and the 5′→3′ Exonuclease Exo1 Have Major Roles in Postreplication Mutation Avoidance in Saccharomyces cerevisiae

REFERENCES

• Bennett, C., A. Lewis, K. Baldwin, and J. Resnick 1993. Lethality induced by a single site-specific double-strand break in a dispensable yeast plasmid. Proc. Natl. Acad. Sci. USA 90:5613–5617.
   PubMed Web of Science ®Google Scholar
• Boeke, J. D., F. LaCroute, and J. Fink 1984. A positive selection for mutants lacking orotidine-5′-phosphate decarboxylase activity in yeast: 5-fluoro-orotic acid resistance. Mol. Gen. Genet. 197:345–346.
   PubMedGoogle Scholar
• Bonneaud, N., K. O. Ozier, G. Y. Li, M. Labouesse, S. L. Minvielle, and J. Lacroute 1991. A family of low and high copy replicative, integrative and single-stranded S. cerevisiae/E. coli shuttle vectors. Yeast 7:609–615.
   PubMed Web of Science ®Google Scholar
• Burns, N., B. Grimwade, M. P. Ross, E. Y. Choi, K. Finberg, G. S. Roeder, and J. Snyder 1994. Large-scale analysis of gene expression, protein localization, and gene disruption in Saccharomyces cerevisiae. Genes Dev. 8:1087–1105.
   PubMed Web of Science ®Google Scholar
• Cooper, D. L., R. S. Lahue, and J. Modrich 1993. Methyl-directed mismatch repair is bidirectional. J. Biol. Chem. 268:11823–11829.
   PubMedGoogle Scholar
• Eissenberg, J. C., R. Ayyagari, X. V. Gomes, and J. Burgers 1997. Mutations in yeast proliferating cell nuclear antigen define distinct sites for interaction with DNA polymerase δ and DNA polymerase ɛ. Mol. Cell. Biol. 17:6367–6378.
   PubMed Web of Science ®Google Scholar
• Fang, W. H., and J. Modrich 1993. Human strand-specific mismatch repair occurs by a bidirectional mechanism similar to that of the bacterial reaction. J. Biol. Chem. 268:11838–11844.
   PubMedGoogle Scholar
• Fijalkowska, I. J., and J. Schaaper 1996. Mutants in the Exo I motif of Escherichia coli dnaQ: defective proofreading and inviability due to error catastrophe. Proc. Natl. Acad. Sci. USA 93:2856–2861.
   PubMedGoogle Scholar
• Fiorentini, P., K. N. Huang, D. X. Tishkoff, R. D. Kolodner, and J. Symington 1997. Exonuclease I of Saccharomyces cerevisiae functions in mitotic recombination in vivo and in vitro. Mol. Cell. Biol. 17:2764–2773.
   PubMed Web of Science ®Google Scholar
• Gietz, R. D., and J. Schiestl 1991. Applications of high efficiency lithium acetate transformation of intact yeast cells using single-stranded nucleic acids as carrier. Yeast 7:253–263.
   PubMed Web of Science ®Google Scholar
• Greene, C. N., and J. Jinks 1997. Frameshift intermediates in homopolymer runs are removed efficiently by yeast mismatch repair proteins. Mol. Cell. Biol. 17:2844–2850.
   PubMedGoogle Scholar
• Johnson, R. E., G. K. Kovvali, S. N. Guzder, N. S. Amin, C. Holm, Y. Habraken, P. Sung, L. Prakash, and J. Prakash 1996. Evidence for involvement of yeast proliferating cell nuclear antigen in DNA mismatch repair. J. Biol. Chem. 271:27987–27990.
   PubMedGoogle Scholar
• Johnson, R. E., G. K. Kovvali, L. Prakash, and J. Prakash 1995. Requirement of the yeast RTH1 5′ to 3′ exonuclease for the stability of simple repetitive DNA. Science 269:238–240.
   PubMed Web of Science ®Google Scholar
• Kesti, T., and J. Syvaoja 1991. Identification and tryptic cleavage of the catalytic core of HeLa and calf thymus DNA polymerase ɛ. J. Biol. Chem. 266:6336–6341.
   PubMedGoogle Scholar
• Kirchner, J., H. T. Tran, and M. A. Resnick. Unpublished data.
   Google Scholar
• Kokoska, R. J., L. Stefanovic, H. T. Tran, M. A. Resnick, D. A. Gordenin, and J. Petes 1998. Destabilization of yeast micro- and minisatellite DNA sequences by mutations affecting a nuclease involved in Okazaki fragment processing (rad27) and DNA polymerase δ (pol3-t). Mol. Cell. Biol. 18:2779–2788.
   PubMedGoogle Scholar
• Kornberg, A., T. Baker 1992. DNA replication, 2nd ed. Freeman, New York, N.Y.
   Google Scholar
• Kroutil, L. C., K. Register, K. Bebenek, and J. Kunkel 1996. Exonucleolytic proofreading during replication of repetitive DNA. Biochemistry 35:1046–1053.
   PubMed Web of Science ®Google Scholar
• Lahue, R. S., K. G. Au, and J. Modrich 1989. DNA mismatch correction in a defined system. Science 245:160–164.
   PubMed Web of Science ®Google Scholar
• Lea, D. E., and J. Coulson 1949. The distribution of the number of mutants in bacterial populations. J. Genet. 49:264–285.
   PubMed Web of Science ®Google Scholar
• Longley, M. J., A. J. Pierce, and J. Modrich 1997. DNA polymerase δ is required for human mismatch repair in vitro. J. Biol. Chem. 272:10917–10921.
   PubMed Web of Science ®Google Scholar
• Modrich, P., and J. Lahue 1996. Mismatch repair in replication fidelity, genetic recombination, and cancer biology. Annu. Rev. Biochem. 65:101–133.
   PubMed Web of Science ®Google Scholar
• Morrison, A., J. B. Bell, T. A. Kunkel, and J. Sugino 1991. Eukaryotic DNA polymerase amino acid sequence required for 3′ to 5′ exonuclease activity. Proc. Natl. Acad. Sci. USA 88:9473–9477.
   PubMedGoogle Scholar
• Morrison, A., A. L. Johnston, L. H. Johnston, and J. Sugino 1993. Pathway correcting DNA replication errors in S. cerevisiae. EMBO J. 12:1467–1473.
   PubMed Web of Science ®Google Scholar
• Morrison, A., and J. Sugino 1994. The 3′ to 5′ exonucleases of both DNA polymerase δ and ɛ participate in correcting errors of DNA replication in S. cerevisiae. Mol. Gen. Genet. 242:289–296.
   PubMedGoogle Scholar
• Protein Data Base. 1998, copyright date. [Online.] http://www.ncbi.nlm.nih.gov/cgi-bin/BLAST/nph-blast?Jform=1 [13 January 1999, last date accessed.]
   Google Scholar
• Sambrook, J., E. F. Fritsch, T. Maniatis 1989. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
   Google Scholar
• Saparbaev, M., L. Prakash, and J. Prakash 1996. Requirement of mismatch repair genes MSH2 and MSH3 in the RAD1-RAD10 pathway of mitotic recombination in Saccharomyces cerevisiae. Genetics 142:727–736.
   PubMed Web of Science ®Google Scholar
• S. cerevisiae DNA Data Base. 1998, copyright date. [Online.] http://genome-www2.stanford.edu/cgi-bin/SGD/nph-blast2sgd [13 January 1999, last date accessed.]
   Google Scholar
• Schaaper, R. M. 1993. Base selection, proofreading, and mismatch repair during DNA replication in Escherichia coli. J. Biol. Chem. 268:23762–23765.
   PubMed Web of Science ®Google Scholar
• Schaaper, R. M. 1988. Mechanisms of mutagenesis in the Escherichia coli mutator mutD5: role of DNA mismatch repair. Proc. Natl. Acad. Sci. USA 85:8126–8130.
   PubMed Web of Science ®Google Scholar
• Selva, E. M., L. New, G. F. Crouse, and J. Lahue 1995. Mismatch correction acts as a barrier to homeologous recombination in Saccharomyces cerevisiae. Genetics 139:1175–1188.
   PubMed Web of Science ®Google Scholar
• Sherman, F., G. F. Fink, J. B. Hicks 1986. Methods in yeast genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
   Google Scholar
• Sia, E. A., R. J. Kokoska, M. Dominska, P. Greenwell, and J. Petes 1997. Microsatellite instability in yeast: dependence on repeat unit size and DNA mismatch repair genes. Mol. Cell. Biol. 17:2851–2858.
   PubMedGoogle Scholar
• Simon, M., L. Giot, and J. Faye 1991. The 3′ to 5′ exonuclease activity located in the DNA polymerase δ subunit of Saccharomyces cerevisiae is required for accurate replication. EMBO J. 10:2165–2170.
   PubMedGoogle Scholar
• Strand, M., M. C. Earley, G. F. Crouse, and J. Petes 1995. Mutations in the MSH3 gene preferentially lead to deletions within tracts of simple repetitive DNA in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 92:10418–10421.
   PubMed Web of Science ®Google Scholar
• Sugawara, N., F. Paques, M. Colaiacovo, and J. Haber 1997. Role of Saccharomyces cerevisiae Msh2 and Msh3 repair proteins in double-strand break-induced recombination. Proc. Natl. Acad. Sci. USA 94:9214–9219.
   PubMed Web of Science ®Google Scholar
• Sugino, A. 1995. Yeast DNA polymerases and their role at the replication fork. Trends Biochem. Sci. 20:319–323.
   PubMed Web of Science ®Google Scholar
• Szankasi, P., and J. Smith 1995. A role for exonuclease I from S. pombe in mutation avoidance and mismatch correction. Science 267:1166–1169.
   PubMed Web of Science ®Google Scholar
• Thomas, D. C., J. D. Roberts, and J. Kunkel 1991. Heteroduplex repair in extracts of human HeLa cells. J. Biol. Chem. 266:3744–3751.
   PubMed Web of Science ®Google Scholar
• Tishkoff, D. X., A. L. Boerger, P. Bertrand, N. Filosi, G. M. Gaida, M. F. Kane, and J. Kolodner 1997. Identification and characterization of Saccharomyces cerevisiae EXO1, a gene encoding an exonuclease that interacts with MSH2. Proc. Natl. Acad. Sci. USA 94:7487–7492.
   PubMed Web of Science ®Google Scholar
• Tran, H., N. Degtyareva, D. Gordenin, and J. Resnick 1997. Altered replication and inverted repeats induce mismatch repair-independent recombination between highly diverged DNAs in yeast. Mol. Cell. Biol. 17:1027–1036.
   PubMedGoogle Scholar
• Tran, H. T., J. D. Keen, M. Kricker, M. A. Resnick, and J. Gordenin 1997. Hypermutability of homonucleotide runs in mismatch repair and DNA polymerase proofreading yeast mutants. Mol. Cell. Biol. 17:2859–2865.
   PubMed Web of Science ®Google Scholar
• Tran, T. H., N. P. Degtyareva, N. N. Koloteva, A. Sugino, H. Masumoto, D. A. Gordenin, and J. Resnick 1995. Replication slippage between distant short repeats in Saccharomyces cerevisiae depends on the direction of replication and the RAD50 and RAD52 genes. Mol. Cell. Biol. 15:5607–5617.
   PubMedGoogle Scholar
• Tran, T. H., D. Gordenin, and J. Resnick 1996. The prevention of repeat-associated deletions in Saccharomyces cerevisiae by mismatch repair depends on size and origin of deletions. Genetics 143:1579–1587.
   PubMedGoogle Scholar
• Umar, A., A. B. Buermeyer, J. A. Simon, D. C. Thomas, A. B. Clark, R. M. Liskay, and J. Kunkel 1996. Requirement for PCNA in DNA mismatch repair at a step preceding DNA resynthesis. Cell 87:65–73.
   PubMed Web of Science ®Google Scholar
• Viswanathan, M., and J. Lovett 1998. Single-strand DNA-specific exonucleases in Escherichia coli: roles in repair and mutation avoidance. Genetics 149:7–16.
   PubMed Web of Science ®Google Scholar
• Wach, A., A. Brachat, R. Pohlmann, and J. Philippsen 1994. New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae. Yeast 10:1793–1808.
   PubMed Web of Science ®Google Scholar