Skip to main content
PMC home page
Genetics logoLink to Genetics
. 2003 Sep;165(1):65–81. doi: 10.1093/genetics/165.1.65

Genomic instability induced by mutations in Saccharomyces cerevisiae POL1.

Pedro J A Gutiérrez 1, Teresa S-F Wang 1
PMCID: PMC1462734  PMID: 14504218

Abstract

Mutations of chromosome replication genes can be one of the early events that promote genomic instability. Among genes that are involved in chromosomal replication, DNA polymerase alpha is essential for initiation of replication and lagging-strand synthesis. Here we examined the effect of two mutations in S. cerevisiae POL1, pol1-1 and pol1-17, on a microsatellite (GT)(16) tract. The pol1-17 mutation elevated the mutation rate 13-fold by altering sequences both inside and downstream of the (GT)(16) tract, whereas the pol1-1 mutation increased the mutation rate 54-fold by predominantly altering sequences downstream of the (GT)(16) tract in a RAD52-dependent manner. In a rad52 null mutant background pol1-1 and pol1-17 also exhibited different plasmid and chromosome loss phenotypes. Deletions of mismatch repair (MMR) genes induce a differential synergistic increase in the mutation rates of pol1-1 and pol1-17. These findings suggest that perturbations of DNA replication in these two pol1 mutants are caused by different mechanisms, resulting in various types of mutations. Thus, mutations of POL1 can induce a variety of mutator phenotypes and can be a source of genomic instability in cells.

Full Text

The Full Text of this article is available as a PDF (321.3 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Adams Martin A., Dionne I., Wellinger R. J., Holm C. The function of DNA polymerase alpha at telomeric G tails is important for telomere homeostasis. Mol Cell Biol. 2000 Feb;20(3):786–796. doi: 10.1128/mcb.20.3.786-796.2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bhaumik D., Wang T. S. Mutational effect of fission yeast polalpha on cell cycle events. Mol Biol Cell. 1998 Aug;9(8):2107–2123. doi: 10.1091/mbc.9.8.2107. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Boddy M. N., Russell P. DNA replication checkpoint. Curr Biol. 2001 Nov 27;11(23):R953–R956. doi: 10.1016/s0960-9822(01)00572-3. [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. Copeland W. C., Lam N. K., Wang T. S. Fidelity studies of the human DNA polymerase alpha. The most conserved region among alpha-like DNA polymerases is responsible for metal-induced infidelity in DNA synthesis. J Biol Chem. 1993 May 25;268(15):11041–11049. [PubMed] [Google Scholar]
  6. Dahlén Maria, Sunnerhagen Per, Wang Teresa S-F. Replication proteins influence the maintenance of telomere length and telomerase protein stability. Mol Cell Biol. 2003 May;23(9):3031–3042. doi: 10.1128/MCB.23.9.3031-3042.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Delarue M., Poch O., Tordo N., Moras D., Argos P. An attempt to unify the structure of polymerases. Protein Eng. 1990 May;3(6):461–467. doi: 10.1093/protein/3.6.461. [DOI] [PubMed] [Google Scholar]
  8. Diede S. J., Gottschling D. E. Telomerase-mediated telomere addition in vivo requires DNA primase and DNA polymerases alpha and delta. Cell. 1999 Dec 23;99(7):723–733. doi: 10.1016/s0092-8674(00)81670-0. [DOI] [PubMed] [Google Scholar]
  9. Franklin M. C., Wang J., Steitz T. A. Structure of the replicating complex of a pol alpha family DNA polymerase. Cell. 2001 Jun 1;105(5):657–667. doi: 10.1016/s0092-8674(01)00367-1. [DOI] [PubMed] [Google Scholar]
  10. 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]
  11. Henderson S. T., Petes T. D. Instability of simple sequence DNA in Saccharomyces cerevisiae. Mol Cell Biol. 1992 Jun;12(6):2749–2757. doi: 10.1128/mcb.12.6.2749. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Herskowitz I., Jensen R. E. Putting the HO gene to work: practical uses for mating-type switching. Methods Enzymol. 1991;194:132–146. doi: 10.1016/0076-6879(91)94011-z. [DOI] [PubMed] [Google Scholar]
  13. Ito J., Braithwaite D. K. Compilation and alignment of DNA polymerase sequences. Nucleic Acids Res. 1991 Aug 11;19(15):4045–4057. doi: 10.1093/nar/19.15.4045. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Johnson R. E., Kovvali G. K., Guzder S. N., Amin N. S., Holm C., Habraken Y., Sung P., Prakash L., Prakash S. Evidence for involvement of yeast proliferating cell nuclear antigen in DNA mismatch repair. J Biol Chem. 1996 Nov 8;271(45):27987–27990. doi: 10.1074/jbc.271.45.27987. [DOI] [PubMed] [Google Scholar]
  15. 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]
  16. Kai Mihoko, Wang Teresa S-F. Checkpoint activation regulates mutagenic translesion synthesis. Genes Dev. 2003 Jan 1;17(1):64–76. doi: 10.1101/gad.1043203. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Kirchner J. M., Tran H., Resnick M. A. A DNA polymerase epsilon mutant that specifically causes +1 frameshift mutations within homonucleotide runs in yeast. Genetics. 2000 Aug;155(4):1623–1632. doi: 10.1093/genetics/155.4.1623. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Kokoska R. J., Stefanovic L., DeMai J., Petes T. D. Increased rates of genomic deletions generated by mutations in the yeast gene encoding DNA polymerase delta or by decreases in the cellular levels of DNA polymerase delta. Mol Cell Biol. 2000 Oct;20(20):7490–7504. doi: 10.1128/mcb.20.20.7490-7504.2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Lindahl T., Wood R. D. Quality control by DNA repair. Science. 1999 Dec 3;286(5446):1897–1905. doi: 10.1126/science.286.5446.1897. [DOI] [PubMed] [Google Scholar]
  20. Liu V. F., Bhaumik D., Wang T. S. Mutator phenotype induced by aberrant replication. Mol Cell Biol. 1999 Feb;19(2):1126–1135. doi: 10.1128/mcb.19.2.1126. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Lucchini G., Muzi Falconi M., Pizzagalli A., Aguilera A., Klein H. L., Plevani P. Nucleotide sequence and characterization of temperature-sensitive pol1 mutants of Saccharomyces cerevisiae. Gene. 1990 May 31;90(1):99–104. doi: 10.1016/0378-1119(90)90444-v. [DOI] [PubMed] [Google Scholar]
  22. 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]
  23. 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]
  24. 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]
  25. Pavlov Y. I., Shcherbakova P. V., Kunkel T. A. In vivo consequences of putative active site mutations in yeast DNA polymerases alpha, epsilon, delta, and zeta. Genetics. 2001 Sep;159(1):47–64. doi: 10.1093/genetics/159.1.47. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Pizzagalli A., Valsasnini P., Plevani P., Lucchini G. DNA polymerase I gene of Saccharomyces cerevisiae: nucleotide sequence, mapping of a temperature-sensitive mutation, and protein homology with other DNA polymerases. Proc Natl Acad Sci U S A. 1988 Jun;85(11):3772–3776. doi: 10.1073/pnas.85.11.3772. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Rigaut G., Shevchenko A., Rutz B., Wilm M., Mann M., Séraphin B. A generic protein purification method for protein complex characterization and proteome exploration. Nat Biotechnol. 1999 Oct;17(10):1030–1032. doi: 10.1038/13732. [DOI] [PubMed] [Google Scholar]
  28. Rose M., Winston F. Identification of a Ty insertion within the coding sequence of the S. cerevisiae URA3 gene. Mol Gen Genet. 1984;193(3):557–560. doi: 10.1007/BF00382100. [DOI] [PubMed] [Google Scholar]
  29. Ruskin B., Fink G. R. Mutations in POL1 increase the mitotic instability of tandem inverted repeats in Saccharomyces cerevisiae. Genetics. 1993 May;134(1):43–56. doi: 10.1093/genetics/134.1.43. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Schweitzer J. K., Livingston D. M. Expansions of CAG repeat tracts are frequent in a yeast mutant defective in Okazaki fragment maturation. Hum Mol Genet. 1998 Jan;7(1):69–74. doi: 10.1093/hmg/7.1.69. [DOI] [PubMed] [Google Scholar]
  31. Sherman F. Getting started with yeast. Methods Enzymol. 1991;194:3–21. doi: 10.1016/0076-6879(91)94004-v. [DOI] [PubMed] [Google Scholar]
  32. Sia E. A., Kokoska R. J., Dominska M., Greenwell P., Petes T. D. Microsatellite instability in yeast: dependence on repeat unit size and DNA mismatch repair genes. Mol Cell Biol. 1997 May;17(5):2851–2858. doi: 10.1128/mcb.17.5.2851. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Strand M., Prolla T. A., Liskay R. M., Petes T. D. Destabilization of tracts of simple repetitive DNA in yeast by mutations affecting DNA mismatch repair. Nature. 1993 Sep 16;365(6443):274–276. doi: 10.1038/365274a0. [DOI] [PubMed] [Google Scholar]
  34. Tran H. T., Degtyareva N. P., Koloteva N. N., Sugino A., Masumoto H., Gordenin D. A., Resnick M. A. Replication slippage between distant short repeats in Saccharomyces cerevisiae depends on the direction of replication and the RAD50 and RAD52 genes. Mol Cell Biol. 1995 Oct;15(10):5607–5617. doi: 10.1128/mcb.15.10.5607. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Tran H. T., Gordenin D. A., Resnick M. A. The prevention of repeat-associated deletions in Saccharomyces cerevisiae by mismatch repair depends on size and origin of deletions. Genetics. 1996 Aug;143(4):1579–1587. doi: 10.1093/genetics/143.4.1579. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Tran H., Degtyareva N., Gordenin D., Resnick M. A. Altered replication and inverted repeats induce mismatch repair-independent recombination between highly diverged DNAs in yeast. Mol Cell Biol. 1997 Feb;17(2):1027–1036. doi: 10.1128/mcb.17.2.1027. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Waga S., Bauer G., Stillman B. Reconstitution of complete SV40 DNA replication with purified replication factors. J Biol Chem. 1994 Apr 8;269(14):10923–10934. [PubMed] [Google Scholar]
  38. Waga S., Stillman B. Anatomy of a DNA replication fork revealed by reconstitution of SV40 DNA replication in vitro. Nature. 1994 May 19;369(6477):207–212. doi: 10.1038/369207a0. [DOI] [PubMed] [Google Scholar]
  39. Walworth N. C. Cell-cycle checkpoint kinases: checking in on the cell cycle. Curr Opin Cell Biol. 2000 Dec;12(6):697–704. doi: 10.1016/s0955-0674(00)00154-x. [DOI] [PubMed] [Google Scholar]
  40. Wang J., Sattar A. K., Wang C. C., Karam J. D., Konigsberg W. H., Steitz T. A. Crystal structure of a pol alpha family replication DNA polymerase from bacteriophage RB69. Cell. 1997 Jun 27;89(7):1087–1099. doi: 10.1016/s0092-8674(00)80296-2. [DOI] [PubMed] [Google Scholar]
  41. Wierdl M., Dominska M., Petes T. D. Microsatellite instability in yeast: dependence on the length of the microsatellite. Genetics. 1997 Jul;146(3):769–779. doi: 10.1093/genetics/146.3.769. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Wierdl M., Greene C. N., Datta A., Jinks-Robertson S., Petes T. D. Destabilization of simple repetitive DNA sequences by transcription in yeast. Genetics. 1996 Jun;143(2):713–721. doi: 10.1093/genetics/143.2.713. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Xie Y., Counter C., Alani E. Characterization of the repeat-tract instability and mutator phenotypes conferred by a Tn3 insertion in RFC1, the large subunit of the yeast clamp loader. Genetics. 1999 Feb;151(2):499–509. doi: 10.1093/genetics/151.2.499. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES