Skip to main content
Genetics logoLink to Genetics
. 2002 Nov;162(3):1131–1145. doi: 10.1093/genetics/162.3.1131

Alleles of the yeast Pms1 mismatch-repair gene that differentially affect recombination- and replication-related processes.

Caroline Welz-Voegele 1, Jana E Stone 1, Phuoc T Tran 1, Hutton M Kearney 1, R Michael Liskay 1, Thomas D Petes 1, Sue Jinks-Robertson 1
PMCID: PMC1462331  PMID: 12454061

Abstract

Mismatch-repair (MMR) systems promote eukaryotic genome stability by removing errors introduced during DNA replication and by inhibiting recombination between nonidentical sequences (spellchecker and antirecombination activities, respectively). Following a common mismatch-recognition step effected by MutS-homologous Msh proteins, homologs of the bacterial MutL ATPase (predominantly the Mlh1p-Pms1p heterodimer in yeast) couple mismatch recognition to the appropriate downstream processing steps. To examine whether the processing steps in the spellchecker and antirecombination pathways might differ, we mutagenized the yeast PMS1 gene and screened for mitotic separation-of-function alleles. Two alleles affecting only the antirecombination function of Pms1p were identified, one of which changed an amino acid within the highly conserved ATPase domain. To more specifically address the role of ATP binding/hydrolysis in MMR-related processes, we examined mutations known to compromise the ATPase activity of Pms1p or Mlh1p with respect to the mitotic spellchecker and antirecombination activities and with respect to the repair of mismatches present in meiotic recombination intermediates. The results of these analyses confirm a differential requirement for the Pms1p ATPase activity in replication vs. recombination processes, while demonstrating that the Mlh1p ATPase activity is important for all examined MMR-related functions.

Full Text

The Full Text of this article is available as a PDF (184.2 KB).

Selected References

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

  1. Ali J. A., Jackson A. P., Howells A. J., Maxwell A. The 43-kilodalton N-terminal fragment of the DNA gyrase B protein hydrolyzes ATP and binds coumarin drugs. Biochemistry. 1993 Mar 16;32(10):2717–2724. doi: 10.1021/bi00061a033. [DOI] [PubMed] [Google Scholar]
  2. Argueso Juan Lucas, Smith Daniel, Yi James, Waase Marc, Sarin Sumeet, Alani Eric. Analysis of conditional mutations in the Saccharomyces cerevisiae MLH1 gene in mismatch repair and in meiotic crossing over. Genetics. 2002 Mar;160(3):909–921. doi: 10.1093/genetics/160.3.909. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Ban C., Junop M., Yang W. Transformation of MutL by ATP binding and hydrolysis: a switch in DNA mismatch repair. Cell. 1999 Apr 2;97(1):85–97. doi: 10.1016/s0092-8674(00)80717-5. [DOI] [PubMed] [Google Scholar]
  4. Ban C., Yang W. Crystal structure and ATPase activity of MutL: implications for DNA repair and mutagenesis. Cell. 1998 Nov 13;95(4):541–552. doi: 10.1016/s0092-8674(00)81621-9. [DOI] [PubMed] [Google Scholar]
  5. Bartel P., Chien C. T., Sternglanz R., Fields S. Elimination of false positives that arise in using the two-hybrid system. Biotechniques. 1993 Jun;14(6):920–924. [PubMed] [Google Scholar]
  6. Boeke J. D., LaCroute F., Fink G. R. A positive selection for mutants lacking orotidine-5'-phosphate decarboxylase activity in yeast: 5-fluoro-orotic acid resistance. Mol Gen Genet. 1984;197(2):345–346. doi: 10.1007/BF00330984. [DOI] [PubMed] [Google Scholar]
  7. Bärtsch S., Kang L. E., Symington L. S. RAD51 is required for the repair of plasmid double-stranded DNA gaps from either plasmid or chromosomal templates. Mol Cell Biol. 2000 Feb;20(4):1194–1205. doi: 10.1128/mcb.20.4.1194-1205.2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Chen W., Jinks-Robertson S. Mismatch repair proteins regulate heteroduplex formation during mitotic recombination in yeast. Mol Cell Biol. 1998 Nov;18(11):6525–6537. doi: 10.1128/mcb.18.11.6525. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Datta A., Adjiri A., New L., Crouse G. F., Jinks Robertson S. Mitotic crossovers between diverged sequences are regulated by mismatch repair proteins in Saccaromyces cerevisiae. Mol Cell Biol. 1996 Mar;16(3):1085–1093. doi: 10.1128/mcb.16.3.1085. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Datta A., Hendrix M., Lipsitch M., Jinks-Robertson S. Dual roles for DNA sequence identity and the mismatch repair system in the regulation of mitotic crossing-over in yeast. Proc Natl Acad Sci U S A. 1997 Sep 2;94(18):9757–9762. doi: 10.1073/pnas.94.18.9757. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Detloff P., Sieber J., Petes T. D. Repair of specific base pair mismatches formed during meiotic recombination in the yeast Saccharomyces cerevisiae. Mol Cell Biol. 1991 Feb;11(2):737–745. doi: 10.1128/mcb.11.2.737. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Drotschmann K., Aronshtam A., Fritz H. J., Marinus M. G. The Escherichia coli MutL protein stimulates binding of Vsr and MutS to heteroduplex DNA. Nucleic Acids Res. 1998 Feb 15;26(4):948–953. doi: 10.1093/nar/26.4.948. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Dutta R., Inouye M. GHKL, an emergent ATPase/kinase superfamily. Trends Biochem Sci. 2000 Jan;25(1):24–28. doi: 10.1016/s0968-0004(99)01503-0. [DOI] [PubMed] [Google Scholar]
  14. Fan Q., Xu F., Petes T. D. Meiosis-specific double-strand DNA breaks at the HIS4 recombination hot spot in the yeast Saccharomyces cerevisiae: control in cis and trans. Mol Cell Biol. 1995 Mar;15(3):1679–1688. doi: 10.1128/mcb.15.3.1679. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Fleig U. N., Pridmore R. D., Philippsen P. Construction of LYS2 cartridges for use in genetic manipulations of Saccharomyces cerevisiae. Gene. 1986;46(2-3):237–245. doi: 10.1016/0378-1119(86)90408-7. [DOI] [PubMed] [Google Scholar]
  16. Flores-Rozas H., Clark D., Kolodner R. D. Proliferating cell nuclear antigen and Msh2p-Msh6p interact to form an active mispair recognition complex. Nat Genet. 2000 Nov;26(3):375–378. doi: 10.1038/81708. [DOI] [PubMed] [Google Scholar]
  17. 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]
  18. Fogel S., Mortimer R., Lusnak K., Tavares F. Meiotic gene conversion: a signal of the basic recombination event in yeast. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 2):1325–1341. doi: 10.1101/sqb.1979.043.01.152. [DOI] [PubMed] [Google Scholar]
  19. Grenert J. P., Johnson B. D., Toft D. O. The importance of ATP binding and hydrolysis by hsp90 in formation and function of protein heterocomplexes. J Biol Chem. 1999 Jun 18;274(25):17525–17533. doi: 10.1074/jbc.274.25.17525. [DOI] [PubMed] [Google Scholar]
  20. Guarné A., Junop M. S., Yang W. Structure and function of the N-terminal 40 kDa fragment of human PMS2: a monomeric GHL ATPase. EMBO J. 2001 Oct 1;20(19):5521–5531. doi: 10.1093/emboj/20.19.5521. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Hall M. C., Jordan J. R., Matson S. W. Evidence for a physical interaction between the Escherichia coli methyl-directed mismatch repair proteins MutL and UvrD. EMBO J. 1998 Mar 2;17(5):1535–1541. doi: 10.1093/emboj/17.5.1535. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Hall M. C., Matson S. W. The Escherichia coli MutL protein physically interacts with MutH and stimulates the MutH-associated endonuclease activity. J Biol Chem. 1999 Jan 15;274(3):1306–1312. doi: 10.1074/jbc.274.3.1306. [DOI] [PubMed] [Google Scholar]
  23. Hall Mark C., Shcherbakova Polina V., Kunkel Thomas A. Differential ATP binding and intrinsic ATP hydrolysis by amino-terminal domains of the yeast Mlh1 and Pms1 proteins. J Biol Chem. 2001 Nov 20;277(5):3673–3679. doi: 10.1074/jbc.M106120200. [DOI] [PubMed] [Google Scholar]
  24. 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]
  25. Harfe B. D., Jinks-Robertson S. Mismatch repair proteins and mitotic genome stability. Mutat Res. 2000 Jun 30;451(1-2):151–167. doi: 10.1016/s0027-5107(00)00047-6. [DOI] [PubMed] [Google Scholar]
  26. Harfe B. D., Minesinger B. K., Jinks-Robertson S. Discrete in vivo roles for the MutL homologs Mlh2p and Mlh3p in the removal of frameshift intermediates in budding yeast. Curr Biol. 2000 Feb 10;10(3):145–148. doi: 10.1016/s0960-9822(00)00314-6. [DOI] [PubMed] [Google Scholar]
  27. Hunter N., Borts R. H. Mlh1 is unique among mismatch repair proteins in its ability to promote crossing-over during meiosis. Genes Dev. 1997 Jun 15;11(12):1573–1582. doi: 10.1101/gad.11.12.1573. [DOI] [PubMed] [Google Scholar]
  28. 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]
  29. Kramer W., Kramer B., Williamson M. S., Fogel S. Cloning and nucleotide sequence of DNA mismatch repair gene PMS1 from Saccharomyces cerevisiae: homology of PMS1 to procaryotic MutL and HexB. J Bacteriol. 1989 Oct;171(10):5339–5346. doi: 10.1128/jb.171.10.5339-5346.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Lamers M. H., Perrakis A., Enzlin J. H., Winterwerp H. H., de Wind N., Sixma T. K. The crystal structure of DNA mismatch repair protein MutS binding to a G x T mismatch. Nature. 2000 Oct 12;407(6805):711–717. doi: 10.1038/35037523. [DOI] [PubMed] [Google Scholar]
  31. Longtine M. S., McKenzie A., 3rd, Demarini D. J., Shah N. G., Wach A., Brachat A., Philippsen P., Pringle J. R. Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast. 1998 Jul;14(10):953–961. doi: 10.1002/(SICI)1097-0061(199807)14:10<953::AID-YEA293>3.0.CO;2-U. [DOI] [PubMed] [Google Scholar]
  32. 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]
  33. Modrich P., Lahue R. Mismatch repair in replication fidelity, genetic recombination, and cancer biology. Annu Rev Biochem. 1996;65:101–133. doi: 10.1146/annurev.bi.65.070196.000533. [DOI] [PubMed] [Google Scholar]
  34. Muhlrad D., Hunter R., Parker R. A rapid method for localized mutagenesis of yeast genes. Yeast. 1992 Feb;8(2):79–82. doi: 10.1002/yea.320080202. [DOI] [PubMed] [Google Scholar]
  35. Nag D. K., White M. A., Petes T. D. Palindromic sequences in heteroduplex DNA inhibit mismatch repair in yeast. Nature. 1989 Jul 27;340(6231):318–320. doi: 10.1038/340318a0. [DOI] [PubMed] [Google Scholar]
  36. Nicholson A., Hendrix M., Jinks-Robertson S., Crouse G. F. Regulation of mitotic homeologous recombination in yeast. Functions of mismatch repair and nucleotide excision repair genes. Genetics. 2000 Jan;154(1):133–146. doi: 10.1093/genetics/154.1.133. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Obmolova G., Ban C., Hsieh P., Yang W. Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA. Nature. 2000 Oct 12;407(6805):703–710. doi: 10.1038/35037509. [DOI] [PubMed] [Google Scholar]
  38. Pang Q., Prolla T. A., Liskay R. M. Functional domains of the Saccharomyces cerevisiae Mlh1p and Pms1p DNA mismatch repair proteins and their relevance to human hereditary nonpolyposis colorectal cancer-associated mutations. Mol Cell Biol. 1997 Aug;17(8):4465–4473. doi: 10.1128/mcb.17.8.4465. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Perkins D. D. Biochemical Mutants in the Smut Fungus Ustilago Maydis. Genetics. 1949 Sep;34(5):607–626. doi: 10.1093/genetics/34.5.607. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Prodromou C., Roe S. M., O'Brien R., Ladbury J. E., Piper P. W., Pearl L. H. Identification and structural characterization of the ATP/ADP-binding site in the Hsp90 molecular chaperone. Cell. 1997 Jul 11;90(1):65–75. doi: 10.1016/s0092-8674(00)80314-1. [DOI] [PubMed] [Google Scholar]
  41. Prodromou C., Roe S. M., Piper P. W., Pearl L. H. A molecular clamp in the crystal structure of the N-terminal domain of the yeast Hsp90 chaperone. Nat Struct Biol. 1997 Jun;4(6):477–482. doi: 10.1038/nsb0697-477. [DOI] [PubMed] [Google Scholar]
  42. Prolla T. A., Christie D. M., Liskay R. M. Dual requirement in yeast DNA mismatch repair for MLH1 and PMS1, two homologs of the bacterial mutL gene. Mol Cell Biol. 1994 Jan;14(1):407–415. doi: 10.1128/mcb.14.1.407. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Stapleton A., Petes T. D. The Tn3 beta-lactamase gene acts as a hotspot for meiotic recombination in yeast. Genetics. 1991 Jan;127(1):39–51. doi: 10.1093/genetics/127.1.39. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Sung P., Trujillo K. M., Van Komen S. Recombination factors of Saccharomyces cerevisiae. Mutat Res. 2000 Jun 30;451(1-2):257–275. doi: 10.1016/s0027-5107(00)00054-3. [DOI] [PubMed] [Google Scholar]
  45. Tomer Guy, Buermeyer Andrew B., Nguyen Megan M., Liskay R. Michael. Contribution of human mlh1 and pms2 ATPase activities to DNA mismatch repair. J Biol Chem. 2002 Mar 15;277(24):21801–21809. doi: 10.1074/jbc.M111342200. [DOI] [PubMed] [Google Scholar]
  46. Tran P. T., Liskay R. M. Functional studies on the candidate ATPase domains of Saccharomyces cerevisiae MutLalpha. Mol Cell Biol. 2000 Sep;20(17):6390–6398. doi: 10.1128/mcb.20.17.6390-6398.2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Umar A., Buermeyer A. B., Simon J. A., Thomas D. C., Clark A. B., Liskay R. M., Kunkel T. A. Requirement for PCNA in DNA mismatch repair at a step preceding DNA resynthesis. Cell. 1996 Oct 4;87(1):65–73. doi: 10.1016/s0092-8674(00)81323-9. [DOI] [PubMed] [Google Scholar]
  48. Vojtek A. B., Hollenberg S. M., Cooper J. A. Mammalian Ras interacts directly with the serine/threonine kinase Raf. Cell. 1993 Jul 16;74(1):205–214. doi: 10.1016/0092-8674(93)90307-c. [DOI] [PubMed] [Google Scholar]
  49. Wach A., Brachat A., Pöhlmann R., Philippsen P. New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae. Yeast. 1994 Dec;10(13):1793–1808. doi: 10.1002/yea.320101310. [DOI] [PubMed] [Google Scholar]
  50. White M. A., Dominska M., Petes T. D. Transcription factors are required for the meiotic recombination hotspot at the HIS4 locus in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1993 Jul 15;90(14):6621–6625. doi: 10.1073/pnas.90.14.6621. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Wigley D. B., Davies G. J., Dodson E. J., Maxwell A., Dodson G. Crystal structure of an N-terminal fragment of the DNA gyrase B protein. Nature. 1991 Jun 20;351(6328):624–629. doi: 10.1038/351624a0. [DOI] [PubMed] [Google Scholar]
  52. Wild R. Biennial conference of the Medical Association, Palmerston North, February 15-18, 1971. Twelfth memorial oration. N Z Med J. 1971 Mar;73(466):162–166. [PubMed] [Google Scholar]
  53. Williamson M. S., Game J. C., Fogel S. Meiotic gene conversion mutants in Saccharomyces cerevisiae. I. Isolation and characterization of pms1-1 and pms1-2. Genetics. 1985 Aug;110(4):609–646. doi: 10.1093/genetics/110.4.609. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. de Graaf B., Bekkering H., Erasmus C., Bles W. Influence of visual, vestibular, cervical, and somatosensory tilt information on ocular rotation and perception of the horizontal. J Vestib Res. 1992;2(1):15–30. [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES