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. 2002 Mar;160(3):909–921. doi: 10.1093/genetics/160.3.909

Analysis of conditional mutations in the Saccharomyces cerevisiae MLH1 gene in mismatch repair and in meiotic crossing over.

Juan Lucas Argueso 1, Daniel Smith 1, James Yi 1, Marc Waase 1, Sumeet Sarin 1, Eric Alani 1
PMCID: PMC1462004  PMID: 11901110

Abstract

In mismatch repair (MMR), members of the MLH gene family have been proposed to act as key molecular matchmakers to coordinate mismatch recognition with downstream repair functions that result in mispair excision. Two members of this gene family, MLH1 and MLH3, have also been implicated in meiotic crossing over. These diverse roles suggest that a mutational analysis of MLH genes could provide reagents required to identify interactions between gene products and to test whether the different roles ascribed to a subset of these genes can be separated. In this report we show that in Saccharomyces cerevisiae the mlh1Delta mutation confers inviability in pol3-01 strain backgrounds that are defective in the Poldelta proofreading exonuclease activity. This phenotype was exploited to identify four mlh1 alleles that each confer a temperature-sensitive phenotype for viability in pol3-01 strains. In three different mutator assays, strains bearing conditional mlh1 alleles displayed wild-type or nearly wild-type mutation rates at 26 degrees. At 35 degrees, these strains exhibited mutation rates that approached those observed in mlh1Delta mutants. The mutator phenotype exhibited in mlh1-I296S strains was partially suppressed at 35 degrees by EXO1 overexpression. The mlh1-F228S and -I296S mutations conferred a separation-of-function phenotype in meiosis; both mlh1-F228S and -I296S strains displayed strong defects in meiotic mismatch repair but showed nearly wild-type levels of crossing over, suggesting that the conditional mutations differentially affected MLH1 functions. These genetic studies suggest that the conditional mlh1 mutations can be used to separate the MMR and meiotic crossing-over functions of MLH1 and to identify interactions between MLH1 and downstream repair components.

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Selected References

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  1. Abdullah M. F., Borts R. H. Meiotic recombination frequencies are affected by nutritional states in Saccharomycescerevisiae. Proc Natl Acad Sci U S A. 2001 Nov 27;98(25):14524–14529. doi: 10.1073/pnas.201529598. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Alani E., Reenan R. A., Kolodner R. D. Interaction between mismatch repair and genetic recombination in Saccharomyces cerevisiae. Genetics. 1994 May;137(1):19–39. doi: 10.1093/genetics/137.1.19. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Allers T., Lichten M. Differential timing and control of noncrossover and crossover recombination during meiosis. Cell. 2001 Jul 13;106(1):47–57. doi: 10.1016/s0092-8674(01)00416-0. [DOI] [PubMed] [Google Scholar]
  4. Allers T., Lichten M. Intermediates of yeast meiotic recombination contain heteroduplex DNA. Mol Cell. 2001 Jul;8(1):225–231. doi: 10.1016/s1097-2765(01)00280-5. [DOI] [PubMed] [Google Scholar]
  5. Amin N. S., Nguyen M. N., Oh S., Kolodner R. D. exo1-Dependent mutator mutations: model system for studying functional interactions in mismatch repair. Mol Cell Biol. 2001 Aug;21(15):5142–5155. doi: 10.1128/MCB.21.15.5142-5155.2001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Au K. G., Welsh K., Modrich P. Initiation of methyl-directed mismatch repair. J Biol Chem. 1992 Jun 15;267(17):12142–12148. [PubMed] [Google Scholar]
  7. 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]
  8. 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]
  9. Chakraverty R. K., Hickson I. D. Defending genome integrity during DNA replication: a proposed role for RecQ family helicases. Bioessays. 1999 Apr;21(4):286–294. doi: 10.1002/(SICI)1521-1878(199904)21:4<286::AID-BIES4>3.0.CO;2-Z. [DOI] [PubMed] [Google Scholar]
  10. Chen C., Merrill B. J., Lau P. J., Holm C., Kolodner R. D. Saccharomyces cerevisiae pol30 (proliferating cell nuclear antigen) mutations impair replication fidelity and mismatch repair. Mol Cell Biol. 1999 Nov;19(11):7801–7815. doi: 10.1128/mcb.19.11.7801. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Christianson T. W., Sikorski R. S., Dante M., Shero J. H., Hieter P. Multifunctional yeast high-copy-number shuttle vectors. Gene. 1992 Jan 2;110(1):119–122. doi: 10.1016/0378-1119(92)90454-w. [DOI] [PubMed] [Google Scholar]
  12. 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]
  13. 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]
  14. Detloff P., White M. A., Petes T. D. Analysis of a gene conversion gradient at the HIS4 locus in Saccharomyces cerevisiae. Genetics. 1992 Sep;132(1):113–123. doi: 10.1093/genetics/132.1.113. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. 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]
  16. Fiorentini P., Huang K. N., Tishkoff D. X., Kolodner R. D., Symington L. S. Exonuclease I of Saccharomyces cerevisiae functions in mitotic recombination in vivo and in vitro. Mol Cell Biol. 1997 May;17(5):2764–2773. doi: 10.1128/mcb.17.5.2764. [DOI] [PMC free article] [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. Gangloff S., McDonald J. P., Bendixen C., Arthur L., Rothstein R. The yeast type I topoisomerase Top3 interacts with Sgs1, a DNA helicase homolog: a potential eukaryotic reverse gyrase. Mol Cell Biol. 1994 Dec;14(12):8391–8398. doi: 10.1128/mcb.14.12.8391. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Gu L., Hong Y., McCulloch S., Watanabe H., Li G. M. ATP-dependent interaction of human mismatch repair proteins and dual role of PCNA in mismatch repair. Nucleic Acids Res. 1998 Mar 1;26(5):1173–1178. doi: 10.1093/nar/26.5.1173. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Guarente L. Synthetic enhancement in gene interaction: a genetic tool come of age. Trends Genet. 1993 Oct;9(10):362–366. doi: 10.1016/0168-9525(93)90042-g. [DOI] [PubMed] [Google Scholar]
  22. Habraken Y., Sung P., Prakash L., Prakash S. ATP-dependent assembly of a ternary complex consisting of a DNA mismatch and the yeast MSH2-MSH6 and MLH1-PMS1 protein complexes. J Biol Chem. 1998 Apr 17;273(16):9837–9841. doi: 10.1074/jbc.273.16.9837. [DOI] [PubMed] [Google Scholar]
  23. 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]
  24. 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]
  25. 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]
  26. 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]
  27. Hillers K. J., Stahl F. W. The conversion gradient at HIS4 of Saccharomyces cerevisiae. I. Heteroduplex rejection and restoration of Mendelian segregation. Genetics. 1999 Oct;153(2):555–572. doi: 10.1093/genetics/153.2.555. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Hollingsworth N. M., Ponte L., Halsey C. MSH5, a novel MutS homolog, facilitates meiotic reciprocal recombination between homologs in Saccharomyces cerevisiae but not mismatch repair. Genes Dev. 1995 Jul 15;9(14):1728–1739. doi: 10.1101/gad.9.14.1728. [DOI] [PubMed] [Google Scholar]
  29. Hopper A. K., Magee P. T., Welch S. K., Friedman M., Hall B. D. Macromolecule synthesis and breakdown in relation to sporulation and meiosis in yeast. J Bacteriol. 1974 Aug;119(2):619–628. doi: 10.1128/jb.119.2.619-628.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. 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]
  31. 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]
  32. Khazanehdari K. A., Borts R. H. EXO1 and MSH4 differentially affect crossing-over and segregation. Chromosoma. 2000;109(1-2):94–102. doi: 10.1007/s004120050416. [DOI] [PubMed] [Google Scholar]
  33. Kirkpatrick D. T., Ferguson J. R., Petes T. D., Symington L. S. Decreased meiotic intergenic recombination and increased meiosis I nondisjunction in exo1 mutants of Saccharomyces cerevisiae. Genetics. 2000 Dec;156(4):1549–1557. doi: 10.1093/genetics/156.4.1549. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Kolodner R. D., Marsischky G. T. Eukaryotic DNA mismatch repair. Curr Opin Genet Dev. 1999 Feb;9(1):89–96. doi: 10.1016/s0959-437x(99)80013-6. [DOI] [PubMed] [Google Scholar]
  35. Langland G., Kordich J., Creaney J., Goss K. H., Lillard-Wetherell K., Bebenek K., Kunkel T. A., Groden J. The Bloom's syndrome protein (BLM) interacts with MLH1 but is not required for DNA mismatch repair. J Biol Chem. 2001 Apr 26;276(32):30031–30035. doi: 10.1074/jbc.M009664200. [DOI] [PubMed] [Google Scholar]
  36. 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]
  37. 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]
  38. Nicolas A., Treco D., Schultes N. P., Szostak J. W. An initiation site for meiotic gene conversion in the yeast Saccharomyces cerevisiae. Nature. 1989 Mar 2;338(6210):35–39. doi: 10.1038/338035a0. [DOI] [PubMed] [Google Scholar]
  39. 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]
  40. Pedrazzi G., Perrera C., Blaser H., Kuster P., Marra G., Davies S. L., Ryu G. H., Freire R., Hickson I. D., Jiricny J. Direct association of Bloom's syndrome gene product with the human mismatch repair protein MLH1. Nucleic Acids Res. 2001 Nov 1;29(21):4378–4386. doi: 10.1093/nar/29.21.4378. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. 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]
  42. Prolla T. A., Pang Q., Alani E., Kolodner R. D., Liskay R. M. MLH1, PMS1, and MSH2 interactions during the initiation of DNA mismatch repair in yeast. Science. 1994 Aug 19;265(5175):1091–1093. doi: 10.1126/science.8066446. [DOI] [PubMed] [Google Scholar]
  43. Reenan R. A., Kolodner R. D. Characterization of insertion mutations in the Saccharomyces cerevisiae MSH1 and MSH2 genes: evidence for separate mitochondrial and nuclear functions. Genetics. 1992 Dec;132(4):975–985. doi: 10.1093/genetics/132.4.975. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Rocco V., de Massy B., Nicolas A. The Saccharomyces cerevisiae ARG4 initiator of meiotic gene conversion and its associated double-strand DNA breaks can be inhibited by transcriptional interference. Proc Natl Acad Sci U S A. 1992 Dec 15;89(24):12068–12072. doi: 10.1073/pnas.89.24.12068. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Ross-Macdonald P., Roeder G. S. Mutation of a meiosis-specific MutS homolog decreases crossing over but not mismatch correction. Cell. 1994 Dec 16;79(6):1069–1080. doi: 10.1016/0092-8674(94)90037-x. [DOI] [PubMed] [Google Scholar]
  46. Rossignol J. L., Nicolas A., Hamza H., Langin T. Origins of gene conversion and reciprocal exchange in Ascobolus. Cold Spring Harb Symp Quant Biol. 1984;49:13–21. doi: 10.1101/sqb.1984.049.01.004. [DOI] [PubMed] [Google Scholar]
  47. Sancar A., Hearst J. E. Molecular matchmakers. Science. 1993 Mar 5;259(5100):1415–1420. doi: 10.1126/science.8451638. [DOI] [PubMed] [Google Scholar]
  48. Schmutte C., Sadoff M. M., Shim K. S., Acharya S., Fishel R. The interaction of DNA mismatch repair proteins with human exonuclease I. J Biol Chem. 2001 Jun 26;276(35):33011–33018. doi: 10.1074/jbc.M102670200. [DOI] [PubMed] [Google Scholar]
  49. Sokolsky T., Alani E. EXO1 and MSH6 are high-copy suppressors of conditional mutations in the MSH2 mismatch repair gene of Saccharomyces cerevisiae. Genetics. 2000 Jun;155(2):589–599. doi: 10.1093/genetics/155.2.589. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Stebbins C. E., Russo A. A., Schneider C., Rosen N., Hartl F. U., Pavletich N. P. Crystal structure of an Hsp90-geldanamycin complex: targeting of a protein chaperone by an antitumor agent. Cell. 1997 Apr 18;89(2):239–250. doi: 10.1016/s0092-8674(00)80203-2. [DOI] [PubMed] [Google Scholar]
  51. 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]
  52. Sun H., Treco D., Schultes N. P., Szostak J. W. Double-strand breaks at an initiation site for meiotic gene conversion. Nature. 1989 Mar 2;338(6210):87–90. doi: 10.1038/338087a0. [DOI] [PubMed] [Google Scholar]
  53. Szankasi P., Smith G. R. A role for exonuclease I from S. pombe in mutation avoidance and mismatch correction. Science. 1995 Feb 24;267(5201):1166–1169. doi: 10.1126/science.7855597. [DOI] [PubMed] [Google Scholar]
  54. Tishkoff D. X., Boerger A. L., Bertrand P., Filosi N., Gaida G. M., Kane M. F., Kolodner R. D. Identification and characterization of Saccharomyces cerevisiae EXO1, a gene encoding an exonuclease that interacts with MSH2. Proc Natl Acad Sci U S A. 1997 Jul 8;94(14):7487–7492. doi: 10.1073/pnas.94.14.7487. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. 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]
  56. 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]
  57. 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]
  58. Tran P. T., Simon J. A., Liskay R. M. Interactions of Exo1p with components of MutLalpha in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 2001 Jul 31;98(17):9760–9765. doi: 10.1073/pnas.161175998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  59. Tsubouchi H., Ogawa H. Exo1 roles for repair of DNA double-strand breaks and meiotic crossing over in Saccharomyces cerevisiae. Mol Biol Cell. 2000 Jul;11(7):2221–2233. doi: 10.1091/mbc.11.7.2221. [DOI] [PMC free article] [PubMed] [Google Scholar]
  60. Viswanathan M., Burdett V., Baitinger C., Modrich P., Lovett S. T. Redundant exonuclease involvement in Escherichia coli methyl-directed mismatch repair. J Biol Chem. 2001 Jun 19;276(33):31053–31058. doi: 10.1074/jbc.M105481200. [DOI] [PubMed] [Google Scholar]
  61. 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]
  62. 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]
  63. White J. H., Lusnak K., Fogel S. Mismatch-specific post-meiotic segregation frequency in yeast suggests a heteroduplex recombination intermediate. Nature. 1985 May 23;315(6017):350–352. doi: 10.1038/315350a0. [DOI] [PubMed] [Google Scholar]
  64. 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]
  65. Winston F., Dollard C., Ricupero-Hovasse S. L. Construction of a set of convenient Saccharomyces cerevisiae strains that are isogenic to S288C. Yeast. 1995 Jan;11(1):53–55. doi: 10.1002/yea.320110107. [DOI] [PubMed] [Google Scholar]
  66. Zubenko G. S., Jones E. W. Protein degradation, meiosis and sporulation in proteinase-deficient mutants of Saccharomyces cerevisiae. Genetics. 1981 Jan;97(1):45–64. doi: 10.1093/genetics/97.1.45. [DOI] [PMC free article] [PubMed] [Google Scholar]

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