Skip to main content
The EMBO Journal logoLink to The EMBO Journal
. 1998 Nov 2;17(21):6412–6425. doi: 10.1093/emboj/17.21.6412

Distinct roles of two separable in vitro activities of yeast Mre11 in mitotic and meiotic recombination.

M Furuse 1, Y Nagase 1, H Tsubouchi 1, K Murakami-Murofushi 1, T Shibata 1, K Ohta 1
PMCID: PMC1170966  PMID: 9799249

Abstract

In Saccharomyces cerevisiae, Mre11 protein is involved in both double-strand DNA break (DSB) repair and meiotic DSB formation. Here, we report the correlation of nuclease and DNA-binding activities of Mre11 with its functions in DNA repair and meiotic DSB formation. Purified Mre11 bound to DNA efficiently and was shown to have Mn2+-dependent nuclease activities. A point mutation in the N-terminal phosphoesterase motif (Mre11D16A) resulted in the abolition of nuclease activities but had no significant effect on DNA binding. The wild-type level of nuclease activity was detected in a C-terminal truncated protein (Mre11DeltaC49), although it had reduced DNA-binding activity. Phenotypes of the corresponding mutations were also analyzed. The mre11D16A mutation conferred methyl methanesulfonate-sensitivity to mitotic cells and caused the accumulation of unprocessed meiotic DSBs. The mre11DeltaC49 mutant exhibited almost wild-type phenotypes in mitosis. However, in meiosis, no DSB formation could be detected and an aberrant chromatin configuration was observed at DSB sites in the mre11DeltaC49 mutant. These results indicate that Mre11 has two separable functional domains: the N-terminal nuclease domain required for DSB repair, and the C-terminal dsDNA-binding domain essential to its meiotic functions such as chromatin modification and DSB formation. Keywords: DNA binding/double-strand break repair/DSB formation/Mre11/nuclease

Full Text

The Full Text of this article is available as a PDF (756.2 KB).

Selected References

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

  1. Ajimura M., Leem S. H., Ogawa H. Identification of new genes required for meiotic recombination in Saccharomyces cerevisiae. Genetics. 1993 Jan;133(1):51–66. doi: 10.1093/genetics/133.1.51. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Alani E., Padmore R., Kleckner N. Analysis of wild-type and rad50 mutants of yeast suggests an intimate relationship between meiotic chromosome synapsis and recombination. Cell. 1990 May 4;61(3):419–436. doi: 10.1016/0092-8674(90)90524-i. [DOI] [PubMed] [Google Scholar]
  3. Anderson D. G., Kowalczykowski S. C. The recombination hot spot chi is a regulatory element that switches the polarity of DNA degradation by the RecBCD enzyme. Genes Dev. 1997 Mar 1;11(5):571–581. doi: 10.1101/gad.11.5.571. [DOI] [PubMed] [Google Scholar]
  4. Bergerat A., de Massy B., Gadelle D., Varoutas P. C., Nicolas A., Forterre P. An atypical topoisomerase II from Archaea with implications for meiotic recombination. Nature. 1997 Mar 27;386(6623):414–417. doi: 10.1038/386414a0. [DOI] [PubMed] [Google Scholar]
  5. Boulton S. J., Jackson S. P. Components of the Ku-dependent non-homologous end-joining pathway are involved in telomeric length maintenance and telomeric silencing. EMBO J. 1998 Mar 16;17(6):1819–1828. doi: 10.1093/emboj/17.6.1819. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Boulton S. J., Jackson S. P. Saccharomyces cerevisiae Ku70 potentiates illegitimate DNA double-strand break repair and serves as a barrier to error-prone DNA repair pathways. EMBO J. 1996 Sep 16;15(18):5093–5103. [PMC free article] [PubMed] [Google Scholar]
  7. Cao L., Alani E., Kleckner N. A pathway for generation and processing of double-strand breaks during meiotic recombination in S. cerevisiae. Cell. 1990 Jun 15;61(6):1089–1101. doi: 10.1016/0092-8674(90)90072-m. [DOI] [PubMed] [Google Scholar]
  8. Carlson M., Botstein D. Two differentially regulated mRNAs with different 5' ends encode secreted with intracellular forms of yeast invertase. Cell. 1982 Jan;28(1):145–154. doi: 10.1016/0092-8674(82)90384-1. [DOI] [PubMed] [Google Scholar]
  9. Carney J. P., Maser R. S., Olivares H., Davis E. M., Le Beau M., Yates J. R., 3rd, Hays L., Morgan W. F., Petrini J. H. The hMre11/hRad50 protein complex and Nijmegen breakage syndrome: linkage of double-strand break repair to the cellular DNA damage response. Cell. 1998 May 1;93(3):477–486. doi: 10.1016/s0092-8674(00)81175-7. [DOI] [PubMed] [Google Scholar]
  10. Church G. M., Gilbert W. Genomic sequencing. Proc Natl Acad Sci U S A. 1984 Apr;81(7):1991–1995. doi: 10.1073/pnas.81.7.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Cohen P. T., Collins J. F., Coulson A. F., Berndt N., da Cruz e Silva O. B. Segments of bacteriophage lambda (orf 221) and phi 80 are homologous to genes coding for mammalian protein phosphatases. Gene. 1988 Sep 15;69(1):131–134. doi: 10.1016/0378-1119(88)90385-x. [DOI] [PubMed] [Google Scholar]
  12. Connelly J. C., Leach D. R. The sbcC and sbcD genes of Escherichia coli encode a nuclease involved in palindrome inviability and genetic recombination. Genes Cells. 1996 Mar;1(3):285–291. doi: 10.1046/j.1365-2443.1996.23024.x. [DOI] [PubMed] [Google Scholar]
  13. Cool M., Malone R. E. Molecular and genetic analysis of the yeast early meiotic recombination genes REC102 and REC107/MER2. Mol Cell Biol. 1992 Mar;12(3):1248–1256. doi: 10.1128/mcb.12.3.1248. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Dolganov G. M., Maser R. S., Novikov A., Tosto L., Chong S., Bressan D. A., Petrini J. H. Human Rad50 is physically associated with human Mre11: identification of a conserved multiprotein complex implicated in recombinational DNA repair. Mol Cell Biol. 1996 Sep;16(9):4832–4841. doi: 10.1128/mcb.16.9.4832. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Engebrecht J. A., Voelkel-Meiman K., Roeder G. S. Meiosis-specific RNA splicing in yeast. Cell. 1991 Sep 20;66(6):1257–1268. doi: 10.1016/0092-8674(91)90047-3. [DOI] [PubMed] [Google Scholar]
  16. Fan Q. Q., Petes T. D. Relationship between nuclease-hypersensitive sites and meiotic recombination hot spot activity at the HIS4 locus of Saccharomyces cerevisiae. Mol Cell Biol. 1996 May;16(5):2037–2043. doi: 10.1128/mcb.16.5.2037. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Game J. C., Mortimer R. K. A genetic study of x-ray sensitive mutants in yeast. Mutat Res. 1974 Sep;24(3):281–292. doi: 10.1016/0027-5107(74)90176-6. [DOI] [PubMed] [Google Scholar]
  18. Griffith J. P., Kim J. L., Kim E. E., Sintchak M. D., Thomson J. A., Fitzgibbon M. J., Fleming M. A., Caron P. R., Hsiao K., Navia M. A. X-ray structure of calcineurin inhibited by the immunophilin-immunosuppressant FKBP12-FK506 complex. Cell. 1995 Aug 11;82(3):507–522. doi: 10.1016/0092-8674(95)90439-5. [DOI] [PubMed] [Google Scholar]
  19. Guerini D., Klee C. B. Cloning of human calcineurin A: evidence for two isozymes and identification of a polyproline structural domain. Proc Natl Acad Sci U S A. 1989 Dec;86(23):9183–9187. doi: 10.1073/pnas.86.23.9183. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Haber J. E. In vivo biochemistry: physical monitoring of recombination induced by site-specific endonucleases. Bioessays. 1995 Jul;17(7):609–620. doi: 10.1002/bies.950170707. [DOI] [PubMed] [Google Scholar]
  21. Hashimoto-Gotoh T., Mizuno T., Ogasahara Y., Nakagawa M. An oligodeoxyribonucleotide-directed dual amber method for site-directed mutagenesis. Gene. 1995 Jan 23;152(2):271–275. doi: 10.1016/0378-1119(94)00750-m. [DOI] [PubMed] [Google Scholar]
  22. Ivanov E. L., Korolev V. G., Fabre F. XRS2, a DNA repair gene of Saccharomyces cerevisiae, is needed for meiotic recombination. Genetics. 1992 Nov;132(3):651–664. doi: 10.1093/genetics/132.3.651. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Johzuka K., Ogawa H. Interaction of Mre11 and Rad50: two proteins required for DNA repair and meiosis-specific double-strand break formation in Saccharomyces cerevisiae. Genetics. 1995 Apr;139(4):1521–1532. doi: 10.1093/genetics/139.4.1521. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Keeney S., Giroux C. N., Kleckner N. Meiosis-specific DNA double-strand breaks are catalyzed by Spo11, a member of a widely conserved protein family. Cell. 1997 Feb 7;88(3):375–384. doi: 10.1016/s0092-8674(00)81876-0. [DOI] [PubMed] [Google Scholar]
  25. Keeney S., Kleckner N. Communication between homologous chromosomes: genetic alterations at a nuclease-hypersensitive site can alter mitotic chromatin structure at that site both in cis and in trans. Genes Cells. 1996 May;1(5):475–489. doi: 10.1046/j.1365-2443.1996.d01-257.x. [DOI] [PubMed] [Google Scholar]
  26. Kironmai K. M., Muniyappa K. Alteration of telomeric sequences and senescence caused by mutations in RAD50 of Saccharomyces cerevisiae. Genes Cells. 1997 Jul;2(7):443–455. doi: 10.1046/j.1365-2443.1997.1330331.x. [DOI] [PubMed] [Google Scholar]
  27. Kissinger C. R., Parge H. E., Knighton D. R., Lewis C. T., Pelletier L. A., Tempczyk A., Kalish V. J., Tucker K. D., Showalter R. E., Moomaw E. W. Crystal structures of human calcineurin and the human FKBP12-FK506-calcineurin complex. Nature. 1995 Dec 7;378(6557):641–644. doi: 10.1038/378641a0. [DOI] [PubMed] [Google Scholar]
  28. Klapholz S., Esposito R. E. A new mapping method employing a meiotic rec-mutant of yeast. Genetics. 1982 Mar;100(3):387–412. doi: 10.1093/genetics/100.3.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Kon N., Krawchuk M. D., Warren B. G., Smith G. R., Wahls W. P. Transcription factor Mts1/Mts2 (Atf1/Pcr1, Gad7/Pcr1) activates the M26 meiotic recombination hotspot in Schizosaccharomyces pombe. Proc Natl Acad Sci U S A. 1997 Dec 9;94(25):13765–13770. doi: 10.1073/pnas.94.25.13765. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Kramer K. M., Brock J. A., Bloom K., Moore J. K., Haber J. E. Two different types of double-strand breaks in Saccharomyces cerevisiae are repaired by similar RAD52-independent, nonhomologous recombination events. Mol Cell Biol. 1994 Feb;14(2):1293–1301. doi: 10.1128/mcb.14.2.1293. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. doi: 10.1038/227680a0. [DOI] [PubMed] [Google Scholar]
  32. Leach D. R., Lloyd R. G., Coulson A. F. The SbcCD protein of Escherichia coli is related to two putative nucleases in the UvrA superfamily of nucleotide-binding proteins. Genetica. 1992;87(2):95–100. doi: 10.1007/BF00120998. [DOI] [PubMed] [Google Scholar]
  33. Lee S. E., Moore J. K., Holmes A., Umezu K., Kolodner R. D., Haber J. E. Saccharomyces Ku70, mre11/rad50 and RPA proteins regulate adaptation to G2/M arrest after DNA damage. Cell. 1998 Aug 7;94(3):399–409. doi: 10.1016/s0092-8674(00)81482-8. [DOI] [PubMed] [Google Scholar]
  34. Loidl J., Klein F., Scherthan H. Homologous pairing is reduced but not abolished in asynaptic mutants of yeast. J Cell Biol. 1994 Jun;125(6):1191–1200. doi: 10.1083/jcb.125.6.1191. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Malone R. E., Bullard S., Hermiston M., Rieger R., Cool M., Galbraith A. Isolation of mutants defective in early steps of meiotic recombination in the yeast Saccharomyces cerevisiae. Genetics. 1991 May;128(1):79–88. doi: 10.1093/genetics/128.1.79. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Matsuura S., Tauchi H., Nakamura A., Kondo N., Sakamoto S., Endo S., Smeets D., Solder B., Belohradsky B. H., Der Kaloustian V. M. Positional cloning of the gene for Nijmegen breakage syndrome. Nat Genet. 1998 Jun;19(2):179–181. doi: 10.1038/549. [DOI] [PubMed] [Google Scholar]
  37. Mezard C., Nicolas A. Homologous, homeologous, and illegitimate repair of double-strand breaks during transformation of a wild-type strain and a rad52 mutant strain of Saccharomyces cerevisiae. Mol Cell Biol. 1994 Feb;14(2):1278–1292. doi: 10.1128/mcb.14.2.1278. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Milne G. T., Jin S., Shannon K. B., Weaver D. T. Mutations in two Ku homologs define a DNA end-joining repair pathway in Saccharomyces cerevisiae. Mol Cell Biol. 1996 Aug;16(8):4189–4198. doi: 10.1128/mcb.16.8.4189. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Moore J. K., Haber J. E. Cell cycle and genetic requirements of two pathways of nonhomologous end-joining repair of double-strand breaks in Saccharomyces cerevisiae. Mol Cell Biol. 1996 May;16(5):2164–2173. doi: 10.1128/mcb.16.5.2164. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Nairz K., Klein F. mre11S--a yeast mutation that blocks double-strand-break processing and permits nonhomologous synapsis in meiosis. Genes Dev. 1997 Sep 1;11(17):2272–2290. doi: 10.1101/gad.11.17.2272. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Nakagawa T., Ogawa H. Involvement of the MRE2 gene of yeast in formation of meiosis-specific double-strand breaks and crossover recombination through RNA splicing. Genes Cells. 1997 Jan;2(1):65–79. doi: 10.1046/j.1365-2443.1997.d01-283.x. [DOI] [PubMed] [Google Scholar]
  42. Nugent C. I., Bosco G., Ross L. O., Evans S. K., Salinger A. P., Moore J. K., Haber J. E., Lundblad V. Telomere maintenance is dependent on activities required for end repair of double-strand breaks. Curr Biol. 1998 May 21;8(11):657–660. doi: 10.1016/s0960-9822(98)70253-2. [DOI] [PubMed] [Google Scholar]
  43. Ogawa H., Johzuka K., Nakagawa T., Leem S. H., Hagihara A. H. Functions of the yeast meiotic recombination genes, MRE11 and MRE2. Adv Biophys. 1995;31:67–76. doi: 10.1016/0065-227x(95)99383-z. [DOI] [PubMed] [Google Scholar]
  44. Ohta K., Nicolas A., Furuse M., Nabetani A., Ogawa H., Shibata T. Mutations in the MRE11, RAD50, XRS2, and MRE2 genes alter chromatin configuration at meiotic DNA double-stranded break sites in premeiotic and meiotic cells. Proc Natl Acad Sci U S A. 1998 Jan 20;95(2):646–651. doi: 10.1073/pnas.95.2.646. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Ohta K., Shibata T., Nicolas A. Changes in chromatin structure at recombination initiation sites during yeast meiosis. EMBO J. 1994 Dec 1;13(23):5754–5763. doi: 10.1002/j.1460-2075.1994.tb06913.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Paull T. T., Gellert M. The 3' to 5' exonuclease activity of Mre 11 facilitates repair of DNA double-strand breaks. Mol Cell. 1998 Jun;1(7):969–979. doi: 10.1016/s1097-2765(00)80097-0. [DOI] [PubMed] [Google Scholar]
  47. Petrini J. H., Walsh M. E., DiMare C., Chen X. N., Korenberg J. R., Weaver D. T. Isolation and characterization of the human MRE11 homologue. Genomics. 1995 Sep 1;29(1):80–86. doi: 10.1006/geno.1995.1217. [DOI] [PubMed] [Google Scholar]
  48. Rockmill B., Engebrecht J. A., Scherthan H., Loidl J., Roeder G. S. The yeast MER2 gene is required for chromosome synapsis and the initiation of meiotic recombination. Genetics. 1995 Sep;141(1):49–59. doi: 10.1093/genetics/141.1.49. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Sharples G. J., Leach D. R. Structural and functional similarities between the SbcCD proteins of Escherichia coli and the RAD50 and MRE11 (RAD32) recombination and repair proteins of yeast. Mol Microbiol. 1995 Sep;17(6):1215–1217. doi: 10.1111/j.1365-2958.1995.mmi_17061215_1.x. [DOI] [PubMed] [Google Scholar]
  50. Shinohara A., Ogawa T. Homologous recombination and the roles of double-strand breaks. Trends Biochem Sci. 1995 Oct;20(10):387–391. doi: 10.1016/s0968-0004(00)89085-4. [DOI] [PubMed] [Google Scholar]
  51. Tavassoli M., Shayeghi M., Nasim A., Watts F. Z. Cloning and characterisation of the Schizosaccharomyces pombe rad32 gene: a gene required for repair of double strand breaks and recombination. Nucleic Acids Res. 1995 Feb 11;23(3):383–388. doi: 10.1093/nar/23.3.383. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Towbin H., Staehelin T., Gordon J. Electrophoretic transfer of proteins from polyacrylamide gels to nitrocellulose sheets: procedure and some applications. Proc Natl Acad Sci U S A. 1979 Sep;76(9):4350–4354. doi: 10.1073/pnas.76.9.4350. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Trujillo K. M., Yuan S. S., Lee E. Y., Sung P. Nuclease activities in a complex of human recombination and DNA repair factors Rad50, Mre11, and p95. J Biol Chem. 1998 Aug 21;273(34):21447–21450. doi: 10.1074/jbc.273.34.21447. [DOI] [PubMed] [Google Scholar]
  54. Tsubouchi H., Ogawa H. A novel mre11 mutation impairs processing of double-strand breaks of DNA during both mitosis and meiosis. Mol Cell Biol. 1998 Jan;18(1):260–268. doi: 10.1128/mcb.18.1.260. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Tsukamoto Y., Ikeda H. Double-strand break repair mediated by DNA end-joining. Genes Cells. 1998 Mar;3(3):135–144. doi: 10.1046/j.1365-2443.1998.00180.x. [DOI] [PubMed] [Google Scholar]
  56. Tsukamoto Y., Kato J., Ikeda H. Budding yeast Rad50, Mre11, Xrs2, and Hdf1, but not Rad52, are involved in the formation of deletions on a dicentric plasmid. Mol Gen Genet. 1997 Aug;255(5):543–547. doi: 10.1007/s004380050527. [DOI] [PubMed] [Google Scholar]
  57. Tsukamoto Y., Kato J., Ikeda H. Hdf1, a yeast Ku-protein homologue, is involved in illegitimate recombination, but not in homologous recombination. Nucleic Acids Res. 1996 Jun 1;24(11):2067–2072. doi: 10.1093/nar/24.11.2067. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Varon R., Vissinga C., Platzer M., Cerosaletti K. M., Chrzanowska K. H., Saar K., Beckmann G., Seemanová E., Cooper P. R., Nowak N. J. Nibrin, a novel DNA double-strand break repair protein, is mutated in Nijmegen breakage syndrome. Cell. 1998 May 1;93(3):467–476. doi: 10.1016/s0092-8674(00)81174-5. [DOI] [PubMed] [Google Scholar]
  59. Weiner B. M., Kleckner N. Chromosome pairing via multiple interstitial interactions before and during meiosis in yeast. Cell. 1994 Jul 1;77(7):977–991. doi: 10.1016/0092-8674(94)90438-3. [DOI] [PubMed] [Google Scholar]
  60. Wu T. C., Lichten M. Meiosis-induced double-strand break sites determined by yeast chromatin structure. Science. 1994 Jan 28;263(5146):515–518. doi: 10.1126/science.8290959. [DOI] [PubMed] [Google Scholar]
  61. Zhuo S., Clemens J. C., Stone R. L., Dixon J. E. Mutational analysis of a Ser/Thr phosphatase. Identification of residues important in phosphoesterase substrate binding and catalysis. J Biol Chem. 1994 Oct 21;269(42):26234–26238. [PubMed] [Google Scholar]

Articles from The EMBO Journal are provided here courtesy of Nature Publishing Group

RESOURCES