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. 1995 Aug;140(4):1199–1211. doi: 10.1093/genetics/140.4.1199

The Role of DNA Repair Genes in Recombination between Repeated Sequences in Yeast

B Liefshitz 1, A Parket 1, R Maya 1, M Kupiec 1
PMCID: PMC1206687  PMID: 7498763

Abstract

The presence of repeated sequences in the genome represents a potential source of karyotypic instability. Genetic control of recombination is thus important to preserve the integrity of the genome. To investigate the genetic control of recombination between repeated sequences, we have created a series of isogenic strains in which we could assess the role of genes involved in DNA repair in two types of recombination: direct repeat recombination and ectopic gene conversion. Naturally occurring (Ty elements) and artificially constructed repeats could be compared in the same cell population. We have found that direct repeat recombination and gene conversion have different genetic requirements. The role of the RAD51, RAD52, RAD54, RAD55, and RAD57 genes, which are involved in recombinational repair, was investigated. Based on the phenotypes of single and double mutants, these genes can be divided into three functional subgroups: one composed of RAD52, a second one composed of RAD51 and RAD54, and a third one that includes the RAD55 and RAD57 genes. Among seven genes involved in excision repair tested, only RAD1 and RAD10 played a role in the types of recombination studied. We did not detect a differential effect of any rad mutation on Ty elements as compared to artificially constructed repeats.

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Selected References

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  1. Aguilera A., Klein H. L. Genetic control of intrachromosomal recombination in Saccharomyces cerevisiae. I. Isolation and genetic characterization of hyper-recombination mutations. Genetics. 1988 Aug;119(4):779–790. doi: 10.1093/genetics/119.4.779. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Aguilera A., Klein H. L. Yeast intrachromosomal recombination: long gene conversion tracts are preferentially associated with reciprocal exchange and require the RAD1 and RAD3 gene products. Genetics. 1989 Dec;123(4):683–694. doi: 10.1093/genetics/123.4.683. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Alani E., Cao L., Kleckner N. A method for gene disruption that allows repeated use of URA3 selection in the construction of multiply disrupted yeast strains. Genetics. 1987 Aug;116(4):541–545. doi: 10.1534/genetics.112.541.test. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bankmann M., Prakash L., Prakash S. Yeast RAD14 and human xeroderma pigmentosum group A DNA-repair genes encode homologous proteins. Nature. 1992 Feb 6;355(6360):555–558. doi: 10.1038/355555a0. [DOI] [PubMed] [Google Scholar]
  5. Bardwell A. J., Bardwell L., Iyer N., Svejstrup J. Q., Feaver W. J., Kornberg R. D., Friedberg E. C. Yeast nucleotide excision repair proteins Rad2 and Rad4 interact with RNA polymerase II basal transcription factor b (TFIIH). Mol Cell Biol. 1994 Jun;14(6):3569–3576. doi: 10.1128/mcb.14.6.3569. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bardwell A. J., Bardwell L., Tomkinson A. E., Friedberg E. C. Specific cleavage of model recombination and repair intermediates by the yeast Rad1-Rad10 DNA endonuclease. Science. 1994 Sep 30;265(5181):2082–2085. doi: 10.1126/science.8091230. [DOI] [PubMed] [Google Scholar]
  7. Basile G., Aker M., Mortimer R. K. Nucleotide sequence and transcriptional regulation of the yeast recombinational repair gene RAD51. Mol Cell Biol. 1992 Jul;12(7):3235–3246. doi: 10.1128/mcb.12.7.3235. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. 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]
  9. Borts R. H., Lichten M., Haber J. E. Analysis of meiosis-defective mutations in yeast by physical monitoring of recombination. Genetics. 1986 Jul;113(3):551–567. doi: 10.1093/genetics/113.3.551. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Couto L. B., Friedberg E. C. Nucleotide sequence of the wild-type RAD4 gene of Saccharomyces cerevisiae and characterization of mutant rad4 alleles. J Bacteriol. 1989 Apr;171(4):1862–1869. doi: 10.1128/jb.171.4.1862-1869.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Egel R. Intergenic conversion and reiterated genes. Nature. 1981 Mar 19;290(5803):191–192. doi: 10.1038/290191a0. [DOI] [PubMed] [Google Scholar]
  12. Emery H. S., Schild D., Kellogg D. E., Mortimer R. K. Sequence of RAD54, a Saccharomyces cerevisiae gene involved in recombination and repair. Gene. 1991 Jul 31;104(1):103–106. doi: 10.1016/0378-1119(91)90473-o. [DOI] [PubMed] [Google Scholar]
  13. Fishman-Lobell J., Haber J. E. Removal of nonhomologous DNA ends in double-strand break recombination: the role of the yeast ultraviolet repair gene RAD1. Science. 1992 Oct 16;258(5081):480–484. doi: 10.1126/science.1411547. [DOI] [PubMed] [Google Scholar]
  14. Fishman-Lobell J., Rudin N., Haber J. E. Two alternative pathways of double-strand break repair that are kinetically separable and independently modulated. Mol Cell Biol. 1992 Mar;12(3):1292–1303. doi: 10.1128/mcb.12.3.1292. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Friedberg E. C. Deoxyribonucleic acid repair in the yeast Saccharomyces cerevisiae. Microbiol Rev. 1988 Mar;52(1):70–102. doi: 10.1128/mr.52.1.70-102.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Game J. C. DNA double-strand breaks and the RAD50-RAD57 genes in Saccharomyces. Semin Cancer Biol. 1993 Apr;4(2):73–83. [PubMed] [Google Scholar]
  17. Harrington J. J., Lieber M. R. Functional domains within FEN-1 and RAD2 define a family of structure-specific endonucleases: implications for nucleotide excision repair. Genes Dev. 1994 Jun 1;8(11):1344–1355. doi: 10.1101/gad.8.11.1344. [DOI] [PubMed] [Google Scholar]
  18. Hastings P. J., Quah S. K., von Borstel R. C. Spontaneous mutation by mutagenic repair of spontaneous lesions in DNA. Nature. 1976 Dec 23;264(5588):719–722. doi: 10.1038/264719a0. [DOI] [PubMed] [Google Scholar]
  19. Jackson J. A., Fink G. R. Gene conversion between duplicated genetic elements in yeast. Nature. 1981 Jul 23;292(5821):306–311. doi: 10.1038/292306a0. [DOI] [PubMed] [Google Scholar]
  20. Jinks-Robertson S., Petes T. D. Chromosomal translocations generated by high-frequency meiotic recombination between repeated yeast genes. Genetics. 1986 Nov;114(3):731–752. doi: 10.1093/genetics/114.3.731. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Kadyk L. C., Hartwell L. H. Sister chromatids are preferred over homologs as substrates for recombinational repair in Saccharomyces cerevisiae. Genetics. 1992 Oct;132(2):387–402. doi: 10.1093/genetics/132.2.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Kans J. A., Mortimer R. K. Nucleotide sequence of the RAD57 gene of Saccharomyces cerevisiae. Gene. 1991 Aug 30;105(1):139–140. doi: 10.1016/0378-1119(91)90527-i. [DOI] [PubMed] [Google Scholar]
  23. Kass D. H., Batzer M. A., Deininger P. L. Gene conversion as a secondary mechanism of short interspersed element (SINE) evolution. Mol Cell Biol. 1995 Jan;15(1):19–25. doi: 10.1128/mcb.15.1.19. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Klein H. L. Different types of recombination events are controlled by the RAD1 and RAD52 genes of Saccharomyces cerevisiae. Genetics. 1988 Oct;120(2):367–377. doi: 10.1093/genetics/120.2.367. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Klein H. L., Petes T. D. Intrachromosomal gene conversion in yeast. Nature. 1981 Jan 15;289(5794):144–148. doi: 10.1038/289144a0. [DOI] [PubMed] [Google Scholar]
  26. Kupiec M., Petes T. D. Meiotic recombination between repeated transposable elements in Saccharomyces cerevisiae. Mol Cell Biol. 1988 Jul;8(7):2942–2954. doi: 10.1128/mcb.8.7.2942. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Lichten M., Borts R. H., Haber J. E. Meiotic gene conversion and crossing over between dispersed homologous sequences occurs frequently in Saccharomyces cerevisiae. Genetics. 1987 Feb;115(2):233–246. doi: 10.1093/genetics/115.2.233. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Lichten M., Haber J. E. Position effects in ectopic and allelic mitotic recombination in Saccharomyces cerevisiae. Genetics. 1989 Oct;123(2):261–268. doi: 10.1093/genetics/123.2.261. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Lin F. L., Sperle K., Sternberg N. Intermolecular recombination between DNAs introduced into mouse L cells is mediated by a nonconservative pathway that leads to crossover products. Mol Cell Biol. 1990 Jan;10(1):103–112. doi: 10.1128/mcb.10.1.103. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Louis E. J., Haber J. E. Mitotic recombination among subtelomeric Y' repeats in Saccharomyces cerevisiae. Genetics. 1990 Mar;124(3):547–559. doi: 10.1093/genetics/124.3.547. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Lovett S. T., Mortimer R. K. Characterization of null mutants of the RAD55 gene of Saccharomyces cerevisiae: effects of temperature, osmotic strength and mating type. Genetics. 1987 Aug;116(4):547–553. doi: 10.1093/genetics/116.4.547. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Lovett S. T. Sequence of the RAD55 gene of Saccharomyces cerevisiae: similarity of RAD55 to prokaryotic RecA and other RecA-like proteins. Gene. 1994 May 3;142(1):103–106. doi: 10.1016/0378-1119(94)90362-x. [DOI] [PubMed] [Google Scholar]
  33. Madura K., Prakash S. Nucleotide sequence, transcript mapping, and regulation of the RAD2 gene of Saccharomyces cerevisiae. J Bacteriol. 1986 Jun;166(3):914–923. doi: 10.1128/jb.166.3.914-923.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Malone R. E., Esposito R. E. The RAD52 gene is required for homothallic interconversion of mating types and spontaneous mitotic recombination in yeast. Proc Natl Acad Sci U S A. 1980 Jan;77(1):503–507. doi: 10.1073/pnas.77.1.503. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Maryon E., Carroll D. Characterization of recombination intermediates from DNA injected into Xenopus laevis oocytes: evidence for a nonconservative mechanism of homologous recombination. Mol Cell Biol. 1991 Jun;11(6):3278–3287. doi: 10.1128/mcb.11.6.3278. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. McDonald J. P., Rothstein R. Unrepaired heteroduplex DNA in Saccharomyces cerevisiae is decreased in RAD1 RAD52-independent recombination. Genetics. 1994 Jun;137(2):393–405. doi: 10.1093/genetics/137.2.393. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Melamed C., Nevo Y., Kupiec M. Involvement of cDNA in homologous recombination between Ty elements in Saccharomyces cerevisiae. Mol Cell Biol. 1992 Apr;12(4):1613–1620. doi: 10.1128/mcb.12.4.1613. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Milne G. T., Weaver D. T. Dominant negative alleles of RAD52 reveal a DNA repair/recombination complex including Rad51 and Rad52. Genes Dev. 1993 Sep;7(9):1755–1765. doi: 10.1101/gad.7.9.1755. [DOI] [PubMed] [Google Scholar]
  39. Nevo-Caspi Y., Kupiec M. Transcriptional induction of Ty recombination in yeast. Proc Natl Acad Sci U S A. 1994 Dec 20;91(26):12711–12715. doi: 10.1073/pnas.91.26.12711. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Ogawa T., Yu X., Shinohara A., Egelman E. H. Similarity of the yeast RAD51 filament to the bacterial RecA filament. Science. 1993 Mar 26;259(5103):1896–1899. doi: 10.1126/science.8456314. [DOI] [PubMed] [Google Scholar]
  41. Ozenberger B. A., Roeder G. S. A unique pathway of double-strand break repair operates in tandemly repeated genes. Mol Cell Biol. 1991 Mar;11(3):1222–1231. doi: 10.1128/mcb.11.3.1222. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Paetkau D. W., Riese J. A., MacMorran W. S., Woods R. A., Gietz R. D. Interaction of the yeast RAD7 and SIR3 proteins: implications for DNA repair and chromatin structure. Genes Dev. 1994 Sep 1;8(17):2035–2045. doi: 10.1101/gad.8.17.2035. [DOI] [PubMed] [Google Scholar]
  43. Parket A., Inbar O., Kupiec M. Recombination of Ty elements in yeast can be induced by a double-strand break. Genetics. 1995 May;140(1):67–77. doi: 10.1093/genetics/140.1.67. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Parket A., Kupiec M. Ectopic recombination between Ty elements in Saccharomyces cerevisiae is not induced by DNA damage. Mol Cell Biol. 1992 Oct;12(10):4441–4448. doi: 10.1128/mcb.12.10.4441. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Perozzi G., Prakash S. RAD7 gene of Saccharomyces cerevisiae: transcripts, nucleotide sequence analysis, and functional relationship between the RAD7 and RAD23 gene products. Mol Cell Biol. 1986 May;6(5):1497–1507. doi: 10.1128/mcb.6.5.1497. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Prado F., Aguilera A. Role of reciprocal exchange, one-ended invasion crossover and single-strand annealing on inverted and direct repeat recombination in yeast: different requirements for the RAD1, RAD10, and RAD52 genes. Genetics. 1995 Jan;139(1):109–123. doi: 10.1093/genetics/139.1.109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Prakash S., Prakash L., Burke W., Montelone B. A. Effects of the RAD52 Gene on Recombination in SACCHAROMYCES CEREVISIAE. Genetics. 1980 Jan;94(1):31–50. doi: 10.1093/genetics/94.1.31. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Prakash S., Sung P., Prakash L. DNA repair genes and proteins of Saccharomyces cerevisiae. Annu Rev Genet. 1993;27:33–70. doi: 10.1146/annurev.ge.27.120193.000341. [DOI] [PubMed] [Google Scholar]
  49. Quah S. K., von Borstel R. C., Hastings P. J. The origin of spontaneous mutation in Saccharomyces cerevisiae. Genetics. 1980 Dec;96(4):819–839. doi: 10.1093/genetics/96.4.819. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Rattray A. J., Symington L. S. Multiple pathways for homologous recombination in Saccharomyces cerevisiae. Genetics. 1995 Jan;139(1):45–56. doi: 10.1093/genetics/139.1.45. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Rattray A. J., Symington L. S. Use of a chromosomal inverted repeat to demonstrate that the RAD51 and RAD52 genes of Saccharomyces cerevisiae have different roles in mitotic recombination. Genetics. 1994 Nov;138(3):587–595. doi: 10.1093/genetics/138.3.587. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Resnick M. A., Martin P. The repair of double-strand breaks in the nuclear DNA of Saccharomyces cerevisiae and its genetic control. Mol Gen Genet. 1976 Jan 16;143(2):119–129. doi: 10.1007/BF00266917. [DOI] [PubMed] [Google Scholar]
  53. Reynolds R. J., Friedberg E. C. Molecular mechanisms of pyrimidine dimer excision in Saccharomyces cerevisiae: incision of ultraviolet-irradiated deoxyribonucleic acid in vivo. J Bacteriol. 1981 May;146(2):692–704. doi: 10.1128/jb.146.2.692-704.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  54. Rothstein R. J. One-step gene disruption in yeast. Methods Enzymol. 1983;101:202–211. doi: 10.1016/0076-6879(83)01015-0. [DOI] [PubMed] [Google Scholar]
  55. Saeki T., Machida I., Nakai S. Genetic control of diploid recovery after gamma-irradiation in the yeast Saccharomyces cerevisiae. Mutat Res. 1980 Dec;73(2):251–265. doi: 10.1016/0027-5107(80)90192-x. [DOI] [PubMed] [Google Scholar]
  56. Schiestl R. H., Gietz R. D. High efficiency transformation of intact yeast cells using single stranded nucleic acids as a carrier. Curr Genet. 1989 Dec;16(5-6):339–346. doi: 10.1007/BF00340712. [DOI] [PubMed] [Google Scholar]
  57. Schiestl R. H., Prakash S. RAD1, an excision repair gene of Saccharomyces cerevisiae, is also involved in recombination. Mol Cell Biol. 1988 Sep;8(9):3619–3626. doi: 10.1128/mcb.8.9.3619. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Schiestl R. H., Prakash S. RAD10, an excision repair gene of Saccharomyces cerevisiae, is involved in the RAD1 pathway of mitotic recombination. Mol Cell Biol. 1990 Jun;10(6):2485–2491. doi: 10.1128/mcb.10.6.2485. [DOI] [PMC free article] [PubMed] [Google Scholar]
  59. Shinohara A., Ogawa H., Ogawa T. Rad51 protein involved in repair and recombination in S. cerevisiae is a RecA-like protein. Cell. 1992 May 1;69(3):457–470. doi: 10.1016/0092-8674(92)90447-k. [DOI] [PubMed] [Google Scholar]
  60. Sikorski R. S., Hieter P. A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics. 1989 May;122(1):19–27. doi: 10.1093/genetics/122.1.19. [DOI] [PMC free article] [PubMed] [Google Scholar]
  61. Steele D. F., Morris M. E., Jinks-Robertson S. Allelic and ectopic interactions in recombination-defective yeast strains. Genetics. 1991 Jan;127(1):53–60. doi: 10.1093/genetics/127.1.53. [DOI] [PMC free article] [PubMed] [Google Scholar]
  62. Sung P. Catalysis of ATP-dependent homologous DNA pairing and strand exchange by yeast RAD51 protein. Science. 1994 Aug 26;265(5176):1241–1243. doi: 10.1126/science.8066464. [DOI] [PubMed] [Google Scholar]
  63. Sung P., Reynolds P., Prakash L., Prakash S. Purification and characterization of the Saccharomyces cerevisiae RAD1/RAD10 endonuclease. J Biol Chem. 1993 Dec 15;268(35):26391–26399. [PubMed] [Google Scholar]
  64. Thomas B. J., Rothstein R. The genetic control of direct-repeat recombination in Saccharomyces: the effect of rad52 and rad1 on mitotic recombination at GAL10, a transcriptionally regulated gene. Genetics. 1989 Dec;123(4):725–738. doi: 10.1093/genetics/123.4.725. [DOI] [PMC free article] [PubMed] [Google Scholar]
  65. Tomkinson A. E., Bardwell A. J., Bardwell L., Tappe N. J., Friedberg E. C. Yeast DNA repair and recombination proteins Rad1 and Rad10 constitute a single-stranded-DNA endonuclease. Nature. 1993 Apr 29;362(6423):860–862. doi: 10.1038/362860a0. [DOI] [PubMed] [Google Scholar]
  66. Verhage R., Zeeman A. M., de Groot N., Gleig F., Bang D. D., van de Putte P., Brouwer J. The RAD7 and RAD16 genes, which are essential for pyrimidine dimer removal from the silent mating type loci, are also required for repair of the nontranscribed strand of an active gene in Saccharomyces cerevisiae. Mol Cell Biol. 1994 Sep;14(9):6135–6142. doi: 10.1128/mcb.14.9.6135. [DOI] [PMC free article] [PubMed] [Google Scholar]
  67. Von Borstel R. C., Cain K. T., Steinberg C. M. Inheritance of spontaneous mutability in yeast. Genetics. 1971 Sep;69(1):17–27. doi: 10.1093/genetics/69.1.17. [DOI] [PMC free article] [PubMed] [Google Scholar]
  68. Watkins J. F., Sung P., Prakash L., Prakash S. The Saccharomyces cerevisiae DNA repair gene RAD23 encodes a nuclear protein containing a ubiquitin-like domain required for biological function. Mol Cell Biol. 1993 Dec;13(12):7757–7765. doi: 10.1128/mcb.13.12.7757. [DOI] [PMC free article] [PubMed] [Google Scholar]
  69. Wilcox D. R., Prakash L. Incision and postincision steps of pyrimidine dimer removal in excision-defective mutants of Saccharomyces cerevisiae. J Bacteriol. 1981 Nov;148(2):618–623. doi: 10.1128/jb.148.2.618-623.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]

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