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. 1994 Jul;14(7):4802–4814. doi: 10.1128/mcb.14.7.4802

Induction of recombination between homologous and diverged DNAs by double-strand gaps and breaks and role of mismatch repair.

S D Priebe 1, J Westmoreland 1, T Nilsson-Tillgren 1, M A Resnick 1
PMCID: PMC358853  PMID: 8007979

Abstract

Sequence homology is expected to influence recombination. To further understand mechanisms of recombination and the impact of reduced homology, we examined recombination during transformation between plasmid-borne DNA flanking a double-strand break (DSB) or gap and its chromosomal homolog. Previous reports have concentrated on spontaneous recombination or initiation by undefined lesions. Sequence divergence of approximately 16% reduced transformation frequencies by at least 10-fold. Gene conversion patterns associated with double-strand gap repair of episomal plasmids or with plasmid integration were analyzed by restriction endonuclease mapping and DNA sequencing. For episomal plasmids carrying homeologous DNA, at least one input end was always preserved beyond 10 bp, whereas for plasmids carrying homologous DNA, both input ends were converted beyond 80 bp in 60% of the transformants. The system allowed the recovery of transformants carrying mixtures of recombinant molecules that might arise if heteroduplex DNA--a presumed recombination intermediate--escapes mismatch repair. Gene conversion involving homologous DNAs frequently involved DNA mismatch repair, directed to a broken strand. A mutation in the PMS1 mismatch repair gene significantly increased the fraction of transformants carrying a mixture of plasmids for homologous DNAs, indicating that PMS1 can participate in DSB-initiated recombination. Since nearly all transformants involving homeologous DNAs carried a single recombinant plasmid in both Pms+ and Pms- strains, stable heteroduplex DNA appears less likely than for homologous DNAs. Regardless of homology, gene conversion does not appear to occur by nucleolytic expansion of a DSB to a gap prior to recombination. The results with homeologous DNAs are consistent with a recombinational repair model that we propose does not require the formation of stable heteroduplex DNA but instead involves other homology-dependent interactions that allow recombination-dependent DNA synthesis.

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Selected References

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

  1. Ahn B. Y., Dornfeld K. J., Fagrelius T. J., Livingston D. M. Effect of limited homology on gene conversion in a Saccharomyces cerevisiae plasmid recombination system. Mol Cell Biol. 1988 Jun;8(6):2442–2448. doi: 10.1128/mcb.8.6.2442. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bailis A. M., Arthur L., Rothstein R. Genome rearrangement in top3 mutants of Saccharomyces cerevisiae requires a functional RAD1 excision repair gene. Mol Cell Biol. 1992 Nov;12(11):4988–4993. doi: 10.1128/mcb.12.11.4988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bailis A. M., Rothstein R. A defect in mismatch repair in Saccharomyces cerevisiae stimulates ectopic recombination between homeologous genes by an excision repair dependent process. Genetics. 1990 Nov;126(3):535–547. doi: 10.1093/genetics/126.3.535. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bennett C. B., Lewis A. L., Baldwin K. K., Resnick M. A. Lethality induced by a single site-specific double-strand break in a dispensable yeast plasmid. Proc Natl Acad Sci U S A. 1993 Jun 15;90(12):5613–5617. doi: 10.1073/pnas.90.12.5613. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Bianchi M., DasGupta C., Radding C. M. Synapsis and the formation of paranemic joints by E. coli RecA protein. Cell. 1983 Oct;34(3):931–939. doi: 10.1016/0092-8674(83)90550-0. [DOI] [PubMed] [Google Scholar]
  6. Birnboim H. C. A rapid alkaline extraction method for the isolation of plasmid DNA. Methods Enzymol. 1983;100:243–255. doi: 10.1016/0076-6879(83)00059-2. [DOI] [PubMed] [Google Scholar]
  7. Borts R. H., Leung W. Y., Kramer W., Kramer B., Williamson M., Fogel S., Haber J. E. Mismatch repair-induced meiotic recombination requires the pms1 gene product. Genetics. 1990 Mar;124(3):573–584. doi: 10.1093/genetics/124.3.573. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Claverys J. P., Lacks S. A. Heteroduplex deoxyribonucleic acid base mismatch repair in bacteria. Microbiol Rev. 1986 Jun;50(2):133–165. doi: 10.1128/mr.50.2.133-165.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. DasGupta C., Radding C. M. Lower fidelity of RecA protein catalysed homologous pairing with a superhelical substrate. Nature. 1982 Jan 7;295(5844):71–73. doi: 10.1038/295071a0. [DOI] [PubMed] [Google Scholar]
  10. Donahue T. F., Farabaugh P. J., Fink G. R. The nucleotide sequence of the HIS4 region of yeast. Gene. 1982 Apr;18(1):47–59. doi: 10.1016/0378-1119(82)90055-5. [DOI] [PubMed] [Google Scholar]
  11. 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]
  12. Formosa T., Alberts B. M. DNA synthesis dependent on genetic recombination: characterization of a reaction catalyzed by purified bacteriophage T4 proteins. Cell. 1986 Dec 5;47(5):793–806. doi: 10.1016/0092-8674(86)90522-2. [DOI] [PubMed] [Google Scholar]
  13. Gietz R. D., Sugino A. New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites. Gene. 1988 Dec 30;74(2):527–534. doi: 10.1016/0378-1119(88)90185-0. [DOI] [PubMed] [Google Scholar]
  14. Guild W. R., Shoemaker N. B. Intracellular competition for a mismatch recogition system and marker-specific rescue of transforming DNA from inactivation by ultraviolet irradiation. Mol Gen Genet. 1974;128(4):291–300. doi: 10.1007/BF00268517. [DOI] [PubMed] [Google Scholar]
  15. Harris S., Rudnicki K. S., Haber J. E. Gene conversions and crossing over during homologous and homeologous ectopic recombination in Saccharomyces cerevisiae. Genetics. 1993 Sep;135(1):5–16. doi: 10.1093/genetics/135.1.5. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Hoffman C. S., Winston F. A ten-minute DNA preparation from yeast efficiently releases autonomous plasmids for transformation of Escherichia coli. Gene. 1987;57(2-3):267–272. doi: 10.1016/0378-1119(87)90131-4. [DOI] [PubMed] [Google Scholar]
  17. Huang L. S., Ripps M. E., Korman S. H., Deckelbaum R. J., Breslow J. L. Hypobetalipoproteinemia due to an apolipoprotein B gene exon 21 deletion derived by Alu-Alu recombination. J Biol Chem. 1989 Jul 5;264(19):11394–11400. [PubMed] [Google Scholar]
  18. Ito H., Fukuda Y., Murata K., Kimura A. Transformation of intact yeast cells treated with alkali cations. J Bacteriol. 1983 Jan;153(1):163–168. doi: 10.1128/jb.153.1.163-168.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Jinks-Robertson S., Michelitch M., Ramcharan S. Substrate length requirements for efficient mitotic recombination in Saccharomyces cerevisiae. Mol Cell Biol. 1993 Jul;13(7):3937–3950. doi: 10.1128/mcb.13.7.3937. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. 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]
  21. Larionov V., Kouprina N., Eldarov M., Perkins E., Porter G., Resnick M. A. Transformation-associated recombination between diverged and homologous DNA repeats is induced by strand breaks. Yeast. 1994 Jan;10(1):93–104. doi: 10.1002/yea.320100109. [DOI] [PubMed] [Google Scholar]
  22. Learn B. A., Grafstrom R. H. Methyl-directed repair of frameshift heteroduplexes in cell extracts from Escherichia coli. J Bacteriol. 1989 Dec;171(12):6473–6481. doi: 10.1128/jb.171.12.6473-6481.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Miller H. Practical aspects of preparing phage and plasmid DNA: growth, maintenance, and storage of bacteria and bacteriophage. Methods Enzymol. 1987;152:145–170. doi: 10.1016/0076-6879(87)52016-x. [DOI] [PubMed] [Google Scholar]
  24. Modrich P. Mechanisms and biological effects of mismatch repair. Annu Rev Genet. 1991;25:229–253. doi: 10.1146/annurev.ge.25.120191.001305. [DOI] [PubMed] [Google Scholar]
  25. Myerowitz R., Hogikyan N. D. A deletion involving Alu sequences in the beta-hexosaminidase alpha-chain gene of French Canadians with Tay-Sachs disease. J Biol Chem. 1987 Nov 15;262(32):15396–15399. [PubMed] [Google Scholar]
  26. Mézard C., Pompon D., Nicolas A. Recombination between similar but not identical DNA sequences during yeast transformation occurs within short stretches of identity. Cell. 1992 Aug 21;70(4):659–670. doi: 10.1016/0092-8674(92)90434-e. [DOI] [PubMed] [Google Scholar]
  27. New L., Liu K., Crouse G. F. The yeast gene MSH3 defines a new class of eukaryotic MutS homologues. Mol Gen Genet. 1993 May;239(1-2):97–108. doi: 10.1007/BF00281607. [DOI] [PubMed] [Google Scholar]
  28. 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]
  29. Pavan W. J., Hieter P., Reeves R. H. Modification and transfer into an embryonal carcinoma cell line of a 360-kilobase human-derived yeast artificial chromosome. Mol Cell Biol. 1990 Aug;10(8):4163–4169. doi: 10.1128/mcb.10.8.4163. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Petit M. A., Dimpfl J., Radman M., Echols H. Control of large chromosomal duplications in Escherichia coli by the mismatch repair system. Genetics. 1991 Oct;129(2):327–332. doi: 10.1093/genetics/129.2.327. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Pompon D., Nicolas A. Protein engineering by cDNA recombination in yeasts: shuffling of mammalian cytochrome P-450 functions. Gene. 1989 Nov 15;83(1):15–24. doi: 10.1016/0378-1119(89)90399-5. [DOI] [PubMed] [Google Scholar]
  32. Ray B. L., White C. I., Haber J. E. Heteroduplex formation and mismatch repair of the "stuck" mutation during mating-type switching in Saccharomyces cerevisiae. Mol Cell Biol. 1991 Oct;11(10):5372–5380. doi: 10.1128/mcb.11.10.5372. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Rayssiguier C., Thaler D. S., Radman M. The barrier to recombination between Escherichia coli and Salmonella typhimurium is disrupted in mismatch-repair mutants. Nature. 1989 Nov 23;342(6248):396–401. doi: 10.1038/342396a0. [DOI] [PubMed] [Google Scholar]
  34. 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]
  35. Resnick M. A., Skaanild M., Nilsson-Tillgren T. Lack of DNA homology in a pair of divergent chromosomes greatly sensitizes them to loss by DNA damage. Proc Natl Acad Sci U S A. 1989 Apr;86(7):2276–2280. doi: 10.1073/pnas.86.7.2276. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Resnick M. A. The repair of double-strand breaks in DNA; a model involving recombination. J Theor Biol. 1976 Jun;59(1):97–106. doi: 10.1016/s0022-5193(76)80025-2. [DOI] [PubMed] [Google Scholar]
  37. Resnick M. A., Zgaga Z., Hieter P., Westmoreland J., Fogel S., Nilsson-Tillgren T. Recombinant repair of diverged DNAs: a study of homoeologous chromosomes and mammalian YACs in yeast. Mol Gen Genet. 1992 Jul;234(1):65–73. doi: 10.1007/BF00272346. [DOI] [PubMed] [Google Scholar]
  38. Rudin N., Haber J. E. Efficient repair of HO-induced chromosomal breaks in Saccharomyces cerevisiae by recombination between flanking homologous sequences. Mol Cell Biol. 1988 Sep;8(9):3918–3928. doi: 10.1128/mcb.8.9.3918. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. 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]
  40. Schultes N. P., Szostak J. W. Decreasing gradients of gene conversion on both sides of the initiation site for meiotic recombination at the ARG4 locus in yeast. Genetics. 1990 Dec;126(4):813–822. doi: 10.1093/genetics/126.4.813. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Shen P., Huang H. V. Effect of base pair mismatches on recombination via the RecBCD pathway. Mol Gen Genet. 1989 Aug;218(2):358–360. doi: 10.1007/BF00331291. [DOI] [PubMed] [Google Scholar]
  42. Shen P., Huang H. V. Homologous recombination in Escherichia coli: dependence on substrate length and homology. Genetics. 1986 Mar;112(3):441–457. doi: 10.1093/genetics/112.3.441. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Stoppa-Lyonnet D., Carter P. E., Meo T., Tosi M. Clusters of intragenic Alu repeats predispose the human C1 inhibitor locus to deleterious rearrangements. Proc Natl Acad Sci U S A. 1990 Feb;87(4):1551–1555. doi: 10.1073/pnas.87.4.1551. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Strathern J. N., Klar A. J., Hicks J. B., Abraham J. A., Ivy J. M., Nasmyth K. A., McGill C. Homothallic switching of yeast mating type cassettes is initiated by a double-stranded cut in the MAT locus. Cell. 1982 Nov;31(1):183–192. doi: 10.1016/0092-8674(82)90418-4. [DOI] [PubMed] [Google Scholar]
  45. 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]
  46. Sun H., Treco D., Szostak J. W. Extensive 3'-overhanging, single-stranded DNA associated with the meiosis-specific double-strand breaks at the ARG4 recombination initiation site. Cell. 1991 Mar 22;64(6):1155–1161. doi: 10.1016/0092-8674(91)90270-9. [DOI] [PubMed] [Google Scholar]
  47. Szostak J. W., Orr-Weaver T. L., Rothstein R. J., Stahl F. W. The double-strand-break repair model for recombination. Cell. 1983 May;33(1):25–35. doi: 10.1016/0092-8674(83)90331-8. [DOI] [PubMed] [Google Scholar]
  48. Thaler D. S., Stahl F. W. DNA double-chain breaks in recombination of phage lambda and of yeast. Annu Rev Genet. 1988;22:169–197. doi: 10.1146/annurev.ge.22.120188.001125. [DOI] [PubMed] [Google Scholar]
  49. Waldman A. S., Liskay R. M. Differential effects of base-pair mismatch on intrachromosomal versus extrachromosomal recombination in mouse cells. Proc Natl Acad Sci U S A. 1987 Aug;84(15):5340–5344. doi: 10.1073/pnas.84.15.5340. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Ward A. C. Single-step purification of shuttle vectors from yeast for high frequency back-transformation into E. coli. Nucleic Acids Res. 1990 Sep 11;18(17):5319–5319. doi: 10.1093/nar/18.17.5319. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. 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]
  52. Zenvirth D., Arbel T., Sherman A., Goldway M., Klein S., Simchen G. Multiple sites for double-strand breaks in whole meiotic chromosomes of Saccharomyces cerevisiae. EMBO J. 1992 Sep;11(9):3441–3447. doi: 10.1002/j.1460-2075.1992.tb05423.x. [DOI] [PMC free article] [PubMed] [Google Scholar]

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