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. 1993 Jul;134(3):685–700. doi: 10.1093/genetics/134.3.685

Positive and Negative Regulatory Elements Control Expression of the Yeast Retrotransposon Ty3

V W Bilanchone 1, J A Claypool 1, P T Kinsey 1, S B Sandmeyer 1
PMCID: PMC1205508  PMID: 8394262

Abstract

We report the results of an analysis of Ty3 transcription and identification of Ty3 regions that mediate pheromone and mating-type regulation to coordinate its expression with the yeast life cycle. A set of strains was constructed which was isogenic except for the number of Ty3 elements, which varied from zero to three. Analysis of Ty3 expression in these strains showed that each of the three elements was transcribed and that each element was regulated. Dissection of the long terminal repeat regulatory region by Northern blot analysis of deletion mutants and reporter gene analysis showed that the upstream junction of Ty3 with flanking chromosomal sequences contained a negative control region. A 19-bp fragment (positions 56-74) containing one consensus copy and one 7 of 8-bp match to the pheromone response element (PRE) consensus was sufficient to mediate pheromone induction in either haploid cell type. Deletion of this region, however, did not abolish expression, indicating that other sequences also activate transcription. A 24-bp block immediately downstream of the PRE region contained a sequence similar to the a1-α2 consensus that conferred mating-type control. A single base pair mutation in the region separating the PRE and a1-α2 sequences blocked pheromone induction, but not mating-type control. Thus, the long terminal repeat of Ty3 is a compact, highly regulated, mobile promoter which is responsive to cell type and mating.

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Selected References

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  1. Bender A., Sprague G. F., Jr MAT alpha 1 protein, a yeast transcription activator, binds synergistically with a second protein to a set of cell-type-specific genes. Cell. 1987 Aug 28;50(5):681–691. doi: 10.1016/0092-8674(87)90326-6. [DOI] [PubMed] [Google Scholar]
  2. Boeke J. D., Garfinkel D. J., Styles C. A., Fink G. R. Ty elements transpose through an RNA intermediate. Cell. 1985 Mar;40(3):491–500. doi: 10.1016/0092-8674(85)90197-7. [DOI] [PubMed] [Google Scholar]
  3. Company M., Adler C., Errede B. Identification of a Ty1 regulatory sequence responsive to STE7 and STE12. Mol Cell Biol. 1988 Jun;8(6):2545–2554. doi: 10.1128/mcb.8.6.2545. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Dolan J. W., Kirkman C., Fields S. The yeast STE12 protein binds to the DNA sequence mediating pheromone induction. Proc Natl Acad Sci U S A. 1989 Aug;86(15):5703–5707. doi: 10.1073/pnas.86.15.5703. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Elder R. T., Loh E. Y., Davis R. W. RNA from the yeast transposable element Ty1 has both ends in the direct repeats, a structure similar to retrovirus RNA. Proc Natl Acad Sci U S A. 1983 May;80(9):2432–2436. doi: 10.1073/pnas.80.9.2432. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Elder R. T., St John T. P., Stinchcomb D. T., Davis R. W., Scherer S., Davis R. W. Studies on the transposable element Ty1 of yeast. I. RNA homologous to Ty1. II. Recombination and expression of Ty1 and adjacent sequences. Cold Spring Harb Symp Quant Biol. 1981;45(Pt 2):581–591. doi: 10.1101/sqb.1981.045.01.075. [DOI] [PubMed] [Google Scholar]
  7. Errede B., Ammerer G. STE12, a protein involved in cell-type-specific transcription and signal transduction in yeast, is part of protein-DNA complexes. Genes Dev. 1989 Sep;3(9):1349–1361. doi: 10.1101/gad.3.9.1349. [DOI] [PubMed] [Google Scholar]
  8. Farabaugh P., Liao X. B., Belcourt M., Zhao H., Kapakos J., Clare J. Enhancer and silencerlike sites within the transcribed portion of a Ty2 transposable element of Saccharomyces cerevisiae. Mol Cell Biol. 1989 Nov;9(11):4824–4834. doi: 10.1128/mcb.9.11.4824. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Feinberg A. P., Vogelstein B. "A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity". Addendum. Anal Biochem. 1984 Feb;137(1):266–267. doi: 10.1016/0003-2697(84)90381-6. [DOI] [PubMed] [Google Scholar]
  10. Feinberg A. P., Vogelstein B. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem. 1983 Jul 1;132(1):6–13. doi: 10.1016/0003-2697(83)90418-9. [DOI] [PubMed] [Google Scholar]
  11. Fields S., Herskowitz I. Regulation by the yeast mating-type locus of STE12, a gene required for cell-type-specific expression. Mol Cell Biol. 1987 Oct;7(10):3818–3821. doi: 10.1128/mcb.7.10.3818. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Flanagan J. R., Becker K. G., Ennist D. L., Gleason S. L., Driggers P. H., Levi B. Z., Appella E., Ozato K. Cloning of a negative transcription factor that binds to the upstream conserved region of Moloney murine leukemia virus. Mol Cell Biol. 1992 Jan;12(1):38–44. doi: 10.1128/mcb.12.1.38. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Flanagan J. R., Krieg A. M., Max E. E., Khan A. S. Negative control region at the 5' end of murine leukemia virus long terminal repeats. Mol Cell Biol. 1989 Feb;9(2):739–746. doi: 10.1128/mcb.9.2.739. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Fujita A., Misumi Y., Ikehara Y., Kobayashi H. The yeast SFL2 gene may be necessary for mating-type control. Gene. 1992 Mar 1;112(1):85–90. doi: 10.1016/0378-1119(92)90306-a. [DOI] [PubMed] [Google Scholar]
  15. Fulton A. M., Rathjen P. D., Kingsman S. M., Kingsman A. J. Upstream and downstream transcriptional control signals in the yeast retrotransposon, TY. Nucleic Acids Res. 1988 Jun 24;16(12):5439–5458. doi: 10.1093/nar/16.12.5439. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Goutte C., Johnson A. D. a1 protein alters the DNA binding specificity of alpha 2 repressor. Cell. 1988 Mar 25;52(6):875–882. doi: 10.1016/0092-8674(88)90429-1. [DOI] [PubMed] [Google Scholar]
  17. Guarente L., Lalonde B., Gifford P., Alani E. Distinctly regulated tandem upstream activation sites mediate catabolite repression of the CYC1 gene of S. cerevisiae. Cell. 1984 Feb;36(2):503–511. doi: 10.1016/0092-8674(84)90243-5. [DOI] [PubMed] [Google Scholar]
  18. Guarente L., Mason T. Heme regulates transcription of the CYC1 gene of S. cerevisiae via an upstream activation site. Cell. 1983 Apr;32(4):1279–1286. doi: 10.1016/0092-8674(83)90309-4. [DOI] [PubMed] [Google Scholar]
  19. Hagen D. C., McCaffrey G., Sprague G. F., Jr Pheromone response elements are necessary and sufficient for basal and pheromone-induced transcription of the FUS1 gene of Saccharomyces cerevisiae. Mol Cell Biol. 1991 Jun;11(6):2952–2961. doi: 10.1128/mcb.11.6.2952. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Hansen L. J., Chalker D. L., Sandmeyer S. B. Ty3, a yeast retrotransposon associated with tRNA genes, has homology to animal retroviruses. Mol Cell Biol. 1988 Dec;8(12):5245–5256. doi: 10.1128/mcb.8.12.5245. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Hartig A., Holly J., Saari G., MacKay V. L. Multiple regulation of STE2, a mating-type-specific gene of Saccharomyces cerevisiae. Mol Cell Biol. 1986 Jun;6(6):2106–2114. doi: 10.1128/mcb.6.6.2106. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Herskowitz I., Jensen R. E. Putting the HO gene to work: practical uses for mating-type switching. Methods Enzymol. 1991;194:132–146. doi: 10.1016/0076-6879(91)94011-z. [DOI] [PubMed] [Google Scholar]
  23. Hicks J. B., Herskowitz I. Evidence for a new diffusible element of mating pheromones in yeast. Nature. 1976 Mar 18;260(5548):246–248. doi: 10.1038/260246a0. [DOI] [PubMed] [Google Scholar]
  24. Hwang-Shum J. J., Hagen D. C., Jarvis E. E., Westby C. A., Sprague G. F., Jr Relative contributions of MCM1 and STE12 to transcriptional activation of a- and alpha-specific genes from Saccharomyces cerevisiae. Mol Gen Genet. 1991 Jun;227(2):197–204. doi: 10.1007/BF00259671. [DOI] [PubMed] [Google Scholar]
  25. 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]
  26. Jarvis E. E., Clark K. L., Sprague G. F., Jr The yeast transcription activator PRTF, a homolog of the mammalian serum response factor, is encoded by the MCM1 gene. Genes Dev. 1989 Jul;3(7):936–945. doi: 10.1101/gad.3.7.936. [DOI] [PubMed] [Google Scholar]
  27. Jarvis E. E., Hagen D. C., Sprague G. F., Jr Identification of a DNA segment that is necessary and sufficient for alpha-specific gene control in Saccharomyces cerevisiae: implications for regulation of alpha-specific and a-specific genes. Mol Cell Biol. 1988 Jan;8(1):309–320. doi: 10.1128/mcb.8.1.309. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Johnson A. D., Herskowitz I. A repressor (MAT alpha 2 Product) and its operator control expression of a set of cell type specific genes in yeast. Cell. 1985 Aug;42(1):237–247. doi: 10.1016/s0092-8674(85)80119-7. [DOI] [PubMed] [Google Scholar]
  29. Julius D., Blair L., Brake A., Sprague G., Thorner J. Yeast alpha factor is processed from a larger precursor polypeptide: the essential role of a membrane-bound dipeptidyl aminopeptidase. Cell. 1983 Mar;32(3):839–852. doi: 10.1016/0092-8674(83)90070-3. [DOI] [PubMed] [Google Scholar]
  30. Keleher C. A., Goutte C., Johnson A. D. The yeast cell-type-specific repressor alpha 2 acts cooperatively with a non-cell-type-specific protein. Cell. 1988 Jun 17;53(6):927–936. doi: 10.1016/s0092-8674(88)90449-7. [DOI] [PubMed] [Google Scholar]
  31. Keleher C. A., Passmore S., Johnson A. D. Yeast repressor alpha 2 binds to its operator cooperatively with yeast protein Mcm1. Mol Cell Biol. 1989 Nov;9(11):5228–5230. doi: 10.1128/mcb.9.11.5228. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Keleher C. A., Redd M. J., Schultz J., Carlson M., Johnson A. D. Ssn6-Tup1 is a general repressor of transcription in yeast. Cell. 1992 Feb 21;68(4):709–719. doi: 10.1016/0092-8674(92)90146-4. [DOI] [PubMed] [Google Scholar]
  33. Kinsey P. T., Sandmeyer S. B. Adjacent pol II and pol III promoters: transcription of the yeast retrotransposon Ty3 and a target tRNA gene. Nucleic Acids Res. 1991 Mar 25;19(6):1317–1324. doi: 10.1093/nar/19.6.1317. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Kronstad J. W., Holly J. A., MacKay V. L. A yeast operator overlaps an upstream activation site. Cell. 1987 Jul 31;50(3):369–377. doi: 10.1016/0092-8674(87)90491-0. [DOI] [PubMed] [Google Scholar]
  35. Kunkel T. A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc Natl Acad Sci U S A. 1985 Jan;82(2):488–492. doi: 10.1073/pnas.82.2.488. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Kurjan J., Hall B. D. Mutations at the Saccharomyces cerevisiae SUP4 tRNA(Tyr) locus: isolation, genetic fine-structure mapping, and correlation with physical structure. Mol Cell Biol. 1982 Dec;2(12):1501–1513. doi: 10.1128/mcb.2.12.1501. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Liao X. B., Clare J. J., Farabaugh P. J. The upstream activation site of a Ty2 element of yeast is necessary but not sufficient to promote maximal transcription of the element. Proc Natl Acad Sci U S A. 1987 Dec;84(23):8520–8524. doi: 10.1073/pnas.84.23.8520. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. MacKay V. L., Welch S. K., Insley M. Y., Manney T. R., Holly J., Saari G. C., Parker M. L. The Saccharomyces cerevisiae BAR1 gene encodes an exported protein with homology to pepsin. Proc Natl Acad Sci U S A. 1988 Jan;85(1):55–59. doi: 10.1073/pnas.85.1.55. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Majors J. The structure and function of retroviral long terminal repeats. Curr Top Microbiol Immunol. 1990;157:49–92. doi: 10.1007/978-3-642-75218-6_3. [DOI] [PubMed] [Google Scholar]
  40. Marsh L., Neiman A. M., Herskowitz I. Signal transduction during pheromone response in yeast. Annu Rev Cell Biol. 1991;7:699–728. doi: 10.1146/annurev.cb.07.110191.003411. [DOI] [PubMed] [Google Scholar]
  41. McCaffrey G., Clay F. J., Kelsay K., Sprague G. F., Jr Identification and regulation of a gene required for cell fusion during mating of the yeast Saccharomyces cerevisiae. Mol Cell Biol. 1987 Aug;7(8):2680–2690. doi: 10.1128/mcb.7.8.2680. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. McMaster G. K., Carmichael G. G. Analysis of single- and double-stranded nucleic acids on polyacrylamide and agarose gels by using glyoxal and acridine orange. Proc Natl Acad Sci U S A. 1977 Nov;74(11):4835–4838. doi: 10.1073/pnas.74.11.4835. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Miller A. M., MacKay V. L., Nasmyth K. A. Identification and comparison of two sequence elements that confer cell-type specific transcription in yeast. Nature. 1985 Apr 18;314(6012):598–603. doi: 10.1038/314598a0. [DOI] [PubMed] [Google Scholar]
  44. Mukai Y., Harashima S., Oshima Y. AAR1/TUP1 protein, with a structure similar to that of the beta subunit of G proteins, is required for a1-alpha 2 and alpha 2 repression in cell type control of Saccharomyces cerevisiae. Mol Cell Biol. 1991 Jul;11(7):3773–3779. doi: 10.1128/mcb.11.7.3773. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Mullins M. C., Rio D. C., Rubin G. M. cis-acting DNA sequence requirements for P-element transposition. Genes Dev. 1989 May;3(5):729–738. doi: 10.1101/gad.3.5.729. [DOI] [PubMed] [Google Scholar]
  46. Pelham H. R., Bienz M. A synthetic heat-shock promoter element confers heat-inducibility on the herpes simplex virus thymidine kinase gene. EMBO J. 1982;1(11):1473–1477. doi: 10.1002/j.1460-2075.1982.tb01340.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Pirtle R., Kashdan M., Pirtle I., Dudock B. The nucleotide sequence of a major species of leucine tRNA from bovine liver. Nucleic Acids Res. 1980 Feb 25;8(4):805–815. [PMC free article] [PubMed] [Google Scholar]
  48. Roeder G. S., Rose A. B., Pearlman R. E. Transposable element sequences involved in the enhancement of yeast gene expression. Proc Natl Acad Sci U S A. 1985 Aug;82(16):5428–5432. doi: 10.1073/pnas.82.16.5428. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Rose M., Casadaban M. J., Botstein D. Yeast genes fused to beta-galactosidase in Escherichia coli can be expressed normally in yeast. Proc Natl Acad Sci U S A. 1981 Apr;78(4):2460–2464. doi: 10.1073/pnas.78.4.2460. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Rosen C. A., Sodroski J. G., Haseltine W. A. The location of cis-acting regulatory sequences in the human T cell lymphotropic virus type III (HTLV-III/LAV) long terminal repeat. Cell. 1985 Jul;41(3):813–823. doi: 10.1016/s0092-8674(85)80062-3. [DOI] [PubMed] [Google Scholar]
  51. 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]
  52. Russell D. W., Jensen R., Zoller M. J., Burke J., Errede B., Smith M., Herskowitz I. Structure of the Saccharomyces cerevisiae HO gene and analysis of its upstream regulatory region. Mol Cell Biol. 1986 Dec;6(12):4281–4294. doi: 10.1128/mcb.6.12.4281. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Saiki R. K., Gelfand D. H., Stoffel S., Scharf S. J., Higuchi R., Horn G. T., Mullis K. B., Erlich H. A. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science. 1988 Jan 29;239(4839):487–491. doi: 10.1126/science.2448875. [DOI] [PubMed] [Google Scholar]
  54. Sandmeyer S. B., Bilanchone V. W., Clark D. J., Morcos P., Carle G. F., Brodeur G. M. Sigma elements are position-specific for many different yeast tRNA genes. Nucleic Acids Res. 1988 Feb 25;16(4):1499–1515. doi: 10.1093/nar/16.4.1499. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Scott M. P., Tamkun J. W., Hartzell G. W., 3rd The structure and function of the homeodomain. Biochim Biophys Acta. 1989 Jul 28;989(1):25–48. doi: 10.1016/0304-419x(89)90033-4. [DOI] [PubMed] [Google Scholar]
  56. Sengupta P., Cochran B. H. The PRE and PQ box are functionally distinct yeast pheromone response elements. Mol Cell Biol. 1990 Dec;10(12):6809–6812. doi: 10.1128/mcb.10.12.6809. [DOI] [PMC free article] [PubMed] [Google Scholar]
  57. Sikorski R. S., Boguski M. S., Goebl M., Hieter P. A repeating amino acid motif in CDC23 defines a family of proteins and a new relationship among genes required for mitosis and RNA synthesis. Cell. 1990 Jan 26;60(2):307–317. doi: 10.1016/0092-8674(90)90745-z. [DOI] [PubMed] [Google Scholar]
  58. Siliciano P. G., Tatchell K. Identification of the DNA sequences controlling the expression of the MAT alpha locus of yeast. Proc Natl Acad Sci U S A. 1986 Apr;83(8):2320–2324. doi: 10.1073/pnas.83.8.2320. [DOI] [PMC free article] [PubMed] [Google Scholar]
  59. Simons R. W., Kleckner N. Translational control of IS10 transposition. Cell. 1983 Sep;34(2):683–691. doi: 10.1016/0092-8674(83)90401-4. [DOI] [PubMed] [Google Scholar]
  60. Sprague G. F., Jr Signal transduction in yeast mating: receptors, transcription factors, and the kinase connection. Trends Genet. 1991 Nov-Dec;7(11-12):393–398. [PubMed] [Google Scholar]
  61. Struhl K., Stinchcomb D. T., Scherer S., Davis R. W. High-frequency transformation of yeast: autonomous replication of hybrid DNA molecules. Proc Natl Acad Sci U S A. 1979 Mar;76(3):1035–1039. doi: 10.1073/pnas.76.3.1035. [DOI] [PMC free article] [PubMed] [Google Scholar]
  62. Tatchell K., Nasmyth K. A., Hall B. D., Astell C., Smith M. In vitro mutation analysis of the mating-type locus in yeast. Cell. 1981 Nov;27(1 Pt 2):25–35. doi: 10.1016/0092-8674(81)90357-3. [DOI] [PubMed] [Google Scholar]
  63. Thomas P. S. Hybridization of denatured RNA and small DNA fragments transferred to nitrocellulose. Proc Natl Acad Sci U S A. 1980 Sep;77(9):5201–5205. doi: 10.1073/pnas.77.9.5201. [DOI] [PMC free article] [PubMed] [Google Scholar]
  64. Trueheart J., Boeke J. D., Fink G. R. Two genes required for cell fusion during yeast conjugation: evidence for a pheromone-induced surface protein. Mol Cell Biol. 1987 Jul;7(7):2316–2328. doi: 10.1128/mcb.7.7.2316. [DOI] [PMC free article] [PubMed] [Google Scholar]
  65. Van Arsdell S. W., Stetler G. L., Thorner J. The yeast repeated element sigma contains a hormone-inducible promoter. Mol Cell Biol. 1987 Feb;7(2):749–759. doi: 10.1128/mcb.7.2.749. [DOI] [PMC free article] [PubMed] [Google Scholar]
  66. Williams F. E., Trumbly R. J. Characterization of TUP1, a mediator of glucose repression in Saccharomyces cerevisiae. Mol Cell Biol. 1990 Dec;10(12):6500–6511. doi: 10.1128/mcb.10.12.6500. [DOI] [PMC free article] [PubMed] [Google Scholar]
  67. Yu K., Elder R. T. A region internal to the coding sequences is essential for transcription of the yeast Ty-D15 element. Mol Cell Biol. 1989 Sep;9(9):3667–3678. doi: 10.1128/mcb.9.9.3667. [DOI] [PMC free article] [PubMed] [Google Scholar]

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