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. 1999 Apr;151(4):1365–1378. doi: 10.1093/genetics/151.4.1365

Specific components of the SAGA complex are required for Gcn4- and Gcr1-mediated activation of the his4-912delta promoter in Saccharomyces cerevisiae.

A M Dudley 1, L J Gansheroff 1, F Winston 1
PMCID: PMC1460567  PMID: 10101163

Abstract

Mutations selected as suppressors of Ty or solo delta insertion mutations in Saccharomyces cerevisiae have identified several genes, SPT3, SPT7, SPT8, and SPT20, that encode components of the SAGA complex. However, the mechanism by which SAGA activates transcription of specific RNA polymerase II-dependent genes is unknown. We have conducted a fine-structure mutagenesis of one widely used SAGA-dependent promoter, the delta element of his4-912delta, to identify sequence elements important for its promoter activity. Our analysis has characterized three delta regions necessary for full promoter activity and accurate start site selection: an upstream activating sequence, a TATA region, and an initiator region. In addition, we have shown that factors present at the adjacent UASHIS4 (Gcn4, Bas1, and Pho2) also activate the delta promoter in his4-912delta. Our results suggest a model in which the delta promoter in his4-912delta is primarily activated by two factors: Gcr1 acting at the UASdelta and Gcn4 acting at the UASHIS4. Finally, we tested whether activation by either of these factors is dependent on components of the SAGA complex. Our results demonstrate that Spt3 and Spt20 are required for full delta promoter activity, but that Gcn5, another member of SAGA, is not required. Spt3 appears to be partially required for activation of his4-912delta by both Gcr1 and Gcn4. Thus, our work suggests that SAGA exerts a large effect on delta promoter activity through a combination of smaller effects on multiple factors.

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Selected References

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  1. Arndt K. M., Ricupero S. L., Eisenmann D. M., Winston F. Biochemical and genetic characterization of a yeast TFIID mutant that alters transcription in vivo and DNA binding in vitro. Mol Cell Biol. 1992 May;12(5):2372–2382. doi: 10.1128/mcb.12.5.2372. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Arndt K. M., Wobbe C. R., Ricupero-Hovasse S., Struhl K., Winston F. Equivalent mutations in the two repeats of yeast TATA-binding protein confer distinct TATA recognition specificities. Mol Cell Biol. 1994 Jun;14(6):3719–3728. doi: 10.1128/mcb.14.6.3719. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Arndt K. T., Styles C., Fink G. R. Multiple global regulators control HIS4 transcription in yeast. Science. 1987 Aug 21;237(4817):874–880. doi: 10.1126/science.3303332. [DOI] [PubMed] [Google Scholar]
  4. Arndt K., Fink G. R. GCN4 protein, a positive transcription factor in yeast, binds general control promoters at all 5' TGACTC 3' sequences. Proc Natl Acad Sci U S A. 1986 Nov;83(22):8516–8520. doi: 10.1073/pnas.83.22.8516. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Berroteran R. W., Ware D. E., Hampsey M. The sua8 suppressors of Saccharomyces cerevisiae encode replacements of conserved residues within the largest subunit of RNA polymerase II and affect transcription start site selection similarly to sua7 (TFIIB) mutations. Mol Cell Biol. 1994 Jan;14(1):226–237. doi: 10.1128/mcb.14.1.226. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Brazas R. M., Stillman D. J. The Swi5 zinc-finger and Grf10 homeodomain proteins bind DNA cooperatively at the yeast HO promoter. Proc Natl Acad Sci U S A. 1993 Dec 1;90(23):11237–11241. doi: 10.1073/pnas.90.23.11237. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Brow D. A., Guthrie C. Spliceosomal RNA U6 is remarkably conserved from yeast to mammals. Nature. 1988 Jul 21;334(6179):213–218. doi: 10.1038/334213a0. [DOI] [PubMed] [Google Scholar]
  8. Brownell J. E., Zhou J., Ranalli T., Kobayashi R., Edmondson D. G., Roth S. Y., Allis C. D. Tetrahymena histone acetyltransferase A: a homolog to yeast Gcn5p linking histone acetylation to gene activation. Cell. 1996 Mar 22;84(6):843–851. doi: 10.1016/s0092-8674(00)81063-6. [DOI] [PubMed] [Google Scholar]
  9. Chen W., Struhl K. Yeast mRNA initiation sites are determined primarily by specific sequences, not by the distance from the TATA element. EMBO J. 1985 Dec 1;4(12):3273–3280. doi: 10.1002/j.1460-2075.1985.tb04077.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Clark-Adams C. D., Norris D., Osley M. A., Fassler J. S., Winston F. Changes in histone gene dosage alter transcription in yeast. Genes Dev. 1988 Feb;2(2):150–159. doi: 10.1101/gad.2.2.150. [DOI] [PubMed] [Google Scholar]
  11. Coney L. R., Roeder G. S. Control of yeast gene expression by transposable elements: maximum expression requires a functional Ty activator sequence and a defective Ty promoter. Mol Cell Biol. 1988 Oct;8(10):4009–4017. doi: 10.1128/mcb.8.10.4009. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Devlin C., Tice-Baldwin K., Shore D., Arndt K. T. RAP1 is required for BAS1/BAS2- and GCN4-dependent transcription of the yeast HIS4 gene. Mol Cell Biol. 1991 Jul;11(7):3642–3651. doi: 10.1128/mcb.11.7.3642. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Drysdale C. M., Dueñas E., Jackson B. M., Reusser U., Braus G. H., Hinnebusch A. G. The transcriptional activator GCN4 contains multiple activation domains that are critically dependent on hydrophobic amino acids. Mol Cell Biol. 1995 Mar;15(3):1220–1233. doi: 10.1128/mcb.15.3.1220. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Eisenmann D. M., Arndt K. M., Ricupero S. L., Rooney J. W., Winston F. SPT3 interacts with TFIID to allow normal transcription in Saccharomyces cerevisiae. Genes Dev. 1992 Jul;6(7):1319–1331. doi: 10.1101/gad.6.7.1319. [DOI] [PubMed] [Google Scholar]
  15. Eisenmann D. M., Dollard C., Winston F. SPT15, the gene encoding the yeast TATA binding factor TFIID, is required for normal transcription initiation in vivo. Cell. 1989 Sep 22;58(6):1183–1191. doi: 10.1016/0092-8674(89)90516-3. [DOI] [PubMed] [Google Scholar]
  16. Elble R. A simple and efficient procedure for transformation of yeasts. Biotechniques. 1992 Jul;13(1):18–20. [PubMed] [Google Scholar]
  17. 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]
  18. Farabaugh P. J., Fink G. R. Insertion of the eukaryotic transposable element Ty1 creates a 5-base pair duplication. Nature. 1980 Jul 24;286(5771):352–356. doi: 10.1038/286352a0. [DOI] [PubMed] [Google Scholar]
  19. Fassler J. S., Winston F. Isolation and analysis of a novel class of suppressor of Ty insertion mutations in Saccharomyces cerevisiae. Genetics. 1988 Feb;118(2):203–212. doi: 10.1093/genetics/118.2.203. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Fassler J. S., Winston F. The Saccharomyces cerevisiae SPT13/GAL11 gene has both positive and negative regulatory roles in transcription. Mol Cell Biol. 1989 Dec;9(12):5602–5609. doi: 10.1128/mcb.9.12.5602. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. 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]
  22. Grant P. A., Duggan L., Côté J., Roberts S. M., Brownell J. E., Candau R., Ohba R., Owen-Hughes T., Allis C. D., Winston F. Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones: characterization of an Ada complex and the SAGA (Spt/Ada) complex. Genes Dev. 1997 Jul 1;11(13):1640–1650. doi: 10.1101/gad.11.13.1640. [DOI] [PubMed] [Google Scholar]
  23. Grant P. A., Duggan L., Côté J., Roberts S. M., Brownell J. E., Candau R., Ohba R., Owen-Hughes T., Allis C. D., Winston F. Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones: characterization of an Ada complex and the SAGA (Spt/Ada) complex. Genes Dev. 1997 Jul 1;11(13):1640–1650. doi: 10.1101/gad.11.13.1640. [DOI] [PubMed] [Google Scholar]
  24. Hahn S., Hoar E. T., Guarente L. Each of three "TATA elements" specifies a subset of the transcription initiation sites at the CYC-1 promoter of Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1985 Dec;82(24):8562–8566. doi: 10.1073/pnas.82.24.8562. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Happel A. M., Swanson M. S., Winston F. The SNF2, SNF5 and SNF6 genes are required for Ty transcription in Saccharomyces cerevisiae. Genetics. 1991 May;128(1):69–77. doi: 10.1093/genetics/128.1.69. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Harbury P. A., Struhl K. Functional distinctions between yeast TATA elements. Mol Cell Biol. 1989 Dec;9(12):5298–5304. doi: 10.1128/mcb.9.12.5298. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Hekmatpanah D. S., Young R. A. Mutations in a conserved region of RNA polymerase II influence the accuracy of mRNA start site selection. Mol Cell Biol. 1991 Nov;11(11):5781–5791. doi: 10.1128/mcb.11.11.5781. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Hinnebusch A. G. A hierarchy of trans-acting factors modulates translation of an activator of amino acid biosynthetic genes in Saccharomyces cerevisiae. Mol Cell Biol. 1985 Sep;5(9):2349–2360. doi: 10.1128/mcb.5.9.2349. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Hinnebusch A. G., Lucchini G., Fink G. R. A synthetic HIS4 regulatory element confers general amino acid control on the cytochrome c gene (CYC1) of yeast. Proc Natl Acad Sci U S A. 1985 Jan;82(2):498–502. doi: 10.1073/pnas.82.2.498. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Hirschman J. E., Durbin K. J., Winston F. Genetic evidence for promoter competition in Saccharomyces cerevisiae. Mol Cell Biol. 1988 Nov;8(11):4608–4615. doi: 10.1128/mcb.8.11.4608. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Ho S. N., Hunt H. D., Horton R. M., Pullen J. K., Pease L. R. Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene. 1989 Apr 15;77(1):51–59. doi: 10.1016/0378-1119(89)90358-2. [DOI] [PubMed] [Google Scholar]
  32. Hope I. A., Struhl K. GCN4 protein, synthesized in vitro, binds HIS3 regulatory sequences: implications for general control of amino acid biosynthetic genes in yeast. Cell. 1985 Nov;43(1):177–188. doi: 10.1016/0092-8674(85)90022-4. [DOI] [PubMed] [Google Scholar]
  33. Horiuchi J., Silverman N., Piña B., Marcus G. A., Guarente L. ADA1, a novel component of the ADA/GCN5 complex, has broader effects than GCN5, ADA2, or ADA3. Mol Cell Biol. 1997 Jun;17(6):3220–3228. doi: 10.1128/mcb.17.6.3220. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Hull M. W., McKune K., Woychik N. A. RNA polymerase II subunit RPB9 is required for accurate start site selection. Genes Dev. 1995 Feb 15;9(4):481–490. doi: 10.1101/gad.9.4.481. [DOI] [PubMed] [Google Scholar]
  35. Jiang Y. W., Stillman D. J. Epigenetic effects on yeast transcription caused by mutations in an actin-related protein present in the nucleus. Genes Dev. 1996 Mar 1;10(5):604–619. doi: 10.1101/gad.10.5.604. [DOI] [PubMed] [Google Scholar]
  36. Jiang Y. W., Stillman D. J. Involvement of the SIN4 global transcriptional regulator in the chromatin structure of Saccharomyces cerevisiae. Mol Cell Biol. 1992 Oct;12(10):4503–4514. doi: 10.1128/mcb.12.10.4503. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Kingston R. E., Bunker C. A., Imbalzano A. N. Repression and activation by multiprotein complexes that alter chromatin structure. Genes Dev. 1996 Apr 15;10(8):905–920. doi: 10.1101/gad.10.8.905. [DOI] [PubMed] [Google Scholar]
  38. 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]
  39. Li W. Z., Sherman F. Two types of TATA elements for the CYC1 gene of the yeast Saccharomyces cerevisiae. Mol Cell Biol. 1991 Feb;11(2):666–676. doi: 10.1128/mcb.11.2.666. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. 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]
  41. Madison J. M., Dudley A. M., Winston F. Identification and analysis of Mot3, a zinc finger protein that binds to the retrotransposon Ty long terminal repeat (delta) in Saccharomyces cerevisiae. Mol Cell Biol. 1998 Apr;18(4):1879–1890. doi: 10.1128/mcb.18.4.1879. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Madison J. M., Winston F. Evidence that Spt3 functionally interacts with Mot1, TFIIA, and TATA-binding protein to confer promoter-specific transcriptional control in Saccharomyces cerevisiae. Mol Cell Biol. 1997 Jan;17(1):287–295. doi: 10.1128/mcb.17.1.287. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Maicas E., Friesen J. D. A sequence pattern that occurs at the transcription initiation region of yeast RNA polymerase II promoters. Nucleic Acids Res. 1990 Jun 11;18(11):3387–3393. doi: 10.1093/nar/18.11.3387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Pinto I., Ware D. E., Hampsey M. The yeast SUA7 gene encodes a homolog of human transcription factor TFIIB and is required for normal start site selection in vivo. Cell. 1992 Mar 6;68(5):977–988. doi: 10.1016/0092-8674(92)90040-j. [DOI] [PubMed] [Google Scholar]
  45. Prelich G., Winston F. Mutations that suppress the deletion of an upstream activating sequence in yeast: involvement of a protein kinase and histone H3 in repressing transcription in vivo. Genetics. 1993 Nov;135(3):665–676. doi: 10.1093/genetics/135.3.665. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Roberts S. M., Winston F. Essential functional interactions of SAGA, a Saccharomyces cerevisiae complex of Spt, Ada, and Gcn5 proteins, with the Snf/Swi and Srb/mediator complexes. Genetics. 1997 Oct;147(2):451–465. doi: 10.1093/genetics/147.2.451. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Roberts S. M., Winston F. SPT20/ADA5 encodes a novel protein functionally related to the TATA-binding protein and important for transcription in Saccharomyces cerevisiae. Mol Cell Biol. 1996 Jun;16(6):3206–3213. doi: 10.1128/mcb.16.6.3206. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Rudolph H., Hinnen A. The yeast PHO5 promoter: phosphate-control elements and sequences mediating mRNA start-site selection. Proc Natl Acad Sci U S A. 1987 Mar;84(5):1340–1344. doi: 10.1073/pnas.84.5.1340. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Santisteban M. S., Arents G., Moudrianakis E. N., Smith M. M. Histone octamer function in vivo: mutations in the dimer-tetramer interfaces disrupt both gene activation and repression. EMBO J. 1997 May 1;16(9):2493–2506. doi: 10.1093/emboj/16.9.2493. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Sherwood P. W., Osley M. A. Histone regulatory (hir) mutations suppress delta insertion alleles in Saccharomyces cerevisiae. Genetics. 1991 Aug;128(4):729–738. doi: 10.1093/genetics/128.4.729. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. 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]
  52. Smith M. M., Yang P., Santisteban M. S., Boone P. W., Goldstein A. T., Megee P. C. A novel histone H4 mutant defective in nuclear division and mitotic chromosome transmission. Mol Cell Biol. 1996 Mar;16(3):1017–1026. doi: 10.1128/mcb.16.3.1017. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  54. Steger D. J., Workman J. L. Remodeling chromatin structures for transcription: what happens to the histones? Bioessays. 1996 Nov;18(11):875–884. doi: 10.1002/bies.950181106. [DOI] [PubMed] [Google Scholar]
  55. Struhl K. Yeast transcriptional regulatory mechanisms. Annu Rev Genet. 1995;29:651–674. doi: 10.1146/annurev.ge.29.120195.003251. [DOI] [PubMed] [Google Scholar]
  56. Thanos D., Maniatis T. Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome. Cell. 1995 Dec 29;83(7):1091–1100. doi: 10.1016/0092-8674(95)90136-1. [DOI] [PubMed] [Google Scholar]
  57. Tice-Baldwin K., Fink G. R., Arndt K. T. BAS1 has a Myb motif and activates HIS4 transcription only in combination with BAS2. Science. 1989 Nov 17;246(4932):931–935. doi: 10.1126/science.2683089. [DOI] [PubMed] [Google Scholar]
  58. Türkel S., Liao X. B., Farabaugh P. J. GCR1-dependent transcriptional activation of yeast retrotransposon Ty2-917. Yeast. 1997 Aug;13(10):917–930. doi: 10.1002/(SICI)1097-0061(199708)13:10<917::AID-YEA148>3.0.CO;2-G. [DOI] [PubMed] [Google Scholar]
  59. Winston F., Chaleff D. T., Valent B., Fink G. R. Mutations affecting Ty-mediated expression of the HIS4 gene of Saccharomyces cerevisiae. Genetics. 1984 Jun;107(2):179–197. doi: 10.1093/genetics/107.2.179. [DOI] [PMC free article] [PubMed] [Google Scholar]
  60. Winston F., Dollard C., Malone E. A., Clare J., Kapakos J. G., Farabaugh P., Minehart P. L. Three genes are required for trans-activation of Ty transcription in yeast. Genetics. 1987 Apr;115(4):649–656. doi: 10.1093/genetics/115.4.649. [DOI] [PMC free article] [PubMed] [Google Scholar]
  61. 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]
  62. Winston F., Durbin K. J., Fink G. R. The SPT3 gene is required for normal transcription of Ty elements in S. cerevisiae. Cell. 1984 Dec;39(3 Pt 2):675–682. doi: 10.1016/0092-8674(84)90474-4. [DOI] [PubMed] [Google Scholar]
  63. Wolberger C. Homeodomain interactions. Curr Opin Struct Biol. 1996 Feb;6(1):62–68. doi: 10.1016/s0959-440x(96)80096-0. [DOI] [PubMed] [Google Scholar]
  64. Xu H., Kim U. J., Schuster T., Grunstein M. Identification of a new set of cell cycle-regulatory genes that regulate S-phase transcription of histone genes in Saccharomyces cerevisiae. Mol Cell Biol. 1992 Nov;12(11):5249–5259. doi: 10.1128/mcb.12.11.5249. [DOI] [PMC free article] [PubMed] [Google Scholar]

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