Skip to main content
PMC home page
Molecular and Cellular Biology logoLink to Molecular and Cellular Biology
. 1996 Jul;16(7):3651–3657. doi: 10.1128/mcb.16.7.3651

Identifying a species-specific region of yeast TF11B in vivo.

S P Shaw 1, J Wingfield 1, M J Dorsey 1, J Ma 1
PMCID: PMC231360  PMID: 8668181

Abstract

The general transcription factor IIB (TFIIB) is required for RNA polymerase II transcription in eukaryotes. It provides a physical link between the TATA-binding protein (TBP) and the RNA polymerase and is a component previously suggested to respond to transcriptional activators in vitro. In this report, we compare the yeast (Saccharomyces cerevisiae) and human forms of the protein in yeast cells to study their functional differences. We demonstrate that human TFIIB fails to functionally replace yeast TFIIB in yeast cells. By analyzing various human-yeast hybrid TFIIB molecules, we show that a 14-amino-acid region at the amino terminus of the first repeat of yeast TFIIB plays an important role in determining species specificity in vivo. In addition, we identify four amino acids in this region that are critical for an amphipathic helix unique to yeast TFIIB. By site-directed mutagenesis analyses we demonstrate that these four amino acids are important for yeast TFIIB's activity in vivo. Finally, we show that mutations in the species-specific region of yeast TFIIB can differentially affect the expression of genes activated by different activators in vivo. These results provide strong evidence suggesting that yeast TFIIB is involved in the process of transcriptional activation in living cells.

Full Text

The Full Text of this article is available as a PDF (748.5 KB).

Selected References

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

  1. Bagby S., Kim S., Maldonado E., Tong K. I., Reinberg D., Ikura M. Solution structure of the C-terminal core domain of human TFIIB: similarity to cyclin A and interaction with TATA-binding protein. Cell. 1995 Sep 8;82(5):857–867. doi: 10.1016/0092-8674(95)90483-2. [DOI] [PubMed] [Google Scholar]
  2. Baniahmad A., Ha I., Reinberg D., Tsai S., Tsai M. J., O'Malley B. W. Interaction of human thyroid hormone receptor beta with transcription factor TFIIB may mediate target gene derepression and activation by thyroid hormone. Proc Natl Acad Sci U S A. 1993 Oct 1;90(19):8832–8836. doi: 10.1073/pnas.90.19.8832. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Barberis A., Müller C. W., Harrison S. C., Ptashne M. Delineation of two functional regions of transcription factor TFIIB. Proc Natl Acad Sci U S A. 1993 Jun 15;90(12):5628–5632. doi: 10.1073/pnas.90.12.5628. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Berger S. L., Piña B., Silverman N., Marcus G. A., Agapite J., Regier J. L., Triezenberg S. J., Guarente L. Genetic isolation of ADA2: a potential transcriptional adaptor required for function of certain acidic activation domains. Cell. 1992 Jul 24;70(2):251–265. doi: 10.1016/0092-8674(92)90100-q. [DOI] [PubMed] [Google Scholar]
  5. Boeke J. D., Trueheart J., Natsoulis G., Fink G. R. 5-Fluoroorotic acid as a selective agent in yeast molecular genetics. Methods Enzymol. 1987;154:164–175. doi: 10.1016/0076-6879(87)54076-9. [DOI] [PubMed] [Google Scholar]
  6. Buratowski S., Hahn S., Guarente L., Sharp P. A. Five intermediate complexes in transcription initiation by RNA polymerase II. Cell. 1989 Feb 24;56(4):549–561. doi: 10.1016/0092-8674(89)90578-3. [DOI] [PubMed] [Google Scholar]
  7. Buratowski S., Zhou H. Functional domains of transcription factor TFIIB. Proc Natl Acad Sci U S A. 1993 Jun 15;90(12):5633–5637. doi: 10.1073/pnas.90.12.5633. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Chao D. M., Gadbois E. L., Murray P. J., Anderson S. F., Sonu M. S., Parvin J. D., Young R. A. A mammalian SRB protein associated with an RNA polymerase II holoenzyme. Nature. 1996 Mar 7;380(6569):82–85. doi: 10.1038/380082a0. [DOI] [PubMed] [Google Scholar]
  9. Chevray P. M., Nathans D. Protein interaction cloning in yeast: identification of mammalian proteins that react with the leucine zipper of Jun. Proc Natl Acad Sci U S A. 1992 Jul 1;89(13):5789–5793. doi: 10.1073/pnas.89.13.5789. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Colgan J., Wampler S., Manley J. L. Interaction between a transcriptional activator and transcription factor IIB in vivo. Nature. 1993 Apr 8;362(6420):549–553. doi: 10.1038/362549a0. [DOI] [PubMed] [Google Scholar]
  11. Colicelli J., Birchmeier C., Michaeli T., O'Neill K., Riggs M., Wigler M. Isolation and characterization of a mammalian gene encoding a high-affinity cAMP phosphodiesterase. Proc Natl Acad Sci U S A. 1989 May;86(10):3599–3603. doi: 10.1073/pnas.86.10.3599. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Cormack B. P., Strubin M., Ponticelli A. S., Struhl K. Functional differences between yeast and human TFIID are localized to the highly conserved region. Cell. 1991 Apr 19;65(2):341–348. doi: 10.1016/0092-8674(91)90167-w. [DOI] [PubMed] [Google Scholar]
  13. Côté J., Quinn J., Workman J. L., Peterson C. L. Stimulation of GAL4 derivative binding to nucleosomal DNA by the yeast SWI/SNF complex. Science. 1994 Jul 1;265(5168):53–60. doi: 10.1126/science.8016655. [DOI] [PubMed] [Google Scholar]
  14. Gill G., Tjian R. A highly conserved domain of TFIID displays species specificity in vivo. Cell. 1991 Apr 19;65(2):333–340. doi: 10.1016/0092-8674(91)90166-v. [DOI] [PubMed] [Google Scholar]
  15. Giniger E., Varnum S. M., Ptashne M. Specific DNA binding of GAL4, a positive regulatory protein of yeast. Cell. 1985 Apr;40(4):767–774. doi: 10.1016/0092-8674(85)90336-8. [DOI] [PubMed] [Google Scholar]
  16. Goodrich J. A., Hoey T., Thut C. J., Admon A., Tjian R. Drosophila TAFII40 interacts with both a VP16 activation domain and the basal transcription factor TFIIB. Cell. 1993 Nov 5;75(3):519–530. doi: 10.1016/0092-8674(93)90386-5. [DOI] [PubMed] [Google Scholar]
  17. Ha I., Lane W. S., Reinberg D. Cloning of a human gene encoding the general transcription initiation factor IIB. Nature. 1991 Aug 22;352(6337):689–695. doi: 10.1038/352689a0. [DOI] [PubMed] [Google Scholar]
  18. Ha I., Roberts S., Maldonado E., Sun X., Kim L. U., Green M., Reinberg D. Multiple functional domains of human transcription factor IIB: distinct interactions with two general transcription factors and RNA polymerase II. Genes Dev. 1993 Jun;7(6):1021–1032. doi: 10.1101/gad.7.6.1021. [DOI] [PubMed] [Google Scholar]
  19. Hahn S. Transcription. Clamping the TBP stirrup. Nature. 1995 Oct 12;377(6549):480–481. doi: 10.1038/377480a0. [DOI] [PubMed] [Google Scholar]
  20. Himmelfarb H. J., Pearlberg J., Last D. H., Ptashne M. GAL11P: a yeast mutation that potentiates the effect of weak GAL4-derived activators. Cell. 1990 Dec 21;63(6):1299–1309. doi: 10.1016/0092-8674(90)90425-e. [DOI] [PubMed] [Google Scholar]
  21. Hisatake K., Malik S., Roeder R. G., Horikoshi M. Conserved structural motifs between Xenopus and human TFIIB. Nucleic Acids Res. 1991 Dec 11;19(23):6639–6639. doi: 10.1093/nar/19.23.6639. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Hoey T., Weinzierl R. O., Gill G., Chen J. L., Dynlacht B. D., Tjian R. Molecular cloning and functional analysis of Drosophila TAF110 reveal properties expected of coactivators. Cell. 1993 Jan 29;72(2):247–260. doi: 10.1016/0092-8674(93)90664-c. [DOI] [PubMed] [Google Scholar]
  23. Ingles C. J., Shales M., Cress W. D., Triezenberg S. J., Greenblatt J. Reduced binding of TFIID to transcriptionally compromised mutants of VP16. Nature. 1991 Jun 13;351(6327):588–590. doi: 10.1038/351588a0. [DOI] [PubMed] [Google Scholar]
  24. Joliot V., Demma M., Prywes R. Interaction with RAP74 subunit of TFIIF is required for transcriptional activation by serum response factor. Nature. 1995 Feb 16;373(6515):632–635. doi: 10.1038/373632a0. [DOI] [PubMed] [Google Scholar]
  25. Kim J. L., Nikolov D. B., Burley S. K. Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature. 1993 Oct 7;365(6446):520–527. doi: 10.1038/365520a0. [DOI] [PubMed] [Google Scholar]
  26. Kim T. K., Roeder R. G. Proline-rich activator CTF1 targets the TFIIB assembly step during transcriptional activation. Proc Natl Acad Sci U S A. 1994 May 10;91(10):4170–4174. doi: 10.1073/pnas.91.10.4170. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Kim Y. J., Björklund S., Li Y., Sayre M. H., Kornberg R. D. A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II. Cell. 1994 May 20;77(4):599–608. doi: 10.1016/0092-8674(94)90221-6. [DOI] [PubMed] [Google Scholar]
  28. Kim Y., Geiger J. H., Hahn S., Sigler P. B. Crystal structure of a yeast TBP/TATA-box complex. Nature. 1993 Oct 7;365(6446):512–520. doi: 10.1038/365512a0. [DOI] [PubMed] [Google Scholar]
  29. Knaus R., Pollock R., Guarente L. Yeast SUB1 is a suppressor of TFIIB mutations and has homology to the human co-activator PC4. EMBO J. 1996 Apr 15;15(8):1933–1940. [PMC free article] [PubMed] [Google Scholar]
  30. Koleske A. J., Buratowski S., Nonet M., Young R. A. A novel transcription factor reveals a functional link between the RNA polymerase II CTD and TFIID. Cell. 1992 May 29;69(5):883–894. doi: 10.1016/0092-8674(92)90298-q. [DOI] [PubMed] [Google Scholar]
  31. Koleske A. J., Young R. A. An RNA polymerase II holoenzyme responsive to activators. Nature. 1994 Mar 31;368(6470):466–469. doi: 10.1038/368466a0. [DOI] [PubMed] [Google Scholar]
  32. Lee S., Hahn S. Model for binding of transcription factor TFIIB to the TBP-DNA complex. Nature. 1995 Aug 17;376(6541):609–612. doi: 10.1038/376609a0. [DOI] [PubMed] [Google Scholar]
  33. Lessard J. L. Two monoclonal antibodies to actin: one muscle selective and one generally reactive. Cell Motil Cytoskeleton. 1988;10(3):349–362. doi: 10.1002/cm.970100302. [DOI] [PubMed] [Google Scholar]
  34. Li Y., Flanagan P. M., Tschochner H., Kornberg R. D. RNA polymerase II initiation factor interactions and transcription start site selection. Science. 1994 Feb 11;263(5148):805–807. doi: 10.1126/science.8303296. [DOI] [PubMed] [Google Scholar]
  35. Liao S. M., Zhang J., Jeffery D. A., Koleske A. J., Thompson C. M., Chao D. M., Viljoen M., van Vuuren H. J., Young R. A. A kinase-cyclin pair in the RNA polymerase II holoenzyme. Nature. 1995 Mar 9;374(6518):193–196. doi: 10.1038/374193a0. [DOI] [PubMed] [Google Scholar]
  36. Lin Y. S., Green M. R. Mechanism of action of an acidic transcriptional activator in vitro. Cell. 1991 Mar 8;64(5):971–981. doi: 10.1016/0092-8674(91)90321-o. [DOI] [PubMed] [Google Scholar]
  37. Lin Y. S., Ha I., Maldonado E., Reinberg D., Green M. R. Binding of general transcription factor TFIIB to an acidic activating region. Nature. 1991 Oct 10;353(6344):569–571. doi: 10.1038/353569a0. [DOI] [PubMed] [Google Scholar]
  38. Ma J., Ptashne M. Deletion analysis of GAL4 defines two transcriptional activating segments. Cell. 1987 Mar 13;48(5):847–853. doi: 10.1016/0092-8674(87)90081-x. [DOI] [PubMed] [Google Scholar]
  39. Maldonado E., Reinberg D. News on initiation and elongation of transcription by RNA polymerase II. Curr Opin Cell Biol. 1995 Jun;7(3):352–361. doi: 10.1016/0955-0674(95)80090-5. [DOI] [PubMed] [Google Scholar]
  40. Malik S., Hisatake K., Sumimoto H., Horikoshi M., Roeder R. G. Sequence of general transcription factor TFIIB and relationships to other initiation factors. Proc Natl Acad Sci U S A. 1991 Nov 1;88(21):9553–9557. doi: 10.1073/pnas.88.21.9553. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Nikolov D. B., Chen H., Halay E. D., Usheva A. A., Hisatake K., Lee D. K., Roeder R. G., Burley S. K. Crystal structure of a TFIIB-TBP-TATA-element ternary complex. Nature. 1995 Sep 14;377(6545):119–128. doi: 10.1038/377119a0. [DOI] [PubMed] [Google Scholar]
  42. Ossipow V., Tassan J. P., Nigg E. A., Schibler U. A mammalian RNA polymerase II holoenzyme containing all components required for promoter-specific transcription initiation. Cell. 1995 Oct 6;83(1):137–146. doi: 10.1016/0092-8674(95)90242-2. [DOI] [PubMed] [Google Scholar]
  43. Ozer J., Moore P. A., Bolden A. H., Lee A., Rosen C. A., Lieberman P. M. Molecular cloning of the small (gamma) subunit of human TFIIA reveals functions critical for activated transcription. Genes Dev. 1994 Oct 1;8(19):2324–2335. doi: 10.1101/gad.8.19.2324. [DOI] [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. Piña B., Berger S., Marcus G. A., Silverman N., Agapite J., Guarente L. ADA3: a gene, identified by resistance to GAL4-VP16, with properties similar to and different from those of ADA2. Mol Cell Biol. 1993 Oct;13(10):5981–5989. doi: 10.1128/mcb.13.10.5981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Roberts S. G., Green M. R. Activator-induced conformational change in general transcription factor TFIIB. Nature. 1994 Oct 20;371(6499):717–720. doi: 10.1038/371717a0. [DOI] [PubMed] [Google Scholar]
  47. Roberts S. G., Ha I., Maldonado E., Reinberg D., Green M. R. Interaction between an acidic activator and transcription factor TFIIB is required for transcriptional activation. Nature. 1993 Jun 24;363(6431):741–744. doi: 10.1038/363741a0. [DOI] [PubMed] [Google Scholar]
  48. Sauer F., Fondell J. D., Ohkuma Y., Roeder R. G., Jäckle H. Control of transcription by Krüppel through interactions with TFIIB and TFIIE beta. Nature. 1995 May 11;375(6527):162–164. doi: 10.1038/375162a0. [DOI] [PubMed] [Google Scholar]
  49. Stringer K. F., Ingles C. J., Greenblatt J. Direct and selective binding of an acidic transcriptional activation domain to the TATA-box factor TFIID. Nature. 1990 Jun 28;345(6278):783–786. doi: 10.1038/345783a0. [DOI] [PubMed] [Google Scholar]
  50. Swaffield J. C., Bromberg J. F., Johnston S. A. Alterations in a yeast protein resembling HIV Tat-binding protein relieve requirement for an acidic activation domain in GAL4. Nature. 1992 Jun 25;357(6380):698–700. doi: 10.1038/357698a0. [DOI] [PubMed] [Google Scholar]
  51. Thompson C. M., Koleske A. J., Chao D. M., Young R. A. A multisubunit complex associated with the RNA polymerase II CTD and TATA-binding protein in yeast. Cell. 1993 Jul 2;73(7):1361–1375. doi: 10.1016/0092-8674(93)90362-t. [DOI] [PubMed] [Google Scholar]
  52. Tsuboi A., Conger K., Garrett K. P., Conaway R. C., Conaway J. W., Arai N. RNA polymerase II initiation factor alpha from rat liver is almost identical to human TFIIB. Nucleic Acids Res. 1992 Jun 25;20(12):3250–3250. doi: 10.1093/nar/20.12.3250. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Wampler S. L., Kadonaga J. T. Functional analysis of Drosophila transcription factor IIB. Genes Dev. 1992 Aug;6(8):1542–1552. doi: 10.1101/gad.6.8.1542. [DOI] [PubMed] [Google Scholar]
  54. Wilson C. J., Chao D. M., Imbalzano A. N., Schnitzler G. R., Kingston R. E., Young R. A. RNA polymerase II holoenzyme contains SWI/SNF regulators involved in chromatin remodeling. Cell. 1996 Jan 26;84(2):235–244. doi: 10.1016/s0092-8674(00)80978-2. [DOI] [PubMed] [Google Scholar]
  55. Xiao H., Pearson A., Coulombe B., Truant R., Zhang S., Regier J. L., Triezenberg S. J., Reinberg D., Flores O., Ingles C. J. Binding of basal transcription factor TFIIH to the acidic activation domains of VP16 and p53. Mol Cell Biol. 1994 Oct;14(10):7013–7024. doi: 10.1128/mcb.14.10.7013. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Yamashita S., Hisatake K., Kokubo T., Doi K., Roeder R. G., Horikoshi M., Nakatani Y. Transcription factor TFIIB sites important for interaction with promoter-bound TFIID. Science. 1993 Jul 23;261(5120):463–466. doi: 10.1126/science.8332911. [DOI] [PubMed] [Google Scholar]
  57. Yocum R. R., Hanley S., West R., Jr, Ptashne M. Use of lacZ fusions to delimit regulatory elements of the inducible divergent GAL1-GAL10 promoter in Saccharomyces cerevisiae. Mol Cell Biol. 1984 Oct;4(10):1985–1998. doi: 10.1128/mcb.4.10.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Zawel L., Reinberg D. Common themes in assembly and function of eukaryotic transcription complexes. Annu Rev Biochem. 1995;64:533–561. doi: 10.1146/annurev.bi.64.070195.002533. [DOI] [PubMed] [Google Scholar]

Articles from Molecular and Cellular Biology are provided here courtesy of Taylor & Francis

RESOURCES