Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1995 Nov 11;23(21):4345–4352. doi: 10.1093/nar/23.21.4345

Acanthamoeba castellanii contains a ribosomal RNA enhancer binding protein which stimulates TIF-IB binding and transcription under stringent conditions.

Q Yang 1, C A Radebaugh 1, W Kubaska 1, G K Geiss 1, M R Paule 1
PMCID: PMC307389  PMID: 7501455

Abstract

The intergenic spacer (IGS) of Acanthamoeba castellanii rRNA genes contains repeated elements which are weak enhancers for transcription by RNA polymerase I. A protein, EBF, was identified and partially purified which binds to the enhancers and to several other sequences within the IGS, but not to other DNA fragments, including the rRNA core promoter. No consensus binding sequence could be discerned in these fragments and bound factor is in rapid equilibrium with unbound. EBF has functional characteristics similar to vertebrate upstream binding factors (UBF). Not only does it bind to the enhancer and other IGS elements, but it also stimulates binding of TIF-IB, the fundamental transcription initiation factor, to the core promoter and stimulates transcription from the promoter. Attempts to identify polypeptides with epitopes similar to rat or Xenopus laevis UBF suggest that structurally the protein from A.castellanii is not closely related to vertebrate UBF.

Full text

PDF
4345

Images in this article

4347Image
on p.4347
4348Image
on p.4348
4348Image
on p.4348
4349Image
on p.4349
4350Image
on p.4350
4350Image
on p.4350
4351Image
on p.4351
4351Image
on p.4351

Selected References

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

  1. Bachvarov D., Normandeau M., Moss T. Heterogeneity in the Xenopus ribosomal transcription factor xUBF has a molecular basis distinct from that in mammals. FEBS Lett. 1991 Aug 19;288(1-2):55–59. doi: 10.1016/0014-5793(91)81002-p. [DOI] [PubMed] [Google Scholar]
  2. Bateman E., Iida C. T., Kownin P., Paule M. R. Footprinting of ribosomal RNA genes by transcription initiation factor and RNA polymerase I. Proc Natl Acad Sci U S A. 1985 Dec;82(23):8004–8008. doi: 10.1073/pnas.82.23.8004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bazett-Jones D. P., Leblanc B., Herfort M., Moss T. Short-range DNA looping by the Xenopus HMG-box transcription factor, xUBF. Science. 1994 May 20;264(5162):1134–1137. doi: 10.1126/science.8178172. [DOI] [PubMed] [Google Scholar]
  4. Bell S. P., Jantzen H. M., Tjian R. Assembly of alternative multiprotein complexes directs rRNA promoter selectivity. Genes Dev. 1990 Jun;4(6):943–954. doi: 10.1101/gad.4.6.943. [DOI] [PubMed] [Google Scholar]
  5. Bell S. P., Learned R. M., Jantzen H. M., Tjian R. Functional cooperativity between transcription factors UBF1 and SL1 mediates human ribosomal RNA synthesis. Science. 1988 Sep 2;241(4870):1192–1197. doi: 10.1126/science.3413483. [DOI] [PubMed] [Google Scholar]
  6. Bell S. P., Pikaard C. S., Reeder R. H., Tjian R. Molecular mechanisms governing species-specific transcription of ribosomal RNA. Cell. 1989 Nov 3;59(3):489–497. doi: 10.1016/0092-8674(89)90032-9. [DOI] [PubMed] [Google Scholar]
  7. Clos J., Buttgereit D., Grummt I. A purified transcription factor (TIF-IB) binds to essential sequences of the mouse rDNA promoter. Proc Natl Acad Sci U S A. 1986 Feb;83(3):604–608. doi: 10.1073/pnas.83.3.604. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Comai L., Tanese N., Tjian R. The TATA-binding protein and associated factors are integral components of the RNA polymerase I transcription factor, SL1. Cell. 1992 Mar 6;68(5):965–976. doi: 10.1016/0092-8674(92)90039-f. [DOI] [PubMed] [Google Scholar]
  9. Comai L., Zomerdijk J. C., Beckmann H., Zhou S., Admon A., Tjian R. Reconstitution of transcription factor SL1: exclusive binding of TBP by SL1 or TFIID subunits. Science. 1994 Dec 23;266(5193):1966–1972. doi: 10.1126/science.7801123. [DOI] [PubMed] [Google Scholar]
  10. Copenhaver G. P., Putnam C. D., Denton M. L., Pikaard C. S. The RNA polymerase I transcription factor UBF is a sequence-tolerant HMG-box protein that can recognize structured nucleic acids. Nucleic Acids Res. 1994 Jul 11;22(13):2651–2657. doi: 10.1093/nar/22.13.2651. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Cormack B. P., Struhl K. The TATA-binding protein is required for transcription by all three nuclear RNA polymerases in yeast cells. Cell. 1992 May 15;69(4):685–696. doi: 10.1016/0092-8674(92)90232-2. [DOI] [PubMed] [Google Scholar]
  12. Dunaway M. A transcription factor, TFIS, interacts with both the promoter and enhancer of the Xenopus rRNA genes. Genes Dev. 1989 Nov;3(11):1768–1778. doi: 10.1101/gad.3.11.1768. [DOI] [PubMed] [Google Scholar]
  13. Eberhard D., Tora L., Egly J. M., Grummt I. A TBP-containing multiprotein complex (TIF-IB) mediates transcription specificity of murine RNA polymerase I. Nucleic Acids Res. 1993 Sep 11;21(18):4180–4186. doi: 10.1093/nar/21.18.4180. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Gong X., Radebaugh C. A., Geiss G. K., Simon M. N., Paule M. R. Site-directed photo-cross-linking of rRNA transcription initiation complexes. Mol Cell Biol. 1995 Sep;15(9):4956–4963. doi: 10.1128/mcb.15.9.4956. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Hisatake K., Nishimura T., Maeda Y., Hanada K., Song C. Z., Muramatsu M. Cloning and structural analysis of cDNA and the gene for mouse transcription factor UBF. Nucleic Acids Res. 1991 Sep 11;19(17):4631–4637. doi: 10.1093/nar/19.17.4631. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Iida C. T., Kownin P., Paule M. R. Ribosomal RNA transcription: proteins and DNA sequences involved in preinitiation complex formation. Proc Natl Acad Sci U S A. 1985 Mar;82(6):1668–1672. doi: 10.1073/pnas.82.6.1668. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Iida C. T., Paule M. R. Purification of components required for accurate transcription of ribosomal RNA from Acanthamoeba castellanii. Nucleic Acids Res. 1992 Jun 25;20(12):3211–3221. doi: 10.1093/nar/20.12.3211. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Jantzen H. M., Admon A., Bell S. P., Tjian R. Nucleolar transcription factor hUBF contains a DNA-binding motif with homology to HMG proteins. Nature. 1990 Apr 26;344(6269):830–836. doi: 10.1038/344830a0. [DOI] [PubMed] [Google Scholar]
  19. Kassavetis G. A., Braun B. R., Nguyen L. H., Geiduschek E. P. S. cerevisiae TFIIIB is the transcription initiation factor proper of RNA polymerase III, while TFIIIA and TFIIIC are assembly factors. Cell. 1990 Jan 26;60(2):235–245. doi: 10.1016/0092-8674(90)90739-2. [DOI] [PubMed] [Google Scholar]
  20. Kassavetis G. A., Joazeiro C. A., Pisano M., Geiduschek E. P., Colbert T., Hahn S., Blanco J. A. The role of the TATA-binding protein in the assembly and function of the multisubunit yeast RNA polymerase III transcription factor, TFIIIB. Cell. 1992 Dec 11;71(6):1055–1064. doi: 10.1016/0092-8674(92)90399-w. [DOI] [PubMed] [Google Scholar]
  21. Keys D. A., Vu L., Steffan J. S., Dodd J. A., Yamamoto R. T., Nogi Y., Nomura M. RRN6 and RRN7 encode subunits of a multiprotein complex essential for the initiation of rDNA transcription by RNA polymerase I in Saccharomyces cerevisiae. Genes Dev. 1994 Oct 1;8(19):2349–2362. doi: 10.1101/gad.8.19.2349. [DOI] [PubMed] [Google Scholar]
  22. Kuhn A., Deppert U., Grummt I. A 140-base-pair repetitive sequence element in the mouse rRNA gene spacer enhances transcription by RNA polymerase I in a cell-free system. Proc Natl Acad Sci U S A. 1990 Oct;87(19):7527–7531. doi: 10.1073/pnas.87.19.7527. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Kuhn A., Grummt I. Dual role of the nucleolar transcription factor UBF: trans-activator and antirepressor. Proc Natl Acad Sci U S A. 1992 Aug 15;89(16):7340–7344. doi: 10.1073/pnas.89.16.7340. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Labhart P., Reeder R. H. Enhancer-like properties of the 60/81 bp elements in the ribosomal gene spacer of Xenopus laevis. Cell. 1984 May;37(1):285–289. doi: 10.1016/0092-8674(84)90324-6. [DOI] [PubMed] [Google Scholar]
  25. Learned R. M., Learned T. K., Haltiner M. M., Tjian R. T. Human rRNA transcription is modulated by the coordinate binding of two factors to an upstream control element. Cell. 1986 Jun 20;45(6):847–857. doi: 10.1016/0092-8674(86)90559-3. [DOI] [PubMed] [Google Scholar]
  26. Lobo S. M., Tanaka M., Sullivan M. L., Hernandez N. A TBP complex essential for transcription from TATA-less but not TATA-containing RNA polymerase III promoters is part of the TFIIIB fraction. Cell. 1992 Dec 11;71(6):1029–1040. doi: 10.1016/0092-8674(92)90397-u. [DOI] [PubMed] [Google Scholar]
  27. McStay B., Frazier M. W., Reeder R. H. xUBF contains a novel dimerization domain essential for RNA polymerase I transcription. Genes Dev. 1991 Nov;5(11):1957–1968. doi: 10.1101/gad.5.11.1957. [DOI] [PubMed] [Google Scholar]
  28. McStay B., Hu C. H., Pikaard C. S., Reeder R. H. xUBF and Rib 1 are both required for formation of a stable polymerase I promoter complex in X. laevis. EMBO J. 1991 Aug;10(8):2297–2303. doi: 10.1002/j.1460-2075.1991.tb07766.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Miller K. G., Tower J., Sollner-Webb B. A complex control region of the mouse rRNA gene directs accurate initiation by RNA polymerase I. Mol Cell Biol. 1985 Mar;5(3):554–562. doi: 10.1128/mcb.5.3.554. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Moss T., Stefanovsky V. Y. Promotion and regulation of ribosomal transcription in eukaryotes by RNA polymerase I. Prog Nucleic Acid Res Mol Biol. 1995;50:25–66. doi: 10.1016/s0079-6603(08)60810-7. [DOI] [PubMed] [Google Scholar]
  31. O'Mahony D. J., Rothblum L. I. Identification of two forms of the RNA polymerase I transcription factor UBF. Proc Natl Acad Sci U S A. 1991 Apr 15;88(8):3180–3184. doi: 10.1073/pnas.88.8.3180. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Pape L. K., Windle J. J., Mougey E. B., Sollner-Webb B. The Xenopus ribosomal DNA 60- and 81-base-pair repeats are position-dependent enhancers that function at the establishment of the preinitiation complex: analysis in vivo and in an enhancer-responsive in vitro system. Mol Cell Biol. 1989 Nov;9(11):5093–5104. doi: 10.1128/mcb.9.11.5093. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Paule M. R., Bateman E., Hoffman L., Iida C., Imboden M., Kubaska W., Kownin P., Li H., Lofquist A., Risi P. Initiation and regulation mechanisms of ribosomal RNA transcription in the eukaryote Acanthamoeba castellanii. 1991 May 29-Jun 12Mol Cell Biochem. 104(1-2):119–126. doi: 10.1007/BF00229811. [DOI] [PubMed] [Google Scholar]
  34. Paule M. R. Transcription initiation. In search of the single factor. Nature. 1990 Apr 26;344(6269):819–820. doi: 10.1038/344819a0. [DOI] [PubMed] [Google Scholar]
  35. Pikaard C. S., McStay B., Schultz M. C., Bell S. P., Reeder R. H. The Xenopus ribosomal gene enhancers bind an essential polymerase I transcription factor, xUBF. Genes Dev. 1989 Nov;3(11):1779–1788. doi: 10.1101/gad.3.11.1779. [DOI] [PubMed] [Google Scholar]
  36. Pikaard C. S., Pape L. K., Henderson S. L., Ryan K., Paalman M. H., Lopata M. A., Reeder R. H., Sollner-Webb B. Enhancers for RNA polymerase I in mouse ribosomal DNA. Mol Cell Biol. 1990 Sep;10(9):4816–4825. doi: 10.1128/mcb.10.9.4816. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Pikaard C. S., Smith S. D., Reeder R. H., Rothblum L. rUBF, an RNA polymerase I transcription factor from rats, produces DNase I footprints identical to those produced by xUBF, its homolog from frogs. Mol Cell Biol. 1990 Jul;10(7):3810–3812. doi: 10.1128/mcb.10.7.3810. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Putnam C. D., Copenhaver G. P., Denton M. L., Pikaard C. S. The RNA polymerase I transactivator upstream binding factor requires its dimerization domain and high-mobility-group (HMG) box 1 to bend, wrap, and positively supercoil enhancer DNA. Mol Cell Biol. 1994 Oct;14(10):6476–6488. doi: 10.1128/mcb.14.10.6476. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Radebaugh C. A., Matthews J. L., Geiss G. K., Liu F., Wong J. M., Bateman E., Camier S., Sentenac A., Paule M. R. TATA box-binding protein (TBP) is a constituent of the polymerase I-specific transcription initiation factor TIF-IB (SL1) bound to the rRNA promoter and shows differential sensitivity to TBP-directed reagents in polymerase I, II, and III transcription factors. Mol Cell Biol. 1994 Jan;14(1):597–605. doi: 10.1128/mcb.14.1.597. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Reeder R. H. Regulatory elements of the generic ribosomal gene. Curr Opin Cell Biol. 1989 Jun;1(3):466–474. doi: 10.1016/0955-0674(89)90007-0. [DOI] [PubMed] [Google Scholar]
  41. Reeder R. H., Roan J. G., Dunaway M. Spacer regulation of Xenopus ribosomal gene transcription: competition in oocytes. Cell. 1983 Dec;35(2 Pt 1):449–456. doi: 10.1016/0092-8674(83)90178-2. [DOI] [PubMed] [Google Scholar]
  42. Sadowski C. L., Henry R. W., Lobo S. M., Hernandez N. Targeting TBP to a non-TATA box cis-regulatory element: a TBP-containing complex activates transcription from snRNA promoters through the PSE. Genes Dev. 1993 Aug;7(8):1535–1548. doi: 10.1101/gad.7.8.1535. [DOI] [PubMed] [Google Scholar]
  43. Schnapp A., Grummt I. Transcription complex formation at the mouse rDNA promoter involves the stepwise association of four transcription factors and RNA polymerase I. J Biol Chem. 1991 Dec 25;266(36):24588–24595. [PubMed] [Google Scholar]
  44. Schultz M. C., Reeder R. H., Hahn S. Variants of the TATA-binding protein can distinguish subsets of RNA polymerase I, II, and III promoters. Cell. 1992 May 15;69(4):697–702. doi: 10.1016/0092-8674(92)90233-3. [DOI] [PubMed] [Google Scholar]
  45. Smith S. D., O'Mahony D. J., Kinsella B. T., Rothblum L. I. Transcription from the rat 45S ribosomal DNA promoter does not require the factor UBF. Gene Expr. 1993;3(3):229–236. [PMC free article] [PubMed] [Google Scholar]
  46. Smith S. D., Oriahi E., Lowe D., Yang-Yen H. F., O'Mahony D., Rose K., Chen K., Rothblum L. I. Characterization of factors that direct transcription of rat ribosomal DNA. Mol Cell Biol. 1990 Jun;10(6):3105–3116. doi: 10.1128/mcb.10.6.3105. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Smith S. D., Oriahi E., Yang-Yen H. F., Xie W. Q., Chen C., Rothblum L. I. Interaction of RNA polymerase I transcription factors with a promoter in the nontranscribed spacer of rat ribosomal DNA. Nucleic Acids Res. 1990 Apr 11;18(7):1677–1685. doi: 10.1093/nar/18.7.1677. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Sollner-Webb B., Mougey E. B. News from the nucleolus: rRNA gene expression. Trends Biochem Sci. 1991 Feb;16(2):58–62. doi: 10.1016/0968-0004(91)90025-q. [DOI] [PubMed] [Google Scholar]
  49. Sollner-Webb B., Pape L., Ryan K., Mougey E. B., Poretta R., Nikolov E., Paalman M. H., Lazdins I., Martin C. Expression of mouse and frog rRNA genes: transcription and processing. 1991 May 29-Jun 12Mol Cell Biochem. 104(1-2):149–154. doi: 10.1007/BF00229814. [DOI] [PubMed] [Google Scholar]
  50. Taggart A. K., Fisher T. S., Pugh B. F. The TATA-binding protein and associated factors are components of pol III transcription factor TFIIIB. Cell. 1992 Dec 11;71(6):1015–1028. doi: 10.1016/0092-8674(92)90396-t. [DOI] [PubMed] [Google Scholar]
  51. White R. J., Jackson S. P. Mechanism of TATA-binding protein recruitment to a TATA-less class III promoter. Cell. 1992 Dec 11;71(6):1041–1053. doi: 10.1016/0092-8674(92)90398-v. [DOI] [PubMed] [Google Scholar]
  52. Wolffe A. P. Architectural transcription factors. Science. 1994 May 20;264(5162):1100–1101. doi: 10.1126/science.8178167. [DOI] [PubMed] [Google Scholar]
  53. Yang Q., Zwick M. G., Paule M. R. Sequence organization of the Acanthamoeba rRNA intergenic spacer: identification of transcriptional enhancers. Nucleic Acids Res. 1994 Nov 11;22(22):4798–4805. doi: 10.1093/nar/22.22.4798. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES