Skip to main content
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1990 Apr 11;18(7):1805–1811. doi: 10.1093/nar/18.7.1805

Two complex regions, including a TATA sequence, are required for transcription by RNA polymerase I in Neurospora crassa.

B M Tyler 1
PMCID: PMC330599  PMID: 2139932

Abstract

In order to define the RNA polymerase I transcriptional apparatus and how it might interact with regulatory signals, the DNA sequences necessary for 40S rRNA transcription in Neurospora crassa were determined. A systematic set of deletion, substitution and insertion mutations were assayed in a homologous in vitro system. The sequences required for transcription of the gene consist of two large domains (I and II) from -113 to -37, and -29 to +4, respectively. Complete deletion of either domain abolished transcription. Upstream sequences confer a small stimulation of transcription. Domain II includes a TATA sequence at -5 which is sensitive to a small (2 bp) substitution and which is conserved among the large rRNA genes of many organisms. Domain I includes a sequence, termed the 'Ribo box', which is also required for transcription of the Neurospora 5S rRNA genes (1), and which occurs in the 5' region of a Neurospora ribosomal protein gene. The 5S and 40S Ribo boxes are shown to be functionally interchangeable.

Full text

PDF
1805

Images in this article

Selected References

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

  1. Alberghina F. A., Sturani E., Gohlke J. R. Levels and rates of synthesis of ribosomal ribonucleic acid, transfer ribonucleic acid, and protein in Neurospora crassa in different steady states of growth. J Biol Chem. 1975 Jun 25;250(12):4381–4388. [PubMed] [Google Scholar]
  2. Balzi E., Di Pietro A., Goffeau A., van Heerikhuizen H., Klootwijk J. The RNA polymerase I initiation site and the external transcribed spacer of the fission yeast Schizosaccharomyces pombe ribosomal RNA genes. Gene. 1985;39(2-3):165–172. doi: 10.1016/0378-1119(85)90310-5. [DOI] [PubMed] [Google Scholar]
  3. Barthelmess I. B. Mutants affecting amino acid cross-pathway control in Neurospora crassa. Genet Res. 1982 Apr;39(2):169–185. doi: 10.1017/s0016672300020863. [DOI] [PubMed] [Google Scholar]
  4. Bateman E., Paule M. R. Regulation of eukaryotic ribosomal RNA transcription by RNA polymerase modification. Cell. 1986 Nov 7;47(3):445–450. doi: 10.1016/0092-8674(86)90601-x. [DOI] [PubMed] [Google Scholar]
  5. 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]
  6. Birnboim H. C., Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 1979 Nov 24;7(6):1513–1523. doi: 10.1093/nar/7.6.1513. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Buttgereit D., Pflugfelder G., Grummt I. Growth-dependent regulation of rRNA synthesis is mediated by a transcription initiation factor (TIF-IA). Nucleic Acids Res. 1985 Nov 25;13(22):8165–8180. doi: 10.1093/nar/13.22.8165. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Cassidy B., Haglund R., Rothblum L. I. Regions upstream from the core promoter of the rat ribosomal gene are required for the formation of a stable transcription initiation complex by RNA polymerase I in vitro. Biochim Biophys Acta. 1987 Jul 14;909(2):133–144. doi: 10.1016/0167-4781(87)90035-2. [DOI] [PubMed] [Google Scholar]
  9. Geever R. F., Case M. E., Tyler B. M., Buxton F., Giles N. H. Point mutations and DNA rearrangements 5' to the inducible qa-2 gene of Neurospora allow activator protein-independent transcription. Proc Natl Acad Sci U S A. 1983 Dec;80(23):7298–7302. doi: 10.1073/pnas.80.23.7298. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Gokal P. K., Cavanaugh A. H., Thompson E. A., Jr The effects of cycloheximide upon transcription of rRNA, 5 S RNA, and tRNA genes. J Biol Chem. 1986 Feb 25;261(6):2536–2541. [PubMed] [Google Scholar]
  11. Grummt I. Nucleotide sequence requirements for specific initiation of transcription by RNA polymerase I. Proc Natl Acad Sci U S A. 1982 Nov;79(22):6908–6911. doi: 10.1073/pnas.79.22.6908. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Hill D. E., Hope I. A., Macke J. P., Struhl K. Saturation mutagenesis of the yeast his3 regulatory site: requirements for transcriptional induction and for binding by GCN4 activator protein. Science. 1986 Oct 24;234(4775):451–457. doi: 10.1126/science.3532321. [DOI] [PubMed] [Google Scholar]
  13. Indik Z. K., Tartof K. D. Glutamate tRNA genes are adjacent to 5S RNA genes in Drosophila and reveal a conserved upstream sequence (the ACT-TA box). Nucleic Acids Res. 1982 Jul 24;10(14):4159–4172. doi: 10.1093/nar/10.14.4159. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Kempers-Veenstra A. E., Musters W., Dekker A. F., Klootwijk J., Planta R. J. Deletion mapping of the yeast Pol I promoter. Curr Genet. 1985;10(4):253–260. doi: 10.1007/BF00365621. [DOI] [PubMed] [Google Scholar]
  15. Kohorn B. D., Rae P. M. Localization of DNA sequences promoting RNA polymerase I activity in Drosophila. Proc Natl Acad Sci U S A. 1983 Jun;80(11):3265–3268. doi: 10.1073/pnas.80.11.3265. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Kownin P., Bateman E., Paule M. R. Eukaryotic RNA polymerase I promoter binding is directed by protein contacts with transcription initiation factor and is DNA sequence-independent. Cell. 1987 Aug 28;50(5):693–699. doi: 10.1016/0092-8674(87)90327-8. [DOI] [PubMed] [Google Scholar]
  17. Kownin P., Iida C. T., Brown-Shimer S., Paule M. R. The ribosomal RNA promoter of Acanthamoeba castellanii determined by transcription in a cell-free system. Nucleic Acids Res. 1985 Sep 11;13(17):6237–6248. doi: 10.1093/nar/13.17.6237. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. 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]
  19. 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]
  20. 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]
  21. Morton D. G., Sprague K. U. In vitro transcription of a silkworm 5S RNA gene requires an upstream signal. Proc Natl Acad Sci U S A. 1984 Sep;81(17):5519–5522. doi: 10.1073/pnas.81.17.5519. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Norrander J., Kempe T., Messing J. Construction of improved M13 vectors using oligodeoxynucleotide-directed mutagenesis. Gene. 1983 Dec;26(1):101–106. doi: 10.1016/0378-1119(83)90040-9. [DOI] [PubMed] [Google Scholar]
  23. Pribnow D. Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter. Proc Natl Acad Sci U S A. 1975 Mar;72(3):784–788. doi: 10.1073/pnas.72.3.784. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Reeder R. H., Pennock D., McStay B., Roan J., Tolentino E., Walker P. Linker scanner mutagenesis of the Xenopus laevis ribosomal gene promoter. Nucleic Acids Res. 1987 Sep 25;15(18):7429–7441. doi: 10.1093/nar/15.18.7429. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Rubacha A., Sumner W., 3rd, Richter L., Beckingham K. Conserved 5' flank homologies in dipteran 5S RNA genes that would function on 'A' form DNA. Nucleic Acids Res. 1984 Nov 12;12(21):8193–8207. doi: 10.1093/nar/12.21.8193. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Selker E. U., Morzycka-Wroblewska E., Stevens J. N., Metzenberg R. L. An upstream signal is required for in vitro transcription of Neurospora 5S RNA genes. Mol Gen Genet. 1986 Oct;205(1):189–192. doi: 10.1007/BF02428052. [DOI] [PubMed] [Google Scholar]
  27. Sollner-Webb B., Tower J. Transcription of cloned eukaryotic ribosomal RNA genes. Annu Rev Biochem. 1986;55:801–830. doi: 10.1146/annurev.bi.55.070186.004101. [DOI] [PubMed] [Google Scholar]
  28. Sturani E., Costantini M. G., Zippel R., Alberghina F. A. Regulation of RNA synthesis in Neurospora crassa. An analysis of a shift-up. Exp Cell Res. 1976 May;99(2):245–252. doi: 10.1016/0014-4827(76)90580-2. [DOI] [PubMed] [Google Scholar]
  29. Sturani E., Magnani F., Alberghina F. A. Inhibition of ribosomal RNA synthesis during a shift-down transition of growth in Neurospora crassa. Biochim Biophys Acta. 1973 Aug 24;319(2):153–164. doi: 10.1016/0005-2787(73)90006-3. [DOI] [PubMed] [Google Scholar]
  30. Tower J., Culotta V. C., Sollner-Webb B. Factors and nucleotide sequences that direct ribosomal DNA transcription and their relationship to the stable transcription complex. Mol Cell Biol. 1986 Oct;6(10):3451–3462. doi: 10.1128/mcb.6.10.3451. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Tower J., Sollner-Webb B. Transcription of mouse rDNA is regulated by an activated subform of RNA polymerase I. Cell. 1987 Sep 11;50(6):873–883. doi: 10.1016/0092-8674(87)90514-9. [DOI] [PubMed] [Google Scholar]
  32. Tyler B. M., Giles N. H. Accurate transcription of homologous 5S rRNA and tRNA genes and splicing of tRNA in vitro by soluble extracts of Neurospora. Nucleic Acids Res. 1984 Jul 25;12(14):5737–5755. doi: 10.1093/nar/12.14.5737. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Tyler B. M., Giles N. H. Structure of a Neurospora RNA polymerase I promoter defined by transcription in vitro with homologous extracts. Nucleic Acids Res. 1985 Jun 25;13(12):4311–4332. doi: 10.1093/nar/13.12.4311. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Tyler B. M. Transcription of Neurospora crassa 5 S rRNA genes requires a TATA box and three internal elements. J Mol Biol. 1987 Aug 20;196(4):801–811. doi: 10.1016/0022-2836(87)90406-2. [DOI] [PubMed] [Google Scholar]
  35. Vieira J., Messing J. Production of single-stranded plasmid DNA. Methods Enzymol. 1987;153:3–11. doi: 10.1016/0076-6879(87)53044-0. [DOI] [PubMed] [Google Scholar]
  36. Wilson E. T., Larson D., Young L. S., Sprague K. U. A large region controls tRNA gene transcription. J Mol Biol. 1985 May 25;183(2):153–163. doi: 10.1016/0022-2836(85)90209-8. [DOI] [PubMed] [Google Scholar]
  37. Windle J. J., Sollner-Webb B. Two distant and precisely positioned domains promote transcription of Xenopus laevis rRNA genes: analysis with linker-scanning mutants. Mol Cell Biol. 1986 Dec;6(12):4585–4593. doi: 10.1128/mcb.6.12.4585. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Yamamoto O., Takakusa N., Mishima Y., Kominami R., Muramatsu M. Determination of the promoter region of mouse ribosomal RNA gene by an in vitro transcription system. Proc Natl Acad Sci U S A. 1984 Jan;81(2):299–303. doi: 10.1073/pnas.81.2.299. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES