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. 1993 Jul 11;21(14):3233–3238. doi: 10.1093/nar/21.14.3233

Promoter opening (melting) and transcription initiation by RNA polymerase I requires neither nucleotide beta,gamma hydrolysis nor protein phosphorylation.

A K Lofquist 1, H Li 1, M A Imboden 1, M R Paule 1
PMCID: PMC309760  PMID: 7688114

Abstract

With some bacterial RNA polymerases and in eukaryotic RNA polymerase II, DNA melting during initiation requires the coupling of energy derived from beta,gamma hydrolysis of ATP. A detailed analysis of this possible requirement for eukaryotic RNA polymerase I reveals no such requirement. However, in some cases, beta,gamma non-hydrolyzable derivatives (beta,gamma imido or methylene) of nucleotide substrates have been found to significantly inhibit transcription initiation because of their inefficient use as the first nucleotide of the transcript. In addition, the results presented here show that protein kinase activity is not required as an integral part of transcription initiation by RNA polymerase I. Prior phosphorylation of proteins participating in the process is not ruled out.

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Selected References

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

  1. Akiyama T., Ishida J., Nakagawa S., Ogawara H., Watanabe S., Itoh N., Shibuya M., Fukami Y. Genistein, a specific inhibitor of tyrosine-specific protein kinases. J Biol Chem. 1987 Apr 25;262(12):5592–5595. [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. Bateman E., Paule M. R. Events during eucaryotic rRNA transcription initiation and elongation: conversion from the closed to the open promoter complex requires nucleotide substrates. Mol Cell Biol. 1988 May;8(5):1940–1946. doi: 10.1128/mcb.8.5.1940. [DOI] [PMC free article] [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. Bunick D., Zandomeni R., Ackerman S., Weinmann R. Mechanism of RNA polymerase II--specific initiation of transcription in vitro: ATP requirement and uncapped runoff transcripts. Cell. 1982 Jul;29(3):877–886. doi: 10.1016/0092-8674(82)90449-4. [DOI] [PubMed] [Google Scholar]
  6. Cavanaugh A. H., Thompson E. A., Jr Hormonal regulation of transcription of rDNA. Initiation of transcription by RNA polymerase I in vitro. J Biol Chem. 1986 Sep 25;261(27):12738–12744. [PubMed] [Google Scholar]
  7. Chesnut J. D., Stephens J. H., Dahmus M. E. The interaction of RNA polymerase II with the adenovirus-2 major late promoter is precluded by phosphorylation of the C-terminal domain of subunit IIa. J Biol Chem. 1992 May 25;267(15):10500–10506. [PubMed] [Google Scholar]
  8. Gokal P. K., Mahajan P. B., Thompson E. A. Hormonal regulation of transcription of rDNA. Formation of initiated complexes by RNA polymerase I in vitro. J Biol Chem. 1990 Sep 25;265(27):16234–16243. [PubMed] [Google Scholar]
  9. Herendeen D. R., Kassavetis G. A., Geiduschek E. P. A transcriptional enhancer whose function imposes a requirement that proteins track along DNA. Science. 1992 May 29;256(5061):1298–1303. doi: 10.1126/science.1598572. [DOI] [PubMed] [Google Scholar]
  10. 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]
  11. 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]
  12. Kassavetis G. A., Blanco J. A., Johnson T. E., Geiduschek E. P. Formation of open and elongating transcription complexes by RNA polymerase III. J Mol Biol. 1992 Jul 5;226(1):47–58. doi: 10.1016/0022-2836(92)90123-2. [DOI] [PubMed] [Google Scholar]
  13. Kownin P., Bateman E., Paule M. R. Effects of single-base substitutions within the Acanthamoeba castellanii rRNA promoter on transcription and on binding of transcription initiation factor and RNA polymerase I. Mol Cell Biol. 1988 Feb;8(2):747–753. doi: 10.1128/mcb.8.2.747. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. 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]
  15. Kustu S., North A. K., Weiss D. S. Prokaryotic transcriptional enhancers and enhancer-binding proteins. Trends Biochem Sci. 1991 Nov;16(11):397–402. doi: 10.1016/0968-0004(91)90163-p. [DOI] [PubMed] [Google Scholar]
  16. Laybourn P. J., Dahmus M. E. Phosphorylation of RNA polymerase IIA occurs subsequent to interaction with the promoter and before the initiation of transcription. J Biol Chem. 1990 Aug 5;265(22):13165–13173. [PubMed] [Google Scholar]
  17. Learned R. M., Tjian R. In vitro transcription of human ribosomal RNA genes by RNA polymerase I. J Mol Appl Genet. 1982;1(6):575–584. [PubMed] [Google Scholar]
  18. Luse D. S., Kochel T., Kuempel E. D., Coppola J. A., Cai H. Transcription initiation by RNA polymerase II in vitro. At least two nucleotides must be added to form a stable ternary complex. J Biol Chem. 1987 Jan 5;262(1):289–297. [PubMed] [Google Scholar]
  19. Mahajan P. B., Gokal P. K., Thompson E. A. Hormonal regulation of transcription of rDNA. The role of TFIC in formation of initiation complexes. J Biol Chem. 1990 Sep 25;265(27):16244–16247. [PubMed] [Google Scholar]
  20. Mahajan P. B., Thompson E. A. Hormonal regulation of transcription of rDNA. Purification and characterization of the hormone-regulated transcription factor IC. J Biol Chem. 1990 Sep 25;265(27):16225–16233. [PubMed] [Google Scholar]
  21. Ninfa A. J., Reitzer L. J., Magasanik B. Initiation of transcription at the bacterial glnAp2 promoter by purified E. coli components is facilitated by enhancers. Cell. 1987 Sep 25;50(7):1039–1046. doi: 10.1016/0092-8674(87)90170-x. [DOI] [PubMed] [Google Scholar]
  22. O'Mahony D. J., Xie W. Q., Smith S. D., Singer H. A., Rothblum L. I. Differential phosphorylation and localization of the transcription factor UBF in vivo in response to serum deprivation. In vitro dephosphorylation of UBF reduces its transactivation properties. J Biol Chem. 1992 Jan 5;267(1):35–38. [PubMed] [Google Scholar]
  23. Paule M. R., Iida C. T., Perna P. J., Harris G. H., Knoll D. A., D'Alessio J. M. In vitro evidence that eukaryotic ribosomal RNA transcription is regulated by modification of RNA polymerase I. Nucleic Acids Res. 1984 Nov 12;12(21):8161–8180. doi: 10.1093/nar/12.21.8161. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Payne J. M., Laybourn P. J., Dahmus M. E. The transition of RNA polymerase II from initiation to elongation is associated with phosphorylation of the carboxyl-terminal domain of subunit IIa. J Biol Chem. 1989 Nov 25;264(33):19621–19629. [PubMed] [Google Scholar]
  25. Perna P. J., Harris G. H., Iida C. T., Kownin P., Bugren S., Paule M. R. The start site of the Acanthamoeba castellanii ribosomal RNA transcription unit. Gene Expr. 1992;2(1):71–78. [PMC free article] [PubMed] [Google Scholar]
  26. Popham D. L., Szeto D., Keener J., Kustu S. Function of a bacterial activator protein that binds to transcriptional enhancers. Science. 1989 Feb 3;243(4891):629–635. doi: 10.1126/science.2563595. [DOI] [PubMed] [Google Scholar]
  27. Rhodes G., Chamberlin M. J. Kinetic analysis of ribonucleic acid chain initiation by Escherichia coli Ribonucleic acid polymerase bound to DNA. J Biol Chem. 1975 Dec 10;250(23):9112–9120. [PubMed] [Google Scholar]
  28. 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]
  29. Schnapp A., Pfleiderer C., Rosenbauer H., Grummt I. A growth-dependent transcription initiation factor (TIF-IA) interacting with RNA polymerase I regulates mouse ribosomal RNA synthesis. EMBO J. 1990 Sep;9(9):2857–2863. doi: 10.1002/j.1460-2075.1990.tb07475.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Secrist J. P., Sehgal I., Powis G., Abraham R. T. Preferential inhibition of the platelet-derived growth factor receptor tyrosine kinase by staurosporine. J Biol Chem. 1990 Nov 25;265(33):20394–20400. [PubMed] [Google Scholar]
  31. 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]
  32. Spindler S. R., Duester G. L., D'Alessio J. M., Paule M. R. A rapid and facile procedure for the preparation of RNA polymerase I from Acanthamoeba castellanii. Purification and subunit structure. J Biol Chem. 1978 Jul 10;253(13):4669–4675. [PubMed] [Google Scholar]
  33. Su W., Porter S., Kustu S., Echols H. DNA-looping and enhancer activity: association between DNA-bound NtrC activator and RNA polymerase at the bacterial glnA promoter. Proc Natl Acad Sci U S A. 1990 Jul;87(14):5504–5508. doi: 10.1073/pnas.87.14.5504. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Wang W., Carey M., Gralla J. D. Polymerase II promoter activation: closed complex formation and ATP-driven start site opening. Science. 1992 Jan 24;255(5043):450–453. doi: 10.1126/science.1310361. [DOI] [PubMed] [Google Scholar]
  35. Zwick M. G., Imboden M. A., Paule M. R. Specific transcription of an Acanthamoeba castellanii 5S RNA gene in homologous nuclear extracts. Nucleic Acids Res. 1991 Apr 11;19(7):1681–1686. doi: 10.1093/nar/19.7.1681. [DOI] [PMC free article] [PubMed] [Google Scholar]

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