Skip to main content
PMC home page
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1995 Oct;177(20):5756–5761. doi: 10.1128/jb.177.20.5756-5761.1995

Role of curved DNA in binding of Escherichia coli RNA polymerase to promoters.

C A Nickerson 1, E C Achberger 1
PMCID: PMC177394  PMID: 7592319

Abstract

The ability of curved DNA upstream of the -35 region to affect the interaction of Escherichia coli RNA polymerase and promoter DNA was examined through the use of hybrid promoters. These promoters were constructed by substituting the curved DNA from two Bacillus subtilis bacteriophage SP82 promoters for the comparable DNA of the bacteriophage lambda promoters lambda pR and lambda pL. The SP82 promoters possessed intrinsic DNA curvature upstream of their -35 regions, as characterized by runs of adenines in phase with the helical repeat. In vitro, the relative affinities of purified sigma 70-RNA polymerase for the promoters were determined in a competition binding assay. Hybrid promoters derived from lambda pR that contained curved DNA were bound by E. coli RNA polymerase more efficiently than was the original lambda pR. Binding of E. coli RNA polymerase to these hybrid promoters was favored on superhelical DNA templates according to gel retardation analysis. Both the supercoiled and relaxed forms of the hybrid lambda pL series were better competitors for E. coli RNA polymerase binding than was the original lambda pL. The results of DNase I footprinting analysis provided evidence for the wrapping of the upstream curved DNA of the hybrid lambda pR promoters around the E. coli RNA polymerase in a tight, nucleosomal-like fashion. The tight wrapping of the upstream DNA around the polymerase may facilitate the subsequent steps of DNA untwisting and strand separation.

Full Text

The Full Text of this article is available as a PDF (342.0 KB).

Selected References

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

  1. Achberger E. C., Hilton M. D., Whiteley H. R. The effect of the delta subunit on the interaction of Bacillus subtilis RNA polymerase with bases in a SP82 early gene promoter. Nucleic Acids Res. 1982 May 11;10(9):2893–2910. doi: 10.1093/nar/10.9.2893. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Achberger E. C., Whiteley H. R. The interaction of Escherichia coli core RNA polymerase with specificity-determining subunits derived from unmodified and SP82-modified Bacillus subtilis RNA polymerase. J Biol Chem. 1980 Dec 25;255(24):11957–11964. [PubMed] [Google Scholar]
  3. Banner C. D., Moran C. P., Jr, Losick R. Deletion analysis of a complex promoter for a developmentally regulated gene from Bacillus subtilis. J Mol Biol. 1983 Aug 5;168(2):351–365. doi: 10.1016/s0022-2836(83)80023-0. [DOI] [PubMed] [Google Scholar]
  4. Bossi L., Smith D. M. Conformational change in the DNA associated with an unusual promoter mutation in a tRNA operon of Salmonella. Cell. 1984 Dec;39(3 Pt 2):643–652. doi: 10.1016/0092-8674(84)90471-9. [DOI] [PubMed] [Google Scholar]
  5. Bossi L. The hisR locus of Salmonella: nucleotide sequence and expression. Mol Gen Genet. 1983;192(1-2):163–170. doi: 10.1007/BF00327662. [DOI] [PubMed] [Google Scholar]
  6. Bracco L., Kotlarz D., Kolb A., Diekmann S., Buc H. Synthetic curved DNA sequences can act as transcriptional activators in Escherichia coli. EMBO J. 1989 Dec 20;8(13):4289–4296. doi: 10.1002/j.1460-2075.1989.tb08615.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Brosius J., Dull T. J., Sleeter D. D., Noller H. F. Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J Mol Biol. 1981 May 15;148(2):107–127. doi: 10.1016/0022-2836(81)90508-8. [DOI] [PubMed] [Google Scholar]
  8. Deutch A. H., Smith C. J., Rushlow K. E., Kretschmer P. J. Escherichia coli delta 1-pyrroline-5-carboxylate reductase: gene sequence, protein overproduction and purification. Nucleic Acids Res. 1982 Dec 11;10(23):7701–7714. doi: 10.1093/nar/10.23.7701. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Espinosa-Urgel M., Tormo A. Sigma s-dependent promoters in Escherichia coli are located in DNA regions with intrinsic curvature. Nucleic Acids Res. 1993 Aug 11;21(16):3667–3670. doi: 10.1093/nar/21.16.3667. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Fried M. G., Liu G. Molecular sequestration stabilizes CAP-DNA complexes during polyacrylamide gel electrophoresis. Nucleic Acids Res. 1994 Nov 25;22(23):5054–5059. doi: 10.1093/nar/22.23.5054. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Galas D. J., Eggert M., Waterman M. S. Rigorous pattern-recognition methods for DNA sequences. Analysis of promoter sequences from Escherichia coli. J Mol Biol. 1985 Nov 5;186(1):117–128. doi: 10.1016/0022-2836(85)90262-1. [DOI] [PubMed] [Google Scholar]
  12. Gartenberg M. R., Crothers D. M. Synthetic DNA bending sequences increase the rate of in vitro transcription initiation at the Escherichia coli lac promoter. J Mol Biol. 1991 May 20;219(2):217–230. doi: 10.1016/0022-2836(91)90563-l. [DOI] [PubMed] [Google Scholar]
  13. Giladi H., Gottesman M., Oppenheim A. B. Integration host factor stimulates the phage lambda pL promoter. J Mol Biol. 1990 May 5;213(1):109–121. doi: 10.1016/S0022-2836(05)80124-X. [DOI] [PubMed] [Google Scholar]
  14. Hsu L. M., Giannini J. K., Leung T. W., Crosthwaite J. C. Upstream sequence activation of Escherichia coli argT promoter in vivo and in vitro. Biochemistry. 1991 Jan 22;30(3):813–822. doi: 10.1021/bi00217a035. [DOI] [PubMed] [Google Scholar]
  15. Kuhnke G., Fritz H. J., Ehring R. Unusual properties of promoter-up mutations in the Escherichia coli galactose operon and evidence suggesting RNA polymerase-induced DNA bending. EMBO J. 1987 Feb;6(2):507–513. doi: 10.1002/j.1460-2075.1987.tb04782.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Lamond A. I., Travers A. A. Requirement for an upstream element for optimal transcription of a bacterial tRNA gene. Nature. 1983 Sep 15;305(5931):248–250. doi: 10.1038/305248a0. [DOI] [PubMed] [Google Scholar]
  17. Lee G., Talkington C., Pero J. Nucleotide sequence of a promoter recognized by Bacillus subtilis RNA polymerase. Mol Gen Genet. 1980;180(1):57–65. doi: 10.1007/BF00267352. [DOI] [PubMed] [Google Scholar]
  18. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  19. McAllister C. F., Achberger E. C. Effect of polyadenine-containing curved DNA on promoter utilization in Bacillus subtilis. J Biol Chem. 1988 Aug 25;263(24):11743–11749. [PubMed] [Google Scholar]
  20. McAllister C. F., Achberger E. C. Rotational orientation of upstream curved DNA affects promoter function in Bacillus subtilis. J Biol Chem. 1989 Jun 25;264(18):10451–10456. [PubMed] [Google Scholar]
  21. Mizuno T. Static bend of DNA helix at the activator recognition site of the ompF promoter in Escherichia coli. Gene. 1987;54(1):57–64. doi: 10.1016/0378-1119(87)90347-7. [DOI] [PubMed] [Google Scholar]
  22. Mulligan M. E., Hawley D. K., Entriken R., McClure W. R. Escherichia coli promoter sequences predict in vitro RNA polymerase selectivity. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 2):789–800. doi: 10.1093/nar/12.1part2.789. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Nishi T., Itoh S. Enhancement of transcriptional activity of the Escherichia coli trp promoter by upstream A + T-rich regions. Gene. 1986;44(1):29–36. doi: 10.1016/0378-1119(86)90039-9. [DOI] [PubMed] [Google Scholar]
  24. Plaskon R. R., Wartell R. M. Sequence distributions associated with DNA curvature are found upstream of strong E. coli promoters. Nucleic Acids Res. 1987 Jan 26;15(2):785–796. doi: 10.1093/nar/15.2.785. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Pérez-Martín J., Rojo F., de Lorenzo V. Promoters responsive to DNA bending: a common theme in prokaryotic gene expression. Microbiol Rev. 1994 Jun;58(2):268–290. doi: 10.1128/mr.58.2.268-290.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Ross W., Gosink K. K., Salomon J., Igarashi K., Zou C., Ishihama A., Severinov K., Gourse R. L. A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase. Science. 1993 Nov 26;262(5138):1407–1413. doi: 10.1126/science.8248780. [DOI] [PubMed] [Google Scholar]
  27. Verde P., Frunzio R., di Nocera P. P., Blasi F., Bruni C. B. Identification, nucleotide sequence and expression of the regulatory region of the histidine operon of Escherichia coli K-12. Nucleic Acids Res. 1981 May 11;9(9):2075–2086. doi: 10.1093/nar/9.9.2075. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Vieira J., Messing J. The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene. 1982 Oct;19(3):259–268. doi: 10.1016/0378-1119(82)90015-4. [DOI] [PubMed] [Google Scholar]

Articles from Journal of Bacteriology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES