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. 1987 Jun;84(12):4185–4189. doi: 10.1073/pnas.84.12.4185

Modulation of transcription by DNA supercoiling: a deletion analysis of the Escherichia coli gyrA and gyrB promoters.

R Menzel, M Gellert
PMCID: PMC305049  PMID: 3035573

Abstract

Expression of the genes determining the subunits of Escherichia coli DNA gyrase (gyrA and gyrB) is known to be induced by relaxation of the template DNA. In this paper we report a deletion analysis of the gyrA and gyrB promoter regions. We find that a DNA sequence 20 base pairs long that includes the -10 consensus region, the transcription start point, and the first few transcribed bases is responsible for the property of induction by DNA relaxation. We propose a model for relaxation-stimulated transcription in which promoter clearance is the rate-limiting step.

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Selected References

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  1. Borowiec J. A., Gralla J. D. Supercoiling response of the lac ps promoter in vitro. J Mol Biol. 1985 Aug 20;184(4):587–598. doi: 10.1016/0022-2836(85)90305-5. [DOI] [PubMed] [Google Scholar]
  2. Buc H., McClure W. R. Kinetics of open complex formation between Escherichia coli RNA polymerase and the lac UV5 promoter. Evidence for a sequential mechanism involving three steps. Biochemistry. 1985 May 21;24(11):2712–2723. doi: 10.1021/bi00332a018. [DOI] [PubMed] [Google Scholar]
  3. Carpousis A. J., Gralla J. D. Cycling of ribonucleic acid polymerase to produce oligonucleotides during initiation in vitro at the lac UV5 promoter. Biochemistry. 1980 Jul 8;19(14):3245–3253. doi: 10.1021/bi00555a023. [DOI] [PubMed] [Google Scholar]
  4. Deuschle U., Kammerer W., Gentz R., Bujard H. Promoters of Escherichia coli: a hierarchy of in vivo strength indicates alternate structures. EMBO J. 1986 Nov;5(11):2987–2994. doi: 10.1002/j.1460-2075.1986.tb04596.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. DiLauro R., Taniguchi T., Musso R., de Crombrugghe B. Unusual location and function of the operator in the Escherichia coli galactose operon. Nature. 1979 Jun 7;279(5713):494–500. doi: 10.1038/279494a0. [DOI] [PubMed] [Google Scholar]
  6. Drlica K. Biology of bacterial deoxyribonucleic acid topoisomerases. Microbiol Rev. 1984 Dec;48(4):273–289. doi: 10.1128/mr.48.4.273-289.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Gellert M. DNA topoisomerases. Annu Rev Biochem. 1981;50:879–910. doi: 10.1146/annurev.bi.50.070181.004311. [DOI] [PubMed] [Google Scholar]
  8. Grayhack E. J., Yang X. J., Lau L. F., Roberts J. W. Phage lambda gene Q antiterminator recognizes RNA polymerase near the promoter and accelerates it through a pause site. Cell. 1985 Aug;42(1):259–269. doi: 10.1016/s0092-8674(85)80121-5. [DOI] [PubMed] [Google Scholar]
  9. Hansen U. M., McClure W. R. Role of the sigma subunit of Escherichia coli RNA polymerase in initiation. II. Release of sigma from ternary complexes. J Biol Chem. 1980 Oct 25;255(20):9564–9570. [PubMed] [Google Scholar]
  10. Hawley D. K., McClure W. R. Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res. 1983 Apr 25;11(8):2237–2255. doi: 10.1093/nar/11.8.2237. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Holmes D. S., Quigley M. A rapid boiling method for the preparation of bacterial plasmids. Anal Biochem. 1981 Jun;114(1):193–197. doi: 10.1016/0003-2697(81)90473-5. [DOI] [PubMed] [Google Scholar]
  12. Maquat L. E., Thornton K., Reznikoff W. S. lac Promoter mutations located downstream from the transcription start site. J Mol Biol. 1980 May 25;139(3):537–549. doi: 10.1016/0022-2836(80)90145-x. [DOI] [PubMed] [Google Scholar]
  13. Maxam A. M., Gilbert W. A new method for sequencing DNA. Proc Natl Acad Sci U S A. 1977 Feb;74(2):560–564. doi: 10.1073/pnas.74.2.560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. McClure W. R. Mechanism and control of transcription initiation in prokaryotes. Annu Rev Biochem. 1985;54:171–204. doi: 10.1146/annurev.bi.54.070185.001131. [DOI] [PubMed] [Google Scholar]
  15. McKenney K., Shimatake H., Court D., Schmeissner U., Brady C., Rosenberg M. A system to study promoter and terminator signals recognized by Escherichia coli RNA polymerase. Gene Amplif Anal. 1981;2:383–415. [PubMed] [Google Scholar]
  16. Menzel R., Gellert M. Fusions of the Escherichia coli gyrA and gyrB control regions to the galactokinase gene are inducible by coumermycin treatment. J Bacteriol. 1987 Mar;169(3):1272–1278. doi: 10.1128/jb.169.3.1272-1278.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Menzel R., Gellert M. Regulation of the genes for E. coli DNA gyrase: homeostatic control of DNA supercoiling. Cell. 1983 Aug;34(1):105–113. doi: 10.1016/0092-8674(83)90140-x. [DOI] [PubMed] [Google Scholar]
  18. 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]
  19. Munson L. M., Reznikoff W. S. Abortive initiation and long ribonucleic acid synthesis. Biochemistry. 1981 Apr 14;20(8):2081–2085. doi: 10.1021/bi00511a003. [DOI] [PubMed] [Google Scholar]
  20. Russell D. R., Auger E. A., Vermersch P. S., Bennett G. N. Role of DNA regions flanking the tryptophan promoter of Escherichia coli. I. Insertion of synthetic oligonucleotides. Gene. 1984 Dec;32(3):337–348. doi: 10.1016/0378-1119(84)90009-x. [DOI] [PubMed] [Google Scholar]
  21. Sanzey B. Modulation of gene expression by drugs affecting deoxyribonucleic acid gyrase. J Bacteriol. 1979 Apr;138(1):40–47. doi: 10.1128/jb.138.1.40-47.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Stefano J. E., Gralla J. D. Spacer mutations in the lac ps promoter. Proc Natl Acad Sci U S A. 1982 Feb;79(4):1069–1072. doi: 10.1073/pnas.79.4.1069. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Stefano J. E., Gralla J. Lac UV5 transcription in vitro. Rate limitation subsequent to formation of an RNA polymerase-DNA complex. Biochemistry. 1979 Mar 20;18(6):1063–1067. doi: 10.1021/bi00573a020. [DOI] [PubMed] [Google Scholar]
  24. Travers A. A., Burgessrr Cyclic re-use of the RNA polymerase sigma factor. Nature. 1969 May 10;222(5193):537–540. doi: 10.1038/222537a0. [DOI] [PubMed] [Google Scholar]
  25. Tse-Dinh Y. C., Wang J. C. Complete nucleotide sequence of the topA gene encoding Escherichia coli DNA topoisomerase I. J Mol Biol. 1986 Oct 5;191(3):321–331. doi: 10.1016/0022-2836(86)90129-4. [DOI] [PubMed] [Google Scholar]
  26. Wood D. C., Lebowitz J. Effect of supercoiling on the abortive initiation kinetics of the RNA-I promoter of ColE1 plasmid DNA. J Biol Chem. 1984 Sep 25;259(18):11184–11187. [PubMed] [Google Scholar]
  27. Youderian P., Bouvier S., Susskind M. M. Sequence determinants of promoter activity. Cell. 1982 Oct;30(3):843–853. doi: 10.1016/0092-8674(82)90289-6. [DOI] [PubMed] [Google Scholar]

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