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. 1997 Jun;179(11):3528–3533. doi: 10.1128/jb.179.11.3528-3533.1997

In vivo supercoiling of plasmid and chromosomal DNA in an Escherichia coli hns mutant.

F J Mojica 1, C F Higgins 1
PMCID: PMC179144  PMID: 9171396

Abstract

We have used trimethylpsoralen to measure localized levels of unconstrained DNA supercoiling in vivo. The data provide direct evidence that plasmid and chromosomal DNA supercoiling is altered in vivo in an hns mutant. This increase in supercoiling is independent of transcription or changes in the activity of topoisomerase I. These data have implications for the mechanisms by which the chromatin-associated protein H-NS may influence chromosome organization and gene expression.

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Selected References

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  1. Bliska J. B., Cozzarelli N. R. Use of site-specific recombination as a probe of DNA structure and metabolism in vivo. J Mol Biol. 1987 Mar 20;194(2):205–218. doi: 10.1016/0022-2836(87)90369-x. [DOI] [PubMed] [Google Scholar]
  2. Chen D., Bowater R., Dorman C. J., Lilley D. M. Activity of a plasmid-borne leu-500 promoter depends on the transcription and translation of an adjacent gene. Proc Natl Acad Sci U S A. 1992 Sep 15;89(18):8784–8788. doi: 10.1073/pnas.89.18.8784. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Chen D., Bowater R., Lilley D. M. Topological promoter coupling in Escherichia coli: delta topA-dependent activation of the leu-500 promoter on a plasmid. J Bacteriol. 1994 Jun;176(12):3757–3764. doi: 10.1128/jb.176.12.3757-3764.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Cook D. N., Armstrong G. A., Hearst J. E. Induction of anaerobic gene expression in Rhodobacter capsulatus is not accompanied by a local change in chromosomal supercoiling as measured by a novel assay. J Bacteriol. 1989 Sep;171(9):4836–4843. doi: 10.1128/jb.171.9.4836-4843.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Dri A. M., Moreau P. L., Rouvière-Yaniv J. Role of the histone-like proteins OsmZ and HU in homologous recombination. Gene. 1992 Oct 12;120(1):11–16. doi: 10.1016/0378-1119(92)90003-8. [DOI] [PubMed] [Google Scholar]
  6. Drlica K. Control of bacterial DNA supercoiling. Mol Microbiol. 1992 Feb;6(4):425–433. doi: 10.1111/j.1365-2958.1992.tb01486.x. [DOI] [PubMed] [Google Scholar]
  7. Drlica K., Franco R. J., Steck T. R. Rifampin and rpoB mutations can alter DNA supercoiling in Escherichia coli. J Bacteriol. 1988 Oct;170(10):4983–4985. doi: 10.1128/jb.170.10.4983-4985.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Drlica K., Rouviere-Yaniv J. Histonelike proteins of bacteria. Microbiol Rev. 1987 Sep;51(3):301–319. doi: 10.1128/mr.51.3.301-319.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Göransson M., Sondén B., Nilsson P., Dagberg B., Forsman K., Emanuelsson K., Uhlin B. E. Transcriptional silencing and thermoregulation of gene expression in Escherichia coli. Nature. 1990 Apr 12;344(6267):682–685. doi: 10.1038/344682a0. [DOI] [PubMed] [Google Scholar]
  10. Higgins C. F., Dorman C. J., Stirling D. A., Waddell L., Booth I. R., May G., Bremer E. A physiological role for DNA supercoiling in the osmotic regulation of gene expression in S. typhimurium and E. coli. Cell. 1988 Feb 26;52(4):569–584. doi: 10.1016/0092-8674(88)90470-9. [DOI] [PubMed] [Google Scholar]
  11. Higgins C. F., Hinton J. C., Hulton C. S., Owen-Hughes T., Pavitt G. D., Seirafi A. Protein H1: a role for chromatin structure in the regulation of bacterial gene expression and virulence? Mol Microbiol. 1990 Dec;4(12):2007–2012. doi: 10.1111/j.1365-2958.1990.tb00559.x. [DOI] [PubMed] [Google Scholar]
  12. Hinton J. C., Santos D. S., Seirafi A., Hulton C. S., Pavitt G. D., Higgins C. F. Expression and mutational analysis of the nucleoid-associated protein H-NS of Salmonella typhimurium. Mol Microbiol. 1992 Aug;6(16):2327–2337. doi: 10.1111/j.1365-2958.1992.tb01408.x. [DOI] [PubMed] [Google Scholar]
  13. Hulton C. S., Seirafi A., Hinton J. C., Sidebotham J. M., Waddell L., Pavitt G. D., Owen-Hughes T., Spassky A., Buc H., Higgins C. F. Histone-like protein H1 (H-NS), DNA supercoiling, and gene expression in bacteria. Cell. 1990 Nov 2;63(3):631–642. doi: 10.1016/0092-8674(90)90458-q. [DOI] [PubMed] [Google Scholar]
  14. Jordi B. J., Owen-Hughes T. A., Hulton C. S., Higgins C. F. DNA twist, flexibility and transcription of the osmoregulated proU promoter of Salmonella typhimurium. EMBO J. 1995 Nov 15;14(22):5690–5700. doi: 10.1002/j.1460-2075.1995.tb00256.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Lejeune P., Danchin A. Mutations in the bglY gene increase the frequency of spontaneous deletions in Escherichia coli K-12. Proc Natl Acad Sci U S A. 1990 Jan;87(1):360–363. doi: 10.1073/pnas.87.1.360. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Lilley D. Bacterial chromatin. A new twist to an old story. Nature. 1986 Mar 6;320(6057):14–15. doi: 10.1038/320014a0. [DOI] [PubMed] [Google Scholar]
  17. Liu L. F., Wang J. C. Supercoiling of the DNA template during transcription. Proc Natl Acad Sci U S A. 1987 Oct;84(20):7024–7027. doi: 10.1073/pnas.84.20.7024. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Lodge J. K., Kazic T., Berg D. E. Formation of supercoiling domains in plasmid pBR322. J Bacteriol. 1989 Apr;171(4):2181–2187. doi: 10.1128/jb.171.4.2181-2187.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Lynch A. S., Wang J. C. Anchoring of DNA to the bacterial cytoplasmic membrane through cotranscriptional synthesis of polypeptides encoding membrane proteins or proteins for export: a mechanism of plasmid hypernegative supercoiling in mutants deficient in DNA topoisomerase I. J Bacteriol. 1993 Mar;175(6):1645–1655. doi: 10.1128/jb.175.6.1645-1655.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. May G., Dersch P., Haardt M., Middendorf A., Bremer E. The osmZ (bglY) gene encodes the DNA-binding protein H-NS (H1a), a component of the Escherichia coli K12 nucleoid. Mol Gen Genet. 1990 Oct;224(1):81–90. doi: 10.1007/BF00259454. [DOI] [PubMed] [Google Scholar]
  21. McLaren R. S., Newbury S. F., Dance G. S., Causton H. C., Higgins C. F. mRNA degradation by processive 3'-5' exoribonucleases in vitro and the implications for prokaryotic mRNA decay in vivo. J Mol Biol. 1991 Sep 5;221(1):81–95. [PubMed] [Google Scholar]
  22. Mojica F. J., Charbonnier F., Juez G., Rodríguez-Valera F., Forterre P. Effects of salt and temperature on plasmid topology in the halophilic archaeon Haloferax volcanii. J Bacteriol. 1994 Aug;176(16):4966–4973. doi: 10.1128/jb.176.16.4966-4973.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Mojica F. J., Higgins C. F. Localized domains of DNA supercoiling: topological coupling between promoters. Mol Microbiol. 1996 Dec;22(5):919–928. doi: 10.1046/j.1365-2958.1996.01541.x. [DOI] [PubMed] [Google Scholar]
  24. Ni Bhriain N., Dorman C. J., Higgins C. F. An overlap between osmotic and anaerobic stress responses: a potential role for DNA supercoiling in the coordinate regulation of gene expression. Mol Microbiol. 1989 Jul;3(7):933–942. doi: 10.1111/j.1365-2958.1989.tb00243.x. [DOI] [PubMed] [Google Scholar]
  25. Owen-Hughes T. A., Pavitt G. D., Santos D. S., Sidebotham J. M., Hulton C. S., Hinton J. C., Higgins C. F. The chromatin-associated protein H-NS interacts with curved DNA to influence DNA topology and gene expression. Cell. 1992 Oct 16;71(2):255–265. doi: 10.1016/0092-8674(92)90354-f. [DOI] [PubMed] [Google Scholar]
  26. Pavitt G. D., Higgins C. F. Chromosomal domains of supercoiling in Salmonella typhimurium. Mol Microbiol. 1993 Nov;10(3):685–696. doi: 10.1111/j.1365-2958.1993.tb00940.x. [DOI] [PubMed] [Google Scholar]
  27. Pruss G. J., Drlica K. DNA supercoiling and suppression of the leu-500 promoter mutation. J Bacteriol. 1985 Nov;164(2):947–949. doi: 10.1128/jb.164.2.947-949.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Pruss G. J., Drlica K. Topoisomerase I mutants: the gene on pBR322 that encodes resistance to tetracycline affects plasmid DNA supercoiling. Proc Natl Acad Sci U S A. 1986 Dec;83(23):8952–8956. doi: 10.1073/pnas.83.23.8952. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Pruss G. J., Manes S. H., Drlica K. Escherichia coli DNA topoisomerase I mutants: increased supercoiling is corrected by mutations near gyrase genes. Cell. 1982 Nov;31(1):35–42. doi: 10.1016/0092-8674(82)90402-0. [DOI] [PubMed] [Google Scholar]
  30. Py B., Higgins C. F., Krisch H. M., Carpousis A. J. A DEAD-box RNA helicase in the Escherichia coli RNA degradosome. Nature. 1996 May 9;381(6578):169–172. doi: 10.1038/381169a0. [DOI] [PubMed] [Google Scholar]
  31. Rahmouni A. R., Wells R. D. Stabilization of Z DNA in vivo by localized supercoiling. Science. 1989 Oct 20;246(4928):358–363. doi: 10.1126/science.2678475. [DOI] [PubMed] [Google Scholar]
  32. Raji A., Zabel D. J., Laufer C. S., Depew R. E. Genetic analysis of mutations that compensate for loss of Escherichia coli DNA topoisomerase I. J Bacteriol. 1985 Jun;162(3):1173–1179. doi: 10.1128/jb.162.3.1173-1179.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Reed K. C., Mann D. A. Rapid transfer of DNA from agarose gels to nylon membranes. Nucleic Acids Res. 1985 Oct 25;13(20):7207–7221. doi: 10.1093/nar/13.20.7207. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Richardson S. M., Higgins C. F., Lilley D. M. DNA supercoiling and the leu-500 promoter mutation of Salmonella typhimurium. EMBO J. 1988 Jun;7(6):1863–1869. doi: 10.1002/j.1460-2075.1988.tb03019.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Sinden R. R., Carlson J. O., Pettijohn D. E. Torsional tension in the DNA double helix measured with trimethylpsoralen in living E. coli cells: analogous measurements in insect and human cells. Cell. 1980 Oct;21(3):773–783. doi: 10.1016/0092-8674(80)90440-7. [DOI] [PubMed] [Google Scholar]
  36. Sinden R. R., Pettijohn D. E. Chromosomes in living Escherichia coli cells are segregated into domains of supercoiling. Proc Natl Acad Sci U S A. 1981 Jan;78(1):224–228. doi: 10.1073/pnas.78.1.224. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Sinden R. R., Ussery D. W. Analysis of DNA structure in vivo using psoralen photobinding: measurement of supercoiling, topological domains, and DNA-protein interactions. Methods Enzymol. 1992;212:319–335. doi: 10.1016/0076-6879(92)12020-q. [DOI] [PubMed] [Google Scholar]
  38. Stirling D. A., Hulton C. S., Waddell L., Park S. F., Stewart G. S., Booth I. R., Higgins C. F. Molecular characterization of the proU loci of Salmonella typhimurium and Escherichia coli encoding osmoregulated glycine betaine transport systems. Mol Microbiol. 1989 Aug;3(8):1025–1038. doi: 10.1111/j.1365-2958.1989.tb00253.x. [DOI] [PubMed] [Google Scholar]
  39. Tupper A. E., Owen-Hughes T. A., Ussery D. W., Santos D. S., Ferguson D. J., Sidebotham J. M., Hinton J. C., Higgins C. F. The chromatin-associated protein H-NS alters DNA topology in vitro. EMBO J. 1994 Jan 1;13(1):258–268. doi: 10.1002/j.1460-2075.1994.tb06256.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Worcel A., Burgi E. On the structure of the folded chromosome of Escherichia coli. J Mol Biol. 1972 Nov 14;71(2):127–147. doi: 10.1016/0022-2836(72)90342-7. [DOI] [PubMed] [Google Scholar]
  41. Yamada H., Yoshida T., Tanaka K., Sasakawa C., Mizuno T. Molecular analysis of the Escherichia coli hns gene encoding a DNA-binding protein, which preferentially recognizes curved DNA sequences. Mol Gen Genet. 1991 Nov;230(1-2):332–336. doi: 10.1007/BF00290685. [DOI] [PubMed] [Google Scholar]
  42. Zheng G. X., Kochel T., Hoepfner R. W., Timmons S. E., Sinden R. R. Torsionally tuned cruciform and Z-DNA probes for measuring unrestrained supercoiling at specific sites in DNA of living cells. J Mol Biol. 1991 Sep 5;221(1):107–122. doi: 10.1016/0022-2836(91)80208-c. [DOI] [PubMed] [Google Scholar]

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