Localized domains of DNA supercoiling: Topological coupling between promoters

Molecular Microbiology

Volumn 22, Issue 5, 1996, Pages 919-928

  Mojica, Francisco J M ^a   Higgins, Christopher F ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; DNA SUPERCOILING; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; TRANSCRIPTION REGULATION;

EID: 0029799816     PISSN: 0950382X     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2958.1996.01541.x     Document Type: Article

References (52)

1. Baker, T.A., and Kornberg, A. (1988) Transcriptional activation of initiation of replication from the E. coli chromosomal origin: an RNA-DNA hybrid near oriC. Cell 55: 113-123.
2. Bates, A.D., and Maxwell, A. (1993) DNA supercoiling. In DNA Topology. ('In Focus' Series). Rickwood, D. (ed.). Oxford: IRL Press, pp. 17-45.
3. Bolivar, F., Rodríguez, R.L., Betlach, M.C., and Boyer, H.W. (1977) Construction and characterization of new cloning vehicles. I. Ampicillin-resistant derivatives of the plasmid pMB9. Gene 2: 75-93.
4. Bowater, R.P., Chen, D., and Lilley, D.M.J. (1994) Elevated unconstrained supercoiling of plasmid DNA generated by transcription and translation of the tetracycline resistance gene in eubacteria. Biochemistry 33: 9266-9275.
5. Charbonnier, F., and Forterre, P. (1994) Comparison of plasmid DNA topology among mesophilic and thermophilic eubacteria and archaebacteria. J Bacteriol 176: 1251-1259.
6. Chen, D., Bowater, R., Dorman, C.J., and Lilley, D.M.J. (1992) Activity of a plasmid-borne leu-500 promoter depends on the transcription and translation of an adjacent gene. Proc Natl Acad Sci USA 89: 8784-8788.
7. Chen, D., Bowater, R.P., and Lilley, D.M.J. (1993) Activation of the leu-500 promoter: a topological domain generated by divergent transcription in a plasmid. Biochemistry 32: 13162-13170.
8. Chen, D., Bowater, R., and Lilley, D.M.J. (1994) Topological promoter coupling in Escherichia coli: Δtop/4-dependent activation of the leu-500 promoter on a plasmid. J Bacteriol 176: 3757-3764.
9. Cole, R.S. (1971) Inactivation of Escherichia coli, F′ episomes at transfer, and bacteriophage lambda by psoralen plus 360-nm light: significance of deoxyribonucleic acid cross-links. J Bacteriol 107: 846-852.
10. Cook, D.N., Armstrong, G.A., and Hearst, J.E. (1989) 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 171: 4836-4843.
11. Cook, D.N., Ma, D., Pon, N.G., and Hearst, J.E. (1992) Dynamics of DNA supercoiling by transcription in Escherichia coli. Proc Natl Acad Sci USA 89: 10603-10607.
12. DiNardo, S., Voelkel, K.A., Sternglanz, R., Reynolds, A.E., and Wright, A. (1982) Escherichia coli DNA topoisomerase I mutants have compensatory mutations in DNA gyrase genes. Cell 31: 43-51.
13. Dorman, C.J., Lynch, A.S., Ni Bhriain, N., and Higgins, C.F. (1989) DNA supercoiling in Escherichia coli: topA mutations can be suppressed by DNA amplifications involving the tolC locus. Mol Microbiol 3: 531-540.
14. Dower, W.J., Miller, J.F., and Ragsdale, C.W. (1988) High efficiency transformation of E. coli by high voltage electroporation. Nucl Acids Res 16: 6127-6145.
15. Drlica, K. (1992) Control of bacterial DNA supercoiling. Mol Microbiol 6: 425-433.
16. Dröge, P. (1993) Transcription-driven site-specific DNA recombination in vitro. Proc Natl Acad Sci USA 90: 2759-2763.
17. Drolet, M., and Lau, P.C.K. (1992) Mobilization protein-DNA binding and divergent transcription at the transfer origin of the Thiobacillus ferrooxidans pTF1 plasmid. Mol Microbiol 6: 1061-1071.
18. Dubnau, E., and Margolin, P. (1972) Suppression of promoter mutations by the pleiotropic supX mutations. Mol Gen Genet 117: 91-112.
19. Gemmill, R.M., Jones, J.W., Haughn, G.W., and Calvo, J.M. (1983) Transcription initiation sites of the leucine operons of Salmonella typhimurium and Escherichia coli. J Mol Biol 170: 39-59.
20. Hyde, J.E., and Hearst, J.E. (1978) Binding of psoralen derivatives to DNA and chromatin: influence of the ionic environment on dark binding and photoreactivity. Biochemistry 17: 1251-1257.
21. Jupe, E.R., Sinden, R.R., and Cartwright, I.L. (1993) Stably maintained microdomain of localized unrestrained supercoiling at a Drosophila heat shock gene locus. EMBO J 12: 1067-1075.
22. Kato, J., Nishimura, Y., Imamura, R., Niki, H., Hiraga, S., and Suzuki, H. (1990) New topoisomerase essential for chromosome segregation in E. coli. Cell 63: 393-404.
23. Koo, H.S., Wu, H.Y., and Liu, L.F. (1990) Effects of transcription and translation on gyrase-mediated DNA cleavage in Escherichia coli. J Biol Chem 265: 12300-12305.
24. Lilley, D.M., and Higgins, C.F. (1991) Local DNA topology and gene expression: the case of the leu-500 promoter. Mol Microbiol 5: 779-783.
25. Liu, L.F., and Wang, J.C. (1987) Supercoiling of the DNA template during transcription. Proc Natl Acad Sci USA 84: 7024-7027.
26. Ljungman, M., and Hanawalt, P.C. (1992) Localized torsional tension in the DNA of human cells. Proc Natl Acad Sci USA 89: 6055-6059.
27. Ljungman, M., and Hanawalt, P.C. (1995) Presence of negative torsional tension in the promoter region of the transcriptionally poised dihydrofolate reductase gene in vivo. Nucl Acids Res 23: 1782-1789.
28. Lodge, J.K., Kazic, T., and Berg, D.E. (1989) Formation of supercoiling domains in plasmid pBR322. J Bacteriol 171: 2181-2187.
29. Lynch, A.S., and Wang, J.C. (1993) 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 175: 1645-1655.
30. Miller, J.H. (1992) A Short Course in Bacterial Genetics. A Laboratory Manual and Handbook for Escherichia coli and Related Bacteria. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press.
31. Mojica, F.J.M., Charbonnier, F., Juez, G., RodríguezValera, F., and Forterre, P. (1994) Effects of salt and temperature on plasmid topology in the halophilic archaeon Haloferax volcanii. J Bacteriol 176: 4966-4973.
32. Ostrander, E.A., Kurkinen, N.A., and Hallick, L.M. (1988) DNA structural alterations in the SV40 enhancer region are retained in vivo. Virology 165: 274-277.
33. Pettijohn, D.E., and Pfenninger, O. (1980) Supercoils in prokaryotic DNA restrained in vivo. Proc Natl Acad Sci USA 77: 1331-1335.
34. Pruss, G.J., Manes, S.H., and Drlica, K. (1982) Escherichia coli DNA topoisomerase I mutants: increased supercoiling is corrected by mutations near gyrase genes. Cell 31: 35-42.
35. Rahmouni, A.R., and Wells, R.D. (1989) Stabilization of Z DNA in vivo by localized supercoiling. Science 246: 358-363.
36. Rahmouni, A.R., and Wells, R.D. (1992) Direct evidence for the effect of transcription on local DNA supercoiling in vivo. J Mol Biol 223: 131-144.
37. Raji, A., Zabel, D.J., Laufer, C.S., and Depew, R.E. (1985) Genetic analysis of mutations that compensate for loss of Escherichia coli DNA topoisomerase I. J Bacteriol 162: 1173-1179.
38. Reed, K.C., and Mann, D.A. (1985) Rapid transfer of DNA from agarose gels to nylon membranes. Nucl Acids Res 13: 7207-7221.
39. Richardson, J.P. (1991) Preventing the synthesis of unused transcripts by Rho factor. Cell 64: 1047-1049.
40. Richardson, S.M.H., Higgins, C.F., and Lilley, D.M.J. (1988) DNA supercoiling and the leu-500 promoter mutation of Salmonella typhimurium. EMBO J 7: 1863-1869.
41. Shi, Y.B., Spielmann, H.P., and Hearst, J.E. (1988) Base-catalysed reversal of a psoralen-DNA cross-link. Biochemistry 27: 5174-5178.
42. Sinden, R.R., Carlson, J.O., and Pettijohn, D.E. (1980) Torsional tension in the DNA double helix measured with trimethylpsoralen in living E coli cells: analogous measurements in insect and human cells. Cell 21: 773-783.
43. Sinden, R.R., and Ussery, D.W. (1992) Analysis of DNA structure in vivo using psoralen photobinding: measurement of supercoiling, topological domains, and DNA-protein interactions. Meth Enzymol 212: 319-335.
44. Spirito, F., Figueroa-Bossi, N., and Bossi, L. (1994) The relative contributions of transcription and translation to plasmid DNA supercoiling in Salmonella typhimurium. Mol Microbiol 11: 111-122.
45. Tan, J., Shu, L., and Wu, H.Y. (1994) Activation of the leu-500 promoter by adjacent transcription. J Bacteriol 176: 1077-1086.
46. Trucksis, M., and Depew, R.E. (1981) Identification and localization of a gene that specifies production of Escherichia coli DNA topoisomerase I. Proc Natl Acad Sci USA 78: 2164-2168.
47. Trucksis, M., Golub, E.I., Zabel, D.J., and Depew, R.E. (1981) Escherichia coli and Salmonella typhimurium supX genes specify deoxyribonucleic acid topoisomerase I. J Bacteriol 147: 679-681.
48. Wang, J.C. (1987) Recent studies of DNA topoisomerases. Biochim Biophys Acta 909: 1-9.
49. Wong, M.L., and Hsu, M.T. (1989) Linear adenovirus DNA is organized into supercoiled domains in virus particles. Nucl Acids Res 17: 3535-3550.
50. Wu, H.Y., Tan, J., and Fang, M. (1995) Long-range interaction between two promoters: activation of the leu-500 promoter by a distant upstream promoter. Cell 82: 445-451.
51. Yoakum, G.H., and Cole, R.S. (1978) Cross-linking and relaxation of supercoiled DNA by psoralen and light. Biochim Biophys Acta 521: 529-546.
52. Zheng, G., Kochel, T., Hoepfner, R.W., Timmons, S.E., and Sinden, R.R. (1991) Torsionally tuned cruciform and Z-DNA probes for measuring unrestrained supercoiling at specific sites in DNA of living cells. J Mol Biol 221: 107-122.