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DNA supercoiling and transcription: topological coupling of promoters

Published online by Cambridge University Press:  17 March 2009

David M. J. Lilley
Affiliation:
CRC Nucleic Acid Structure Research Group, Department of Biochemistry, University of Dundee, Dundee DDt 4HN, UK
Dongrong Chen
Affiliation:
CRC Nucleic Acid Structure Research Group, Department of Biochemistry, University of Dundee, Dundee DDt 4HN, UK
Richard P. Bowater
Affiliation:
CRC Nucleic Acid Structure Research Group, Department of Biochemistry, University of Dundee, Dundee DDt 4HN, UK

Extract

DNA supercoiling is a consequence of the double-stranded nature of DNA. When a linear DNA molecule is ligated into a covalently closed circle, the two strands become intertwined like the links of a chain, and will remain so unless one of the strands is broken. The number of times one strand is linked with the other is described by a fundamental property of DNA supercoiling, the linking number (Lk).

Type
Research Article
Copyright
Copyright © Cambridge University Press 1996

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References

Allard, J. D. & Bertrand, K. P. (1992). Membrane topology of the PBR322 tetracycline resistance protein. J. Biol. Chem. 267, 1780917819.CrossRefGoogle ScholarPubMed
Amouyal, M. & Buc, H. (1987). Topological unwinding of strong and weak promoters by RNA polymerase. A comparison between the lac wild-type and the UV5 sites of Escherichia colt. J. Molec. Biol. 195, 795808.CrossRefGoogle Scholar
Bliska, J. B. & Cozzarelli, N. R. (1987). Use of site-specific recombination as a probe of DNA structure and function. J. Molec. Biol. 194, 205218.CrossRefGoogle Scholar
Bowater, R., Aboul-Ela, F. & Lilley, D. M. J. (1991). Large-scale stable opening of supercoiled DNA in response to temperature and supercoiling in A + T rich regions that promote low-salt cruciform extrusion. Biochemistry 30, 1149511506.CrossRefGoogle Scholar
Bowater, R. P., Chen, D. & Lilley, D. M. J. (1994a). Elevated unconstrained supercoiling of plasmid DNA generated by transcription and translation of the tetracycline resistance gene in eubacteria. Biochemistry 33, 92669275.CrossRefGoogle ScholarPubMed
Bowater, R. P., Chen, D. & Lilley, D. M. J. (1994b). Modulation of tyrT promoter activity by template supercoiling in vivo. EMBO J. 13, 56475655.CrossRefGoogle ScholarPubMed
Brill, S. J. & Sternglanz, R. (1988). Transcription-dependent DNA supercoiling in yeast DNA topoisomerase mutants. Cell 54, 403411.CrossRefGoogle ScholarPubMed
Brown, P. O. & Cozzarelli, N. R. (1979). A sign inversion mechanism for enzymatic supercoiling of DNA. Science 206, 10811083.CrossRefGoogle ScholarPubMed
Champoux, J. J. & Dulbecco, R. (1972). An activity from mammalian cells that untwists superhelical DNA – A possible swivel for DNA replication. Proc. Natl. Acad. Sci. USA 69, 143146.CrossRefGoogle ScholarPubMed
Chen, D., Bowater, R., Dorman, C. & Lilley, D. M. J. (1992). Activity of a plasmidborne leu-500 promoter depends on the transcription and translation of an adjacent gene. Proc. Natl. Acad. Sci. USA 89, 87848788.CrossRefGoogle ScholarPubMed
Chen, D., Bowater, R. & Lilley, D. M. J. (1993). Activation of the leu-500 promoter: A topological domain generated by divergent transcription in a plasmid. Biochemistry 32, 1316213170.CrossRefGoogle ScholarPubMed
Chen, D., Bowater, R. & Lilley, D. M. J. (1994). Topological promoter coupling in Escherichia coli: δtopA-dependent activation of the leu-500 promoter on a plasmid. J. Bacteriol. 76, 37573764.CrossRefGoogle Scholar
Cook, D. N., Ma, D., Pon, N. G. & Hearst, J. E. (1992). Dynamics of DNA supercoiling by transcription in Escherichia-coli. Proc Natl Acad Sci USA 89, 1060310607.CrossRefGoogle ScholarPubMed
De Boer, H. A., Comstock, L. J. & Vasser, M. (1983). The tac promoter: a functional hybrid derived from the trp and lac promoters. Proc. Natl. Acad. Sci. USA 80, 2125.CrossRefGoogle ScholarPubMed
Depew, R. E. & Wang, J. C. (1975). Conformational fluctuations of DNA helix. Proc. Natl. Acad. Sci. USA 72, 42754279.CrossRefGoogle ScholarPubMed
Deuschle, U., Kammerer, W., Gentz, R. & Bujard, H. (1986). Promoters of Escherichia coli: a hierarchy of in vivo strength indicates alternate structures. EMBO J. 5, 29872994.CrossRefGoogle ScholarPubMed
Di Nardo, S., Voelkel, K. A., Sternglanz, R., Reynolds, A. E. & Wright, A. (1982). Escherichia coli DNA topoisomerase I mutants have compensatory mutations in DNA gyrase genes. Cell 31, 4351.CrossRefGoogle ScholarPubMed
Dröge, P. & Nordheim, A. (1991). Transcription-induced conformational change in a topologically closed DNA domain. Nucleic Acids Res. 19, 29412946.CrossRefGoogle Scholar
Dubnau, E. & Margolin, P. (1972). Suppression of promoter mutations by the pleiotropic supX mutations. Mol. Gen. Genet. 117, 91112.CrossRefGoogle ScholarPubMed
Eckert, B. & Beck, C. F. (1989). Topology of the transposon Tn10-encoded tetracycline resistance protein within the inner membrane of Escherichia coli. J. Biol. Chem. 264, 1166311670.CrossRefGoogle ScholarPubMed
Engle, E. C., Manes, S. H. & Drlica, K. (1982). Differential effects of antibiotics inhibiting gyrase. J. Bacteriol. 149, 9298.CrossRefGoogle ScholarPubMed
Fuller, F. B. (1971). The writhing number of a space curve. Proc. Natl. Acad Sci, USA 68, 815819.CrossRefGoogle ScholarPubMed
Gellert, M., Mizuuchi, K., O'Dea, M. H. & Nash, H. A. (1976). DNA gyrase: An enzyme that introduces superhelical turns into DNA. Proc. Natl. Acad. Sci. USA 73, 38723876.CrossRefGoogle ScholarPubMed
Gellert, M., Mizuuchi, K., O'Dea, M. H., Ohmori, H. & Tomizawa, J. (1979). DNA gyrase and DNA supercoiling. Cold Spring Harbor Symp. Quant. Biol. 43, 3540.CrossRefGoogle ScholarPubMed
Gemmill, R. M., Tripp, M., Friedman, S. B. & Calvo, J. M. (1984). Promoter mutation causing catabolite repression of the Salmonella typhimurium leucine operon. J. Bacteriol. 158, 948953.CrossRefGoogle ScholarPubMed
Greaves, D. R., Patient, R. K. & Lilley, D. M. J. (1985). Facile cruciform formation by an (A – T)34 sequence from a Xenopus globin gene. J. Molec. Biol. 185, 461478.CrossRefGoogle Scholar
Haughn, G. W., Wessler, S. R., Gemmill, R. M. & Calvo, J. M. (1986). High A + T content conserved in DNA sequences upstream of leuABCD in Escherichia coli and Salmonella typhimurium. J. Bacteriol. 166, 11131117.CrossRefGoogle Scholar
Higgins, N. P., Peebles, C. I., Sugino, A. & Cozzarelli, N. R. (1978). Purification of the subunits of Escherichia coli DNA gyrase and the reconstitution of its enzymatic activity. Proc. Natl. Acad. Sci. USA 75, 17731777.CrossRefGoogle ScholarPubMed
Horowitz, D. S. & Wang, J. C. (1984). Torsional rigidity of DNA and length dependence of the free energy of DNA supercoiling. J. Molec. Biol. 173, 7591.CrossRefGoogle ScholarPubMed
Javor, G. T. (1974). Inhibition of ribonucleic acid synthesis by nalidixic acid in Escherichia coli. J. Bacteriol. 120, 282286.CrossRefGoogle ScholarPubMed
Kano, Y., Miyashita, T., Nakamura, H., Kuroki, K., Nagata, A. & Imamoto, F. (1981). In vivo correlation between DNA supercoiling and transcription. Gene 13, 173184.Google ScholarPubMed
Kirkegaard, K. & Wang, J. C. (1978). Escherichia coli DNA topoisomerase I catalyzed linking of single-stranded rings of complementary base sequences. Nucleic Acids Res. 5, 38113820.CrossRefGoogle ScholarPubMed
Koshland, D. & Botstein, D. (1982). Evidence for posttranslational translocation of β-lactamase across the bacterial inner membrane. Cell 30, 893902.CrossRefGoogle ScholarPubMed
Kowalski, D., Natale, D. A. & Eddy, M. J. (1988). Stable DNA unwinding, not ‘breathing’, accounts for single-strand-specific nuclease hypersensitivity of specific A + T rich sequences. Proc. Natl. Acad. Sci. USA 85, 94649468.CrossRefGoogle Scholar
Kreuzer, K. N. & Cozzarelli, N. R. (1980). Formation and resolution of DNA catenanes by DNA gyrase. Cell 20, 245254.CrossRefGoogle ScholarPubMed
Lamond, A. I. (1985). Supercoiling response of a bacterial †RNA gene. EMBO J. 4, 501507.CrossRefGoogle Scholar
Lee, F. S. & Bauer, W. R. (1985). Temperature-dependence of the gel electrophoretic mobility of superhelical DNA. Nucleic Acids Res. 13, 16651682.CrossRefGoogle ScholarPubMed
Lilley, D. M. J. (1980). The inverted repeat as a recognisable structural feature in supercoiled DNA molecules. Proc. Natl. Acad. Sci. USA 77, 64686472.CrossRefGoogle Scholar
Liu, L. F., Liu, C. C. & Alberts, B. M. (1980). Type II DNA topoisomerases: Enzymes that can unknot a topologically knotted DNA molecule via a reversible double-strand break. Cell 19, 697707.CrossRefGoogle Scholar
Liu, L. F. & Wang, J. C. (1987). Supercoiling of the DNA template during transcription. Proc. Natl. Acad. Sci. USA 84, 70247027.CrossRefGoogle ScholarPubMed
Lockshon, D. & Morris, D. R. (1983). Positively supercoiled plasmid DNA is produced by treatment of Escherichia coli with DNA gyrase inhibitors. Nucleic Acids Res. 11, 29993017.CrossRefGoogle ScholarPubMed
Lodge, J. K., Kazik, T. & Berg, D. E. (1989). Formation of supercoiling domains in plasmid pBR.322. J. Bacteriol. 171, 21812187.CrossRefGoogle Scholar
Lyamichev, V., Mirkin, S. M. & Frank-Kamenetskii, M. D. (1986). Structures of homopurine-homopyrimidine tract in superhelical DNA. J. Biomol. Struc. & Dynamics 3, 667669.CrossRefGoogle ScholarPubMed
Lynch, A. S. & 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, 16451655.CrossRefGoogle ScholarPubMed
Margolin, P., Zumstein, L., Sternglanz, R. & Wang, J. C. (1985). The Escherichia coli supX locus is top A, the structural gene for DNA topoisomerase I. Proc. Natl. Acad. Sci. USA 82, 54375441.CrossRefGoogle Scholar
McClellan, J. A., Boublikova, P., Palecek, E. & Lilley, D. M. J. (1990). Superhelical torsion in cellular DNA responds directly to environmental and genetic factors. Proc. Natl. Acad. Sci. USA 87, 83738377.CrossRefGoogle ScholarPubMed
McClellan, J. A. & Lilley, D. M. J. (1991). Structural alteration in alternating adenine-thymine sequences in positively supercoiled DNA. J. Molec. Biol. 219, 145149.CrossRefGoogle ScholarPubMed
Menzel, R. & Gellert, M. (1983). Regulation of the genes for E. coli DNA gyrase: homeostatic control of DNA supercoiling. Cell 34, 105113.CrossRefGoogle ScholarPubMed
Mizuuchi, K., O'Dea, M. H. & Gellert, M. (1978). DNA gyrase: Subunit structure and ATPase activity of the purified enzyme. Proc. Natl. Acad. Sci. USA 75, 59605963.CrossRefGoogle ScholarPubMed
Mukai, F. H. & Margolin, P. (1963). Analysis of unlinked suppressors of a o° mutation in Salmonella. Proc. Natl. Acad. Sci. USA 50, 140148.CrossRefGoogle Scholar
Ostrander, E. A., Benedetti, P. & Wang, J. C. (1990). Template supercoiling by a chimera of yeast GAL4 protein and phage T7 RNA polymerase. Science 249, 12611265.CrossRefGoogle ScholarPubMed
Panayotatos, N. & Wells, R. D. (1981). Cruciform structures in supercoiled DNA. Nature 289, 466470.CrossRefGoogle ScholarPubMed
Peck, L. J., Nordheim, A., Rich, A. & Wang, J. C. (1982). Flipping of cloned d(pCpG)n.d(pCpG)n DNA sequences from right- to left-handed helical structure by salt, Co(III), or negative supercoiling. Proc. Natl. Acad. Sci. USA 79, 45604564.CrossRefGoogle ScholarPubMed
Pruss, G. (1985). DNA topoisomerase I mutants. Increased heterogeneity in linking number and other replicon-dependent changes in DNA supercoiling. J. Molec. Biol. 185, 5163.CrossRefGoogle ScholarPubMed
Pruss, G. & Drlica, K. (1985). DNA supercoiling and suppression of the leu-500 promoter mutation. J. Bacteriol. 164, 947949.CrossRefGoogle ScholarPubMed
Pruss, G. J. & Drlica, K. (1986). Topoisomerase I mutants; the gene on PBR322 that encodes resistance to tetracycline affects plasmid DNA supercoiling. Proc. Natl. Acad. Sci. USA 83, 89528956.CrossRefGoogle ScholarPubMed
Pruss, G. J. & Drlica, K. (1989). DNA supercoiling and prokaryotic transcription. Cell 56, 521523.CrossRefGoogle ScholarPubMed
Pruss, G. J., Manes, S. H. & Drlica, K. (1982). Escherichia coli DNA topoisomerase I mutants: increased supercoiling is corrected by mutations near the gyrase genes. Cell 31, 3542.CrossRefGoogle ScholarPubMed
Pulleyblank, D. E., Shure, M., Tang, D., Vinograd, J. & Vosberg, H.-P. (1975). Action of nicking-closing enzyme on supercoiled and nonsupercoiled closed circular DNA: Formation of a Boltzmann distribution of topological isomers. Proc. Natl. Acad. Sci. USA 72, 42804284.CrossRefGoogle ScholarPubMed
Rahmouni, A. R. & Wells, R. D. (1989). Stabilization of Z-DNA in vivo by localized supercoiling. Science 246, 358363.CrossRefGoogle ScholarPubMed
Rahmouni, A. R. & Wells, R. D. (1992). Direct evidence for the effect of transcription on local DNA supercoiling in vivo. J. Molec. Biol. 223, 131144.CrossRefGoogle ScholarPubMed
Richardson, S. M. H., Higgins, C. F. & Lilley, D. M. J. (1984). The genetic control of DNA supercoiling in Salmonella typhimurium. EMBO J. 3, 17451752.CrossRefGoogle ScholarPubMed
Richardson, S. M. H., Higgins, C. F. & Lilley, D. M. J. (1988). DNA supercoiling and the leu-500 mutation of Salmonella typhimurium. EMBO J. 3, 18631869.CrossRefGoogle Scholar
Sanzey, B. (1979). Modulation of gene expression by drugs affecting deoxyribonucleic acid gyrase. J. Bacteriol. 138, 4047.CrossRefGoogle ScholarPubMed
Singleton, C. K., Klysik, J., Stirdivant, S. M. & Wells, R. D. (1982). Left-handed Z-DNA is induced by supercoiling in physiological ionic conditions. Nature 299, 312316.CrossRefGoogle ScholarPubMed
Smith, G. R. (1981). DNA supercoiling: another level for regulating gene expression. Cell 24, 599600.CrossRefGoogle ScholarPubMed
Sugino, A. & Cozzarelli, N. R. (1980). The intrinsic ATPase of DNA gyrase. J. Biol. Chem. 255, 62996306.CrossRefGoogle ScholarPubMed
Trucksis, M., Golub, E. I., Zabel, D. J. & Depew, R. E. (1981). Escherichia coli and Salmonella typhimurium supX genes specify deoxyribonucleic acid topoisomerase I. J. Bacteriol. 147, 679681.CrossRefGoogle ScholarPubMed
Tsao, Y.-P., Wu, H.-Y. & Liu, L. F. (1989). Transcription-dependent supercoiling of DNA: direct biochemical evidence from in vitro studies. Cell 56, 111118.CrossRefGoogle Scholar
Tse, Y.-C., Kirkegaard, K. & Wang, J. C. (1980). Covalent bonds between protein and DNA. Formation of a phosphotyrosine linkage between certain DNA topoisomerases and DNA. J. Biol. Chem. 255, 55605565.CrossRefGoogle ScholarPubMed
Tse-Dinh, Y. (1985). Regulation of the Escherichia coli DNA topoiosmerase I gene by DNA supercoiling. Nucleic Acids Res. 13, 47514763.CrossRefGoogle Scholar
Tse-Dinh, Y.-C. & Beran, R. K. (1988). Multiple promoters for transcription of the Escherichia coli DNA topoisomerase I gene and their regulation by DNA supercoiling. J. Molec. Biol. 202, 735742.CrossRefGoogle ScholarPubMed
Wang, J. C. (1971). The interaction between DNA and and Escherichia coli protein ω. J. Molec. Biol. 55, 523533.CrossRefGoogle ScholarPubMed
Wang, J. C., Peck, L. J. & Becherer, K. (1983). DNA supercoiling and its effects on DNA structure and function. Cold Spring Harbor Symp. Quant. Biol. 47, 8591.CrossRefGoogle ScholarPubMed
Wu, H.-Y., Shyy, S., Wang, J. C. & Liu, L. F. (1988). Transcription generates positively and negatively supercoiled domains in the template. Cell 53, 433440.CrossRefGoogle ScholarPubMed
Zacharias, W., Jaworski, A., Larson, J. E. & Wells, R. D. (1988). The B-to Z-DNA equilibrium in vivo is perturbed by biological processes. Proc. Natl. Acad. Sci. USA 85, 70697073.CrossRefGoogle ScholarPubMed