DNA supercoiling and transcription: Topological coupling of promoters

Quarterly Reviews of Biophysics

Volumn 29, Issue 3, 1996, Pages 203-225

  Lilley, David M J ^a   Chen, Dongrong ^a   Bowater, Richard P ^a  

^a UNIVERSITY OF DUNDEE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA TOPOISOMERASE;

DNA SUPERCOILING; DNA TRANSCRIPTION; PLASMID; PRIORITY JOURNAL; PROMOTER REGION; REVIEW;

EID: 0029826454     PISSN: 00335835     EISSN: None     Source Type: Journal    
DOI: 10.1017/s0033583500005825     Document Type: Review

References (76)

1. ALLARD, J. D. & BERTRAND, K. P. (1992). Membrane topology of the pBR322 tetracycline resistance protein. J. Biol. Chem. 267, 17809-17819.
2. 5 sites of Escherichia coli. J. Molec. Biol. 195, 793-808.
3. BLISKA, J. B. & COZZARELLI, N. R. (1987). Use of site-specific recombination as a probe of DNA structure and function. J. Molec. Biol. 194, 205-218.
4. 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, 11495-11506.
5. 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, 9266-9275.
6. BOWATER, R. P., CHEN, D. & LILLEY, D. M. J. (1994b). Modulation of tyrT promoter activity by template supercoiling in vivo. EMBO J. 13, 5647-5655.
7. BRILL, S. J. & STERNGLANZ, R. (1988). Transcription-dependent DNA supercoiling in yeast DNA topoisomerase mutants. Cell 54, 403-411.
8. BROWN, P. O. & COZZARELLI, N. R. (1979). A sign inversion mechanism for enzymatic supercoiling of DNA. Science 206, 1081-1083.
9. 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, 143-146.
10. CHEN, D., BOWATER, R., DORMAN, C. & 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.
11. 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, 13162-13170.
12. 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. 176, 3757-3704.
13. 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, 10603-10607.
14. 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, 21-25.
15. DEPEW, R. E. & WANG, J. C. (1975). Conformational fluctuations of DNA helix. Proc. Natl. Acad. Sci. USA 72, 4275-4279.
16. 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, 2987-2994.
17. 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, 43-51.
18. DRÖGE, P. & NORDHEIM, A. (1991). Transcription-induced conformational change in a topologically closed DNA domain. Nucleic Acids Res. 19, 2941-2946.
19. DUBNAU, E. & MARGOLIN, P. (1972). Suppression of promoter mutations by the pleiotropic supX mutations. Mol. Gen. Genet. 117, 91-112.
20. 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, 11663-11670.
21. ENGLE, E. C., MANES, S. H. & DRLICA, K. (1982). Differential effects of antibiotics inhibiting gyrase. J. Bacteriol. 149, 92-98.
22. FULLER, F. B. (1971). The writhing number of a space curve. Proc. Natl. Acad Sci, USA 68, 815-819.
23. 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, 3872-3876.
24. 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, 35-40.
25. 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, 948-953.
26. 34 sequence from a Xenopus globin gene. J. Molec. Biol. 185, 461-478.
27. 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, 1113-1117.
28. 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, 1773-1777.
29. 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, 75-91.
30. JAVOR, G, T. (1974). Inhibition of ribonucleic acid synthesis by nalidixic acid in Escherichia coli. J. Bacteriol. 120, 282-286.
31. KANO, Y., MIYASHITA, T., NAKAMURA, H., KUROKI, K., NAGATA, A. & IMAMOTO, F. (1981). In vivo correlation between DNA supercoiling and transcription. Gene 13, 173-184.
32. 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, 3811-3820.
33. KOSHLAND, D. & BOTSTEIN, D. (1982). Evidence for posttranslational translocation of β-lactamase across the bacterial inner membrane. Cell 30, 893-902.
34. 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, 9464-9468.
35. KREUZER, K. N. & COZZARELLI, N. R. (1980). Formation and resolution of DNA catenanes by DNA gyrase. Cell 20, 245-254.
36. LAMOND, A. I. (1985). Supercoiling response of a bacterial tRNA gene. EMBO J. 4, 501-507.
37. LEE, F. S. & BAUER, W. R. (1985). Temperature-dependence of the gel electrophoretic mobility of superhelical DNA. Nucleic Acids Res. 13, 1665-1682.
38. LILLEY, D. M. J. (1980). The inverted repeat as a recognisable structural feature in supercoiled DNA molecules. Proc. Natl. Acad. Sci. USA 77, 6468-6472.
39. 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, 697-707.
40. LIU, L. F. & WANG, J. C. (1987). Supercoilmg of the DNA template during transcription. Proc. Natl. Acad. Sci. USA 84, 7024-7027.
41. 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, 2999-3017.
42. LODGE, J. K., KAZIK, T. & BERG, D. E. (1989). Formation of supercoiling domains in plasmid pBR322. J. Bacteriol. 171, 2181-2187.
43. LYAMICHEV, V., MIRKIN, S. M. & FRANK-KAMENETSKII, M. D. (1986). Structures of homopurine-homopyrimidine tract in superhelical DNA. J. Biomol. Struc. & Dynamics 3, 667-669.
44. 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, 1645-1655.
45. MARGOLIN, P., ZUMSTEIN, L., STERNGLANZ, R. & WANG, J. G. (1985). The Escherichia coli supX locus is topA, the structural gene for DNA topoisomerase I. Proc. Natl. Acad. Sci. USA 82, 5437-5441.
46. 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, 8373-8377.
47. MCCLELLAN, J. A. & LELLEY, D. M. J. (1991). Structural alteration in alternating adenine-thymine sequences in positively supercoiled DNA. J. Molec. Biol. 219, 145-149.
48. MENZEL, R. & GELLERT, M. (1983). Regulation of the genes for E. coli DNA gyrase: homeostatic control of DNA supercoiling. Cell 34, 105-113.
49. 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, 5960-5963.
50. MUKAI, F. H. & MARGOLIN, P. (1963). Analysis of unlinked suppressors of a 0° mutation in Salmonella. Proc. Natl. Acad. Sci. USA 50, 140-148.
51. 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, 1261-1265.
52. PANAYOTATOS, N. & WELLS, R. D. (1981). Cruciform structures in supercoiled DNA. Nature 289, 466-470.
53. n DNA sequences from right- to left-handed helical structure by salt, Co(III), or negative supercoiling. Proc. Natl. Acad. Sci. USA 79, 4560-4564.
54. PRUSS, G. (1985). DNA topoisomerase I mutants. Increased heterogeneity in linking number and other replicon-dependent changes in DNA supercoiling. J. Molec. Biol. 185, 51-63.
55. PRUSS, G. & DRLICA, K. (1985). DNA supercoiling and suppression of the leu-500 promoter mutation. J. Bacteriol. 164, 947-949.
56. 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, 8952-8956.
57. PRUSS, G. J. & DRLICA, K. (1989). DNA supercoiling and prokaryotic transcription. Cell 56, 531-523.
58. 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, 35-42.
59. 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, 4280-4284.
60. RAHMOUNI, A. R. & WELLS, R. D. (1989). Stabilization of Z-DNA in vivo by localized supercoiling. Science 246, 358-363.
61. RAHMOUNI, A. R. & WELLS, R. D. (1992). Direct evidence for the effect of transcription on local DNA supercoiling in vivo. J. Molec. Biol. 223, 131-144.
62. RICHARDSON, S. M. H., HIGGINS, C. F. & LILLEY, D. M. J. (1984). The genetic control of DNA supercoiling in Salmonella typhimurium. EMBO J. 3, 1745-1752.
63. RICHARDSON, S. M. H., HIGGINS, C. F. & LILLEY, D. M. J. (1988). DNA supercoiling and the leu-500 mutation of Salmonella typhimurium. EMBO J. 7, 1863-1869.
64. SANZEY, B. (1979). Modulation of gene expression by drugs affecting deoxyribonucleic acid gyrase. J. Bacteriol. 138, 40-47.
65. 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, 312-316.
66. SMITH, G. R. (1981). DNA supercoiling: another level for regulating gene expression. Cell 24, 599-600.
67. SUGINO, A. & COZZARELLI, N. R. (1980). The intrinsic ATPase of DNA gyrase. J. Biol. Chem. 255, 6299-6306.
68. TRUCKSIS, M., GOLUB, E. I., ZABEL, D. J. & DEPEW, R. E. (1981). Escherichia coli and Salmonella typhimurium supX genes specify deoxyribonucleic acid topoisomeraseI. J. Bacteriol. 147, 679-681.
69. TSAO, Y.-P., WU, H.-Y. & LIU, L. F. (1989). Transcription-dependent supercoiling of DNA: direct biochemical evidence from in vitro studies. Cell 56, 111-118.
70. 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, 5560-5565.
71. TSE-DINH, Y. (1985). Regulation of the Escherichia coli DNA topoiosmerase I gene by DNA supercoiling. Nucleic Acids Res. 13, 4751-4763.
72. 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, 735-742.
73. WANG, J. C. (1971). The interaction between DNA and and Escherichia coli protein ω. J. Molec. Biol. 55, 523-533.
74. 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, 85-91.
75. WU, H.-Y., SHYY, S., WANG, J. C. & LIU, L. F. (1988). Transcription generates positively and negatively supercoiled domains in the template. Cell 53, 433-440.
76. ZACHASIAS, 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, 7069-7073.