Advertisement

Effects of DNA Supercoiling on Gene Expression

  • James C. Wang
  • A. Simon Lynch

Abstract

It is well known that open complex formation between promoters and RNA polymerase is thermodynamically favored by negative su-percoiling of the DNA template. The effects of template supercoiling on the kinetics of transcription are, however, much more complex even in simple cases involving no regulatory factors; a priori predictions of such effects are at best tenuous. In this chapter, we focus on insights gained from experimental data accumulated in the past two decades on how template supercoiling and transcription affect each other. We begin with a review of the historical link between DNA supercoiling and transcription. This introduction is followed by a brief account of how gene expression is affected upon decreasing the cellular level of gyrase, a DNA topoisomerase that negatively supercoils DNA, or DNA topoisomerase I, an enzyme that specifically relaxes negatively super-coiled DNA. Mechanistic considerations are then presented for several cases of increasing complexity: from the simplest case in which the rate of transcription is determined by that of open complex formation between RNA polymerase and promoter, to cases involving regulatory and auxiliary DNA binding proteins, and finally to cases in which the rate of transcription is determined by a step that occurs after open complex formation.

Keywords

cAMP Receptor Protein Integration Host Factor Catabolite Activator Protein Open Complex Formation Gyrase Gene 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Hayashi M. A DNA-RNA complex as an intermediate of in vitro genetic transcription. Proc Natl Acad Sci USA 1965 54:1736–1743.Google Scholar
  2. 2.
    Vinograd J, Lebowitz J, R. Radloff et al. The twisted circular form of polyoma viral DNA. Proc Natl Acad Sci USA 1965; 53:1104–1111.Google Scholar
  3. 3.
    Hayashi Y, Hayashi M. Template activities of the fX-174 replicative allo-morphic deoxyribonucleic acids. Biochemistry 1971;10:4212–4218.Google Scholar
  4. 4.
    Walter G, Zillig W, Palm P et al. Initiation of DNA-dependent RNA synthesis and the effect of heparin on RNA polymerase. Eur J Biochem 1967; 3:194–201.Google Scholar
  5. 5.
    Chamberlin MJ. The selectivity of transcription. Annu Rev Chem 1974; 43:721–745.Google Scholar
  6. 6.
    Saucier J-M, Wang JC. Angular alteration of the DNA helix by E. coli RNA polymerase. Nature New Biology 1972; 239:167–170.Google Scholar
  7. 7.
    Wang JC, Jacobsen JH, Saucier J-M. Physicochemical studies on interactions between DNA and RNA polymerase. Unwinding of the DNA helix by Escherichia coli RNA polymerase. Nucl Acids Res. 1977; 4:1225–1241.Google Scholar
  8. 8.
    Mirkin SM, Bogdanova ES, Gorlenko ZM et al. DNA supercoiling and transcription in Escherichia coli: Influence of RNA polymerase mutations. Molec Gen Genet 1979; 177:169–175.Google Scholar
  9. 9.
    Gamper HB, Hearst JE. A topological model of transcription based on unwinding angle analysis of E. coli RNA polymerase binary, initiation and ternary complexes. Cell 1982; 29:81–90.Google Scholar
  10. 10.
    Amouyal M, Buc H. Topological unwinding of strong and weak promoters by RNA polymerase. J Mol Biol 1987; 195:795–808.Google Scholar
  11. 11.
    Hsieh T-S, Wang JC. Physicochemical studies on interactions between DNA and RNA polymerase. Ultraviolet absorption measurements. Nucl Acids Res 1978 5:3337–45.Google Scholar
  12. 12.
    Melnikova A, Beakealashvilli R, Mirzabekov AD. A study of unwinding of DNA and shielding of the DNA grooves by RNA polymerase by using methylation with dimethylsulfate. Eur J Biochem 1978; 84:301–9.Google Scholar
  13. 13.
    Siebenlist U. RNA polymerase unwinds an 11-base pair segment of a phage T7 promoter. Nature 1979; 279:651–2.Google Scholar
  14. 14.
    Kirkegaard K, Buc H, Spassky A et al. Mapping of single-stranded regions in duplex DNA at the sequence level: Single-stranded specific cy-tosine methylation in RNA polymerase-promoter complexes. Proc Natl Acad Sci USA 1983; 80:2544–48.Google Scholar
  15. 15.
    Sasse-Dwight S, Gralla JD. KMnO4 as a probe for lac promoter DNA melting and mechanism in vivo. J Biol Chem 1989; 264:8074–81.Google Scholar
  16. 16.
    Bauer W, Vinograd J. Interaction of closed circular DNA with intercalative dyes. II. The free energy of superhelix formation in SV40 DNA. J Mol Biol 1970; 47:419–35.Google Scholar
  17. 17.
    Davidson N. Effect of DNA length on the free energy of binding of an unwinding ligand to a superhelical DNA. J Mol Biol 1972; 66:307–9.Google Scholar
  18. 18.
    Wang JC, Barkley MD, Bourgeois S. Measurements of unwinding of lac operator by repressor. Nature 1974; 251:247.Google Scholar
  19. 19.
    Hsieh T-S, Wang JC. Thermodynamic properties of superhelical DNAs. Biochemistry 1975; 14:527–35.Google Scholar
  20. 20.
    Botchan P, Wang JC, Echols H. Effect of circularity and superhelicity on transcription from bacteriophage ? DNA. Proc Natl Acad Sci USA 1973; 70:3077–81.Google Scholar
  21. 21.
    Wang JC. Interactions between twisted DNAs and enzymes: The effects of superhelical turns. J Mol Biol 1974; 87:797–816.Google Scholar
  22. 22.
    Richardson JP. Effects of supercoiling on transcription from bacteriophage PM2 deoxyribonucleic acid. Biochemistry 1974; 13:3164–9.Google Scholar
  23. 23.
    Richardson JP. Initiation of transcription by Escherichia coli RNA polymerase from supercoiled and nonsupercoiled bacteriophage PM2 DNA. J Mol Biol 1975; 91:477–87.Google Scholar
  24. 24.
    Botchan P, An electron microscopic comparison of transcription on linear and superhelical DNA. J Mol Biol 1976; 105:161–76.Google Scholar
  25. 25.
    Sankaran L, Pogell BM. Differential inhibition of catabolite-sensitive enzyme induction by intercalating dyes. Nature New Biol 1973; 245:257–60.Google Scholar
  26. 26.
    Sanzey B. Modulation of gene expression by drugs affecting deoxyribonucleic acid gyrase. J Bacteriol 1979; 138:40–47.Google Scholar
  27. 27.
    Geliert M, Mizuuchi K,O’Dea MH et al. DNA gyrase: An enzyme that introduces superhelical turns into DNA. Proc Natl Acad Sci USA 1976; 73:3872–6.Google Scholar
  28. 28.
    Geliert M, O’Dea MH, Itoh T et al. Novobiocin and coumermycin inhibit DNA supercoiling catalyzed by DNA gyrase. Proc Natl Acad Sci USA 1976b; 73:4474–8.Google Scholar
  29. 29.
    Wang JC. Interaction between DNA and an Escherichia coli protein co. J Mol Biol 1971; 55:523–33.Google Scholar
  30. 30.
    Sternglanz R, DiNardo S, Voelkel KA et al. Mutations in the gene coding for Escherichia coli DNA topoisomerase I affect transcription and transposition. Proc Natl Acad Sci USA 1981; 78:2747–51.Google Scholar
  31. 31.
    Trucksis M, Depew RW. Identification and localization of a gene that specifies production of Escherichia coli DNA topoisomerase I. Proc Natl Acad Sci USA 1981; 78:2164–8.Google Scholar
  32. 32.
    Mukai FH, Margolin P. Analysis of unlinked suppressors of an 0° mutation in Salmonella. Proc. Natl. Acad. Sci. USA 50:140–148.Google Scholar
  33. 33.
    Margolin P, Zumstein L, Sternglanz R et al. The Escherichia coli supX locus is topA, the structural gene for DNA topoisomerase I. Proc Natl Acad Sci USA 1985; 82:5437–41.Google Scholar
  34. 34.
    Gemmill RM, Tripp, Friedman SB et al. Promoter mutation causing catabolite repression of the Salmonella typhimurium leucine operon. J Bacteriol 1984; 158:948–53.Google Scholar
  35. 35.
    Roth JR, Anton DN, Hartman PE. Histidine regulatory mutants in 5. typhimurium: I. Isolation and general properties. J Mol Biol 1966; 22:305–23.Google Scholar
  36. 36.
    Rudd KE, Menzel R. his operons of Escherichia coli and Salmonella typhimurium are regulated by DNA supercoiling. Proc Natl Acad Sci USA 1987; 84:517–21.Google Scholar
  37. 37.
    Toone MW, Rudd KE, Friessen JD. Mutations causing aminotriazole resistance and temperature sensitivity reside in gyrB, which encodes the B subunit of DNA gyrase. J Bacteriol 19921 174:5479–81.Google Scholar
  38. 38.
    Menzel R, Geliert M. Regulation of the genes for E. coli DNA gyrase: Homeostatic control of DNA supercoiling. Cell 1983; 34:105–13.Google Scholar
  39. 39.
    Menzel R, Geliert M. Modulation of transcription by DNA supercoiling: A deletion analysis of the Escherichia coli gyrA and gyrB promoters. Proc Natl Acad Sci USA 1987; 84:4185–9.Google Scholar
  40. 40.
    Menzel R, Geliert M. Fusions of Escherichia coli gyrA and gyrB control regions to the glactokinase gene are inducible by coumermycin treatment. J Bacteriol 1987b; 169:1272–8.Google Scholar
  41. 41.
    Jovanovich SB, Lebowitz J. Estimation of the effect of coumermycin A1 on Salmonella typhimurium promoters by using random operon fusions. J Bacteriol 1987; 169:4431–5.Google Scholar
  42. 42.
    Pruss GJ, Drlica K. DNA supercoiling and transcription. Cell 1989; 56:521–3.Google Scholar
  43. 43.
    Menzel R, Geliert M. The biochemistry and biology of DNA gyrase. In: Liu L, ed. DNA Topoisomerases and Their Applications in Pharmacology. Academic Press, Orlando, FL In press.Google Scholar
  44. 44.
    Steck TR, Franco RJ, Wang J-Y et al. Topoisomerase mutations affect the relative abundance of many Escherichia coli proteins. Mol Microbiol 1993; 10:473–81.Google Scholar
  45. 45.
    Figueroa N, Wills N, Bossi L. Common sequence determinants of the response of a prokaryotic promoter to DNA bending and supercoiling. EMBO J 1991; 10:941–9.Google Scholar
  46. 46.
    Blanc-Potard A-B, Bossi L. Phenotypic suppression of DNA gyrase deficiencies by a deletion lowering the gene dosage of a major tRNA in Salmonella typhimurium. J Bacteriol 1994; 176:2216–26.Google Scholar
  47. 47.
    Chuang S-E, Daniels DL, Blattner FR. Global regulation of gene expression in Escherichia coli. J Bacteriol 1993; 175:2026–36.Google Scholar
  48. 48.
    Drlica K. Control of bacterial DNA supercoiling. Mol Microbiol 1992; 6:425–33.Google Scholar
  49. 49.
    Tse-Dinh Y-C. Regulation of the Escherichia coli DNA topoisomerase I gene by DNA supercoiling. Nucleic Acids Res 1985; 13:4751–63.Google Scholar
  50. 50.
    Tse-Dinh Y-C, Beran-Steed RK. Multiple promoters for transcription of E. coli topoisomerase I gene and their regulation by DNA supercoiling. J Mol Biol 1982; 202:735–42.Google Scholar
  51. 51.
    Pruss GJ, Manes SH, Drlica K. Escherichia coli DNA topoisomerase I mutants: Increased supercoiling is corrected by mutations near gyrase genes. Cell 1982; 31:35–42.Google Scholar
  52. 52.
    DiNardo S, Voelkel KA, Sternglanz R et al. Escherichia coli DNA topoisomerase I mutants have compensatory mutations in DNA gyrase genes. Cell 1982; 31:43–51.Google Scholar
  53. 53.
    Raji A, Zabel DJ, Laufer CS et al. Genetic analysis of mutations that compensate for loss of Escherichia coli DNA topoisomerase I. J Bacteriol 1985; 162:1173–79.Google Scholar
  54. 54.
    Richardson SMH, Higgins CF, Lilley DMJ. The genetic control of DNA supercoiling in Salmonella typhimurium. EMBO J 1984; 3:1745–52.Google Scholar
  55. 55.
    von Hippel PH, Bear DG, Morgan WD et al. Protein-nucleic acid interactions in transcription: A molecular analysis. Annu Rev Biochem 1984; 53:389–446.Google Scholar
  56. 56.
    McClure WR. Mechanism and control of transcription initiation in prokaryotes. Annu Rev Biochem 1985; 54:171–204.Google Scholar
  57. 57.
    Record Jr MT, Ha J-H, Fisher MA. Use of equilibrium and kinetic measurements to determine the thermodynamic origins of stability and specificity and mechanism of formation of site specific complexes between proteins and helical DNA. Methods Enzymol 1991; 208:291–343.Google Scholar
  58. 58.
    von Hippel PH, Yager TD, Gill SC. Quantitative aspects of the transcription cycle in Escherichia coli. In: McKnight S, Yamamoto K, eds. Transcriptional Regulation. Cold Spring Harbor NY: Cold Spring Harbor Laboratory Press, 1992:179–201.Google Scholar
  59. 59.
    Wood DC, Lebowitz J. Effect of supercoiling on the abortive initiation kinetics of the RNA I promoter of colE1 plasmid DNA. J Biol Chem 1984; 259:11184–87.Google Scholar
  60. 60.
    Malan TP, Kolb A, Buc H et al. Mechanism of CRP-cAMP activation of lac operon transcription initiation activation of the P1 promoter. J Mol Biol 1984; 180:881–909.Google Scholar
  61. 61.
    Buc H, Amouyal M. Superhelix density as an intensive thermodynamic variable. Eckstein F, Lilley DMJ eds. Nucleic Acids and Molecular Biology. vol. 6. New York: Springer-Verlag, 1992:23–54.Google Scholar
  62. 62.
    Bertrand-Burggraf E, Dunand J, Fuchs RPP et al. Kinetic studies of the modulation of ada promoter activity by upstream elements. EMBO J 1990; 9:2265–71.Google Scholar
  63. 63.
    Buc H, McClure WR. 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; 24:2712–23.Google Scholar
  64. 64.
    . Straney DC, Crothers DM. Intermediates in transcription initiation from the Escherichia coli lac UV5 promoter. Cell 1985; 43:449–54.Google Scholar
  65. 65.
    Straney DC, Crothers DM. Comparison of the open complexes formed by RNA polymerase at the E. coli lac UV5 promoter. J Mol Biol 1987; 193:279–92.Google Scholar
  66. 66.
    . Straney DC, Crothers DM. A stressed intermediate in the formation of stably initiated RNA chains at the Escherichia coli lac UV5 promoter. J Mol Biol 1987 193:267–278.Google Scholar
  67. 67.
    . Schickor P, Metzger W, Werel W et al. Topography of intermediates in transcription initiation of E. coli. EMBO J 1990; 9:2215–20.Google Scholar
  68. 68.
    Lavigne M, Herbert M, Kolb A et al. Upstream curved sequences influence the initiation of transcription at the Escherichia coli galactose operon. J Mol Biol 1992; 224:293–306.Google Scholar
  69. 69.
    Crothers DM, Steitz TA. Transcriptional activation by Escherichia coli CAP protein. McKnight SL, Yamamoto KR eds. Transcription Regulation. Cold Spring Harbor NY: Cold Spring Harbor Laboratory Press, 1992:501–34.Google Scholar
  70. 70.
    Heggeler-Bordellier B, Wahli W, Adrian M et al. The apical localization of transcribing RNA polymerases on supercoiled DNA prevents its rotation around the template. EMBO J 1992; 11:667–72.Google Scholar
  71. 71.
    Ross W, Gosink KK, Salomon J et al. A third recognition element in bacterial promoters: DNA binding by the a subunit of RNA polymerase. Science 1993; 262:1407–13.Google Scholar
  72. 72.
    Kammerer W, Deuschle U, Gentz R et al. Functional dissection of Escherichia coli promoters: Information in the transcribed region is involved in late steps of the overall process. EMBO J 1986; 5:2995–3000.Google Scholar
  73. 73.
    Borowiec JA, Gralla JD. Supercoiling response of the lac ps promoter in vitro. J Mol Biol 1985; 184:587–98.Google Scholar
  74. 74.
    . Bossi L, Smith DM. Conformational change in the DNA associated with an unusual promoter mutation in a tRNA Operon of Salmonella. Cell 1984; 39:643–52.Google Scholar
  75. 75.
    Yang H-L, Heller K, Geliert M et al. Differential sensitivity of gene expression in vitro to inhibitors of DNA gyrase. Proc Natl Acad Sci USA 1979; 76:3304–8.Google Scholar
  76. 76.
    . Carty M, Menzel R. Inhibition of DNA gyrase activity in an in vitro transcription-translation system stimulates gyrA expression in a DNA concentration dependent manner. J Mol Biol 1990; 214:397–406.Google Scholar
  77. 77.
    . Bracco L, Kotlarz D, Kolb A et al. Synthetic curved DNA sequences can act as transcriptional activators in Escherichia coli. EMBO J 1989; 8:4289–96.Google Scholar
  78. 78.
    Gartenberg MR, Crothers DM. Synthetic DNA bending sequences increase the rate of in vitro transcription initiation at the Escherichia coli lac promoter. J Mol Biol 1991; 219:217–30.Google Scholar
  79. 79.
    Pérez-Martín J, Rojo F, deLorenzo V. Promoters responsive to DNA bending: A common theme in prokaryotic gene expression. Microbiol Rev 1994; 58:268–90.Google Scholar
  80. 80.
    Giladi H, Koby S, Gottesman ME et al. Supercoiling, integration host factor, and a dual promoter system, participate in the control of the bacteriophage λ pL promoter. J Mol Biol 1992; 224:937–48.Google Scholar
  81. 81.
    Claverie-Martin F, Magasanik B. Role of integration host factor in the regulation of the glnHp2 promoter of Escherichia coli. Proc Natl Acad Sci USA 1991; 88:1631–35.Google Scholar
  82. 82.
    Claverie-Martin F, Magasanik B. Positive and negative effects of DNA bending on activation of transcription from a distant site. J Mol Biol 1992; 227:996–1008.Google Scholar
  83. 83.
    Hochschild A, Ptashne M. Cooperative binding of λ repressors to sites separated by integral turns of the DNA helix. Cell 1986; 44:681–7.Google Scholar
  84. 84.
    Wang JC, Giaever G. Action at a distance along a DNA. Science 1988; 240:300–4.Google Scholar
  85. 85.
    Hochschild A. Protein-protein interactions and DNA loop formation. Cozzarelli NR, Wang JC eds. DNA topology and its biological effects. Cold Spring Harbor, Cold Spring Harbor Laboratory Press, 1990:107–38.Google Scholar
  86. 86.
    Matthews KS. DNA looping. Microbiol Rev 1992; 56:123–6.Google Scholar
  87. 87.
    Kramer H, Amouyal M, Nordheim A et al. DNA supercoiling changes the spacing requirement of two lac operators for DNA loop formation with lac repressor. EMBO J 1988; 7:547–56.Google Scholar
  88. 88.
    Kramer H, Niemoller M, Amouyal M. lac repressor forms loops with linear DNA carrying two suitably spaced lac operators. EMBO J 1987; 6:1481–91.Google Scholar
  89. 89.
    Lobell R, Schlief RF. DNA looping and unlooping by AraC protein. Science 1990; 250:528–32.Google Scholar
  90. 90.
    Whitehall S, Austin S, Dixon R. DNA supercoiling response of the σ54-dependent Klebsiella pneumoniae nifL promoter in vitro. J Mol Biol 1992; 225:591–607.Google Scholar
  91. 91.
    Whitehall S, Austin S, Dixon R. The function of the upstream region of the σ54-d ependent Klebsiella pneumoniae nifL promoter is sensitive to DNA supercoiling. Mol Microbiol 1993; 9:1107–17.Google Scholar
  92. 92.
    Law SM, Bellomy GR, Schlax PJ et al. In vivo thermodynamic analysis of repression with and without looping in lac constructs. J Mol Biol 1993; 230:161–73.Google Scholar
  93. 93.
    Stefano JE, Gralla JD. Kinetic investigation of the mechanism of RNA polymerase binding to mutant lac promoters. J Biol Chem 1979; 255:10423–30.Google Scholar
  94. 94.
    Carpousis AJ, Stefano JE, Gralla JD. 5′ Nucleotide heterogeneity and altered initiation of transcription at mutant lac promoters. J Mol Biol 1982; 157:619–33.Google Scholar
  95. 95.
    Menedez M, Kolb A, Buc H. A new target for CRP action at the malT promoter. EMBO J. 1987; 6:4227–34.Google Scholar
  96. 96.
    Krohn M, Pardon B, Wagner R. Effects of template topology on RNA polymerase pausing during in vitro transcription of the Escherichia coli rrnB leader region. Mol Microbiol 1992; 6:581–9.Google Scholar
  97. 97.
    Peck LJ, Wang JC. Transcriptional block caused by a negative supercoil-ing induced structural change in an alternating CG sequence. Cell 1985; 40:129–37.Google Scholar
  98. 98.
    Brahms JG, Dargouge O, Brahms S et al. Activation of transcription by DNA supercoiling. J Mol Biol 1985; 181:455–65.Google Scholar
  99. 99.
    Dröge P, Pohl FM. The influence of an alternate template conformation on elongating phage T7 RNA polymerase. Nucleic Acids Res 1991; 19:5301–6.Google Scholar
  100. 100.
    Morales NM, Cobourn SD, Müller UR. Effect of in vitro transcription on cruciform stability. Nucleic Acids Res 1990; 18:2777–82.Google Scholar
  101. 101.
    Carty M, Menzel R. The unexpected antitermination of gyrvA-directed transcripts is enhanced by DNA relaxation. Proc Natl Acad Sci USA 1989; 86:8882–6.Google Scholar
  102. 102.
    Telesnitsky APW, Chamberlin MJ. Sequences linked to prokaryotic promoters can affect the efficiency of downstream termination sites. J Mol Biol 1989; 205:315–30.Google Scholar
  103. 103.
    Goliger JA, Yang X, Guo H-C et al. Early transcribed sequences affect termination efficiency of Escherichia coli RNA polymerase. J Mol Biol 1989; 205:331–41.Google Scholar
  104. 104.
    Arnold GF, Tessman I. Regulation of DNA superhelicity by rpoB mutations that suppress defective Rho-mediated transcription termination in Escherichia coli. J Bacteriol 1988; 170:4266–71.Google Scholar
  105. 105.
    Liu LF, Wang JC. Supercoiling of the DNA template during transcription. Proc Natl Acad Sci USA 1987; 84:7024–7.Google Scholar
  106. 106.
    Wang JC. Template topology and transcription. McKnight S, Yamamoto K, eds. Transcriptional Regulation. Cold Spring Harbor NY: Cold Spring Harbor Laboratory Press, 1992:1253–69.Google Scholar
  107. 107.
    Wang JC, Lynch AS. Transcription and DNA supercoiling. Current Op in Gen and Dev 1993; 3:764–8.Google Scholar
  108. 108.
    Dröge P. Protein tracking-induced supercoiling of DNA: A tool to regulate DNA transactions in vivo? Bioessays 1993;16:91–9.Google Scholar
  109. 109.
    Cook DN, Ma D, Hearst JE. Nucleic Acids and Molecular Biology. In: Eckstein F, Lilley DMJ, eds. New York: Springer-Verlag, In press.Google Scholar
  110. 110.
    Wang JC. DNA topoisomerases. Jerusalem Symposium. Ann Rev Biochem 1985; 54:665–97.Google Scholar
  111. 111.
    Wang JC. Recent Studies of DNA Topoisomerases. Harvey Lecture. Biochim Biophys Acta 1987; 909, 1–9.Google Scholar
  112. 112.
    Ostrander EO, Benedetti P, Wang JC. Template supercoiling by a chimera of yeast GAL4 protein-phage T7 RNA polymerase chimera. Science 1990; 249:1261–65.Google Scholar
  113. 113.
    Reaban ME, Griffith JA. Induction of RNA-stabilized DNA conformers by transcription of an immunoglobulin switch region. Nature 1990; 348:342–4.Google Scholar
  114. 114.
    Lodge JK, Kazic T, Berg DE. Formation of supercoiling domains in plas-mid pBR322. J Bacteriol 1989; 171:2181–87.Google Scholar
  115. 115.
    Cook DN, Ma D, Pon NG et al. Dynamics of DNA supercoiling by transcription in Escherichia coli. Proc Natl Acad Sci USA 1992; 89:10603–7.Google Scholar
  116. 116.
    Lynch AS, Wang JC. 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; 175:1645–55.Google Scholar
  117. 117.
    Ma D, Cook DN, Pon NG et al. Efficient anchoring of RNA polymerase in Escherichia coli during coupled transcription-translation of genes encoding integral inner membrane polypeptides. J Biol Chem 1994; 269:15362–70.Google Scholar
  118. 118.
    Liu LF, Wang JC. Micrococcus luteus DNA gyrase: Active components and a model for its supercoiling of DNA. Proc Natl Acad Sci USA 1978; 75:2098–2102.Google Scholar
  119. 119.
    Liu LF, Wang JC. DNA-DNA gyrase complex: the wrapping of the DNA duplex outside the enzyme. Cell 1978;15:979–84.Google Scholar
  120. 120.
    Higgins NP, Cozzarelli NR. The binding of gyrase to DNA: Analysis by retention by nitrocellulose filters. Nucleic Acids Res 1982; 10:6833–47.Google Scholar
  121. 121.
    Koo H-S, Wu H-Y, Liu LF. Effects of transcription and translation on gyrase-mediated DNA cleavage in Escherichia coli. J Biol Chem 1990; 265:12300–5.Google Scholar
  122. 122.
    Condemine G, Smith CL. Transcription regulates oxolinic acid-induced DNA gyrase cleavage at specific sites on the E. coli chromosome. Nucleic Acids Res 1990; 18:7389–96.Google Scholar
  123. 123.
    Rahmouni AR, Wells RD. Stabilization of Z DNA in vivo by localized supercoiling. Science 1989; 246:358–63.Google Scholar
  124. 124.
    Kochel TJ, Sinden RR. Hyperreactivity of B-Z junctions to 4,5′,8-trimethylpsoralen photobinding assayed by an exonuclease III/photoreversal mapping procedure. J Mol Biol 1989; 205:91–102.Google Scholar
  125. 125.
    Jaworski, A., N.P. Higgins NP, Wells RD et al. Topoisomerase mutants and physiological conditions control supercoiling and Z-DNA formation in vivo. J Biol Chem 1991; 266:2576–81.Google Scholar
  126. 126.
    Rahmouni AR, Wells RD. Direct evidence for the effect of transcription on local DNA supercoiling in vivo. J Mol Biol 1992; 223:131–44.Google Scholar
  127. 127.
    McClellan JA, Boublíkova P, Palecek E et al. Superhelical torsion in cellular DNA responds to directly to environmental and genetic factors. Proc Natl Acad Sci USA 1990; 87:8373–7.Google Scholar
  128. 128.
    Dayn A, Malkhosyan S, Mirkin SM. Transcriptionally driven cruciform formation in vivo. Nucleic Acids Res 1992; 20:5991–7.Google Scholar
  129. 129.
    Bowater R, Chen D, Lilley DMJ. Elevated unconstrained supercoiling of plasmid DNA generated by transcription and translation of the tetracycline resistance gene in eubacteria. Biochemistry 1994; In press.Google Scholar
  130. 130.
    Kohwi Y, Malkhosyan SR, Kohi-Shigematsu T. Intramolecular dG22c5dG22c5dC triplex detected in Escherichia coli cells. J Mol Biol 1992; 223:817–22.Google Scholar
  131. 131.
    Worcel A, Burgi E. On the structure of the folded chromosome of Escherichia coli. J Mol Biol 1972; 71:127–47.Google Scholar
  132. 132.
    Pettijohn DE, Hecht R. RNA molecules bound to the folded bacterial genome stabilize DNA folds and segregate domains of supercoiling. Cold Spring Harbor Symp Quantitative Biol 1974; 38:31–42.Google Scholar
  133. 133.
    Pettijohn DE, Pfenninger O. Supercoils in prokaryotic DNA restrained in vivo. Proc Natl Acad Sci USA 1980; 77:1331–5.Google Scholar
  134. 134.
    Sinden RR, Pettijohn DE. Chromosomes in living Escherichia coli cells are segregated into domains of supercoiling. Proc Natl Acad Sci USA 1981; 78:224–8.Google Scholar
  135. 135.
    Miller WG, Simons RW. Chromosomal supercoiling in Escherichia coli. Mol Microbiol 1993; 10:675–84.Google Scholar
  136. 136.
    Pavitt GD, Higgins CF. Chromosomal domains of supercoiling in Salmonella typhimurium. Mol Microbiol 1993; 10:685–96.Google Scholar
  137. 137.
    Lilley DMJ, Higgins CF. Local DNA topology and gene expression: The case of the leu-500 promoter. Mol Microbiol 1993; 5:779–83.Google Scholar
  138. 138.
    Asai T, Chen C-P, Nagata T et al. Transcription in vivo within the replication origin of the Escherichia coli chromosome: A mechanism for activating initiation of replication. Mol Gen Genet 1992; 231:169–78.Google Scholar
  139. 139.
    Dröge P, Transcription-driven site-specific DNA recombination in vitro. Proc Natl Acad Sci USA 1993; 90:2759–63.Google Scholar
  140. 140.
    Kohwi Y, Panchenko Y. Transcription-dependent recombination induced by triple-helix formation. Genes & Devel 1993; 7:1766–78.Google Scholar
  141. 141.
    Richardson SM, Higgins CF, Lilley DM. DNA supercoiling and the leu500 mutation of Salmonella typhimurium. EMBO J 1988; 7:1863–9.Google Scholar
  142. 142.
    Chen D, Bowater R, Dorman CJ et al. Activity of a plasmid-borne leu-500 promoter depends on the transcription and translation of an adjacent gene. Proc Natl Acad Sci USA 1992; 89:8784–8.Google Scholar
  143. 143.
    Chen D, Bowater RP, Lilley DMJ. Activation of the leu-500 promoter: A topological domain generated by divergent transcription in a plasmid. Biochem 1993; 32:13162–70.Google Scholar
  144. 144.
    Chen D, Bowater R, Lilley DMJ. Topological promoter coupling in Escherichia coli: ΔtopA-dependent activation of the leu-500 promoter on a plasmid. J Bacteriol 1994; 176:3757–64.Google Scholar
  145. 145.
    Tan J, Shu L, Wu H-Y. Activation of the leu-500 promoter by adjacent transcription. J Bacteriol 1994; 176:1077–86.Google Scholar
  146. 146.
    Liu LF, Wang JC. In vitro DNA synthesis of primed covalently closed double-stranded templates. I. Studies with Escherichia coli DNA polymerase I. In: Goulian M, Hanawalt P, eds. DNA Synthesis and Its Regulation. Menlo Park: Benjamin Inc., 1975:38–63.Google Scholar
  147. 147.
    Wang JC. The Degree of unwinding of the DNA helix by ethidium. I. Titration of twisted PM2 DNA molecules in alkaline cesium chloride density gradients. J Mol Biol 1974; 89:783–801.Google Scholar
  148. 148.
    Itoh T, Tomizawa J. Formation of an RNA primer for initiation of replication of ColE1 DNA by ribonuclease H. Proc Natl Acad Sci USA 1980; 77:2450–4.Google Scholar
  149. 149.
    Selzer G, Tomizawa JI. Specific cleavage of the p15A primer precursor by ribonuclease H at the origin of DNA replication. Proc Natl Acad Sci USA 1982;79:7082–6.Google Scholar
  150. 150.
    Masukata H, Tomizawa J. Effects of point mutations on formation and structure of RNA primer for ColEl replication. Cell 1984; 36:513–22.Google Scholar
  151. 151.
    Masukata H, Tomizawa J. Control of primer formation of ColEl plasmid replication: Conformational change of the primer transcript. Cell 1986; 44:125–36.Google Scholar
  152. 152.
    Masukata H, Dasgupta S, Tomizawa J. Transcriptional activation of ColEl DNA synthesis by displacement of the nontranscribed strand. Cell 1987; 51:1123–30.Google Scholar
  153. 153.
    Parada CA, Marians KJ. Mechanism of DNA A protein-dependent pBR322 DNA replication. J Biol Chem 1991; 66:18895–906.Google Scholar
  154. 154.
    Marians KJ. Prokaryotic DNA replication. Annu Rev Biochem 192; 61:673–719.Google Scholar
  155. 155.
    Asai T, Kogoma T. Minireview: D-loops and R-loops: Alternative mechanisms for the initiation of chromosome replication in Escherichia coli. J Bacteriol 1994; 176:1807–12.Google Scholar
  156. 156.
    Drolet M, Bi X, Liu LF. Hypernegative supercoiling of the DNA template during transcription elongation in vitro. J Biol Chem 1994; 269:2068–74.Google Scholar

Copyright information

© R.G. Landes Company 1996

Authors and Affiliations

  • James C. Wang
  • A. Simon Lynch

There are no affiliations available

Personalised recommendations