DNA topology-mediated control of global gene expression in Escherichia coli

Annual Review of Genetics

Volumn 36, Issue , 2002, Pages 175-203

  Hatfield, G Wesley ^a   Benham, Craig J ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

DNA supercoiling; Energy charge; Metabolic regulation; SIDD; Transcriptional coupling

Indexed keywords

BACTERIAL GENETICS; CELL ENERGY; CELL GROWTH; CHROMOSOME; CHROMOSOME STRUCTURE; DNA STRUCTURE; DNA SUPERCOILING; ESCHERICHIA COLI; GENE EXPRESSION; NONHUMAN; OPERON; PRIORITY JOURNAL; REGULON; REVIEW;

BASE SEQUENCE; DNA, BACTERIAL; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; GENES, BACTERIAL; MOLECULAR SEQUENCE DATA;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; POSIBACTERIA;

EID: 0036953237     PISSN: 00664197     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.genet.36.032902.111815     Document Type: Review

References (99)

1. Atkinson DE. 1965. Biological feedback control at the molecular level. Science 150:851-57
2. Atkinson DE. 1969. Regulation of enzyme function. Annu. Rev. Microbiol. 23:47-68
3. Benham CJ. 1979. Torsional stress and local denaturation in supercoiled DNA. Proc. Natl. Acad. Sci. USA 76:3870-74
4. Benham CJ. 1980. Theoretical analysis of transitions between B- and Z-conformations in torsionally stressed DNA. Nature 286:637-38
5. Benham CJ. 1990. Transitions in superhelical DNA molecules of specified sequence. J. Chem. Phys. 92:6294-305
6. Benham CJ. 1992. Energetics of the strand separation transition in superhelical DNA. J. Mol. Biol. 225:835-47
7. Benham CJ. 1993. Sites of predicted stress-induced DNA duplex destabilization occur preferentially at regulatory loci. Proc. Natl. Acad. Sci. USA 90:2999-3003
8. Benham CJ. 1996. Duplex destabilization in superhelical DNA is predicted to occur at specific transcriptional regulatory regions. J. Mol. Biol. 255:425-34
9. Benham C, Kohwi-Shigematsu T, Bode J. 1997. Stress-induced duplex DNA destabilization in scaffold/matrix attachment regions. J. Mol. Biol. 274:181-96
10. Bensaid A, Almeida A, Drlica K, Rouviere J. 1996. Cross-talk between topoisomerase I and HU in Escherichia coli. J. Mol. Biol. 256:292-300
11. Bliska JB, Cozzarelli NR. 1987. Use of site-specific recombination as a probe of DNA structure and metabolism in vivo. J. Mol. Biol. 194:205-18
12. Bokal AJ, Ross W, Gaal T, Johnson RC, Gourse RL. 1997. Molecular anatomy of a transcription activation patch: FISRNA polymerase interactions at the Escherichia coli rmB P1 promoter. EMBO J. 16:154-62
13. Bokal AJ, Ross W, Gourse RL. 1995. The transcriptional activator protein FIS: DNA interactions and cooperative interactions with RNA polymerase at the Escherichia coli rmB P1 promoter. J. Mol. Biol. 245:197-207
14. Borowiec JA, Gralla JD. 1985. Supercoiling response of the lac ps promoter in vitro. J. Mol. Biol. 184:587-98
15. Breslauer KJ, Frank R, Blocker H,. Marky LA. 1986. Predicting DNA duplex stability from the base sequence. Proc. Natl. Acad. Sci. USA 83:3746-50
16. Calladine CR. 1997. Understanding DNA: The Molecule and How it Works. New York: Academic
17. Calvo JM, Matthews RG. 1994. The leucine-responsive regulatory protein, a global regulator of metabolism in Escherichia coli. Microbiol. Rev. 58:466-90
18. Chapman AG, Atkinson DE. 1977. Adenine nucleotide concentrations and turnover rates. Their correlation with biological activity in bacteria and yeast. Adv. Microb. Physiol. 15:253-306
19. Chapman AG, Fall L, Atkinson DE. 1971. Adenylate energy charge in Escherichia coli during growth and starvation. J. Bacteriol. 108:1072-86
20. Cortassa S, Aon MA. 1993. Altered topoisomerase activities may be involved in the regulation of DNA supercoiling in aerobic-anaerobic transitions in Escherichia coli. Mol. Cell Biochem. 126:115-24
21. Cozzarelli NR. 1980. DNA gyrase and the supercoiling of DNA. Science 207:953-60
22. Dai X, Greizerstein MB, Nadas Chinni K, Rothman Denes LB. 1997. Supercoil-induced extrusion of a regulatory DNA hairpin. Proc. Natl. Acad. Sci. USA 94:2174-79
23. Dai X, Rothman-Denes LB. 1999. DNA structure and transcription. Curr. Opin. Microbiol. 2:126-30
24. Deibler RW, Rahmati S, Zechiedrich EL, 2001. Topoisomerase IV, alone, unknots DNA in E. coli. Genes Dev. 15:748-61
25. DiNardo S, Voelkel KA, Sternglass R, Reynolds AE, Wright A. 1983. Escherichia coli DNA topoisomerase I mutants have compensatory mutations at or near DNA gyrase genes. Cold Spring Harbor Symp. Quant. Biol. 47:779-84
26. Drew HR, Weeks JR, Travers AA. 1985. Negative supercoiling induces spontaneous unwinding of a bacterial promoter. EMBO J. 4:1025-32
27. Drlica K. 1992. Control of bacterial DNA supercoiling. Mol. Microbiol. 6:425-33
28. Drlica K, Franco RJ. 1988. Inhibitors of DNA topoisomerases. Biochemistry 27:2253-59
29. Drlica K, Zhao X. 1997. DNA gyrase, topoisomerase IV, and the 4-quinolones. Microbiol. Mol. Biol. Rev. 61:377-92
30. Estrem ST, Gaal T, Ross W, Gourse RL. 1998. Identification of an UP element consensus sequence for bacterial promoters. Proc. Natl. Acad. Sci. USA 95:9761-66
31. Friden P, Newman T, Freundlich M. 1982. Nucleotide sequence of the ilvB promoter-regulatory region: a biosynthetic operon controlled by attenuation and cyclic AMP. Proc. Natl. Acad. Sci. USA 79:6156-60
32. Fye RM, Benham CJ. 1999. Exact method for numerically analyzing a model of local denaturation in superhelically stressed DNA. Phys. Rev. 59:3408-26
33. Gemmill RM, Wessler SR, Keller EB, Calvo JM. 1979. leu operon of Salmonella typhimurium is controlled by an attenuation mechanism. Proc. Natl. Acad. Sci. USA 76:4941-45
34. Giaever GN, Snyder L, Wang JC. 1988. DNA supercoiling in vivo. Biophys. Chem. 29:7-15
35. Gosink KK, Ross W, Leirmo S, Osuna R, Finkel SE, et al. 1993. DNA binding and bending are necessary but not sufficient for Fis-dependent activation of rmB P1. J. Bacteriol. 175:1580-89
36. Hauser CA, Hatfield GW. 1983. Nucleotide sequence of the ilvB multivalent attenuator region of Escherichia coli K12. Nucleic Acids Res. 11:127-39
37. Henikoff S, Haughn GW, Calvo JM, Wallace JC. 1988. A large family of bacterial activator proteins. Proc. Natl. Acad. Sci. USA 85:6602-6
38. Higgins CF, Dorman CJ, Stirling DA, Waddell L, Booth IR, et al. 1988. A physiological role for DNA supercoiling in the osmotic regulation of gene expression in S. typhimurium and E. coli. Cell 52:569-84
39. Hsieh LS, Rouviere-Yaniv J, Drlica K. 1991. Bacterial DNA supercoiling and [ATP]/[ADP] ratio: changes associated with salt shock. J. Bacteriol. 173:3914-17
40. Htun H, Dahlberg JE. 1989. Topology and formation of triple-stranded H-DNA. Science 243:1571-76
41. Jensen PR, Loman L, Petra B, Vanderwe C, Westerhouse HV. 1995. Energy buffering of DNA structure fails when Escherichia coli runs out of substrate. J. Bacteriol. 177:3420-26
42. Jones PG, Inouye M. 1994. The cold-shock response - a hot topic. Mol. Microbiol. 11:811-18
43. Jones PG, VanBogelen RA, Neidhardt FC. 1987. Induction of proteins in response to low temperature in Escherichia coli. J. Bacteriol. 169:2092-95
44. Kowalski D, Natale DA, Eddy MJ. 1988. Stable DNA unwinding, not "breathing," accounts for single-strand-specific nuclease hypersensitivity of specific A+T-rich sequences. Proc. Natl. Acad. Sci. USA 85:9464-68
45. Kusano S, Ding QQ, Fujita N, Ishihama A. 1996. Promoter selectivity of Escherichia coli RNA polymerase E sigma 70 and E sigma 38 holoenzymes. Effect of DNA supercoiling. J. Biol. Chem. 271:1998-2004
46. Landick R, Yanofsky C. 1987. Transcription attenuation. See Ref. 58, 1:1276-301
47. Lawther RP, Hatfield GW. 1980. Multivalent translational control of transcription termination at attenuator of ilvGEDA operon of Escherichia coli K-12. Proc. Natl. Acad. Sci. USA 77:1862-66
48. Lilley DM. 1980. The inverted repeat as a recognizable structural feature in super-coiled DNA molecules. Proc. Natl. Acad. Sci. USA 77:6468-72
49. Liu LF, Wang JC. 1987. Supercoiling of the DNA template during transcription. Proc. Natl. Acad. Sci. USA 84:7024-27
50. Liu Y, et al. 2001. DNA supercoiling allows enhancer action over a large distance. Proc. Natl. Acad. Sci. USA 98:14883-88
51. Luttinger A. 1995. The twisted 'life' of DNA in the cell: bacterial topoisomerases. Mol. Microbiol. 15:601-6
52. McEachern F, Fisher LM. 1989. Regulation of DNA supercoiling in Escherichia coli: genetic basis of a compensatory mutation in DNA gyrase. FEBS Lett. 253:67-70
53. Menzel R, Gellert M. 1983. Regulation of the genes for E. coli DNA gyrase: homeostatic control of DNA supercoiling. Cell 34:105-13
54. Michelotti GA, Michelotti EF, Pullner A, Duncan RC, Eick D. 1996. Multiple single-stranded cis elements are associated with activated chromatin of the human c-myc gene in vivo. Mol. Cell Biol. 16:2656-69
55. Mojica FJ, Higgins CF. 1996. Localized domains of DNA supercoiling: topological coupling between promoters. Mol. Microbiol. 22:919-28
56. Muskhelishvili G, Buckle M, Heumann H, Kahmann R, Travers AA. 1997. FIS activates sequential steps during transcription initiation at a stable RNA promoter. EMBO J. 16:3655-65
57. Nargang FE, Subrahmanyam CS, Umbarger HE. 1980. Nucleotide sequence of ilvGEDA operon attenuator region of Escherichia coli. Proc. Natl. Acad. Sci. USA 77:1823-27
58. Neidhardt FC, ed. 1987. Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology. Washington, DC: ASM
59. Neidhardt FC, Savageau MA. 1996. Regulation beyond the operon. See Ref. 58, 2:1310-24
60. Newlands JT, Josaitis CA, Ross W, Gourse RL. 1992. Both fis-dependent and factor-independent upstream activation of the rmB P1 promoter are face of the helix dependent. Nucleic Acids Res. 20:719-26
61. Opel ML, Arfin SM, Hatfield GW. 2001. The effects of DNA supercoiling on the expression of operons of the ilv regulon of Escherichia coli suggest a physiological rationale for divergently transcribed operons. Mol. Microbiol. 39:1109-15
62. Opel ML, Hatfield GW. 2001. DNA supercoiling-dependent transcriptional coupling between the divergently transcribed promoters of the ilvYC operon of Escherichia coli is proportional to promoter strengths and transcript lengths. Mol. Microbiol. 39:191-98
63. Oram M, Fisher LM. 1992. An Escherichia coli DNA topoisomerase I mutant has a compensatory mutation that alters two residues between functional domains of the DNA gyrase A protein. J. Bacteriol. 174:4175-78
64. Parekh BS, Hatfield GW. 1996. Transcriptional activation by protein-induced DNA bending: evidence for a DNA structural transmission model. Proc. Natl. Acad. Sci. USA 93:1173-77
65. Parekh BS, Sheridan SD, Hatfield GW. 1996. Effects of integration host factor and DNA supercoiling on transcription from the ilvPG promoter of Escherichia coli. J. Biol. Chem. 271:20258-64
66. Pettijohn DE, Pfenninger O. 1980. Supercoils in prokaryotic DNA restrained in vivo. Proc. Natl. Acad. Sci. USA 77:1331-35
67. Pokholok DK, Redlak M, Turnboug CL, Dylla S, Holmes WM. 1999. Multiple mechanisms are used for growth rate and stringent control of leuV transcriptional initiation in Escherichia coli. J. Bacteriol. 181:5771-82
68. Pruss GJ, Manes SH, Drlica K. 1982. Escherichia coli DNA topoisomerase I mutants: increased supercoiling is corrected by mutations near gyrase genes. Cell 31:35-42
69. Rahmouni AR, Wells RD. 1989. Stabilization of Z DNA in vivo by localized super-coiling. Science 246:358-63
70. Raji A, Zabel DJ, Laufer CS, Depwe RE. 1985. Genetic analysis of mutations that compensate for loss of Escherichia coli DNA topoisomerase I. J. Bacteriol. 162:1173-79
71. Rhee KY, Opel M, Ito E, Hung SP, Arfin SM, Hatfield GW. 1999. Transcriptional coupling between the divergent promoters of a prototypic LysR-type regulatory system, the ilvYC operon of Escherichia coli. Proc. Natl. Acad. Sci. USA 96:14294-99
72. Rhee KY, Senear DF, Hatfield GW. 1998. Activation of gene expression by a ligand-induced conformational change of a protein-DNA complex. J. Biol. Chem. 273:11257-66
73. Ross W, Gosink KK, Salomon J, Igarashi K, Zou C, et al. 1993. A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase. Science 262:1407-13
74. Ross W, Salomon J, Holmes WM, Gourse RL. 1999. Activation of Escherichia coli leuV transcription by FIS. J. Bacteriol. 181:3864-68
75. Rouviere-Yaniv J. 1978. Localization of the HU protein on the Escherichia coli nucleoid. Cold Spring Harbor Symp. Quant. Biol. 42 (Pt. 1):439-47
76. Rouviere-Yaniv J, Yaniv M, Germond JE. 1979. E. coli DNA binding protein HU forms nucleosomelike structure with circular double-stranded DNA. Cell 17:265-74
77. Sander P, Langert W, Mueller K. 1993. Mechanisms of upstream activation of the rmd promoter P1 of Escherichia coli. J. Biol. Chem 268:16907-16
78. Schell MA. 1993. Molecular biology of the LysR family of transcriptional regulators. Annu. Rev. Microbiol. 47:597-626
79. Sheridan SD, Benham CJ, Hatfield GW. 1998. Activation of gene expression by a novel DNA structural transmission mechanism that requires supercoiling-induced DNA duplex destabilization in an upstream activating sequence. J. Biol. Chem. 273:21298-308
80. Sheridan SD, Benham CJ, Hatfield GW. 1999. Inhibition of DNA supercoiling-dependent transcriptional activation by a distant B-DNA to Z-DNA transition. J. Biol. Chem. 274:8169-74
81. Sheridan SD, Opel ML, Hatfield GW. 2001. Activation and repression of transcription initiation by a distant DNA structural transition. Mol. Microbiol. 40:684-90
82. Sinden RR, Kochel TJ. 1987. Reduced 4,5′,8-trimethylpsoralen cross-linking of left-handed Z-DNA stabilized by DNA supercoiling. Biochemistry 26:1343-50
83. Singleton CK, Klysik J, Stirdiva SM, Wells RD. 1982. Left-handed Z-DNA is induced by supercoiling in physiological ionic conditions. Nature 299:312-16
84. Steck TR, Franco RJ, Wang JY, Drlica K. 1993. Topoisomerase mutations affect the relative abundance of many Escherichia coli proteins. Mol. Microbiol. 10:473-81
85. Steger G. 1994. Thermal denaturation of double-stranded nucleic acids: prediction of temperatures critical for gradient gel electrophoresis and polymerase chain reaction. Nucleic Acids Res. 22:2760-68
86. Sun HZ, Mezei M, Fye R, Benham CJ. 1995. Monte Carlo analysis of conformational transitions in superhelical DNA. J. Chem. Phys. 103:8653-65
87. Tse-Dinh YC. 1985. Regulation of the Escherichia coli DNA topoisomerase I gene by DNA supercoiling. Nucleic Acids Res. 13:4751-63
88. Tse-Dinh YC, Beran RK. 1988. Multiple promoters for transcription of the Escherichia coli DNA topoisomerase I gene and their regulation by DNA supercoiling. J. Mol. Biol. 202:735-42
89. Umbarger HE. 1996. Biosynthesis of the branched-chain amino acids. See Ref. 58, 2:442-57
90. Urios A, Herrera G, Aleixand V, Blanco M. 1990. Expression of the recA gene is reduced in Escherichia coli topoisomerase I mutants. Mutat. Res. 243:267-72
91. Varshavsky AJ, Nedospa SA, Bakayev VV, Bakayeva TG, Georgiev GP. 1977. Histone-like proteins in the purified Escherichia coli deoxyribonucleoprotein. Nucleic Acids Res. 4:2725-45
92. Wang JY, Syvanen M. 1992. DNA twist as a transcriptional sensor for environmental changes. Mol. Microbiol. 6:1861-66
93. Wek RC, Hatfield GW. 1986. Nucleotide sequence and in vivo expression of the ilvY and ilvC genes in Escherichia coli K12. Transcription from divergent overlapping promoters. J. Biol. Chem. 261:2441-50
94. Wek RC, Hatfield GW. 1988. Transcriptional activation at adjacent operators in the divergent-overlapping ilvY and ilvC promoters of Escherichia coli. J. Mol. Biol. 203:643-63
95. Westerhoff HV, van Workum M. 1990. Control of DNA structure and gene expression. Biomed. Biochim. Acta 49:839-53
96. Westerhoff HV, Odea MH, Maxwell A, Gellert M. 1988. DNA supercoiling by DNA gyrase. A static head analysis. Cell Biophys. 12:157-81
97. Winkelman JW, Hatfield GW. 1990. Characterization of the integration host factor binding site in the ilvPG1 promoter region of the ilvGMEDA operon of Escherichia coli. J. Biol. Chem. 265:10055-60
98. Zacharias M, Goringer HU, Wagner R. 1992. Analysis of the Fis-dependent and Fis-independent transcription activation mechanisms of the Escherichia coli ribosomal RNA P1 promoter. Biochemistry 31:2621-28
99. Zechiedrich EL, Khodursk AB, Bachelli S, Schneider R, Chem DR, et al. 2000. Roles of topoisomerases in maintaining steady-state DNA supercoiling in Escherichia coli. J. Biol. Chem 275:8103-13