Activation and repression of transcription initiation by a distant DNA structural transition

Molecular Microbiology

Volumn 40, Issue 3, 2001, Pages 684-690

  Sheridan, S D ^a   Opel, M L ^a   Wesley Hatfield, G ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; DNA B; DNA Z;

ARTICLE; DNA SEQUENCE; DNA STRUCTURE; ESCHERICHIA COLI; GEL ELECTROPHORESIS; GENE EXPRESSION; IN VITRO STUDY; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION;

ESCHERICHIA COLI;

EID: 0035012306     PISSN: 0950382X     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2958.2001.02416.x     Document Type: Article

References (29)

1. Aboul‐Ela, F., Bowater, R.P., Lilley, D.M. (1992) Competing B–Z and helix–coil conformational transitions in supercoiled plasmid DNA. J Biol Chem 267: 1776–1785.
2. Ausubel, F., Brent, R., Kingston, R.E., Moore, D.D., Sideman, J.G., Smith, J.A., Struhl, K. (1993) Current Protocols in Molecular Biology. New York: Greene Publishing Associates and John Wiley and Sons.
3. Benham, C.J. (1981) Theoretical analysis of competitive conformational transitions in torsionally stressed DNA. J Mol Biol 150: 43–68.
4. Bowater, R., Aboul‐Ela, F., Lilley, D.M. (1992) Two‐dimensional gel electrophoresis of circular DNA topoisomers. Methods Enzymol 212: 105–120.
5. Drew, H.R., Weeks, J.R., Travers, A.A. (1985) Negative supercoiling induces spontaneous unwinding of a bacterial promoter. EMBO J 4: 1025–1032.
6. Hamada, H. & Kakunaga, T. (1982) Potential Z‐DNA‐forming sequences are highly dispersed in the human genome. Nature 298: 396–398.
7. Hamada, H., Petrino, M.G., Kakunaga, T. (1982) A novel repeated element with Z‐DNA‐forming potential is widely found in evolutionarily diverse eukaryotic genomes. Proc Natl Acad Sci USA 79: 6465–6469.
8. Herbert, A. & Rich, A. (1996) The biology of left‐handed Z‐DNA. J Biol Chem 271: 11595–11598.
9. Higgins, C.F., Dorman, C.J., Stirling, D.A., Waddell, L., Booth, I.R., May, G., Bremer, E. (1988) A physiological role for DNA supercoiling in the osmotic regulation of gene expression in S. typhimurium and E. coli. Cell 52: 569–584.
10. Van Holde, K. & Zlatanova, J. (1994) Unusual DNA structures, chromatin and transcription. Bioessays 16: 59–68.
11. Hsieh, L.S., Burger, R.M., Drlica, K. (1991) Bacterial DNA supercoiling and [ATP]/[ADP]. Changes associated with a transition to anaerobic growth. J Mol Biol 219: 443–450.
12. Keller, W. (1975) Determination of the number of superhelical turns in simian virus 40 DNA by gel electrophoresis. Proc Natl Acad Sci USA 72: 4876–4880.
13. Marincs, F. & White, D.W. (1996) Regulation of gene expression at a distance: the hypothetical role of regulatory protein‐mediated topological changes of DNA. FEBS Lett 382: 1–5. DOI: 10.1016/0014-5793(96)00139-1
14. Menzel, R. & Gellert, M. (1983) Regulation of the genes for E. coli DNA gyrase: homeostatic control of DNA supercoiling. Cell 34: 105–113.
15. Nordheim, A., Lafer, E.M., Moller, A., Stollar, B.D., Pardue, M.L., Rich, A. (1982) Left‐handed Z‐DNA: a DNA structure with biological function? Prog Clin Biol Res 85 (Part A): 101–113.
16. Parekh, B.S. & Hatfield, G.W. (1996) Transcriptional activation by protein‐induced DNA bending: evidence for a DNA structural transmission model. Proc Natl Acad Sci USA 93: 1173–1177.
17. Parekh, B.S., Sheridan, S.D., Hatfield, G.W. (1996) Effects of integration host factor and DNA supercoiling on transcription from the ilvPG promoter of Escherichia coli. J Biol Chem 271: 20258–20264.
18. Rahmouni, A.R. & Wells, R.D. (1989) Stabilization of Z DNA in vivo by localized supercoiling. Science 246: 358–363.
19. Rahmouni, A.R. & Wells, R.D. (1992) Direct evidence for the effect of transcription on local DNA supercoiling in vivo. J Mol Biol 223: 131–144.
20. Rich, A., Nordheim, A., Wang, A.H. (1984) The chemistry and biology of left‐handed Z‐DNA. Annu Rev Biochem 53: 791–846.
21. Sambrook, J., Fritsch, E.F., Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
22. Schroth, G.P., Chou, P.J., Ho, P.S. (1992) Mapping Z‐DNA in the human genome. Computer‐aided mapping reveals a non‐random distribution of potential Z‐DNA‐forming sequences in human genes. J Biol Chem 267: 11846–11855.
23. Sheridan, S.D., Benham, C.J., Hatfield, G.W. (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: 21298–21308.
24. Sheridan, S.D., Benham, C.J., Hatfield, G.W. (1999) Inhibition of DNA supercoiling‐dependent transcriptional activation by a distant B‐DNA to Z‐DNA transition. J Biol Chem 274: 8169–8174.
25. Singleton, C.K. & Wells, R.D. (1982) The facile generation of covalently closed, circular DNAs with defined negative superhelical densities. Anal Biochem 122: 253–257.
26. Steck, T.R., Franco, R.J., Wang, J.Y., Drlica, K. (1993) Topoisomerase mutations affect the relative abundance of many Escherichia coli proteins. Mol Microbiol 10: 473–481.
27. Thomas, T. & Kiang, D.T. (1988) A twenty‐two‐fold increase in the relative affinity of estrogen receptor to poly‐(dA–dC) poly‐(dG–dT) in the presence of polyamines. Nucleic Acids Res 16: 4705–4720.
28. Wang, J.C. & Lynch, A.S. (1993) Transcription and DNA supercoiling. Curr Opin Genet Dev 3: 764–768.
29. Wang, J.Y. & Syvanen, M. (1992) DNA twist as a transcriptional sensor for environmental changes. Mol Microbiol 6: 1861–1866.