The role of DNA conformation in transcriptional initiation and activation in Escherichia coli

Biological Chemistry

Volumn 378, Issue 7, 1997, Pages 599-607

  Geiselmann, Johannes ^a  

^a UNIVERSITY OF GENEVA   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

CURVED DNA; DNA; DNA BINDING PROTEIN; RNA POLYMERASE;

BACTERIAL GENETICS; DNA CONFORMATION; ESCHERICHIA COLI; GENE ACTIVATION; ISOMERISM; KINETICS; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DNA BINDING; PROTEIN PROTEIN INTERACTION; REVIEW; THERMODYNAMICS; TRANSCRIPTION INITIATION;

DNA, BACTERIAL; ESCHERICHIA COLI; NUCLEIC ACID CONFORMATION; TRANS-ACTIVATION (GENETICS); TRANSCRIPTION, GENETIC;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; PROKARYOTA;

EID: 0030751918     PISSN: 14316730     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (68)

1. Blatter, E.E., Ross, W., Tang, H., Gourse, R.L., and Ebright, R.H. (1994). Domain organization of RNA polymerase alpha subunit: C-terminal 85 amino acids constitute a domain capable of dimerization and DNA binding. Cell 78, 889-896.
2. Brahms, G., Brahms, S., and Magasanik, B. (1995). A sequence-induced superhelical DNA segment serves as transcriptional enhancer. J. Mol. Biol. 246, 35-42.
3. Brody, E.N., Kassavetis, G.A., Ouhammouch, M., Sanders, G.M., Tinker, R.L., and Geiduschek, E.P. (1995). Old phage, new insights: two recently recognized mechanisms of transcriptional regulation in bacteriophage T4 development. FEMS Microbiol. Lett. 128, 1-8.
4. Buc, H., and McClure, W.R. (1985). Kinetics of open complex formation between Escherichia coli RNA polymerase and lacUV5 promoter. Evidence for a sequential mechanism involving three steps. Biochemistry 24, 2712-2723.
5. Buc, H., Amouyal, M., Buckle, M., Herbert, M., Kolb, A., Kotlarz, D., Menendez, M., Rimsky, S., Spassky, A., and Yeramian, E. (1987). Activation of transcription by the cyclic AMP receptor protein. In: RNA-polymerase and the Regulation of Transcription. W.S. Reznikoff, R.R. Burgess, J.E. Dahlberg, C.A. Gross, M.T. Record and M.P. Wickens, eds. (Amsterdam: Elsevier), pp. 115-125.
6. Buckle, M., Buc, H., and Travers, A.A. (1992). DNA deformation in nucleoprotein complexes between RNA polymerase, cAMP receptor protein and the lac UV5 promoter probed by singlet oxygen. EMBOJ. 11, 2619-2625.
7. Busby, S., and Buc, H. (1987). Positive regulation of gene expression by cyclic AMP and its receptor protein in Escherichia coli. Microbiol. Sci. 4, 371-375.
8. Busby, S., and Ebright, R.H. (1994). Promoter structure, promoter recognition, and transcription activation in prokaryotes. Cell 79, 743-746.
9. Busby, S., and Ebright, R.H. (1997). Transcription activation at class II CAP-dependent promoters. Mol. Microbiol. 23, 853-859.
10. Carmona, M., and Magasanik, B. (1996). Activation of transcription at sigma 54-dependent promoters on linear templates requires intrinsic or induced bending of the DNA. J. Mol. Biol. 261, 348-356.
11. Carpousis, A.J., and Gralla, J.D. (1980). Cycling of ribonucleic acid polymerase to produce oligonucleotides during initiation in vitro at the lacUV5 promoter. Biochemistry 19, 3245-3253.
12. Chen, Y., and Helmann, J.D. (1997). DNA-melting at the Bacillus subtilis flagellin promoter nucleates near -10 and expands unidirectionally. J. Mol. Biol. 267, 47-59.
13. Claverie-Martin, F., and Magasanik, B. (1991). Role of integration host factor in the regulation of glnHp2 promoter of Escherichia coli. Proc. Natl. Acad. Sci. USA 88, 1631-1635.
14. 32. J. Mol. Biol. 210, 521-530.
15. 2+ binding and its structural consequences at the transcription start site. Biochemistry 34, 15624-15632.
16. Darst, S.A., Kubalek, E.W., and Kornberg, R.D. (1989). The three-dimensional structure of Escherichia coli RNA polymerase holoenzyme determined by electron crystallography. Nature 340, 730-732.
17. deHaseth, P.L., and Helmann, J.D. (1995). Open complex formation by Escherichia coli RNA polymerase: the mechanism of polymerase-induced strand separation of double helical DNA. Mol. Microbiol. 16, 817-824.
18. Dethiollaz, S., Eichenberger, P., and Geiselmann, J. (1996). Influence of DNA geometry on transcriptional activation in Escherichia coli. EMBO J. 15, 5449-5458.
19. Dove, S.L., Joung, J.K., and Hochschild, A. (1997). Activation of prokaryotic transcription through arbitrary protein-protein contacts. Nature 386, 627-630.
20. Duval-Valentin, G., and Ehrlich, R. (1987). Dynamic and structural characterization of multiple steps during complex formation between E. coli RNA polymerase and tetR promoter from pSC101. Nucleic Acids Res. 15, 575-594.
21. Dykxhoorn, D.M., St. Pierre, R., and Linn, T. (1996). Synthesis of the beta and beta' subunits of Escherichia coli RNA polymerase is autogenously regulated in vivo by both transcriptional and translational mechanisms. Mol. Microbiol. 19, 483-493.
22. Ebright, R.H., and Busby, S. (1995). Escherichia coli RNA polymerase alpha subunit: structure and function. Curr. Op. Genet. Dev. 5, 197-200.
23. Eichenberger, P., Déthiollaz, S., Fujita, N., Ishihama, A., and Geiselmann, J. (1996). Influence of the Location of the cAMP Receptor Protein Binding Site on the geometry of a Transcriptional Activation Complex in Escherichia coli. Biochemistry 35, 15302-15312.
24. Ellinger, T., Behnke, D., Bujard, H., and Gralla, J.D. (1994). Stalling of Escherichia coli RNA polymerase in the + 6 to + 12 region in vivo is associated with tight binding to consensus promoter elements. J. Mol. Biol. 239, 455-465.
25. Fersht, A. (1977). Enzyme Structure and Mechanism (San Francisco: W.H. Freeman and Company).
26. Goosen, N., and van de Putte, P. (1995). The regulation of transcription initiation by integration host factor. Mol. Microbiol. 16, 1-7.
27. Gralla, J.D. (1996). Activation and repression of E coli promoters. Curr. Op. Genet. Dev. 6, 526-530.
28. Gralla, J.D., and Collado-Vides, J. (1996). Organization and function of transcription regulatory elements. In Escherichia coli and Salmonella. F. Neidhardt, ed. (Washington: American Society of Microbiology), pp. 1232-1246.
29. Ishihama, A. (1993). Protein-protein communication within the transcription apparatus. J. Bacteriol. 175, 2483-2489.
30. Jeon, Y.H., Yamazaki, T., Otomo, T., Ishihama, A., and Kyogoku, Y. (1997). Flexible linker in the RNA polymerase alpha subunit facilitates the independent motion of the C-terminal activator contact domain. J. Mol. Biol. 267, 953-962.
31. Kammerer, W., Deuschle, U., Gentz, R., and Bujard, H. (1986). Functional dissection of Escherichia coli promoters: information in the transcribed region is involved in late steps of the overall process. EMBO J. 5, 2995-3000.
32. Komissarova, N., and Kashlev, M. (1997). Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3′ end of the RNA intact and extruded. Proc. Natl. Acad. Sci. USA 94, 1755-1760.
33. Kovacic, R.T. (1987). The 0°C closed complex between Escherichia coli RNA polymerase and two promoters, T7-A3 and lacUV5. J. Biol. Chem. 262, 13654-13661.
34. Krummel, B., and Chamberlin, M.J. (1989). RNA chain initiation by Escherichia coli RNA polymerase. Structural transitions of the enzyme in early ternary complexes. Biochemistry 28, 7829-7842.
35. Lavigne, M., Herbert, M., Kolb, A., and Buc, H. (1992a). Upstream curved sequences influence the initiation of transcription at the Escherichia coli galactose operon. J. Mol. Biol. 224, 293-306.
36. Lavigne, M., Kolb, A., and Buc, H. (1992b). Transcription activation by cAMP receptor protein (CRP) at the Escherichia coli gal P1 promoter. Crucial role for the spacing between the CRP binding site and the -10 region. Biochemistry 31, 9647-9656.
37. Lavigne, M., Kolb, A., Yeramian, E., and Buc, H. (1994). CRP fixes the rotational orientation of covalently closed DNA molecules. EMBOJ. 13, 4983-4990.
38. Lobell, R.B., and Schleif, R. (1991). AraC-DNA looping: orientation and distance-dependent loop breaking by the cyclic AMP receptor protein. J. Mol. Biol. 218, 45-54.
39. McClure, W.R. (1985). Mechanism and control of transcription initiation in prokaryotes. Annu. Rev. Biochem. 54, 171-204.
40. Menendez, M., Kolb, A., and Buc, H. (1987). A new target for CRP action at the malT promoter. EMBO J. 6, 4227-4234.
41. Niu, W., Kim, Y., Tau, G., Heyduk, T., and Ebright, R.H. (1996). Transcription activation at class II CAP-dependent promoters: Two interactions between CAP and RNA polymerase. Cell 87, 1123-1134.
42. Parekh, B.S., and 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.
43. 54-dependent promoter Pu of Pseudomonas putida. Proc. Natl. Acad. Sci. USA 92, 7277-7281.
44. Perez Martin, J., and Espinosa, M. (1994). Correlation between DNA bending and transcriptional activation at a plasmid promoter. J. Mol. Biol. 241, 7-17.
45. Perez Martin, J., Rojo, F., and De Lorenzo, V. (1994). Promoters responsive to DNA bending: a common theme in prokaryotic gene expression. Microbiol. Rev. 58, 268-290.
46. Rao, L., Ross, W., Appleman, J.A., Gaal, T., Leirmo, S., Schlax, P.J., Record, M.T., Jr., and Course, R.L. (1994). Factor independent activation of rrnB P1. An "extended" promoter with an upstream element that dramatically increases promoter strength. J. Mol. Biol. 235, 1421-1435.
47. 70), promoters, and the kinetics of the steps of transcription initiation. In Escherichia coli and Salmonella. F. Neidhardt, ed. (Washington: ASM Press), pp. 792-820.
48. Rees, W.A., Keller, R.W., Vesenka, J.P., Yang, G., and Bustamante, C. (1993). Evidence of DNA bending in transcription complexes images by scanning force microscopy. Science 260, 1646-1649.
49. Rice, P.A., Yang, S., Mizuuchi, K., and Nash, H.A. (1996). Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn. Cell 87, 1295-1306.
50. Richet, E., and Sogaard Andersen, L. (1994). CRP induces the repositioning of MalT at the Escherichia coli malKp promoter primarily through DNA bending. EMBO J. 13, 4558-4567.
51. Richet, E., Vidal Ingigliardi, D., and Raibaud, O. (1991). A new mechanism for coactivation of transcription initiation: repositioning of an activator triggered by the binding of a second activator. Cell 66, 1185-1195.
52. Rippe, K., von Hippel, P.H., and Langowski, J. (1995). Action at a distance: DNA looping and initiation of transcription. Trends. Biochem. Sci. 20, 500-506.
53. Ryu, S., Garges, S., and Adhya, S. (1994). An arcane role of DNA in transcription activation Proc. Natl. Acad. Sci. USA 97, 8582-8586. [published erratum appears in Proc Natl Acad Sci USA 1994 Nov 8:91(23): 11281].
54. Schickor, P., Metzger, W., Werel, W., Lederer, H., and Neumann, H. (1990). Topography of intermediates in transcription initiation of E. coli. EMBO J. 9, 2215-2220.
55. Schlax, P.J., Capp, M.W., and Record, M.T., Jr. (1995). Inhibition of transcription initiation by lac repressor. J. Mol. Biol. 245, 331-350.
56. Schleif, R. (1996). Two positively regulated systems, ara and mal. In Escherichia coli and Salmonella. F. Neidhardt, ed. (Washington: ASM Press), pp. 1300-1309.
57. Straney, D.C., and Crothers, D.M. (1987). A stressed intermediate in the formation of stably initiated RNA chains at the Escherichia coli lacUV5 promoter. J. Mol. Biol. 193, 267-278.
58. Su, T.T., and McClure, W.R. (1994). Selective binding of Escherichia coli RNA polymerase to topoisomers of minicircles carrying the TAC16 and TAC17 promoters. J. Biol. Chem. 269, 13511-13521.
59. Suh, W.C., Ross, W., and Record, M.T., Jr. (1993). Two open complexes and a requirement for Mg2+ to open the lambda PR transcription start site. Science 259, 358-361.
60. Tagami, H., and Aiba, H. (1995). Role of CRP in transcription activation at Escherichia coli lac promoter: CRP is dispensable after the formation of open complex. Nucleic Acids Res. 23, 599-605.
61. van Ulsen, P. (1997). Regulation of transcription initiation from the early promoter of bacteriophage Mu. 125-132. (Abstract)
62. von Hippel, P.H., and Berg, O.G. (1989). Facilitated target location in biological systems. J. Biol. Chem. 264, 675-678.
63. von Hippel, P.H., and Yager, T.D. (1992). The elongation-termination decision in transcription. Science 255, 809-812.
64. von Hippel, P.H., Rees, W.A., Rippe, K., and Wilson, K.S. (1996). Specificity mechanisms in the control of transcription. Biophys. Chem. 59, 231-246.
65. Yager, T.D., and von Hippel, P.H. (1991). A thermodynamic analysis of RNA transcript elongation and termination in Escherichia coli. Biochemistry 30, 1097-1118.
66. Zhou, Y., Merkel, T.J., and Ebright, R.H. (1994a). Characterization of the activating region of Escherichia coli catabolite gene activator protein (CAP). II. Role at Class I and class II CAP-dependent promoters. J. Mol. Biol. 243, 603-610.
67. Zhou, Y., Pendergrast, P.S., Bell, A., Williams, R., Busby, S., and Ebright, R.H. (1994b). The functional subunit of a dimeric transcription activator protein depends on promoter architecture. EMBO J. 13, 4549-4557.
68. Zinkel, S.S., and Crothers, D.M. (1991). Catabolite activator protein-induced DNA bending in transcription initiation. J. Mol. Biol. 219, 201-215.