DNA footprints of the two kinetically significant intermediates in formation of an RNA polymerase-promoter open complex: Evidence that interactions with start site and downstream DNA induce sequential conformational changes in polymerase and DNA

Journal of Molecular Biology

Volumn 283, Issue 4, 1998, Pages 741-756

  Craig, Maria L ^a   Tsodikov, Oleg V ^a   McQuade, Kristi L ^a   Schlax Jr , Peter E ^a   Capp, Michael W ^a   Saecker, Ruth M ^a   Record Jr , M Thomas ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

Footprinting; Open complex formation; RNA polymerase; Transcription initiation; P(R) promoter

Indexed keywords

DEOXYRIBONUCLEASE I; HEPARIN; RNA POLYMERASE;

ARTICLE; BINDING COMPETITION; COMPLEX FORMATION; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; DNA FOOTPRINTING; KINETICS; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROMOTER REGION; START CODON; TEMPERATURE; THERMODYNAMICS;

EID: 0032491380     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2129     Document Type: Article

References (46)

1. Asturias J.F., Meredith G.D., Poglitsch C.L., Kornberg R.D. Two conformations of RNA polymerase II revealed by electron crystallography. J. Mol. Biol. 272:1997;536-540
2. Bokal A.J.I.V., Ross W., Gourse R.L. The transcriptional activator protein FIS DNA interactions and cooperative interactions with RNA polymerase at the Escherichia coli rrnB P1 promoter. J. Mol. Biol. 245:1995;197-207
3. Brenowitz M., Senear D.F., Shea M.A., Ackers G.K. Quantitative DNase footprint titration a method for studying protein-DNA interactions. Methods Enzymol. 130:1986;132-181
4. Buc H., McClure W.R. Kinetics of open complex formation between Escherichia coli RNA polymerase and the lac UV5 promoter. Evidence for a sequential mechanism involving three steps. Biochemistry. 24:1985;2712-2723
5. Burgess R.R., Jendrisak J.J. A procedure for the rapid, large-scale purification of Escherichia coli DNA-dependent RNA polymerase involving polymin P precipitation and DNA-cellulose chromatography. Biochemistry. 14:1975;4634-4638
6. 32 at the groE promoter. J. Mol. Biol. 210:1989;521-530
7. R promoter. 1996;University of Wisconsin-Madison, Madison, WI. PhD thesis
8. 2+ binding and its structural consequences at the transcription start site. Biochemistry. 34:1995;15624-15632
9. Darst S.A., Kubalek E.W., Kornberg R.D. Three-dimensional structure of Escherichia coli RNA polymerase holoenzyme determined by electron crystallography. Nature. 340:1989;730-732
10. deHaseth P.L., Helmann J.D. Open complex formation by Escherichia coli RNA polymerase the mechanism of polymerase-induced strand separation of double helical DNA. Mol. Microbiol. 16:1995;817-824
11. Doublié S., Tabor S., Long A.M., Richardson C.C., Ellenberger T. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution. Nature. 391:1998;251-258
12. Gaal T., Ross W., Blatter E.E., Tang H., Jia X., Krishnan V.V., Assa-Munt N., Ebright R.H., Gourse R.L. DNA-binding determinants of the α subunit of RNA polymerase novel DNA-binding architecture. Genes Dev. 10:1996;16-26
13. Gonzalez N., Wiggs J., Chamberlin M.J. A simple procedure for resolution of Escherichia coli RNA polymerase holoenzyme from core polymerase. Arch. Biochem. Biophys. 182:1977;404-408
14. Ha J.-H., Spolar R.S., Record M.T. Jr. Role of the hydrophobic effect in stability of site-specific protein-DNA complexes. J. Mol. Biol. 209:1989;801-816
15. Hofer B., Muller D., Koster H. The pathway of E. coli RNA polymerase-promoter complex formation as visualized by footprinting. Nucl. Acids Res. 16:1985;5995-6013
16. Johnson M.L., Frasier S.G. Non-linear least-square analysis. Methods Enzymol. 117:1985;301-342
17. Kiefer J.R., Mao C., Braman J.C., Beese L.S. Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal. Nature. 391:1998;304-307
18. Kovacic R.T. The 0°C closed complexes between Escherichia coli RNA polymerase and two promoters, T7-A3 and lacUV5. J. Biol. Chem. 262:1987;13654-13661
19. Lahm A., Suck D. DNase I-induced DNA conformation 2 Å structure of a DNase I-octamer complex. J. Mol. Biol. 262:1991;645-667
20. Lavigne M., Kolb A., Buc H. 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. 31:1992;9647-9656
21. 70 with promoter DNA. Eckstein F., Lilley D.M.J. Nucleic Acids and Molecular Biology. vol. 4:1990;123-151 Springer-Verlag, Berlin
22. Maxam A.M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 65:1980;499-560
23. R promoter Interactions effects of temperature and nucleotides on the kinetics and thermodynamics of open complex formation. 1996;University of Wisconsin-Madison, Madison, WI. PhD thesis
24. Mecsas J., Cowing D.W., Gross C.A. Development of RNA polymerase-promoter contacts during open complex formation. J. Mol. Biol. 220:1991;585-597
25. Nickerson C.A., Achberger E.C. Role of curved DNA in binding to Escherichia coli RNA polymerase to promoters. J. Bacteriol. 177:1995;5756-5761
26. Nudler E., Avetissova E., Markovtsov V., Goldfarb A. Transcription processivity protein-DNA interactions holding together the elongation complex. Science. 273:1996;211-217
27. Pelletier H. Polymerase structures and mechanism. Science. 266:1994;2025-2026
28. Polyakov A., Severinova E., Darst S.A. Three-dimensional structure of E. coli core RNA polymerase promoter binding and elongation conformations of the enzyme. Cell. 83:1995;365-373
29. 70), promoters, and the kinetics of the steps of transcription initiation. Neidhardt F.C. 2nd edit. Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology. vol. 1:1996;792-821 ASM Press, Washington, DC
30. R promoter by salt concentration. Biochemistry. 24:1985;4721-4726
31. R promoter. J. Mol. Biol. 176:1984;495-521
32. R promoter interaction assignment of the kinetic steps corresponding to protein conformational change and DNA opening. J. Mol. Biol. 184:1985;441-453
33. Ross W., Gosink K.K., Salomon J., Igarashi K., Zou C., Ishihama A., Severinov K., Gourse R.L. A third recognition element in bacterial promoters DNA binding by the α subunit of RNA polymerase. Science. 262:1993;1407-1413
34. Schickor P., Metzger W., Werel W., Lederer H., Heumann H. Topography of intermediates in transcription initiation of E. coli. EMBO J. 9:1990;2215-2220
35. R promoter. 1995;University of Wilconsin-Madison, Madison, WI. PhD thesis
36. Selden R.F., Chory J. Rapid estimation of DNA concentration by ethidium bromide dot quantitation. Ausubel F.M., Brent R., Kingston R.E., Moore D.D., Seidman J.G., Smith J.A., Struhl K. Current Protocols in Molecular Biology. vol. 2.6.7:1987;John Wiley & Sons, Inc, NY
37. Severinov K., Darst S.A. A mutant RNA polymerase that forms unusual open promoter complexes. Proc. Natl Acad. Sci. USA. 94:1997;13481-13486
38. Sousa R., Chung Y.J., Rose J.P., Wang B.C. Crystal structure of bacteriophage T7 RNA polymerase at 3.3 Å resolution. Nature. 364:1993;593-599
39. Sousa R., Rose J.P., Wang B.C. The thumb's knuckle. Flexibility in the thumb subdomain of T7 RNA polymerase is revealed by the structure of a chimeric T7/T3 RNAP polymerase. J. Mol. Biol. 244:1994;6-12
40. Spassky L.A., Kirkegaard K., Buc H. Changes in the DNA structure of the lac UV5 promoter during formation of an open complex with Escherichia coli RNA polymerase. Biochemistry. 24:1985;2723-2730
41. Spolar R.S., Record M.T. Jr. Coupling of local folding to site-specific binding of proteins to DNA. Science. 263:1994;777-784
42. Steitz T.A., Smerdom S.J., Jåger J., Joyce C.M. A unified polymerase mechanism for nonhomologous DNA and RNA polymerases. Science. 266:1994;2022-2025
43. 2+. Biochemistry. 31:1992;7815-7825
44. 2+ is required to open the transcription site. Science. 259:1993;358-361
45. R promoter complex formation. 1998;University of Witconsin-Madison, Madison, WI. PhD thesis
46. 70 RNA polymerase. J. Mol. Biol. 283:1998;757-769