A Kinetic Model of Transcription Initiation by RNA Polymerase

Journal of Molecular Biology

Volumn 378, Issue 3, 2008, Pages 520-529

  Xue, Xiao chuan ^a   Liu, Fei ^a   Ou Yang, Zhong can ^a,b  

^a TSINGHUA UNIVERSITY   (China)

^b INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

Author keywords

abortive; escape; RNA polymerase; scrunching; transcription initiation

Indexed keywords

NUCLEOSIDE TRIPHOSPHATE; RNA POLYMERASE;

ARTICLE; DISSOCIATION CONSTANT; DNA RNA HYBRIDIZATION; DNA SEQUENCE; DNA STRAND; DNA TEMPLATE; ENZYME KINETICS; MONTE CARLO METHOD; PRIORITY JOURNAL; TRANSCRIPTION INITIATION;

EID: 42249085944     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2008.03.008     Document Type: Article

References (32)

1. Murakmi K.S., and Darst S.A. Bacterial RNA polymerases: the whole story. Curr. Opin. Struct. Biol. 13 (2003) 31-39
2. Greive S.J., and von Hippel P.H. Thinking quantitatively about transcriptional regulation. Nat. Rev. Mol. Cell Biol. 6 (2005) 221-232
3. Bai L., Santangelo T.J., and Wang M.D. Single-molecule analysis of RNA polymerase transcription. Annu. Rev. Biophys. Biomol. Struct. 35 (2006) 343-360
4. Shundrovsky A., Santangelo T.J., Roberts J.W., and Wang M.D. A single-molecule technique to study sequence-dependent transcription pausing. Biophys. J. 87 (2004) 3945-3953
5. 70 in transcription elongation: single-molecule analysis. Mol. Cell 20 (2004) 347-356
6. McClure W.R., Cech C.L., and Johnston D.E. A steady state assay for the RNA polymerase initiation reaction. J. Biol. Chem. 253 (1978) 8941-8948
7. Smagowicz W., and Scheit K.H. A minimal mechanism for abortive initiation of transcription of T7 DNA. Nucleic Acids Res. 9 (1981) 5845-5854
8. Hsu L.M. Promoter clearance and escape in prokaryotes. Biochim. Biophys. Acta 1577 (2002) 191-207
9. Revyakin A., Liu C.Y., Ebright R.H., and Strick T.R. Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching. Science 314 (2006) 1139-1143
10. Kapanidis A.N., Margeat E., Ho S.O., Kortkhonjia E., Weiss S., and Ebright R.H. Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism. Science 314 (2006) 1144-1147
11. Bai L., Shundrovsky A., and Wang M.D. Sequence-dependent kinetic model for transcription elongation by RNA polymerase. J. Mol. Biol. 344 (2004) 335-349
12. Tadigotla V.R., Maoiléidigh D.O., Sengupta A.M., Epshtein V., Ebright R.H., Nudler E., and Ruckenstein A.E. Thermodynamic and kinetic modeling of transcriptional pausing. Proc. Natl. Acad. Sci. USA 103 (2006) 4439-4444
13. Hsu L.M., Vo N.V., Kane C.M., and Chamberlin M.J. In vitro studies of transcript initiation by Escherichia coli RNA polymerase. 1. RNA chain initiation, abortive initiation, and promoter escape at three bacteriophage promoters. Biochemistry 42 (2003) 3777-3786
14. Vo N.V., Hsu L.M., Kane C.M., and Chamberlin M.J. In vitro studies of transcript initiation by Escherichia coli RNA polymerase. 2. Formation and characterization of two distinct classes of initial transcribing complexes. Biochemistry 42 (2003) 3787-3797
15. Vo N.V., Hsu L.M., Kane C.M., and Chamberlin M.J. In vitro studies of transcript initiation by Escherichia coli RNA polymerase. 3. Influences of individual DNA elements within the promoter recognition region on abortive initiation and promoter escape. Biochemistry 42 (2003) 3798-3811
16. Nudler E., Gusarov I., Avetissova E., Kozlov M., and Goldfarb A. Spatial organization of transcription elongation complex in Escherichia coli. Science 281 (1998) 424-428
17. Korzheva N., Mustaev A., Kozlov M., Malhotra A., Nikiforov V., Goldfarb A., and Darst S.A. A structural model of transcription elongation. Science 289 (2000) 619-625
18. Zhang G. Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 Å resolution. Cell 98 (1999) 811-824
19. Revyakin A., Ebright R.H., and Strick T.R. Promoter unwinding and promoter clearance by RNA polymerase: detection by single-molecule DNA nanomanipulation. Proc. Natl. Acad. Sci. USA 101 (2004) 4776-4780
20. Young B.A., Gruber T.M., and Gross C.A. Views of transcription initiation. Cell 109 (2002) 417-420
21. Pal M., Ponticelli A.S., and Lusel D.S. The role of the transcription bubble and TFIIB in promoter clearance by RNA polymerase II. Mol. Cell 19 (2005) 101-110
22. Liu C.H., and Martin C.T. Promoter clearance by T7 RNA polymerase. J. Biol. Chem. 277 (2002) 2725-2731
23. Gong P., Esposito E.A., and Martin C.T. Initial bubble collapse plays a key role in the transition to elongation in T7 RNA polymerase. J. Biol. Chem. 279 (2004) 44277-44285
24. Santa Lucia J., and Hicks D. The thermodynamics of DNA structural motifs. Annu. Rev. Biophys. Biomol. Struct. 33 (2004) 415-440
25. Sugimoto N., Nakano S., Katoh M., Matsumura A., Nakamuta H., Ohmichi T., et al. Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes. Biochemistry 34 (1995) 11211-11216
26. Maerkl S.J., and Quake S.R. A systems approach to measuring the binding energy landscapes of transcription factors. Science 315 (2007) 233-237
27. Bandwar R.P., and Patel S.S. The energetics of consensus promoter opening by T7 RNA polymerase. J. Mol. Biol. 324 (2002) 63-72
28. Thompson M., and Woodbury N.W. Thermodynamics of specific and nonspecific DNA binding by two DNA-binding domains conjugated to fluorescent probes. Biophys. J. 81 (2006) 17939-18804
29. Margeat E., Kapanidis A.N., Tinnefeld P., Wang Y., Mukhopadhyay J., Ebright R.H., and Weiss S. Direct observation of abortive initiation and promoter escape within single immobilized transcription complexes. Biophys. J. 90 (2006) 1419-1431
30. Straney D.C., and Crothers D.M. Comparison of the open complexes formed by RNA polymerase at the Escherichia coli lac UV5 promoter. J. Mol. Biol. 193 (1987) 279-292
31. Esposito E.A., and Martin C.T. Cross-linking of promoter DNA to T7 RNA polymerase does not prevent formation of a stable elongation complex. J. Biol. Chem. 279 (2004) 44270-44276
32. Rhodes G., and Chamberlin M.J. Ribonucleic acid chain elongation by Escherichia coli ribonucleic acid polymerase I. Isolation of ternary complexes and the kinetics of elongation. J. Biol. Chem. 249 (1974) 6675