T7 RNA polymerase studied by force measurements varying cofactor concentration

Biophysical Journal

Volumn 95, Issue 5, 2008, Pages 2423-2433

  Thomen, P ^a   Lopez, P J ^b   Bockelmann, U ^c   Guillerez, J ^a   Dreyfus, M ^a   Heslot, Francois ^a  

^a ECOLE NORMALE SUPÉRIEURE   (France)

^b Centre National de la Recherche Scientifique   (France)

^c PSL RESEARCH UNIVERSITY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIOPHAGE T7 RNA POLYMERASE; DNA DIRECTED RNA POLYMERASE; MAGNESIUM; NUCLEOTIDE; VIRUS PROTEIN;

ARTICLE; BACTERIOPHAGE T7; COENZYME; ENZYMOLOGY; GENETIC TRANSCRIPTION; GENETICS; METABOLISM;

BACTERIOPHAGE T7; COENZYMES; DNA-DIRECTED RNA POLYMERASES; MAGNESIUM; NUCLEOTIDES; TRANSCRIPTION, GENETIC; VIRAL PROTEINS;

EID: 51649113736     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1529/biophysj.107.125096     Document Type: Article

References (38)

1. Erie, D. A., T. D. Yager, and P. H. Vonhippel. 1992. The single-nucleotide addition cycle in transcription: a biophysical and biochemical perspective. Annu. Rev. Biophys. Biomol. Struct. 21:379-415.
2. Alberts, B., A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter. 2002. Molecular Biology of the Cell, 4th ed. Garland, New York.
3. Davenport, R. J., G. J. L. Wuite, R. Landick, and C. Bustamante. 2000. Single-molecule study of transcriptional pausing and arrest by E-coli RNA polymerase. Science. 287:2497-2500.
4. Wuite, G. J. L., S. B. Smith, M. Young, D. Keller, and C. Bustamante. 2000. Single-molecule studies of the effect of template tension on T7 DNA polymerase activity. Nature. 404:103-106.
5. Smith, D. E., S. J. Tans, S. B. Smith, S. Grimes, D. L. Anderson, and C. Bustamante. 2001. The bacteriophage φ29 portal motor can package DNA against a large internal force. Nature. 413:748-752.
6. Visscher, K., M. J. Schnitzer, and S. M. Block. 1999. Single kinesin molecules studied with a molecular force clamp. Nature. 400:184-189.
7. Schnitzer, M. J., K. Visscher, and S. M. Block. 2000. Force production by single kinesin motors. Nat. Cell Biol. 2:718-723.
8. Wang, M. D., M. J. Schnitzer, H. Yin, R. Landick, J. Gelles, and S. M. Block. 1998. Force and velocity measured for single molecules of RNA polymerase. Science. 282:902-907.
9. Adelman, K., A. La Porta, T. J. Santangelo, J. T. Lis, J. W. Roberts, and M. D. Wang. 2002. Single molecule analysis of RNA polymerase elongation reveals uniform kinetic behavior. Proc. Natl. Acad. Sci. USA. 99:13538-13543.
10. Maier, B., D. Bensimon, and V. Croquette. 2000. Replication by a single DNA polymerase of a stretched single-stranded DNA. Proc. Natl. Acad. Sci. USA. 97:12002-12007.
11. Neuman, K. C., E. A. Abbondanzieri, R. Landick, J. Gelles, and S. M. Block. 2003. Ubiquitous transcriptional pausing is independent of RNA polymerase backtracking. Cell. 115:437-447.
12. Itoh, H., A. Takahashi, K. Adachi, H. Noji, R. Yasuda, M. Yoshida, and K. Kinosita. 2004. Mechanically driven ATP synthesis by F-1-ATPase. Nature. 427:465-468.
13. Abbondanzieri, E. A., W. J. Greenleaf, J. W. Shaevitz, R. Landick, and S. M. Block. 2005. Direct observation of base-pair stepping by RNA polymerase. Nature. 438:460-465.
14. Yin, Y. W., and T. A. Steitz. 2004. The structural mechanism of translocation and helicase activity in T7 RNA polymerase. Cell. 116:393-404.
15. Temiakov, D., V. Patlan, M. Anikin, W. T. McAllister, S. Yokoyama, and D. G. Vassylyev. 2004. Structural basis for substrate selection by T7 RNA polymerase. Cell. 116:381-391.
16. Skinner, G. M., C. G. Baumann, D. M. Quinn, J. E. Molloy, and J. G. Hoggett. 2004. Promoter binding, initiation, and elongation by bacteriophage T7 RNA polymerase: a single-molecule view of the transcription cycle. J. Biol. Chem. 279:3239-3244.
17. Yin, H., M. D. Wang, K. Svoboda, R. Landick, S. M. Block, and J. Gelles. 1995. Transcription against an applied force. Science. 270:1653-1657.
18. Thomen, P., P. J. Lopez, and F. Heslot. 2005. Unravelling the mechanism of RNA-polymerase forward motion by using mechanical force. Phys. Rev. Lett. 94:128102.
19. Yin, Y. W., and A. A. Steitz. 2002. Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase. Science. 298:1387-1395.
20. Tahirov, T. H., D. Temiakov, M. Anikin, V. Patlan, W. T. McAllister, D. G. Vassylyev, and S. Yokoyama. 2002. Structure of a T7 RNA polymerase elongation complex at 2.9 Å resolution. Nature. 420:43-50.
21. Bockelmann, U., P. Thomen, B. Essevaz-Roulet, V. Viasnoff, and F. Heslot. 2002. Unzipping DNA with optical tweezers: high sequence sensitivity and force flips. Biophys. J. 82:1537-1553.
22. Maslak, M., and C. T. Martin. 1994. Effects of solution conditions on the steady-state kinetics of initiation of transcription by T7 RNA polymerase. Biochemistry. 33:6918-6924.
23. Brieba, L. G., V. Gopal, and R. Sousa. 2001. Scanning mutagenesis reveals roles for helix N of the bacteriophage T7 RNA polymerase thumb subdomain in transcription complex stability, pausing, and termination. J. Biol. Chem. 276:10306-10313.
24. Odijk, T. 1995. Stiff chains and filaments under tension. Macromolecules. 28:7016-7018.
25. Tolic-Norrelykke, S. F., A. M. Engh, R. Landick, and J. Gelles. 2004. Diversity in the rates of transcript elongation by single RNA polymerase molecules. J. Biol. Chem. 279:3292-3299.
26. Arnold, S., M. Siemann, K. Scharnweber, M. Werner, S. Baumann, and M. Reuss. 2001. Kinetic modeling and simulation of in vitro transcription by phage T7 RNA polymerase. Biotechnol. Bioeng. 72:548-561.
27. Parrondo, J. M. R., and B. J. De Cisneros. 2002. Energetics of Brownian motors: a review. Appl. Phys. A. 75:179-191.
28. Astumian, R. D. 1997. Thermodynamics and kinetics of a Brownian motor. Science. 276:917-922.
29. Li, Y., S. Korolev, and G. Waksman. 1998. Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation. EMBO J. 17:7514-7525.
30. Doublie, S., S. Tabor, A. M. Long, C. C. Richardson, and T. Ellenberger. 1998. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Åresolution. Nature. 391:251-258.
31. Huang, H. F., R. Chopra, G. L. Verdine, and S. C. Harrison. 1998. Structure of a covalently trapped catalytic complex of HIV-I reverse transcriptase: implications for drug resistance. Science. 282:1669-1675.
32. Guo, Q., and R. Sousa. 2006. Translocation by T7 RNA polymerase: a sensitively Brownian ratchet. J. Mol. Biol. 358:241-254.
33. Marchand, B., E. P. Tchesnokov, and M. Gotte. 2007. The pyrophosphate analogue foscarnet traps the pre-translocational state of HIV-1 reverse transcriptase in a Brownian ratchet model of polymerase translocation. J. Biol. Chem. 282:3337-3346.
34. Brautigam, C. A., and T. A. Steitz. 1998. Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes. Curr. Opin. Struct. Biol. 8:54-63.
35. 2- and other ions in solution: calculation of true concentrations of species present in mixtures of associating ions. Biochem. J. 159:1-5.
36. 2+ dependency of HIV-1 reverse transcription, inhibition by nucleoside analogues and resistance. Nucleic Acids Res. 34:42-52.
37. Young, J. S., W. F. Ramirez, and R. H. Davis. 1997. Modeling and optimization of a batch process for in vitro RNA production. Biotechnol. Bioeng. 56:210-220.
38. Woody, A. Y. M., S. S. Eaton, P. A. Osumi-Davis, and R. W. Woody. 1996. Asp537 and Asp812 in bacteriophage T7 RNA polymerase as metal ion-binding sites studied by EPR, flow-dialysis, and transcription. Biochemistry. 35:144-152.