Table of Contents Author Guidelines Submit a Manuscript
Archaea
Volume 2011, Article ID 608385, 7 pages
http://dx.doi.org/10.1155/2011/608385
Review Article

The Bridge Helix of RNA Polymerase Acts as a Central Nanomechanical Switchboard for Coordinating Catalysis and Substrate Movement

Department of Life Sciences, Imperial College London, Sir Alexander Fleming Building, Exhibition Road, London SW7 2AZ, UK

Received 1 September 2011; Accepted 25 October 2011

Academic Editor: Herman van Tilbeurgh

Copyright © 2011 Robert O. J. Weinzierl. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. F. Brueckner, J. Ortiz, and P. Cramer, “A movie of the RNA polymerase nucleotide addition cycle,” Current Opinion in Structural Biology, vol. 19, no. 3, pp. 294–299, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  2. C. D. Kaplan and R. D. Kornberg, “A bridge to transcription by RNA polymerase,” Journal of Biology, vol. 7, no. 10, article 39, 2008. View at Publisher · View at Google Scholar · View at PubMed
  3. F. Werner and R. O. J. Weinzierl, “A recombinant RNA polymerase II-like enzyme capable of promoter-specific transcription,” Molecular Cell, vol. 10, no. 3, pp. 635–646, 2002. View at Publisher · View at Google Scholar · View at Scopus
  4. S. Naji, S. Grünberg, and M. Thomm, “The RPB7 orthologue E′ is required for transcriptional activity of a reconstituted archaeal core enzyme at low temperatures and stimulates open complex formation,” Journal of Biological Chemistry, vol. 282, no. 15, pp. 11047–11057, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  5. P. Baumann, S. A. Quereshi, and S. P. Jackson, “Transcription: new insights from studies on Archaea,” Trends in Genetics, vol. 11, no. 7, pp. 279–283, 1995. View at Publisher · View at Google Scholar · View at Scopus
  6. J. D. Parvin and P. A. Sharp, “DNA topology and a minimal set of basal factors for transcription by RNA polymerase II,” Cell, vol. 73, no. 3, pp. 533–540, 1993. View at Publisher · View at Google Scholar · View at Scopus
  7. T. Juven-Gershon and J. T. Kadonaga, “Regulation of gene expression via the core promoter and the basal transcriptional machinery,” Developmental Biology, vol. 339, no. 2, pp. 225–229, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  8. F. Werner, “Structural evolution of multisubunit RNA polymerases,” Trends in Microbiology, vol. 16, no. 6, pp. 247–250, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  9. F. Werner and D. Grohmann, “Evolution of multisubunit RNA polymerases in the three domains of life,” Nature Reviews in Microbiology, vol. 9, no. 2, pp. 85–98, 2011. View at Publisher · View at Google Scholar · View at PubMed
  10. W. Hausner, G. Frey, and M. Thomm, “Control regions of an archaeal gene. A TATA box and an initiator element promote cell-free transcription of the tRNA(Val) gene of methanococcus vannielii,” Journal of Molecular Biology, vol. 222, no. 3, pp. 495–508, 1991. View at Google Scholar · View at Scopus
  11. W. Hausner, J. Wettach, C. Hethke, and M. Thomm, “Two transcription factors related with the eucaryal transcription factors TATA-binding protein and transcription factor IIB direct promoter recognition by an archaeal RNA polymerase,” Journal of Biological Chemistry, vol. 271, no. 47, pp. 30144–30148, 1996. View at Publisher · View at Google Scholar · View at Scopus
  12. S. A. Qureshi, S. D. Bell, and S. P. Jackson, “Factor requirements for transcription in the Archaeon Sulfolobus shibatae,” EMBO Journal, vol. 16, no. 10, pp. 2927–2936, 1997. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  13. M. Ouhammouch, F. Werner, R. O. J. Weinzierl, and E. P. Geiduschek, “A fully recombinant system for activator-dependent archaeal transcription,” Journal of Biological Chemistry, vol. 279, no. 50, pp. 51719–51721, 2004. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  14. F. Werner and R. O. J. Weinzierl, “Direct modulation of RNA polymerase core functions by basal transcription factors,” Molecular and Cellular Biology, vol. 25, no. 18, pp. 8344–8355, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  15. F. Werner, S. Wiesler, S. Nottebaum, and R. O. J. Weinzierl, “Modulation of RNA polymerase core functions by basal transcription factor TFB/TFIIB,” Biochemical Society Symposium, vol. 73, pp. 49–58, 2006. View at Google Scholar · View at Scopus
  16. S. C. Wiesler and R. O. Weinzierl, “The linker domain of basal transcription factor TFIIB controls distinct recruitment and transcription stimulation functions,” Nucleic Acids Research, vol. 39, no. 2, pp. 464–474, 2011. View at Publisher · View at Google Scholar · View at PubMed
  17. D. Wang, D. A. Bushnell, K. D. Westover, C. D. Kaplan, and R. D. Kornberg, “Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis,” Cell, vol. 127, no. 5, pp. 941–954, 2006. View at Publisher · View at Google Scholar · View at PubMed
  18. The PyMOL Molecular Graphics System, Version 1.2r3pre, Schrödinger, LLC.
  19. R. P. Kandpal, B. Saviola, and J. Felton, “The era of 'omics unlimited,” BioTechniques, vol. 46, no. 5, pp. 351–355, 2009. View at Publisher · View at Google Scholar · View at PubMed
  20. S. Nottebaum, L. Tan, D. Trzaska, H. C. Carney, and R. O. J. Weinzierl, “The RNA polymerase factory: a robotic in vitro assembly platform for high-throughput production of recombinant protein complexes,” Nucleic Acids Research, vol. 36, no. 1, pp. 245–252, 2008. View at Publisher · View at Google Scholar · View at PubMed
  21. L. Tan, S. Wiesler, D. Trzaska, H. C. Carney, and R. O. J. Weinzierl, “Bridge helix and trigger loop perturbations generate superactive RNA polymerases,” Journal of Biology, vol. 7, no. 10, article 40, 2008. View at Publisher · View at Google Scholar · View at PubMed
  22. R. O. J. Weinzierl, “Nanomechanical constraints acting on the catalytic site of cellular RNA polymerases,” Biochemical Society Transactions, vol. 38, no. 2, pp. 428–432, 2010. View at Publisher · View at Google Scholar · View at PubMed
  23. R. O. J. Weinzierl, “The nucleotide addition cycle of RNA polymerase is controlled by two molecular hinges in the Bridge Helix domain,” BMC Biology, vol. 8, article 134, 2010. View at Publisher · View at Google Scholar · View at PubMed
  24. P. P. Hein and R. Landick, “The bridge helix coordinates movements of modules in RNA polymerase,” BMC Biology, vol. 8, article 141, 2010. View at Publisher · View at Google Scholar · View at PubMed
  25. S. A. Seibold, B. N. Singh, C. Zhang et al., “Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase,” Biochimica et Biophysica Acta, vol. 1799, no. 8, pp. 575–587, 2010. View at Publisher · View at Google Scholar · View at PubMed
  26. M. Jovanovic, P. C. Burrows, D. Bose et al., “Activity map of the Escherichia coli RNA polymerase bridge helix,” Journal of Biological Chemistry, vol. 286, no. 16, pp. 14469–14479, 2011. View at Publisher · View at Google Scholar · View at PubMed
  27. H. Heindl, P. Greenwell, N. Weingarten, T. Kiss, G. Terstyanszky, and R. O. Weinzierl, “Cation-π interactions induce kinking of a molecular hinge in the RNA polymerase bridge-helix domain,” Biochemical Society Transactions, vol. 39, no. 1, pp. 31–35, 2011. View at Publisher · View at Google Scholar · View at PubMed
  28. A. Hirata, B. J. Klein, and K. S. Murakami, “The X-ray crystal structure of RNA polymerase from Archaea,” Nature, vol. 451, no. 7180, pp. 851–854, 2008. View at Publisher · View at Google Scholar · View at PubMed
  29. Y. Korkhin, U. M. Unligil, O. Littlefield et al., “Evolution of complex RNA polymerases: the complete archaeal RNA polymerase structure,” PLoS Biology, vol. 7, no. 5, Article ID e1000102, 2009. View at Publisher · View at Google Scholar · View at PubMed
  30. A. Klug, “A marvellous machine for making messages,” Science, vol. 292, no. 5523, pp. 1844–1846, 2001. View at Publisher · View at Google Scholar · View at PubMed
  31. R. Sousa, “Machinations of a Maxwellian demon,” Cell, vol. 120, no. 2, pp. 155–158, 2005. View at Publisher · View at Google Scholar · View at PubMed
  32. G. Bar-Nahum, V. Epshtein, A. E. Ruckenstein, R. Rafikov, A. Mustaev, and E. Nudler, “A ratchet mechanism of transcription elongation and its control,” Cell, vol. 120, no. 2, pp. 183–193, 2005. View at Publisher · View at Google Scholar · View at PubMed
  33. D. Temiakov, N. Zenkin, M. N. Vassylyeva et al., “Structural basis of transcription inhibition by antibiotic streptolydigin,” Molecular Cell, vol. 19, no. 5, pp. 655–666, 2005. View at Publisher · View at Google Scholar
  34. M. Kireeva, M. Kashlev, and Z. F. Burton, “Translocation by multi-subunit RNA polymerases,” Biochimica et biophysica acta, vol. 1799, no. 5-6, pp. 389–401, 2010. View at Google Scholar
  35. K. D. Westover, D. A. Bushnell, and R. D. Kornberg, “Structural basis of transcription: separation of RNA from DNA by RNA polymerase II,” Science, vol. 303, no. 5660, pp. 1014–1016, 2004. View at Publisher · View at Google Scholar · View at PubMed
  36. G. Zhang, E. A. Campbell, L. Minakhin, C. Richter, K. Severinov, and S. A. Darst, “Crystal structure of thermus aquaticus core RNA polymerase at 3.3 å resolution,” Cell, vol. 98, no. 6, pp. 811–824, 1999. View at Google Scholar
  37. A. L. Gnatt, P. Cramer, J. Fu, D. A. Bushnell, and R. D. Kornberg, “Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 Å resolution,” Science, vol. 292, no. 5523, pp. 1876–1882, 2001. View at Publisher · View at Google Scholar · View at PubMed
  38. P. Cramer, D. A. Bushnell, and R. D. Kornberg, “Structural basis of transcription: RNA polymerase II at 2.8 ångstrom resolution,” Science, vol. 292, no. 5523, pp. 1863–1876, 2001. View at Publisher · View at Google Scholar · View at PubMed
  39. D. G. Vassylyev, S. I. Sekine, O. Laptenko et al., “Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6. Å resolution,” Nature, vol. 417, no. 6890, pp. 712–719, 2002. View at Publisher · View at Google Scholar · View at PubMed
  40. S. Tagami, S. I. Sekine, T. Kumarevel et al., “Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein,” Nature, vol. 468, no. 7326, pp. 978–982, 2010. View at Publisher · View at Google Scholar · View at PubMed
  41. M. Karplus and J. A. McCammon, “Molecular dynamics simulations of biomolecules,” Nature Structural Biology, vol. 9, no. 9, pp. 646–652, 2002. View at Publisher · View at Google Scholar · View at PubMed
  42. T. S. Ream, J. R. Haag, A. T. Wierzbicki et al., “Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V reveal their origins as specialized forms of RNA polymerase II,” Molecular Cell, vol. 33, no. 2, pp. 192–203, 2009. View at Publisher · View at Google Scholar · View at PubMed
  43. N. Miropolskaya, I. Artsimovitch, S. Klimašauskas, V. Nikiforov, and A. Kulbachinskiy, “Allosteric control of catalysis by the F loop of RNA polymerase,” Proceedings of the National Academy of Sciences of the United States of America, vol. 106, no. 45, pp. 18942–18947, 2009. View at Publisher · View at Google Scholar · View at PubMed