Single-molecule imaging reveals mechanisms of protein disruption by a DNA translocase (original) (raw)

References

  1. Jankowsky, E., Gross, C., Shuman, S. & Pyle, A. Active disruption of an RNA-protein interaction by a DExH/D RNA helicase. Science 291, 121–125 (2001)
    Article ADS CAS Google Scholar
  2. Marquis, K. A. et al. SpoIIIE strips proteins off the DNA during chromosome translocation. Genes Dev. 22, 1786–1795 (2008)
    Article CAS Google Scholar
  3. Krejci, L. et al. DNA helicase Srs2 disrupts the Rad51 presynaptic filament. Nature 423, 305–309 (2003)
    Article ADS CAS Google Scholar
  4. Guy, C. P. et al. Rep provides a second motor at the replisome to promote duplication of protein-bound DNA. Mol. Cell 36, 654–666 (2009)
    Article CAS Google Scholar
  5. Singleton, M. R., Dillingham, M., Gaudier, M., Kowalczykowski, S. & Wigley, D. Crystal structure of RecBCD enzyme reveals a machine for processing DNA breaks. Nature 432, 187–193 (2004)
    Article ADS CAS Google Scholar
  6. Bianco, P. R. et al. Processive translocation and DNA unwinding by individual RecBCD enzyme molecules. Nature 409, 374–378 (2001)
    Article ADS CAS Google Scholar
  7. Spies, M., Amitani, I., Baskin, R. & Kowalczykowski, S. RecBCD enzyme switches lead motor subunits in response to chi recognition. Cell 131, 694–705 (2007)
    Article CAS Google Scholar
  8. Taylor, A. F. & Smith, G. R. RecBCD enzyme is a DNA helicase with fast and slow motors of opposite polarity. Nature 423, 889–893 (2003)
    Article ADS CAS Google Scholar
  9. Visnapuu, M.-L. & Greene, E. Single-molecule imaging of DNA curtains reveals intrinsic energy landscapes for nucleosome deposition. Nature Struct. Mol. Biol. 16, 1056–1062 (2009)
    Article CAS Google Scholar
  10. Ishihama, A. Functional modulation of Escherichia coli RNA polymerase. Annu. Rev. Microbiol. 54, 499–518 (2000)
    Article CAS Google Scholar
  11. Herbert, K. M., Greenleaf, W. J. & Block, S. M. Single-molecule studies of RNA polymerase: motoring along. Annu. Rev. Biochem. 77, 149–176 (2008)
    Article CAS Google Scholar
  12. Liu, B., Wong, M. & Alberts, B. A transcribing RNA polymerase molecule survives DNA replication without aborting its growing RNA chain. Proc. Natl Acad. Sci. USA 91, 10660–10664 (1994)
    Article ADS CAS Google Scholar
  13. Liu, B., Wong, M., Tinker, R., Geiduschek, E. & Alberts, B. The DNA replication fork can pass RNA polymerase without displacing the nascent transcript. Nature 366, 33–39 (1993)
    Article ADS CAS Google Scholar
  14. Liu, B. & Alberts, B. Head-on collision between a DNA replication apparatus and RNA polymerase transcription complex. Science 267, 1131–1137 (1995)
    Article ADS CAS Google Scholar
  15. Pomerantz, R. T. & O’Donnell, M. The replisome uses mRNA as a primer after colliding with RNA polymerase. Nature 456, 762–766 (2008)
    Article ADS CAS Google Scholar
  16. Pomerantz, R. T. & O’Donnell, M. Direct restart of a replication fork stalled by a head-on RNA polymerase. Science 327, 590–592 (2010)
    Article ADS CAS Google Scholar
  17. Wright, D. J., King, K. & Modrich, P. The negative charge of Glu-111 is required to activate the cleavage center of EcoRI endonuclease. J. Biol. Chem. 264, 11816–11821 (1989)
    CAS Google Scholar
  18. Epshtein, V. & Toulm, È. F. Rahmouni, A. Borukhov, S. & Nudler, E. Transcription through the roadblocks: the role of RNA polymerase cooperation. EMBO J. 22, 4719–4727 (2003)
    Article CAS Google Scholar
  19. Nudler, E., Kashlev, M., Nikiforov, V. & Goldfarb, A. Coupling between transcription termination and RNA polymerase inchworming. Cell 81, 351–357 (1995)
    Article CAS Google Scholar
  20. Pavco, P. A. & Steege, D. A. Characterization of elongating T7 and SP6 RNA polymerases and their response to a roadblock generated by a site-specific DNA binding protein. Nucleic Acids Res. 19, 4639–4646 (1991)
    Article CAS Google Scholar
  21. Byrd, A. K. & Raney, K. D. Displacement of a DNA binding protein by Dda helicase. Nucleic Acids Res. 34, 3020–3029 (2006)
    Article CAS Google Scholar
  22. Noom, M. C., van den Broek, B., van Mameren, J. & Wuite, G. J. L. Visualizing single DNA-bound proteins using DNA as a scanning probe. Nature Methods 4, 1031–1036 (2007)
    Article CAS Google Scholar
  23. Sadler, J. R., Sasmor, H. & Betz, J. L. A perfectly symmetric lac operator binds the lac repressor very tightly. Proc. Natl Acad. Sci. USA 80, 6785–6789 (1983)
    Article ADS CAS Google Scholar
  24. Lin, S.-Y. & Riggs, A. D. Lac repressor binding to DNA not containing the lac operator and to synthetic poly dAT. Nature 228, 1184–1186 (1970)
    Article ADS CAS Google Scholar
  25. Elf, J., Li, G.-W. & Xie, X. Probing transcription factor dynamics at the single-molecule level in a living cell. Science 316, 1191–1194 (2007)
    Article ADS CAS Google Scholar
  26. Wang, Y. M., Austin, R. H. & Cox, E. C. Single molecule measurements of repressor protein 1D diffusion on DNA. Phys. Rev. Lett. 97, 048302 (2006)
    Article ADS CAS Google Scholar
  27. Studitsky, V. M., Clark, D. J. & Felsenfeld, G. Overcoming a nucleosomal barrier to transcription. Cell 83, 19–27 (1995)
    Article CAS Google Scholar
  28. Bonne-Andrea, C., Wong, M. & Alberts, B. In vitro replication through nucleosomes without histone displacement. Nature 343, 719–726 (1990)
    Article ADS CAS Google Scholar
  29. Eggleston, A. K., O’Neill, T. E., Bradbury, E. M. & Kowalczykowski, S. C. Unwinding of nucleosomal DNA by a DNA helicase. J. Biol. Chem. 270, 2024–2031 (1995)
    Article CAS Google Scholar
  30. Mollazadeh-Beidokhti, L., Deseigne, J., Lacoste, D., Mohammad-Rafiee, F. & Schiessel, H. Stochastic model for nucleosome sliding under an external force. Phys. Rev. E 79, 031922 (2009)
    Article ADS CAS Google Scholar

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