Single-molecule imaging reveals mechanisms of protein disruption by a DNA translocase

Nature

Volumn 468, Issue 7326, 2010, Pages 983-987

  Finkelstein, Ilya J ^a   Visnapuu, Mari Liis ^a   Greene, Eric C ^a  

^a Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARRIER PROTEIN; DNA; ELONGATION FACTOR; HOLOENZYME; REPRESSOR PROTEIN; RNA POLYMERASE;

ENZYME ACTIVITY; IMAGE ANALYSIS; MICROSCOPY; PROTEIN; REAL TIME;

ARTICLE; CHEMOREACTIVITY; CONTROLLED STUDY; GENE DISRUPTION; IMAGE ANALYSIS; MICROSCOPY; MOLECULAR MECHANICS; NANOFABRICATION; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; REPRESSOR GENE;

BACTERIOPHAGE LAMBDA; BIOCATALYSIS; DEOXYRIBONUCLEASE ECORI; DNA; DNA, VIRAL; DNA-BINDING PROTEINS; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; EXODEOXYRIBONUCLEASE V; HOLOENZYMES; LAC REPRESSORS; MICROSCOPY, FLUORESCENCE; MOVEMENT; NUCLEOSOMES; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; QUANTUM DOTS; TIME FACTORS;

EID: 78650307167     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature09561     Document Type: Article

References (30)

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).
2. Marquis, K. A. et al. SpoIIIE strips proteins off the DNA during chromosome translocation. Genes Dev. 22, 1786-1795 (2008).
3. Krejci, L. et al. DNA helicase Srs2 disrupts the Rad51 presynaptic filament. Nature 423, 305-309 (2003).
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).
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).
6. Bianco, P. R. et al. Processive translocation and DNA unwinding by individual RecBCD enzyme molecules. Nature 409, 374-378 (2001).
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).
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).
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).
10. Ishihama, A. Functionalmodulation of Escherichia coliRNA polymerase. Annu. Rev. Microbiol. 54, 499-518 (2000).
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).
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).
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).
14. Liu, B. & Alberts, B. Head-on collision between a DNA replication apparatus and RNA polymerase transcription complex. Science 267, 1131-1137 (1995).
15. Pomerantz, R. T. & O'Donnell, M. The replisome uses mRNA as a primer after colliding with RNA polymerase. Nature 456, 762-766 (2008).
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).
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). (Pubitemid 19185349)
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). (Pubitemid 37162908)
19. Nudler, E., Kashlev, M., Nikiforov, V. & Goldfarb, A. Coupling between transcription termination and RNA polymerase inchworming. Cell 81, 351-357 (1995).
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).
21. Byrd, A. K. & Raney, K. D. Displacement of a DNA binding protein by Dda helicase. Nucleic Acids Res. 34, 3020-3029 (2006).
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).
23. Sadler, J. R., Sasmor, H.&Betz, J. L.Aperfectly symmetric lacoperator binds the lac repressor very tightly. Proc. Natl Acad. Sci. USA 80, 6785-6789 (1983).
24. Lin,S.-Y.&Riggs,A.D. Lac repressor binding toDNAnot containing the lac operator and to synthetic poly dAT. Nature 228, 1184-1186 (1970).
25. Elf, J., Li, G.-W. & Xie, X. Probing transcription factor dynamics at the singlemolecule level in a living cell. Science 316, 1191-1194 (2007).
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).
27. Studitsky, V. M., Clark, D. J. & Felsenfeld, G. Overcoming a nucleosomal barrier to transcription. Cell 83, 19-27 (1995).
28. Bonne-Andrea, C., Wong, M. & Alberts, B. In vitro replication through nucleosomes without histone displacement. Nature 343, 719-726 (1990).
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).
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).