Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner

Nature

Volumn 446, Issue 7137, 2007, Pages 820-823

  Galburt, Eric A ^a,d   Grill, Stephan W ^a,d   Wiedmann, Anna ^b   Lubkowska, Lucyna ^c   Choy, Jason ^e   Nogales, Eva ^a,b   Kashlev, Mikhail ^c   Bustamante, Carlos ^a,b  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c NATIONAL CANCER INSTITUTE   (United States)

^d MAX PLANCK INSTITUT FÜR PHYSIK KOMPLEXER SYSTEME   (Germany)

^e NCI Center for Cancer Research ^*

Author keywords

[No Author keywords available]

Indexed keywords

RNA POLYMERASE II; TRANSCRIPTION FACTOR;

BACTERIUM; ENZYME ACTIVITY; EUKARYOTE; FORCE; RNA; YEAST;

ARTICLE; CELL FUNCTION; DNA HYBRIDIZATION; ENZYME ACTIVATION; ENZYME ASSAY; ENZYME MODIFICATION; ESCHERICHIA COLI; EUKARYOTE; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROTEIN FUNCTION; RNA HYBRIDIZATION; SACCHAROMYCES CEREVISIAE; STATISTICAL SIGNIFICANCE; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION;

ESCHERICHIA COLI; EUKARYOTA; SACCHAROMYCES CEREVISIAE;

EID: 34147206187     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature05701     Document Type: Article

References (28)

1. Roeder, R. G. The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem. Sci. 21, 327-335 (1996).
2. Kireeva, M. L. et al. Nature of the nucleosomal barrier to RNA polymerase II. Mol. Cell 18, 97-108 (2005).
3. Komissarova, N. & Kashlev, M. Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3′ end of the RNA intact and extruded. Proc. Natl Acad. Sci. USA 94, 1755-1760 (1997).
4. Komissarova, N. & Kashlev, M. RNA polymerase switches between inactivated and activated states by translocating back and forth along the DNA and the RNA. J. Biol. Chem. 272, 15329-15338 (1997).
5. Nudler, E., Mustaev, A., Lukhtanov, E. & Goldfarb, A. The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase. Cell 89, 33-41 (1997).
6. Shaevitz, J. W., Abbondanzieri, E. A., Landick, R. & Block, S. M. Backtracking by single RNA polymerase molecules observed at near-base-pair resolution. Nature 426, 684-687 (2003).
7. Davenport, R. J., Wuite, G. J., Landick, R. & Bustamante, C. Single-molecule study of transcriptional pausing and arrest by E. coli RNA polymerase. Science 287, 2497-2500 (2000).
8. Wang, M. D. et al. Force and velocity measured for single molecules of RNA polymerase. Science 282, 902-907 (1998).
9. Hahn, S. Structure and mechanism of the RNA polymerase II transcription machinery. Nature Struct. Mol. Biol. 11, 394-403 (2004).
10. Komissarova, N., Kireeva, M. L., Becker, J., Sidorenkov, I. & Kashlev, M. Engineering of elongation complexes of bacterial and yeast RNA polymerases. Methods Enzymol. 371, 233-251 (2003).
11. Abbondanzieri, E. A., Greenleaf, W. J., Shaevitz, J. W., Landick, R. & Block, S. M. Direct observation of base-pair stepping by RNA polymerase. Nature 438, 460-465 (2005).
12. Moffitt, J., Chemla, Y., Izhaky, D. & Bustamante, C. Differential detection of dual traps improves the spatial resolution of optical tweezers. Proc. Natl Acad. Sci. USA 103, 9006-9011 (2006).
13. Bustamante, C., Marko, J. F., Siggia, E. D. & Smith, S. Entropic elasticity of lambda-phage DNA. Science 265, 1599-1600 (1994).
14. Neuman, K. C., Abbondanzieri, E. A., Landick, R., Gelles, J. & Block, S. M. Ubiquitous transcriptional pausing is independent of RNA polymerase backtracking. Cell 115, 437-447 (2003).
15. Izban, M. G. & Luse, D. S. Factor-stimulated RNA polymerase II transcribes at physiological elongation rates on naked DNA but very poorly on chromatin templates. J. Biol. Chem. 267, 13647-13655 (1992).
16. Forde, N. R., Izhaky, D., Woodcock, G. R., Wuite, G. J. L. & Bustamante, C. Using mechanical force to probe the mechanism of pausing and arrest during continuous elongation by Escherichia coli RNA polymerase. Proc. Natl Acad. Sci. USA 99, 11682-11687 (2002).
17. Yin, H. et al. Transcription against an applied force. Science 270, 1653-1657 (1995).
18. Kulish, D. & Struhl, K. TFIIS enhances transcriptional elongation through an artificial arrest site in vivo. Mol. Cell. Biol. 21, 4162-4168 (2001).
19. Li, P. T. X., Collin, D., Smith, S. B., Bustamante, C. & Tinoco, I. Probing the mechanical folding kinetics of TAR RNA by hopping, force-jump, and force-ramp methods. Biophys. J. 90, 250-260 (2006).
20. Fish, R. N. & Kane, C. M. Promoting elongation with transcript cleavage stimulatory factors. Biochim. Biophys. Acta 1577, 287-307 (2002).
21. Borukhov, S., Lee, J. & Laptenko, O. Bacterial transcription elongation factors: new insights into molecular mechanism of action. Mol. Microbiol. 55, 1315-1324 (2005).
22. Jeon, C. & Agarwal, K. Fidelity of RNA polymerase II transcription controlled by elongation factor TFIIS. Proc. Natl Acad. Sci. USA 93, 13677-13682 (1996).
23. Awrey, D. E. et al. Yeast transcript elongation factor (TFIIS), structure and function. II: RNA polymerase binding, transcript cleavage, and read-through. J. Biol. Chem. 273, 22595-22605 (1998).
24. Weilbaecher, R. G., Awrey, D. E., Edwards, A. M. & Kane, C. M. Intrinsic transcript cleavage in yeast RNA polymerase II elongation complexes. J. Biol. Chem. 278, 24189-24199 (2003).
25. Reines, D. & Mote, J. Jr. Elongation factor SII-dependent transcription by RNA polymerase II through a sequence-specific DNA-binding protein. Proc. Natl Acad. Sci. USA 90, 1917-1921 (1993).
26. Palangat, M., Renner, D. B., Price, D. H. & Landick, R. A negative elongation factor for human RNA polymerase II inhibits the anti-arrest transcript-cleavage factor TFIIS. Proc. Natl Acad. Sci. USA 102, 15036-15041 (2005).
27. Kireeva, M. L., Lubkowska, L., Komissarova, N. & Kashlev, M. Assays and affinity purification of biotinylated and nonbiotinylated forms of double-tagged core RNA polymerase II from Saccharomyces cerevisiae. Methods Enzymol. 370, 138-155 (2003).
28. Smith, S. B., Cui, Y. & Bustamante, C. Optical-trap force transducer that operates by direct measurement of light momentum. Methods Enzymol. 361, 134-162 (2003).