Nano positioning system reveals the course of upstream and nontemplate DNA within the RNA polymerase ii elongation complex

Nucleic Acids Research

Volumn 37, Issue 17, 2009, Pages 5803-5809

  Andrecka, Joanna ^a   Treutlein, Barbara ^a   Arcusa, Maria Angeles Izquierdo ^b   Muschielok, Adam ^a   Lewis, Robert ^a   Cheung, Alan C M ^a   Cramer, Patrick ^a   Michaelis, Jens ^a  

^a UNIVERSITY OF MUNICH   (Germany)

^b UNIVERSITAT JAUME I   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; RNA POLYMERASE II;

ARTICLE; BACTERIUM; CONTROLLED STUDY; CRYSTALLOGRAPHY; DNA FLANKING REGION; EUKARYOTE; FLUORESCENCE RESONANCE ENERGY TRANSFER; NONHUMAN; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DETERMINATION; PROTEIN INTERACTION; PROTEIN STRUCTURE; WILD TYPE; X RAY CRYSTALLOGRAPHY;

BAYES THEOREM; CRYSTALLOGRAPHY, X-RAY; DNA; FLUORESCENCE RESONANCE ENERGY TRANSFER; MODELS, MOLECULAR; RNA; RNA POLYMERASE II; TEMPLATES, GENETIC; TRANSCRIPTION, GENETIC;

EUKARYOTA;

EID: 73049092277     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp601     Document Type: Article

References (40)

1. Cramer, P., Bushnell, D.A. and Kornberg, R.D. (2001) Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science, 292, 1863-1876.
2. Armache, K.-J., Mitterweger, S., Meinhart, A. and Cramer, P. (2005) Structures of complete RNA polymerase II and its subcomplex Rpb4/7. J. Biol. Chem., 280, 7131-7134.
3. Bushnell, D.A. and Kornberg, R.D. (2003) Complete RNA polymerase II at 4.1 Å resolution: implications for the initiation of transcription. Proc. Natl Acad. Sci. USA, 100, 6969-6972.
4. Armache, K.-J., Kettenberger, H. and Cramer, P. (2003) Architecture of the initiation-competent 12-subunit RNA polymerase II. Proc. Natl Acad. Sci. USA, 100, 6964-6968.
5. Gnatt, A.L., Cramer, P., Fu, J., Bushnell, D.A. and Kornberg, R.D. (2001) Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution. Science, 292, 1876-1882.
6. Kettenberger, H., Armache, K.-J. and Cramer, P. (2004) Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. Mol. Cell, 16, 955-965.
7. Westover, K.D., Bushnell, D.A. and Kornberg, R.D. (2004) Structural basis of transcription: separation of RNA from DNA by RNA polymerase II. Science, 303, 1014-1016.
8. Westover, K.D., Bushnell, D.A. and Kornberg, R.D. (2004) Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center. Cell, 119, 481-489.
9. Brueckner, F. and Cramer, P. (2008) Structural basis of transcription inhibition by [alpha]-amanitin and implications for RNA polymerase II translocation. Nat. Struct. Mol. Biol., 15, 811-818.
10. Ha, T., Enderle, T., Ogletree, D.F., Chemla, D.S., Selvin, P.R. and Weiss, S. (1996) Probing the interaction between two single molecules: fluorescence resonance energy transfer between a single donor and a single acceptor. Proc. Natl Acad. Sci. USA, 93, 6264-6268.
11. Joo, C., Balci, H., Ishitsuka, Y., Buranachai, C. and Ha, T. (2008) Advances in single-molecule fluorescence methods for molecular biology. Annu. Rev. Biochem., 77, 51-76.
12. Mekler, V., Kortkhonjia, E., Mukhopadhyay, J., Knight, J., Revyakin, A., Kapanidis, A.N., Niu, W., Ebright, Y.W., Levy, R. and Ebright, R.H. (2002) Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex. Cell, 108, 599-614.
13. Andrecka, J., Lewis, R., Bruckner, F., Lehmann, E., Cramer, P. and Michaelis, J. (2008) Single-molecule tracking of mRNA exiting from RNA polymerase II. Proc. Natl Acad. Sci. USA, 105, 135-140.
14. Knight, J.L., Mekler, V., Mukhopadhyay, J., Ebright, R.H. and Levy, R.M. (2005) Distance-restrained docking of rifampicin and rifamycin SV to RNA polymerase using systematic FRET measurements: developing benchmarks of model quality and reliability. Biophys. J., 88, 925-938.
15. Rasnik, I., Myong, S., Cheng, W., Lohman, T.M. and Ha, T. (2004) DNA-binding orientation and domain conformation of the E. coli rep helicase monomer bound to a partial duplex junction: single-molecule studies of fluorescently labeled enzymes. J. Mol. Biol., 336, 395-408.
16. Margittai, M., Widengren, J., Schweinberger, E., Schroder, G.F., Felekyan, S., Haustein, E., Konig, M., Fasshauer, D., Grubmuller, H., Jahn, R. et al. (2003) Single-molecule fluorescence resonance energy transfer reveals a dynamic equilibrium between closed and open conformations of syntaxin 1. Proc. Natl Acad. Sci. USA, 100, 15516-15521.
17. Muschielok, A., Andrecka, J., Jawhari, A., Bruckner, F., Cramer, P. and Michaelis, J. (2008) A nano-positioning system for macromolecular structural analysis. Nat. Methods, 5, 965-971.
18. Chen, C.Y., Chang, C.C., Yen, C.F., Chiu, M.T. and Chang, W.H. (2009) Mapping RNA exit channel on transcribing RNA polymerase II by FRET analysis. Proc. Natl Acad. Sci. USA, 106, 127-132.
19. Sidorenkov, I., Komissarova, N. and Kashlev, M. (1998) Crutial role of the RNA:DNA hybrid in the processivity of transcription. Mol. Cell, 2, 55-64.
20. Kireeva, M.L., Komissarova, N. and Kashlev, M. (2000) Overextended RNA:DNA hybrid as a negative regulator of RNA polymerase II processivity. J. Mol. Biol., 299, 325-335.
21. Kireeva, M.L., Komissarova, N., Waugh, D.S. and Kashlev, M. (2000) The 8-nucleotide-long RNA:DNA hybrid is a primary stability determinant of the RNA polymerase II elongation complex. J. Biol. Chem., 275, 6530-6536.
22. Wang, D. and Landick, R. (1997) Nuclease cleavage of the upstream half of the nontemplate strand DNA in an Escherichia coli transcription elongation complex causes upstream translocation and transcriptional arrest. J. Biol. Chem., 272, 5989-5994.
23. Nudler, E., Goldfarb, A. and Kashlev, M. (1994) Discontinuous mechanism of transcription elongation. Science, 265, 793-796.
24. Sevostyanova, A., Svetlov, V., Vassylyev, D.G. and Artsimovitch, I. (2008) The elongation factor RfaH and the initiation factor s bind to the same site on the transcription elongation complex. Proc. Natl Acad. Sci. USA, 105, 865-870.
25. Chen, H.-T., Warfield, L. and Hahn, S. (2007) The positions of TFIIF and TFIIE in the RNA polymerase II transcription initiation complex. Nat. Struct. Mol. Biol., 8, 696-703.
26. Vamosi, G., Gohlke, C. and Clegg, R.M. (1996) Fluorescence characteristics of 5-carboxytetramethylrhodamine linked covalently to the 5' end of oligonucleotides: multiple conformers of single-stranded and double-stranded dye-DNA complexes. Biophys. J., 71, 972-994.
27. Emsley, P. and Cowtan, K. (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr., 60, 2126-2132.
28. Afonine, P.V., Grosse-Kunstleve, R.W. and Adams, P.D. (2005) A robust bulk-solvent correction and anisotropic scaling procedure. Acta Crystallogr. D Biol. Crystallogr., 61, 850-855.
29. Naji, S., Bertero, M.G., Spitalny, P., Cramer, P. and Thomm, M. (2008) Structure-function analysis of the RNA polymerase cleft loops elucidates initial transcription, DNA unwinding and RNA displacement. Nucleic Acids Res., 36, 676-687.
30. Rees, W., Keller, R.W., Vesenka, J.P., Yang, G. and Bustamante, C. (1993) Evidence of DNA bending in transcription complexes imaged by scanning force microscopy. Science, 260, 1646-1649.
31. Korzheva, N., Mustaev, A., Kozlov, M., Malhotra, A., Nikiforov, V., Goldfarb, A. and Darst, S.A. (2000) A structural model of transcription elongation. Science, 289, 619-625.
32. Naryshkin, N., Revyakin, A., Kim, Y., Mekler, V. and Ebright, R.H. (2000) Structural organization of the RNA polymerase-promoter open complex. Cell, 101, 601-611.
33. Nechaev, S., Chlenov, M. and Severinov, K. (2000) Dissection of two hallmarks of the open promoter complex by mutation in an RNA polymerase core subunit. J. Biol. Chem., 275, 25516-25522.
34. Severinov, K. and Darst, S.A. (1997) A mutant RNA polymerasethat forms unusual open promoter complexes. Proc. Natl Acad. Sci. USA, 94, 13481-13486.
35. Kuznedelov, K., Korzheva, N., Mustaev, A. and Severinov, K. (2002) Structure-based analysis of RNA polymerase function: the largest subunit's rudder contributes critically to elongation complex stability and is not involved in the maintenance of RNA-DNA hybrid length. EMBO J., 21, 1369-1378.
36. Malagon, F., Kireeva, M.L., Shafer, B.K., Lubkowska, L., Kashlev, M. and Strathern, J.N. (2006) Mutations in the Saccharomyces cerevisiae RPB1 gene conferring hypersensitivity to 6-azauracil. Genetics, 172, 2201-2209.
37. Toulokhonov, I. and Landick, R. (2006) The role of the lid element in transcription by E. coli RNA polymerase. J. Mol. Biol., 361, 644-658.
38. Naryshkina, T., Kuznedelov, K. and Severinov, K. (2006) The role of the largest RNA polymerase subunit lid element in preventing the formation of extended RNA-DNA hybrid. J. Mol. Biol., 361, 634-643.
39. Chen, H.T. and Hahn, S. (2004) Mapping the location of TFIIB within the RNA polymerase II transcription preinitiation complex: a model for the structure of the PIC. Cell, 119, 169-180.
40. Ujvari, A. and Luse, D.S. (2006) RNA emerging from the active site of RNA polymerase II interacts with the Rpb7 subunit. Nat. Struct. Mol. Biol., 13, 4954.