Transcription factors IIF and IIS and nucleoside triphosphate substrates as dynamic probes of the human RNA polymerase II mechanism

Journal of Molecular Biology

Volumn 342, Issue 4, 2004, Pages 1085-1099

  Zhang, Chunfen ^a   Burton, Zachary F ^a  

^a USA ^*  (United States)

Author keywords

NTP driven translocation; RNA polymerase II; transcription factor IIF; transcription factor IIS; transient state kinetics

Indexed keywords

NUCLEOSIDE TRIPHOSPHATE; PHOSPHODIESTERASE; RNA POLYMERASE II; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR 2F; TRANSCRIPTION FACTOR 2S; UNCLASSIFIED DRUG;

ARTICLE; CHEMICAL BOND; CONTROLLED STUDY; ENZYME ANALYSIS; ENZYME CONFORMATION; ENZYME MECHANISM; ENZYME STABILITY; ENZYME SUBSTRATE; HUMAN; HUMAN CELL; ISOMERIZATION; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR PROBE; NONPHOTOCHEMICAL QUENCHING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN PROCESSING; RNA CLEAVAGE; RNA SYNTHESIS; STEADY STATE; TRANSCRIPTION REGULATION;

EID: 4444228491     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.07.070     Document Type: Article

References (50)

1. K.A. Johnson Rapid quench kinetic analysis of polymerases, adenosinetriphosphatases, and enzyme intermediates Methods Enzymol. 249 1995 38 61
2. K.A. Johnson Transient-state kinetic analysis of enzyme reaction pathways Enzymes 20 1992 1 61
3. C. Zhang, H. Yan, and Z.F. Burton Combinatorial control of human RNA polymerase II (RNAP II) pausing and transcript cleavage by transcription factor IIF. Hepatitis {delta} antigen, and stimulatory factor II J. Biol. Chem. 278 2003 50101 50111
4. Y.A. Nedialkov, X.Q. Gong, Y. Yamaguchi, H. Handa, and Z.F. Burton Transient state kinetics of RNA polymerase II elongation Methods Enzymol. 371 2003 252 262
5. Y.A. Nedialkov, X.Q. Gong, S.L. Hovde, Y. Yamaguchi, H. Handa, and J.H. Geiger NTP-driven translocation by human RNA polymerase II J. Biol. Chem. 278 2003 18303 18312
6. 2+ Biochemistry 43 2004 5126 5137
7. 2+ Biochemistry 43 2004 5138 5148
8. E. Bengal, O. Flores, A. Krauskopf, D. Reinberg, and Y. Aloni Role of the mammalian transcription factors IIF, IIS, and IIX during elongation by RNA polymerase II Mol. Cell. Biol. 11 1991 1195 1206
9. M.G. Izban, and D.S. Luse Factor-stimulated RNA polymerase II transcribes at physiological elongation rates on naked DNA but very poorly on chromatin templates J. Biol. Chem. 267 1992 13647 13655
10. L. Lei, D. Ren, and Z.F. Burton The RAP74 subunit of human transcription factor IIF has similar roles in initiation and elongation Mol. Cell. Biol. 19 1999 8372 8382
11. D.B. Renner, Y. Yamaguchi, T. Wada, H. Handa, and D.H. Price A highly purified RNA polymerase II elongation control system J. Biol. Chem. 276 2001 42601 42609
12. S. Tan, T. Aso, R.C. Conaway, and J.W. Conaway Roles for both the RAP30 and RAP74 subunits of transcription factor IIF in transcription initiation and elongation by RNA polymerase II J. Biol. Chem. 269 1994 25684 25691
13. J.D. Funk, Y.A. Nedialkov, D. Xu, and Z.F. Burton A key role for the alpha 1 helix of human RAP74 in the initiation and elongation of RNA chains J. Biol. Chem. 277 2002 46998 47003
14. H. Guo, and D.H. Price Mechanism of DmS-II-mediated pause suppression by Drosophila RNA polymerase II J. Biol. Chem. 268 1993 18762 18770
15. M.G. Izban, and D.S. Luse The polymerase RNA II ternary complex cleaves the nascent transcript in a 3′-5′ direction in the presence of elongation factor SII Genes Dev. 6 1992 1342 1356
16. M.G. Izban, and D.S. Luse The increment of SII-facilitated transcript cleavage varies dramatically between elongation competent and incompetent RNA polymerase II ternary complexes J. Biol. Chem. 268 1993 12874 12885
17. W. Gu, and D. Reines Variation in the size of nascent RNA cleavage products as a function of transcript length and elongation competence J. Biol. Chem. 270 1995 30441 30447
18. H. Kettenberger, K.J. Armache, and P. Cramer Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage Cell 114 2003 347 357
19. 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 292 2001 1876 1882
20. K.D. Westover, D.A. Bushnell, and R.D. Kornberg Structural basis of transcription: separation of RNA from DNA by RNA polymerase II Science 303 2004 1014 1016
21. P. Cramer, D.A. Bushnell, and R.D. Kornberg Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution Science 292 2001 1863 1876
22. T.A. Steitz A mechanism for all polymerases Nature 391 1998 231 232
23. T.A. Steitz, S.J. Smerdon, J. Jager, and C.M. Joyce A unified polymerase mechanism for nonhomologous DNA and RNA polymerases Science 266 1994 2022 2025
24. D.G. Vassylyev, S. Sekine, O. Laptenko, J. Lee, M.N. Vassylyeva, S. Borukhov, and S. Yokoyama Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution Nature 417 2002 712 719
25. V. Sosunov, E. Sosunova, A. Mustaev, I. Bass, V. Nikiforov, and A. Goldfarb Unified two-metal mechanism of RNA synthesis and degradation by RNA polymerase EMBO J. 22 2003 2234 2244
26. S.F. Holmes, and D.A. Erie Downstream DNA sequence effects on transcription elongation. Allosteric binding of nucleoside triphosphates facilitates translocation via a ratchet motion J. Biol. Chem. 278 2003 35597 35608
27. 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 98 1999 811 824
28. J.E. Foster, S.F. Holmes, and D.A. Erie Allosteric binding of nucleoside triphosphates to RNA polymerase regulates transcription elongation Cell 106 2001 243 252
29. X.Q. Gong, Y.A. Nedialkov, and Z.F. Burton Alpha-amanitin blocks translocation by human RNA polymerase II J. Biol. Chem. 279 2004 27422 27427
30. D.A. Bushnell, P. Cramer, and R.D. Kornberg Structural basis of transcription: alpha-amanitin-RNA polymerase II cocrystal at 2.8 Å resolution Proc. Natl Acad. Sci. USA 99 2002 1218 1222
31. M. Palangat, and R. Landick Roles of RNA:DNA hybrid stability, RNA structure, and active site conformation in pausing by human RNA polymerase II J. Mol. Biol. 311 2001 265 282
32. K.C. Neuman, E.A. Abbondanzieri, R. Landick, J. Gelles, and S.M. Block Ubiquitous transcriptional pausing is independent of RNA polymerase backtracking Cell 115 2003 437 447
33. J.W. Shaevitz, E.A. Abbondanzieri, R. Landick, and S.M. Block Backtracking by single RNA polymerase molecules observed at near-base-pair resolution Nature 426 2003 684 687
34. T.W. Traut Physiological concentrations of purines and pyrimidines Mol. Cell. Biochem. 140 1994 1 22
35. M.G. Izban, and D.S. Luse SII-facilitated transcript cleavage in RNA polymerase II complexes stalled early after initiation occurs in primarily dinucleotide increments J. Biol. Chem. 268 1993 12864 12873
36. C.A. Dunlap, and M.D. Tsai Use of 2-aminopurine and tryptophan fluorescence as probes in kinetic analyses of DNA polymerase Beta Biochemistry 41 2002 11226 11235
37. P. Kuzmic Program DYNAFIT for the analysis of enzyme kinetic data: application to HIV proteinase Anal. Biochem. 237 1996 260 273
38. M. Sopta, R.W. Carthew, and J. Greenblatt Isolation of three proteins that bind to mammalian RNA polymerase II J. Biol. Chem. 260 1985 10353 10360
39. R. Landick Active-site dynamics in RNA polymerases Cell 116 2004 351 353
40. H. Wang, and G. Oster Ratchets, power strokes, and molecular motors Appl. Phys. A 75 2002 315 323
41. Y.W. Yin, and T.A. Steitz The structural mechanism of translocation and helicase activity in T7 RNA polymerase Cell 116 2004 393 404
42. D. Temiakov, V. Patlan, M. Anikin, W.T. McAllister, S. Yokoyama, and D.G. Vassylyev Structural basis for substrate selection by T7 RNA polymerase Cell 116 2004 381 391
43. S.J. Johnson, J.S. Taylor, and L.S. Beese Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations Proc. Natl Acad. Sci. USA 100 2003 3895 3900
44. S. Doublie, S. Tabor, A.M. Long, C.C. Richardson, and T. Ellenberger Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 Å resolution Nature 391 1998 251 258
45. A.K. Showalter, and M.D. Tsai A reexamination of the nucleotide incorporation fidelity of DNA polymerases Biochemistry 41 2002 10571 10576
46. B.J. Elmendorf, A. Shilatifard, Q. Yan, J.W. Conaway, and R.C. Conaway Transcription factors TFIIF, ELL, and Elongin negatively regulate SII- induced nascent transcript cleavage by non-arrested RNA polymerase II elongation intermediates J. Biol. Chem. 276 2001 23109 23114
47. A. Gnatt Elongation by RNA polymerase II: structure-function relationship Biochim. Biophys. Acta 1577 2002 175 190
48. D.J. Shapiro, P.A. Sharp, W.W. Wahli, and M.J. Keller A high-efficiency HeLa cell nuclear transcription extract DNA 7 1988 47 55
49. B.Q. Wang, C.F. Kostrub, A. Finkelstein, and Z.F. Burton Production of human RAP30 and RAP74 in bacterial cells Protein Expt. Purif. 4 1993 207 214
50. B.Q. Wang, L. Lei, and Z.F. Burton Importance of codon preference for production of human RAP74 and reconstitution of the RAP30/74 complex Protein Expt. Purif. 5 1994 476 485