Promoter independent abortive transcription assays unravel functional interactions between TFIIB and RNA polymerase

Methods in Molecular Biology

Volumn 977, Issue , 2013, Pages 217-227

  Wiesler, Simone C ^a   Werner, Finn ^a   Weinzierl, Robert O J ^a  

^a NONE

Author keywords

Abortive transcription; Biochemical analysis; High throughput; Luciferase; RNA polymerase; Saturation mutagenesis

Indexed keywords

LUCIFERASE; RNA POLYMERASE; TRANSCRIPTION FACTOR IIB; ARCHAEAL PROTEIN; BACTERIOPHAGE T7 RNA POLYMERASE; DNA DIRECTED RNA POLYMERASE; ESCHERICHIA COLI PROTEIN; VIRUS PROTEIN;

AMINO ACID SUBSTITUTION; ARTICLE; DNA TEMPLATE; GENETIC TRANSCRIPTION; HIGH THROUGHPUT SCREENING; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN RNA BINDING; TRANSCRIPTION INITIATION; X RAY CRYSTALLOGRAPHY; BIOSYNTHESIS; CHEMISTRY; ENZYMOLOGY; GENETICS; METHANOCOCCALES; PROTEIN BINDING; REPORTER GENE; TITRIMETRY;

ARCHAEAL PROTEINS; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI PROTEINS; GENES, REPORTER; LUCIFERASES; METHANOCOCCALES; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; TITRIMETRY; TRANSCRIPTION FACTOR TFIIB; TRANSCRIPTION INITIATION, GENETIC; TRANSCRIPTION, GENETIC; VIRAL PROTEINS;

MLCS; MLOWN;

EID: 84880973608     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-284-1_17     Document Type: Article

References (48)

1. Borukhov S, Nudler E. (2008) RNA poly-merase: the vehicle of transcription. Trends Microbiol 16: 126-134
2. Buratowski S, Hahn S, Guarente L., Sharp P.A. (1989) Five intermediate complexes in transcription initiation by RNA polymerase II. Cell 56: 549-561
3. Buratowski S, Sopta M, Greenblatt J., Sharp P.A. (1991) RNA polymerase II-associated proteins are required for a DNA conformation change in the transcription initiation complex. Proc Natl Acad Sci USA 88: 7509-7513
4. Reese JC (2003) Basal transcription factors. Curr Opin Genet Dev 13: 114-118
5. McClure WR (1985) Mechanism and control of transcription initiation in prokaryotes. Annu Rev Biochem 54: 171-204
6. Walter G, Zillig W, Palm P., Fuchs E. (1967) Initiation of DNA-dependent RNA synthesis and the effect of heparin on RNA polymerase. Eur J Biochem 3: 194-201
7. Chen BS, Hampsey M. (2004) Functional interaction between TFIIB and the Rpb2 sub-unit of RNA polymerase II: implications for the mechanism of transcription initiation. Mol Cell Biol 24: 3983-3991
8. Artsimovitch I, Vassylyev D.G. (2006) Is it easy to stop RNA polymerase? Cell Cycle 5: 399-404
9. Carpousis AJ, Gralla J.D. (1980) Cycling of ribonucleic acid polymerase to produce oligo-nucleotides during initiation in vitro at the lac UV5 promoter. Biochemistry 19: 3245-3253
10. Cheetham GM, Jeruzalmi D, Steitz T.A. (1999) Structural basis for initiation of transcription from an RNA polymerase-promoter complex. Nature 399: 80-83
11. Gnatt AL, Cramer P, Fu J., Bushnell DA, Kornberg R.D. (2001) Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution. Science 292: 1876-1882
12. Kapanidis AN, Margeat E, Ho S.O., Kortkhonjia E., Weiss S, Ebright R.H. (2006) Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism. Science 314: 1144-1147
13. Krummel B, Chamberlin M.J. (1989) RNA chain initiation by Escherichia coli RNA poly-merase. Structural transitions of the enzyme in early ternary complexes. Biochemistry 28: 7829-7842
14. Revyakin A, Liu C, Ebright R.H., Strick T.R. (2006) Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching. Science 314: 1139-1143
15. Orphanides G, Reinberg D. (2002) A unified theory of gene expression. Cell 108: 439-451
16. Ebright RH (2000) RNA polymerase: structural similarities between bacterial RNA poly-merase and eukaryotic RNA polymerase II. J Mol Biol 304: 687-698
17. Cheung AC, Sainsbury S, Cramer P. (2011) Structural basis of initial RNA polymerase II transcription. EMBO J 30(23): 4755-4763
18. Kostrewa D, Zeller ME, Armache K.J., Seizl M., Leike K, Thomm M, Cramer P. (2009) RNA polymerase II-TFIIB structure and mechanism of transcription initiation. Nature 462(7271): 323-330
19. Bushnell DA, Westover KD, Davis R.E., Kornberg R.D. (2004) Structural basis of transcription: an RNA polymerase II-TFIIB cocrystal at 4.5 Angstroms. Science 303: 983-988
20. Liu X, Bushnell DA, Wang D, Calero G., Kornberg R.D. (2010) Structure of an RNA Polymerase II-TFIIB Complex and the Transcription Initiation Mechanism. Science 327(5962): 206-209
21. Chen HT, 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
22. Chen HT, Hahn S. (2003) Binding of TFIIB to RNA polymerase II: mapping the binding site for the TFIIB zinc ribbon domain within the preinitiation complex. Mol Cell 12: 437-447
23. Wang D, Bushnell DA, Westover K.D., Kaplan CD, Kornberg R.D. (2006) Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis. Cell 127: 941-954
24. Boeger H, Bushnell DA, Davis R, Griesenbeck J., Lorch Y, Strattan JS, Westover K.D., Kornberg R.D. (2005) Structural basis of eukaryotic gene transcription. FEBS Lett 579: 899-903
25. Westover KD, Bushnell DA, Kornberg R.D. (2004) Structural basis of transcription: nucleotide selection by rotation in the RNA poly-merase II active center. Cell 119: 481-489
26. Westover KD, Bushnell DA, Kornberg R.D. (2004) Structural basis of transcription: separation of RNA from DNA by RNA polymerase II. Science 303: 1014-1016
27. Bushnell DA, Cramer P, Kornberg R.D. (2002) Structural basis of transcription: alpha-amanitin-RNA polymerase II cocrystal at 2.8 A resolution. Proc Natl Acad Sci USA 99: 1218-1222
28. Cramer P, Bushnell DA, Kornberg R.D. (2001) Structural basis of transcription: RNA poly-merase II at 2.8 angstrom resolution. Science 292: 1863-1876
29. Bell SD, Magill CP, Jackson S.P. (2001) Basal and regulated transcription in Archaea. Biochem Soc Trans 29: 392-395
30. Parvin JD, Sharp P.A. (1993) DNA topology and a minimal set of basal factors for transcription by RNA polymerase II. Cell 73: 533-540
31. Tyree CM, George CP, Lira-DeVito LM, Wampler S.L., Dahmus ME, Zawel L, Kadonaga J.T. (1993) Identification of a minimal set of proteins that is sufficient for accurate initiation of transcription by RNA polymerase II. Genes Dev 7: 1254-1265
32. Naidu S, Friedrich JK, Russell J, Zomerdijk J.C. (2011) TAF1B is a TFIIB-like component of the basal transcription machinery for RNA polymerase I. Science 333: 1640-1642
33. Kassavetis GA, Geiduschek E.P. (2006) Transcription factor TFIIIB and transcription by RNA polymerase III. Biochem Soc Trans 34: 1082-1087
34. Schramm L, Hernandez N. (2002) Recruitment of RNA polymerase III to its target promoters. Genes Dev 16: 2593-2620
35. Weinzierl RO, Wiesler S.C. (2011) Revealing the functions of TFIIB. Transcription 2: 254-257
36. Knutson BA, Hahn S. (2011) Yeast Rrn7 and human TAF1B are TFIIB-related RNA poly-merase I general transcription factors. Science 333: 1637-1640
37. Buratowski S, Zhou H. (1993) Functional domains of transcription factor TFIIB. Proc Natl Acad Sci USA 90: 5633-5637
38. Werner F, Weinzierl R.O. (2005) Direct modulation of RNA polymerase core functions by basal transcription factors. Mol Cell Biol 25: 8344-8355
39. Wiesler SC, Weinzierl R.O. (2011) The linker domain of basal transcription factor TFIIB controls distinct recruitment and transcription stimulation functions. Nucleic Acids Res 39: 464-474
40. Werner F, Weinzierl R.O. (2002) A recombinant RNA polymerase II-like enzyme capable of promoter-specific transcription. Mol Cell 10: 635-646
41. Tan L, Wiesler S, Trzaska D., Carney HC, Weinzierl R.O. (2008) Bridge helix and trigger loop perturbations generate superactive RNA polymerases. J Biol 7: 40
42. Weinzierl RO (2010) The nucleotide addition cycle of RNA polymerase is controlled by two molecular hinges in the Bridge Helix domain. BMC Biol 8: 134
43. Aposhian HV, Kornberg A. (1962) Enzymatic synthesis of deoxyribonucleic acid. IX. The polymerase formed after T2 bacteriophage infection of Escherichia coli: a new enzyme. J Biol Chem 237: 519-525
44. Sun Y, Jacobson KB, Golovlev V. (2007) A multienzyme bioluminescent time-resolved pyrophosphate assay. Anal Biochem 367: 201-209
45. Ronaghi M, Karamohamed S, Pettersson B., Uhlen M, Nyren P. (1996) Real-time DNA sequencing using detection of pyrophosphate release. Anal Biochem 242: 84-89
46. Nyren P, Karamohamed S, Ronaghi M. (1997) Detection of single-base changes using a bioluminometric primer extension assay. Anal Biochem 244: 367-373
47. Karamohamed S, Nyren P. (1999) Real-time detection and quantification of adenosine triphosphate sulfurylase activity by a bioluminometric approach. Anal Biochem 271: 81-85
48. Lahser FC, Malcolm B.A. (2004) A continuous nonradioactive assay for RNA-dependent RNA polymerase activity. Anal Biochem 325: 247-254