Binding of TFIIB to RNA polymerase II: Mapping the binding site for the TFIIB zinc ribbon domain within the preinitiation complex

Molecular Cell

Volumn 12, Issue 2, 2003, Pages 437-447

  Chen, Hung Ta ^a   Hahn, Steven ^a  

^a HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOCKING PROTEIN; HYDROXYL RADICAL; RNA POLYMERASE II; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR IIB; UNCLASSIFIED DRUG;

ARTICLE; ASSAY; BINDING SITE; CONTROLLED STUDY; CROSS LINKING; ENZYME BINDING; GENE MAPPING; GENE MUTATION; MOLECULAR MODEL; MUTATIONAL ANALYSIS; NONHUMAN; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DEGRADATION; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; TRANSCRIPTION INITIATION; ZINC FINGER MOTIF;

RUMEX;

EID: 0141992120     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1097-2765(03)00306-X     Document Type: Article

References (44)

1. Armache K.J., Kettenberger H., Cramer P. Architecture of initiation-competent 12-subunit RNA polymerase II. Proc. Natl. Acad. Sci. USA. 100:2003;6964-6968.
2. Bangur C.S., Pardee T.S., Ponticelli A.S. Mutational analysis of the D1/E1 core helices and the conserved N-terminal region of yeast transcription factor IIB (TFIIB). identification of an N-terminal mutant that stabilizes TATA-binding protein-TFIIB-DNA complexes Mol. Cell. Biol. 17:1997;6784-6793.
3. Barberis A., Muller C.W., Harrison S.C., Ptashne M. Delineation of two functional regions of transcription factor TFIIB. Proc. Natl. Acad. Sci. USA. 90:1993;5628-5632.
4. Bell S.D., Jackson S.P. Transcription in Archaea. Cold Spring Harb. Symp. Quant. Biol. 63:1998;41-51.
5. Bell S.D., Jackson S.P. The role of transcription factor B in transcription initiation and promoter clearance in the archaeon Sulfolobus acidocaldarius. J. Biol. Chem. 275:2000;12934-12940.
6. Buratowski S., Zhou H. Functional domains of transcription factor TFIIB. Proc. Natl. Acad. Sci. USA. 90:1993;5633-5637.
7. Bushnell D.A., Kornberg R.D. Complete, 12-subunit RNA polymerase II at 4.1-A resolution. implications for the initiation of transcription Proc. Natl. Acad. Sci. USA. 100:2003;6969-6973.
8. Chedin S., Ferri M.L., Peyroche G., Andrau J.C., Jourdain S., Lefebvre O., Werner M., Carles C., Sentenac A. The yeast RNA polymerase III transcription machinery. a paradigm for eukaryotic gene activation Cold Spring Harb. Symp. Quant. Biol. 63:1998;381-389.
9. Chen H.T., Legault P., Glushka J., Omichinski J.G., Scott R.A. Structure of a (Cys3His) zinc ribbon, a ubiquitous motif in archaeal and eucaryal transcription. Protein Sci. 9:2000;1743-1752.
10. Chen Y., Ebright Y.W., Ebright R.H. Identification of the target of a transcription activator protein by protein-protein photocrosslinking. Science. 265:1994;90-92.
11. Cho E.J., Buratowski S. Evidence that transcription factor IIB is required for a post-assembly step in transcription initiation. J. Biol. Chem. 274:1999;25807-25813.
12. Cramer P., Bushnell D.A., Kornberg R.D. Structural basis of transcription. RNA polymerase II at 2.8 angstrom resolution Science. 292:2001;1863-1876.
13. Datwyler S.A., Meares C.F. Protein-protein interactions mapped by artificial proteases. where sigma factors bind to RNA polymerase Trends Biochem. Sci. 25:2000;408-414.
14. Ferri M.L., Peyroche G., Siaut M., Lefebvre O., Carles C., Conesa C., Sentenac A. A novel subunit of yeast RNA polymerase III interacts with the TFIIB-related domain of TFIIIB70. Mol. Cell. Biol. 20:2000;488-495.
15. Gnatt A.L., Cramer P., Fu J., Bushnell D.A., Kornberg R.D. Structural basis of transcription. an RNA polymerase II elongation complex at 3.3 A resolution Science. 292:2001;1876-1882.
16. Ha I., Roberts S., Maldonado E., Sun X., Kim L.U., Green M., Reinberg D. Multiple functional domains of human transcription factor IIB. distinct interactions with two general transcription factors and RNA polymerase II Genes Dev. 7:1993;1021-1032.
17. Hahn S., Roberts S. The zinc ribbon domains of the general transcription factors TFIIB and Brf. conserved functional surfaces but different roles in transcription initiation Genes Dev. 14:2000;719-730.
18. Hampsey M. Molecular genetics of the RNA polymerase II general transcriptional machinery. Microbiol. Mol. Biol. Rev. 62:1998;465-503.
19. Han H., Dervan P.B. Visualization of RNA tertiary structure by RNA-EDTA.Fe(II) autocleavage. analysis of tRNA(Phe) with uridine-EDTA.Fe(II) at position 47 Proc. Natl. Acad. Sci. USA. 91:1994;4955-4959.
20. Hawkes N.A., Roberts S.G. The role of human TFIIB in transcription start site selection in vitro and in vivo. J. Biol. Chem. 274:1999;14337-14343.
21. Hisatake K., Roeder R.G., Horikoshi M. Functional dissection of TFIIB domains required for TFIIB-TFIID-promoter complex formation and basal transcription activity. Nature. 363:1993;744-747.
22. Jensen G.J., Meredith G., Bushnell D.A., Kornberg R.D. Structure of wild-type yeast RNA polymerase II and location of Rpb4 and Rpb7. EMBO J. 17:1998;2353-2358.
23. Kassavetis G.A., Letts G.A., Geiduschek E.P. The RNA polymerase III transcription initiation factor TFIIIB participates in two steps of promoter opening. EMBO J. 20:2001;2823-2834.
24. Knaus R., Pollock R., Guarente L. Yeast SUB1 is a suppressor of TFIIB mutations and has homology to the human co-activator PC4. EMBO J. 15:1996;1933-1940.
25. Kosa P.F., Ghosh G., DeDecker B.S., Sigler P.B. The 2.1-A crystal structure of an archaeal preinitiation complex. TATA-box-binding protein/transcription factor (II)B core/TATA-box Proc. Natl. Acad. Sci. USA. 94:1997;6042-6047.
26. Lee T.I., Young R.A. Transcription of eukaryotic protein-coding genes. Annu. Rev. Genet. 34:2000;77-137.
27. Littlefield O., Korkhin Y., Sigler P.B. The structural basis for the oriented assembly of a TBP/TFB/promoter complex. Proc. Natl. Acad. Sci. USA. 96:1999;13668-13673.
28. Magill C.P., Jackson S.P., Bell S.D. Identification of a conserved archaeal RNA polymerase subunit contacted by the basal transcription factor TFB. J. Biol. Chem. 276:2001;46693-46696.
29. Mekler V., Kortkhonjia E., Mukhopadhyay J., Knight J., Revyakin A., Kapanidis A.N., Niu W., Ebright Y.W., Levy R., Ebright R.H. Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex. Cell. 108:2002;599-614.
30. Murakami K.S., Darst S.A. Bacterial RNA polymerases. the wholo story Curr. Opin. Struct. Biol. 13:2003;31-39.
31. Murakami K., Kimura M., Owens J.T., Meares C.F., Ishihama A. The two alpha subunits of Escherichia coli RNA polymerase are asymmetrically arranged and contact different halves of the DNA upstream element. Proc. Natl. Acad. Sci. USA. 94:1997;1709-1714.
32. Murakami K.S., Masuda S., Campbell E.A., Muzzin O., Darst S.A. Structural basis of transcription initiation. an RNA polymerase holoenzyme-DNA complex Science. 296:2002;1285-1290.
33. Nicholls A., Sharp K.A., Honig B. Protein folding and association. insights from the interfacial and thermodynamic properties of hydrocarbons Proteins. 11:1991;281-296.
34. Nikolov D.B., Chen H., Halay E.D., Usheva A.A., Hisatake K., Lee D.K., Roeder R.G., Burley S.K. Crystal structure of a TFIIB-TBP-TATA-element ternary complex. Nature. 377:1995;119-128.
35. Pardee T.S., Bangur C.S., Ponticelli A.S. The N-terminal region of yeast TFIIB contains two adjacent functional domains involved in stable RNA polymerase II binding and transcription start site selection. J. Biol. Chem. 273:1998;17859-17864.
36. Pinto I., Wu W.-H., Na J.G., Hampsey M. Characterization of sua7 mutations defines a domain of TFIIB involved in transcription start site selection in yeast. J. Biol. Chem. 269:1994;30569-30573.
37. Qureshi S.A., Bell S.D., Jackson S.P. Factor requirements for transcription in the Archaeon Sulfolobus shibatae. EMBO J. 16:1997;2927-2936.
38. Ranish J.A., Yudkovsky N., Hahn S. Intermediates in formation and activity of the RNA polymerase II preinitiation complex. holoenzyme recruitment and a postrecruitment role for the TATA box and TFIIB Genes Dev. 13:1999;49-63.
39. Scafe C., Martin C., Nonet M., Podos S., Okamura S., Young R.A. Conditional mutations occur predominantly in highly conserved residues of RNA polymerase II subunits. Mol. Cell. Biol. 10:1990;1270-1275.
40. Schramm L., Hernandez N. Recruitment of RNA polymerase III to its target promoters. Genes Dev. 16:2002;2593-2620.
41. Tsai F.T., Sigler P.B. Structural basis of preinitiation complex assembly on human pol II promoters. EMBO J. 19:2000;25-36.
42. Vassylyev D.G., Sekine S., Laptenko O., Lee J., Vassylyeva M.N., Borukhov S., Yokoyama S. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution. Nature. 417:2002;712-719.
43. Woychik N.A., Hampsey M. The RNA polymerase II machinery. structure illuminates function Cell. 108:2002;453-463.
44. Zhu W., Zeng Q., Coangelo C.M., Lewis M., Summers M.F., Scott R.A. The N-terminal domain of TFIIB from Pyrococcus furiosus forma a zinc ribbon. Nat. Struct. Biol. 3:1996;122-124.