RNA polymerase-DNA interaction: Structures of intermediate, open, and elongation complexes

Cold Spring Harbor Symposia on Quantitative Biology

Volumn 63, Issue , 1998, Pages 11-20

  Ebright, R H ^a  

^a RUTGERS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; ELONGATION FACTOR; RNA POLYMERASE; DNA DIRECTED RNA POLYMERASE III; RNA POLYMERASE II;

CONFERENCE PAPER; CONFORMATIONAL TRANSITION; DNA CROSS LINKING; ELECTRON MICROSCOPY; ENZYME STRUCTURE; MOLECULAR MODEL; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DNA INTERACTION; PROTEIN PROCESSING; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION; TRANSCRIPTION TERMINATION; CARBOXY TERMINAL SEQUENCE; CROSS LINKING; DOWNSTREAM PROCESSING; GENE EXPRESSION; HUMAN; RNA STRUCTURE; RNA SYNTHESIS;

EID: 0032450639     PISSN: 00917451     EISSN: None     Source Type: Book Series    
DOI: 10.1101/sqb.1998.63.11     Document Type: Conference Paper

References (78)

1. Archambault J. and Friesen J. 1993. Genetics of eukaryotic RNA polymerases I, II, and III. Microbiol. Rev. 57: 703.
2. Asturias F., Meredith G., Poglitsch C., and Kornberg R. 1997. Two conformations of RNA polymerase II revealed by electron crystallography. J. Mol. Biol. 272: 536.
3. Bartholomew B., Braun B., Kassavetis G., and Geiduschek E.P. 1994. Probing close contacts of RNA polymerase III transcription complexes with the photoactive nucleoside 4-thiodeoxythymidine. J. Biol. Chem. 269: 18090.
4. Bartholomew B., Durkovich D., Kassavetis G., and Geiduschek E.P. 1993. Orientation and topography of RNA polymerase III in transcription complexes. Mol. Cell. Biol. 13: 942.
5. Busby S. and Ebright R. 1994. Promoter structure, promoter recognition, and transcription activation in prokaryotes. Cell 79: 743.
6. Carlson M. 1997. Genetics of transcriptional regulation in yeast: Connections to the RNA polymerase II CTD. Anna. Rev. Cell Dev. Biol. 13: 1.
7. Chambers R., Wang B., Burton Z., and Dahmus M. 1995. The activity of COOH-terminal domain phosphatase is regulated by a docking site on RNA polymerase II and by the general transcription factors IIF and IIB. J. Biol. Chem. 270: 14962.
8. Chenchick A., Beabealashvilli R., and Mirzabekov A. 1981. Topography of interaction of Escherichia coli RNA polymerase subunits with lacUV5 promoter. FEBS Lett. 128: 46.
9. Corden J. and Patturajan M. 1997. A CTD function linking transcription to splicing. Trends Biochem. Sci. 22: 413.
10. Corden J., Wasylysk B., Buchwalder A., Sassone-Corsi P., Kedinger C., and Chambon P. 1980. Promoter sequences of eukaryotic protein-coding genes. Science 209: 1406.
11. Coulombe B., Li J., and Greenblatt J. 1994. Topological localization of the human transcription factors IIA, IIB, TATA box-binding protein, and RNA polymerase II-associated protein 30 on a class II promoter. J. Biol. Chem. 269: 19962.
12. Dahmus M. 1995. Phosphorylation of the C-terminal domain of RNA polymerase II. Biochim. Biophys. Acta 1261: 171.
13. Darst S., Edwards A., Kubalek E., and Kornberg R. 1991. Three-dimensional structure of yeast RNA polymerase II at 16 Å resolution. Cell 66: 121.
14. d'Aubenton Carafa Y., Brody E., and Thermes C. 1990. Prediction of rho-independent Escherichia coli transcription terminators. J. Mol. Biol. 216: 835.
15. deHaseth P. and Helmann J. 1995. Open complex formation by Escherichia coli RNA polymerase: The mechanism of polymerase-induced strand separation of double helical DNA. Mol Microbiol. 16: 817.
16. deHaseth P., Zupancic M., and Record M. 1998. RNA polymerase-promoter interactions. J. Bacteriol. 180: 3019.
17. Edwards A., Kane C., Young R., and Kornberg R. 1991. Two dissociable subunits of yeast RNA polymerase II stimulate the initiation of transcription at a promoter in vitro. J. Biol. Chem. 266: 71.
18. Forget D., Robert F., Grondin G., Burton Z., Greenblatt J., and Coulombe B. 1997. RAP74 induces promoter contacts by RNA polymerase II upstream and downstream of a DNA bend centered on the TATA box. Proc. Natl. Acad. Sci. 94: 7150.
19. Fu J., Gerstein M., David P., Gnatt A., Bushnell D., Edwards A., and Kornberg R. 1998. Repeated tertiary fold of RNA polymerase II and implications for DNA binding. J. Mol. Biol. 280: 317.
20. Gamper H. and Hearst J. 1982a. A topological model for transcription based on unwinding angle analysis of E. coli RNA polymerase binary, initiation and ternary complexes. Cell 29: 81.
21. _. 1982b. Size of the unwound region of DNA in Escherichia coli RNA polymerase and calf thymus RNA polymerase II ternary complexes. Cold Spring Harbor Symp. Quant. Biol. 47: 455.
22. Geiger J., Hahn S., Lee S., and Sigler P. 1996. Crystal structure of the yeast TFIIA/TBP/DNA complex. Science 272: 830.
23. Gelles J. and Landick R. 1998. RNA polymerase as a molecular motor. Cell 93: 13.
24. Giardina C. and Lis J. 1993. DNA melting on yeast RNA polymerase II promoters. Science 261: 759.
25. Gross C., Lonetto M., and Losick R. 1992. Bacterial sigma factors. In Transcriptional regulation (ed. S. McKnight and K. Yamamoto), p. 129. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
26. Hanna M. and Meares C. 1983. Topography of transcription: Path of the leading end of nascent RNA through the Escherichia coli transcription complex. Proc. Natl. Acad. Sci. 80: 4238.
27. Heumann H., Ricchetti M., and Werel W. 1988. DNA-dependent RNA polymerase of Escherichia coli induces bending or an increased flexibility of DNA by specific complex formation. EMBO J. 7: 4379.
28. Holstege F., van der Vliet P.C., and Timmers H.T. 1996. Opening of an RNA polymerase II promoter occurs in two distinct steps and requires the basal transcription factors IIE and IIH. EMBO J. 15: 1666.
29. Huang X., Lopez de Saro F., and Helmann J. 1997. σ Factor mutations affecting the sequence-selective interaction of RNA polymerase with - 10 region single-stranded DNA. Nucleic Acids Res. 25: 2603.
30. Jensen G., Meredith G., Bushnell D., and Kornberg R. 1998. Structure of wild-type yeast RNA polymerase II and location of Rpb4 and Rpb7. EMBO J. 17: 2353.
31. Kang M. and Dahmus M. 1995. The photoactivated cross-linking of recombinant C-terminal domain to proteins in a HeLa cell transcription extract that comigrate with transcription factors IIE and IIP. J. Biol. Chem. 270: 23390.
32. Kim J., Nikolov D., and Burley S. 1993. Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature 365: 520.
33. Kim T.-K., Lagrange T., Wang Y.-H., Griffith J., Reinberg D., and Ebright R. 1997. Trajectory of DNA in the RNA polymerase II transcription preinitiation complex. Proc. Natl. Acad. Sci. 94: 12268.
34. Kim Y., Geiger J., Hahn S., and Sigler P. 1993. Crystal structure of a yeast TBP/TATA-box complex. Nature 365: 512.
35. Klinger C., Huet J., Song D., Petersen G., Riva M., Bautz E., Sentenac A., Oudet P., and Schultz P. 1996. Localization of yeast RNA polymerase I core subunits by immunoelectron microscopy. EMBO J. 15: 4643.
36. Komissarova N. and Kashlev M. 1997a. RNA polymerase switches between inactivated and activated states by translocating back and forth along the DNA and the RNA. J. Biol. Chem. 272: 15329.
37. _. 1997b. Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3′ end of the RNA intact and extruded. Proc. Natl. Acad. Sci. 94: 1755.
38. Kornberg. R. 1996. RNA polymerase II transcription control. Trends Biochem. Sci. 21: 325.
39. Lagrange T., Kapanidis A., Tang H., Reinberg D., and Ebright R. 1998. New core promoter element in RNA polymerase II-dependent transcription: Sequence-specific DNA binding by transcription factor IIB. Genes Dev. 12: 34.
40. Lagrange T., Kim T.K., Orphanides G., Ebright Y., Ebright R., and Reinberg D. 1996. High-resolution mapping of nucleoprotein complexes by site-specific protein-DNA photocrosslinking: Organization of the human TBP-TFIIA-TFIIB-DNA quaternary complex. Proc. Natl. Acad. Sci. 93: 10620.
41. Lee D. and Landick R. 1992. Structure of RNA and DNA chains in paused transcription complexes containing Escherichia coli RNA polymerase. J. Mol. Biol. 228: 759.
42. Lee S. and Hahn S. 1995. A model for TFIIB binding to the TBP-DNA complex. Nature 376: 609.
43. Leuther K., Bushnell D., and Komberg R. 1996. Two-dimensional crystallography of TFIIB- and IIE-RNA polymerase II complexes: Implications for start site selection and initiation complex formation. Cell 85: 773.
44. Liu K. and Hanna M. 1995. NusA interferes with interactions between the nascent RNA and the C-terminal domain of the alpha subunit of RNA polymerase in Escherichia coli transcription complexes. Proc. Natl. Acad. Sci. 92: 5012.
45. 70 subunit fragment from E. coli RNA polymerase. Cell 87: 127.
46. Marr M. and Roberts J. 1997. Promoter recognition as measured by binding of polymerase to nontemplate strand oligonucleotide. Science 276: 1258.
47. 70-α cross-link to the C-terminal region of a. Biochemistry 33: 12092.
48. Melnikova A., Beabealashvilli R., and Mirzabekov A. 1978. A study of unwinding of DNA and shielding of the DNA grooves by RNA polymerase by using methylation with dimethylsulphate. Eur. J. Biochem. 84: 301.
49. Meredith G., Chang W.-H., Li Y., Bushnell D., Darst S., and Kornberg R. 1996. The C-terminal domain revealed in the structure of RNA polymerase II. J. Mol. Biol. 258: 413.
50. Meyer-Almes F.-J., Heumann H., and Porschke D. 1994. The structure of the RNA polymerase-promoter complex: DNA-bending angle by quantitative electrooptics. J. Mol. Biol. 236: 1.
51. Mooney R., Artsimovitch I., and Landick R. 1998. Information processing by RNA polymerase: Recognition of regulatory signals during RNA chain elongation. J. Bacteriol. 180: 3265.
52. Nikolov D., Chen H., Malay E., Usheva A., Hisatake K., Lee D.K., Roeder R., and Burley S. 1995. Crystal structure of a TFIIB-TBP-TATA-element ternary complex. Nature 377: 119.
53. Nudler E., Mustaev A., Lukhtanov E., and Goldfarb A. 1997. The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase. Cell 89: 33.
54. Nudler E., Gusarov I., Avetissova E., Kozlov M., and Goldfarb A. 1998. Spatial organization of transcription elongation complex in Escherichia coli. Science 281: 424.
55. 70 in an Escherichia coli RNA polymerase-lacUV5 open promoter complex. Biochemistry 37: 7670.
56. Polyakov A., Severinova E., and Darst S. 1995. Three-dimensional structure of E. coli core RNA polymerase: Promoter binding and elongation conformations of the enzyme. Cell 83: 365.
57. Qureshi S. and Jackson S. 1998. Sequence-specific DNA binding by the 5. shibatae TFIIB homolog, TFB, and its effect on promoter strength. Mol. Cell 1: 389.
58. 70), promoters, and the kinetics of the steps of transcription initiation. In Escherichia coli and Salmonella: Cellular and molecular biology (ed. F. Neidhart), p. 792. ASM Press, Washington, D.C.
59. Reeder T. and Hawley D. 1996. Promoter proximal sequences modulate RNA polymerase II elongation by a novel mechanism. Cell 87: 767.
60. 54 holoenzyme by scanning force microscopy. J. Mol. Biol. 270: 125.
61. Robert F., Forget D., Li J., Greenblatt J., and Coulombe B. 1996. Localization of subunits of transcription factors IIE and IIF immediately upstream of the transcriptional initiation site of the adenovirus major late promoter. J. Biol. Chem. 271: 8517.
62. Roberts J. 1995. Transcription termination and its control. In Regulation of gene expression in Escherichia coli (ed. E.C.C. Lin and A. Simon). R.G. Landes, Austin, Texas.
63. 4 as a probe for lac promoter DNA melting and mechanism in vivo. J. Biol. Chem. 264: 8074.
64. Schultz P., Celia H., Riva M., Sentenac A., and Oudet P. 1993. Three-dimensional model of yeast RNA polymerase I determined by electron microscopy of two-dimensional crystals. EMBO J. 12: 2601.
65. Selvin P. 1995. Fluorescence resonance energy transfer. Methods Enzymol. 246: 301.
66. Sentenac A., Riva M., Thuriaux P., Buhler J.-M., Treich I., Carles C., Werner M., Ruet A., Huet J., Mann C, Chiannilkulchai N., Stettler S., and Mariette S. 1992. Yeast RNA polymerase subunits and genes. In Transcriptional regulation (ed. S. McKnight and K. Yamamoto), p. 27. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
67. Shuman S. 1997. Origins of mRNA identity: Capping enzymes bind to the phosphorylated C-terminal domain of RNA polymerase II. Proc. Natl. Acad. Sci. 94: 12758.
68. Sidorenkov I., Komissarova N., and Kashlev M. 1998. Crucial role of the RNA:DNA hybrid in the processivity of transcription. Mol. Cell 2: 55.
69. Siebenlist U., Simpson R., and Gilbert W. 1980. E. coli RNA polymerase interacts homologously with two different promoters. Cell 20: 269.
70. Steinmetz E. 1997. Pre-mRNA processing and the CTD of RNA polymerase II. Cell 89: 491.
71. Tan S., Hunziker Y., Sargent D., and Richmond T. 1996. Crystal structure of a yeast TFIIA/TBP/DNA complex. Nature 381: 127.
72. Tichelaar W., Schutter W., Arnberg A., van Bruggen E., and Slender W. 1983. The quaternary structure of Escherichia coli RNA polymerase studies with (scanning) transmission (immuno)electron microscopy. Eur. J. Biochem. 135: 363.
73. Uptain S.M., Kane C.M., and Chamberlin M.J. 1997. Basic mechanisms of transcription elongation and its regulation. Annu. Rev. Biochem. 66: 117.
74. Usheva A., Maldonado E., Goldring A., Lu H., Houbavi C., Reinberg D., and Aloni Y. 1992. Specific interaction between the nonphosphorylated form of RNA polymerase II and the TATA-binding protein. Cell 69: 871.
75. von Hippel P., Bear D., Morgan W., and McSwiggen J. 1984. Protein-nucleic acid interactions in transcription: A molecular analysis. Annu. Rev. Biochem. 53: 389.
76. Wang W., Carey M., and Gralla J. 1992. Polymerase II promoter activation: Closed complex formation and ATP-driven start site opening. Science 255: 450.
77. Young R. 1991. RNA polymerase II. Annu. Rev. Biochem. 60: 689.
78. 2+ and temperature on formation of the transcription bubble. J. Biol. Chem. 272: 2259.