The many conformational states of RNA polymerase elongation complexes and their roles in the regulation of transcription

Biochimica et Biophysica Acta - Gene Structure and Expression

Volumn 1577, Issue 2, 2002, Pages 224-239

  Erie, Dorothy A ^a  

^a The University of North Carolina at Chapel Hill   (United States)

Author keywords

Backtracking; RNA polymerase; RNA synthesis; Transcription elongation

Indexed keywords

REGULATOR PROTEIN; RNA POLYMERASE;

DNA SEQUENCE; ENZYME CONFORMATION; ENZYME REGULATION; ENZYME STRUCTURE; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL; PROTEIN FUNCTION; REVIEW; RNA CONFORMATION; RNA SEQUENCE; RNA SYNTHESIS; TRANSCRIPTION REGULATION; TRANSCRIPTION TERMINATION;

ALLOSTERIC SITE; BASE SEQUENCE; CATALYSIS; DNA FOOTPRINTING; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; GENE EXPRESSION REGULATION; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; PEPTIDE CHAIN ELONGATION, TRANSLATIONAL; PEPTIDE CHAIN TERMINATION, TRANSLATIONAL; PROTEIN CONFORMATION; RNA; RNA POLYMERASE II; TRANSCRIPTION, GENETIC;

ESCHERICHIA COLI;

EID: 0037073062     PISSN: 01674781     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0167-4781(02)00454-2     Document Type: Review

References (97)

1. Foster J.E., Holmes S.F., Erie D.A. Cell. 106:2001;243-252.
2. Erie D.A., Yager T.D., von Hippel P.H. Annu. Rev. Biophys. Biomol. Struct. 21:1992;379-415.
3. Uptain S.M., Kane C.M., Chamberlin M.J. Annu. Rev. Biochem. 66:1997;117-172.
4. Coulombe B., Burton Z.F. Microbiol. Mol. Biol. Rev. 63:1999;457-478.
5. Landick R. Science. 284:1999;598-599.
6. Mooney R.A., Landick R. Cell. 98:1999;687-690.
7. Gelles J., Landick R. Cell. 93:1998;13-16.
8. von Hippel P.H. Science. 281:1998;660-665.
9. Surratt C.K., Milan S.C., Chamberlin M.J. Proc. Natl. Acad. Sci. U. S. A. 88:1991;7983-7987.
10. Rice G.A., Kane C.M., Chamberlin M.J. Proc. Natl. Acad. Sci. U. S. A. 88:1991;4245-4249.
11. Erie D.A., Hajiseyedjavadi O., Young M.C., von Hippel P.H. Science. 262:1993;867-873.
12. Mustaev A., Kashlev M., Zaychikov E., Grachev M., Goldfarb A. J. Biol. Chem. 268:1993;19185-19187.
13. Chan C.L., Landick R. Conaway R.C., Conaway J.W. Transcription: Mechanisms and Regulation. 1994;297-321 Raven Press, New York.
14. Nudler E., Goldfarb A., Kashlev M. Science. 265:1994;793-796.
15. Wang D., Meier T.I., Chan C.L., Feng G., Lee D.N., Landick R. Cell. 81:1995;341-350.
16. Nudler E., Kashlev M., Nikiforov V., Goldfarb A. Cell. 81:1995;351-357.
17. Artsimovitch I., Landick R. Proc. Natl. Acad. Sci. U. S. A. 97:2000;7070-7075.
18. Komissarova N., Kashlev M. J. Biol. Chem. 272:1997;15329-15338.
19. Komissarova N., Kashlev M. Proc. Natl. Acad. Sci. U. S. A. 94:1997;1755-1760.
20. Yager T.D., von Hippel P.H. Biochemistry. 30:1991;1097-1118.
21. Metzger W., Schickor P., Heuman H. EMBO. 8:1989;2745-2754.
22. Arndt K.M., Chamberlin M.J. J. Mol. Biol. 213:1990;79-108.
23. Kashlev M., Nudler E., Goldfarb A., White T., Kutter E. Cell. 75:1993;147-154.
24. Feng G.H., Lee D.N., Wang D., Chan C.L., Landick R. J. Biol. Chem. 269:1994;22282-22294.
25. Burova E., Gottesman M.E. Mol. Microbiol. 17:1995;633-641.
26. Burova E., Hung S.C., Sagitov V., Stitt B.L., Gottesman M.E. J. Bacteriol. 177:1995;1388-1392.
27. Conaway J.W., Conaway R.C. Annu. Rev. Biochem. 68:1999;301-319.
28. Hung S.C., Gottesman M.E. J. Mol. Biol. 247:1995;428-442.
29. Zellars M., Squires C.L. Mol. Microbiol. 32:1999;1296-1304.
30. Yarnell W.S., Roberts J.W. Science. 284:1999;611-615.
31. Pasman Z., von Hippel P.H. Biochemistry. 39:2000;5573-5585.
32. Liu B., Wong M.L., Tinker R.L., Geiduschek E.P., Alberts B.M. Nature. 366:1993;33-39.
33. Liu B., Wong M.L., Alberts B.M. Proc. Natl. Acad. Sci. U. S. A. 91:1994;10660-10664.
34. Alberts B.M., Liu B. Science. 267:1995;1131-1137.
35. Thomas M.J., Platas A.A., Hawley D.K. Cell. 93:1998;627-637.
36. Matsuzaki H., Kassavetis G.A., Geiduschek E.P. J. Mol. Biol. 235:1994;1173-1192.
37. Jing D.H., Dong F., Latham G.J., von Hippel P.H. J. Biol. Chem. 274:1999;27287-27298.
38. Borukhov S., Polyakov A., Nikiforov V., Goldfarb A. Proc. Natl. Acad. Sci. U. S. A. 89:1992;8899-8902.
39. Borukhov S., Goldfarb A. Methods Enzymol. 274:1996;315-326.
40. Chamberlin M.J. Harvey Lect. 88:1992;1-21.
41. Yin H., Artsimovitch I., Landick R., Gelles J. Proc. Natl. Acad. Sci. U. S. A. 96:1999;13124-13129.
42. Zhang G., Campbell E.A., Minakhin L., Richter C., Severinov K., Darst S.A. Cell. 98:1999;811-824.
43. Borukhov S., Sagitov V., Goldfarb A. Cell. 72:1993;459-466.
44. Hogan B.P., Hartsch T., Erie D.A. J. Biol. Chem. 277:2001;967-975.
45. Drivdahl R.H., Kutter E.M. J. Bacteriol. 172:1990;2716-2727.
46. Cramer P., Bushnell D.A., Kornberg R.D. Science. 292:2001;1863-1876.
47. Gnatt A.L., Cramer P., Fu J., Bushnell D.A., Kornberg R.D. Science. 292:2001;1876-1882.
48. Korzheva N., Mustaev A., Kozlov M., Malhotra A., Nikiforov V., Goldfarb A., Darst S. Science. 289:2000;619-625.
49. Nudler E., Mustaev A., Lukhtanov E., Goldfarb A. Cell. 89:1997;33-41.
50. Reeder T.C., Hawley D.K. Cell. 87:1996;767-777.
51. Borukhov S., Lee J., Goldfarb A. J. Biol. Chem. 266:1991;23932-23935.
52. Markovtsov V., Mustaev A., Goldfarb A. Proc. Natl. Acad. Sci. U. S. A. 93:1996;3221-3226.
53. Guajardo R., Sousa R. J. Mol. Biol. 265:1997;8-19.
54. Guthold M., Erie D.A. CHEMBIOCHEM. 2:2001;167-170.
55. Erijman L., Clegg R.M. Biophys. J. 75:1998;453-462.
56. Davenport R.J., Wuite G.J., Landick R., Bustamante C. Science. 287:2000;2497-2500.
57. Slepneva I.A., Weiner L.M. FEBS Lett. 130:1981;283-286.
58. Slepneva I.A. Mol. Biol. Rep. 6:1980;31-34.
59. Shimamoto N., Wu F.Y., Wu C.W. Biochemistry. 20:1981;4745-4755.
60. Shimamoto N., Wu C.W. Biochemistry. 19:1980;849-856.
61. Shimamoto N., Wu C.W. Biochemistry. 19:1980;842-848.
62. Nierman W.C., Chamberlin M.J. J. Biol. Chem. 255:1980;4495-4500.
63. Schulz A.R. Enzyme Kinetics: From Distase to Multi-Enzyme Systems. 1994;133-152 Cambridge Univ. Press, Cambridge.
64. Segel I.H. Enzyme Kinetics: Behavior and Analysis of Rapid Equilibrium and Steady State Enzyme Systems. 1975;227-272 Wiley, New York.
65. Polyakov A., Severinova E., Darst S.A. Cell. 83:1995;365-373.
66. Gaal T., Bartlett M.S., Ross W., Turnbough C.L., Gourse R.L. Science. 278:1997;2092-2097.
67. Xue Y., Hogan B.P., Erie D.A. Biochemistry. 39:2000;14356-14362.
68. Toulme F., Mosrin-Huaman C., Sparkowski J., Das A., Leng M., Rahmouni A.R. EMBO J. 19:2000;6853-6859.
69. Marr M.T., Roberts J.W. Mol. Cell. 6:2000;1275-1285.
70. Palangat M., Landick R. J. Mol. Biol. 311:2001;265-282.
71. Krummel B., Chamberlin M.J. J. Mol. Biol. 225:1992;221-237.
72. Krummel B., Chamberlin M.J. J. Mol. Biol. 225:1992;239-250.
73. Kays A.R., Schepartz A. Chem. Biol. 7:2000;601-610.
74. Landick R. Cell. 88:1997;741-744.
75. Reines D. J. Biol. Chem. 267:1992;3795-3800.
76. Reines D., Chamberlin M.J., Kane C.M. J. Biol. Chem. 264:1989;10799-10809.
77. Reines D., Conaway J.W., Conaway R.C. Trends Biochem. Sci. 21:1996;351-355.
78. Reines D., Conaway R.C., Conaway J.W. Curr. Opin. Cell Biol. 11:1999;342-346.
79. Reines D., Mote J. Jr. Proc. Natl. Acad. Sci. U. S. A. 90:1993;1917-1921.
80. Sluder A.E., Greenleaf A.L., Price D.H. J. Biol. Chem. 264:1989;8963-8969.
81. Rudd M.D., Izban M.G., Luse D.S. Proc. Natl. Acad. Sci. U. S. A. 91:1994;8057-8061.
82. Wang D., Hawley D.K. Proc. Natl. Acad. Sci. U. S. A. 90:1993;843-847.
83. Korzheva N., Mustaev A., Nudler E., Nikiforov V., Goldfarb A. Cold Spring Harbor Symp. Quant. Biol. 63:1998;337-345.
84. Koulich D., Orlova M., Malhotra A., Sali A., Darst S.A., Borukhov S. J. Biol. Chem. 272:1997;7201-7210.
85. Stebbins C.E., Borukhov S., Orlova M., Polyakov A., Goldfarb A., Darst S.A. Nature. 373:1995;636-640.
86. Loizos N., Darst S.A. J. Biol. Chem. 274:1999;23378-23386.
87. Polyakov A., Richter C., Malhotra A., Koulich D., Borukhov S., Darst S.A. J. Mol. Biol. 281:1998;465-473.
88. Chan C.L., Wang D., Landick R. J. Mol. Biol. 268:1997;54-68.
89. Artsimovitch I., Landick R. Genes Dev. 12:1998;3110-3122.
90. Toulokhonov I., Artsimovitch I., Landick R. Science. 292:2001;730-733.
91. Hsu L.M., Vo N.V., Chamberlin M.J. Proc. Natl. Acad. Sci. U. S. A. 92:1995;11588-11592.
92. Minakhin L., Nechaev S., Campbell E.A., Severinov K. J. Bacteriol. 183:2001;71-76.
93. Johnson K.A. Annu. Rev. Biochem. 62:1993;685-713.
94. Donlin M.J., Patel S.S., Johnson K.A. Biochemistry. 30:1991;538-546.
95. Wong I., Patel S.S., Johnson K.A. Biochemistry. 30:1991;526-537.
96. Armstrong V.W., Yee D., Eckstein F. Biochemistry. 18:1979;4120-4123.
97. B. Krummel, PhD Thesis, University of California-Berkeley, 1993.