Downstream DNA sequence effects on transcription elongation: Allosteric binding of nucleoside triphosphates facilitates translocation via a ratchet motion

Journal of Biological Chemistry

Volumn 278, Issue 37, 2003, Pages 35597-35608

  Holmes, Shannon F ^a,c   Erie, Dorothy A ^a,b  

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

^b UNIVERSITY OF NORTH CAROLINA   (United States)

^c NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSIS; CONFORMATIONS; ENZYMES; ESCHERICHIA COLI; RNA;

TRANSCRIPTIONAL REGULATION;

DNA;

DNA; DNA BASE; NUCLEOSIDE TRIPHOSPHATASE; RNA POLYMERASE; RNA POLYMERASE II; STREPTOLYDIGIN;

ALLOSTERISM; ARTICLE; BASE PAIRING; BINDING SITE; CATALYSIS; DNA SEQUENCE; DNA TRANSCRIPTION; ENZYME ACTIVATION; ENZYME BINDING; ENZYME CONFORMATION; ENZYME KINETICS; ENZYME MECHANISM; ESCHERICHIA COLI; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN TRANSPORT; TRANSCRIPTION REGULATION; YEAST;

ALLOSTERIC REGULATION; AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; CONSERVED SEQUENCE; DEOXYRIBONUCLEOTIDES; DNA, BACTERIAL; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; HUMANS; KINETICS; MOLECULAR SEQUENCE DATA; PEPTIDE CHAIN ELONGATION, TRANSLATIONAL; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SEQUENCE HOMOLOGY, NUCLEIC ACID; TEMPLATES, GENETIC; THERMUS THERMOPHILUS; TRANSCRIPTION, GENETIC;

ESCHERICHIA COLI;

EID: 0041315524     PISSN: 00219258     EISSN: None     Source Type: Journal    
DOI: 10.1074/jbc.M304496200     Document Type: Article

References (60)

1. Foster, J. E., Holmes, S. F., and Erie, D. A. (2001) Cell 106, 243-252
2. Erie, D. A., Hajiseyedjavadi, O., Young, M. C., and von Hippel, P. H. (1993) Science 262, 867-873
3. Erie, D. A., Yager, T. D., and von Hippel, P. H. (1992) Annu. Rev. Biophys. Biomol. Struct. 21, 379-415
4. Davenport, R. J., Wuite, G. J., Landick, R., and Bustamante, C. (2000) Science 287, 2497-2500
5. Matsuzaki, H., Kassavetis, G. A., and Geiduschek, E. P. (1994) J. Mol. Biol. 235, 1173-1192
6. Yin, H., Artsimovitch, I., Landick, R., and Gelles, J. (1999) Proc. Natl. Acad. Sci. U. S. A. 96, 13124-13129
7. Coulombe, B., and Burton, Z. F. (1999) Microbiol. Mol. Biol. Rev. 63, 457-478
8. Guthold, M., and Erie, D. A. (2001) Chembiochem 2, 167-170
9. Kubori, T., and Shimamoto, N. (1996) J. Mol. Biol. 256, 449-457
10. Erie, D. A. (2002) Biochim. Biophys. Acta 1577, 224-239
11. Landick, R. (1997) Cell 88, 741-744
12. Chan, C. L., Wang, D., and Landick, R. (1997) J. Mol. Biol. 268, 54-68
13. Chan, C. L., and Landick, R. (1997) J. Mol. Biol. 268, 37-53
14. Lee, D. N., Phung, L., Stewart, J., and Landick, R. (1990) J. Biol. Chem. 265, 15145-15153
15. Landick, R., and Yanofsky, C. (1984) J. Biol. Chem. 259, 11550-11555
16. Landick, R., and Yanofsky, C. (1987) J. Mol. Biol. 196, 363-377
17. Wang, D., Meier, T. I., Chan, C. L., Feng, G., Lee, D. N., and Landick, R. (1995) Cell 81, 341-350
18. Levin, J. R., and Chamberlin, M. J. (1987) J. Mol. Biol. 196, 61-84
19. Fivaz, J., Bassi, M. C., Pinaud, S., and Mirkovitch, J. (2000) Gene (Amst.) 255, 185-194
20. Aranda, A., and Proudfoot, N. J. (1999) Mol. Cell. Biol. 19, 1251-1261
21. Telesnitsky, A., and Chamberlin, M. J. (1989) Biochemistry 28, 5210-5218
22. Reynolds, R., Bermudez-Cruz, R. M., and Chamberlin, M. J. (1992) J. Mol. Biol. 224, 31-51
23. Reynolds, R., and Chamberlin, M. J. (1992) J. Mol. Biol. 224, 53-63
24. Uptain, S. M., and Chamberlin, M. J. (1997) Proc. Natl. Acad. Sci. U. S. A. 94, 13548-13553
25. Burgess, R. R., and Jendrisak, J. J. (1975) Biochemistry 14, 4634-4638
26. Kuzmic, P. (1996) Anal. Biochem. 237, 260-273
27. Anderson, K. S., Sikorski, J. A., and Johnson, K. A. (1988) Biochemistry 27, 7395-7406
28. Cramer, P., Bushnell, D. A., and Kornberg, R. D. (2001) Science 292, 1863-1876
29. Forde, N. R., Izhaky, D., Woodcock, G. R., Wuite, G. J., and Bustamante, C. (2002) Proc. Natl. Acad. Sci. U. S. A. 99, 11682-11687
30. Neff, N. F., and Chamberlin, M. J. (1980) Biochemistry 19, 3005-3015
31. Levin, J. R., Krummel, B., and Chamberlin, M. J. (1987) J. Mol. Biol. 196, 85-100
32. Artsimovitch, I., and Landick, R. (2000) Proc. Natl. Acad. Sci. U. S. A. 97, 7090-7095
33. Palangat, M., and Landick, R. (2001) J. Mol. Biol. 311, 265-282
34. Komissarova, N., and Kashlev, M. (1997) J. Biol. Chem. 272, 15329-15338
35. Landick, R. (1999) Science 284, 598-599
36. Tomizawa, J., and Masukata, H. (1987) Cell 51, 623-630
37. Wilson, K. S., and von Hippel, P. H. (1995) Proc. Natl. Acad. Sci. U. S. A. 92, 8793-8797
38. Gusarov, I., and Nudler, E. (1999) Mol. Cell 3, 495-504
39. Rosenberg, M., and Court, D. (1979) Annu. Rev. Genet. 13, 319-353
40. Gnatt, A. L., Cramer, P., Fu, J., Bushnell, D. A., and Kornberg, R. D. (2001) Science 292, 1876-1882
41. Korzheva, N., Mustaev, A., Kozlov, M., Malhotra, A., Nikiforov, V., Goldfarb, A., and Darst, S. A. (2000) Science 289, 619-625
42. Zhang, G., Campbell, E. A., Minakhin, L., Richter, C., Severinov, K., and Darst, S. A. (1999) Cell 98, 811-824
43. Vassylyev, D. G., Sekine, S., Laptenko, O., Lee, J., Vassylyeva, M. N., Borukhov, S., and Yokoyama, S. (2002) Nature 417, 712-719
44. Heisler, L. M., Suzuki, H., Landick, R., and Gross, C. A. (1993) J. Biol. Chem. 268, 25369-25375
45. Severinov, K., Soushko, M., Goldfarb, A., and Nikiforov, V. (1993) J. Biol. Chem. 268, 14820-14825
46. Yang, X., and Price, C. W. (1995) J. Biol. Chem. 270, 23930-23933
47. McClure, W. R. (1980) J. Biol. Chem. 255, 1610-1616
48. Cassani, G., Burgess, R. R., Goodman, H. M., and Gold, L. (1971) Nat. New Biol. 230, 197-200
49. Jin, D. J., and Gross, C. A. (1991) J. Biol. Chem. 266, 14478-14485
50. Walker, J. E., Saraste, M., Runswick, M. J., and Gay, N. J. (1982) EMBO J. 1, 945-951
51. Leipe, D. D., Wolf, Y. I., Koonin, E. V., and Aravind, L. (2002) J. Mol. Biol. 317, 41-72
52. Kull, F. J., Vale, R. D., and Fletterick, R. J. (1998) J. Muscle Res. Cell Motil. 19, 877-886
53. Via, A., Ferre, F., Brannetti, B., Valencia, A., and Helmer-Citterich, M. (2000) J. Mol. Biol. 303, 455-465
54. Pargellis, C., Tong, L., Churchill, L., Cirillo, P. F., Gilmore, T., Graham, A. G., Grob, P. M., Hickey, E. R., Moss, N., Pav, S., and Regan, J. (2002) Nat. Struct. Biol. 9, 268-272
55. Tahirov, T. H., Temiakov, D., Anikin, M., Patlan, V., McAllister, W. T., Vassylyev, D. G., and Yokoyama, S. (2002) Nature 420, 43-50
56. Nedialkov, Y. A., Gong, X. Q., Hovde, S. L., Yamaguchi, Y., Handa, H., Geiger, J. H., Yan, H., and Burton, Z. F. (2003) J. Biol. Chem. 278, 18303-18312
57. Shimamoto, N., and Wu, C. W. (1980) Biochemistry 19, 842-848
58. Barshop, B. A., Wrenn, R. F., and Frieden, C. (1983) Anal. Biochem. 130, 134-145
59. Zimmerle, C. T., and Frieden, C. (1989) Biochem. J. 258, 381-387
60. Zhou, T., Radaev, S., Rosen, B. P., and Gatti, D. L. (2000) EMBO J. 19, 4838-4845