Strand opening-deficient Escherichia coli RNA polymerase facilitates investigation of closed complexes with promoter DNA: Effects of DNA sequence and temperature

Journal of Biological Chemistry

Volumn 282, Issue 29, 2007, Pages 21319-21326

  Cook, Victoria M ^a   DeHaseth, Pieter L ^a  

^a CASE WESTERN RESERVE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIOPHAGES; BINDING SITES; DNA SEQUENCES; ENZYMES; RNA;

CLOSED COMPLEX FORMATION; PROMOTER DNA; RNAPOLYMERASE;

ESCHERICHIA COLI;

DEOXYRIBONUCLEASE I; DOUBLE STRANDED DNA; RNA POLYMERASE;

ARTICLE; BACTERIOPHAGE LAMBDA; BACTERIUM MUTANT; BASE PAIRING; COMPLEX FORMATION; CONTROLLED STUDY; DNA SEQUENCE; ESCHERICHIA COLI; LOW TEMPERATURE; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN PROTEIN INTERACTION; TEMPERATURE SENSITIVITY;

BASE SEQUENCE; DEOXYRIBONUCLEASE I; DNA; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; KINETICS; MODELS, CHEMICAL; MOLECULAR SEQUENCE DATA; POTASSIUM PERMANGANATE; PROMOTER REGIONS (GENETICS); TEMPERATURE;

ENTEROBACTERIA PHAGE LAMBDA; ESCHERICHIA COLI;

EID: 34547113065     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M702232200     Document Type: Article

References (40)

1. Gross, C., Chan, C., Dombroski, A., Gruber, T., Sharp, M., Tupy, J., and Young, B. A. (1998) Cold Spring Harbor Symp. Quant. Biol. 63, 141-155
2. deHaseth, P. L., Zupancic, M., and Record, M. T., Jr. (1998) J. Bacteriol. 180, 3019-3025
3. Record, M. T., Jr., Reznikoff, W. S., Craig, M. L., McQuade, K. L., and Schlax, P. J. (1996) in Escherichia coli and Salmonella, Cellular and Molecular Biology (Neidhardt, F. C., ed) pp. 792-820, American Society for Microbiology, Washington, D. C.
4. Sen, R., Nagai, H., and Shimamoto, N. (2000) J. Boil. Chem. 275, 10899-10904
5. Mulligan, M. E., Brosius, J., and McClure, W. R. (1985) J. Biol. Chem. 260, 3529-3538
6. Saecker, R. M., Tsodikov, O. V., McQuade, K. L., Schlax, P. E., Capp, M. W., and Record, M. T., Jr. (2002) J. Mol. Biol. 319, 649-671
7. Craig, M. L., Tsodikov, O. V., McQuade, K. L., Schlax, Jr., P. E., Capp, M. W., Saecker, R. M., and Record, M. T., Jr. (1998) J. Mol. Biol. 283, 741-756
8. deHaseth, P. L., Lohman, T. M., Burgess, R. R., and Record, M. T., Jr. (1978) Biochemistry 17, 1612-1622
9. Craig, M. L., Suh, W.-C., and Record, M. T. J. (1995) Biochemistry 34, 15624-15632
10. Kovacic, R. T. (1987) J. Biol. Chem. 262, 13654-13661
11. Roy, S., Semsey, S., Liu, M., Gussin, G., and Adhya, S. (2004) J. Mol. Biol. 344, 609-618
12. Li, X.-Y., and McClure, W. R. (1998) J. Biol. Chem. 273, 23549-23557
13. Zhang, X., Rheeder, T., and Schleif, R. (1996) J. Mol. Biol. 258, 14-24
14. Niedziela-Majka, A., and Heyduk, T. (2005) J. Biol. Chem. 280, 38219-38227
15. Sun, L., Dove, S., Panaghie, G., deHaseth, P. L., and Hochschild, A. (2004) J. Mol. Biol. 343, 1171-1182
16. Zhi, H., and Jin, D. J. (2003) Methods Enzymol. 370, 174-180
17. Panaghie, G., Aiyar, S. E., Bobb, K. L., Hayward, R. S., and deHaseth, P. L. (2000) J. Mol. Biol. 299, 1217-1230
18. Brenowitz, M., Senear, D. F., Shea, M. A., and Ackers, G. K. (1986) Methods Enzymol. 130, 132-181
19. Schroeder, L. A., and deHaseth, P. L. (2005) J. Biol. Chem. 280, 17422-17429
20. McKane, M., and Gussin, G. N. (2000) J. Mol. Biol. 299, 337-349
21. Roe, J. H., Burgess, R. R., and Record, M. T. (1984) J. Mol. Biol. 176, 495-521
22. Szoke, P. A., Allen, T. A., and deHaseth, P. L. (1987) Biochemistry 26, 6188-6194
23. Melançon, P., Burgess, R. R., and Record, M. T., Jr. (1983) Biochemistry 22, 5169-5176
24. Murakami, K. S., Masuda, S., Campbell, E. A., Muzzin, O., and Darst, S. A. (2002) Science 296, 1285-1290
25. Helmann, J. D., and deHaseth, P. L. (1999) Biochemistry 37, 5959-5967
26. Fenton, M. S., Lee, S. J., and Gralla, J. D. (2000) EMBO J. 19, 1130-1137
27. Burr, T., Mitchell, J., Kolb, A., Minchin, S., and Busby, S. (2000) Nucleic Acids Res. 28, 1864-1870
28. Feklistov, A., Barinova, N., Sevostyanova, A., Heyduk, E., Bass, I., Vvedenskaya, I., Kuznedelov, K., Merkiene, E., Stavrovskaya, E., Klimasauskas, S., Nikiforov, V., Heyduk, T., Severinov, K., and Kulbachinskiy, A. (2006) Mol. Cell 23, 97-107
29. Haugen, S. P., Berkmen, M. B., Ross, W., Gaal, T., Ward, C., and Gourse, R. L. (2006) Cell 125, 1069-1082
30. Moyle, H., Waldburger, C., and Susskind, M. M. (1991) J. Bacteriol. 173, 1944-1950
31. Liu, M., Tolstorukov, M., Zhurkin, V., Garges, S., and Adhya, S. (2004) Proc. Natl. Acad. Sci. U. S. A. 101, 6911-6916
32. Ozoline, O. N., and Tsyganov, M. A. (1995) Nucleic Acids Res. 23, 4533-4541
33. Lew, C. H., and Gralla, J. D. (2004) Biochemistry 43, 12660-12666
34. McClure, W. R. (1980) Proc. Natl. Acad. Sci. U. S. A. 77, 5634-5638
35. Roberts, J. W., and Roberts, C. W. (1996) Cell 86, 495-501
36. Stefano, J. E., and Gralla, J. D. (1982) Proc. Natl. Acad. Sci. U. S. A. 79, 1069-1072
37. Ayers, D. G., Auble, D. T., and deHaseth, P. L. (1989) J. Mol. Biol. 207, 749-756
38. Warne, S. E., and deHaseth, P. L. (1993) Biochemistry 32, 6134-6140
39. Lisser, S., and Margalit, H. (1993) Nucleic Acids Res. 21, 1507-1516
40. Tsujikawa, L., Tsodikov, O. V., and deHaseth, P. L. (2002) Proc. Natl. Acad. Sci. U. S. A. 99, 3493-3498