A consensus adenine at position -11 of the nontemplate strand of bacterial promoter is important for nucleation of promoter melting

Journal of Biological Chemistry

Volumn 281, Issue 18, 2006, Pages 12362-12369

  Heyduk, Ewa ^a   Kuznedelov, Konstantin ^b   Severinov, Konstantin ^b,c   Heyduk, Tomasz ^a  

^a SAINT LOUIS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b RUTGERS UNIVERSITY   (United States)

^c RUTGERS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; CORRELATION METHODS; DNA; FREE ENERGY; MATHEMATICAL MODELS; MUTAGENESIS; RNA;

ADENINE; HEPARIN-RESISTANT PROMOTER; NONNATIVE THYMINE; NONTEMPLATE STRAND OF BACTERIAL;

PROTEINS;

ADENINE; DOUBLE STRANDED DNA; HEPARIN; RNA POLYMERASE; SINGLE STRANDED DNA; THYMINE;

ARTICLE; BACTERIAL GENE; BASE MISPAIRING; BINDING AFFINITY; CONTROLLED STUDY; GENE MUTATION; GENETIC TRANSCRIPTION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; TRANSCRIPTION INITIATION;

ADENINE; BASE PAIR MISMATCH; DNA; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; HEPARIN; KINETICS; MANGANESE COMPOUNDS; MODELS, GENETIC; MUTATION; OXIDES; PROMOTER REGIONS (GENETICS); THERMODYNAMICS; TIME FACTORS;

BACTERIA (MICROORGANISMS);

EID: 33744958373     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M601364200     Document Type: Article

References (35)

1. deHaseth, P. L., Zupancic, M. L., and Record, M. T., Jr. (1998) J. Bacteriol. 180, 3019-3025
2. Record, M. T., Jr., Reznikoff, W. S., Craig, M. L., McQuade, K. L., and Schlax, P. J. (1996) Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd Ed. (Neidhardt, F. C., Curtis, R., III, Ingraham, J. L., Lin, E. C. C., Low, K. R., Magasanik, B., Reznikoff, W. S., Riley, M., Schaechter, M., and Umbarger, H. E., eds) pp. 792-820, American Society for Microbiology Press, Washington, D. C.
3. Helmann, J. D., and deHaseth, P. L. (1999) Biochemistry 38, 5959-5967
4. Roe, J-H., Burgess, R. R., and Record, M. T., Jr. (1984) J. Mol. Biol. 176, 495-521
5. Roe, J-H., Burgess, R. R., and Record, M. T., Jr. (1985) J. Mol. Biol. 184, 441-453
6. Roe, J-H., and Record, M. T., Jr. (1985) Biochemistry 24, 4721-4726
7. Saecker, R. M., Tsodikov, O. V., McQuade, K. L., Schlax, P. E., Jr., Capp, M. W., and Record, M. T., Jr. (2002) J. Mol. Biol. 319, 649-671
8. Li, X-Y., and McClure, W. R. (1998) J. Biol. Chem. 273, 23558-23566
9. Chen, Y-F., and Helmann, J. D. (1997) J. Mol. Biol. 267, 47-59
10. Severinov, K., and Darst, S. A. (1997) Proc. Natl. Acad. Sci. U. S. A. 94, 13481-13486
11. Suh, W-C., Ross, W., and Record, M. T., Jr. (1993) Science 259, 358-361
12. Juang, Y-L., and Helmann, J. D. (1995) Biochemistry 34, 8465-8473
13. Rowe-Magnus, D. A., and Spiegelman, G. B. (1998) Proc. Natl. Acad. Sci. U. S. A. 95, 5305-5310
14. Ring, B. Z., Yarnell, W. S., and Roberts, J. W. (1996) Cell 86, 485-493
15. Marr, M. T., and Roberts, J. W. (1997) Science 276, 1258-1260
16. Huang, X., Lopez de Saro, F. J., and Helmann, J. D. (1997) Nucleic Acids Res. 25, 2603-2609
17. Guo, Y., and Gralla, J. D. (1998) Proc. Natl. Acad. Sci. U. S. A. 95, 11655-11660
18. Callaci, S., and Heyduk, T. (1998) Biochemstry 37, 3312-3320
19. Young, B. A., Gruber, T. M., and Gross, C. A. (2004) Science 303, 1382-1384
20. Niedziela-Majka, A., and Heyduk, T. (2005) J. Biol. Chem. 280, 38219-38227
21. Lisser, S., and Margalit, H. (1993) Nucleic Acids Res. 21, 1507-1516
22. Matlock, D. L., and Heyduk, T. (2000) Biochemistry 39, 12274-12283
23. Lee, H. J., Lim, H. M., and Adhya, S. (2004) J. Biol. Chem. 279, 16899-16902
24. Tsujikawa, L., Strainic, M. G., Watrob, H., Barkley, M. D., and deHaseth, P. L. (2002) Biochemistry 41, 15334-15341
25. Stivers, J. T., and Jiang, Y. L. (2003) Chem. Rev. 103, 2729-2759
26. Burgess, R. R., and Jendrisak, J. J. (1975) Biochemistry 14, 4634-4638
27. Polyakov, A., Severinova, E., and Darst, S. A. (1995) Cell 83, 365-373
28. Hager, D. A., Jin, D. J., and Burgess, R. R. (1990) Biochemistry 29, 7890-7894
29. Callaci, S., Heyduk, E., and Heyduk, T. (1998) J. Biol. Chem. 273, 32995-33001
30. Fried, M., and Crothers, D. M. (1981) Nucleic Acids Res. 9, 6505-6525
31. Roberts, C. W., and Roberts, J. W. (1996) Cell 86, 495-501
32. Kool, E. T. (2001) Annu. Rev. Biophys. Biomol. Struct. 30, 1-22
33. Krosky, D. J., Schwarz, F. P., and Stivers, J. T. (2004) Biochemistry 43, 4188-4195
34. Slupphaug, G., Mol, C. D., Kavli, B., Arvai, A. S., Krokan, H. E., and Tainer, J. A. (1996) Nature 384, 87-92
35. Altan-Bonnet, G., Libchaber, A., and Krichevsky, O. (2003) Phys. Rev. Lett. 90, 1-4