A critical role of downstream RNA polymerase-promoter interactions in the formation of initiation complex

Journal of Biological Chemistry

Volumn 286, Issue 25, 2011, Pages 22600-22608

  Mekler, Vladimir ^a   Minakhin, Leonid ^a   Severinov, Konstantin ^a,b,c  

^a RUTGERS UNIVERSITY   (United States)

^b RUTGERS UNIVERSITY   (United States)

^c RUSSIAN ACADEMY OF SCIENCES   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

CRITICAL LENGTH; DNA MELTING; FLUORESCENT METHODS; NEW MODEL; PROMOTER COMPLEXES; PROMOTER ELEMENTS; PROMOTER FRAGMENTS; RNA POLYMERASE; START POINT; STRUCTURAL DETERMINANTS; TRANSCRIPTION ACTIVITY; TRANSCRIPTION START SITE;

COMPLEXATION; MELTING; RNA;

TRANSCRIPTION;

BACTERIAL DNA; DOWNSTREAM FORK JUNCTION PROMOTER FRAGMENT; RNA POLYMERASE; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; CRYSTAL STRUCTURE; DNA DENATURATION; ESCHERICHIA COLI; FLUOROMETRY; GENETIC TRANSCRIPTION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN ANALYSIS; PROTEIN DNA BINDING; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION REGULATION;

BASE SEQUENCE; DNA PROBES; DNA, BACTERIAL; DNA, SINGLE-STRANDED; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; MODELS, MOLECULAR; PROMOTER REGIONS, GENETIC; PROTEIN BINDING; PROTEIN CONFORMATION; THERMUS; TRANSCRIPTION, GENETIC;

EID: 79959360447     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M111.247080     Document Type: Article

References (52)

1. Buc, H., and McClure, W. R. (1985) Biochemistry 24, 2712-2723
2. deHaseth, P. L., Zupancic, M. L., and Record, M. T., Jr. (1998) J. Bacteriol. 180, 3019-3025
3. Sclavi, B. (2009) in RNA Polymerases as Molecular Motors (Buc, H., and Strick, T., eds) pp. 38-68, RCS Publishing, Cambridge, UK
4. Kirkegaard, K., Buc, H., Spassky, A., and Wang, J. C. (1983) Proc. Natl. Acad. Sci. U.S.A. 80, 2544-2548
5. Sasse-Dwight, S., and Gralla, J. D. (1989) J. Biol. Chem. 264, 8074-8081
6. Roberts, C. W., and Roberts, J. W. (1996) Cell 86, 495-501
7. Marr, M. T., and Roberts, J. W. (1997) Science 276, 1258-1260
8. Guo, Y., and Gralla, J. D. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 11655-11660
9. Mekler, V., Pavlova, O., and Severinov, K. (2011) J. Biol. Chem. 286, 270-279
10. Lim, H. M., Lee, H. J., Roy, S., and Adhya, S. (2001) Proc. Natl. Acad. Sci. U.S.A. 98, 14849-14852
11. 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
12. Sclavi, B., Zaychikov, E., Rogozina, A., Walther, F., Buckle, M., and Heumann, H. (2005) Proc. Natl. Acad. Sci. U.S.A. 102, 4706-4711
13. Murakami, K. S., Masuda, S., and Darst, S. A. (2002) Science 296, 1280-1284
14. Vassylyev, D. G., Sekine, S., Laptenko, O., Lee, J., Vassylyeva, M. N., Borukhov, S., and Yokoyama, S. (2002) Nature 417, 712-719
15. Bartlett, M. S., Gaal, T., Ross, W., and Gourse, R. L. (1998) J. Mol. Biol. 279, 331-345
16. Ederth, J., Artsimovitch, I., Isaksson, L. A., and Landick, R. (2002) J. Biol. Chem. 277, 37456-37463
17. Young, B. A., Gruber, T. M., and Gross, C. A. (2004) Science 303, 1382-1384
18. Davis, C. A., Bingman, C. A., Landick, R., Record, M. T., Jr., and Saecker, R. M. (2007) Proc. Natl. Acad. Sci. U.S.A. 104, 7833-7838
19. Mukhopadhyay, J., Das, K., Ismail, S., Koppstein, D., Jang, M., Hudson, B., Sarafianos, S., Tuske, S., Patel, J., Jansen, R., Irschik, H., Arnold, E., and Ebright, R. H. (2008) Cell 135, 295-307
20. Rutherford, S. T., Villers, C. L., Lee, J. H., Ross, W., and Gourse, R. L. (2009) Genes Dev. 23, 236-248
21. Cámara, B., Liu, M., Reynolds, J., Shadrin, A., Liu, B., Kwok, K., Simpson, P., Weinzierl, R., Severinov, K., Cota, E., Matthews, S., and Wigneshweraraj, S. R. (2010) Proc. Natl. Acad. Sci. U.S.A. 107, 2247-2252
22. Murakami, K. S., Masuda, S., Campbell, E. A., Muzzin, O., and Darst, S. A. (2002) Science 296, 1285-1290
23. Matlock, D. L., and Heyduk, T. (2000) Biochemistry 39, 12274-12283
24. Guo, Y., Lew, C. M., and Gralla, J. D. (2000) Genes Dev. 14, 2242-2255
25. Tsujikawa, L., Tsodikov, O. V., and deHaseth, P. L. (2002) Proc. Natl. Acad. Sci. U.S.A. 99, 3493-3498
26. Fenton, M. S., and Gralla, J. D. (2003) J. Biol. Chem. 278, 39669-39674
27. Severinova, E., Severinov, K., Fenyö, D., Marr, M., Brody, E. N., Roberts, J. W., Chait, B. T., and Darst, S. A. (1996) J. Mol. Biol. 263, 637-647
28. Nechaev, S., and Severinov, K. (1999) J. Mol. Biol. 289, 815-826
29. Ederth, J., Isaksson, L. A., and Abdulkarim, F. (2002) Mol. Genet. Genomics 267, 587-592
30. Mekler, V., Kortkhonjia, E., Mukhopadhyay, J., Knight, J., Revyakin, A., Kapanidis, A. N., Niu, W., Ebright, Y. W., Levy, R., and Ebright, R. H. (2002) Cell 108, 599-614
31. Hesselbach, B. A., and Nakada, D. (1975) Nature 258, 354-357
32. Colland, F., Orsini, G., Brody, E. N., Buc, H., and Kolb, A. (1998) Mol. Microbiol. 27, 819-829
33. McCullagh, M., Zhang, L., Karaba, A. H., Zhu, H., Schatz, G. C., and Lewis, F. D. (2008) J. Phys. Chem. B 112, 11415-11421
34. Craig, M. L., Tsodikov, O. V., McQuade, K. L., Schlax, P. E., Jr., Capp, M. W., Saecker, R. M., and Record, M. T., Jr. (1998) J. Mol. Biol. 283, 741-756
35. Pfeffer, S. R., Stahl, S. J., and Chamberlin, M. J. (1977) J. Biol. Chem. 252, 5403-5407
36. Brodolin, K., Zenkin, N., Mustaev, A., Mamaeva, D., and Heumann, H. (2004) Nat. Struct. Mol. Biol. 11, 551-557
37. Carpousis, A. J., and Gralla, J. D. (1985) J. Mol. Biol. 183, 165-177
38. Hsu, L. M. (2002) Biochim. Biophys. Acta 1577, 191-207
39. Kapanidis, A. N., Margeat, E., Ho, S. O., Kortkhonjia, E., Weiss, S., and Ebright, R. H. (2006) Science 314, 1144-1147
40. Revyakin, A., Liu, C., Ebright, R. H., and Strick, T. R. (2006) Science 314, 1139-1143
41. Mooney, R. A., Darst, S. A., and Landick, R. (2005) Mol. Cell 20, 335-345
42. Gourse, R. L. (1988) Nucleic Acids Res. 16, 9789-9809
43. Wigneshweraraj, S. R., Burrows, P. C., Severinov, K., and Buck, M. (2005) J. Biol. Chem. 280, 36176-36184
44. Kontur, W. S., Saecker, R. M., Capp, M. W., and Record, M. T., Jr. (2008) J. Mol. Biol. 376, 1034-1047
45. Murakami, K. S., and Darst, S. A. (2003) Curr. Opin. Struct. Biol. 13, 31-39
46. Kontur, W. S., Saecker, R. M., Davis, C. A., Capp, M. W., and Record, M. T., Jr. (2006) Biochemistry 45, 2161-2177
47. Dedrick, R. L., and Chamberlin, M. J. (1985) Biochemistry 24, 2245-2253
48. Helmann, J. D., and deHaseth, P. L. (1999) Biochemistry 38, 5959-5967
49. Zenkin, N., and Severinov, K. (2004) Proc. Natl. Acad. Sci. U.S.A. 101, 4396-4400
50. Schroder, O., Geiduschek, E. P., and Kassavetis, G. A. (2003) Proc. Natl. Acad. Sci. U.S.A. 100, 934-939
51. Lawson, C. L., Swigon, D., Murakami, K. S., Darst, S. A., Berman, H. M., and Ebright, R. H. (2004) Curr. Opin. Struct. Biol. 14, 10-20
52. Saecker, R. M., Record, M. T. J., and Dehaseth, P. L. (2011) J. Mol. Biol. doi: 10.1016/j.jmb.2011.01.018