Transcription Factor B Contacts Promoter DNA Near the Transcription Start Site of the Archaeal Transcription Initiation Complex

Journal of Biological Chemistry

Volumn 279, Issue 4, 2004, Pages 2825-2831

  Renfrow, Matthew B ^a,c   Naryshkin, Nikolai ^b,d   Lewis, L Michelle ^a,e   Chen, Hung Ta ^a,f   Ebright, Richard H ^b   Scott, Robert A ^a,g  

^a University of Georgia ^*  (United States)

^b RUTGERS UNIVERSITY   (United States)

^c FLORIDA STATE UNIVERSITY   (United States)

^d PTC THERAPEUTICS   (United States)

^e DIVERSA CORPORATION   (United States)

^f HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^g UNIVERSITY OF GEORGIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; CATALYST ACTIVITY; CHEMICAL ACTIVATION; CROSSLINKING; CRYSTALLOGRAPHY; DNA; ENZYME KINETICS; MOLECULAR STRUCTURE; RNA; SURFACE TOPOGRAPHY;

GENE TRANSCRIPTION; HOMOLOGY;

GENETIC ENGINEERING;

DNA; RNA POLYMERASE; TATA BINDING PROTEIN; TRANSCRIPTION FACTOR;

AMINO TERMINAL SEQUENCE; ARCHAEBACTERIUM; ARTICLE; CELL FREE SYSTEM; COMPLEX FORMATION; CROSS LINKING; CRYSTALLOGRAPHY; DERIVATIZATION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DNA INTERACTION; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION REGULATION;

ARCHAEAL PROTEINS; BASE SEQUENCE; DNA, ARCHAEAL; DNA-BINDING PROTEINS; GENE EXPRESSION REGULATION, ARCHAEAL; MOLECULAR SEQUENCE DATA; PROMOTER REGIONS (GENETICS); TRANSCRIPTION FACTOR TFIIB; TRANSCRIPTION FACTORS, TFII; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION, GENETIC;

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA; PYROCOCCUS; PYROCOCCUS FURIOSUS;

EID: 1642453651     PISSN: 00219258     EISSN: None     Source Type: Journal    
DOI: 10.1074/jbc.M311433200     Document Type: Article

References (64)

1. Hampsey, M. (1998) Microbiol. Mol. Biol. Rev. 62, 465-503
2. Lee, T. I., and Young, R. A. (2000) Annu. Rev. Genet 34, 77-137
3. Ebright, R. H. (2000) J. Mol. Biol. 304, 687-698
4. Woychik, N. A., and Hampsey, M. (2002) Cell 108, 453-463
5. Soppa, J. (1999) Mol. Microbiol. 31, 1295-1305
6. Bell, S. D., Magill, C. P., and Jackson, S. P. (2001) Biochem. Soc. Trans. 29, 392-395
7. Hausner, W., Wettach, J., Hethke, C., and Thomm, M. (1996) J. Biol. Chem. 271, 30144-30148
8. Hethke, C., Geerling, A. C., Hausner, W., de Vos, W. M., and Thomm, M. (1996) Nucleic Acids Res. 24, 2369-2376
9. Hethke, C., Bergerat, A., Hausner, W., Forterre, P., and Thomm, M. (1999) Genetics 152, 1325-1333
10. Lewis, L. M. (2000) Structural and Functional Characterization of the Transcription Preinitiation Complex from Pyrococcus furiosus. Ph.D. dissertation, University of Georgia, Athens
11. Hausner, W., and Thomm, M. (2001) J. Bacteriol. 183, 3025-3031
12. Thomsen, J., De Biase, A., Kaczanowski, S., Macario, A. J., Thomm, M., Zielenkiewicz, P., MacColl, R., and Conway de Macario, E. (2001) J. Mol. Biol. 309, 589-603
13. Qureshi, S. A., and Jackson, S. P. (1998) Mol. Cell 1, 389-400
14. Zhang, G., Campbell, E. A., Minakhin, L., Richter, C., Severinov, K., and Darst, S. A. (1999) Cell 98, 811-824
15. Cramer, P., Bushnell, D. A., Fu, J., Gnatt, A. L., Maier-Davis, B., Thompson, N. E., Burgess, R. R., Edwards, A. M., David, P. R., and Kornberg, R. D. (2000) Science 288, 640-649
16. Cramer, P., Bushnell, D. A., and Kornberg, R. D. (2001) Science 292, 1863-1876
17. Armache, K. J., Kettenberger, H., and Cramer, P. (2003) Proc. Natl. Acad. Sci. U. S. A. 100, 6964-6968
18. Murakami, K. S., Masuda, S., and Darst, S. A. (2002) Science 296, 1280-1284
19. Vassylyev, D. G., Sekine, S., Laptenko, O., Lee, J., Vassylyeva, M. N., Borukhov, S., and Yokoyama, S. (2002) Nature 417, 712-719
20. Bushnell, D. A., and Kornberg, R. D. (2003) Proc. Natl. Acad. Sci. U. S. A. 100, 6969-6973
21. Bartlett, M. S., Thomm, M., and Geiduschek, E. P. (2000) Nat. Struct. Biol. 7, 782-785
22. Bell, S. D., and Jackson, S. P. (2000) Nat. Struct. Biol. 7, 703-705
23. Todone, F., Brick, P., Werner, F., Weinzierl, R. O., and Onesti, S. (2001) Mol. Cell 8, 1137-1143
24. Kim, J. L., Nikolov, D. B., and Burley, S. K. (1993) Nature 365, 520-527
25. Kim, Y., Geiger, J. H., Hahn, S., and Sigler, P. B. (1993) Nature 365, 512-520
26. Nikolov, D. B., Chen, H., Halay, E. D., Usheva, A. A., Hisatake, K., Lee, D. K., Roeder, R. G., and Burley, S. K. (1995) Nature 377, 119-128
27. Kosa, P. F., Ghosh, G., DeDecker, B. S., and Sigler, P. B. (1997) Proc. Natl. Acad. Sci. U. S. A. 94, 6042-6047
28. Littlefield, O., Korkhin, Y., and Sigler, P. B. (1999) Proc. Natl. Acad. Sci. U. S. A. 96, 13668-13673
29. Tsai, F. T., and Sigler, P. B. (2000) EMBO J. 19, 25-36
30. Rowlands, T., Baumann, P., and Jackson, S. P. (1994) Science 264, 1326-1329
31. Buratowski, S., and Zhou, H. (1993) Proc. Natl. Acad. Sci. U. S. A. 90, 5633-5637
32. Barberis, A., Muller, C. W., Harrison, S. C., and Ptashne, M. (1993) Proc. Natl. Acad. Sci. U. S. A. 90, 5628-5632
33. Bell, S. D., and Jackson, S. P. (2000) J. Biol. Chem. 275, 12934-12940
34. Magill, C. P., Jackson, S. P., and Bell, S. D. (2001) J. Biol. Chem. 276, 46693-46696
35. Zhu, W., Zeng, Q., Colangelo, C. M., Lewis, M., Summers, M. F., and Scott, R. A. (1996) Nat. Struct. Biol. 3, 122-124
36. Chen, H. T., Legault, P., Glushka, J., Omichinski, J. G., and Scott, R. A. (2000) Protein Sci. 9, 1743-1752
37. Pinto, I., Wu, W. H., Na, J. G., and Hampsey, M. (1994) J. Biol. Chem. 269, 30569-30573
38. Bangur, C. S., Pardee, T. S., and Ponticelli, A. S. (1997) Mol. Cell. Biol. 17, 6784-6793
39. Pardee, T. S., Bangur, C. S., and Ponticelli, A. S. (1998) J. Biol. Chem. 273, 17859-17864
40. Cho, E. J., and Buratowski, S. (1999) J. Biol. Chem. 274, 25807-25813
41. Hawkes, N. A., and Roberts, S. G. (1999) J. Biol. Chem. 274, 14337-14343
42. Zhang, D. Y., Carson, D. J., and Ma, J. (2002) Nucleic Acids Res. 30, 3078-3085
43. Lagrange, T., Kim, T. K., Orphanides, G., Ebright, Y. W., Ebright, R. H., and Reinberg, D. (1996) Proc. Natl. Acad. Sci. U. S. A. 93, 10620-10625
44. Kim, T. K., Lagrange, T., Wang, Y. H., Griffith, J. D., Reinberg, D., and Ebright, R. H. (1997) Proc. Natl. Acad. Sci. U. S. A. 94, 12268-12273
45. Kim, T. K., Ebright, R. H., and Reinberg, D. (2000) Science 288, 1418-1422
46. Naryshkin, N., Revyakin, A., Kim, Y., Mekler, V., and Ebright, R. H. (2000) Cell 101, 601-611
47. Naryshkin, N., Kim, Y., Dong, Q., and Ebright, R. H. (2001) Methods Mol. Biol. 148, 337-361
48. Bryant, F. O., and Adams, M. W. (1989) J. Biol. Chem. 264, 5070-5079
49. Burgess, R. R., and Jendrisak, J. J. (1975) Biochemistry 14, 4634-4638
50. Thomm, M. (1990) in Archaea: A Lab Manual (Robb, F. T., ed) pp. 297-301, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
51. Tabor, S., and Richardson, C. C. (1985) Proc. Natl. Acad. Sci. U. S. A. 82, 1074-1078
52. Zeng, Q., Lewis, L. M., Colangelo, C. M., Dong, J., and Scott, R. A. (1996) J. Biol. Inorg. Chem. 1, 162-168
53. Spitalny, P., and Thomm, M. (2003) J. Biol. Chem. 278, 30497-30505
54. Cech, C. L., and McClure, W. R. (1980) Biochemistry 19, 2440-2447
55. Bell, S. D., and Jackson, S. P. (1998) Trends Microbiol. 6, 222-228
56. Chen, H.-T. (2000) Structural Study of Eucaryl and Archaeal Transcription Factors TF(II)B. M.Sc. thesis University of Georgia, Athens
57. 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
58. Murakami, K. S., Masuda, S., Campbell, E. A., Muzzin, O., and Darst, S. A. (2002) Science 296, 1285-1290
59. Lagrange, T., Kapanidis, A. N., Tang, H., Reinberg, D., and Ebright, R. H. (1998) Genes Dev. 12, 34-44
60. Lee, S., and Hahn, S. (1995) Nature 376, 609-612
61. Bell, S. D., Kosa, P. L., Sigler, P. B., and Jackson, S. P. (1999) Proc. Natl. Acad. Sci. U. S. A. 96, 13662-13667
62. Campbell, E. A., Muzzin, O., Chlenov, M., Sun, J. L., Olson, C. A., Weinman, O., Trester-Zedlitz, M. L., and Darst, S. A. (2002) Mol. Cell 9, 527-539
63. Severinov, K., Fenyo, D., Severinova, E., Mustaev, A., Chait, B. T., Goldfarb, A., and Darst, S. A. (1994) J. Biol. Chem. 269, 20826-20828
64. Chen, H.-T., and Hahn, S. (2003) Mol. Cell 12, 437-447