Transcription factor-dependent DNA bending governs promoter recognition by the mitochondrial RNA polymerase

Journal of Biological Chemistry

Volumn 286, Issue 44, 2011, Pages 38805-38813

  Tang, Guo Qing ^a   Deshpande, Aishwarya P ^a   Patel, Smita S ^a  

^a RUTGERS ROBERT WOOD JOHNSON MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONAL CHANGE; CONFORMATIONAL STATE; DNA BENDING; DNA BINDING; INDUCED-FIT MECHANISM; INITIATION FACTORS; PROMOTER RECOGNITION; PROMOTER SEQUENCES; RNA POLYMERASE; RNA SYNTHESIS; SELECTIVE BINDING; SPECIFIC SITES;

DNA; GENES; MACHINERY; MITOCHONDRIA; RNA; TRANSCRIPTION FACTORS; YEAST;

TRANSCRIPTION;

CURVED DNA; MITOCHONDRIAL RNA POLYMERASE; MTF1 PROTEIN; RNA POLYMERASE; RPO41 PROTEIN; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

ARTICLE; CATALYSIS; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; DNA BINDING; DNA SEQUENCE; ENZYME ACTIVE SITE; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; RNA SYNTHESIS; SACCHAROMYCES CEREVISIAE;

ANISOTROPY; DNA; DNA-DIRECTED RNA POLYMERASES; FLUORESCENCE RESONANCE ENERGY TRANSFER; KINETICS; MITOCHONDRIA; MITOCHONDRIAL PROTEINS; OLIGONUCLEOTIDES; PROMOTER REGIONS, GENETIC; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

SACCHAROMYCES CEREVISIAE;

EID: 80055070163     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M111.261966     Document Type: Article

References (54)

1. Reznikoff, W. S., Siegele, D. A., Cowing, D. W., and Gross, C. A. (1985) Annu. Rev. Genet. 19, 355-387
2. Verrijzer, C. P., and Tjian, R. (1996) Trends Biochem. Sci. 21, 338-342
3. Soppa, J. (1999) Mol. Microbiol 31, 1295-1305
4. McAllister, W. T. (1993) Cell Mol. Biol. Res. 39, 385-391
5. Masters, B. S., Stohl, L. L., and Clayton, D. A. (1987) Cell 51, 89-99
6. Fisher, R. P., and Clayton, D. A. (1988) Mol. Cell Biol. 8, 3496-3509
7. Falkenberg, M., Gaspari, M., Rantanen, A., Trifunovic, A., Larsson, N. G., and Gustafsson, C. M. (2002) Nat. Genet. 31, 289-294
8. Matsushima, Y., Garesse, R., and Kaguni, L. S. (2004) J. Biol. Chem. 279, 26900-26905
9. Shutt, T. E., Lodeiro, M. F., Cotney, J., Cameron, C. E., and Shadel, G. S. (2010) Proc. Natl. Acad. Sci. U.S.A. 107, 12133-12138
10. Sologub, M., Litonin, D., Anikin, M., Mustaev, A., and Temiakov, D. (2009) Cell 139, 934-944
11. Tang, G. Q., Paratkar, S., and Patel, S. S. (2009) J. Biol. Chem. 284, 5514-5522
12. Levens, D., Lustig, A., and Rabinowitz, M. (1981) J. Biol. Chem. 256, 1474-1481
13. Jang, S. H., and Jaehning, J. A. (1991) J. Biol. Chem. 266, 22671-22677
14. Schubot, F. D., Chen, C. J., Rose, J. P., Dailey, T. A., Dailey, H. A., and Wang, B. C. (2001) Protein Sci. 10, 1980-1988
15. Biswas, T. K., Edwards, J. C., Rabinowitz, M., and Getz, G. S. (1985) Proc. Natl. Acad. Sci. U.S.A. 82, 1954-1958
16. Schinkel, A. H., Groot Koerkamp, M. J., and Tabak, H. F. (1988) EMBO J. 7, 3255-3262
17. Xu, B., and Clayton, D. A. (1992) Nucleic Acids Res. 20, 1053-1059
18. Matsunaga, M., and Jaehning, J. A. (2004) J. Biol. Chem. 279, 44239-44242
19. Gaspari, M., Falkenberg, M., Larsson, N. G., and Gustafsson, C. M. (2004) EMBO J. 23, 4606-4614
20. Shadel, G. S., and Clayton, D. A. (1995) Mol. Cell Biol. 15, 2101-2108
21. Paratkar, S., and Patel, S. S. (2010) J. Biol. Chem. 285, 3949-3956
22. Savkina, M., Temiakov, D., McAllister, W. T., and Anikin, M. (2010) J. Biol. Chem. 285, 3957-3964
23. Matsunaga, M., Jang, S. H., and Jaehning, J. A. (2004) Protein Expr. Purif. 35, 126-130
24. Tang, G. Q., and Patel, S. S. (2006) Biochemistry 45, 4936-4946
25. Tang, G. Q., and Patel, S. S. (2006) Biochemistry 45, 4947-4956
26. Clegg, R. M. (1992) Methods Enzymol. 211, 353-388
27. Biswas, T. K. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 9338-9342
28. Biswas, T. K., and Getz, G. S. (1986) J. Biol. Chem. 261, 3927-3930
29. Schinkel, A. H., Groot Koerkamp, M. J., Teunissen, A. W., and Tabak, H. F. (1988) Nucleic Acids Res. 16, 9147-9163
30. Yin, Y. W., and Steitz, T. A. (2002) Science 298, 1387-1395
31. Rippe, K., Guthold, M., von Hippel, P. H., and Bustamante, C. (1997) J. Mol. Biol. 270, 125-138
32. Rivetti, C., Guthold, M., and Bustamante, C. (1999) EMBO J. 18, 4464-4475
33. Bandwar, R. P., and Patel, S. S. (2002) J. Mol. Biol. 324, 63-72
34. 70), Promoters, and the Kinetics of the Steps of Transcription Initiation, 2nd Ed., ASM Press, Washington D.C.
35. Jiang, H., Sun, W., Wang, Z., Zhang, J., Chen, D., and Murchie, A. I. (2011) Nucleic Acids Res. 39, 5119-5130
36. Biswas, T. K., and Getz, G. S. (1990) J. Biol. Chem. 265, 19053-19059
37. Biswas, T. K., Ticho, B., and Getz, G. S. (1987) J. Biol. Chem. 262, 13690-13696
38. Coulombe, B., and Burton, Z. F. (1999) Microbiol Mol. Biol. Rev. 63, 457-478
39. Pérez-Martin, J., and de Lorenzo, V. (1997) Annu. Rev. Microbiol 51, 593-628
40. Heumann, H., Ricchetti, M., and Werel, W. (1988)EMBOJ. 7, 4379-4381
41. Bartlett, M. S. (2005) Curr. Opin. Microbiol 8, 677-684
42. Lee, T. I., and Young, R. A. (2000) Annu. Rev. Genet. 34, 77-137
43. Winkler, F. K., Banner, D. W., Oefner, C., Tsernoglou, D., Brown, R. S., Heathman, S. P., Bryan, R. K., Martin, P. D., Petratos, K., and Wilson, K. S. (1993) EMBO J. 12, 1781-1795
44. Kalodimos, C. G., Biris, N., Bonvin, A. M., Levandoski, M. M., Guennuegues, M., Boelens, R., and Kaptein, R. (2004) Science 305, 386-389
45. Nagaich, A. K., Appella, E., and Harrington, R. E. (1997) J. Biol. Chem. 272, 14842-14849
46. Jen-Jacobson, L. (1997) Biopolymers 44, 153-180
47. Albright, R. A., and Matthews, B. W. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 3431-3436
48. Wang, H., Yang, Y., Schofield, M. J., Du, C., Fridman, Y., Lee, S. D., Larson, E. D., Drummond, J. T., Alani, E., Hsieh, P., and Erie, D. A. (2003) Proc. Natl. Acad. Sci. U.S.A. 100, 14822-14827
49. Erie, D. A., Yang, G., Schultz, H. C., and Bustamante, C. (1994) Science 266, 1562-1566
50. Post, C. B., and Ray, W. J., Jr. (1995) Biochemistry 34, 15881-15885
51. Chen, X. J., and Butow, R. A. (2005) Nat. Rev. Genet. 6, 815-825
52. Diffley, J. F., and Stillman, B. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 7864-7868
53. Diffley, J. F., and Stillman, B. (1992) J. Biol. Chem. 267, 3368-3374
54. Kim, H., Tang, G. Q., Patel, S. S., and Ha, T. (2011) Nucleic Acids Res. doi: 10.1093/nar/gkr736