Isomerization of a binary sigma–promoter DNA complex by transcription activators (original) (raw)

References

  1. Gross, C.A. et al. The functional and regulatory roles of sigma factors in transcription. Cold Spring Harb. Symp. Quant. Biol. 63, 141– 155 (1998).
    Article CAS PubMed Google Scholar
  2. Sasse-Dwight, S. & Gralla, J.D. Role of eukaryotic-type functional domains found in the prokaryotic enhancer receptor factor σ54. Cell 62, 945– 954 (1990).
    Article CAS PubMed Google Scholar
  3. Reitzer, L.J. & Magasanik, B. Transcription of glnA in E. coli is stimulated by activator bound to sites far from the promoter . Cell 45, 785–792 (1986).
    Article CAS PubMed Google Scholar
  4. Popham, D.L., Szeto, D., Keener, J. & Kustu, S. Function of a bacterial activator protein that binds to transcriptional enhancers. Science 243, 629–635 ( 1989).
    Article CAS PubMed Google Scholar
  5. Wedel, A. & Kustu, S. The bacterial enhancer-binding protein NtrC is a molecular machine: ATP hydrolysis is coupled to transcriptional activation. Genes Dev. 9, 2042– 2052 (1995).
    Article CAS PubMed Google Scholar
  6. Cannon, W., Gallegos, M.T., Casaz, P. & Buck, M. Amino terminal sequences of σN (σ54) inhibit RNA polymerase isomerisation. Genes Dev. 13, 357– 370 (1999).
    Article CAS PubMed PubMed Central Google Scholar
  7. Neuwald, A.F., Aravind, L., Spouge, J.L. & Koonin, E.V. AAA+: a class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Genome Res. 9, 27– 43 (1999).
    CAS PubMed Google Scholar
  8. Wang, J.T., Syed, A. & Gralla, J.D. Multiple pathways to bypass the enhancer requirement of sigma 54 RNA polymerase: roles for DNA and protein determinants. Proc. Natl. Acad. Sci. USA 94, 9538–9543 ( 1997).
    Article CAS PubMed PubMed Central Google Scholar
  9. Gallegos, M.T. & Buck, M. Sequences in region I required for binding to early melted DNA and their involvement in sigma-DNA isomerisation . J. Mol. Biol. 297, 849– 859 (2000).
    Article CAS PubMed Google Scholar
  10. Hsieh, M. & Gralla, J.D. Analysis of the N-terminal leucine heptad and hexad repeats of sigma 54. J. Mol. Biol. 239, 15–24 (1994).
    Article CAS PubMed Google Scholar
  11. Hsieh, M., Tintut, Y. & Gralla, J.D. Functional roles for the glutamines within the glutamine-rich region of the transcription factor sigma 54. J. Biol. Chem. 269, 373–378 (1994).
    CAS PubMed Google Scholar
  12. Syed, A. & Gralla, J.D. Identification of an N-terminal region of sigma 54 required for enhancer responsiveness. J. Bacteriol. 180, 5619–5625 ( 1998).
    CAS PubMed PubMed Central Google Scholar
  13. Merrick, M.J. In a class of its own-the RNA polymerase sigma factor sigma 54 (sigma N). Mol. Microbiol. 10, 903–909 (1993).
    Article CAS PubMed Google Scholar
  14. Morris, L., Cannon, W., Claverie-Martin, F., Austin, S. & Buck, M. DNA distortion and nucleation of local DNA unwinding within sigma-54 (σN) holoenzyme closed promoter complexes. J. Biol. Chem. 269, 11563–11571 (1994).
    CAS PubMed Google Scholar
  15. Wang, J.T., Syed, A., Hsieh, M. & Gralla, J.D. Converting Escherichia coli RNA polymerase into an enhancer-responsive enzyme: role of an NH2-terminal leucine patch in sigma 54. Science 270, 992–994 ( 1995).
    Article CAS PubMed Google Scholar
  16. Wang, J.T. & Gralla, J.D. The transcription initiation pathway of sigma 54 mutants that bypass the enhancer protein requirement. Implications for the mechanism of activation. J. Biol. Chem. 271 , 32707–32713 (1996).
    Article CAS PubMed Google Scholar
  17. Gallegos, M.T. & Buck, M. Sequences in σN determining holoenzyme formation and properties. J. Mol. Biol. 288, 539–553 ( 1999).
    Article CAS PubMed Google Scholar
  18. Casaz, P. & Buck, M. Probing the assembly of transcription initiation complexes through changes in σN protease sensitivity . Proc. Natl. Acad. Sci. USA 94, 12145– 12150 (1997).
    Article CAS PubMed PubMed Central Google Scholar
  19. Casaz, P. & Buck, M. Region I modifies DNA binding domain conformation of sigma 54 holoenzyme. J. Mol. Biol. 285, 507–514 (1999).
    Article CAS PubMed Google Scholar
  20. Chaney, M. & Buck, M. The sigma 54 DNA-binding domain includes a determinant of enhancer responsiveness. Mol. Microbiol. 33, 1200–1209 (1999).
    Article CAS PubMed Google Scholar
  21. Guo, Y., Wang, L. & Gralla, J.D. A fork junction DNA-protein switch that controls promoter melting by the bacterial enhancer-dependent sigma factor. EMBO J. 18, 3736–3745 (1999).
    Article CAS PubMed PubMed Central Google Scholar
  22. Wang, L. & Gralla, J.D. Multiple in vivo roles for the −12-region elements of sigma 54 promoters. J. Bacteriol. 180, 5626–5631 (1998).
    CAS PubMed PubMed Central Google Scholar
  23. Buck, M. & Cannon, W. Specific binding of the transcription factor sigma-54 to promoter DNA. Nature 358, 422 –424 (1992).
    Article CAS PubMed Google Scholar
  24. Weiss, D.S., Batut, J., Klose, K.E., Keener, J. & Kustu, S. The phosphorylated form of the enhancer-binding protein NTRC has an ATPase activity that is essential for activation of transcription . Cell 67, 155–167 (1991).
    Article CAS PubMed Google Scholar
  25. González, V., Olvera, L., Soberón, X. & Morett, E. In vivo studies on the positive control function of NifA: a conserved hydrophobic amino acid patch at the central domain involved in transcriptional activation. Mol. Microbiol. 28, 55– 67 (1998).
    Article PubMed Google Scholar
  26. Wang, Y.K. & Hoover, T.R. Alterations within the activation domain of the sigma 54-dependent activator DctD that prevent transcriptional activation. J. Bacteriol. 179, 5812– 5819 (1997).
    Article CAS PubMed PubMed Central Google Scholar
  27. Oguiza, J.A., Gallegos, M.T., Chaney, M.K., Cannon, W.V. & Buck, M. Involvement of the σN DNA-binding domain in open complex formation. Mol. Microbiol. 33 , 873–885 (1999).
    Article CAS PubMed Google Scholar
  28. Jovanovic, G., Rakonjac, J. & Model, P. In vivo and in vitro activities of the Escherichia coli σ54 transcription activator, PspF, and its DNA-binding mutant, PspFΔHTH . J. Mol. Biol. 285, 469– 483 (1999).
    Article CAS PubMed Google Scholar
  29. Austin, S., Buck, M., Cannon, W., Eydmann, T. & Dixon, R. Purification and in vitro activities of the native nitrogen fixation control proteins NifA and NifL. J. Bacteriol. 176, 3460–3465 ( 1994).
    Article CAS PubMed PubMed Central Google Scholar
  30. Hunt, T.P. & Magasanik, B. Transcription of glnA by purified Escherichia coli components: core RNA polymerase and the products of glnF, glnG, and glnL. Proc. Natl. Acad. Sci. USA 82, 8453–8457 ( 1985).
    Article CAS PubMed PubMed Central Google Scholar
  31. Klose, K.E., North, A.K., Stedman, K.M. & Kustu, S. The major dimerization determinants of the nitrogen regulatory protein NtrC from enteric bacteria lie in its carboxy-terminal domain. J. Mol. Biol. 241 , 233–245 (1994).
    Article CAS PubMed Google Scholar
  32. Rombel, I., North, A., Hwang, I., Wyman, C. & Kustu, S. The bacterial enhancer-binding protein NtrC as a molecular machine. Cold Spring Harb. Symp. Quant. Biol. 63, 157–166 (1998).
    Article CAS PubMed Google Scholar
  33. Lee, J.H. & Hoover, T.R. Protein crosslinking studies suggest that Rhizobium meliloti C4-dicarboxylic acid transport protein D, a sigma 54-dependent transcriptional activator, interacts with sigma 54 and the beta subunit of RNA polymerase. Proc. Natl. Acad. Sci. USA 92, 9702–9706 ( 1995).
    Article CAS PubMed PubMed Central Google Scholar
  34. Gallegos, M.T., Cannon, W. & Buck, M. Functions of the σ54 region I in trans and implications for transcription activation. J. Biol. Chem. 274, 25285–25290 (1999).
    Article CAS PubMed Google Scholar
  35. Buckle, M., Pemberton, I.K., Jacquet, M.A. & Buc, H. The kinetics of sigma subunit directed promoter recognition by E. coli RNA polymerase. J. Mol. Biol. 285, 955–964 (1999).
    Article CAS PubMed Google Scholar
  36. Reinberg et al. The RNA polymerase II general transcription factors: past, present and future. Cold Spring Harb. Symp. Quant. Biol. 63, 83– 103 (1998).
    Article CAS PubMed Google Scholar
  37. Fu, J. et al. Yeast RNA polymerase II at 5 Å resolution. Cell 98, 799–810 (1999).
    Article CAS PubMed Google Scholar
  38. Zhang, G. et al. Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 Å resolution. Cell 98, 811– 824 (1999).
    Article CAS PubMed Google Scholar
  39. Tinker-Kulberg, R.L., Fu, T.J., Geiduschek, E.P. & Kassavetis, G.A. A direct interaction between a DNA-tracking protein and a promoter recognition protein: implications for searching DNA sequence. EMBO J. 15, 5032–5039 (1996).
    Article CAS PubMed PubMed Central Google Scholar
  40. Cannon, W. et al. Core RNA polymerase and promoter DNA interactions of purified domains of sigma N: bipartite functions. J. Mol. Biol. 248, 781–803 (1995).
    Article CAS PubMed Google Scholar

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