Structure of the RNA Polymerase Core-Binding Domain of σ54 Reveals a Likely Conformational Fracture Point

Journal of Molecular Biology

Volumn 390, Issue 1, 2009, Pages 70-82

  Hong, Eunmi ^a,b   Doucleff, Michaeleen ^a,b   Wemmer, David E ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

bacterial transcription; gene regulation; NMR structure; RNA polymerase; 54

Indexed keywords

RNA POLYMERASE;

AMINO TERMINAL SEQUENCE; AQUIFEX AEOLICUS; ARTICLE; CARBOXY TERMINAL SEQUENCE; ENZYME BINDING; ENZYME CONFORMATION; HYDROPHOBICITY; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN DOMAIN; SURFACE PROPERTY;

AQUIFEX AEOLICUS; BACTERIA (MICROORGANISMS);

EID: 67349263052     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2009.04.070     Document Type: Article

References (42)

1. Cramer P. Multisubunit RNA polymerases. Curr. Opin. Struct. Biol. 12 (2002) 89-97
2. Kornberg R.D. The molecular basis of eukaryotic transcription. Proc. Natl Acad. Sci. USA 104 (2007) 12955-12961
3. Burgess R.R., Travers A.A., Dunn J.J., and Bautz E.K. Factor stimulating transcription by RNA polymerase. Nature 221 (1969) 43-46
4. Hirschman J., Wong P.K., Sei K., Keener J., and Kustu S. Products of nitrogen regulatory genes ntrA and ntrC of enteric bacteria activate glnA transcription in vitro: evidence that the ntrA product is a sigma factor. Proc. Natl Acad. Sci. USA 82 (1985) 7525-7529
5. Murakami K.S., and Darst S.A. Bacterial RNA polymerases: the wholo story. Curr. Opin. Struct. Biol. 13 (2003) 31-39
6. Mooney R.A., Darst S.A., and Landick R. Sigma and RNA polymerase: an on-again, off-again relationship?. Mol. Cell 20 (2005) 335-345
7. Gallegos M.T., and Buck M. Sequences in sigma(54) region I required for binding to early melted DNA and their involvement in sigma-DNA isomerisation. J. Mol. Biol. 297 (2000) 849-859
8. Fisher M.A., Grimm D., Henion A.K., Elias A.F., Stewart P.E., Rosa P.A., and Gherardini F.C. Borrelia burgdorferi sigma54 is required for mammalian infection and vector transmission but not for tick colonization. Proc. Natl Acad. Sci. USA 102 (2005) 5162-5167
9. Saldias M.S., Lamothe J., Wu R., and Valvano M.A. Burkholderia cenocepacia requires the RpoN sigma factor for biofilm formation and intracellular trafficking within macrophages. Infect. Immun. 76 (2008) 1059-1067
10. Cannon W.V., Chaney M.K., Wang X., and Buck M. Two domains within sigmaN (sigma54) cooperate for DNA binding. Proc. Natl Acad. Sci. USA 94 (1997) 5006-5011
11. 54 N-terminal sequences identifies regions involved in positive and negative regulation. J. Mol. Biol. 292 (1999) 229-239
12. Wong C., Tintut Y., and Gralla J.D. The domain structure of sigma 54 as determined by analysis of a set of deletion mutants. J. Mol. Biol. 236 (1994) 81-90
13. Doucleff M., Pelton J.G., Lee P.S., Nixon B.T., and Wemmer D.E. Structural basis of DNA recognition by the alternative sigma-factor, sigma54. J. Mol. Biol. 369 (2007) 1070-1078
14. Wigneshweraraj S.R., Burrows P.C., Bordes P., Schumacher J., Rappas M., Finn R.D., et al. The second paradigm for activation of transcription. Prog. Nucleic Acid Res. Mol. Biol. 79 (2005) 339-369
15. Jain D., Nickels B.E., Sun L., Hochschild A., and Darst S.A. Structure of a ternary transcription activation complex. Mol. Cell 13 (2004) 45-53
16. Sorenson M.K., Ray S.S., and Darst S.A. Crystal structure of the flagellar sigma/anti-sigma complex sigma(28)/FlgM reveals an intact sigma factor in an inactive conformation. Mol. Cell 14 (2004) 127-138
17. Campbell E.A., Muzzin O., Chlenov M., Sun J.L., Olson C.A., Weinman O., et al. Structure of the bacterial RNA polymerase promoter specificity sigma subunit. Mol. Cell 9 (2002) 527-539
18. Murakami K.S., Masuda S., Campbell E.A., Muzzin O., and Darst S.A. Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex. Science 296 (2002) 1285-1290
19. Svergun D.I., Malfois M., Koch M.H., Wigneshweraraj S.R., and Buck M. Low resolution structure of the sigma54 transcription factor revealed by X-ray solution scattering. J. Biol. Chem. 275 (2000) 4210-4214
20. Rappas M., Schumacher J., Beuron F., Niwa H., Bordes P., Wigneshweraraj S., et al. Structural insights into the activity of enhancer-binding proteins. Science 307 (2005) 1972-1975
21. Tintut Y., and Gralla J.D. PCR mutagenesis identifies a polymerase-binding sequence of sigma 54 that includes a sigma 70 homology region. J. Bacteriol. 177 (1995) 5818-5825
22. 70 family of sigma factors. Genome Biol. 4 (2003) 203
23. Vassylyev D.G., Sekine S., Laptenko O., Lee J., Vassylyeva M.N., Borukhov S., and Yokoyama S. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution. Nature 417 (2002) 712-719
24. Schwartz E.C., Shekhtman A., Dutta K., Pratt M.R., Cowburn D., Darst S., and Muir T.W. A full-length group 1 bacterial sigma factor adopts a compact structure incompatible with DNA binding. Chem. Biol. 15 (2008) 1091-1103
25. Sasse-Dwight S., and Gralla J.D. Role of eukaryotic-type functional domains found in the prokaryotic enhancer receptor factor sigma 54. Cell 62 (1990) 945-954
26. Missailidis S., Cannon W.V., Drake A., Wang X.Y., and Buck M. Analysis of the architecture of the transcription factor sigma N (sigma 54) and its domains by circular dichroism. Mol. Microbiol. 24 (1997) 653-664
27. Tintut Y., Wong C., Jiang Y., Hsieh M., and Gralla J.D. RNA polymerase binding using a strongly acidic hydrophobic-repeat region of sigma 54. Proc. Natl Acad. Sci. USA 91 (1994) 2120-2124
28. Cannon W., Missailidis S., Smith C., Cottier A., Austin S., Moore M., and Buck M. Core RNA polymerase and promoter DNA interactions of purified domains of sigma N: bipartite functions. J. Mol. Biol. 248 (1995) 781-803
29. Gallegos M.T., and Buck M. Sequences in sigmaN determining holoenzyme formation and properties. J. Mol. Biol. 288 (1999) 539-553
30. Qiao F., and Bowie J.U. The many faces of SAM. Sci. STKE 2005 (2005) re7
31. Haney P., Konisky J., Koretke K.K., Luthey-Schulten Z., and Wolynes P.G. Structural basis for thermostability and identification of potential active site residues for adenylate kinases from the archaeal genus Methanococcus. Proteins 28 (1997) 117-130
32. Bose D., Pape T., Burrows P.C., Rappas M., Wigneshweraraj S.R., Buck M., and Zhang X. Organization of an activator-bound RNA polymerase holoenzyme. Mol. Cell 32 (2008) 337-346
33. Chen B., Doucleff M., Wemmer D.E., De Carlo S., Huang H.H., Nogales E., et al. ATP ground- and transition states of bacterial enhancer binding AAA+ ATPases support complex formation with their target protein, sigma54. Structure 15 (2007) 429-440
34. Delaglio F., Grzesiek S., Vuister G.W., Zhu G., Pfeifer J., and Bax A. NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6 (1995) 277-293
35. Goddard T., and Kneller D.G. SPARKY (2004), University of California, San Francisco, CA
36. Ferentz A.E., and Wagner G. NMR spectroscopy: a multifaceted approach to macromolecular structure. Q. Rev. Biophys. 33 (2000) 29-65
37. Cornilescu G., Delaglio F., and Bax A. Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J. Biomol. NMR 13 (1999) 289-302
38. Guntert P. Automated NMR structure calculation with CYANA. Methods Mol. Biol. 278 (2004) 353-378
39. Laskowski R.A., Rullmannn J.A., MacArthur M.W., Kaptein R., and Thornton J.M. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 8 (1996) 477-486
40. DeLano W.L. Use of PYMOL as a communications tool for molecular science. Abstr. Pap.-Am. Chem. Soc. 229 (2004) U313-U314
41. Koradi, R., Billeter, M. & Wüthrich, K. (1996). MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graphics, 14, 51-55, 29-32.
42. Baker N.A., Sept D., Joseph S., Holst M.J., and McCammon J.A. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl Acad. Sci. USA 98 (2001) 10037-10041