Structural Basis of DNA Recognition by the Alternative Sigma-factor, σ54

Journal of Molecular Biology

Volumn 369, Issue 4, 2007, Pages 1070-1078

  Doucleff, Michaeleen ^a   Pelton, Jeffrey G ^a   Lee, Peter S ^a   Nixon, B Tracy ^b   Wemmer, David E ^a  

^a LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

Protein DNA complex; RNA polymerase; RpoN box; Sigma 54; Transcription initiation

Indexed keywords

SIGMA FACTOR; SIGMA FACTOR RPON;

ARTICLE; CARBOXY TERMINAL SEQUENCE; DNA PROTEIN COMPLEX; DNA STRUCTURE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN INTERACTION; PROTEIN MOTIF; TRANSCRIPTION INITIATION;

BACTERIA (MICROORGANISMS);

EID: 34248578701     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.04.019     Document Type: Article

References (32)

1. Young B.A., Gruber T.M., and Gross C.A. Views of transcription initiation. Cell 109 (2002) 417-420
2. Murakami K.S., and Darst S.A. Bacterial RNA polymerases: the wholo story. Curr. Opin. Struct. Biol. 13 (2003) 31-39
3. Wedel A., Weiss D.S., Popham D., Droge P., and Kustu S. A bacterial enhancer functions to tether a transcriptional activator near a promoter. Science 248 (1990) 486-490
4. Rappas M., Bose D., and Zhang X. Bacterial enhancer-binding proteins: unlocking sigma(54)-dependent gene transcription. Curr. Opin. Struct. Biol. 17 (2007) 110-116
5. 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
6. Correa N.E., Lauriano C.M., McGee R., and Klose K.E. Phosphorylation of the flagellar regulatory protein FlrC is necessary for Vibrio cholerae motility and enhanced colonization. Mol. Microbiol. 35 (2000) 743-755
7. 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
8. Ray P., Hall R.J., Finn R.D., Chen S., Patwardhan A., Buck M., and van Heel M. Conformational changes of Escherichia coli sigma54-RNA-polymerase upon closed-promoter complex formation. J. Mol. Biol. 354 (2005) 201-205
9. Lane W.J., and Darst S.A. The structural basis for promoter -35 element recognition by the group IV sigma factors. PLoS. Biol. 4 (2006) e269
10. 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
11. 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
12. Barrios H., Valderrama B., and Morett E. Compilation and analysis of sigma(54)-dependent promoter sequences. Nucl. Acids Res. 27 (1999) 4305-4313
13. 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
14. Burrows P.C., Severinov K., Ishihama A., Buck M., and Wigneshweraraj S.R. Mapping sigma 54-RNA polymerase interactions at the -24 consensus promoter element. J. Biol. Chem. 278 (2003) 29728-29743
15. Doucleff M., Malak L.T., Pelton J.G., and Wemmer D. E. The C-terminal RpoN domain of sigma54 forms an unpredicted helix-turn-helix motif similar to domains of sigma70. J. Biol. Chem. 280 (2005) 41530-41536
16. Gajiwala K.S., and Burley S.K. Winged helix proteins. Curr. Opin. Struct. Biol. 10 (2000) 110-116
17. Wang L., and Gralla J.D. Roles for the C-terminal region of sigma 54 in transcriptional silencing and DNA binding. J. Biol. Chem. 276 (2001) 8979-8986
18. Tucker-Kellogg L., Rould M.A., Chambers K.A., Ades S.E., Sauer R.T., and Pabo C.O. Engrailed (Gln50-→Lys) homeodomain-DNA complex at 1.9 Å resolution: structural basis for enhanced affinity and altered specificity. Structure 5 (1997) 1047-1054
19. Khan H., Buck M., and Dixon R. Deletion loop mutagenesis of the nifL promoter from Klebsiella pneumoniae: role of the -26 to -12 region in promoter function. Gene 45 (1986) 281-288
20. 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
21. 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
22. Wigneshweraraj S.R., Kuznedelov K., Severinov K., and Buck M. Multiple roles of the RNA polymerase beta subunit flap domain in sigma 54-dependent transcription. J. Biol. Chem. 278 (2003) 3455-3465
23. 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
24. Johnson B.A., and Blevins B.A. NMRView: a computer program for the visualization and analysis of NMR data. J. Biomol. NMR 4 (1994) 603-614
25. Iwahara J., Wojciak J.M., and Clubb R.T. Improved NMR spectra of a protein-DNA complex through rational mutagenesis and the application of a sensitivity optimized isotope-filtered NOESY experiment. J. Biomol. NMR 19 (2001) 231-241
26. Pierre P., and Gueron G. Exchangeable proton NMR without base-line distorsion, using new strong-pulse sequences. J. Am. Chem. Soc. 104 (1982) 7310-7311
27. Zwahlen C., Legault P., F., V. S. J., Greenblatt J., Konrat R., and Kay L.E. Methods for measurement of intermolecular NOEs by multinuclear NMR spectroscopy: application to a bacteriophage lambda N-peptide/boxB RNA complex. J. Am. Chem. Soc. 119 (1997) 6711-6721
28. Kuboniwa H., Grzesiek S., Delaglio F., and Bax A. Measurement of HN-H alpha J couplings in calcium-free calmodulin using new 2D and 3D water-flip-back methods. J. Biomol. NMR 4 (1994) 871-878
29. Guntert P. Automated NMR structure calculation with CYANA. Methods Mol. Biol. 278 (2004) 353-378
30. Schwieters C.D., Kuszewski J.J., Tjandra N., and Clore G.M. The Xplor-NIH NMR molecular structure determination package. J. Magn. Reson. 160 (2003) 65-73
31. Iwahara J., Iwahara M., Daughdrill G.W., Ford J., and Clubb R.T. The structure of the Dead ringer-DNA complex reveals how AT-rich interaction domains (ARIDs) recognize DNA. EMBO J. 21 (2002) 1197-1209
32. Kuszewski J., Schwieters C., and Clore G.M. Improving the accuracy of NMR structures of DNA by means of a database potential of mean force describing base-base positional interactions. J. Am. Chem. Soc. 123 (2001) 3903-3918