Spacing between core recognition motifs determines relative orientation of AraR monomers on bipartite operators

Nucleic Acids Research

Volumn 41, Issue 1, 2013, Pages 639-647

  Jain, Deepti ^a   Nair, Deepak T ^a  

^a TATA INSTITUTE OF FUNDAMENTAL RESEARCH   (India)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; DOUBLE STRANDED DNA; MONOMER; PROTEIN ARAR; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; BACILLUS SUBTILIS; COMPLEX FORMATION; CONTROLLED STUDY; DNA HELIX; DNA SEQUENCE; GENE EXPRESSION REGULATION; MOLECULAR INTERACTION; MOLECULAR RECOGNITION; NONHUMAN; OPERATOR GENE; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN DOMAIN; PROTEIN MOTIF; STRUCTURE ACTIVITY RELATION; TRANSCRIPTION REGULATION;

BACTERIAL PROTEINS; DNA, BACTERIAL; MODELS, MOLECULAR; NUCLEOTIDE MOTIFS; OPERATOR REGIONS, GENETIC; PROTEIN BINDING; REPRESSOR PROTEINS;

BACILLUS SUBTILIS;

EID: 84871771101     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks962     Document Type: Article

References (32)

1. Mota, L.J., Tavares, P. and Sa-Nogueira, I. (1999) Mode of action of AraR, the key regulator of L-arabinose metabolism in Bacillus subtilis. Mol. Microbiol., 33, 476-489.
2. Raposo, M.P., Inacio, J.M., Mota, L.J. and de Sa-Nogueira, I. (2004) Transcriptional regulation of genes encoding arabinan-degrading enzymes in Bacillus subtilis. J. Bacteriol., 186, 1287-1296.
3. Mota, L.J., Sarmento, L.M. and de Sa-Nogueira, I. (2001) Control of the arabinose regulon in Bacillus subtilis by AraR in vivo: crucial roles of operators, cooperativity, and DNA looping. J. Bacteriol., 183, 4190-4201.
4. Sa-Nogueira, I. and Mota, L.J. (1997) Negative regulation of L-arabinose metabolism in Bacillus subtilis: characterization of the araR (araC) gene. J. Bacteriol., 179, 1598-1608.
5. Sa-Nogueira, I., Nogueira, T.V., Soares, S. and de Lencastre, H. (1997) The Bacillus subtilis L-arabinose (ara) operon: nucleotide sequence, genetic organization and expression. Microbiology, 143(Pt 3), 957-969.
6. Sa-Nogueira, I. and Ramos, S.S. (1997) Cloning, functional analysis, and transcriptional regulation of the Bacillus subtilis araE gene involved in L-arabinose utilization. J. Bacteriol., 179, 7705-7711.
7. Franco, I.S., Mota, L.J., Soares, C.M. and de Sa-Nogueira, I. (2007) Probing key DNA contacts in AraR-mediated transcriptional repression of the Bacillus subtilis arabinose regulon. Nucleic Acids Res., 35, 4755-4766.
8. Franco, I.S., Mota, L.J., Soares, C.M. and de Sa-Nogueira, I. (2006) Functional domains of the Bacillus subtilis transcription factor AraR and identification of amino acids important for nucleoprotein complex assembly and effector binding. J. Bacteriol., 188, 3024-3036.
9. Prochazkova, K., Cermakova, K., Pachl, P., Sieglova, I., Fabry, M., Otwinowski, Z. and Rezacova, P. (2012) Structure of the effector-binding domain of the arabinose repressor AraR from Bacillus subtilis. Acta Crystallogr. D Biol. Crystallogr., 68, 176-185.
10. Z. Otwinowski and Minor, M., (1997) Processing of X-ray Diffraction Data Collected in Oscillation Mode. Methods in Enzymology, 276: C.W. Carter, Jr. & R. M. Sweet, Eds., Academic Press (New York) 307-326.
11. Sheldrick, G.M. (2008) A short history of SHELX. Acta Crystallogr. A, 64, 112-122.
12. Emsley, P. and Cowtan, K. (2004) Coot: model building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr., 60, 2126-2132.
13. Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S. et al. (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr., 54, 905-921.
14. Vagin, A. and Teplyakov, A. (1997) MOLREP and automated program for molecular replacement. J. Appl. Crystallogr., 30, 1022-1025.
15. Adams, P.D., Afonine, P.V., Bunkoczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.W., Kapral, G.J., Grosse-Kunstleve, R.W. et al. (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr, 66, 213-221.
16. Winn, M.D., Murshudov, G.N. and Papiz, M.Z. (2003) Macromolecular TLS refinement in REFMAC at moderate resolutions. Methods Enzymol., 374, 300-321.
17. Winn, M.D., Ballard, C.C., Cowtan, K.D., Dodson, E.J., Emsley, P., Evans, P.R., Keegan, R.M., Krissinel, E.B., Leslie, A.G., McCoy, A. et al. (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr. D Biol. Crystallogr., 67, 235-242.
18. Laskowski, R.A., MacArthur, M.W., Moss, D.S. and Thornton, J. (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr., 266
19. Lavery, R., Moakher, M., Maddocks, J.H., Petkeviciute, D. and Zakrzewska, K. (2009) Conformational analysis of nucleic acids revisited: curves+. Nucleic Acids Res., 37, 5917-5929.
20. Lawrence, M.C. and Colman, P.M. (1993) Shape complementarity at protein/protein interfaces. J. Mol. Biol., 234, 946-950.
21. Haydon, D.J. and Guest, J.R. (1991) A new family of bacterial regulatory proteins. FEMS Microbiol. Lett., 63, 291-295.
22. Rigali, S., Derouaux, A., Giannotta, F. and Dusart, J. (2002) Subdivision of the helix-turn-helix GntR family of bacterial regulators in the FadR, HutC, MocR, and YtrA subfamilies. J. Biol. Chem., 277, 12507-12515.
23. Hoskisson, P.A. and Rigali, S. (2009) Chapter 1: Variation in form and function the helix-turn-helix regulators of the GntR superfamily. Adv. Appl. Microbiol., 69, 1-22.
24. Xu, Y., Heath, R.J., Li, Z., Rock, C.O. and White, S.W. (2001) The FadR.DNA complex. Transcriptional control of fatty acid metabolism in Escherichia coli. J. Biol. Chem., 276, 17373-17379.
25. van Aalten, D.M., DiRusso, C.C. and Knudsen, J. (2001) The structural basis of acyl coenzyme A-dependent regulation of the transcription factor FadR. EMBO J., 20, 2041-2050.
26. Scully, K.M., Jacobson, E.M., Jepsen, K., Lunyak, V., Viadiu, H., Carriere, C., Rose, D.W., Hooshmand, F., Aggarwal, A.K. and Rosenfeld, M.G. (2000) Allosteric effects of Pit-1 DNA sites on long-term repression in cell type specification. Science, 290, 1127-1131.
27. Remenyi, A., Tomilin, A., Pohl, E., Lins, K., Philippsen, A., Reinbold, R., Scholer, H.R. and Wilmanns, M. (2001) Differential dimer activities of the transcription factor Oct-1 by DNA-induced interface swapping. Mol. Cell, 8, 569-580.
28. Horvath, M.M., Wang, X., Resnick, M.A. and Bell, D.A. (2007) Divergent evolution of human p53 binding sites: cell cycle versus apoptosis. PLoS Genet., 3, e127.
29. Gajiwala, K.S., Chen, H., Cornille, F., Roques, B.P., Reith, W., Mach, B. and Burley, S.K. (2000) Structure of the winged-helix protein hRFX1 reveals a new mode of DNA binding. Nature, 403, 916-921.
30. Kitayner, M., Rozenberg, H., Kessler, N., Rabinovich, D., Shaulov, L., Haran, T.E. and Shakked, Z. (2006) Structural basis of DNA recognition by p53 tetramers. Mol. Cell, 22, 741-753.
31. Muller, J., Barker, A., Oehler, S. and Muller-Hill, B. (1998) Dimeric lac repressors exhibit phase-dependent co-operativity. J. Mol. Biol., 284, 851-857.
32. Zhang, Y., McEwen, A.E., Crothers, D.M. and Levene, S.D. (2006) Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA looping. PLoS One, 1, e136.