Insights into the Nature of DNA Binding of AbrB-like Transcription Factors

Structure

Volumn 16, Issue 11, 2008, Pages 1702-1713

  Sullivan, Daniel M ^a   Bobay, Benjamin G ^a,b   Kojetin, Douglas J ^c   Thompson, Richele J ^a   Rance, Mark ^c   Strauch, Mark A ^d   Cavanagh, John ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b North Carolina Research Campus Kannapolis ^*  (United States)

^c UNIVERSITY OF CINCINNATI COLLEGE OF MEDICINE   (United States)

^d UNIVERSITY OF MARYLAND DENTAL SCHOOL   (United States)

Author keywords

DNA; PROTEINS

Indexed keywords

ABH TRANSCRIPTION FACTOR; ABRB TRANSCRIPTION FACTOR; DEOXYRIBONUCLEASE I; SPOVT TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; BACILLUS SUBTILIS; DNA BINDING; DNA FOOTPRINTING; DNA METHYLATION; DNA STRUCTURE; ENZYME SPECIFICITY; MOLECULAR CLONING; MOLECULAR DYNAMICS; MUTAGENESIS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DNA INTERACTION; PROTEIN EXPRESSION; PROTEIN FUNCTION; PROTEIN PURIFICATION;

BACILLUS SUBTILIS; BACTERIAL PROTEINS; BINDING SITES; DNA; DNA-BINDING PROTEINS; HYDROGEN BONDING; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; PROTEIN CONFORMATION; THERMODYNAMICS; TRANSCRIPTION FACTORS;

BACILLUS SUBTILIS;

EID: 55449107986     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2008.08.014     Document Type: Article

References (44)

1. Aertsen A., and Michiels C.W. Stress and how bacteria cope with death and survival. Crit. Rev. Microbiol. 30 (2004) 263-273
2. Bagyan I., Hobot J., and Cutting S. A compartmentalized regulator of developmental gene expression in Bacillus subtilis. J. Bacteriol. 178 (1996) 4500-4507
3. Bobay B.G., Benson L., Naylor S., Feeney B., Clark A.C., Goshe M.B., Strauch M.A., Thompson R., and Cavanagh J. Evaluation of the DNA binding tendencies of the transition state regulator AbrB. Biochemistry 43 (2004) 16106-16118
4. Bobay B.G., Andreeva A., Mueller G.A., Cavanagh J., and Murzin A.G. Revised structure of the AbrB N-terminal domain unifies a diverse superfamily of putative DNA-binding proteins. FEBS Lett. 579 (2005) 5669-5674
5. Bobay B.G., Mueller G.A., Thompson R.J., Murzin A.G., Venters R.A., Strauch M.A., and Cavanagh J. NMR structure of AbhN and comparison with AbrBN: FIRST insights into the DNA binding promiscuity and specificity of AbrB-like transition state regulator proteins. J. Biol. Chem. 281 (2006) 21399-21409
6. Cavanagh J., Thompson R., Bobay B., Benson L.M., and Naylor S. Stoichiometries of protein-protein/DNA binding and conformational changes for the transition-state regulator AbrB measured by pseudo cell-size exclusion chromatography-mass spectrometry. Biochemistry 41 (2002) 7859-7865
7. Chou J.J., Gaemers S., Howder B., Louis J.M., and Bax A. A simple apparatus for generating stretched polyacrylamide gels, yielding uniform alignment of proteins and detergent micelles. J. Biomol. NMR 21 (2001) 377-382
8. Clore G.M., Driscoll P.C., Wingfield P.T., and Gronenborn A.M. Analysis of the backbone dynamics of interleukin-1 β using two-dimensional inverse detected heteronuclear 15N-1H NMR spectroscopy. Biochemistry 29 (1990) 7387-7401
9. Coles M., Djuranovic S., Soding J., Frickey T., Koretke K., Truffault V., Martin J., and Lupas A.N. AbrB-like transcription factors assume a swapped hairpin fold that is evolutionarily related to double-ψ β barrels. Structure 13 (2005) 919-928
10. d'Auvergne E.J., and Gooley P.R. Optimisation of NMR dynamic models I. Minimisation algorithms and their performance within the model-free and Brownian rotational diffusion spaces. J. Biomol. NMR 40 (2008) 107-119
11. 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
12. Dominguez C., Boelens R., and Bonvin A.M. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J. Am. Chem. Soc. 125 (2003) 1731-1737
13. Dong T.C., Cutting S.M., and Lewis R.J. DNA-binding studies on the Bacillus subtilis transcriptional regulator and AbrB homologue, SpoVT. FEMS Microbiol. Lett. 233 (2004) 247-256
14. Furbass R., Gocht M., Zuber P., and Marahiel M.A. Interaction of AbrB, a transcriptional regulator from Bacillus subtilis with the promoters of the transition state-activated genes tycA and spoVG. Mol. Gen. Genet. 225 (1991) 347-354
15. Hubbard S.J., and Thornton J.M. NACCESS Computer Program (1993), Department of Biochemistry and Molecular Biology, University College London, London
16. Jarymowycz V.A., and Stone M.J. Fast time scale dynamics of protein backbones: NMR relaxation methods, applications, and functional consequences. Chem. Rev. 106 (2006) 1624-1671
17. Johnson B.A., and Blevins R.A. NMR View: a computer program for the visualization and analysis of NMR data. J. Biomol. NMR 4 (1994) 603-614
18. Kneller J.M., Lu M., and Bracken C. An effective method for the discrimination of motional anisotropy and chemical exchange. J. Am. Chem. Soc. 124 (2002) 1852-1853
19. 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
20. Lipari G., and Sabo A. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1 Theory and range of validity. J. Am. Chem. Soc. 104 (1982) 4546-4559
21. Lipari G., and Sabo A. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results. J. Am. Chem. Soc. 104 (1982) 4560-4570
22. Lipsitz R.S., and Tjandra N. Residual dipolar couplings in NMR structure analysis. Annu. Rev. Biophys. Biomol. Struct. 33 (2004) 387-413
23. Lu X.J., and Olson W.K. 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res. 31 (2003) 5108-5121
24. Nakano M.M., and Zuber P. Mutational analysis of the regulatory region of the srfA operon in Bacillus subtilis. J. Bacteriol. 175 (1993) 3188-3191
25. Phillips Z.E., and Strauch M.A. Role of Cys54 in AbrB multimerization and DNA-binding activity. FEMS Microbiol. Lett. 203 (2001) 207-210
26. Ptashne M. Gene regulation by proteins acting nearby and at a distance. Nature 322 (1986) 697-701
27. Schleif R. Gene regulation: why should DNA loop?. Nature 327 (1987) 369-370
28. Schleif R. DNA looping. Annu. Rev. Biochem. 61 (1992) 199-223
29. Shcheptov M., Chyu G., Bagyan I., and Cutting S. Characterization of csgA, a new member of the forespore-expressed sigmaG-regulon from Bacillus subtilis. Gene 184 (1997) 133-140
30. Sonenshein A.L., Hoch J.A., and Losick R. Bacillus subtilis and Its Closest Relatives: From Genes to Cells (2002), ASM Press, Washington, D.C.
31. Strauch M.A. AbrB modulates expression and catabolite repression of a Bacillus subtilis ribose transport operon. J. Bacteriol. 177 (1995) 6727-6731
32. Strauch M.A. Delineation of AbrB-binding sites on the Bacillus subtilis spo0H, kinB, ftsAZ, and pbpE promoters and use of a derived homology to identify a previously unsuspected binding site in the bsuB1 methylase promote. J. Bacteriol. 177 (1995) 6999-7002
33. Strauch M.A. In vitro binding affinity of the Bacillus subtilis AbrB protein to six different DNA target regions. J. Bacteriol. 177 (1995) 4532-4536
34. Strauch M.A. Dissection of the Bacillus subtilis spoOE binding site for the global regulator AbrB reveals smaller recognition elements. Mol. Gen. Genet. 250 (1996) 742-749
35. Strauch M.A., and Hoch J.A. Transition-state regulators: sentinels of Bacillus subtilis post-exponential gene expression. Mol. Microbiol. 7 (1993) 337-342
36. Strauch M.A., and Ayazifar M. Bent DNA is found in some, but not all, regions recognized by the Bacillus subtilis AbrB protein. Mol. Gen. Genet. 246 (1995) 756-760
37. Strauch M.A., Perego M., Burbulys D., and Hoch J.A. The transition state transcription regulator AbrB of Bacillus subtilis is autoregulated during vegetative growth. Mol. Microbiol. 3 (1989) 1203-1209
38. Theobald D.L., and Wuttke D.S. THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures. Bioinformatics 22 (2006) 2171-2172
39. Theobald D.L., and Wuttke D.S. Accurate structural correlations from maximum likelihood superpositions. PLoS Comput. Biol. 4 (2008) e43
40. Vaughn J.L., Feher V., Naylor S., Strauch M.A., and Cavanagh J. Novel DNA binding domain and genetic regulation model of Bacillus subtilis transition state regulator abrB. Nat. Struct. Biol. 7 (2000) 1139-1146
41. Vaughn J.L., Feher V.A., Bracken C., and Cavanagh J. The DNA-binding domain in the Bacillus subtilis transition-state regulator AbrB employs significant motion for promiscuous DNA recognition. J. Mol. Biol. 305 (2001) 429-439
42. Xu K., and Strauch M.A. In vitro selection of optimal AbrB-binding sites: comparison to known in vivo sites indicates flexibility in AbrB binding and recognition of three-dimensional DNA structures. Mol. Microbiol. 19 (1996) 145-158
43. Xu K., and Strauch M.A. DNA-binding activity of amino-terminal domains of the Bacillus subtilis AbrB protein. J. Bacteriol. 183 (2001) 4094-4098
44. Xu K., Clark D., and Strauch M.A. Analysis of abrB mutations, mutant proteins, and why abrB does not utilize a perfect consensus in the -35 region of its σ A promoter. J. Biol. Chem. 271 (1996) 2621-2626