Systematic mutational analysis of the LytTR DNA binding domain of Staphylococcus aureusvirulence gene transcription factor Agra

Nucleic Acids Research

Volumn 42, Issue 20, 2014, Pages 12523-12536

  Nicod, Sophie S ^a   Weinzierl, Robert O J ^a   Burchell, Lynn ^a   Escalera Maurer, Andres ^a   James, Ellen H ^a   Wigneshweraraj, Sivaramesh ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; DNA BINDING PROTEIN; PROTEIN LYTTR; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR AGRA; TYROSINE; UNCLASSIFIED DRUG; BACTERIAL PROTEIN; PROTEIN BINDING; TRANSACTIVATOR PROTEIN; VIRULENCE FACTOR;

AMINO ACID SUBSTITUTION; ARTICLE; BACTERIAL STRAIN; BACTERIAL VIRULENCE; BETA SHEET; CONTROLLED STUDY; CRYSTAL STRUCTURE; DNA BINDING; ESCHERICHIA COLI; IN VITRO STUDY; IN VIVO STUDY; MOLECULAR DYNAMICS; MUTAGENESIS; MUTATIONAL ANALYSIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN DOMAIN; STAPHYLOCOCCUS AUREUS; STRUCTURE ACTIVITY RELATION; TRANSCRIPTION INITIATION; CHEMISTRY; GENETICS; METABOLISM; MUTATION; PATHOGENICITY; PROTEIN TERTIARY STRUCTURE;

BACTERIAL PROTEINS; MUTAGENESIS; MUTATION; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; STAPHYLOCOCCUS AUREUS; STRUCTURE-ACTIVITY RELATIONSHIP; TRANS-ACTIVATORS; TRANSCRIPTIONAL ACTIVATION; VIRULENCE FACTORS;

EID: 84922951754     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku1015     Document Type: Article

References (32)

1. Gao, R. and Stock, A.M. (2009) Biological insights from structures of two-component proteins. Annu. Rev. Microbiol., 63, 133-154.
2. Galperin, M.Y. (2006) Structural classification of bacterial response regulators: diversity of output domains and domain combinations. J. Bacteriol., 188, 4169-4182.
3. Nikolskaya, A.N. and Galperin, M.Y. (2002) A novel type of conserved DNA-binding domain in the transcriptional regulators of the AlgR/AgrA/LytR family. Nucleic Acids Res., 30, 2453-2459.
4. Sidote, D.J., Barbieri, C.M., Wu, T. and Stock, A.M. (2008) Structure of the Staphylococcus aureus AgrA LytTR domain bound to DNA reveals a beta fold with an unusual mode of binding. Structure, 16, 727-735.
5. McGowan, S., Lucet, I.S., Cheung, J.K., Awad, M.M., Whisstock, J.C. and Rood, J.I. (2002) The FxRxHrS motif: a conserved region essential for DNA binding of the VirR response regulator from Clostridium perfringens. J. Mol. Biol., 322, 997-1011.
6. Lizewski, S.E., Lundberg, D.S. and Schurr, M.J. (2002) The transcriptional regulator AlgR is essential for Pseudomonas aeruginosa pathogenesis. Infect. Immun., 70, 6083-6093.
7. Miller, D.P., Frederick, J.R., Sarkar, J. and Marconi, R.T. (2014) The Treponema denticola AtcR LytTR domain-containing response regulator interacts with three architecturally distinct promoter elements: implications for understanding the molecular signaling mechanisms that drive the progression of periodontal disease. Mol. Oral Microbiol., 29, 219-232.
8. Novick, R.P. (2003) Autoinduction and signal transduction in the regulation of staphylococcal virulence. Mol. Microbiol., 48, 1429-1449.
9. Fournier, B. (2008) Global regulators of Staphylococcus aureus virulence genes. In: Lindsay, JA (ed). Staphylococcus: Molecular Genetics. Caister Academic Press, Norfolk, pp. 131-183.
10. Queck, S.Y., Jameson-Lee, M., Villaruz, A.E., Bach, T.H., Khan, B.A., Sturdevant, D.E., Ricklefs, S.M., Li, M. and Otto, M. (2008) RNAIII-independent target gene control by the agr quorum-sensing system: insight into the evolution of virulence regulation in Staphylococcus aureus. Mol. Cell, 32, 150-158.
11. Sun, F., Liang, H., Kong, X., Xie, S., Cho, H., Deng, X., Ji, Q., Zhang, H., Alvarez, S., Hicks, L.M. et al. (2012) Quorum-sensing agr mediates bacterial oxidation response via an intramolecular disulfide redox switch in the response regulator AgrA. Proc. Natl. Acad. Sci. U.S.A., 109, 9095-9100.
12. Koenig, R.L., Ray, J.L., Maleki, S.J., Smeltzer, M.S. and Hurlburt, B.K. (2004) Staphylococcus aureus AgrA binding to the RNAIII-agr regulatory region. J. Bacteriol., 186, 7549-7555.
13. Rechtin, T.M., Gillaspy, A.F., Schumacher, M.A., Brennan, R.G., Smeltzer, M.S. and Hurlburt, B.K. (1999) Characterization of the SarA virulence gene regulator of Staphylococcus aureus. Mol. Microbiol., 33, 307-316.
14. Reyes, D., Andrey, D.O., Monod, A., Kelley, W.L., Zhang, G. and Cheung, A.L. (2011) Coordinated regulation by AgrA, SarA, and SarR to control agr expression in Staphylococcus aureus. J. Bacteriol., 193, 6020-6031.
15. Cheung, A.L., Nishina, K.A., Trotonda, M.P. and Tamber, S. (2008) The SarA protein family of Staphylococcus aureus. Int. J. Biochem. Cell Biol., 40, 355-361.
16. Reynolds, J. and Wigneshweraraj, S. (2011) Molecular insights into the control of transcription initiation at the Staphylococcus aureus agr operon. J. Mol. Biol., 412, 862-881.
17. Novick, R.P. (1991) Genetic systems in staphylococci. Methods Enzymol., 204, 587-636.
18. James, E.H., Edwards, A.M. and Wigneshweraraj, S. (2013) Transcriptional downregulation of agr expression in Staphylococcus aureus during growth in human serum can be overcome by constitutively active mutant forms of the sensor kinase AgrC. FEMS Microbiol. Lett., 349, 153-162.
19. Charpentier, E., Anton, A.I., Barry, P., Alfonso, B., Fang, Y. and Novick, R.P. (2004) Novel cassette-based shuttle vector system for gram-positive bacteria. Appl. Environ. Microbiol., 70, 6076-6085.
20. Wormann, M.E., Corrigan, R.M., Simpson, P.J., Matthews, S.J. and Grundling, A. (2011) Enzymatic activities and functional interdependencies of Bacillus subtilis lipoteichoic acid synthesis enzymes. Mol. Microbiol., 79, 566-583.
21. Gordon, J.C., Myers, J.B., Folta, T., Shoja, V., Heath, L.S. and Onufriev, A. (2005) H++: a server for estimating pKas and adding missing hydrogens to macromolecules. Nucleic Acids Res., 33, W368-W371.
22. Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W. and Klein, M.L. (1983) Comparison of simple potential functions for simulating liquid water. J. Chem. Phys., 79, 926-935.
23. Ponder, J.W. and Case, D.A. (2003) Force fields for protein simulations. Adv. Protein Chem., 66, 27-85.
24. Salomon-Ferrer, R., Case, D.A. and Walker, R.C. (2013) An overview of the Amber biomolecular simulation package. WIREs Comput. Mol. Sci., 3, 195-210.
25. Ryckaert, J.P., Ciccotti, G. and Berendsen, H.J.C. (1977) Numerical-integration of Cartesian equations of motion of a system with constraints-molecular-dynamics of N-alkanes. J. Comput. Phys., 23, 327-341.
26. Essmann, U., Perera, L., Berkowitz, M.L., Darden, T., Lee, H. and Pedersen, L.G. (1995) A smooth particle mesh Ewald method. J. Chem. Phys., 103, 8577-8593.
27. Pierce, L.C., Salomon-Ferrer, R., Augusto, F., de Oliveira C., McCammon, J.A. and Walker, R.C. (2012) Routine access to millisecond time scale events with accelerated molecular dynamics. J. Chem. Theory Comput., 8, 2997-3002.
28. Humphrey, W., Dalke, A. and Schulten, K. (1996) VMD: visual molecular dynamics. J. Mol. Graph., 14, 33-38.
29. Tsompanidou, E., Sibbald, M.J., Chlebowicz, M.A., Dreisbach, A., Back, J.W., van Dijl, J.M., Buist, G. and Denham, E.L. (2011) Requirement of the agr locus for colony spreading of Staphylococcus aureus. J. Bacteriol., 193, 1267-1272.
30. Markwick, P.R. and McCammon, J.A. (2011) Studying functional dynamics in bio-molecules using accelerated molecular dynamics. Phys. Chem. Chem. Phys., 13, 20053-20065.
31. Shopsin, B., Drlica-Wagner, A., Mathema, B., Adhikari, R.P., Kreiswirth, B.N. and Novick, R.P. (2008) Prevalence of agr dysfunction among colonizing Staphylococcus aureus strains. J. Infect. Dis., 198, 1171-1174.
32. Sully, E.K., Malachowa, N., Elmore, B.O., Alexander, S.M., Femling, J.K., Gray, B.M., DeLeo, F.R., Otto, M., Cheung, A.L., Edwards, B.S. et al. (2014) Selective chemical inhibition of agr quorum sensing in Staphylococcus aureus promotes host defense with minimal impact on resistance. PLoS Pathogens, 10, e1004174.