Molecules and Cells

Korean Society for Molecular and Cellular Biology (한국분자세포생물학회)
권호 표지
DOI QR코드

DOI QR Code

Crystal Structure of the Pneumococcal Vancomycin-Resistance Response Regulator DNA-Binding Domain

  • Received : 2020.11.30
  • Accepted : 2021.02.25
  • Published : 2021.03.31
Download PDF
⟨ Previous Next ⟩

Abstract

Vancomycin response regulator (VncR) is a pneumococcal response regulator of the VncRS two-component signal transduction system (TCS) of Streptococcus pneumoniae. VncRS regulates bacterial autolysis and vancomycin resistance. VncR contains two different functional domains, the N-terminal receiver domain and C-terminal effector domain. Here, we investigated VncR C-terminal DNA binding domain (VncRc) structure using a crystallization approach. Crystallization was performed using the micro-batch method. The crystals diffracted to a 1.964 Å resolution and belonged to space group P212121. The crystal unit-cell parameters were a = 25.71 Å, b = 52.97 Å, and c = 60.61 Å. The structure of VncRc had a helix-turn-helix motif highly similar to the response regulator PhoB of Escherichia coli. In isothermal titration calorimetry and size exclusion chromatography results, VncR formed a complex with VncS, a sensor histidine kinase of pneumococcal TCS. Determination of VncR structure will provide insight into the mechanism by how VncR binds to target genes.

Keywords

References

  1. Adams, P.D., Afonine, P.V., Bunkoczi, G., Chen, V.B., Echols, N., Headd, J.J., Hung, L.W., Jain, S., Kapral, G.J., Grosse Kunstleve, R.W., et al. (2011). The Phenix software for automated determination of macromolecular structures. Methods 55, 94-106. https://doi.org/10.1016/j.ymeth.2011.07.005
  2. Blanco, A.G., Sola, M., Gomis-Ruth, F.X., and Coll, M. (2002). Tandem DNA recognition by PhoB, a two-component signal transduction transcriptional activator. Structure 10, 701-713. https://doi.org/10.1016/S0969-2126(02)00761-X
  3. Chetty, C. and Kreger, A. (1981). Role of autolysin in generating the pneumococcal purpura-producing principle. Infect. Immun. 31, 339-344. https://doi.org/10.1128/iai.31.1.339-344.1981
  4. Emsley, P. and Cowtan, K. (2004). Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126-2132. https://doi.org/10.1107/S0907444904019158
  5. Gao, M. and Skolnick, J. (2008). DBD-Hunter: a knowledge-based method for the prediction of DNA-protein interactions. Nucleic Acids Res. 36, 3978-3992. https://doi.org/10.1093/nar/gkn332
  6. Gao, R., Mack, T.R., and Stock, A.M. (2007). Bacterial response regulators: versatile regulatory strategies from common domains. Trends Biochem. Sci. 32, 225-234. https://doi.org/10.1016/j.tibs.2007.03.002
  7. Ghosh, P., Shah, M., Ravichandran, S., Park, S.S., Iqbal, H., Choi, S., Kim, K.K., and Rhee, D.K. (2019). Pneumococcal VncR strain-specifically regulates capsule polysaccharide synthesis. Front. Microbiol. 10, 2279. https://doi.org/10.3389/fmicb.2019.02279
  8. Haas, W., Sublett, J., Kaushal, D., and Tuomanen, E.I. (2004). Revising the role of the pneumococcal vex-vncRS locus in vancomycin tolerance. J. Bacteriol. 186, 8463-8471. https://doi.org/10.1128/JB.186.24.8463-8471.2004
  9. Jeong, S., Ahn, J., Kwon, A.R., and Ha, N.C. (2020). Cleavage-dependent activation of ATP-dependent protease HslUV from Staphylococcus aureus. Mol. Cells 43, 694-704. https://doi.org/10.14348/molcells.2020.0074
  10. Martner, A., Dahlgren, C., Paton, J.C., and Wold, A.E. (2008). Pneumolysin released during Streptococcus pneumoniae autolysis is a potent activator of intracellular oxygen radical production in neutrophils. Infect. Immun. 76, 4079-4087. https://doi.org/10.1128/IAI.01747-07
  11. Novak, R., Charpentier, E., Braun, J.S., and Tuomanen, E. (2000). Signal transduction by a death signal peptide: uncovering the mechanism of bacterial killing by penicillin. Mol. Cell 5, 49-57. https://doi.org/10.1016/S1097-2765(00)80402-5
  12. Novak, R., Henriques, B., Charpentier, E., Normark, S., and Tuomanen, E. (1999). Emergence of vancomycin tolerance in Streptococcus pneumoniae. Nature 399, 590-593. https://doi.org/10.1038/21202
  13. Otwinowski, Z. and Minor, W. (1997). Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326. https://doi.org/10.1016/S0076-6879(97)76066-X
  14. Paterson, G.K., Blue, C.E., and Mitchell, T.J. (2006). Role of two-component systems in the virulence of Streptococcus pneumoniae. J. Med. Microbiol. 55, 355-363. https://doi.org/10.1099/jmm.0.46423-0
  15. Robertson, G.T., Zhao, J., Desai, B.V., Coleman, W.H., Nicas, T.I., Gilmour, R., Grinius, L., Morrison, D.A., and Winkler, M.E. (2002). Vancomycin tolerance induced by erythromycin but not by loss of vncRS, vex3, or pep27 function in Streptococcus pneumoniae. J. Bacteriol. 184, 6987-7000. https://doi.org/10.1128/JB.184.24.6987-7000.2002
  16. Seo, H.S., Michalek, S.M., and Nahm, M.H. (2008). Lipoteichoic acid is important in innate immune responses to gram-positive bacteria. Infect. Immun. 76, 206-213. https://doi.org/10.1128/IAI.01140-07
  17. Sheffield, P., Garrard, S., and Derewenda, Z. (1999). Overcoming expression and purification problems of RhoGDI using a family of "parallel" expression vectors. Protein Expr. Purif. 15, 34-39. https://doi.org/10.1006/prep.1998.1003
  18. Stock, A.M., Robinson, V.L., and Goudreau, P.N. (2000). Two-component signal transduction. Annu. Rev. Biochem. 69, 183-215. https://doi.org/10.1146/annurev.biochem.69.1.183
  19. Sung, H., Shin, H.B., Kim, M.N., Lee, K., Kim, E.C., Song, W., Jeong, S.H., Lee, W.G., Park, Y.J., and Eliopoulos, G.M. (2006). Vancomycin-tolerant Streptococcus pneumoniae in Korea. J. Clin. Microbiol. 44, 3524-3528. https://doi.org/10.1128/JCM.00558-06
  20. Throup, J.P., Koretke, K.K., Bryant, A.P., Ingraham, K.A., Chalker, A.F., Ge, Y., Marra, A., Wallis, N.G., Brown, J.R., Holmes, D.J., et al. (2000). A genomic analysis of two-component signal transduction in Streptococcus pneumoniae. Mol. Microbiol. 35, 566-576. https://doi.org/10.1046/j.1365-2958.2000.01725.x
  21. Tilley, S.J., Orlova, E.V., Gilbert, R.J., Andrew, P.W., and Saibil, H.R. (2005). Structural basis of pore formation by the bacterial toxin pneumolysin. Cell 121, 247-256. https://doi.org/10.1016/j.cell.2005.02.033