Molecules and Cells

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

DOI QR Code

A Novel Tetrameric Assembly Configuration in VV2_1132, a LysR-Type Transcriptional Regulator in Vibrio vulnificus

  • Jang, Yongdae (Research Institute for Agriculture and Life Sciences, Center for Food and Bioconvergence, Center for Food Safety and Toxicology, Seoul National University) ;
  • Choi, Garam (Research Institute for Agriculture and Life Sciences, Center for Food and Bioconvergence, Center for Food Safety and Toxicology, Seoul National University) ;
  • Hong, Seokho (Research Institute for Agriculture and Life Sciences, Center for Food and Bioconvergence, Center for Food Safety and Toxicology, Seoul National University) ;
  • Jo, Inseong (Research Institute for Agriculture and Life Sciences, Center for Food and Bioconvergence, Center for Food Safety and Toxicology, Seoul National University) ;
  • Ahn, Jinsook (Research Institute for Agriculture and Life Sciences, Center for Food and Bioconvergence, Center for Food Safety and Toxicology, Seoul National University) ;
  • Choi, Sang Ho (Research Institute for Agriculture and Life Sciences, Center for Food and Bioconvergence, Center for Food Safety and Toxicology, Seoul National University) ;
  • Ha, Nam-Chul (Research Institute for Agriculture and Life Sciences, Center for Food and Bioconvergence, Center for Food Safety and Toxicology, Seoul National University)
  • Received : 2017.09.04
  • Accepted : 2018.01.08
  • Published : 2018.04.30
Download PDF
⟨ Previous Next ⟩

Abstract

LysR-type transcriptional regulators (LTTRs) contain an N-terminal DNA binding domain (DBD) and a C-terminal regulatory domain (RD). Typically, LTTRs function as homotetramers. VV2_1132 was identified in Vibrio vulnificus as an LTTR that is a homologue of HypT (also known as YjiE or QseD) in Escherichia coli. In this study, we determined the crystal structure of full-length VV2_1132 at a resolution of $2.2{\AA}$, thereby revealing a novel combination of the domains in the tetrameric assembly. Only one DBD dimer in the tetramer can bind to DNA, because the DNA binding motifs of the other DBD dimer are completely buried in the tetrameric assembly. Structural and functional analyses of VV2_1132 suggest that it might not perform the same role as E. coli HypT, indicating that further study is required to elucidate the function of this gene in V. vulnificus. The unique structure of VV2_1132 extends our knowledge of LTTR function and mechanisms of action.

Keywords

References

  1. 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. https://doi.org/10.1107/S0907444909052925
  2. Alanazi, A.M., Neidle, E.L., and Momany, C. (2013). The DNAbinding domain of BenM reveals the structural basis for the recognition of a T-N11-A sequence motif by LysR-type transcriptional regulators. Acta Crystallogr. D Biol. Crystallogr. 69, 1995-2007. https://doi.org/10.1107/S0907444913017320
  3. Choi, H., Kim, S., Mukhopadhyay, P., Cho, S., Woo, J., Storz, G., and Ryu, S.E. (2001). Structural basis of the redox switch in the OxyR transcription factor. Cell 105, 103-113. https://doi.org/10.1016/S0092-8674(01)00300-2
  4. Drazic, A., Gebendorfer, K.M., Mak, S., Steiner, A., Krause, M., Bepperling, A., and Winter, J. (2014). Tetramers are the activation-competent species of the HOCl-specific transcription factor HypT. J. Biol. Chem. 289, 977-986. https://doi.org/10.1074/jbc.M113.521401
  5. Drazic, A., Miura, H., Peschek, J., Le, Y., Bach, N.C., Kriehuber, T., and Winter, J. (2013a). Methionine oxidation activates a transcription factor in response to oxidative stress. Proc. Natl. Acad. Sci. USA 110, 9493-9498. https://doi.org/10.1073/pnas.1300578110
  6. Drazic, A., Tsoutsoulopoulos, A., Peschek, J., Gundlach, J., Krause, M., Bach, N.C., Gebendorfer, K.M., and Winter, J. (2013b). Role of cysteines in the stability and DNA-binding activity of the hypochloritespecific transcription factor HypT. PLoS One 8, e75683. https://doi.org/10.1371/journal.pone.0075683
  7. 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
  8. Gebendorfer, K.M., Drazic, A., Le, Y., Gundlach, J., Bepperling, A., Kastenmuller, A., Ganzinger, K.A., Braun, N., Franzmann, T.M., and Winter, J. (2012). Identification of a hypochlorite-specific transcription factor from Escherichia coli. J. Biol. Chem. 287, 6892-6903. https://doi.org/10.1074/jbc.M111.287219
  9. Guerrero, S.A., Hecht, H.J., Hofmann, B., Biebl, H., and Singh, M. (2001). Production of selenomethionine-labelled proteins using simplified culture conditions and generally applicable host/vector systems. Appl. Microbiol. Biotechnol. 56, 718-723. https://doi.org/10.1007/s002530100690
  10. Habdas, B.J., Smart, J., Kaper, J.B., and Sperandio, V. (2010). The LysR-type transcriptional regulator QseD alters type three secretion in enterohemorrhagic Escherichia coli and motility in K-12 Escherichia coli. J. Bacteriol. 192, 3699-3712. https://doi.org/10.1128/JB.00382-10
  11. Jang, K.K., Gil, S.Y., Lim, J.G., and Choi, S.H. (2016). Regulatory characteristics of vibrio vulnificus gbpA gene encoding a mucin-binding protein essential for pathogenesis. J. Biol. Chem. 291, 5774-5787. https://doi.org/10.1074/jbc.M115.685321
  12. Jang, Y., Choi, G., Jo, I., Choi, S., and Ha, N. (2017). Purification, crystallization, and preliminary X-ray crystallographic analysis of VV2_1132, a LysR-type transcriptional regulator from Vibrio vulnificus. Biodesign 5, 44-48.
  13. Jo, I., Chung, I.Y., Bae, H.W., Kim, J.S., Song, S., Cho, Y.H., and Ha, N.C. (2015). Structural details of the OxyR peroxide-sensing mechanism. Proc. Natl. Acad. Sci. USA 112, 6443-6448. https://doi.org/10.1073/pnas.1424495112
  14. Jo, I., Kim, D., Bang, Y.J., Ahn, J., Choi, S.H., and Ha, N.C. (2017). The hydrogen peroxide hypersensitivity of OxyR2 in Vibrio vulnificus depends on conformational constraints. J. Biol. Chem. 292, 7223-7232. https://doi.org/10.1074/jbc.M116.743765
  15. Jones, M.K., and Oliver, J.D. (2009). Vibrio vulnificus: disease and pathogenesis. Infect. Immun. 77, 1723-1733. https://doi.org/10.1128/IAI.01046-08
  16. Kim, B.S., Hwang, J., Kim, M.H., and Choi, S.H. (2011a). Cooperative regulation of the Vibrio vulnificus nan gene cluster by NanR protein, cAMP receptor protein, and N-acetylmannosamine 6-phosphate. J. Biol. Chem. 286, 40889-40899. https://doi.org/10.1074/jbc.M111.300988
  17. Kim, H.U., Kim, S.Y., Jeong, H., Kim, T.Y., Kim, J.J., Choy, H.E., Yi, K.Y., Rhee, J.H., and Lee, S.Y. (2011b). Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery. Mol. Syst. Biol. 7, 460.
  18. Lim, J.G., and Choi, S.H. (2014). IscR is a global regulator essential for pathogenesis of Vibrio vulnificus and induced by host cells. Infect. Immun. 82, 569-578. https://doi.org/10.1128/IAI.01141-13
  19. Lochowska, A., Iwanicka-Nowicka, R., Plochocka, D., and Hryniewicz, M.M. (2001). Functional dissection of the LysR-type CysB transcriptional regulator. Regions important for DNA binding, inducer response, oligomerization, and positive control. J. Biol. Chem. 276, 2098-2107. https://doi.org/10.1074/jbc.M007192200
  20. Maddocks, S.E., and Oyston, P.C. (2008). Structure and function of the LysR-type transcriptional regulator (LTTR) family proteins. Microbiology 154, 3609-3623. https://doi.org/10.1099/mic.0.2008/022772-0
  21. Milton, D.L., O'Toole, R., Horstedt, P., and Wolf-Watz, H. (1996). Flagellin A is essential for the virulence of Vibrio anguillarum. J. Bacteriol. 178, 1310-1319. https://doi.org/10.1128/jb.178.5.1310-1319.1996
  22. Muraoka, S., Okumura, R., Ogawa, N., Nonaka, T., Miyashita, K., and Senda, T. (2003). Crystal structure of a full-length LysR-type transcriptional regulator, CbnR: unusual combination of two subunit forms and molecular bases for causing and changing DNA bend. J. Mol. Biol. 328, 555-566. https://doi.org/10.1016/S0022-2836(03)00312-7
  23. Otwinowski, Z., and Minor, W. (1997). Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326.
  24. Park, N., Song, S., Choi, G., Jang, K.K., Jo, I., Choi, S.H., and Ha, N.C. (2017a). Crystal Structure of the Regulatory Domain of AphB from Vibrio vulnificus, a Virulence Gene Regulator. Mol. Cells 40, 299-306. https://doi.org/10.14348/molcells.2017.0015
  25. Park, S., Ha, S., and Kim, Y. (2017b). The Protein Crystallography Beamlines at the Pohang Light Source II. Biodesign 5, 30-34.
  26. Sambrook, J., Russell, D.W., and Sambrook, J. (2006). The condensed protocols from Molecular cloning : a laboratory manual (Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press).
  27. Simon, R., Priefer, U., and Puhler, A. (1983). A broad host range mobilization system for invivo genetic-engineering - transposon mutagenesis in gram-negative bacteria. Bio-Technol 1, 784-791. https://doi.org/10.1038/nbt1183-784
  28. Taylor, J.L., De Silva, R.S., Kovacikova, G., Lin, W., Taylor, R.K., Skorupski, K., and Kull, F.J. (2012). The crystal structure of AphB, a virulence gene activator from Vibrio cholerae, reveals residues that influence its response to oxygen and pH. Mol. Microbiol. 83, 457-470. https://doi.org/10.1111/j.1365-2958.2011.07919.x
  29. 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. https://doi.org/10.1107/S0907444910045749
  30. Zhou, X., Lou, Z., Fu, S., Yang, A., Shen, H., Li, Z., Feng, Y., Bartlam, M., Wang, H., and Rao, Z. (2010). Crystal structure of ArgP from Mycobacterium tuberculosis confirms two distinct conformations of full-length LysR transcriptional regulators and reveals its function in DNA binding and transcriptional regulation. J. Mol. Biol. 396, 1012-1024. https://doi.org/10.1016/j.jmb.2009.12.033

Cited by

  1. Crystal Structure of LysB4, an Endolysin from Bacillus cereus-Targeting Bacteriophage B4 vol.42, pp.1, 2019, https://doi.org/10.14348/molcells.2018.0379
  2. Structural basis for HOCl recognition and regulation mechanisms of HypT, a hypochlorite-specific transcriptional regulator vol.116, pp.9, 2018, https://doi.org/10.1073/pnas.1811509116
  3. Crystal Structure of the Regulatory Domain of MexT, a Transcriptional Activator of the MexEF-OprN Efflux Pump in Pseudomonas aeruginosa vol.42, pp.12, 2019, https://doi.org/10.14348/molcells.2019.0168