Structural Basis of Resistance of Helicobacterpylori DnaK to Antimicrobial Peptide Pyrrhocoricin

Authors: Musammat F. Nahar, Anna Roujeinikova

Abstract:

Bacterial molecular chaperone DnaK plays an essential role in protein folding, stress response and transmembrane targeting of proteins. DnaKs from many bacterial species, including Escherichia coli, Salmonella typhimurium and Haemophilus infleunzae are the molecular targets for the insect-derived antimicrobial peptide pyrrhocoricin. Pyrrhocoricin-like peptides bind in the substrate recognition tunnel. Despite the high degree of crossspecies sequence conservation in the substrate-binding tunnel, some bacteria are not sensitive to pyrrhocoricin. This work addresses the molecular mechanism of resistance of Helicobacter pylori DnaK to pyrrhocoricin. Homology modelling, structural and sequence analysis identify a single aminoacid substitution at the interface between the lid and the β-sandwich subdomains of the DnaK substrate-binding domain as the major determinant for its resistance.

Keywords: Helicobacter pylori, molecular chaperone DnaK, pyrrhocoricin, structural biology.

Digital Object Identifier (DOI): doi.org/10.5281/zenodo.1080714

References:

[1] A. Covacci, J. L. Telford, G. Del Giudice et al., "Helicobacter pylori virulence and genetic geography," Science, vol. 284, no. 5418, pp. 1328-33, May 21, 1999.
[2] B. J. Marshall, and J. R. Warren, "Unidentified curved bacilli in the stomach of patients with gastritis and peptic ulceration," Lancet, vol. 1, no. 8390, pp. 1311-5, Jun 16, 1984.
[3] R. M. Peek, Jr., and M. J. Blaser, "Helicobacter pylori and gastrointestinal tract adenocarcinomas," Nat Rev Cancer, vol. 2, no. 1, pp. 28-37, Jan, 2002.
[4] A. C. Ford, B. C. Delaney, D. Forman et al., "Eradication therapy for peptic ulcer disease in Helicobacter pylori positive patients," Cochrane Database Syst Rev, no. 2, pp. CD003840, 2006.
[5] N. Uemura, T. Mukai, S. Okamoto et al., "Effect of Helicobacter pylori eradication on subsequent development of cancer after endoscopic resection of early gastric cancer," Cancer Epidemiol Biomarkers Prev, vol. 6, no. 8, pp. 639-42, Aug, 1997.
[6] G. Treiber, S. Ammon, E. Schneider et al., "Amoxicillin/metronidazole/omeprazole/clarithromycin: a new, short quadruple therapy for Helicobacter pylori eradication," Helicobacter, vol. 3, no. 1, pp. 54-8, Mar, 1998.
[7] N. Broutet, S. Tchamgoue, E. Pereira et al., "Risk factors for failure of Helicobacter pylori therapy--results of an individual data analysis of 2751 patients," Aliment Pharmacol Ther, vol. 17, no. 1, pp. 99-109, Jan, 2003.
[8] G. Kragol, S. Lovas, G. Varadi et al., "The antibacterial peptide pyrrhocoricin inhibits the ATPase actions of DnaK and prevents chaperone-assisted protein folding," Biochemistry, vol. 40, no. 10, pp. 3016-26, Mar 13, 2001.
[9] L. Otvos, Jr., K. Bokonyi, I. Varga et al., "Insect peptides with improved protease-resistance protect mice against bacterial infection," Protein Sci, vol. 9, no. 4, pp. 742-9, Apr, 2000.
[10] M. P. Mayer, and B. Bukau, "Hsp70 chaperones: cellular functions and molecular mechanism," Cell Mol Life Sci, vol. 62, no. 6, pp. 670-84, Mar, 2005.
[11] M. Liebscher, and A. Roujeinikova, "Allosteric coupling between the lid and interdomain linker in DnaK revealed by inhibitor binding studies," J Bacteriol, vol. 191, no. 5, pp. 1456-62, Mar, 2009.
[12] G. Kragol, R. Hoffmann, M. A. Chattergoon et al., "Identification of crucial residues for the antibacterial activity of the proline-rich peptide, pyrrhocoricin," Eur J Biochem, vol. 269, no. 17, pp. 4226- 37, Sep, 2002.
[13] A. Sali, and T. L. Blundell, "Comparative protein modelling by satisfaction of spatial restraints," J Mol Biol, vol. 234, no. 3, pp. 779-815, Dec 5, 1993.
[14] A. Fiser, R. K. Do, and A. Sali, "Modeling of loops in protein structures," Protein Sci, vol. 9, no. 9, pp. 1753-73, Sep, 2000.
[15] M. J. Sippl, "Recognition of errors in three-dimensional structures of proteins," Proteins, vol. 17, no. 4, pp. 355-62, Dec, 1993.
[16] M. Wiederstein, and M. J. Sippl, "ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins," Nucleic Acids Res, vol. 35, no. Web Server issue, pp. W407-10, Jul, 2007.
[17] B. Wallner, and A. Elofsson, "Can correct protein models be identified?," Protein Sci, vol. 12, no. 5, pp. 1073-86, May, 2003.
[18] J. U. Bowie, R. Luthy, and D. Eisenberg, "A method to identify protein sequences that fold into a known three-dimensional structure," Science, vol. 253, no. 5016, pp. 164-70, Jul 12, 1991.
[19] N. Guex, and M. C. Peitsch, "SWISS-MODEL and the Swiss- PdbViewer: an environment for comparative protein modeling," Electrophoresis, vol. 18, no. 15, pp. 2714-23, Dec, 1997.
[20] W. L. DeLano, "The PyMOL Molecular Graphics System: Version 0.90 (DeLano Scientific, Palo Alto, CA)," 2003.
[21] X. Zhu, X. Zhao, W. F. Burkholder et al., "Structural analysis of substrate binding by the molecular chaperone DnaK," Science, vol. 272, no. 5268, pp. 1606-14, Jun 14, 1996.
[22] P. Emsley, and K. Cowtan, "Coot: model-building tools for molecular graphics," Acta Crystallogr D Biol Crystallogr, vol. 60, no. Pt 12 Pt 1, pp. 2126-32, Dec, 2004.
[23] A. Roujeinikova, "Crystal structure of the cell wall anchor domain of MotB, a stator component of the bacterial flagellar motor: implications for peptidoglycan recognition," Proc Natl Acad Sci U S A, vol. 105, no. 30, pp. 10348-53, Jul 29, 2008.