Molecular basis for inhibition of adhesin-mediated bacterial-host interactions through a peptide-binding domain

Shuaiqi Guo, Hossein Zahiri, Corey Stevens, Daniel C. Spaanderman, Lech-Gustav Milroy, Christian Ottmann, Luc Brunsveld, Ilja K. Voets, Peter L. Davies (Corresponding author)

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Abstract

Infections typically begin with pathogens adhering to host cells. For bacteria, this adhesion can occur through specific ligand-binding domains. We identify a 20-kDa peptide-binding domain (PBD) in a 1.5-MDa RTX adhesin of a Gram-negative marine bacterium that colonizes diatoms. The crystal structure of this Ca2+-dependent PBD suggests that it may bind the C termini of host cell-surface proteins. A systematic peptide library analysis reveals an optimal tripeptide sequence with 30-nM affinity for the PBD, and X-ray crystallography details its peptide-protein interactions. Binding of the PBD to the diatom partner of the bacteria can be inhibited or competed away by the peptide, providing a molecular basis for inhibiting bacterium-host interactions. We further show that this PBD is found in other bacteria, including human pathogens such as Vibrio cholerae and Aeromonas veronii. Here, we produce the PBD ortholog from A. veronii and demonstrate, using the same peptide inhibitor, how pathogens may be prevented from adhering to their hosts.

Original languageEnglish
Article number110002
Number of pages16
JournalCell Reports
Volume37
Issue number7
DOIs
Publication statusPublished - 16 Nov 2021

Funding

We thank Dr. John Allingham for the use of the home source X-ray diffractometer at Queen’s University, as well as staff members at the Canadian Light Source in Saskatoon, Canada, and the PETRA III facility at DESY in Hamburg, Germany, for access to data collection at these synchrotrons. We are grateful to Dr. EonSeon Jin, Hanyang University, Seoul, for the gift of the diatom, C. neogracile, and to Dr. Saeed Rismani Yazdi for assistance with the diatom cultures. We are indebted to Mr. Kim Munro at the Protein Function Discovery Unit at Queen’s University for assistance with acquiring and interpreting ITC data, and to Mr. Rob Eves for completing the binding studies with AvPBD. We thank Ms. Irene van Oekel for preliminary tests on the binding of peptidyl ligands to MpPBD and Mr. Joost van Dongen for analytical support. This project was funded by a Natural Science and Engineering Research Council (NSERC) Discovery Grant ( RGPIN-2016-04810 , to P.L.D., who holds the Canadian Research Chair in Protein Engineering). I.K.V. acknowledges financial support from the European Union ( ERC-2014-StG contract no. 635928 ) and the Dutch Science Foundation (NWO ECHO Grant No. 712.016.002 ). We thank Dr. John Allingham for the use of the home source X-ray diffractometer at Queen's University, as well as staff members at the Canadian Light Source in Saskatoon, Canada, and the PETRA III facility at DESY in Hamburg, Germany, for access to data collection at these synchrotrons. We are grateful to Dr. EonSeon Jin, Hanyang University, Seoul, for the gift of the diatom, C. neogracile, and to Dr. Saeed Rismani Yazdi for assistance with the diatom cultures. We are indebted to Mr. Kim Munro at the Protein Function Discovery Unit at Queen's University for assistance with acquiring and interpreting ITC data, and to Mr. Rob Eves for completing the binding studies with AvPBD. We thank Ms. Irene van Oekel for preliminary tests on the binding of peptidyl ligands to MpPBD and Mr. Joost van Dongen for analytical support. This project was funded by a Natural Science and Engineering Research Council (NSERC) Discovery Grant (RGPIN-2016-04810, to P.L.D. who holds the Canadian Research Chair in Protein Engineering). I.K.V. acknowledges financial support from the European Union (ERC-2014-StG contract no. 635928) and the Dutch Science Foundation (NWO ECHO Grant No. 712.016.002). S.G. and P.L.D. conceived the study, designed the experiments, and wrote the manuscript. S.G. performed the co-crystallization, data collection, and structure determination of the X-ray crystal structures. S.G. performed the FP binding experiments and analyzed the data with the assistance of D.C.S. L.-G.M. and D.C.S. performed the peptide synthesis and purification. H.Z. and C.S. performed the diatom binding experiments and analyzed the data. C.O. L.B. and I.K.V. provided critical feedback to S.G. throughout the project and contributed to the critical editing of drafts of the manuscript. The authors declare no competing interests.

FundersFunder number
Natural Sciences and Engineering Research Council of CanadaRGPIN-2016-04810
European Commission
Hanyang University
Nederlandse Organisatie voor Wetenschappelijk Onderzoek712.016.002

    Keywords

    • anti-adhesion
    • bacteria-host interaction
    • bacterial adhesins
    • chemical biology
    • peptide inhibitors
    • peptide-binding domain
    • structural biology
    • X-ray crystallography

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