Diversification of β-augmentation interactions between CDI toxin/immunity proteins

Robert P. Morse, Julia L.E. Willett, Parker M. Johnson, Jing Zheng, Alfredo Credali, Angelina Iniguez, James S. Nowick, Christopher S. Hayes, Celia W. Goulding

Research output: Contribution to journalArticlepeer-review

26 Scopus citations

Abstract

Contact-dependent growth inhibition (CDI) is a widespread mechanism of inter-bacterial competition mediated by the CdiB/CdiA family of two-partner secretion proteins. CdiA effectors carry diverse C-terminal toxin domains (CdiA-CT), which are delivered into neighboring target cells to inhibit growth. CDI+ bacteria also produce CdiI immunity proteins that bind specifically to cognate CdiA-CT toxins and protect the cell from auto-inhibition. Here, we compare the structures of homologous CdiA-CT/CdiI complexes from Escherichia coli EC869 and Yersinia pseudotuberculosis YPIII to explore the evolution of CDI toxin/immunity protein interactions. Both complexes share an unusual β-augmentation interaction, in which the toxin domain extends a β-hairpin into the immunity protein to complete a six-stranded anti-parallel sheet. However, the specific contacts differ substantially between the two complexes. The EC869 β-hairpin interacts mainly through direct H-bond and ion-pair interactions, whereas the YPIII β-hairpin pocket contains more hydrophobic contacts and a network of bridging water molecules. In accord with these differences, we find that each CdiI protein only protects target bacteria from its cognate CdiA-CT toxin. The compact β-hairpin binding pocket within the immunity protein represents a tractable system for the rationale design of small molecules to block CdiA-CT/CdiI complex formation. We synthesized a macrocyclic peptide mimic of the β-hairpin from EC869 toxin and solved its structure in complex with cognate immunity protein. These latter studies suggest that small molecules could potentially be used to disrupt CDI toxin/immunity complexes.

Original languageEnglish (US)
Pages (from-to)3766-3784
Number of pages19
JournalJournal of Molecular Biology
Volume427
Issue number23
DOIs
StatePublished - Nov 20 2015

Bibliographical note

Funding Information:
This research was supported by the National Institutes of Health ( GM102318 to C.S.H. and C.W.G.) and the National Science Foundation ( CHE-1058825 to J.S.N. and DGE-1144085 to J.L.E.W.). Structure determination was, in part, supported by the Advanced Light Source ( U.S. Department of Energy under Contract No. DE-AC02-05CH11231 ) at Berkeley National Laboratories and the Stanford Synchrotron Radiation Lightsource (supported in part by National Institutes of Health P41 GM103393 and U.S. Department of Energy DE-AC02-76SF00515 ). Funding for open access charge is from National Institutes of Health . We would like to thank the staff at Advanced Light Source and Stanford Synchrotron Radiation Lightsource for their invaluable help in data collection. We would also like to thank Elias Gerrick and Sonya Donato for technical support. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.

Publisher Copyright:
© 2015 Elsevier Ltd.

Keywords

  • DNase
  • bacterial competition
  • interspecies growth inhibition
  • toxin/immunity proteins

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