Diversification of β-Augmentation Interactions between CDI Toxin/Immunity Proteins

• Published in: Journal of molecular biology 2015-11, Vol.427 (23), p.3766-3784
• Main Authors: Morse, Robert P., Willett, Julia L.E., Johnson, Parker M., Zheng, Jing, Credali, Alfredo, Iniguez, Angelina, Nowick, James S., Hayes, Christopher S., Goulding, Celia W.
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; bacterial competition; Bacterial Proteins - chemistry; Bacterial Proteins - immunology; Bacterial Proteins - metabolism; Bacterial Toxins - chemistry; Bacterial Toxins - genetics; Bacterial Toxins - immunology; Bacterial Toxins - metabolism; Crystallography, X-Ray; DNase; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - genetics; Escherichia coli Proteins - metabolism; interspecies growth inhibition; Membrane Proteins - chemistry; Membrane Proteins - metabolism; Models, Molecular; Molecular Sequence Data; Multiprotein Complexes; Protein Conformation; Protein Interaction Domains and Motifs; Protein Interaction Mapping; Structure-Activity Relationship; toxin/immunity proteins; Yersinia pseudotuberculosis - chemistry; Yersinia pseudotuberculosis - growth & development
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2015.09.020

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. [Display omitted] •Contact-dependent growth inhibition is a widespread mechanism of inter-bacterial competition.•Toxins inhibit neighboring cells and immunity proteins protect against auto-inhibition.•A toxin/immunity complex family interface is mediated by toxin β-hairpin interaction.•Among this complex family, each immunity protein only neutralizes cognate toxin.•A toxin β-hairpin mimic binds immunity protein and could disrupt complex formation.