A diverse family of protein antibiotics inhibits the BAM complex by β-signal mimicry

A variety of protein antibiotics, known as lectin-like protein antibiotics (Llps), battle Pseudomonas by blocking the BAM complex, a crucial component of the beta-barrel assembly machinery. These Llps consist of either one or two beta;-lectin domains, along with a C-terminal peptide. The two-domain L-type pyocins of P. aeruginosa bind to BamA's extracellular loop 6, inhibiting the complex by delivering the C-terminal peptide to BamA's beta;-strand 1.

However, the universality of this mechanism and how Llps adapt to sequence differences among BamA across different species were not well understood.

To address this, researchers tested 238 Llps against 101 Pseudomonas isolates with sequenced genomes. The results revealed that susceptibility to these antibiotics is primarily determined by BamA's extracellular loop 6. This loop shows variability in length, leading Llps to adopt three distinct targeting modes: short-loop and long-loop specialists, and broad-range dual targeters, which have emerged multiple times.

In a significant breakthrough, the researchers obtained the 2.66 angstrom cryo-electron microscopy structure of a two-domain LlpA bound to BAM. This structure elucidates the altered recognition of BamA's extracellular loop 6 by Llps, with loop 6 being bound by a single face of the N-terminal beta-lectin domain instead of the inter-domain cleft.

This finding explains how single-domain LlpBs still target BamA and why the second lectin domain has been lost in certain Llps. Additionally, the study demonstrates that the mechanism by which Llps inhibit BAM is shared among them, with a hypervariable C-terminal peptide binding to BamA's beta-strand 1. This peptide inhibits the BAM insertase by imitating the beta-signal found in BamA's substrates.

These findings collectively offer a comprehensive overview of Llp diversity and the fundamental principles behind their mechanisms. The researchers conclude that Llps serve as versatile, multi-interface scaffolds that can be fine-tuned for precise BAM-directed antibacterials. This opens up new possibilities for developing targeted medications, particularly against economically important plant pathogens like Pseudomonas.