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bioRxiv · 10.64898/2026.05.12.724579

Structural modularity of receptor-binding proteins underlies host-range strategy diversification in Klebsiella pneumoniae phages

R. Panicker, V.·Smug, B. J.·Klein-Sousa, V.·Enright, M. C.·Taylor, N. M. I.·Drulis-Kawa, Z.·Mostowy, R. J.
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Abstract

Bacteriophage receptor-binding proteins (RBPs) determine bacterial host recognition and are central to phage host-range evolution, yet the structural principles governing how RBPs diversify and expand host range remain not fully understood. Although phage RBPs are thought to evolve through modular exchange of receptor-binding domains, it is unclear how this modularity is organised across diverse RBP architectures, at what structural scales recombination operates, and how it shapes host-range breadth. Here we combined large-scale AlphaFold3 structural modelling, domain-level annotation, de novo pseudo-domain segmentation, sequence modularity analysis and experimentally determined host-range phenotypes across 192 Klebsiella pneumoniae phages and 382 high-confidence RBPs spanning up to 96 K-types. We generated the first system-wide structural atlas of K. pneumoniae phage RBPs, resolving 39 structurally distinct RBP-classes. Although capsule-degrading beta-helix depolymerases dominated numerically, 161 RBPs across 37 RBP-classes employed non-depolymerase architectures, including 18 novel RBP-classes. Structural and sequence analyses show that this diversity arose through modular reuse of structural domains rather than independent invention. Conserved N-terminal scaffolds linked depolymerase and non-depolymerase RBPs across morphotypes, while receptor-binding regions diversified through recombination operating at and beyond domain boundaries. We found recent modular exchange both within genera, where capsule-specific and capsule-independent RBPs can be swapped to alter host-range strategy, and across morphotypes, where depolymerase modules moved between distant lineages altering capsule specificity. Together, these architectures resolve into six receptor-recognition strategies, establishing multi-scale modularity as the primary organising principle of RBP diversification and a structure-informed framework for guiding phage isolation and engineering against K. pneumoniae. The complete atlas is freely accessible as an interactive community resource at Klebsiella-Phage-RBP-Atlas.

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R. Panicker, V., Smug, B. J., Klein-Sousa, V., Enright, M. C., Taylor, N. M. I., Drulis-Kawa, Z., Mostowy, R. J.. 2026-05-14. Structural modularity of receptor-binding proteins underlies host-range strategy diversification in Klebsiella pneumoniae phages. https://doi.org/10.64898/2026.05.12.724579

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