Structural Superimposition

Abstact

Bacteriophages face intense competition within bacterial populations. Although bacteria encode diverse anti-phage mechanisms, strategies protecting virions at the host surface remain poorly understood. Here, we develop a receptor-centered discovery approach that captures phage proteins bound to host receptors during infection. Applying this strategy to bacteriophage lambda and its outer-membrane receptor LamB, we identify Lom as a phage-encoded outer membrane protein that binds LamB. Structural, biochemical, and functional analyses show that Lom occupies the same LamB surface recognized by the receptor-binding protein gpJ, thereby reducing phage adsorption through receptor occlusion. Ribosome profiling indicates that lom is strongly expressed during late lytic growth and is also expressed during lysogeny, consistent with a role in receptor-level superinfection exclusion. Foldseek analyses identify structurally related Lom-like proteins in diverse temperate phages, raising the possibility that receptor occlusion is a more widespread strategy. These findings establish a framework for discovering receptor-level phage competition mechanisms.