Predicted Structures of Ceduovirus Adhesion Devices Highlight Unique Architectures Reminiscent of Bacterial Secretion System VI.

Abstract

Bacteriophages, or phages, are sophisticated nanomachines that efficiently infect bacteria. Their infection of lactic acid bacteria (LAB) used in fermentation can lead to significant industrial losses. Among phages that infect monoderm bacteria, those with siphovirion morphology characterized by a long, non-contractile tail are predominant. The initial stage of phage infection involves precise host recognition and binding. To achieve this, phages feature host adhesion devices (HADs) located at the distal end of their tails, which have evolved to recognize specific proteinaceous or saccharidic receptors on the host cell wall. Ceduovirus represents a group of unique lytic siphophages that specifically infect the LAB Lactococcus lactis by targeting proteinaceous receptors. Despite having compact genomes, most of their structural genes are poorly annotated and the architecture and function of their HADs remain unknown. Here we used AlphaFold3 to explore the Ceduovirus HADs and their interaction with the host. We show that Ceduovirus HADs exhibit unprecedented features among bacteriophages infecting Gram⁺, share structural similarities with bacterial secretion system VI, and combine both saccharide and protein-binding modules. Moreover, we could annotate the majority of Ceduovirus genes encoding structural proteins by leveraging their predicted structures, highlighting AlphaFold's significant contribution to phage genome annotation.