Structure of the host-recognition device of Staphylococcus aureus phage phi 11

Staphylococcus aureus is a Gram-positive bacterium that causes a wide range of infections. It is a leading cause of bacteremia, infective endocarditis, as well as osteoarticular, skin and soft tissue, pleuropulmonary and device related infections1. Methicillin-resistant S. aureus (MRSA) remains a severe global problem threatening the health care system as resistance restricts treatment options to a few drugs of last resort. All S. aureus genomes sequenced to date contain one or several prophages2,3. Most S. aureus phages can be integrated into the bacterial chromosome or exist as extra-chromosomal elements. It is known that many of these phages encode a large variety of S. aureus virulence or fitness factors that allow the bacterium to escape the host immune system. Among all mobile genetic elements in S. aureus, phages are probably most efficient in mediating horizontal gene transfer of virulence or resistance genes between strains, and across species or even genus. Therefore, phages play important roles in staphylococcal pathogenicity and adaptation of S. aureus to different hostile environments2,3. The large number of staphylococcal phages sequenced to date display an extensive mosaicism in their gene structure, which is a consequence of gene shuffling among different phages that can infect staphylococcal species. The resulting mosaic gene organization is consistent with a modular evolution involving exchanges of genome modules by horizontal transfer and genetic recombination. The genetic exchanges of modules can involve single genes, protein domains, groups of genes, or even functional modules3. Although phages are the most abundant and diversified biological entity on earth, each phage can only infect a limited number of bacterial strains. This specific phage-host interaction is determined, in part, by the protein recognition device located at the tip of the phage tail, which engages a receptor at the bacterial cell surface. Since bacterial cell wall polysaccharides or glycopolymers project from the cell surface and are thus easily accessible, they are the most common molecules targeted by bacteriophages4,5,6. The cell wall of S. aureus typically contains poly-ribitol phosphate type wall teichoic acid (WTA), which is modified with D-alanine and N-acetyl-glucosamine (GlcNAc). S. aureus ϕ11 is often used as model to study horizontal gene transfer of virulence genes7. Recently it was shown that ϕ11 requires GlcNAc residues on WTA for adsorption8. Gp45 of ϕ11 was identified and characterized as the receptor-binding protein (RBP) of ϕ11 9. Furthermore, it was shown that ϕ11 was unable to bind to the cell wall in the absence of WTA–GlcNAc, identifying glycosylated WTA as the receptor. Phages adopt a two-fold strategy for host adhesion. They first deploy adhesion modules on fibers or on capsid or tail that recognize the host’s cell wall glycan structures in a reversible way: this allows cell wall scanning in search for the final, specific receptor, to which they bind irreversibly10,11,12. This final receptor can be a protein, generally membrane embedded12,13, or a cell wall polysaccharide as observed in the case of lactococcal phages4,5,6. Attachment to membrane protein often requires a unique and strong attachment of the phage’s tail tip, as observed in phage T5 14,15. In contrast, the loose affinity observed between saccharides and proteins requires the presence of several attachment sites provided by a multimeric RBP carrying device, the baseplate16,17,18,19. In order to provide a foundation for understanding the initial recognition mechanism of phage ϕ11 and its receptor in the cell wall of S. aureus, we embarked on structural analyses of the Gp45 and baseplate of ϕ11 using X-ray crystallography and electron microscopy. The RBP structure reveals a trimer with a complex fold that can be divided, from N- to C-terminus, into a “stem”, a “platform” and a “tower”. The stem is formed by a long, severely bent triple α-helical coiled coil that features three interruptions: the first and third interruptions are both β-hairpin structures and the second is a short disordered region. A putative “hinge”-like feature is located between the second and the third interruption. The stem is followed by a “platform” of three β-propellers, and the protein terminates with a “tower” formed by a repetitive all-β domain. Platform and tower are interconnected by a fifth short triple helix buried inside of the protein on the molecule’s longest three-fold axis. An unusual iron is located at the C-terminal end of the first coiled coil and may play a role in mediating flexibility or conformational rearrangements within the helical domain. Six copies of the trimer assemble around the baseplate core. This hexameric organization is commonly observed in lactococcal Siphoviridae17,18, and it is compatible with host adhesion and infection in the absence of an activation step.