Analysis of phage-resistant mechanisms in Staphylococcus aureus SA003 reveals a different binding mechanism for the closely related Twort-like phages phiSA012 and phiSA039

We have previously generated strains of Staphylococcus aureus SA003 resistant to its specific phage {phi}SA012 through long-term coevolution experiment. However, the DNA mutations responsible for the phenotypic change of phage resistance are unknown. Whole-genome analysis revealed six genes that acquired unique point mutations: five missense mutations and one nonsense mutation. Moreover, one deletion, 1.779-bp, resulted in the deletion of the genes encoding glycosyltransferase, TarS, and iron-sulfure repair protein, ScdA. The deletion occurred from the second round of coculture (SA003R2) and remained through the last round. The {phi}SA012 infection toward SA003R2 had decreased to 79.77{+/-}7.50% according to plating efficiency. Complementation of the phage-resistant strain by the wild-type allele showed two mutated host genes were linked to the inhibition of post-adsorption, and five genes were linked to phage adsorption of {phi}SA012. Unlike {phi}SA012, infection by {phi}SA039, a close relative of {phi}SA012, onto SA003R2 was impaired drastically. Complementation of SA003R2 by wild-type tarS restores the infectivity of {phi}SA039. Thus, we concluded that {phi}SA039 requires {beta}-GlcNAc in Wall Teichoic Acid (WTA) for its binding. In silico analysis of the {phi}SA039 genome revealed that several proteins in the tail and baseplate region were different from {phi}SA012; notably the partial deletion of orf96 of {phi}SA039, a homolog of orf99 of {phi}SA012. Orf100 of {phi}SA039, a homolog of Orf103 of {phi}SA012, a previously reported receptor binding protein (RBP), had low similarity (86%) to that of {phi}SA012. The difference in tail and baseplate proteins might be the factor for specificity difference between {phi}SA012 and {phi}SA039.