Yersiniophage ϕR1-37 is a tailed bacteriophage having a 270 kb DNA genome with thymidine replaced by deoxyuridine

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Abstract
BacteriophageϕR1-37 was isolated based on its ability to infect strain YeO3-R1, a virulence-plasmid-cured O antigen-negative derivative ofYersinia enterocoliticaserotype O : 3. In this study, the phage receptor was found to be a structure in the outer core hexasaccharide ofY. enterocoliticaO : 3 LPS. The phage receptor was present in the outer core of strains of many otherY. enterocoliticaserotypes, but also in someYersinia intermediastrains. Surprisingly, the receptor structure resided in the O antigen ofYersinia pseudotuberculosisO : 9. Electron microscopy demonstrated thatϕR1-37 particles have an icosahedral head of 88 nm, a short neck of 10 nm, a long contractile tail of 236 nm, and tail fibres of at least 86 nm. This implies that the phage belongs to the orderCaudoviralesand the familyMyoviridaein the ICTV (International Committee for Taxonomy of Viruses) classification.ϕR1-37 was found to have a lytic life cycle, with eclipse and latent periods of 40 and 50 min, respectively, and a burst size of ∼80 p.f.u. per infected cell. Restriction digestions and PFGE showed that theϕR1-37 genome was dsDNA and ∼270 kb in size. Enzymically hydrolysed DNA was subjected to HPLC-MS/MS analysis, which demonstrated that theϕR1-37 genome is composed of DNA in which thymidine (T) is >99 % replaced by deoxyuridine (dU). The only organisms known to have similar DNA are theBacillus subtilis-specific bacteriophages PBS1 and PBS2. N-terminal amino acid sequences of four major structural proteins did not show any similarity to (viral) protein sequences in databases, indicating that close relatives ofϕR1-37 have not yet been characterized. Genes for two of the structural proteins, p24 and p46, were identified from the partially sequencedϕR1-37 genome.