Characterization of the Genome, Proteome, and Structure of Yersiniophage φR1-37

The bacteriophage vB_YecM-phi R1-37 (phi R1-37) is a lytic yersiniophage that can propagate naturally in different Yersinia species carrying the correct lipopolysaccharide receptor. This large-tailed phage has deoxyuridine (dU) instead of thymidine in its DNA. In this study, we determined the genomic sequence of phage phi R1-37, mapped parts of the phage transcriptome, characterized the phage particle proteome, and characterized the virion structure by cryo-electron microscopy and image reconstruction. The 262,391-bp genome of phi R1-37 is one of the largest sequenced phage genomes, and it contains 367 putative open reading frames (ORFs) and 5 tRNA genes. Mass-spectrometric analysis identified 69 phage particle structural proteins with the genes scattered throughout the genome. A total of 269 of the ORFs (73%) lack homologues in sequence databases. Based on terminator and promoter sequences identified from the intergenic regions, the phage genome was predicted to consist of 40 to 60 transcriptional units. Image reconstruction revealed that the phi R1-37 capsid consists of hexameric capsomers arranged on a T = 27 lattice similar to the bacteriophage phi KZ. The tail of phi R1-37 has a contractile sheath. We conclude that phage phi R1-37 is a representative of a novel phage type that carries the dU-containing genome in a phi KZ-like head.