Sequencing

of the attB attP junction in this lysogen confirms the attP site of φX216 to be in the 3’ end of the predicted integrase gene corresponding to phage genome integration at tRNA-Phe (attB) [8]. Figure 2 φX216 genome annotation. Gene clusters and their predicted functions are indicated in different colors. Predicted capsid structural and assembly genes are shown in lime, host lysis proteins are shown in blue, genes required for phage tail structure and assembly are shown in cyan, and genes encoding proteins involved in lysogeny and DNA replication are shown in magenta. The phage attachment site (attP) is indicated by a yellow triangle. Sequence numbering is shown above Based on its genome sequence, φX216 is a P2-like member of the Myoviridae subgroup Proteasome inhibitor A. Its shares 99.8% pair-wise identity with φ52237 isolated from B. pseudomallei Pasteur 52237 (GenBank: DQ087285.2) [8]. There are 55 differences observed between φX216 and φ52237, which were independently

confirmed by both Illumina and Sanger sequencing. The majority of these differences, cluster within a six gene region predicted to be associated with tail structure and assembly although only 14 are missense mutations resulting in amino acid alterations. However, these mutations are of no biological Trichostatin A solubility dmso consequence since φ52237 and φX216 were found to have identical host ranges (see Additional file 1). Illumina sequencing also produced a second 1,141-bp contig independent of the φX216 genome contig. This contig has 100% pairwise identity with the highly active IS407a insertion element found in the B. mallei genome [11]. At present we do not know whether this contig is the result of IS407a insertion in a sub-population of φX216 virions during preparation of the B. mallei lysates used for Illumina sequencing or an integral part of φX216 DNA. However, since the IS407a insertion was absent from the genome sequence

obtained these by Sanger sequencing it is unlikely an indigenous part of the φX216 genome. Burkholderia P2-like prophage distribution and correlation with ϕX216 host range Although φX216 has a broad B. pseudomallei host range it fails to form plaques on approximately 22% of the strains tested in this study. We sought to determine if this was perhaps due to infection immunity conferred by the presence of related prophages. To that end, we designed a series of multiplex and individual PCR probes based on six isolated or predicted Burkholderia P2-like phages from Ronning et al. [8]. These included three subgroup A (φE202, φK96243 and φ52237/φX216) and three subgroup B (φE12-2, GI15, PI-E264-2) P2-like phages (see Additional file 2) [8]. PCR probes were designed to identify candidate P2-like prophages with increasing levels of relatedness to φX216/φ52237. The P2-like 1 and P2-like 2 probes amplify regions in the capsid gene (gene #6; for gene numbers see GenBank: JX681814) and Fels-2 gene (gene #29) and are conserved in both P2-like A and B subgroups.