Pseudo-pac site sequences of P22
Salmonella enterica sv. Typhimurium and its bacteriophage P22 are a model system for the study of horizontal gene transfer by generalized transduction. Typically, P22's DNA packaging machinery initiates packaging when a short sequence of DNA, known as the pac site, is recognized on the P22 genome. However, pseudo-pac sites residing in the host's genome can lead to the erroneous packaging and subsequent generalized transduction of Salmonella DNA. While the general genomic locations of the S. Typhimurium pseudo-pac sites are known, the sequences themselves have not yet been determined.  To identify the pseudo-pac site sequences we used visualization of P22 sequencing reads mapped to the host Salmonella genomes to define regions of generalized transduction initiation and the likely locations of pseudo-pac sites. We searched each genome region for the sequence with the highest similarity to the P22 pac site and aligned the resulting sequence matches. We built a regular expression from the alignment and used it to search the genomes of two P22-susceptible Salmonella strains- LT2 and 14028S- for sequence matches. The final regular expression successfully identified pseudo-pac sites in both LT2 and 14028S that correspond with generalized transduction initiation sites in mapped read coverages. The pseudo-pac site sequences identified in this study can be used to predict locations of generalized transduction in other P22-susceptible hosts or to force generalized transduction at specific locations in P22-susceptible hosts with genetic engineering. Furthermore, the bioinformatics approach used to identify the S. Typhimurium pseudo-pac sites in this study could be applied to other phage-host systems.