Genomics and Proteomics of Mycobacteriophage Patience, an Accidental Tourist in the Mycobacterium Neighborhood

Pope, Welkin H.; Jacobs-Sera, Deborah; Russell, Daniel A.; Rubin, Daniel H. F.; Kajee, Afsana; Msibi, Zama N. P.; Larsen, Michelle H.; Jacobs, William R.; Lawrence, Jeffrey G.; Hendrix, Roger W.; Hatfull, Graham F.

Patience represents an intriguing example of a virus that has successfully entered the mycobacterial genetic neighborhood in its relatively recent evolutionary history. Its overall GC content and codon usage profiles are distinctly different from those of its mycobacterial host, suggesting that it primarily evolved in a moderate-GC (~50%) environment. Growth in high-GC bacteria may have required multiple events, including acquisition of part of a tail gene (gene 47) by lateral gene transfer. Nonetheless, the mismatch between viral and host genomic profiles does not appear to have been a substantial impediment to host range expan-sion, although the highly expressed viral genes are under codon selection for more efficient translation by the host apparatus. Interestingly, although Patience conceivably could have responded by acquisition of a tRNA repertoire to facilitate phage gene expression, this has not occurred; the only phage-carried tRNA is tRNA-Gln (UUG), and CAA is not a rare codon in the Patience genome (see Fig. S3 in the supplemental material).