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.

Here, we describe mycobacteriophage Patience, a newly isolated phage of M. smegmatis mc 2 155 that is a singleton with no close relatives and has a GC content of 50.3%, representing the extreme low end of the percent GC spectrum for mycobacteriophages. Of the predicted 109 Patience protein-coding genes, 61% are "orphams" with no close mycobacteriophage relatives in the Phamerator_285 database, and most of the 48 genes with homologues in other mycobacteriophages are most closely related to those in clusters H, R, and D, which also have below-average GC contents. However, Patience has a distinctly different codon usage profile from both its host and other mycobacteriophages and an abundance of codons that are rarely used in the host. Proteomic analysis using mass spectrometry provides evidence for expression of at least 83 Patience proteins, two of which are from cryptic open reading frames (ORFs) embedded within annotated genes. We propose that Patience is a relatively recent visitor to the Mycobacterium neighborhood, having evolved primarily in lower-GC hosts within the Actinomycetales, and is in the process of adapting to growth in its new high-GC genetic environment.