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.

Mycobacteriophages such as Twister (65% GC) and KayaCho (70% GC), with nucleotide compositions similar to that of M. smegmatis, have similar synonymous codon distributions (see Fig. S3 and S4 in the supplemental material). In contrast, Patience codon usage patterns are distinctly different, with notably different distributions of codons with respect to their third-position content relative to M. smegmatis ( Fig. 6A ; see also Fig. S3 and S4 ). There are a total of nine switches to a different most commonly used synonymous codon from M. smegmatis, seven of which are NNU codons that are rarely used in the host (five with normalized Fig. S3] ). In total, NNU codons (except CGU, for which there is a cognate host tRNA) represent over 25% of all Patience codons; in contrast, these are only 5% of M. smegmatis codons. This represents an extreme end of a trend between the usage of NNU codons and the overall GC content of the phage, where usage of NNU increases as percent GC decreases (Fig. S5 ).