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.

Of the total of 81 Patience proteins identified in infected cells, only one-gp47-was not identified in the late-infected (2.5-hpostinfection) sample. Patience gp47 was identified in the earlyinfected sample and is presumably not expressed late in infection but also is turned over rapidly ( Fig. 5 ; see also Table S1 in the supplemental material). Many of the virion proteins (genes 1 to 40) are expressed at higher levels (using peptide spectral count as a surrogate for expression) in the late-infected sample, although there is also substantial expression of many of these at the early time. Of the 29 annotated proteins not identified in any of the samples, 11 are predicted to be smaller than 10 kDa and may have escaped detection if they are not expressed at high levels. Twelve are predicted to be membrane or wall associated and are likely excluded from the soluble fractions used for analysis. Peptide abundance in infected cells is expected to generally correlate with expression, although other factors such as protein size and trypsin cleavage efficiencies influence peptide detection.