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 genome organization. Genome annotation of Patience indicates that all open reading frames and one tRNA gene are transcribed in the same direction ( Fig. 5 ; Table 1 ). The overall coding capacity is 94.9%, and there are no intergenic spaces greater than 250 bp. The recognizable virion structure and assembly functions lie within the gene 4 to 39 region, and the siphoviral syntenic arrangement of terminase, portal, protease, capsid, headtail connector proteins, major tail subunit, tail assembly chaperones, tape measure, and minor tail protein genes is observed, spanning 32 kbp of the genome (14) . This is atypically long not only because of the long tape measure gene corresponding to the long phage tail but because of a dozen genes of mostly unknown function located between the terminase large subunit (gene 6) and portal (gene 8) genes, between the portal (gene 8) and protease (gene 19) genes, and between the MuF-like gene (gene 20) and the putative scaffolding gene (gene 22) (Fig. 5) ; most of these are orphams (i.e., they do not have a close mycobacteriophage rela-tive), with the exceptions of genes 10 and 18 (Fig. 5 ). Gene 7 encodes a putative Endo VII protein and has weak similarity (Ͻ30% identity) to genes in phages Konstantine and Predator Table S1 in the supplemental material.