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.

Isolation and genome sequencing of mycobacteriophage Patience. Mycobacteriophage Patience was isolated by direct plating of an environmental sample taken from near the Nelson Mandela School of Medicine at the University of KwaZulu-Natal (UKZN), Durban, South Africa, using M. smegmatis mc 2 155 as a host (3) . Isolation and purification of Patience were components of a 2-week workshop on mycobacterial genetics offered in July 2009; the genome was sequenced at the University of Pittsburgh and annotated in a second 2-week workshop at UKZN in July 2011. Patience forms normal-size hazy (~1-mm-diameter) plaques on M. smegmatis mc 2 155 at 37°C under standard conditions, although we have been unsuccessful in recovering stable lysogens. It can easily be propagated on solid media to titers greater than 10 10 PFU/ml. The genome is 70,506 bp long, circularly permuted, and presumably terminally redundant. For linear presentation, coordinate 1 is designated the beginning of an open reading frame upstream of the large terminase subunit consistent with the organization of the cluster H phages that contain homologues of the first open reading frame at their left ends (7) . The GenBank submission (JN412589) has been reported previously (3) . Genome annotation identified 109 putative open reading frames (ORFs) and one tRNA gene (Table 1) ; one additional ORF was annotated using mass spectrometry analysis (see below).