Abstract

Mycobacteriophage Squid is a temperate phage that infects Mycobacterium smegmatis, a close relative of M. tuberculosis. Temperate phages can integrate their genome into the bacterial host genome and form lysogens. However, a definitive integrase-encoding gene was not identified during annotation of the Squid genome, suggesting that it does not integrate its genome with the host’s but rather maintains it as a plasmid-like structure. Analysis of Squid’s genome annotation showed that the protein product of gene 67 shared 97.5% homology with ParG, a plasmid partition protein required for partition of bacterial plasmids. Ongoing studies may reveal additional Par sequences and a plasmid-like structure within the host cell lysogen.

Squid has extensive homology with other sequenced cluster B1 phages. A possible “stoperator,” or repressor-binding sequence, was also identified in Squid. The 11 base pair sequence was found in 20 separate locations in Squid’s genome, 13 of which were in intergenic regions. When searched for in other B subclusters, this sequence was found in B4 phages, but not found in B2, B3, or B5 phages. If the putative stoperator sequence identified for Squid is a viable repressor-binding site, then immunity will only be shown between B1 and B4 phages. We are currently performing immunity assays on the Squid lysogen across the B subclusters to confirm or reject the B1 stoperator sequence proposed.