Mycobacteriophages: Windows into Tuberculosis

What Are Mycobacteriophages?Mycobacteriophages are viruses that infect mycobacterial hosts, such as Mycobacterium tuberculosis and Mycobacterium smegmatis [1].Because the discovery and genomic characterization of mycobacteriophages has been the focus of integrated research and education programs, including the Phage Hunters Integrating Research and Education (PHIRE) and the Howard Hughes Medical Institute Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (HHMI SEA-PHAGES), thousands of phages have been isolated using a single host strain, M. smegmatis mc 2 155, over 500 of which have been completely sequenced [2][3][4][5].These are mostly from environmental samples, but mycobacteriophages have also been isolated from stool samples of tuberculosis patients [6], although these have yet to be genomically analyzed.Clearly, these mycobacteriophages represent only a tiny piece of the overall phage population, which is predicted to include 10 31 particles, making them the majority of all life-forms in the biosphere [7].Mycobacteriophages display a remarkable genetic diversity (Figure 1).About 30 distinct types (called clusters, or singletons if they have no relatives) that share little or no nucleotide sequence similarity have been identified.Many of the clusters span sufficient diversity that the genomes warrant division into subclusters (Figure 1).However, the genomes are characteristically mosaic in their architecture [8], which is readily evident from the shared genes revealed by amino acid sequence comparisons [9].There is also considerable range in overall guanine plus cytosine content (GC%), from 50.3% to 70%, with an average of 64% (M.smegmatis is 67.3%).Thus, phage GC% does not necessarily match that of its host, and the consequent mismatch of codon usage profiles does not appear to be detrimental.Because new mycobacteriophages lacking extensive DNA similarity with the extant collection are still being discovered, and as there are at least seven singletons for which no relatives have been isolated, we clearly have yet to saturate the diversity of this particular population.The pace of discovery is rapid, so the profile of diversity is constantly changing.The collection of .50,000genes can be sorted into .3,900groups (phamilies) according to their shared amino acid sequences.Most of these phamilies (,75%) do not have homologues outside of the mycobacteriophages and are of unknown function.Extrapolation to the broader population suggests that phages have the largest repertoire of unexplored sequences in nature.Genetic studies with mycobacteriophage Giles show that 45% of the genes are nonessential for lytic growth, raising questions as to how and why they were acquired [10].