Exploring the Mycobacteriophage Metaproteome: Phage Genomics as an Educational Platform

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Abstract
Bacteriophages are the most abundant forms of life in the biosphere and carry genomes characterized by high genetic diversity and mosaic architectures. The complete sequences of 30 mycobacteriophage genomes show them collectively to encode 101 tRNAs, three tmRNAs, and 3,357 proteins belonging to 1,536 “phamilies” of related sequences, and a statistical analysis predicts that these represent approximately 50% of the total number of phamilies in the mycobacteriophage population. These phamilies contain 2.19 proteins on average; more than half (774) of them contain just a single protein sequence. Only six phamilies have representatives in more than half of the 30 genomes, and only three—encoding tape-measure proteins, lysins, and minor tail proteins—are present in all 30 phages, although these phamilies are themselves highly modular, such that no single amino acid sequence element is present in all 30 mycobacteriophage genomes. Of the 1,536 phamilies, only 230 (15%) have amino acid sequence similarity to previously reported proteins, reflecting the enormous genetic diversity of the entire phage population. The abundance and diversity of phages, the simplicity of phage isolation, and the relatively small size of phage genomes support bacteriophage isolation and comparative genomic analysis as a highly suitable platform for discovery-based education. Bacteriophages are viruses that infect bacterial hosts and are estimated to be the most numerous biological entities in the biosphere. Insights into the genetic diversity of the bacteriophage population and the evolutionary mechanisms that give rise to it can be obtained using comparative genomic analyses. The genomic analysis of 30 complete mycobacteriophages—viruses that infect mycobacterial hosts—reveals them to be genetically diverse and to contain many previously unidentified genes. The high diversity and relatively small genome sizes of these phages provide an ideal platform for introducing high school and undergraduate students to the research laboratory, isolating and naming novel viruses, and determining their genomic sequences. The thrill of discovering new viruses and previously unidentified genes, coupled with ownership of individual phage projects, provides strong motivations for students to engage in and pursue scientific research.