Expanding the Diversity of Mycobacteriophages: Insights into Genome Architecture and Evolution

Abstract

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists.

Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere

“…Similar cassette sequences were also found for other T4-like viruses, suggesting that homologous recombination may substantially contribute to the evolution of (these) viral genomes (7). In summary, the genomes of tailed bacterial viruses evolve by a combination of genetic drift, extensive illegitimate and homologous recombination, genomic segment duplications and inversions, as well as the acquisition of diverse mobile elements, such as inteins, transposons, and mobile homing endonuclease genes (110,207).…”

“…These viruses are revealed as important players in carbon and energy cycling in the oceans and other natural environments and as major agents in the ecology and evolution of their cellular hosts (34,59,235). (iv) The isolation and characterization of new viruses have accelerated (22,207,294). This has been especially important for the archaeal viruses, where the discovery of new viruses and of new virus types had lagged behind bacteriophage discovery (205,213).…”

Using undergraduate research to develop transferable skills for the modern workforce

“…If developed and implemented effectively, an ALURE can provide the benefits of one-on-one research internships through normal coursework activities for hundreds of students, many of who would otherwise not engage in undergraduate research 27 . The real-world nature of research is a key motivator for student engagement in ALUREs, and in many cases their learning outcomes have directly contributed to research publications 13,28,29 .…”

The Use of Phage for Detection, Antibiotic Sensitivity Testing and Enumeration

“…The collection of Mycobacteriophage is continually being expanded due to an education programme developed by researchers at the University of Pittsburgh, supported by the Howard Hughes Medical Institute Science Education Alliance. This has recently resulted in the publication of a multi-author paper describing the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations by freshmen attending Universities across within the United States (Pope et al, 2011).…”

“…The comparative genomic analysis of mycobacteriophage reveals that they have relatively large genomes (average length approx. 70 kbp), contain large numbers of previously unidentified genes, and are highly diverse at both the nucleotide and amino acid sequence levels (Pedulla et al, 2003;Hatfull et al, 2010;Pope et al, 2011). Once inside the host cell the phage take over the host cell biosynthetic machinery and use this to replicate themselves, usually producing hundreds of progeny phage per infected cell (Figure 2).…”