Chapter 5 : Molecular Genetics of Mycobacteriophages

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Mycobacteriophages are viruses that infect mycobacterial hosts including and . The first mycobacteriophages were isolated in the late 1940s using as a host ( ), followed by isolation of phages that infect ( ). The application of phages with distinct host preferences to typing clinical mycobacterial isolates was recognized, and numerous studies on mycobacteriophage typing were published over the subsequent 30 years ( ). In the 1950s a variety of further investigations focusing on the biology of these phages and their potential applications were initiated including studies on generalized transduction ( ), viral morphology ( ), lysogeny ( ), transfection of phage DNA ( ), and other biochemical features ( ). These early contributions provided a critical foundation for the further characterization and application of mycobacteriophages to tuberculosis research that emerged from them.

Citation: Hatfull G. 2014. Molecular Genetics of Mycobacteriophages, p 81-119. In Hatfull G, Jacobs W (ed), Molecular Genetics of Mycobacteria, Second Edition. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MGM2-0032-2013
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Figure 1

Mycobacteriophage morphologies. Three examples of virion morphologies are illustrated. Phaedrus and Babsiella exhibit siphoviral morphologies with long flexible tails; Phaedrus has an isometric head, whereas the Babsiella head is prolate. Cali is an example of myoviral morphology. Scale bar is 100 nm.

Citation: Hatfull G. 2014. Molecular Genetics of Mycobacteriophages, p 81-119. In Hatfull G, Jacobs W (ed), Molecular Genetics of Mycobacteria, Second Edition. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MGM2-0032-2013
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Figure 2

Dotplot comparison of 285 mycobacteriophage genomes. A concatenated file of 285 mycobacteriophage nucleotide sequences was compared against itself using the Gepard program ( ) to generate the dotplot. The order of the genomes was arranged such that genomically related phages were adjacent to each other in this file, and the clusters of related phages (Clusters A, B, C, etc.) are shown above the plot. Five of the genomes are singletons with no closely related phages and are denoted collectively as Sin.

Citation: Hatfull G. 2014. Molecular Genetics of Mycobacteriophages, p 81-119. In Hatfull G, Jacobs W (ed), Molecular Genetics of Mycobacteria, Second Edition. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MGM2-0032-2013
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Figure 3

Comparison of mycobacteriophage Che9d and Jabbawokkie genome maps. Mycobacteriophages Che9d and Jabbawokkie are grouped into Subcluster F2, and their genome maps are shown as represented by the Phamerator program ( ). Each genome is shown with markers, and the shading between the genomes reflects nucleotide sequence similarity determined by BLASTN, spectrum-colored with the greatest similarity in purple and the least in red. Protein-coding genes are shown as colored boxes above or below the genomes, reflecting rightward or leftward transcription, respectively. Each gene is assigned a phamily (Pham) designation based on amino acid sequence similarity (see text), as shown above or below each box, with the number of phamily members shown in parentheses; genes shown as white boxes are orphams and have no other phamily members. Putative gene functions are indicated.

Citation: Hatfull G. 2014. Molecular Genetics of Mycobacteriophages, p 81-119. In Hatfull G, Jacobs W (ed), Molecular Genetics of Mycobacteria, Second Edition. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MGM2-0032-2013
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Figure 4

Functional genomics of mycobacteriophage Giles. A map of the mycobacteriophage Giles was generated using Phamerator and annotated as described for Fig. 3. Boxes below the genome indicate whether the gene is nonessential for lytic growth (yellow), likely essential (blue), or essential (green). Arrows indicate genes expressed in lysogeny (red) or early (green) or late (purple) lytic growth, with line thickness reflecting transcription strength. Reproduced with permission from Dedrick et al. ( ).

Citation: Hatfull G. 2014. Molecular Genetics of Mycobacteriophages, p 81-119. In Hatfull G, Jacobs W (ed), Molecular Genetics of Mycobacteria, Second Edition. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MGM2-0032-2013
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Figure 5

Genome map of mycobacteriophage Alma. The genome map of mycobacteriophage Alma was generated using Phamerator and is illustrated as described for Fig. 3 . Alma is a Subcluster A6 phage and shares the features of other Cluster A phages in having multiple binding sites for its repressor protein (gp75). These stoperator sites are indicated by vertical arrows, and the orientation of the asymmetric sites relative to genome orientation are shown as (-) or (+). Stoperators were identified as sequences corresponding to the consensus sequence 5′-GATGAGTGTCAAG with no more than a single mismatch. Note that the stoperator consensus sequences can differ for different Subcluster A phages ( ).

Citation: Hatfull G. 2014. Molecular Genetics of Mycobacteriophages, p 81-119. In Hatfull G, Jacobs W (ed), Molecular Genetics of Mycobacteria, Second Edition. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MGM2-0032-2013
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Figure 6

A model for mycobacteriophage diversity. The large number of different types of mycobacteriophages isolated on mc155 can be explained by a model in which phages can readily infect new bacterial hosts—either by a switch or an expansion of host range—using a highly diverse bacterial population that includes many closely related strains. As such, phages with distinctly different genome sequences and GC% contents infecting distantly related bacterial hosts, such as those to the left (red) or right (blue) extremes of a spectrum of hosts, can migrate across a microbial landscape through multiple steps. Each host switch occurs at a relatively high frequency (∼1 in 10 particles, or an average of about one every 10 bursts of lytic growth) and much faster than either amelioration of phage GC% to its new host or genetic recombination. Two phages (such as those shown in red and blue) can thus “arrive” at a common host ( mc155) but be of distinctly different types (clusters, subclusters, and singletons). Reproduced with permission from Jacobs-Sera et al. ( ).

Citation: Hatfull G. 2014. Molecular Genetics of Mycobacteriophages, p 81-119. In Hatfull G, Jacobs W (ed), Molecular Genetics of Mycobacteria, Second Edition. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MGM2-0032-2013
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