Abstract
BackgroundMycobacteriophages are viruses that infect Mycobacterium hosts. A large collection of phages known to infect the same bacterial host strain – Mycobacterium smegmatis mc2155 – exhibit substantial diversity and characteristically mosaic architectures. The well-studied lytic mycobacteriophage D29 appears to be a deletion derivative of a putative temperate parent, although its parent has yet to be identified.ResultsHere we describe three newly-isolated temperate phages – Kerberos, Pomar16 and StarStuff – that are related to D29, and are predicted to be very close relatives of its putative temperate parent, revealing the repressor and additional genes that are lost in D29. Transcriptional profiles show the patterns of both lysogenic and lytic gene expression and identify highly-expressed, abundant, stable, small non-coding transcripts made from the Pleft early lytic promoter, and which are toxic to M. smegmatis.ConclusionsComparative genomics of phages D29, Kerberos, Pomar16 and StarStuff provide insights into bacteriophage evolution, and comparative transcriptomics identifies the pattern of lysogenic and lytic expression with unusual features including highly expressed, small, non-coding RNAs.
Highlights
Mycobacteriophages are viruses that infect Mycobacterium hosts
Relationships of phages StarStuff, Pomar16, and Kerberos to phage D29 Subcluster A2 includes over 70 individual isolates, and they are sufficiently similar by average nucleotide identity comparisons to be grouped together, they encompass considerable genomic variation [15]
There are 25 small insertions and deletions, and StarStuff, L5, and D29 are homoimmune StarStuff makes turbid plaques that are somewhat smaller than D29 on M. smegmatis (Fig. 2a), and as expected, StarStuff lysogens confer superinfection immunity to itself, D29, and L5, preventing infection at even the highest phage titer (Fig. 2b)
Summary
Mycobacteriophages are viruses that infect Mycobacterium hosts. A large collection of phages known to infect the same bacterial host strain – Mycobacterium smegmatis mc2155 – exhibit substantial diversity and characteristically mosaic architectures. Mycobacteriophages – viruses infecting mycobacterial hosts – have been studied since their first isolation in the 1940’s and represent one of the largest genomically characterized group of phages [1]. Mycobacteriophage D29 was isolated from a soil sample in California, and shown to infect both saprophytic (e.g. Mycobacterium smegmatis) and pathogenic (e.g. Mycobacterium tuberculosis) strains of mycobacteria [2]. The sequencing of over 1300 mycobacteriophage genomes [14, 15] shows them to be highly diverse, forming at least 30 distinct genomic types, currently represented as Clusters A-Z, and six singleton phages (those with no close relatives). Phages L5 and D29 are both members of Subcluster A2
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