Genome Sequences of Mycobacteriophages Kerberos, Pomar16, and StarStuff

A Review on Mycobacteriophages: From Classification to Applications

Mycobacterial infections are a group of life-threatening conditions triggered by fast- or slow-growing mycobacteria. Some mycobacteria, such as Mycobacterium tuberculosis, promote the deaths of millions of lives throughout the world annually. The control of mycobacterial infections is influenced by the challenges faced in the diagnosis of these bacteria and the capability of these pathogens to develop resistance against common antibiotics. Detection of mycobacterial infections is always demanding due to the intracellular nature of these pathogens that, along with the lipid-enriched structure of the cell wall, complicates the access to the internal contents of mycobacterial cells. Moreover, recent studies depicted that more than 20% of M. tuberculosis (Mtb) infections are multi-drug resistant (MDR), and only 50% of positive MDR-Mtb cases are responsive to standard treatments. Similarly, the susceptibility of nontuberculosis mycobacteria (NTM) to first-line tuberculosis antibiotics has also declined in recent years. Exploiting mycobacteriophages as viruses that infect mycobacteria has significantly accelerated the diagnosis and treatment of mycobacterial infections. This is because mycobacteriophages, regardless of their cycle type (temperate/lytic), can tackle barriers in the mycobacterial cell wall and make the infected bacteria replicate phage DNA along with their DNA. Although the infectivity of the majority of discovered mycobacteriophages has been evaluated in non-pathogenic M. smegmatis, more research is still ongoing to find mycobacteriophages specific to pathogenic mycobacteria, such as phage DS6A, which has been shown to be able to infect members of the M. tuberculosis complex. Accordingly, this review aimed to introduce some potential mycobacteriophages in the research, specifically those that are infective to the three troublesome mycobacteria, M. tuberculosis, M. avium subsp. paratuberculosis (MAP), and M. abscessus, highlighting their theranostic applications in medicine.

Mycobacteriophage Fruitloop gp52 inactivates Wag31 (DivIVA) to prevent heterotypic superinfection

Bacteriophages engage in complex dynamic interactions with their bacterial hosts and with each other. Bacteria have numerous mechanisms to resist phage infection, and phages must co-evolve by overcoming bacterial resistance or by choosing an alternative host. Phages also compete with each other, both during lysogeny by prophage-mediated defense against viral attack and by superinfection exclusion during lytic replication. Phages are enormously diverse genetically and are replete with small genes of unknown function, many of which are not required for lytic growth, but which may modulate these bacteria-phage and phage-phage dynamics. Using cellular toxicity of phage gene overexpression as an assay, we identified the 93-residue protein gp52 encoded by Cluster F mycobacteriophage Fruitloop. The toxicity of Fruitloop gp52 overexpression results from interaction with and inactivation of Wag31 (DivIVA), an essential Mycobacterium smegmatis protein organizing cell wall biosynthesis at the growing cellular poles. Fruitloop gene 52 is expressed early in lytic growth and is not required for normal Fruitloop lytic replication but interferes with Subcluster B2 phages such as Hedgerow and Rosebush. We conclude that Hedgerow and Rosebush are Wag31-dependent phages and that Fruitloop gp52 confers heterotypic superinfection exclusion by inactivating Wag31.

Expression and evolutionary patterns of mycobacteriophage D29 and its temperate close relatives

Background

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. 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.

Results

Here 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 P_left early lytic promoter, and which are toxic to M. smegmatis.

Conclusions

Comparative 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.

Electronic supplementary material

The online version of this article (10.1186/s12866-017-1131-2) contains supplementary material, which is available to authorized users.