Phage cluster relationships identified through single gene analysis

Abstract

BackgroundPhylogenetic comparison of bacteriophages requires whole genome approaches such as dotplot analysis, genome pairwise maps, and gene content analysis. Currently mycobacteriophages, a highly studied phage group, are categorized into related clusters based on the comparative analysis of whole genome sequences. With the recent explosion of phage isolation, a simple method for phage cluster prediction would facilitate analysis of crude or complex samples without whole genome isolation and sequencing. The hypothesis of this study was that mycobacteriophage-cluster prediction is possible using comparison of a single, ubiquitous, semi-conserved gene. Tape Measure Protein (TMP) was selected to test the hypothesis because it is typically the longest gene in mycobacteriophage genomes and because regions within the TMP gene are conserved.ResultsA single gene, TMP, identified the known Mycobacteriophage clusters and subclusters using a Gepard dotplot comparison or a phylogenetic tree constructed from global alignment and maximum likelihood comparisons. Gepard analysis of 247 mycobacteriophage TMP sequences appropriately recovered 98.8% of the subcluster assignments that were made by whole-genome comparison. Subcluster-specific primers within TMP allow for PCR determination of the mycobacteriophage subcluster from DNA samples. Using the single-gene comparison approach for siphovirus coliphages, phage groupings by TMP comparison reflected relationships observed in a whole genome dotplot comparison and confirm the potential utility of this approach to another widely studied group of phages.ConclusionsTMP sequence comparison and PCR results support the hypothesis that a single gene can be used for distinguishing phage cluster and subcluster assignments. TMP single-gene analysis can quickly and accurately aid in mycobacteriophage classification.

Understanding the enormous diversity of bacteriophages: The tailed phages that infect the bacterial family Enterobacteriaceae

“…The phages in our panel have a 96.4% chance of being assigned to the correct cluster by their MCP sequence. This is remarkably similar to the reported 97.6% correlation between Siphoviridae and Myoviridae mycobacteriophage TMP sequence and cluster (Smith et al , 2013). The correlation between subcluster membership and MCP type is also strong but not universal.…”

“…Recent studies have shown that the tail tape measure protein (TMP) type correlates well with clusters for Siphoviridae and Myoviridae phages that infect Mycobacteria smegmatis (Smith et al , 2013), but the short tails of the Podoviridae have no TMP. In fact, there is no known tail protein that is common to all types of tails and, as mentioned above, phage DNA replication/metabolism and lysis mechanisms are sufficiently diverse that homologous proteins are not universally utilized.…”

Mycobacteriophage-drived diversification of Mycobacterium abscessus

“…The TMP was selected because it is typically the longest gene in mycobacteriophage genomes and because regions within the TMP gene are conserved [37]. We could annotate 135 TMPs which clustered into thirteen groups and four singletons using orthoMCL.…”

Genome sequence of a cluster A13 mycobacteriophage detected in Mycobacterium phlei over a half century ago

“…ORF 6 and ORF 7 encoding the lysine A and holin proteins, respectively, may form a second, 'lysis module' involved in bacterial cell lysis. Smith et al [9] suggested that sequence comparison and phylogenetic analysis of the TMP may be useful for distinguishing mycobacteriophages belonging to various subclusters. In our analyses, the TMP of Phlei phage shared the greatest, but still very low, amino acid similarity (41 % identity), with a subcluster A2 mycobacterium phage (EagleEye, accession no.…”