Abstract
Transposable phages, also called saltoviruses, of which the Escherichia coli phage Mu is the reference, are temperate phages that multiply their genome through replicative transposition at multiple sites in their host chromosome. The viral genome is packaged together with host DNA at both ends. In the present work, genome sequencing of three Pseudomonas aeruginosa transposable phages, HW12, 2P1, and Ab30, incidentally gave us access to the location of thousands of replicative integration sites and revealed the existence of a variable number of hotspots. Taking advantage of deep sequencing, we then designed an experiment to study 13,000,000 transposon integration sites of bacteriophage Ab30. The investigation revealed the presence of 42 transposition hotspots adjacent to bacterial interspersed mosaic elements (BIME) accounting for 5% of all transposition sites. The rest of the sites appeared widely distributed with the exception of coldspots associated with low G-C content segments, including the putative O-antigen biosynthesis cluster. Surprisingly, 0.4% of the transposition events occurred in a copy of the phage genome itself, indicating that the previously described immunity against such events is slightly leaky. This observation allowed drawing an image of the phage chromosome supercoiling into four loops.
Highlights
Transposable phages, which include the Escherichia coli Mu and similar Mu-like phages, are temperate phages that can persist in their host as a prophage [1]
The Different Transposition Site Distributions Observed in the Three Phages
All three phages belong to the D3112 group, Ab30 clustered in the DMS3 subgroup, 2P1 in the D3112 subgroup, whereas HW12 was more distantly related
Summary
Transposable phages, which include the Escherichia coli Mu and similar Mu-like phages, are temperate phages that can persist in their host as a prophage [1]. The phage DNA is injected together with the MuN protein present in the virion, which binds to the ends of the viral genome and converts it into a noncovalently closed circle prior to integration into the host genome. The phage genome is multiplied by replicative transposition at 50–200 sites per bacterial genome with no specificity for a particular insertion site, and packaged together with host DNA flanking the phage genome insertion site [2]. 50–150 base-pairs of DNA fragments of the E. coli host genome on the left side from which packaging is initiated [3] and a few hundred base-pairs up to 2–3 kb on the right side resulting from full-head packaging [4]. Two phage-coded proteins, MuA and MuB, are essential for Mu transposition
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