Transposable phages and prophages (the proposed “Saltoviridae” family) have been detected in a large fraction of bacterial phyla. Eschericha coli phage Mu and Burkholderia cepacia BcepMu (or Pseudomonas aeruginosa phage B3) stand as the paradigms for two genetic organisations of the “Saltoviridae” genomes, with the immunity repressor vs. late positive regulator at the left end, and two vs. three transposition proteins (including one DDE recombinase). Transposition proteins of the two types are distant enough to belong to distinct protein famlilies (Uniprot, ACLAME etc.) and contain different pfam domains.
The first BcepMu/B3-like prophage in a proteobacterium was described in Pectobacterium atrosepticum (ECA41, Evans et al., 2010, FEMS Microbiol Lett 304, 195–202). More recently we identified a very similar prophage in the course of annotating the genomic sequence of a related plant pathogen, Dickeya dianthicola RNS04.9.
Starting with this prophage nucleotide sequence, we could identify many complete BcepMu/B3-like prophages in other enterobacteria. The vast majority appears to be functional since they are flanked by a 6 bp direct repeat, as reported by Evans et al. for ECA41 and contrary to Mu-like phages, which generate a 5 bp direct repeat.
Amazingly, BcepMu/B3-like prophages in E.coli carry an invertible region and its cognate invertase, as do Mu and its close relative D108, which as a result can switch host range (van de Putte et al. 1980, Nature. 286, 218-22.).
The B3-like prophages described here and the newly identified Mu-like (Cazares et al. BMC Genomics 2014, 15, 1146) phages and prophages in pseudomonads enlarge the “Saltoviridae” family and should allow for a more refined classification of these ubiquitous “re-arrangers” of host genomes.