The complete genome sequence of Clostridium difficile phage ϕC2 and comparisons to ϕCD119 and inducible prophages of CD630

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Abstract
The complete genomic sequence of a previously characterized temperate phage of Clostridium difficile, ϕC2, is reported. The genome is 56 538 bp and organized into 84 putative ORFs in six functional modules. The head and tail structural proteins showed similarities to that of C. difficile phage ϕCD119 and Streptococcus pneumoniae phage EJ-1, respectively. Homologues of structural and replication proteins were found in prophages 1 and 2 of the sequenced C. difficile CD630 genome. A putative holin appears unique to the C. difficile phages and was functional when expressed in Escherichia coli. Nucleotide sequence comparisons of ϕC2 to ϕCD119 and the CD630 prophage sequences showed relatedness between ϕC2 and the prophages, but less so to ϕCD119. ϕC2 integrated into a gene encoding a putative transcriptional regulator of the gntR family. ϕC2, ϕCD119 and CD630 prophage 1 genomes had a Cdu1-attP-integrase arrangement, suggesting that the pathogenicity locus (PaLoc) of C. difficile, flanked by cdu1, has phage origins. The attP sequences of ϕC2, ϕCD119 and CD630 prophages were dissimilar. ϕC2-related sequences were found in 84 % of 37 clinical C. difficile isolates and typed reference strains.