The complete genome sequence of Clostridium difficile phage ?C2 and comparisons to ?CD119 and inducible prophages of CD630

摘要

The complete genomic sequence of a previously characterized temperate phage of Clostridium difficile, ?C2, 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 ?CD119 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 ?C2 to ?CD119 and the CD630 prophage sequences showed relatedness between ?C2 and the prophages, but less so to ?CD119. ?C2 integrated into a gene encoding a putative transcriptional regulator of the gntR family. ?C2, ?CD119 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 ?C2, ?CD119 and CD630 prophages were dissimilar. ?C2-related sequences were found in 84?% of 37 clinical C. difficile isolates and typed reference strains.