title: The complete genome sequence of Clostridium difficile phage phiC2 and comparisons to phiCD119 and inducible prophages of CD630.
abstract: 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.
authors.affiliation: National University of Singapore, Yong Loo Lin School of Medicine, Department of Microbiology, 5 Science Drive 2, #05-03, 117597, Singapore.
authors.forename: Shan
authors.initials: S
authors.lastname: Goh
authors.affiliation: National University of Singapore, Yong Loo Lin School of Medicine, Department of Microbiology, 5 Science Drive 2, #05-03, 117597, Singapore.
authors.forename: Peh Fern
authors.initials: PF
authors.lastname: Ong
authors.affiliation: National University of Singapore, Yong Loo Lin School of Medicine, Department of Microbiology, 5 Science Drive 2, #05-03, 117597, Singapore.
authors.forename: Keang Peng
authors.initials: KP
authors.lastname: Song
authors.affiliation: Division of Microbiology and Infectious Diseases, The Western Australian Centre for Pathology and Medical Research, Nedlands, WA 6009, Australia.|Microbiology and Immunology, School of Biomedical, Biomolecular and Chemical Sciences, The University of Western Australia, Queen Elizabeth II Medical Centre, Nedlands, WA 6009, Australia.
authors.forename: Thomas V
authors.initials: TV
authors.lastname: Riley
authors.affiliation: Microbiology and Immunology, School of Biomedical, Biomolecular and Chemical Sciences, The University of Western Australia, Queen Elizabeth II Medical Centre, Nedlands, WA 6009, Australia.
authors.forename: Barbara J
authors.initials: BJ
authors.lastname: Chang
mesh_terms: D000595:Amino Acid Sequence; D001287:Attachment Sites, Microbiological / Q000235:genetics; D001435:Bacteriophages / Q000235:genetics*; D001483:Base Sequence; D016360:Clostridioides difficile / Q000821:virology*; D004279:DNA, Viral / Q000737:chemistry* / Q000235:genetics; D016679:Genome, Viral; D046529:Microscopy, Electron, Transmission; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D039002:Prophages / Q000235:genetics; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D013296:Streptococcus pneumoniae / Q000821:virology; D015678:Viral Structural Proteins / Q000235:genetics; D014771:Virion / Q000648:ultrastructure; D014779:Virus Replication / Q000235:genetics
chemical_list: D004279:DNA, Viral; D015678:Viral Structural Proteins