title: CRISPR inhibition of prophage acquisition in Streptococcus pyogenes.
abstract: Streptococcus pyogenes, one of the major human pathogens, is a unique species since it has acquired diverse strain-specific virulence properties mainly through the acquisition of streptococcal prophages. In addition, S. pyogenes possesses clustered regularly interspaced short palindromic repeats (CRISPR)/Cas systems that can restrict horizontal gene transfer (HGT) including phage insertion. Therefore, it was of interest to examine the relationship between CRISPR and acquisition of prophages in S. pyogenes. Although two distinct CRISPR loci were found in S. pyogenes, some strains lacked CRISPR and these strains possess significantly more prophages than CRISPR harboring strains. We also found that the number of spacers of S. pyogenes CRISPR was less than for other streptococci. The demonstrated spacer contents, however, suggested that the CRISPR appear to limit phage insertions. In addition, we found a significant inverse correlation between the number of spacers and prophages in S. pyogenes. It was therefore suggested that S. pyogenes CRISPR have permitted phage insertion by lacking its own spacers. Interestingly, in two closely related S. pyogenes strains (SSI-1 and MGAS315), CRISPR activity appeared to be impaired following the insertion of phage genomes into the repeat sequences. Detailed analysis of this prophage insertion site suggested that MGAS315 is the ancestral strain of SSI-1. As a result of analysis of 35 additional streptococcal genomes, it was suggested that the influences of the CRISPR on the phage insertion vary among species even within the same genus. Our results suggested that limitations in CRISPR content could explain the characteristic acquisition of prophages and might contribute to strain-specific pathogenesis in S. pyogenes.
authors.affiliation: Section of Bacterial Pathogenesis, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.
authors.forename: Takashi
authors.initials: T
authors.lastname: Nozawa
authors.forename: Nayuta
authors.initials: N
authors.lastname: Furukawa
authors.forename: Chihiro
authors.initials: C
authors.lastname: Aikawa
authors.forename: Takayasu
authors.initials: T
authors.lastname: Watanabe
authors.forename: Bijaya
authors.initials: B
authors.lastname: Haobam
authors.forename: Ken
authors.initials: K
authors.lastname: Kurokawa
authors.forename: Fumito
authors.initials: F
authors.lastname: Maruyama
authors.forename: Ichiro
authors.initials: I
authors.lastname: Nakagawa
mesh_terms: D021901:DNA, Intergenic / Q000235:genetics; D056426:Genetic Loci / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics; D006801:Humans; D055029:Inverted Repeat Sequences / Q000235:genetics*; D010802:Phylogeny; D039002:Prophages / Q000502:physiology*; D011995:Recombination, Genetic / Q000235:genetics; D017384:Sequence Deletion / Q000235:genetics; D013297:Streptococcus pyogenes / Q000235:genetics* / Q000821:virology*; D016662:Virus Integration / Q000502:physiology
chemical_list: D021901:DNA, Intergenic