Phylogenetic relationship of prophages is affected by CRISPR selection in Group A Streptococcus

Shunsuke Yamada; Masaki Shibasaki; Kazunori Murase; Takayasu Watanabe; Chihiro Aikawa; Takashi Nozawa; Ichiro Nakagawa

doi:10.1186/s12866-019-1393-y

Phylogenetic relationship of prophages is affected by CRISPR selection in Group A Streptococcus

BMC Microbiol. 2019 Jan 28;19(1):24. doi: 10.1186/s12866-019-1393-y.

Authors

Shunsuke Yamada¹, Masaki Shibasaki², Kazunori Murase³, Takayasu Watanabe⁴, Chihiro Aikawa¹, Takashi Nozawa¹, Ichiro Nakagawa⁵

Affiliations

¹ Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan.
² Department of Oral Implantology and Regenerative Dental Medicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, 113-8510, Japan.
³ Department of Infectious Diseases, Faculty of Medicine, Miyazaki University, Miyazaki, 889-1692, Japan.
⁴ Department of Chemistry, School of Dentistry, Nihon University, Tokyo, 101-8310, Japan.
⁵ Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan. nakagawa.ichiro.7w@kyoto-u.ac.jp.

Abstract

Background: Group A Streptococcus (GAS) is a major human pathogen, which is associated with a wide spectrum of invasive diseases, such as pharyngitis, scarlet fever, rheumatic fever, and streptococcal toxic shock syndrome (STSS). It is hypothesized that differences in GAS pathogenicity are related to the acquisition of diverse bacteriophages (phages). Nevertheless, the GAS genome also harbors clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (cas) genes, which play an important role in eliminating foreign DNA, including those of phages. However, the structure of prophages in GAS strains is mosaic, and the phylogenetic relationship between prophages and CRISPR is not clear. In this study, we analyzed CRISPR and prophage structure using 118 complete genome sequences of GAS strains to elucidate the relationship between two genomic elements. Additionally, phylogenetic and M-type analyses were performed.

Results: Of the 118 GAS strains, 80 harbored type I-C and/or II-A CRISPR/cas loci. A total of 553 spacer sequences were identified from CRISPR/cas loci and sorted into 229 patterns. We identified and classified 373 prophages into 14 groups. Some prophage groups shared a common integration site, and were related to M-type. We further investigated the correlation between spacer sequences and prophages. Of the 229 spacer sequence patterns, 203 were similar to that of other GAS prophages. No spacer showed similarity with that of a specific prophage group with mutL integration site. Moreover, the average number of prophages in strains with type II-A CRISPR was significantly less than that in type I-C CRISPR and non-CRISPR strains. However, there was no statistical difference between the average number of prophages in type I-C strains and that in non-CRISPR strains.

Conclusions: Our results indicated that type II-A CRISPR may play an important role in eliminating phages and that the prophage integration site may be an important criterion for the acceptance of foreign DNA by GAS. M type, spacer sequence, and prophage group data were correlated with the phylogenetic relationships of GAS. Therefore, we hypothesize that genetic characteristics and/or phylogenetic relationships of GAS may be estimated by analyzing its spacer sequences.

Keywords: CRISPR/cas; Group a Streptococcus; Prophage.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Clustered Regularly Interspaced Short Palindromic Repeats*
Evolution, Molecular
Genome, Bacterial
Phylogeny*
Prophages / classification*
Streptococcus pyogenes / genetics*
Streptococcus pyogenes / virology
Virus Integration