CRISPR Distribution within the Escherichia coli Species Is Not Suggestive of Immunity-Associated Diversifying Selection

• DOI: 10.1128/jb.01307-10
• Publication Date: 2011-03-19T03:19:44Z
• Authors: Marie Touchon; Sophie Charpentier; Olivier Clermont; Eduardo P. C. Rocha; Erick Denamur; Catherine Branger
• Keywords: DNA, Bacterial; 570; 0303 health sciences; [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]; 000; Genotype; Molecular Sequence Data; Genetic Variation; Sequence Analysis, DNA; [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]; Bacterial Typing Techniques; 3. Good health; Evolution, Molecular; 03 medical and health sciences; Escherichia coli; Animals; Cluster Analysis; Humans; Selection, Genetic; Phylogeny; Multilocus Sequence Typing; Repetitive Sequences, Nucleic Acid

ABSTRACTIn order to get further insights into the role of the clustered, regularly interspaced, short palindromic repeats (CRISPRs) inEscherichia coli, we analyzed the CRISPR diversity in a collection of 290 strains, in the phylogenetic framework of the strains represented by multilocus sequence typing (MLST). The set included 263 naturalE. coliisolates exposed to various environments and isolated over a 20-year period from humans and animals, as well as 27 fully sequenced strains. Our analyses confirm that there are two largely independent pairs of CRISPR loci (CRISPR1 and -2 and CRISPR3 and -4), each associated with a different type ofcasgenes (Ecoli and Ypest, respectively), but that each pair of CRISPRs has similar dynamics. Strikingly, the major phylogenetic group B2 is almost devoid of CRISPRs. The majority of genomes analyzed lack Ypestcasgenes and contain CRISPR3 with spacers matching Ypestcasgenes. The analysis of relatedness between strains in terms of spacer repertoire and the MLST tree shows a pattern where closely related strains (MLST phylogenetic distance of <0.005 corresponding to at least hundreds of thousands of years) often exhibit identical CRISPRs while more distantly related strains (MLST distance of >0.01) exhibit completely different CRISPRs. This suggests rare but radical turnover of spacers in CRISPRs rather than CRISPR gradual change. We found no link between the presence, size, or content of CRISPRs and the lifestyle of the strains. Our data suggest that, within theE. colispecies, CRISPRs do not have the expected characteristics of a classical immune system.