Networking clusters and sequence characteristics of clustered regularly interspaced short palindromic repeats (CRISPR) direct repeats and their evolutionary comparison with cas1 genes in lactic acid bacteria

Clustered regularly interspaced short palindromic repeats (CRISPR) widely spread in Archaea and bacteria are an acquired immunity system, which resisted on the infection of exogenous chromosome according to a mechanism similar to RNA interference. In this study, evolutionary origin and sequence feature of totally 211 CRISPRs in 192 of 588 lactic acid bacteria genomes covered 18 genera of 5 phyla were employed, and comparative analysis of direct repeats (DRs), cas1 (CRISPR-associated) genes and 16s rRNA were performed as well. In summary, 11 clusters of CRISPRs were identified based on DRs, and sequence similarity among genera even species were determined. In GC content investigation, complementary sequences and the symmetry in DRs of all clusters can opportunely construct the stem-loop secondary structure, moreover, the GC% level of spacers in one CRISPR locus was comparable, which suggested that foreign sequences with similar GC% were more likely to be inserted into the LAB genomes as a new spacer. cas1 coevolved with DRs as a whole phylogenetic cassette, while it was slightly more conservative. Besides, the distribution of cas1 and DRs was found very different with 16s rRNA in clusters, and it implied the possibility of horizontal gene transfer of LAB CRISPR loci.