CRISPR-Cas systems are present predominantly on chromosome and its relationship with MEGs in Vibrio species.

Abstract

Bacteria have developed diverse strategies to counteract virus predation, one of which is the clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR associated (Cas) proteins immune defense system. In this study, the structure and function of the CRISPR-Cas system in 120 Vibrio strains were analyzed by bioinformatics methods, as well as the correlation between CRISPR and mobile genetic elements (MEGs). Only 61 Vibrio strains contained one or more CRISPR structures, and finally 102 CRISPRs were identified. The typical repeat size was 28bp, and the total length of CRISPRs is nearly 60bp, which was the most stable length of CRISPR in Vibrio strains. The types of CRISPR-Cas present in 61 strains were I-C, I-E, I-F, II-B, III-B, III-D and the rare type IV systems. Through principal component analysis, we found that Cas gene was most closely related to CRISPR. In addition, phages and plasmids were also highly correlated, showing negative correlation with CRISPR-Cas system. CRISPR-Cas predominantly present on chromosome within Vibrio while rarely in plasmids. Comparing the structural characteristics of plasmids containing CRISPR and without CRISPR, we found plasmid pMBL287 with CRISPR contained a bacteriophage f237, with more MGES, suggesting the diversity was greater. In addition, the same mobile genetic elements IS256 and ISL3 were found in the upstream and downstream of CRISPR. This study provides the prevalence, diversity and phylogenetic distribution of CRISPR-Cas in Vibrio, revealing which type of CRISPR-Cas system is predominant, and the factors affecting its function, as well as its relationship with mobile genetic elements.