Analysis of a CRISPR-Cas system and a genomic island, MGIVvuTF3, in complete genome of Vibrio vulnificus TF3

Abstract:

[Objective] In order to dig interesting genetic regions and explore whether CRISPR-Cas systems exist, the draft genome of Vibrio vulnificus TF3 was analyzed. [Methods] We isolated V. vulnificus strain TF3 from the diseased shrimp Litopenaeus vannamei, and then obtained its genome sequence by Illumina Miseq sequencing. The genomic annotation showed that there was a CRISPR-Cas system in V. vulnificus TF3, named CRISPR-Cas_TF3. After further analysis, we found that the CRISPR-Cas_TF3 located in a genomic island, named MGIVvuTF3. The characteristics and sources of CRISPR-Cas_TF3 and MGIVvuTF3 were analyzed using bioinformatic methods. [Results] We found the CRISPR-Cas_TF3 belonged to type I-E CRISPR-Cas system similar to that of Escherichia coli. The CRISPR-Cas_TF3 contained eight cas genes with the order, cas3-cas8e-cse2-cas6-cas7-cas5-cas1-cas2. CRISPR-Cas_TF3 had 50 repeats sequences separated by 49 spacer sequences. MGIVvuTF3 featured attL/attR sequences, and key genes participating in site-specific integration, excision, and transfer, and thus it manifested that MGIVvuTF3 represents a genomic island. MGIVvuTF3 had highly similarity to a genomic island, MGIVch0395, found in V. cholerae O395. However, the two genomic islands also had two distinct differences, namely, they had completely different spacer sequences and each of them had several particular predicted genes. [Conclusion] MGIVvuTF3 harboring CRISPR-Cas_TF3is most likely obtained through horizontal gene transfer, and therefore the CRISPR-Cas_TF3 system may transfer horizontally by means of MGIVvuTF3.

Key words:CRISPR;cas genes;genomic island;Vibrio vulnificus