创伤弧菌TF3全基因组包含的CRISPR-Cas系统及MGIVvuTF3基因岛分析

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

摘要:

[目的]分析创伤弧菌（Vibrio vulnificus）全基因组框架序列，挖掘感兴趣的遗传位点，探索其是否具有CRISPR系统及其特征。[方法]在病虾体内分离获得了一株创伤弧菌TF3，通过Illumina Miseq测序得到基因组框架序列。经注释分析发现其基因组中存在一个CRISPR-Cas系统，命名为CRISPR-Cas_TF3，进一步分析发现CRISPR-Cas_TF3位于一个基因岛上，将该基因岛命名为MGIVvuTF3。对CRISPR-Cas_TF3及MGIVvuTF3的特征和来源进行了分析。[结果]CRISPR-Cas_TF3属于与大肠杆菌类似的Ι-E型CRISPR-Cas系统，CRISPR-Cas_TF3包括8个cas基因，其排列为cas3-cas8e-cse2-cas6-cas7-cas5-cas1-cas2；具有50个重复序列，每二个重复序列间为一个Spacer序列。MGIVvuTF3具有attL和attR序列，含有位点特异性整合、剪切、转移相关的基因。MGIVvuTF3与霍乱弧菌O395基因组中的一个基因岛MGIVch0395具较高相似性，二者最显著的差别在于Spacer序列完全不同，以及各有几个非保守的预测基因。[结论]MGIVvuTF3及CRISPR-Cas_TF3极有可能通过基因水平转移获得，并且CRISPR-Cas_TF3系统可以借助MGIVvuTF3实现水平转移。

关键词:CRISPR;cas基因;基因岛;创伤弧菌

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