大肠埃希菌CRISPRs间隔序列的来源研究

A study on the source of spacers in the clustered regularly interspaced short palindromic repeats in the genome of Escherichia coli

目的研究大肠埃希菌全基因组中规律成簇的间隔短回文重复序列(CRISPRs)的间隔序列分布及来源规律。方法通过BLAST、CRISPRs finder、ClustalX和CRISPRTarget分析CRISPR/Cas、间隔序列及其来源。结果 203株大肠埃希菌中74.4%含有I-E CRISPR/Cas,9.4%含有I-F CRISPR/Cas,17.2%存在CRISPR3-4;CRISPR1,CRISPR2,CRISPR3和CRISPR4的间隔序列数目范围分别为1-25、1-27、4-7和2-22;其独特间隔序列数目分别为339、346、57和66。CRISPRTarget分析I-E和I-F CRISPR/Cas的间隔序列分别匹配816条质粒和293条噬菌体,2 428条质粒和139条噬菌体,差异有统计学意义(χ~2=319.30,P<0.01)。结论大肠埃希菌中CRISPR/Cas分布广泛,I-E和I-F CRISPR/Cas可能发挥不同的免疫功能。

Objective To investigate the distribution and source of spacers in the clustered regularly interspaced short palindromic repeats(CRISPRs) from whole genome sequencing of Escherichia coli. Methods BLAST, CRISPRs finder, Clustal X, and CRISPRTarget were used to analyze CRISPR/Cas systems, spacers, and their sources, respectively. A chi-square test was used to compare and analyze the distribution of the sources of the spacers. Results Results indicated that 74.4% of 203 strains contained the I-E CRISPR/Cas system while 9.4% contained the I-F CRISPR/Cas system;only 17.2% had the CRISPR3/4 array. In CRISPR1, the number of spacers ranged from 1-25. In CRISPR2, the number of spacers ranged from 1-27. In CRISPR3, the number of spacers ranged from 4-17. In CRISPR4, the number of spacers ranged from 2-22. According to sequencing using Clustal X, the spacers were classified into 346, 341, 57, and 66 types of unique spacers in each CRISPR locus. Results indicated that I-E CRISPR/Cas spacers matched sequences found in 816 plasmids and 293 phages and that I-F CRISPR/Cas spacers matched sequences found in 2,428 plasmids and 139 phages. The distributions of the I-E and I-F CRISPR spacer matches differed significantly(χ~2=319.30, P<0.01). Conclusion This study found that CRISPR/Cas systems are widely distributed in E. coli and that I-E and I-F CRISPR/Cas systems may have different immune functions.