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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
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摘要 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.
作者 梁文娟 崔聪聪 段广才 刘慧莹 徐亚珂 郗园林 杨海燕 陈帅印 LIANG Wen-juan;CUI Cong-cong;DUAN Guang-cai;LIU Hui-ying;XU Ya-ke;XI Yuan-lin;YANG Hai-yan;CHEN Shuai-yin(Department of Epidemiology and Statistics,School of Public Health,Xinxiang Medical University,Xinxiang,China 453003;Department of Epidemiology,College of Public Health,Zhengzhou University,Zhengzhou,China 450001;Henan Innovation Center of Molecular Diagnosis and Laboratory Medicine,Xinxiang Medical University,Xinxiang,China 453003)
出处 《中国病原生物学杂志》 CSCD 北大核心 2019年第2期137-140,共4页 Journal of Pathogen Biology
基金 国家重大科技专项(No.2013ZX10004607) 新乡医学院分子诊断与医学检验技术河南省协同创新中心项目(No.XTCX-2015-PY4) 新乡医学院博士启动课题项目(No.XYBSKYZZ201805).
关键词 规律成簇的间隔短回文重复序列 间隔序列 噬菌体 质粒 大肠埃希菌 CRISPR spacer phage plasmid Escherichia coli
作者简介 通讯作者:段广才,E-mail:gcduan@zzu.edu.cn;梁文娟(1983-),女,河南辉县人,博士,讲师。研究方向:分子流行病学。E-mail:wenwen3_1@126.com.
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