志贺菌中成簇的规律间隔短回文重复序列的特点及其关联性分析

doi:10.13481/j.1671-587x.20180604

吉林大学学报(医学版) ›› 2018, Vol. 44 ›› Issue (06): 1131-1137.doi: 10.13481/j.1671-587x.20180604

志贺菌中成簇的规律间隔短回文重复序列的特点及其关联性分析

王颖芳^1,2, 王鹏飞^2,3, 段广才², 郗园林², 张晓萌⁴, 詹煜慧⁴

1. 河南科技大学医学院公共卫生教研室, 河南洛阳 471023;
2. 郑州大学公共卫生学院流行病学教研室, 河南郑州 450001;
3. 河南科技大学医院, 河南洛阳 471023;
4. 河南科技大学医学院, 河南洛阳 471023

收稿日期:2018-02-09 出版日期:2018-11-28 发布日期:2018-11-28
通讯作者: 段广才,教授,博士研究生导师(Tel:0371-67781964,E-mail:gcduan@zzu.edu.cn) E-mail:gcduan@zzu.edu.cn
作者简介:王颖芳(1977-),女,河南省开封市人,讲师,医学博士,主要从事分子流行病学方面的研究。
基金资助:
国家科技部重大专项资助课题（2013ZX10004607，2018ZX10301407）

Characteristics of clustered regularly interspaced short palindromic repeats in Shigella and their correlation analysis

WANG Yingfang^1,2, WANG Pengfei^2,3, DUAN Guangcai², XI Yuanlin², ZHANG Xiaomeng⁴, ZHAN Yuhui⁴

1. Department of Public Health, College of Medical Sciences, Henan University of Science and Technology, Luoyang 471023, China;
2. Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China;
3. Hospitalof Henan University of Science and Technology, Luoyang 471023, China;
4. College of Medical Sciences, Henan University of Science and Technology, Luoyang 471023, China

Received:2018-02-09 Online:2018-11-28 Published:2018-11-28

摘要/Abstract

摘要： 目的：利用数据库和临床分离的志贺菌菌株分析志贺菌中成簇的规律间隔短回文重复序列（CRISPR）的特点，探讨CRISPR-Q1的特性及CRISPR间的关联性。方法：根据志贺菌基因组数据库利用引物序列和PCR扩增获得志贺菌的CRISPR序列信息，采用多序列比对等方法获得每个菌株中CRISPR的分布、间隔序列数及序列特点；利用BLAST分析CRISPR-Q1中重复序列和间隔序列，检测重复序列和间隔序列在菌株中的分布特点以及CRISPR-Q1在菌株中的位置及特征；分析数据库和实验室中志贺菌CRISPR-Q1中间隔序列数与CRISPR1或CRISPR2的关系。结果：在数据库107株志贺菌中，106株志贺菌含有CRISPR1或CRISPR2，8株志贺菌的CRISPR1或CRISPR2含有多个间隔序列；106株志贺菌含有CRISPR-Q1，其中有13株志贺菌的CRISPR-Q1中有多个间隔序列。在实验室12株志贺菌中，有6株含有CRISPR1或CRISPR2，12株均含有CRISPR-Q1；CRISPR-Q1间隔序列中的一部分（约35 bp）在同一个菌株的染色体基因组上分布广泛，重复序列同样如此，CRISPR-Q1中还存在基因外重复序列（REP）元素。数据库志贺菌中的CRISPR-Q1间隔序列数与CRISPR1和CRISPR2有关联（χ²=61.6，P<0.01），实验室志贺菌中的CRISPR-Q1间隔序列数与CRISPR1和CRISPR2有关联（P=0.015）。结论：CRISPR-Q1在志贺菌中广泛分布，其序列中存在REP元素；志贺菌的CRISPR1和CRISPR2与CRISPR-Q1有关联。

关键词: 志贺菌, 成簇的规律间隔短回文重复序列, 间隔序列, 基因外重复序列

Abstract: Objective: To analyze the characteristics of clustered regularly interspaced short palindromic repeats (CRISPR) in Shigella from the database and clinic, and to explore the characteristics of CRISPR-Q1 and the correlations among CRISPRs.Methods: According to the genome database of Shigella, the primer sequences and PCR amplication were used to obtain the CRISPR sequences of Shigella, and the multiple sequence alignment was used to analyze the CRISPR distribution, the number and features of spacer; BLAST was used to analyze the repeats and spacers in CRISPR-Q1;the distribution characteristics of the repeats and spacers in Shigella and the location and features of CRISPR-Q1 in the strain were detected; the relationships between the spacer number of CRISPR-Q1 and CRISPR1/CRISPR2 in the database and laboratory were analyzed.Results: Among 107 Shigella strains in the database, 106 Shigella strains contained CRISPR1 or CRISPR2, 8 Shigella strains contained severial spacers; 106 Shigella strains contained CRISPR-Q1, and 13 Shigella strains contained severial spacers.A total of 6 among 12 Shigella strains in the laboratory contained CRISPR1 or CRISPR2, all of the 12 strains contained CRISPR-Q1. A portion of the CRISPR-Q1 spacer (about 35 bp) widely distributed in the genome of the same strain of chromosome, as was the repeat sequence; CRISPR-Q1 contained the repetitive extragenic palindromic elements (REP). The spacer number of CRISPR-Q1 was related to the CRISPR1 or CRISPR2 of Shigella in the database(χ²=61.60,P<0.01) and in the laboratory (P=0.015).Conclusion: CRISPR-Q1 widely distributes in Shigella and the REP elements can be found in CRISPR-Q1.There are correlations between CRISPR1 or CRISPR2 and CRISPR-Q1 in Shigella.

Key words: Shigella, clustered regularly interspaced short palindromic repeats, spacer, repetitive extragenic palindromic

中图分类号:

王颖芳, 王鹏飞, 段广才, 郗园林, 张晓萌, 詹煜慧. 志贺菌中成簇的规律间隔短回文重复序列的特点及其关联性分析[J]. 吉林大学学报(医学版), 2018, 44(06): 1131-1137.

WANG Yingfang, WANG Pengfei, DUAN Guangcai, XI Yuanlin, ZHANG Xiaomeng, ZHAN Yuhui. Characteristics of clustered regularly interspaced short palindromic repeats in Shigella and their correlation analysis[J]. Journal of Jilin University(Medicine Edition), 2018, 44(06): 1131-1137.

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志贺菌中成簇的规律间隔短回文重复序列的特点及其关联性分析

Characteristics of clustered regularly interspaced short palindromic repeats in Shigella and their correlation analysis

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