O157∶H7型大肠埃希菌CRISPR/Cas系统结构的生物信息学分析

doi:10.16431/j.cnki.1671-7236.2020.02.006

摘要/Abstract

摘要： 为了解O157∶H7型大肠埃希菌中成簇的规律间隔短回文重复序列（clustered regularly interspaced short palindromic repeats，CRISPR）分布和结构特征及cas基因分布情况，本试验通过GenBank数据库和CRISPRdb database获得92株O157∶H7型大肠埃希菌全基因组序列、CRISPR位点位置、CRISPR的侧翼序列及cas基因簇的序列范围，利用多序列比对、启动子预测和RNA二级结构预测等方法分析细菌中CRISPR系统的特点。结果显示，O157∶H7型大肠埃希菌的基因组存在3个CRISPR位点（CRISPR1、CRISPR2和CRISPR3），每个CRISPR位点上的序列一致；CRISPR1和CRISPR2的重复序列可形成茎环状结构，环上的碱基易发生变化；CRISPR2中存在一段长451 bp的序列（命名为序列X），该序列X将CRISPR2分为2个部分CRISPR2a和CRISPR2b，其碱基A和T比例为74%，在91株O157∶H7型大肠埃希菌中均存在该序列，在该序列中可预测出至少有1个启动子和9个转录因子结合位点；侧翼序列中的疑似前导序列位于CRISPR2下游，序列长340 bp，其碱基A和T比例为69%，在92株O157∶H7型细菌中均存在该序列，其可预测出至少有1个启动子和3个转录因子结合位点；在20株O157∶H7型大肠埃希菌的全基因组序列中，有15株具有完整的cas基因簇，有5株缺乏cas3基因。本试验结果表明，O157∶H7型大肠埃希菌的CRISPR系统结构稳定，序列具有较高保守性，cas基因簇也相对保守。CRISPR2的结构与其他类型大肠埃希菌有较大差别。本研究发现的序列X在O157∶H7型大肠埃希菌分布广泛且序列保守，可作为鉴定O157∶H7型大肠埃希菌的潜在分子靶标。

关键词: O157∶H7型大肠埃希菌; CRISPR; cas

Abstract: To know the distribution and structural characteristics of clustered regular interleaved short palindromic repeats (CRISPR) and distribution of cas genes in Escherichia coli O157∶H7,complete genome sequence,CRISPR position,CRISPR flanking sequence and cas gene clusters sequence of 92 strains Escherichia coli O157∶H7 were obtained through GenBank database and CRISPRdb database,then multiple sequence alignment,promoter prediction and RNA secondary structure prediction were used to obtain the CRISPR system.The results showed that the genomes of Escherichia coli O157∶H7 had three CRISPR loci,(CRISPR1,CRISPR2 and CRISPR3),and the gene sequences at each CRISPR locus were highly consistent.The repeats of CRISPR1 and CRISPR2 could form the stem ring structure,and the bases were easily changed on the ring.There was a sequence X which was 451 bp in CRISPR2,and it divided CRISPR2 into two parts (CRISPR2a and CRISPR2b).The ratio of base A to T of the segment X in CRISPR2 was 74% and the sequence was found in 91 strains of O157∶H7 Escherichia coli,in which at least 1 promoter and 9 transcription factor binding sites could be predicted.The ratio of base A to T of suspected leader which located in CRISPR2 downstream was not less than 69%,the sequence was 340 bp and the sequence was available in 92 strains of bacteria,which could predict at least 1 promoter and 3 transcription factor binding sites.In these 20 strains of Escherichia coli,15 strains had complete cas gene clusters,5 strains lacked cas3 gene.The CRISPR structure and cas gene cluster of Escherichia coli O157∶H7 were relatively stable,the CRISPR sequence was highly conservative.The CRISPR2 structure was different from other types.The sequence X found in this study was widely distributed and conserved in Escherichia coli O157∶H7,which could be used as a potential molecular target to identify Escherichia coli O157∶H7.

Key words: Escherichia coli O157∶H7; CRISPR; cas

中图分类号:

S852.61

王鹏飞, 王颖芳, 段广才, 詹煜慧, 陈帅印, 郗园林, 徐亚珂. O157∶H7型大肠埃希菌CRISPR/Cas系统结构的生物信息学分析[J]. 中国畜牧兽医, 2020, 47(2): 363-371.

WANG Pengfei, WANG Yingfang, DUAN Guangcai, ZHAN Yuhui, CHEN Shuaiyin, XI Yuanlin, XU Yake. A Bioinformatics Analysis of CRISPR/Cas Structure in Escherichia coli O157∶H7[J]. China Animal Husbandry and Veterinary Medicine, 2020, 47(2): 363-371.

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