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

Abstract

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

CLC Number:

S852.61

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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A Bioinformatics Analysis of CRISPR/Cas Structure in Escherichia coli O157∶H7

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