Bioinformatics Analysis Of CRISPR Structures And Featurein Shigella, Escherichia Coli And Salmonella

Shigella, Escherichia coli and Salmonella are pathogens of intestinal disease that impact human health seriously and pose serious economic burden on family and society. What’s more, the emergence of antimicrobial resistance has made it more difficult to its prevention and control. Antibiotic resistance may be acquired by gene mutation and acquisition of exogenous resistant genes, horizontal gene transfer makes bacteria resist more extensive antibiotics. Clustered regularly interspaced short palindromic repeats(CRISPR) worked as a acquired immunity system of bacteria, obtains the exogenous genes to resist foreign genetic elements.ObjectiveThis research conducted a systematic analysis of CRISPR in Shigella, Escherichia coli and Salmonella database to elaborate CRISPR characteristics of different bacteria and explore formation mechanism of spacer sequences. And in-depth analyse provides the reference for the further studies on the mechanism and characteristics of CRISPR/Cas.Methods1. The CRISPR information of Shigella(7), Escherichia Coli(39) and Salmonella(52) are derived from CRISPRdb. The genomes of 107 Shigella strains are from Gen Bank. The 12 clinical Shigella and 33 spacers of CRISPR of clinical Shigella were also analyzed.2. The CRISPR structures of Shigella, Escherichia Coli and Salmonella are analyzed by multiple sequence alignment. The repeats of CRISPR are analyzed by Weblogo and RNAfold. The homology tree of cas1 and cas2 are analyzed by DNAMAN. The spacers are analyzed by CRISPRTarget and BLAST.Results1. The CRISPRs are similar among Shigella, Escherichia coli and Salmonella. The Shigella have the CRISPR1/2(CRISPR1, CRISPR2) and CRISPR3, the Escherichia colicontain CRISPR1/2, CRISPR3/4(CRISPR3, CRISPR4) and we also find the new CRISPR, CRISPR5/6(CRISPR5 and CRISPR6), the Salmonella are mainly the CRISPR1/2, the CRISPR5/6 is also new-found.2. The identity positions of upstream flanking sequence of CRISPR1/2 in Escherichia coli and Salmonella are 69.5%(34), 93.5%(35), and the downstream are 92.3%(32), 91.4%(32). The downstream of CRISPR1 and upstream of CRISPR2 are divided into two or three groups and the CRISPR3/4 and CRISPR5/6 have similar with CRISPR1/2. The percentage of unique spacers in different CRISPR are different, the CRISPR1/2 and CRISPR5/6 in Salmonella are 33.6%, 68.6%, CRISPR1/2, CRISPR3/4 and CRISPR5/6 are 54.3%, 47.4% and 68.6%.3. There is some bases change between the first and terminal repeats of some CRISPRs by analyzing the Shigella of Gen Bank. Cas depletion was common in Shigella and IS sequences were found both in cas genes cluster and flank of CRISPR. The cas1 and cas2 of Shigella are divided into two parts; the similarity is not lower than 70%. The numbers of spacers of CRISPR-Q1 are in contact with the existence of CRISPR1/CRISPR2.4. According to analysis of spacers, the spacers formation contain three types, I spacer matches one gene segment which may be the coding region, non-coding region or the combination of coding and non-coding sequence. II spacer may match two or more genes segment, this kind of spacer may be formed by splicing and fusing of more than one gene segment. III spacer is undetermined. according to the coding products of matching gene of spacer, the products contain many types, some are Cas proteins, some are associated with bacterial survival, some are associated with the structure themselves and some are functional protein.Conclusion1. There are CRISPRs in Shigella,Escherichia Coli and Salmonella.2. The identitypositions of flanking sequences indifferent CRISPR of Shigella,Escherichia Coli and Salmonella are different.3. The conservation of repeat sequence in different CRISPR ofShigella are different. Cas genes cluster exist in Shigella and are frequent absence.4. Spacers have many formation and matching genes of spacers have rich coding product which contain multiple types.