Detection and homology analysis of clustered regularly interspaced short palindromic repeats in Shigella

Abstract

Objective To detect the clustered regularly interspaced short palindromic repeats(CRISPR)of Shigella,and to analyze the characteristics and homology of their repeats and spacers with complete genome Shigellain GenBank.Methods The CRISPR were obtained by PCR amplification method,and the homology of repeats and spacers was analyzed by bioinformatics;multiple sequence alignment was used to analyze the features of spacers and the relationship between the spacers and flanking sequences;BLAST was used to analyze the homology between the spacers and plasmids and phages;weblogo was used to analyze the frequency of the bases of the repeats and RNAfold was used to predict the secondary structures of the repeats RNA;homology clustering analysis of repeats was performed and BLAST was used to analyze the homology of the repeats with other bacteria.Results All 3studied clinical strains and 9complete genome Shigella contained different number of CRISPR.In the same CRISPR,the spacers were similar or different;the partial sequences of the spacers in some CRISPR and flanking sequences of CRISPR had the same sequences.Some spacers possible came from the splicing and gene recombination between the informational genes and operational genes.There may be relationship between the repeats which were not completely conserved and bacterial evolution.The differences of the bases of the repeats affected the length of stem,thus affected the stability of the secondary structure and the function of CRISPR.The repeats had high similarity with the several individual species of distant relationships.Conclusion The different CRISPR structures exist in Shigella,and the conservation of the repeats in different CRISPR is different.The partial sequences of some spacers have homology with the flanking sequences of CRISPR,and some spacers come from the gene splicing.