title: Studying the features of 57 confirmed CRISPR loci in 29 strains of Escherichia coli.
abstract: Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) system is a novel type of innate defense system in prokaryotes for destruction of exogenous elements. To gain further insight into behavior and organization of the system, the extensive analysis of the available sequenced genomes is necessary. The dynamic nature of CRISPR loci is possibly valuable for typing and relative analyses of strains and microbial population. There are a few orderly bioinformatics investigations about the structure of CRISPR sequences in the Escherichia coli strains. In this study, 57 CRISPR loci were selected from 32 Escherichia coli strains to investigate their structural characteristics and potential functions using bioinformatics tools. Our results showed that most strains contained several loci that mainly included conserved direct repeats, while the spacers were highly variable. Moreover, RNA analysis of the sequences indicated that all loci could form stable RNA secondary structures and showed homology mostly with phages compared to plasmids. Only three strains included cas genes around their loci.
authors: Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.|Pharmaceutical Science Research Center, Shiraz University of Medical Science, Shiraz, Iran.
authors: Seyyed Soheil
authors: SS
authors: Rahmatabadi
authors: Pharmaceutical Science Research Center, Shiraz University of Medical Science, Shiraz, Iran.
authors: Navid
authors: N
authors: Nezafat
authors: Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.|Pharmaceutical Science Research Center, Shiraz University of Medical Science, Shiraz, Iran.
authors: Manica
authors: M
authors: Negahdaripour
authors: Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.|Pharmaceutical Science Research Center, Shiraz University of Medical Science, Shiraz, Iran.
authors: Nasim
authors: N
authors: Hajighahramani
authors: Pharmaceutical Science Research Center, Shiraz University of Medical Science, Shiraz, Iran.
authors: Mohammad Hossein
authors: MH
authors: Morowvat
authors: Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.|Pharmaceutical Science Research Center, Shiraz University of Medical Science, Shiraz, Iran.|Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.
authors: Younes
authors: Y
authors: Ghasemi
mesh_terms: D001435:Bacteriophages / Q000235:genetics; D064112:Clustered Regularly Interspaced Short Palindromic Repeats / Q000235:genetics*; D019295:Computational Biology; D004269:DNA, Bacterial / Q000235:genetics*; D021901:DNA, Intergenic / Q000235:genetics; D004279:DNA, Viral / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics*; D010957:Plasmids / Q000235:genetics
chemical_list: D004269:DNA, Bacterial; D021901:DNA, Intergenic; D004279:DNA, Viral
keywords: CRISPR; Cas; Direct repeat; Escherichia coli; RNA structure