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Investigating CRISPR-Cas systems in Clostridium botulinum via bioinformatics tools

The Clustered regularly interspaced short palindromic repeats (CRISPR) systems are a type of innate immunity found in some prokaryotes, which protect them against alien genetic elements by targeting foreign nucleic acids. Some other functions are also attributed to these systems. Clostridium botulin...

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Bibliographic Details
Published in:Infection, genetics and evolution genetics and evolution, 2017-10, Vol.54, p.355-373
Main Authors: Negahdaripour, Manica, Nezafat, Navid, Hajighahramani, Nasim, Rahmatabadi, Seyyed Soheil, Ghasemi, Younes
Format: Article
Language:English
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Summary:The Clustered regularly interspaced short palindromic repeats (CRISPR) systems are a type of innate immunity found in some prokaryotes, which protect them against alien genetic elements by targeting foreign nucleic acids. Some other functions are also attributed to these systems. Clostridium botulinum bacteria produce botulinum neurotoxins (BoNT), one of the deadliest known toxins for humans and some animals. Food poisoning due to these bacteria is still a challenge in food industries. On the other hand, BoNT has been widely investigated for therapeutic applications including different muscle disorders. Bont genes may be located on bacterial chromosomes, plasmids, or even prophages. Generally, the genomes of Cl. botulinum show a high level of plasticity. In order to investigate the presence and characteristics of CRISPRs in these anaerobe bacteria, an in silico study on 113 CRISPR arrays identified in 38 Cl. botulinum strains was performed. A high occurrence of CRISPR arrays (80%) were found, with a remarkable frequency on plasmids. Several (CRISPR-associated) Cas proteins from different types were recognized in the studied strains, which were mostly Cas6. The CRISPR-Cas systems were identified as type I or III, but no type II. The spacers showed more homology with bacterial plasmids than phages. Active CRISPR-Cas systems can prevent the transfer of foreign genes, which may also include bont genes. This study provides the first insight into the probable roles of CRISPR-Cas systems in Cl. botulinum strains such as toxigenicity. [Display omitted] •A high prevalence of CRISPRs in Clostridium botulinum suggests their importance.•The CRISPR-Cas systems were identified as type I or III, and no type II.•Spacers showed more identities with plasmids than phages.•Plasmid and toxin gene transfer among some strains may be inhibited by CRISPRs.•CRISPR systems probably impact toxin production in Cl. botulinum.
ISSN:1567-1348
1567-7257
DOI:10.1016/j.meegid.2017.06.027