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PLoS One. 2015 Jul 31;10(7):e0133661. doi: 10.1371/journal.pone.0133661. eCollection 2015.

Occurrence and Diversity of CRISPR-Cas Systems in the Genus Bifidobacterium.

Author information

1
Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina, United States of America.
2
Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy.
3
School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Western Road, Cork, Ireland.
4
Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Villaviciosa, Asturias, Spain.

Abstract

CRISPR-Cas systems constitute adaptive immune systems for antiviral defense in bacteria. We investigated the occurrence and diversity of CRISPR-Cas systems in 48 Bifidobacterium genomes to gain insights into the diversity and co-evolution of CRISPR-Cas systems within the genus and investigate CRISPR spacer content. We identified the elements necessary for the successful targeting and inference of foreign DNA in select Type II CRISPR-Cas systems, including the tracrRNA and target PAM sequence. Bifidobacterium species have a very high frequency of CRISPR-Cas occurrence (77%, 37 of 48). We found that many Bifidobacterium species have unusually large and diverse CRISPR-Cas systems that contain spacer sequences showing homology to foreign genetic elements like prophages. A large number of CRISPR spacers in bifidobacteria show perfect homology to prophage sequences harbored in the chromosomes of other species of Bifidobacterium, including some spacers that self-target the chromosome. A correlation was observed between strains that lacked CRISPR-Cas systems and the number of times prophages in that chromosome were targeted by other CRISPR spacers. The presence of prophage-targeting CRISPR spacers and prophage content may shed light on evolutionary processes and strain divergence. Finally, elements of Type II CRISPR-Cas systems, including the tracrRNA and crRNAs, set the stage for the development of genome editing and genetic engineering tools.

PMID:
26230606
PMCID:
PMC4521832
DOI:
10.1371/journal.pone.0133661
[Indexed for MEDLINE]
Free PMC Article

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