Occurrence and diversity of CRISPR-Cas systems in the genus Bifidobacterium
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Date
2015
Authors
Briner, Alexandra E.
Lugli, Gabriele A.
Milani, Christian
Duranti, Sabrina
Turroni, Francesca
Gueimonde, Miguel
Margolles, Abelardo
van Sinderen, Douwe
Ventura, Marco
Barrangou, Rodolphe
Journal Title
Journal ISSN
Volume Title
Publisher
Public Library of Science
Published Version
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.
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Keywords
Comparative genomics , Adaptive immunity , Streptococcus thermophilus , Acquired resistance , Rna , Dna , Evolution , Bacteria , Classification , Endonuclease
Citation
Briner AE, Lugli GA, Milani C, Duranti S, Turroni F, Gueimonde M, et al. (2015) Occurrence and Diversity of CRISPR-Cas Systems in the Genus Bifidobacterium. PLoS ONE 10(7): e0133661. doi:10.1371/journal.pone.0133661