Occurrence and Diversity of CRISPR-Cas Systems in the Genus Bifidobacterium: e0133661

• Published in: PloS one Vol. 10; no. 7
• Main Authors: Briner, Alexandra E, Lugli, Gabriele Andrea, Milani, Christian, Duranti, Sabrina, Turroni, Francesca, Gueimonde, Miguel, Margolles, Abelardo, Sinderen, Douwe van, Ventura, Marco, Barrangou, Rodolphe
• Format: Journal Article
• Language: English
• Published: 01.07.2015
• Subjects: Bifidobacterium
• ISSN: 1932-6203
• DOI: 10.1371/journal.pone.0133661

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.