title: Occurrence and Diversity of CRISPR-Cas Systems in the Genus Bifidobacterium.
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.
authors.affiliation: Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina, United States of America.
authors.forename: Alexandra E
authors.initials: AE
authors.lastname: Briner
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy.
authors.forename: Gabriele Andrea
authors.initials: GA
authors.lastname: Lugli
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy.
authors.forename: Christian
authors.initials: C
authors.lastname: Milani
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy.
authors.forename: Sabrina
authors.initials: S
authors.lastname: Duranti
authors.affiliation: School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Western Road, Cork, Ireland.
authors.forename: Francesca
authors.initials: F
authors.lastname: Turroni
authors.affiliation: Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Villaviciosa, Asturias, Spain.
authors.forename: Miguel
authors.initials: M
authors.lastname: Gueimonde
authors.affiliation: Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Villaviciosa, Asturias, Spain.
authors.forename: Abelardo
authors.initials: A
authors.lastname: Margolles
authors.affiliation: School of Microbiology and Alimentary Pharmabiotic Centre, University College Cork, Western Road, Cork, Ireland.
authors.forename: Douwe
authors.initials: D
authors.lastname: van Sinderen
authors.affiliation: Laboratory of Probiogenomics, Department of Life Sciences, University of Parma, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Ventura
authors.affiliation: Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina, United States of America.
authors.forename: Rodolphe
authors.initials: R
authors.lastname: Barrangou
mesh_terms: D001644:Bifidobacterium / Q000235:genetics*; D064113:CRISPR-Cas Systems / Q000235:genetics*; D002876:Chromosomes, Bacterial / Q000235:genetics; D064112:Clustered Regularly Interspaced Short Palindromic Repeats / Q000235:genetics; D004247:DNA / Q000235:genetics; D019143:Evolution, Molecular; D014644:Genetic Variation / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics; D039002:Prophages / Q000235:genetics
chemical_list: D004247:DNA