title: Detecting natural adaptation of the Streptococcus thermophilus CRISPR-Cas systems in research and classroom settings.
abstract: CRISPR (clustered regularly interspaced short palindromic repeats)-Cas systems have been adapted into a powerful genome-editing tool. The basis for the flexibility of the tool lies in the adaptive nature of CRISPR-Cas as a bacterial immune system. Here, we describe a protocol to experimentally demonstrate the adaptive nature of this bacterial immune system by challenging the model organism for the study of CRISPR adaptation, Streptococcus thermophilus, with phages in order to detect natural CRISPR immunization. A bacterial culture is challenged with lytic phages, the surviving cells are screened by PCR for expansion of their CRISPR array and the newly acquired specificities are mapped to the genome of the phage. Furthermore, we offer three variants of the assay to (i) promote adaptation by challenging the system using defective viruses, (ii) challenge the system using plasmids to generate plasmid-resistant strains and (iii) bias the system to obtain natural immunity against a specifically targeted DNA sequence. The core protocol and its variants serve as a means to explore CRISPR adaptation, discover new CRISPR-Cas systems and generate bacterial strains that are resistant to phages or refractory to undesired genes or plasmids. In addition, the core protocol has served in teaching laboratories at the undergraduate level, demonstrating both its robust nature and educational value. Carrying out the core protocol takes 4 h of hands-on time over 7 d. Unlike sequence-based methods for detecting natural CRISPR adaptation, this phage-challenge-based approach results in the isolation of CRISPR-immune bacteria for downstream characterization and use.
authors.affiliation: Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Québec, Canada.|Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, Québec, Canada.
authors.forename: Alexander P
authors.initials: AP
authors.lastname: Hynes
authors.affiliation: Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Québec, Canada.|Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, Québec, Canada.
authors.forename: Marie-Laurence
authors.initials: ML
authors.lastname: Lemay
authors.affiliation: Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Québec, Canada.
authors.forename: Luc
authors.initials: L
authors.lastname: Trudel
authors.affiliation: Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Québec, Canada.
authors.forename: Hélène
authors.initials: H
authors.lastname: Deveau
authors.affiliation: Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Québec, Canada.|Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, Québec, Canada.
authors.forename: Michel
authors.initials: M
authors.lastname: Frenette
authors.affiliation: Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Québec, Canada.|Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, Québec, Canada.|Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec, Québec, Canada.
authors.forename: Denise M
authors.initials: DM
authors.lastname: Tremblay
authors.affiliation: Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, Québec, Canada.|Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, Québec, Canada.|Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec, Québec, Canada.
authors.forename: Sylvain
authors.initials: S
authors.lastname: Moineau
mesh_terms: D000222:Adaptation, Physiological; D001435:Bacteriophages / Q000502:physiology; D064113:CRISPR-Cas Systems; D012106:Research; D048249:Streptococcus thermophilus / Q000235:genetics* / Q000276:immunology / Q000502:physiology* / Q000821:virology; D013663:Teaching