CRISPR–Cas in mobile genetic elements: counter-defence and beyond

• Published in: Nature reviews. Microbiology Vol. 17; no. 8; pp. 513 - 525
• Main Authors: Faure, Guilhem, Shmakov, Sergey A., Yan, Winston X., Cheng, David R., Scott, David A., Peters, Joseph E., Makarova, Kira S., Koonin, Eugene V.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.08.2019; Nature Publishing Group
• Subjects: 631/181/2474; 631/181/2481; 631/181/735; 631/208/212/2305; 631/326/1320; 631/326/1321; 631/326/325; 631/326/4041; 631/326/432; 631/326/596; Analysis; Archaea; Archaea - genetics; Bacteria - genetics; Bacteriophages - genetics; Biomedical and Life Sciences; CRISPR; CRISPR-Cas Systems; DNA sequencing; DNA Transposable Elements; DNA viruses; Evolution, Molecular; Gene Transfer, Horizontal; Infectious Diseases; Interspersed Repetitive Sequences; Life Sciences; Medical Microbiology; Microbiology; Nucleotide sequencing; Parasitology; Plasmids; Prophages; Recombination, Genetic; Ribonucleic acid; RNA; Target recognition; Transposons; Virology; Viruses
• ISSN: 1740-1526; 1740-1534
• DOI: 10.1038/s41579-019-0204-7

The principal function of CRISPR–Cas systems in archaea and bacteria is defence against mobile genetic elements (MGEs), including viruses, plasmids and transposons. However, the relationships between CRISPR–Cas and MGEs are far more complex. Several classes of MGE contributed to the origin and evolution of CRISPR–Cas, and, conversely, CRISPR–Cas systems and their components were recruited by various MGEs for functions that remain largely uncharacterized. In this Analysis article, we investigate and substantially expand the range of CRISPR–Cas components carried by MGEs. Three groups of Tn7-like transposable elements encode ‘minimal’ type I CRISPR–Cas derivatives capable of target recognition but not cleavage, and another group encodes an inactivated type V variant. These partially inactivated CRISPR–Cas variants might mediate guide RNA-dependent integration of the respective transposons. Numerous plasmids and some prophages encode type IV systems, with similar predicted properties, that appear to contribute to competition among plasmids and between plasmids and viruses. Many prokaryotic viruses also carry CRISPR mini-arrays, some of which recognize other viruses and are implicated in inter-virus conflicts, and solitary repeat units, which could inhibit host CRISPR–Cas systems. CRISPR–Cas systems in bacteria and archaea have multifaceted evolutionary relationships with mobile genetic elements (MGEs), including viruses, plasmids and transposons. CRISPR–Cas systems or their components have also been recruited by MGEs on many independent occasions. In this Analysis article, Koonin and colleagues investigate and substantially expand the range of CRISPR–Cas components carried by MGEs.