CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) systems are adaptive immune systems that protect bacteria and archaea from invading mobile genetic elements (MGEs). The Cas protein-CRISPR RNA (crRNA) complex uses complementarity of the crRNA “guide” region to specifically recognize the invader genome. CRISPR effectors that perform targeted destruction of the foreign genome have emerged independently as multi-subunit protein complexes (Class 1 systems) and as single multi-domain proteins (Class 2). These different CRISPR-Cas systems can cleave RNA, DNA, and protein in an RNA-guided manner to eliminate the invader, and in some cases, they initiate programmed cell death/dormancy. The versatile mechanisms of the different CRISPR-Cas systems to target and destroy nucleic acids have been adapted to develop various programmable-RNA-guided tools and have revolutionized the development of fast, accurate, and accessible genomic applications. In this review, we present the structure and interference mechanisms of different CRISPR-Cas systems and an analysis of their unified features. The three types of Class 1 systems (I, III, and IV) have a conserved right-handed helical filamentous structure that provides a backbone for sequence-specific targeting while using unique proteins with distinct mechanisms to destroy the invader. Similarly, all three Class 2 types (II, V, and VI) have a bilobed architecture that binds the RNA-DNA/RNA hybrid and uses different nuclease domains to cleave invading MGEs. Additionally, we highlight the mechanistic similarities of CRISPR-Cas enzymes with other RNA cleaving enzymes and briefly present the evolutionary routes of the different CRISPR-Cas systems.

CRISPR-Cas

crRNA

RNA binding protein

Cascade

Cas3

Cas10

CasDinG

Cas9

Cas12

Cas13

Mobile genetic elements

Streptococcus pyogenes Cas9

clustered regularly interspaced short palindromic repeats-CRISPR-associated

CRISPR-associated complex for antiviral defense

CRISPR-associated transposase

protospacer adjacent motif

protospacer flanking sequence

trans-activating crRNA

non-target strand DNA

higher eukaryotes and prokaryotes nucleotide-binding

CRISPR associated Rossman fold

repeat-associated mysterious proteins

Francisella novicida Cas12a

tetratricopeptide repeat Caspase HetF associated with TPRs

© 2024 THE AUTHORS. Published by Elsevier Inc on behalf of American Society for Biochemistry and Molecular Biology.