Structural rearrangements allow nucleic acid discrimination by type I-D Cascade

• Published in: Nature communications Vol. 13; no. 1; pp. 2829 - 11
• Main Authors: Schwartz, Evan A., McBride, Tess M., Bravo, Jack P. K., Wrapp, Daniel, Fineran, Peter C., Fagerlund, Robert D., Taylor, David W.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 20.05.2022; Nature Publishing Group; Nature Portfolio
• Subjects: 101/28; 631/337/4041/3196; 631/535/1258/1259; Adaptive systems; Binding; CRISPR; CRISPR-Associated Proteins - metabolism; CRISPR-Cas Systems; Deoxyribonucleic acid; DNA; DNA - metabolism; DNA Cleavage; Humanities and Social Sciences; Immune system; multidisciplinary; Nucleic Acids; Phages; Prokaryotes; Proteins; RNA; Science; Science (multidisciplinary); Single-stranded DNA; Substrate inhibition
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-022-30402-8

CRISPR-Cas systems are adaptive immune systems that protect prokaryotes from foreign nucleic acids, such as bacteriophages. Two of the most prevalent CRISPR-Cas systems include type I and type III. Interestingly, the type I-D interference proteins contain characteristic features of both type I and type III systems. Here, we present the structures of type I-D Cascade bound to both a double-stranded (ds)DNA and a single-stranded (ss)RNA target at 2.9 and 3.1 Å, respectively. We show that type I-D Cascade is capable of specifically binding ssRNA and reveal how PAM recognition of dsDNA targets initiates long-range structural rearrangements that likely primes Cas10d for Cas3′ binding and subsequent non-target strand DNA cleavage. These structures allow us to model how binding of the anti-CRISPR protein AcrID1 likely blocks target dsDNA binding via competitive inhibition of the DNA substrate engagement with the Cas10d active site. This work elucidates the unique mechanisms used by type I-D Cascade for discrimination of single-stranded and double stranded targets. Thus, our data supports a model for the hybrid nature of this complex with features of type III and type I systems. I-D CRISPR-Cascade can target both single-stranded and double-stranded nucleic acids. Here, Schwartz et. al determine these structures and reveal large-scale rearrangements that allow for target discrimination and destruction.