Structures of the RNA-guided surveillance complex from a bacterial immune system

Abstract

Bacterial cells use CRISPRs (clustered regularly interspaced short palindromic repeats) to defend against invading phages. The central catalytic component in this process is Cascade, a 12-subunit complex consisting of proteins and RNA. The structure of Cascade, free and bound to target RNA, has now been solved by cryoelectron microscopy and three-dimensional reconstruction. These structures show the changes in architecture that are induced by target binding, and will assist future studies addressing how these conformational changes affect restriction of the phage. Bacteria and archaea acquire resistance to viruses and plasmids by integrating short fragments of foreign DNA into clustered regularly interspaced short palindromic repeats (CRISPRs). These repetitive loci maintain a genetic record of all prior encounters with foreign transgressors1,2,3,4,5,6. CRISPRs are transcribed and the long primary transcript is processed into a library of short CRISPR-derived RNAs (crRNAs) that contain a unique sequence complementary to a foreign nucleic-acid challenger7,8,9,10,11,12. In Escherichia coli, crRNAs are incorporated into a multisubunit surveillance complex called Cascade (CRISPR-associated complex for antiviral defence), which is required for protection against bacteriophages13,14. Here we use cryo-electron microscopy to determine the subnanometre structures of Cascade before and after binding to a target sequence. These structures reveal a sea-horse-shaped architecture in which the crRNA is displayed along a helical arrangement of protein subunits that protect the crRNA from degradation while maintaining its availability for base pairing. Cascade engages invading nucleic acids through high-affinity base-pairing interactions near the 5′ end of the crRNA. Base pairing extends along the crRNA, resulting in a series of short helical segments that trigger a concerted conformational change. This conformational rearrangement may serve as a signal that recruits a trans-acting nuclease (Cas3) for destruction of invading nucleic-acid sequences.