Structure basis for single-strand nucleic acid targeting by IscB and variants

Abstract

Transposon-encoded IscB has been established as the evolutionary ancestor of CRISPR-Cas9. This compact RNA-guided endonuclease has since been engineered for genome editing applications. We previously repurposed IscB and Cas9 as efficient RNA editors by removing their double-stranded DNA recognition module, the TAM/PAM-interacting domain. Here, we report four cryo-EM structures of IscB in complex with single-stranded nucleic acid (ssNA) targets to illuminate its mechanistic underpinnings. Structural analysis reveals that IscB initially facilitates formation of a 10-nt seed duplex with ssNA; however, further base-pairing is blocked by an alternatively positioned HNH nuclease that acts as a conformational roadblock. In this intermediate state, neither HNH nor RuvC is competent for target cleavage: the HNH domain is occluded by the roadblock configuration, while the RuvC active site is obstructed by the guide RNA. Only upon full duplex formation do additional base pairs between the guide RNA and ssNA dislodge the HNH roadblock, simultaneously exposing the RuvC nuclease active site. We propose that an analogous conformational checkpoint governs IscB activity during dsDNA target interrogation. Guided by these structural insights, we introduced mutations to either enhance ssNA binding or relieve the conformational checkpoint, both of which significantly improved RNA-targeting efficiency of IscB.