Substrate-induced remodeling of protein disordered loops activates Csm DNases

Type III-A Csm systems show two distinct activities: the synthesis of cyclic oligoadenylates by the Csm1 (Cas10) Palm domain and DNA cleavage by the Csm1 histidine-aspartate (HD) domain, both of which are to be activated by the cognate target RNAs (CTR) and regulated in the spatiotemporal fashion. However, it remains elusive how the Csm DNase is activated. Here, we show that the activation occurs at the stage of substrate binding via two main steps: (i) recognition of CTR triggers the Csm effector to develop substrate binding potential, enabling the HD domain of Csm1 subunit to bind single-stranded DNA (ssDNA) substrate; (ii) ssDNA substrate induces the formation of substrate channel where key amino acids within Csm1 HD domain interact with ssDNA substrate, delivering it to the active cavity for cleavage. A tripartite structural element in the Csm1 HD domain, including the catalytic cavity and two disordered loop segments (L1, L2), was found to function in the substrate channel formation. A model is presented to account for the Csm DNase activation in which remodeling of L2 functions as the trigger. The resulting knowledge of this work provides a basis for further optimization of Csm DNase-based nucleic acid detection tools.