Allosteric regulation in CRISPR/Cas1-Cas2 protospacer acquisition mediated by DNA in association with Cas2

Cas1 and Cas2 are highly conserved proteins across CRISPR-Cas systems and play a significant role in protospacer acquisition. Here we study the protospacer (or ps) DNA binding, recognition, and response to cleavage on the protospacer-adjacent-motif complementary sequence or PAMc by Cas1-Cas2, implementing all-atom molecular dynamics simulations. First, we noticed that two active sites of Cas1&1′ bind asymmetrically to two identical PAMc in the simulation. For psDNA containing only one PAMc to be recognized, it is then found that the non-PAMc association site remains destabilized until after the bound PAMc being cleaved. Thus, correlation appears to exist between the two active sites, which can be allosterically mediated by psDNA and Cas2&2′ in bridging. To substantiate such findings, we further simulated Cas1-Cas2 in complex with synthesized psDNA sequences psL and psH, which have been measured with low and high efficiency in acquisition, respectively. Notably, such inter-site correlation becomes largely enhanced for Cas1-Cas2 in complex with psH, and remains low with psL. Hence, our studies demonstrate that PAMc recognition and cleavage in one active site of Cas1-Cas2 allosterically regulates non-PAMc association/reaction in the other site, and such allosteric regulation is mediated by non-catalytic Cas2 and DNA protospacer in acquisition.