Domain dynamics and plasticity of the transposon-encoded Cascade-TniQ system

Cascade is a type 1, class 1 CRISPR-Cas system with a variety of roles in prokaryote defense, specifically against DNA-based viruses. Though defense against viruses is a robust role in and of itself, the utility of these systems does not end here. Recent studies in Vibrio Cholerae have demonstrated that a transposon, Tn6677, encodes a variant of the ‘standard’ type 1F Cascade present in these systems. This variant complexes with a homodimer of the transposition protein TniQ and is responsible for directing the integration activity of a heteromeric transposase, resulting in a site-specific transposition of Tn6677. This integration process starts with binding of Cascade’s DNA target sequence to the Cascade-TniQ complex, and this step is the focus of the present work. Here, Molecular Dynamics (MD) simulations have been employed to understand the large-scale conformational changes associated with DNA binding, the mutual dynamics of the protein components, and the transition to the ‘locked’ configuration. Model systems built using the RNA- and DNA-bound cryo-EM structures comprising roughly half-million atoms have been simulated over the microsecond time range. As a result, we have discovered notable changes in the dynamics of Cas8 and the TniQ homodimer. Furthermore, comparative studies of the RNA and DNA-bound states suggest a distinct change in the role of Cas8 in the RNA and DNA bound states. In summary, our outcomes provide the first all-atom dynamic representation of one of the largest CRISPR systems, with information that can contribute to understanding the mechanism of nucleic acid binding and, eventually, to transposase recruitment itself.