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

Date
March 20, 2022

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.

Presenter

Speakers

Speaker Image for Giulia Palermo
University of California

Related Products

Thumbnail for Molecular dynamics reveal base pair embedding and disruption as a key determinant for the genome editing selectivity in CRISPR-Cas9
Molecular dynamics reveal base pair embedding and disruption as a key determinant for the genome editing selectivity in CRISPR-Cas9
CRISPR-Cas9 is the forefront technology for editing the genome. In this system, the Cas9 protein is programmed with guide RNAs to process DNA sequences that match the guide RNA forming an RNA:DNA hybrid structure…
Thumbnail for Molecular mechanism of SARS-CoV-2 detection by emerging CRISPR-Cas technologies
Molecular mechanism of SARS-CoV-2 detection by emerging CRISPR-Cas technologies
Recent advances in the rapid detection of the SARS-CoV-2 coronavirus have been achieved through the DETECTR technology, which harnesses the novel CRISPR-Cas12a genome-editing system for nucleic acid detection…
Thumbnail for COMP Poster Session:
COMP Poster Session:
: [COMP] Division of Computers in Chemistry
Thumbnail for Genome editing systems: A tight interplay between electrostatics and conformational dynamics
Genome editing systems: A tight interplay between electrostatics and conformational dynamics
Gene editing is a process in which the DNA of an organism is deliberately altered, modified, or corrected at specific locations within its genome…