Binding Kinetics Oppositely Regulates type II Topoisomerase Relaxation and Decatenation Activities

TL;DR

This study reveals how the binding kinetics of type II topoisomerases differentially regulate their ability to decatenate DNA and relax supercoils, with implications for genome stability.

Contribution

It demonstrates that modulating topo II binding kinetics can oppositely influence decatenation and relaxation activities, combining single-molecule experiments and molecular dynamics simulations.

Findings

Faster dissociation accelerates decatenation.

Slower dissociation enhances relaxation.

Binding kinetics modulate topo II activity in vivo.

Abstract

Type II Topoisomerases (topo II) are critical to simplify genome topology during transcription and replication. They identify topological problems and resolve them by passing a double-stranded DNA segment through a transient break in another segment. The precise mechanisms underpinning topo IIs ability to maintain a topologically simple genome are not fully understood. Here, we investigate how binding kinetics affects the resolution of two distinct forms of topological entanglement: decatenation and torsional relaxation. First, by single-molecule measurements, we quantify how monovalent cation concentration affects the dissociation rate of topo II from DNA. Second, we discover that increasing dissociation rates accelerate decatenation while slowing down relaxation catalytic activities. Finally, by using molecular dynamics simulations, we uncover that this opposite behaviour is due to a trade-off between search of target through facilitated diffusion and processivity of the enzyme in catenated versus supercoiled DNA. Thus, our findings reveal that a modulation of topo II binding kinetics can oppositely regulate its topological simplification activity, and in turn can have a significant impact in vivo.