Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB

Abstract

The manoeuvres involved in replication and transcription lead to a build-up of twisting or torsional strain in DNA, and the job of relieving the strain falls to the topoisomerases. Type IB topoisomerases (TopIBs) cut one DNA strand, allow it to swivel around its partner, then rejoin the ends. This removes both positive and negative supercoils. Direct monitoring of a single TopIB molecule now shows that, unlike other topoisomerases, it does not remove a fixed number of supercoils. Rather, the number of supercoils removed, via a mechanism involving friction between rotating DNA and the enzyme cavity, depends on the torque stored in the DNA. The introduction of friction as a factor in DNA–topoisomerase interactions may have important implications for DNA–enzyme interactions in general. The cover depicts TopIB in action. Topoisomerases relieve the torsional strain in DNA that is built up during replication and transcription. They are vital for cell proliferation1,2,3 and are a target for poisoning by anti-cancer drugs4,5. Type IB topoisomerase (TopIB) forms a protein clamp around the DNA duplex6,7,8 and creates a transient nick that permits removal of supercoils. Using real-time single-molecule observation, we show that TopIB releases supercoils by a swivel mechanism that involves friction between the rotating DNA and the enzyme cavity: that is, the DNA does not freely rotate. Unlike a nicking enzyme, TopIB does not release all the supercoils at once, but it typically does so in multiple steps. The number of supercoils removed per step follows an exponential distribution. The enzyme is found to be torque-sensitive, as the mean number of supercoils per step increases with the torque stored in the DNA. We propose a model for topoisomerization in which the torque drives the DNA rotation over a rugged periodic energy landscape in which the topoisomerase has a small but quantifiable probability to religate the DNA once per turn.