Different propensities for gate opening in gyrases and topoisomerase IV

The bacterial type IIA topoisomerases gyrase and topoisomerase IV (Topo IV) catalyze DNA supercoiling and decatenation (gyrase), or DNA relaxation and decatenation (Topo IV) in ATP-dependent reactions. Most bacteria contain both gyrase and Topo IV, which jointly remove torsional stress during replication: gyrase removes positive supercoils ahead of the replication fork, while Topo IV decatenates pre-catenanes behind the fork and the catenated daughter chromosomes. Some bacteria, including Mycobacterium tuberculosis, contain only a gyrase, which then needs to perform both reactions. The molecular determinants for the predominant activity of type IIA topoisomerases are unclear. We hypothesize that the prevalent activity is connected to the stabilities of the DNA- and C-gates. In a comparative single-molecule FRET study of Bacillus subtilis and M. tuberculosis gyrase and B. subtilis Topo IV, we show that the DNA-gates are less stable than the C-gates in all three enzymes. The stabilities of the DNA-gates of gyrase and Topo IV are similar. Strikingly, the C-gates in both gyrases are highly stable, but the C-gate in Topo IV is markedly less stable. Our results suggest that the stability of the C-gate of type IIA topoisomerases is linked to their activities.