Recognition of DNA knots by type II DNA topoisomerases is facilitated by DNA supercoiling
speaker: Andrzej Stasiak (Université de Lausanne)abstract: During normal cell growth, various DNA transactions are facilitated by topoisomerase-mediated passage of one DNA segment through another. These strand passages can inadvertently lead to the formation of DNA knots, which are highly deleterious for living cells if not removed efficiently (1). Type IIA DNA topoisomerases, can use the free energy of ATP hydrolysis to decrease knotting level significantly below the equilibrium value for DNA rings subject to random passages between colliding segments (2). This topo II ability has been recognized as an important physiological mechanism ensuring efficient DNA unknotting and decatenation. However, the original study establishing that type II DNA topoisomerases actively unknot DNA also revealed that this ability decreases sharply with increasing DNA length (2). Therefore, active unknotting would be doomed to be ineffective for long DNA molecules, but that is exactly where active unknotting would be needed. While seeking an explanation as to why an evolutionarily selected system should be ineffective in unknotting of long DNA molecules, we recognised that original studies establishing that preferential unknotting ability of type II DNA topoisomerase sharply decreases with DNA size were performed using torsionally relaxed DNA (2). It is known, however, that naturally occurring DNA is frequently under torsional tension (3), the best-known examples of this state being negatively supercoiled bacterial plasmids. To investigate the potential effects of torsional constraints on the activity of type IIA topoisomerases, we have performed Brownian dynamics simulations to examine how negative supercoiling affects the structure of knotted DNA molecules and whether DNA supercoiling can cause knotted regions to be recognized specifically and then unknotted by topoisomerases. We observed that DNA supercoiling results in the tightening of knots, which leads directly to an increase in curvature of the knotted regions, in turn rendering these more likely to be bound and unknotted by type IIA topoisomerases.
1. Deibler, R.W., Mann, J.K., Sumners, D.W. and Zechiedrich, L. (2007) Hin-mediated DNA knotting and recombining promote replicon dysfunction and mutation. BMC Mol Biol, 8, 44.
2. Rybenkov, V.V., Ullsperger, C., Vologodskii, A.V. and Cozzarelli, N.R. (1997) Simplification of DNA topology below equilibrium values by type II topoisomerases. Science, 277, 690-693.
3. Travers, A. and Muskhelishvili, G. (2007) A common topology for bacterial and eukaryotic transcription initiation? EMBO Rep, 8, 147-151.
This is joint work with Guillaume Witz and Giovanni Dietler.
timetable:
Wed 15 Jun, 11:30 - 12:30, Aula Dini
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