Topoisomerase VI is a chirally-selective, preferential DNA decatenase

Abstract

DNA topoisomerase VI (topo VI) is a type IIB DNA topoisomerase found predominantly in archaea and some bacteria, but also in plants and algae. Since its discovery, topo VI has been proposed to be a DNA decatenase, however robust evidence and a mechanism for its preferential decatenation activity was lacking. Using single-molecule magnetic tweezers measurements and supporting ensemble biochemistry, we demonstrate that Methanosarcina mazei topo VI preferentially unlinks, or decatenates, DNA crossings, in comparison to relaxing supercoils, through a preference for certain DNA crossing geometries. In addition, topo VI demonstrates a dramatic increase in ATPase activity, DNA binding and rate of strand passage, with increasing DNA writhe, providing further evidence that topo VI is a DNA crossing sensor. Our study strongly suggests that topo VI has evolved an intrinsic preference for the unknotting and decatenation of interlinked chromosomes by sensing and preferentially unlinking DNA crossings with geometries close to 90°.

Evolution and diversity of the TopoVI and TopoVI-like subunits with extensive divergence of the TOPOVIBL subunit

“…As suggested by recent biochemical studies, this may be linked to specific substrate recognition. The proposition of TopoVI binding to DNA crossing is interesting with respect to the topological status of sister chromatids after DNA replication (McKie et al ., 2022) and some factors may tether TopoVI to replication forks or intermediates. Understanding these TopoVI biochemical properties might also help to elucidate TopoVIL activity.…”

“…As A. thaliana TopoVIA/B mutants are defective in endoreduplication, it was proposed that the TopoVI decatenation activity is involved in resolving catenated chromatids generated by endoreduplication. In fact, although TopoVI possesses both relaxation and decatenation activities, it was shown that Methanosarcina mazei TopoVI is preferentially a decatenase in vitro (McKie et al, 2022). Interestingly, the functional link with DNA replication is also supported by the interaction detected by immunoprecipitation between Pyrococcus abyssi TopoVI and the replication fork components PCNA, NusC and RFC (Ren et al, 2009).…”

“…As A. thaliana TopoVIA/B mutants are defective in endoreduplication, it was proposed that the TopoVI decatenation activity is involved in resolving catenated chromatids generated by endoreduplication. In fact, although TopoVI possesses both relaxation and decatenation activities, it was shown that Methanosarcina mazei TopoVI is preferentially a decatenase in vitro (McKie et al, 2022).…”