Topoisomerases maintain topological homeostasis of bacterial chromosomes by catalysing changes in DNA linking number. The resolution of RNA entanglements occurring in the cell would also require catalytic action of topoisomerases. We describe RNA topoisomerase and hydrolysis activities in DNA topoisomerase I (topo I) from mycobacteria. The interaction of topo I with mRNA, tRNA and rRNA suggested its role in some aspect of RNA metabolism; the enzyme participates in rRNA maturation via its RNA hydrolysis activity. Accumulation of rRNA precursors in a topo I knockdown strain and the rescue of rRNA processing deficiency in RNaseE knockdown cells by topo I expression indicated the enzyme’s back-up support to RNases involved in rRNA processing. We demonstrate that the active-site tyrosine of the enzyme mediates catalytic reactions with both DNA/RNA substrates, and RNA topoisomerase activity can follow two reaction paths in contrast to its DNA topoisomerase activity. Mutation in the canonical proton relay pathway impacts DNA topoisomerase activity whilst retaining activity on RNA substrates. The mycobacterial topo I thus exemplifies the resourcefulness and parsimony of biological catalysis in harnessing the limited chemical repertoire at its disposal to find common solutions to mechanistically related challenges of phosphodiester breakage/exchange reactions in DNA and RNA that are essential for cell survival.

拓扑异构酶通过催化DNA连接数的变化来维持细菌染色体的拓扑稳态。解决细胞中发生的RNA缠结还需要拓扑异构酶的催化作用。我们描述了分枝杆菌的RNA拓扑异构酶和DNA拓扑异构酶I（拓扑I）中的水解活性。topo I与mRNA，tRNA和rRNA的相互作用表明其在RNA代谢的某些方面起作用。该酶通过以下途径参与rRNA的成熟其RNA水解活性。topo I敲除菌株中rRNA前体的积累以及通过topo I表达挽救RNaseE敲除细胞中rRNA加工缺陷的迹象表明该酶对参与rRNA加工的RNase提供了备份支持。我们证明，该酶的活性位点酪氨酸介导与两个DNA / RNA底物的催化反应，与它的DNA拓扑异构酶活性相反，RNA拓扑异构酶活性可以遵循两个反应路径。典型的质子传递途径中的突变影响DNA拓扑异构酶的活性，同时保留对RNA底物的活性。