RNA topoisomerase is prevalent in all domains of life and associates with polyribosomes in animals

Abstract

DNA Topoisomerases are essential to resolve topological problems during DNA metabolism in all species. However, the prevalence and function of RNA topoisomerases remain uncertain. Here, we show that RNA topoisomerase activity is prevalent in Type IA topoisomerases from bacteria, archaea, and eukarya. Moreover, this activity always requires the conserved Type IA core domains and the same catalytic residue used in DNA topoisomerase reaction; however, it does not absolutely require the non-conserved carboxyl-terminal domain (CTD), which is necessary for relaxation reactions of supercoiled DNA. The RNA topoisomerase activity of human Top3β differs from that of Escherichia coli topoisomerase I in that the former but not the latter requires the CTD, indicating that topoisomerases have developed distinct mechanisms during evolution to catalyze RNA topoisomerase reactions. Notably, Top3β proteins from several animals associate with polyribosomes, which are units of mRNA translation, whereas the Top3 homologs from E. coli and yeast lack the association. The Top3β-polyribosome association requires TDRD3, which directly interacts with Top3β and is present in animals but not bacteria or yeast. We propose that RNA topoisomerases arose in the early RNA world, and that they are retained through all domains of DNA-based life, where they mediate mRNA translation as part of polyribosomes in animals.

Synthesizing topological structures containing RNA

“…More recently, several other DNA Topos were also reported to have RNA Topo activity2627. Unlike DNA Topos, the research on RNA Topos is belated and rare, mainly due to the lack of proper RNA Topo probes.…”

“…We tested E. coli DNA Topo I (denoted as Topo I afterwards for clarity) for the RNA Topo assay, and in contrast to previous report21, we find that Topo I indeed possesses RNA Topo activity. (While we were preparing the paper, the RNA Topo activity of Topo I was independently reported27. )…”

“…21). Besides, better sensitivity would circumvent the inconvenience associated with the use of autoradiography with 32 P-labelled RNA as described in the recent study27.…”

“…A key residue is R173, which interacts with the −4 position cytosine base via hydrogen bonding. Previous studies demonstrated that the R173A point mutation displays an ∼100-fold decrease in the relaxation activity of supercoiled (sc) plasmid DNA44 and completely loses the ability to relax the helix-based ssRNA probe27. With our junction-based probes of both ssDNA (a previously prepared ssDNA trefoil knot, dTK j )28 and ssRNA ( TK j ), the R173A mutant was investigated regarding its relaxation activities of ssDNA and ssRNA.…”

“…21). Based on this, RNA Topo activity has also been recently found in other Type IA DNA Topos2627, including the human DNA Topo 3β (ref 26), which is crucial to neurodevelopment. RNA topology and RNA Topos, similar to their DNA counterparts, have the potential to transform our understanding of fundamental RNA biology.…”