Type IA topoisomerases can be "magicians" for both DNA and RNA in all domains of life

Abstract

Topoisomerases solve critical topological problems in DNA metabolism and have long been regarded as the "magicians" of the DNA world. Here we present views from 2 of our recent studies indicating that Type IA topoisomerases from all domains of life often possess dual topoisomerase activities for both DNA and RNA. In animals, one of the 2 Type IA topoisomerases, Top3β, contains an RNA-binding domain, possesses RNA topoisomerase activity, binds mRNAs, interacts with mRNA-binding proteins, and associates with active mRNA translation machinery. The RNA-binding domain is required for Top3β to bind mRNAs and promote normal neurodevelopment. Top3β forms a highly conserved complex with Tudor-domain-containing 3 (TDRD3), a protein known to interact with translation factors, histones, RNA polymerase II, single stranded DNA and RNA. Top3β requires TDRD3 for its association with the mRNA translation machinery. We suggest that Type IA topoisomerases can be "magicians" for not only DNA, but also RNA; and they may solve topological problems for both nucleic acids in all domains of life. In animals, Top3β-TDRD3 is a dual-activity topoisomerase complex that can act on DNA to stimulate transcription, and on mRNA to promote translation.

Keywords: FMRP; TDRD3; Top3α; Top3β; polyribosomes; topoisomerase.

Figure 1.

Type IA topoisomerases have evolved from single proteins with dual activities in microorganisms to multi-protein complexes with restricted activities in animals. Schematic representation of evolution of Type IA topoisomerases in DNA and RNA metabolism. In E. coli, both Type IA enzymes (Top1 and Top3) have dual activities for DNA and RNA. In yeast, the only Type IA enzyme is part of a complex (Top3-Rmi1) that also has dual activities for DNA and RNA. In animals, only one of the 2 Type IA paralogs, Top3β, has dual activity, whereas Top3α has activity for only DNA. Interestingly, Top3β, but not Top3α, contains an RNA-binding domain (RGG box) that is required for its RNA topoisomerase activity. Moreover, the 2 Top3 paralogs comprise 2 distinct complexes, with the Top3β complex containing a RNA binding protein (FMRP), whereas the Top3α complex containing a DNA helicase (BLM). These data argue that Type IA topoisomerases have evolved into 2 functional distinct complexes in animals, one for RNA and DNA (Top3β-TDRD3-FMRP), and one for DNA only (Top3α-Rmi1-Rmi2-BLM). This figure is adapted from Fig. 7A of a previous publication.

Figure 2.

RNA topoisomerase activity is prevalent in Type IA topoisomerases from all 3 domains of life. (A) Schematic representation of the RNA topoisomerase assay. A synthetic circular RNA substrate contains 2 pairs of complementary regions (red and green) separated by single-stranded spacers (black). Through strand passage reactions, this substrate is converted to a trefoil knot in which the 2 pairs of complementary regions can form normal double helices. (B) Schematic representation of the domain structures of Type IA topoisomerases from different species (left) and their RNA topoisomerase activity. The conserved core domains and the non-conserved CTDs, including Zn-fingers (orange boxes), are indicated. Their RNA topoisomerase activity was shown on the right. Fig. 2A is adapted from Fig. 4 of the previous paper. Fig. 2B is adapted from 4 figures of another paper.

Figure 3.

Type IA topoisomerases in eukaryotes have evolved into 2 distinct homologous complexes in animals and plants; the RNA topoisomerase activity of Type IA topoisomerases may have arisen earlier during evolution; (A) Schematic presentations show evolution of Top3 into 2 homologous complexes in eukaryotes, Top3α-RMI1 and Top3β-TDRD3, which have distinct functions in DNA and RNA metabolism, respectively. Yeast has a single copy of Top3 and RMI, which forms a complex required for maintenance of genomic stability. In Fungi like Mucor circinelloides and Rhizopus microspores, we predict that the Top3 enzyme has evolved into 2 paralogous complexes: Top3α-RMI1 and Top3β-TDRD3. Both complexes are also conserved in plants and animals. Top3α-RMI1 retains its function in DNA metabolism and maintenance of genomic stability, while Top3β-TDRD3 works in both DNA and RNA metabolism. The subunits of the 2 Top3 complexes, RMI1 and TDRD3, also share homology at their N-terminus, and emerged in above mentioned species of fungi. Their unique C-terminal domains provide protein-protein binding surfaces which target their respective topoisomerases to specific regulators, such as RMI2 or FMRP. Surprisingly, the C-terminal domains of TDRD3 in plants has more resemblance to those of fungi than to those of animals: they lack the UBA, TUDOR, and FMRP-interaction domains, but have the RGG-box which is also present in TDRD3 of several fungi species. Fungi and plants do not have orthologs of FMRP, which binds to the C-terminus of animal TDRD3. Accession numbers of Top3α, Top3β, RMI, TDRD3 homologs of M. circinelloides (Mc) and R. microsporus (Rm) are mentioned here. McTop3α - EPB81200, McRMI - EPB83693, RmTop3α - CEI89638, RmRMI - CEI87462, Mc Top3β - EPB85471, McTDRD3 - EPB83703, RmTop3β CEG78805 and RmTDRD3 GAN02671. (B) A model of origin and evolution of Type IA topoisomerases and their activity for RNA and DNA. It has been postulated that life starts with a pool of self-replicating RNAs; and there exists an RNA world with RNA genome before the current DNA world. We propose that Type IA enzymes may originate in the RNA world to solve RNA topological problems. When the RNA world evolved and was eventually replaced by the DNA world, these enzymes retained their RNA topoisomerase activity while developing a new activity for DNA. This may explain the prevalence of the RNA topoisomerase activity in Type IA enzymes from all 3 domains. Fig. 3A and 3B are reproduced from Fig. 7 and Fig. S7 of a previous publication.

Figure 4.

Models for why RNA metabolism may create topological problems that need an RNA topoisomerase to solve. (A)(B) Models to illustrate that Top3β may catalyze catenation or decatenation of 2 mRNA circles, thus enhancing or inhibiting translation (B) or transport of mRNAs (C). It has been shown that mRNA circles can form when 2 ends of mRNA interacting with a common protein. (C) A model illustrates that helical torsions may arise when a translating ribosome or a helicase unwinds a duplex region in an mRNA hairpin. If the hairpin is bound to an immobile mRNP or cellular matrix, the helical torsion will not be relieved by rotation. Such torsion may impede progression of ribosomes or RNA helicases during translation or transport. Top3β can relax the helical torsion through its strand passage activity. (D) Top3β may interconvert circular RNAs to knots or catenane structures, which may affect the function of these RNAs. (E) A linear mRNA may form an intramocular knot, which may block progression of translating ribosomes. Top3β may catalyze knotting or unknotting of the linear mRNA, and thus affect translation. (F) Two linear mRNAs get entangled with each other, which may interfere with their functions. Top3β may catalyze entangling or segregation of these mRNAs, thus affecting their functions. This figure was adapted from Fig. S7 of a previous publication.