Molecular evolution of DNA topoisomerase III beta (TOP3B) in Metazoa
DNA topoisomerase III beta (TOP3B) is unique because it acts on both DNA and RNA substrates to regulate gene expression and genomic stability. Mutations in human TOP3B are linked to neurodevelopmental and cognitive disorders, highlighting its relevance for human health. Despite the emerging importance of TOP3B, their precise cellular functions and evolutionary history remain poorly understood. Here we present the most comprehensive phylogenetic and protein structure comparative analyses of TOP3B. We confirmed that TOP3B is widespread and conserved across Metazoa. Subdomain IV was identified as the most conserved TOP3B region, in agreement with its role in providing the structural foundation for the protein. On the contrary, subdomain II was the less conserved, possibly by being the most structurally flexible of all TOP3B regions. Moreover, we identified a subset of TOP3B sites that interact with the TDRD3 auxiliary factor highly conserved among humans and other species. In contrast, TOP3B residue at position 472, previously associated with schizophrenia, is highly variable across animals, suggesting a more specific role in humans and related species. Finally, we showed that all TOP3B CXXC zinc finger motifs previously identified at the protein C-terminal region are retained across metazoans. We also found that the two major methylation sites known to regulate TOP3B activity are located in the most conserved section of the C-terminal arginine-glycine-glycine (RGG) box, suggesting that a similar regulatory mechanism may operate throughout metazoans. Overall, the data provided here lays the framework for a better understanding of the evolution and functional roles of TOP3B.