DNA topoisomerase III beta (TOP3B) is unique by operating 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, its precise cellular functions and evolutionary history remain poorly understood. Here, we show that TOP3B is conserved across main metazoan groups and evolved under strong purifying selection. Subdomain IV was identified as the most conserved TOP3B region, in agreement with its role in providing the structural foundation of the protein. On the contrary, subdomain II is the less conserved, possibly because it is the most structurally flexible region of all TOP3B regions. Interestingly, 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 show 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 region of the C-terminal arginine-glycine-glycine (RGG) box, suggesting that a similar regulatory mechanism may operate throughout animals. Overall, our results provide a better understanding of the evolution and functional roles of TOP3B.

DNA 拓扑异构酶 III beta (TOP3B) 是独一无二的，它同时作用于 DNA 和 RNA 底物以调节基因表达和基因组稳定性。人类TOP3B突变与神经发育和认知障碍有关，突出了其与人类健康的相关性。尽管 TOP3B 的重要性日益凸显，但其精确的细胞功能和进化历史仍知之甚少。在这里，我们表明 TOP3B 在主要后生动物群中是保守的，并在强净化选择下进化。亚域 IV 被确定为最保守的 TOP3B 区域，与其在提供蛋白质结构基础方面的作用一致。相反，子域 II 的保守性较低，可能是因为它是所有 TOP3B 区域中结构最灵活的区域。有趣的是，以前与精神分裂症相关的 TOP3B 残基在 472 位的残基在动物之间变化很大，表明在人类和相关物种中具有更具体的作用。最后，我们表明，先前在蛋白质 C 末端区域鉴定的所有 TOP3B CXXC 锌指基序都保留在后生动物中。我们还发现，已知调节 TOP3B 活性的两个主要甲基化位点位于 C 端精氨酸-甘氨酸-甘氨酸 (RGG) 盒的最保守区域，这表明类似的调节机制可能在整个动物中起作用。总体而言，我们的结果提供了对 TOP3B 的演变和功能作用的更好理解。