Type IA topoisomerases: a phylogenomic and biochemical analysis of Methanosarcina acetivorans C2A TopoIII

Abstract

The characterization of the ω protein, eventually renamed to Escherichia coli Topoisomerase I (EcoTopoI), by Prof. James C Wang opened the door to the previously unknown world of molecular machines that manipulate DNA topology. Since then, topoisomerases have been demonstrated to be vital instruments of the cellular machinery in a wide array of processes that are essential for life such as DNA synthesis, DNA repair and chromosome segregation. Their essentiality is further exemplified through the fact that these molecular machines have been identified in every species sequenced to date regardless of domain. As a result, they remain to be a therapeutic target of interest with numerous drugs in various stages of development. Each class of topoisomerase has its own phylogenetic distribution. The focus of this study is the type IA topoisomerase III (TopoIII). From mice to men, higher order eukaryotes contain two TopoIII enzymes while lower order eukaryotes such as yeast contain a single TopoIII. Sequence examination and biochemical studies reveal that this is not the result of gene duplication. Instead, these enzymes have distinct biological roles. Methanosarcinales is the only sequenced archaeal order with this distinct distribution of two TopoIIIs. And yet, there is little information currently available on archaeal TopoIII. Here we report on Methanosarcina acetivorans TopoIIIα (MacTopoIIIα) as the first biochemically characterized mesophilic archaeal topoisomerase. The ensuing study delves into the biochemical properties of a singular topoisomerase from a relatively unexplored domain and utilizes a large-scale phylogenomic approach to illustrate the therapeutic potential of the specific class to which it belongs. This report provides the first analysis of over 2000 topoisomerase sequences from the type IA class.