Phylogenomics of DNA topoisomerases: their origin and putative roles in the emergence of modern organisms

Abstract

Topoisomerases are essential enzymes that solve topological problems arising from the double-helical structure of DNA. As a consequence, one should have naively expected to find homologous topoisomerases in all cellular organisms, dating back to their last common ancestor. However, as observed for other enzymes working with DNA, this is not the case. Phylogenomics analyses indicate that different sets of topoisomerases were present in the most recent common ancestors of each of the three cellular domains of life (some of them being common to two or three domains), whereas other topoisomerases families or subfamilies were acquired in a particular domain, or even a particular lineage, by horizontal gene transfers. Interestingly, two groups of viruses encode topoisomerases that are only distantly related to their cellular counterparts. To explain these observations, we suggest that topoisomerases originated in an ancestral virosphere, and that various subfamilies were later on transferred independently to different ancient cellular lineages. We also proposed that topoisomerases have played a critical role in the origin of modern genomes and in the emergence of the three cellular domains.

Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus

“…The V2H scenario would require an additional evolutionary mechanism (or constraint) forcing the sequences of the EhV homologs to be placed near the basis of eukaryotic trees without long branches. It should be noted that branches longer for viruses than for their eukaryotic hosts are often obtained by phylogenetic tree reconstruction (Moreira and Brochier-Armanet 2008;Claverie et al 2009;Forterre and Gadelle 2009). In the H2V scenario, the viral acquisition of the sphingolipid enzyme genes was probably gradual, through multiple HGT events, rather than through a single en bloc transfer of multiple genes.…”

DNA topology and transcription

“…DNA topoisomerases-the enzymes which modulate the topological state of genome-are vital and common to all cellular organisms. 13,14 Topoisomerases introduce a transient break in the DNA backbone and allow the release of mechanical stress from the double helix (Fig. 1A, left).…”

DNA-DNA Recognition: From Tight Contact to Fatal Attraction

“…DNA topology has been the subject of adaptive pressure in organisms that live at different temperatures for maintaining the balance between the melting potential and functional stability (Forterre and Gadelle, 2009). In addition, it is well known that the dynamics of plectonemic DNA supercoiling plays a critical role in promoting interactions between remote sites in processes such as transcription initiation and site-specific recombination (Kanaar and Cozzarelli, 1992;Travers and Muskhelishvili, 2007).…”