Paralogy in the Evolution of RNA and DNA Enzymatic Machinery

Abstract

The current model of early evolution posits that one of the earliest biological systems was an RNA-world, in which RNA played the role of both genome and catalyst. This system was augmented by the evolution of protein enzymes, and later by the evolution of a DNA genome. In general, the evolution of proteins is marked by gene duplications, producing divergent paralogs, and conservation of domains, allowing novel combinations of functions. We examined datasets of proteins that interact with RNA and DNA in various processes, as well as those involved in nucleic-acid biosynthesis, under the hypothesis that in both the evolution of the RNA-protein world and in the evolution of the DNA genome many genes underwent duplications and evolved into some of the novel protein functions required by these new systems. Picking only enzymes that have been previously identified as ancient, we found trends of homology and domain duplication between nucleic-acid biosynthetic enzymes and RNA and DNA machinery, suggesting an ancestral link between the production and curation of nucleic-acid monomers and polymers. Additionally, evidence of homology between RNA and DNA machinery implies some duplication of RNA-related functions in the genesis of DNA genomes.