Recontextualizing Eukaryogenesis via Computational Analysis of RNA Processing in 16,449 Archaeal Genomes

The analysis of proteins related to RNA processing reveals intriguing aspects of the evolutionary transition from archaea to eukaryotes. Eukaryagenesis is the process in which the first eukaryote came into existence, with multiple hypotheses on the order of events. These hypothesis often focus on the mitochondria and cell skeletal structure, without much discussion on eukaryotic signature proteins(ESP). ESP is integral in increasing the longevity of RNA and for the increase in the variety of proteins able to be produced which ultimately increases fitness of eukaryotes. 16,449 genomes and 10 proteins were acquired and BLAST was run for each superclass for each protein. BLAST scores were compared between superclasses and analyzed. Results for proteins such as Prp9, Rex3, Histone H2A, H2B, and Histone 3 indicate that there is no substantial difference between BLAST results implying a transitional state consistent with E3 model. The results for Smd3 and Ceg1 highlight that a group of Asgardarchaeota and Diaforarchaearchaea were different to other types of archaea. These groups likely underwent similar environmental pressures giving organisms with these genes higher fitness. These early genes evolved into their eukaryotic versions, while other genes like Histone 4, Abd1, and Lsm2 may have had ancestral prototypes present across archaea. Gene prototypes likely served different purposes, but the presence of such prototypes imply that evolution of the nucleus was likely independent from the presence of the mitochondria.