Deamination of tRNA molecules has already been shown in holozoan species with the evolution deemed to have occurred within the ancestor to the choanoflagellates, metazoans and filastereans. The aim of this project is to determine an estimate of the origin of evolution for this process, by providing evidence for this outside of the holozoans to the opisthokonts and further still, across the eukaryotic supergroup if possible. The determination of a time frame for this allows theories to be drawn regarding the possible expansion of this.
This research project used bioinformatic techniques modified from Southworth et al., (2018) in order to analyse the genomes of species: Thecamonas trahens (Apusozoa), Fonticula alba (Opisthokonta), Leishmania tarentolae (Excavata), Chondrus crispus (Archaeplastida), Chlamydomonas reinhardtii (Archaeplastida) and Bigelowiella natans (Rhizaria). The optimal codons for each species were determined using programs CodonW and SMALT in order to see whether these perfectly matched the most abundant tRNA species, or whether deamination is a possible explanation for why there is a lack of perfect matches. Other techniques such as tRNAscan-SE-2.0 analyses on whole genome sequences for some species under investigation, were utilised in order to see what tRNA genes are present, by analysing transcripts of the species.
BLAST analysis of modified and unmodified tRNA genes identified using the tRNAscan output of their genome files showed that both copies were present within the species F. alba and T. trahens. SMALT analyses of these transcriptome files identified multiple copies of both variations within additional eukaryotic species which fall on the opposite side of the eukaryotic root to the original species.
Initial results of T. trahens and F. alba provided direct evidence for the evolution of deamination of tRNA being ancestral to the Opisthokonta group, and allowed this research to undertake analysis of multiple additional species outside of the opisthokonts, where direct evidence for deamination of tRNAs was identified within rhizarians (SAR), archaeplastids and excavates.
The aims this research project set out with have been achieved as the dataset generated by this work provides evidence for deamination being an ancestral eukaryotic trait. One
explanation could be that this has undergone an expansion; from the deamination of the previously identified arginine, isoleucine, serine and threonine amino acid tRNAs in bacterial species, through their symbiosis with Archaea, forming the eukaryotes.
|Date of Award||2023|
|Supervisor||Martin Carr (Co-Supervisor) & Chris Cooper (Co-Supervisor)|