Selective advantage of the tRNA I34 Deamination in Eukaryotes

Introduction: A tRNA modification which deaminates adenosine into inosine at position 34 of tRNAs for the threonine, alanine, proline, serine, isoleucine, leucine, valine and arginine (TAPSILVR) amino acids within eukaryotes is carried out by an enzyme known as hetADAT. This deamination allows for certain codons, known as ADAT preferred codons, to be recognised by tRNA types which are usually non-complementary.

Aims: By looking at the patterns of codon usage within 33 different protists from a range of eukaryotic supergroups, an estimation into the origins of the TAPSILVR tRNA deamination in eukaryotes can be proposed. Secondly, by determining the codon usage of the protists, whether or not the TAPSILVR tRNA deamination allows for the selection of the ADAT preferred codons due to translational efficiency and/or accuracy can also be examined.

Methodology: Optimal codons were identified for each of the 33 protists with the use of CodonW and expression data provided by the NCBI SRA. Under a selection model, the optimal codons are those which correspond to the most abundant tRNA molecules, therefore, the number of genes present with each protist’s genome was found for each tRNA. Certain patterns in the tRNA copy numbers can also show consistency with the presence of the I34 tRNA deamination. A34 tRNA molecules were modified to show the I34 deamination and screened for within available small tRNA data in order to provide evidence for the presence of the deamination.

Results: The codon usage of the majority of the protists along with their tRNA gene copy numbers showed consistency with not only the use of the I34 tRNA deamination but also for the selection of the ADAT preferred codons due to the deamination. tRNA molecules modified with the I34
deamination were found in species belonging to the eukaryotic supergroups of Amoebozoa, Opisthokonta, Excavata, Alveolata and Stramenopiles.

Conclusions: The presence of the I34 tRNA deamination has now been found in eukaryotic supergroups across the eukaryotic tree of life, whilst a selective pressure towards the use of ADAT preferred codons has been found to affect the codon usage bias of organisms from all of the eukaryotic supergroups researched. Therefore, this study has provided evidence that the origin of the I34 tRNA deamination carried out by hetADAT lies in the last common ancestor of the eukaryotes, where it most likely provided an advantage for the use of ADAT preferred codons.