What is it about?
Codon-pair frequencies are not normally distributed which makes it difficult to compare viral genomes (with limited numbers of codon pairs) with host genomes (with large data sets). By clustering codons according to the strength of network interactions of the associated tRNAs we observed that the codon-pair frequencies still correlate well with known phylogenetic groups. Most interestingly, we observed that there are particular biases in the third nucleotide position of the first codon. This position is often associated with synonymous mutations and a bias suggests a role beyond protein coding. We demonstrate that the bias is broadly present in all genomes analyzed and postulate that it plays a role in translation efficiency.
Featured Image
Why is it important?
Codon pairs are used in phylogenetic analyses, and disruptions to codon or codon-pair frequencies are used to attenuate viruses. The discovery of biases related to the strength of the associated tRNA network interactions can be used to refine phylogenetic models and codon-pair disruption strategies.
Perspectives
I did post-doctoral work in a laboratory that explored ribosome structure and function. It was really cool to find a connection between that and my current work with viral vaccines. It took a few attempts to find the best journal for publishing this work because of it affects a couple of different areas of study and I am grateful for the reviewers who also had to have the broad scope of knowledge to review it.
Ewan Plant
US Food & Drug Administration
Read the Original
This page is a summary of: Bias at the third nucleotide of codon pairs in virus and host genomes, Scientific Reports, March 2022, Springer Science + Business Media,
DOI: 10.1038/s41598-022-08570-w.
You can read the full text:
Contributors
The following have contributed to this page
