CODONS

A genetic code is a set of rules that governs the link between codons in DNA and amino acids in protein. There are 64 triplets of nucleotides in the genetic code. Except for methionine and tryptophan, other amino acids are being encoded by more than one codon. This scenario is known as codon degeneracy. Synonymous codon is a terminology to describe all codons that coded for same amino acids. These codons are unequally distributed where some codons are used preferentially than another to code a respective amino acids.

Translation of base triplets for genetic code with the help of codon wheel (Source:https://www.shutterstock.com/image-vector/translation-base-triplets-genetic-code-help-339833039)

The frequency of codon usage varies across species and across gene within a genome. Since synonymous codon usage does not alter the amino acids sequence, these changes were thought not to affect selection under the neutral theory of evolution. However, the codon usage bias has been proven hugely influencing the translation efficiency and accuracy. Nevertheless, the codon usage bias has been reported as an essential genomic feature that occur in prokaryotes, unicellular eukaryotes and higher organisms like human.

In terms of evolution selection, codon usage bias is an outcome of neutral evolutionary process such as mutational bias or selective pressure as optimizing the efficiency of translation is also known as natural selection. The pattern of codon bias can also be shaped by differences in nucleotide composition of the genes especially the GC content of coding regions. Different organism contains different amount GC genes within their genome. GC content have been revealed to be correlated to codon usage bias, gene length, gene density, replication timing and methylation.

Codon usage pattern is not only essential in revealing the evolution of the species, but, in pathogenic organism this pattern provides insights about the host-pathogen co-evolution and adaptation of pathogens to specific host.

INDICES :

1. Effective Number of Codons is a standard measurement used to measure the influence of codon usage bias from the equally distributed synonymous codons. This indices is independent of gene length and amino acids composition. There have been reported by the researchers about the range of ENC value where 20, the case of extreme which consider one particular codon was assigned to one amino acid, and 61, indicates the codons have been chosen equally likely. In order to determine the codon usage pattern ENC against the genetic content (G+C) at synonymous sites were plotted. This plotting is referenced for Homosapiens, Saccharomyces cerevisiae, Escherichia coli, Bacillus subtilis, Dictyostellium discoideum and Drosophila melanogaster.

2. Relative synonymous codon usage (RSCU) is another indices of codon usage bias. This indices is measured as a ratio of observed frequency of codons to the expected frequency for all the synonymous codons of same amino acids equally. RSCU is an independent value which capable of reflecting the bias of synonymous codon usage.

3. Codon Adaptation Index is an indices to determine the extension of codon bias by discovering the level of gene expression. Journals claimed that the CAI value ranges from 0 to 1 where the higher the value the stronger the codon usage bias.

It’s simple yet hope it’s informative.

Best Regards,

Ms Rinaa Ramesh

Bioinformatics Analyst, BG Support & Services, Malaysia

Email: rinaa@biogsupport.com