The genetic information in DNA is transcribed into mRNA then translated into protein, in which codons played important roles during the process. Total 64 combinations of nucleotide triplet (codon) encode all 22 amino acids. Each amino acid corresponds to at least one codon, e.g. methionine and tryptophan. In other cases, amino acids are encoded by 2 to 6 different codons. The codons encode the same amino acid are referred as synonymous codons. The frequency of synonymous codon usage varies widely among different organisms, and these differences have important implications for the regulation of protein expression. In the process of protein synthesis, a particular species tends to use a set of specific codons, which are called optimal codons. This phenomenon is also known as codon usage bias. So the use of different species in the codon usage bias, optimizing the use of codons can increase the protein expression.

At the same time, accurate polypeptide elongation could minimize the energy waste caused by translation errors. Therefore, a codon with optimal translation speed and high fidelity will result high translation efficiency and an increased protein expression. The combination of codons and translation efficiency are not only contributing to the codon usage bias of the whole genome, but also the distribution of codons with different translation efficiency in different regions. The codon usage bias in different regions can regulate genes expression at different stages, such as affecting the mRNA expression during transcription, the speed and accuracy of translation, and the folding of polypeptide.

https://www.synbio-tech.com/codon-usage-bias/