The relationship between synonymous codon usage and gene function, protein folding and protein structure

Genetic information is transferred in the form of triplet, also called genetic code or codon. It is well known that synonymous codons are often used with different frequencies. This phenomenon is called codon bias. The degree of codon bias has been found to be highly variable among genes from different species. Some researches show that there are high correlations between codon usage, tRNA abundance and gene expression. Most researches studied the gene codon usage in some lower species such as bacteria, yeast, C. elegans, drosophila, Arabidopsis and so on. Few researches were focused on higher species such as rodent, primate animals and other mammals. Some researches were carried on to study the codon usage of genes in organelles. Morton studied the codon usage of genes in chloroplast in plants and found that the codon usage was divergent between chloroplast genes in land plants. To reveal the relationship between protein function and codon usage bias, we should extensively study the codon use frequencies of genes with different functions and from different species. Several methods have been used to study the gene codon bias in different species. The relative synonymous codon use frequencies (RSCU) of 135 MHC genes from four mammal species are analyzed using hierarchical cluster method. The result suggests that gene function is the dominant factor that determines codon usage bias, while species is a minor factor that determines further difference in codon usage bias for genes with similar functions.