Synonymous codon usage and its bias in the bacterial proteomes primarily offset GC content variation to maintain optimal amino acid compositions

Abstract

Codon usage bias is the preferential or non-random synonymous codon usage among species. A recent review concluded that their biases are a complex phenomenon influenced by numerous factors, including genome composition, GC content, expression level, length of genes, and recombination rates. In this paper, I present a new plot chart and show a more straightforward explanation of the primary function of the synonymous codon usage and its bias.

First, I calculated each protein's amino acid compositions and its gene's nucleotide compositions from the publicly available proteome cording sequence data set of 23 different bacteria. Next, I calculated the maximum and minimum GC contents of the possible gene variations of the amino acid composition of each protein. And then, they were plotted together by their actual GC content on a scatter plot.

The plot showed a clear tendency. Proteins with lower actual GC content genes are coded for by genes closer to the minimum possible GC content. On the other hand, proteins with higher actual GC content genes are coded for by genes closer to the maximum possible GC content. This tendency indicates that synonymous codon usage bias is uniformly working toward offsetting the variation in GC content. Meanwhile, all plots of maximum and minimum values were aligned in a row within a narrow band for each. Therefore, I considered that the optimal range of amino acid composition of the proteome is relatively limited and that organisms use this GC offset function to meet the range conditions.

Synonymous codons are part of the genetic code table. Therefore, if synonymous codons and their usage bias have a GC offset function to maintain the optimal amino acid composition, it must be considered a fundamental function of the genetic code table assignment.