Average codon usage pattern of Escherichia coli K-12

Awareness of different codon usage pattern in different microorganisms led to the concept of codon optimization in genetic engineering studies. Briefly, codon optimization seeks to adjust the codon usage profile of a heterologous gene to match that of the host organism to help ensure higher expression levels. In cases where codon optimization was not done, codons in the gene that are less frequently used in the host species might not be efficiently translated, and this would result in poorer translation level. But, at the fundamental level, codon usage pattern of an organism holds greater implications than its role in informing codon optimization for heterologous gene expression. Specifically, understanding the codon usage pattern of a species could guide thinking on the evolutionary forces experienced by the species. This work sought to determine the codon usage pattern of the model prokaryotic organism, <i>Escherichia coli </i>K-12 through analysing codon usage for all genes at the global level using an in-house MATLAB software. Results reveal that codon AGA and AGG are less frequently used in <i>E. coli </i>K-12. Preference for codons for each amino acid was determined, and are as follows: phenylalanine (TTT), leucine (CTG), isoleucine (ATT), valine (GTG), serine (TCG), proline (CCA and CCG), threonine (ACC), alanine (GCG), tyrosine (TAT), histidine (CAT), glutamine (CAG), asparagine (AAC), lysine (AAA), aspartate (GAT), glutamate (GAA), cysteine (TGC), arginine (CGC), serine (AGC), and glycine (GGC). Overall, the data reveals that codon usage is fairly well distributed between alternative codons for each amino acid except for leucine, and lysine. But, this does not necessarily imply that <i>E. coli </i>K-12 has a deficit in availability of amino-acyl tRNA for less often used codons. This work should find utility in informing heterologous gene expression in <i>E. coli </i>K-12, as well as more fundamental studies seeking to understand why <i>E. coli </i>K-12 chose such a codon usage pattern. <br><br>