Codon usage pattern of all genes in Escherichia coli K-12

Since its elucidation, the codon table has played a pivotal role in aiding our understanding of how cells read the sequence in DNA and translate it into a protein sequence. But, at a fundamental level, we still do not understand why the codon table is degenerate such that different codons could encode the same amino acid. More intriguingly, different number of codons are used to encode different amino acids. These mysteries await resolution through fundamental research, but, at the applied level, codon usage patterns of cells have been known to impact on the efficiency in which a gene can be expressed. Specifically, genes with less often used codons could not be translated into proteins efficiently, thereby, resulting in a low expression level. This work took a different perspective in understanding the codon usage pattern of a cell. In particular, a global approach was taken to calculate the codon usage pattern of all genes in <i>Escherichia coli</i> K-12 using information from the reference genome of <i>E. coli</i> K-12 MG1655 (Genbank accession number: NCBI Reference Sequence: NC_000913.3) Through analysis with an in-house MATLAB software, the codon usage pattern of all genes revealed that codons, AGA and AGG, were minimally used by the bacterium. This holds implications at different levels. Both codons were part of 6 codons that could encode arginine, which suggests that some genes could not be efficiently translated into the corresponding proteins if they sport the minimally used codons. This meant that analysing the codon usage pattern of a cell at the genome level could help uncover genes that are no longer needed by the cell. Specifically, the logic flows that since a gene could not be expressed efficiently, it has likely lost physiological relevance and might be a relic of evolution. Hence, profiling the codon usage pattern of a cell could become a useful tool for determining putative genes that are no longer required by the cell. Overall, this work should lend insights into the preferred codon usage pattern of this biotechnology workhorse as well as serving as a first demonstration of an approach useful for uncovering genes that are no longer relevant in the cell’s current evolutionary trajectory. <br><br>