Codon Effect on the Entire Genome Based upon Genome-Wide Recoded Escherichia coli

Synonymous codon mutation can influence transcription and translation through gene expression. Researchers have studied how altering codons is linked to expression. However, they did not investigate the correlations at a whole genome level. We classified 1090 genes encoding proteins and analyzed their sequence properties in both strains of Escherichia coli with the entire genome recoded before and after codon alterations. It was observed that expression levels of the genes associated with cell membrane almost increase, while those related to protein production nearly decrease. Regarding to cytosolic metabolism, the overall expression of TCA cycle goes up, while glycolysis holds most genes with lessened expressions. The different values of A+T content, global and local codon usage, and stability of mRNA structure impacts expression ratios in an ambiguous degree, suggesting us take more parameters at cell level into account.