Stop Codon Usage Varies on CDS Length, Nucleotide Compositions, and Peptide Instability in Six Escherichia coli Strains.

Citation: Chua, SCH, Ling, MHT. 2021. Stop Codon Usage Varies on CDS Length, Nucleotide Compositions, and Peptide Instability in Six Escherichia coli Strains. EC Clinical and Medical Case Reports 4(2): 39-46.

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Prokaryotic stop codon usage has been shown to be influenced by GC content and release factor abundance. However, it is unlikely that GC content and release factors are the only factors influencing stop codon usage as nucleotide compositions and peptide properties have also been shown to influence codon usage biasness; of which, stop codon usage is a specific instance of codon usage bias. Here, the stop codon usage frequencies, nucleotide compositions, and peptide properties in six strains of E. coli (MG1655, W3110, BL21, O25b:H4, O157:H7, and 58-3) were examined. Our results suggest that the stop codon usage frequencies of pathogenic strains O157:H7 and O25b:H4 are significantly different to other strains (Chi-Square ≥ 7.241, p-value ≤ 2.7E-02), suggesting different evolutionary paths between pathogenic and non-pathogenic strains of E. coli. The average lengths, nucleotide compositions, and peptide instability between the stop codons are significantly different in all cases (F ≥ 3.07, p-value ≤ 4.7E-02) except for average thymine composition in E. coli 58-3. This suggests a relationship between stop codon usage and nucleotide compositions, other than GC content, and/or peptide properties.