Strand-specific mutational bias influences codon usage of weakly expressed genes in Escherichia coli.

According to the selection-mutation-drift theory of molecular evolution, mutation predominates in determining codon usage bias (CUB) in weakly expressed genes (WEG) whereas selection predominates in determining CUB in highly expressed genes (HEG). Strand-specific mutational bias causes compositional asymmetry of the nucleotides between leading and lagging strands (LaS) in bacterial chromosomes. Keeping in view the aforementioned points, CUB between the strands were compared in Escherichia coli chromosome. In comparison with HEG, codon usage of WEG was observed to be more biased toward strands: G ending codons were significantly more in leading strands than in LaS and the reverse was true for the C ending codons. In case of WEG, the GC(3) skews were found to be significantly different between the strands. This suggests that strand-specific mutational bias influences codon usage of WEG to a greater extent than that of HEG. The differential effect of strand-specific mutational bias in E. coli might be attributed to stronger purifying selection in the HEG than the WEG. The observation here in E. coli supports the SMD theory of molecular evolution.