Codon and base biases after the initiation codon of the open reading frames in the Escherichia coli genome and their influence on the translation efficiency

Nucleotide sequences around the boundaries of all open reading frames in th e Escherichia coli whole genome were analyzed, Characteristic base biases w ere observed after the initiation codon and before the termination codon. W e examined the effect of the base sequence after the initiation codon on th e translation efficiency, by introducing mutations after the initiation cod on of the E. coli dihydrofolate reductase (DHFR) gene, considering codon an d base biases, and using in vitro and in vivo translation systems. In both assay systems, the two most frequent second codons, AAA and AAU, enhanced t he translation efficiency compared with the wild type, whereas the effects of lower frequency codons were not significant. Experiments using 16S rRNA variants with mutations in the putative complementary sequence to the regio n downstream of the initiation codon showed that the translation efficiency of none of the DHFR mutants was affected. These results demonstrate that t he statistically most frequent sequences for the second codon enhance trans lation efficiency, and this effect seems to be independent of base pairing between mRNA and 16S rRNA.