Translation rates of individual codons are not correlated with tRNA abundances or with frequencies of utilization in Escherichia coli

Abstract

We analyzed 12 individual codons, which differed widely with respect to the frequency of use in Escherichia coli and the abundance of the corresponding tRNAs, for their influence on the coupling between transcription and translation. This was probed by determining the effects of codon substitutions in the leader peptide gene on transcription past the pyrE attenuator, as described previously by Bonekamp et al. (F. Bonekamp, H. D. Andersen, T. Christensen, and K. F. Jensen, Nucleic Acids Res. 13:4113-4123, 1985). In principle, the results revealed that either RNA polymerase or the (leading) ribosomes pass the different codon strings at different rates. However, under the assumption that the rate of transcription elongation is unaffected by the sequence changes, the results may be interpreted as indicating that different codons are translated at different rates and that these rates do not generally reflect the concentrations of the corresponding tRNAs or the frequencies with which the codons are used in E. coli. Moreover, it seems that codon synonyms that are served by the same isoaccepting tRNA species can deviate as much from each other in translational behavior as synonymous codons that are served by isoacceptors present in the cell in widely different amounts can.