Attenuation of co-transcriptional-translation density in Escherichia coli reveals crucial determinants of protein synthesis

Mathias Heltberg, Niels Bohr Institute, University of Copenhagen

Authors: Mathias Heltberg, Orr Schlesinger, Yonatan Chemla, Eden Ozer, Ryan Marshall, Vincent Noireaux, Mogens H Jensen, Lital Alfonta
Protein synthesis in living cells has been thoroughly investigated and characterized over the past 60 years. However, some fundamental issues remain unresolved, including the reasons for genetic code redundancy and codon bias. In this study, we changed the kinetics of the E. coli transcription and translation processes by mutating the promoter and ribosome binding domains and by using genetic code expansion. The results expose a counterintuitive phenomenon, whereby an increase in the initiation rates of transcription and translation lead to a decrease in protein expression. This effect can be rescued by introducing slow translating codons into the beginning of the gene, by shortening gene length or by reducing initiation rates. Based on the results, we developed a biophysical model, which suggests that the density of co-transcriptional translation plays a role in bacterial protein synthesis. These findings indicate how codon bias may be used for recombinant protein over-expression purposes, and at the fundamental level how cells use codon bias to tune translation speed and protein synthesis.