Mechanistic Modeling of In Vivo Translation in Escherichia coli Reliably Identifies Well-Adapted and Optimized RNA Sequences

Translation elongation is a multifaceted process that intricately links translational resource availability to the biophysical effects arising from the interaction of mRNA sequences, ribosomes, and nascent polypeptide chains. Optimizing (heterologous) gene expression via codon usage or tRNA preference alone may yield suboptimal outcomes. In this study, we present a comprehensive mechanistic model that accounts for the competition of tRNAs at the ribosomal A-site, internal Shine–Dalgarno sequence interactions, and the decelerating effects of positively charged peptide patches. Our model offers a holistic perspective on the effects of translational elongation, including growth rate-dependent variation in translational rates by 22 to 25% between slow- and fast-growing Escherichia coli cells. We emphasize that endogenous E. coli sequences typically adapt to these effects, particularly in highly expressed genes, where adaptation ensures efficient translation. Conversely, heterologous gene sequences from Saccharomyces cerevisiae are predicted to exhibit lower translational elongation rates by 14 to 70% compared to the homologous isoform. Simulated elongation profiles not only underscore potential sites for translation engineering but also suggest feasible synonymous codon exchanges. The implications of our model extend beyond mere codon usage adaptation and shed light on the key factors influencing translation efficiency (e.g., codons for positively charged amino acids reduced elongation rates by ∼6%). This study provides a nuanced understanding of the intricate dynamics governing translation in E. coli.