Mistranslation drives the evolution of robustness in TEM-1 β-lactamase

Abstract

How biological systems such as proteins achieve robustness to ubiquitous perturbations is a fundamental biological question. Such perturbations include errors that introduce phenotypic mutations into nascent proteins during the translation of mRNA. These errors are remarkably frequent. They are also costly, because they reduce protein stability and help create toxic misfolded proteins. Adaptive evolution might reduce these costs of protein mistranslation by two principal mechanisms. The first increases the accuracy of translation via synonymous "high fidelity" codons at especially sensitive sites. The second increases the robustness of proteins to phenotypic errors via amino acids that increase protein stability. To study how these mechanisms are exploited by populations evolving in the laboratory, we evolved the antibiotic resistance gene TEM-1 in Escherichia coli hosts with either normal or high rates of mistranslation. We analyzed TEM-1 populations that evolved under relaxed and stringent selection for antibiotic resistance by single molecule real-time sequencing. Under relaxed selection, mistranslating populations reduce mistranslation costs by reducing TEM-1 expression. Under stringent selection, they efficiently purge destabilizing amino acid changes. More importantly, they accumulate stabilizing amino acid changes rather than synonymous changes that increase translational accuracy. In the large populations we study, and on short evolutionary timescales, the path of least resistance in TEM-1 evolution consists of reducing the consequences of translation errors rather than the errors themselves. molecular evolution | mutational robustness | phenotypic mutations | protein stability | antibiotic resistance

Mistranslation can enhance fitness through purging of deleterious mutations

“…We subjected each population to four cycles (‘generations') of mutation (with a mutation rate of ≈0.7 mutations per variant) and selection1129 on increasing concentrations of cefotaxime (Fig. 1).…”

“…Under stabilizing selection, mistranslation may decrease mistranslation rates or increase robustness to mistranslation51128. How the effects of mistranslation interact under stabilizing and directional selection remains an important question for future work.…”

Translational fidelity and mistranslation in the cellular response to stress

“…In other cases where mistranslation is very high, however, cells have been shown to develop robustness to increased error rates by increasing protein turnover to maintain proteome homeostasis 99 . In effect, if cells can maintain viability when translation fidelity is initially reduced, the accompanying increase in mistranslation (for example, adaptive mistranslation) can be beneficial by promoting phenotypic heterogeneity and increasing the probability of successfully adapting to stress 115,116 . Given that specific mechanisms such as aaRS oxidation impair quality control on exposure to stress, adaptive mistranslation provides a potentially potent mechanism to promote survival (Fig.…”

A structure-based deep learning framework for protein engineering

“…Only three of thirty positions identified by the model were also identified by either Rosetta or FoldX, which also largely identified separate residues. Furthermore, in TEM-1 β-lactamase, each of these methods uniquely identified stabilizing mutations reported elsewhere in the literature 17,18 (SI Fig. 13).…”