Large-Effect Beneficial Synonymous Mutations Mediate Rapid and Parallel Adaptation in a Bacterium

Abstract

Contrary to previous understanding, recent evidence indicates that synonymous codon changes may sometimes face strong selection. However, it remains difficult to generalize the nature, strength, and mechanism(s) of such selection. Previously, we showed that synonymous variants of a key enzyme-coding gene (fae) of Methylobacterium extorquens AM1 decreased enzyme production and reduced fitness dramatically. We now show that during laboratory evolution, these variants rapidly regained fitness via parallel yet variant-specific, highly beneficial point mutations in the N-terminal region of fae. These mutations (including four synonymous mutations) had weak but consistently positive impacts on transcript levels, enzyme production, or enzyme activity. However, none of the proposed mechanisms (including internal ribosome pause sites or mRNA structure) predicted the fitness impact of evolved or additional, engineered point mutations. This study shows that synonymous mutations can be fixed through strong positive selection, but the mechanism for their benefit varies depending on the local sequence context.

Lateral Gene Transfer Dynamics in the Ancient Bacterial GenusStreptomyces

“…Estimated point mutation rates are also lower in genes that are conserved across most bacteria than in genes conserved in all Streptomyces species. The effects of evolutionary distance and gene data set on inferred mutation rate are stronger in synonymous sites, suggesting widespread fitness effects of synonymous mutations in Streptomyces core genes, as has been shown in a variety of bacteria and eukaryotes (38–41). These results suggest that comparisons of evolutionary event rates between bacterial groups can be strengthened through normalizing rates based on evolutionary distance between samples within each group.…”

The fitness landscape of the codon space across environments

“…The distribution of fitness effects of synonymous mutations Previous studies have shown that synonymous mutations can directly affect fitness (e.g., Firnberg et al 2014;Hunt et al 2014;Lind et al 2010) and impact the ability of populations to adapt to new environments (Agashe et al 2016;Bailey et al 2014). For example, Bailey et al (2014) found that two synonymous mutations were responsible for adaptation of Pseudomonas fluorescens to a new medium by increasing the expression of a gene involved in glucose metabolism.…”

“…For example, Bailey et al (2014) found that two synonymous mutations were responsible for adaptation of Pseudomonas fluorescens to a new medium by increasing the expression of a gene involved in glucose metabolism. In a more recent study in Methylobacterium extorquens, Agashe et al (2016) found that the deleterious effect of synonymous mutations in a medium with methylamine as the sole carbon source could be rescued by different mutations, including four synonymous mutations that increased transcription and protein production levels. The impact of synonymous mutations at the genome-wide level was also found in patterns of codon usage bias (syno-nymous codons are used at different frequencies) across genomes.…”

RNA Structural Determinants of Optimal Codons Revealed by MAGE-Seq

“…However, in our RCS analysis the extent to which mutant RNA structures contained beneficial and not deleterious base-pairings predicted the fitness of synonymous mutants both at the beginning of the gene and far beyond the start codon, augmenting more general predictors based on RNA folding energy and ribosome binding(Salis et al, 2009). The use of gene-specific empirical metrics such as RCS may therefore be useful in cases when general metrics fail to predict the effects of synonymous changes(Agashe et al, 2016; Knöppel et al, 2016). These results can also help to explain biases toward stronger minimum free energy in later gene regions(Gu et al, 2010), since a stronger local fold in later regions of the gene is less likely to interact with upstream RNA structures.…”