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

Mol Biol Evol. 2016 Jun;33(6):1542-53. doi: 10.1093/molbev/msw035. Epub 2016 Feb 23.


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.

Keywords: Shine–Dalgarno sequence; codon use; epistasis; fitness; mRNA folding..

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptation, Physiological / genetics
  • Bacterial Proteins / genetics*
  • Bacterial Proteins / metabolism
  • Biological Evolution
  • Carbon-Nitrogen Ligases / genetics*
  • Carbon-Nitrogen Ligases / metabolism
  • Codon
  • Epistasis, Genetic
  • Evolution, Molecular
  • Genetic Fitness*
  • Methylobacterium extorquens / enzymology
  • Methylobacterium extorquens / genetics*
  • Methylobacterium extorquens / metabolism
  • Mutation*
  • Protein Biosynthesis
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Ribosomes / genetics
  • Ribosomes / metabolism
  • Selection, Genetic
  • Silent Mutation


  • Bacterial Proteins
  • Codon
  • RNA, Messenger
  • Carbon-Nitrogen Ligases
  • Fae protein, Methylobacterium extorquens