Data from: Unraveling the causes of adaptive benefits of synonymous mutations in TEM-1 β-lactamase

While synonymous mutations were long thought to be without phenotypic
consequences, there is growing evidence they can affect gene expression,
protein folding and ultimately the fitness of an organism. In only a few
cases have the mechanisms by which synonymous mutations affect the
phenotype been elucidated. We previously identified 48 mutations in TEM-1
β-lactamase that increased resistance of Escherichia coli to cefotaxime,
10 of which were synonymous. To better understand the molecular mechanisms
underlying the beneficial effect of synonymous mutations, we made a series
of measurements for a panel containing the 10 synonymous together with 10
non-synonymous mutations as a reference. Whereas messenger levels were
unaffected, we found that total and functional TEM protein levels were
higher for 5 out of 10 synonymous mutations. These observations suggest
that some of these mutations act on translation or a downstream process.
Similar effects were observed for some small-benefit non-synonymous
mutations, suggesting a similar causal mechanism. For the synonymous
mutations, we found that the cost of resistance scales with TEM protein
levels. A resistance landscape for four synonymous mutations revealed
strong epistasis: None of the combinations of mutations exceeded the
resistance of the largest-effect mutation and there were synthetically
neutral combinations. By considering combined effects of these mutations,
we could infer that functional TEM protein level is a multi-dimensional
phenotype. These results suggest that synonymous mutations may have
beneficial effects by increasing the expression of an enzyme with low
substrate activity, which may be realized via multiple, yet unknown,
post-transcriptional mechanisms.