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Background  An issue associated with efficient bioethanol production is the fact that the desired product is toxic to the biocatalyst. Among other effects, ethanol has previously been found to influence the membrane of  E. coli  in a dose-dependent manner and induce changes in the lipid composition of the plasma membrane. We describe here the characterization of a collection of ethanol-tolerant strains derived from the ethanologenic  Escherichia coli  strain FBR5.    Results  Membrane permeability assays indicate that many of the strains in the collection have alterations in membrane permeability and/or responsiveness of the membrane to environmental changes such as temperature shifts or ethanol exposure. However, analysis of the strains by gas chromatography and mass spectrometry revealed no qualitative changes in the acyl chain composition of membrane lipids in response to ethanol or temperature. To determine whether these strains contain any mutations that might contribute to ethanol tolerance or changes in membrane permeability, we sequenced the entire genome of each strain. Unexpectedly, none of the strains displayed mutations in genes known to control membrane lipid synthesis, and a few strains carried no mutations at all. Interestingly, we found that four independently-isolated strains acquired an identical C → A (V244 V) silent mutation in the ferric citrate transporter gene  fecA . Further, we demonstrated that either a deletion of  fecA  or over-expression of  fecA  can confer increased ethanol survival, suggesting that any misregulation of  fecA  expression affects the cellular response to ethanol.    Conclusions  The fact that no mutations were observed in several ethanol-tolerant strains suggested that epigenetic mechanisms play a role in  E. coli  ethanol tolerance and membrane permeability. Our data also represent the first direct phenotypic evidence that the  fecA  gene plays a role in ethanol tolerance. We propose that the recurring silent mutation may exert an effect on phenotype by altering RNA-mediated regulation of  fecA  expression.    Electronic supplementary material  The online version of this article (10.1186/s12866-018-1180-1) contains supplementary material, which is available to authorized users.

A Recurrent Silent Mutation Implicates fecA in Ethanol Tolerance by Escherichia coli