Transcriptomic analysis of carboxylic acid challenge in Escherichia coli: beyond membrane damage

PLoS One. 2014 Feb 28;9(2):e89580. doi: 10.1371/journal.pone.0089580. eCollection 2014.

Abstract

Carboxylic acids are an attractive biorenewable chemical. Enormous progress has been made in engineering microbes for production of these compounds though titers remain lower than desired. Here we used transcriptome analysis of Escherichia coli during exogenous challenge with octanoic acid (C8) at pH 7.0 to probe mechanisms of toxicity. This analysis highlights the intracellular acidification and membrane damage caused by C8 challenge. Network component analysis identified transcription factors with altered activity including GadE, the activator of the glutamate-dependent acid resistance system (AR2) and Lrp, the amino acid biosynthesis regulator. The intracellular acidification was quantified during exogenous challenge, but was not observed in a carboxylic acid producing strain, though this may be due to lower titers than those used in our exogenous challenge studies. We developed a framework for predicting the proton motive force during adaptation to strong inorganic acids and carboxylic acids. This model predicts that inorganic acid challenge is mitigated by cation accumulation, but that carboxylic acid challenge inverts the proton motive force and requires anion accumulation. Utilization of native acid resistance systems was not useful in terms of supporting growth or alleviating intracellular acidification. AR2 was found to be non-functional, possibly due to membrane damage. We proposed that interaction of Lrp and C8 resulted in repression of amino acid biosynthesis. However, this hypothesis was not supported by perturbation of lrp expression or amino acid supplementation. E. coli strains were also engineered for altered cyclopropane fatty acid content in the membrane, which had a dramatic effect on membrane properties, though C8 tolerance was not increased. We conclude that achieving higher production titers requires circumventing the membrane damage. As higher titers are achieved, acidification may become problematic.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Carboxylic Acids / metabolism
  • Cell Membrane / metabolism
  • Escherichia coli / metabolism*
  • Escherichia coli Proteins / metabolism*
  • Gene Expression Regulation, Bacterial

Substances

  • Carboxylic Acids
  • Escherichia coli Proteins

Grant support

This work was supported by the National Science Foundation (NSF) Engineering Research Center for Biorenewable Chemicals (CBiRC), NSF award number EEC-0813570. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.