RNase E-dependent degradation of tnaA mRNA encoding tryptophanase is prerequisite for the induction of acid resistance in Escherichia coli

<jats:title>Abstract</jats:title><jats:p>Acid-resistance systems are essential for pathogenic <jats:italic>Escherichia coli</jats:italic> to survive in the strongly acidic environment of the human stomach (pH < 2.5). Among these, the glutamic acid decarboxylase (GAD) system is the most effective. However, the precise mechanism of GAD induction is unknown. We previously reported that a <jats:italic>tolC</jats:italic> mutant lacking the TolC outer membrane channel was defective in GAD induction. Here, we show that indole, a substrate of TolC-dependent efflux pumps and produced by the tryptophanase encoded by the <jats:italic>tnaA</jats:italic> gene, negatively regulates GAD expression. GAD expression was restored by deleting <jats:italic>tnaA</jats:italic> in the <jats:italic>tolC</jats:italic> mutant; in wild-type <jats:italic>E. coli</jats:italic>, it was suppressed by adding indole to the growth medium. RNA-sequencing revealed that <jats:italic>tnaA</jats:italic> mRNA levels drastically decreased upon exposure to moderately acidic conditions (pH 5.5). This decrease was suppressed by RNase E deficiency. Collectively, our results demonstrate that the RNase E-dependent degradation of <jats:italic>tnaA</jats:italic> mRNA is accelerated upon acid exposure, which decreases intracellular indole concentrations and triggers GAD induction.</jats:p>