Non-canonical activation of OmpR drives acid and osmotic stress responses in single bacterial cells

Smarajit Chakraborty,Jie Yan,Leslie K Morgan,Ricksen S Winardhi,Linda J Kenney

doi:10.1038/s41467-017-02030-0

Abstract

Unlike eukaryotes, bacteria undergo large changes in osmolality and cytoplasmic pH. It has been described that during acid stress, bacteria internal pH promptly acidifies, followed by recovery. Here, using pH imaging in single living cells, we show that following acid stress, bacteria maintain an acidic cytoplasm and the osmotic stress transcription factor OmpR is required for acidification. The activation of this response is non-canonical, involving a regulatory mechanism requiring the OmpR cognate kinase EnvZ, but not OmpR phosphorylation. Single cell analysis further identifies an intracellular pH threshold ~6.5. Acid stress reduces the internal pH below this threshold, increasing OmpR dimerization and DNA binding. During osmotic stress, the internal pH is above the threshold, triggering distinct OmpR-related pathways. Preventing intracellular acidification of Salmonella renders it avirulent, suggesting that acid stress pathways represent a potential therapeutic target. These results further emphasize the advantages of single cell analysis over studies of population averages.

Highlights

Unlike eukaryotes, bacteria undergo large changes in osmolality and cytoplasmic pH
We provide evidence that the E. coli strain MC4100 responds differently to extracellular acid or osmotic stress compared to the probiotic Nissle strain[13,14] and to MG1655, a sequenced strain[15]
Typhimurium reduced its intracellular pH in response to external acid stress in an OmpRdependent manner[2], in contrast to previous studies in E. coli that reported a rapid recovery within minutes[17,18]

Summary

Introduction

Bacteria undergo large changes in osmolality and cytoplasmic pH. It has been described that during acid stress, bacteria internal pH promptly acidifies, followed by recovery. Using pH imaging in single living cells, we show that following acid stress, bacteria maintain an acidic cytoplasm and the osmotic stress transcription factor OmpR is required for acidification. The activation of this response is non-canonical, involving a regulatory mechanism requiring the OmpR cognate kinase EnvZ, but not OmpR phosphorylation. Preventing intracellular acidification of Salmonella renders it avirulent, suggesting that acid stress pathways represent a potential therapeutic target These results further emphasize the advantages of single cell analysis over studies of population averages. This study identifies a pH threshold in bacteria, below which OmpR phosphorylation is low, but dimerization is high and DNA binding is driven by an acid-dependent conformational change in OmpR. Unique genes are expressed above and below this threshold, allowing integration of osmotic and acid stress signals

Methods

Results

Conclusion