Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli.

Sang Woo Seo,Donghyuk Kim,Edward J O’Brien,Bernhard O Palsson,Richard Szubin

doi:10.1038/ncomms8970

Abstract

The regulators GadE, GadW and GadX (which we refer to as GadEWX) play a critical role in the transcriptional regulation of the glutamate-dependent acid resistance (GDAR) system in Escherichia coli K-12 MG1655. However, the genome-wide regulatory role of GadEWX is still unknown. Here we comprehensively reconstruct the genome-wide GadEWX transcriptional regulatory network and RpoS involvement in E. coli K-12 MG1655 under acidic stress. Integrative data analysis reveals that GadEWX regulons consist of 45 genes in 31 transcription units and 28 of these genes were associated with RpoS-binding sites. We demonstrate that GadEWX directly and coherently regulate several proton-generating/consuming enzymes with pairs of negative-feedback loops for pH homeostasis. In addition, GadEWX regulate genes with assorted functions, including molecular chaperones, acid resistance, stress response and other regulatory activities. These results show how GadEWX simultaneously coordinate many cellular processes to produce the overall response of E. coli to acid stress.

Highlights

The regulators GadE, GadW and GadX play a critical role in the transcriptional regulation of the glutamate-dependent acid resistance (GDAR) system in Escherichia coli K-12 MG1655
One of the most well-studied model organisms, Escherichia coli K-12 MG1655, has sophisticated acid resistance (AR) systems to survive in acidic pH environments
Several binding sites of GadEWX have been characterized in E. coli by in vitro DNA-binding experiments and mutation analysis[16,17,18,27,29,30,31,32,33,34,35,36,37]

Summary

Introduction

The regulators GadE, GadW and GadX (which we refer to as GadEWX) play a critical role in the transcriptional regulation of the glutamate-dependent acid resistance (GDAR) system in Escherichia coli K-12 MG1655. We comprehensively reconstruct the genome-wide GadEWX transcriptional regulatory network and RpoS involvement in E. coli K-12 MG1655 under acidic stress. GadEWX regulate genes with assorted functions, including molecular chaperones, acid resistance, stress response and other regulatory activities. A complete reconstruction of the GadEWX transcriptional regulatory networks under acidic stress would reveal the detailed mechanism of GadEWX regulation and its role in coordinating all cellular functions in response to acid stress. We measure transcription levels of genes in the wild-type strain and knockout mutants of each TF on a genome scale to identify causal transcriptional regulatory relationships From these data, we identify that the GadEWX regulatory networks maintain intracellular proton concentration by regulating proton-efflux/influx system and proton-generating/ consuming metabolic enzymes and interconnecting the tree of them with pairs of negative-feedback loops. Reconstruction of the GadEWX regulatory networks provides a comprehensive view of the coordinative genome-wide regulatory roles of these TFs under acidic stress

Methods

Results

Conclusion