Defining the regulon of genes controlled by σE , a key regulator of the cell envelope stress response in Streptomyces coelicolor.

Ngat T Tran,Mark J Buttner,Daniela Pinto,Govind Chandra,Hee‐Jeon Hong,Xiaoluo Huang,Maureen J Bibb,Matthew I Hutchings,Thorsten Mascher,Matthew J Bush

doi:10.1111/mmi.14250

Abstract

SummaryThe extracytoplasmic function (ECF) σ factor, σE, is a key regulator of the cell envelope stress response in Streptomyces coelicolor. Although its role in maintaining cell wall integrity has been known for over a decade, a comprehensive analysis of the genes under its control has not been undertaken. Here, using a combination of chromatin immunoprecipitation‐sequencing (ChIP‐seq), microarray transcriptional profiling and bioinformatic analysis, we attempt to define the σE regulon. Approximately half of the genes identified encode proteins implicated in cell envelope function. Seventeen novel targets were validated by S1 nuclease mapping or in vitro transcription, establishing a σE‐binding consensus. Subsequently, we used bioinformatic analysis to look for conservation of the σE target promoters identified in S. coelicolor across 19 Streptomyces species. Key proteins under σE control across the genus include the actin homolog MreB, three penicillin‐binding proteins, two L,D‐transpeptidases, a LytR‐CpsA‐Psr‐family protein predicted to be involved in cell wall teichoic acid deposition and a predicted MprF protein, which adds lysyl groups to phosphatidylglycerol to neutralize membrane surface charge. Taken together, these analyses provide biological insight into the σE‐mediated cell envelope stress response in the genus Streptomyces.

Highlights

The bacterial cell envelope, made up of the cell wall and cell membranes, is critical in counteracting the high intracellular osmotic pressure to maintain cell shape (Silhavy et al, 2010)
We first constructed a strain of S. coelicolor that lacked sigE at its native locus but expressed an N-terminally triple-FLAG-tagged version of σE from the ΦBT1 integration site
The congenic wild-type S. coelicolor strain M600 was used as a negative control to eliminate any false signals that might arise from cross-reaction of the anti-FLAG antibody with other Difco Nutient Agar (DNA) binding proteins

Summary

Introduction

The bacterial cell envelope, made up of the cell wall and cell membranes, is critical in counteracting the high intracellular osmotic pressure to maintain cell shape (Silhavy et al, 2010). Despite the critical role of σE in modulating the cell envelope stress response in S. coelicolor, only two in vivo targets have so far been described: the hrdD gene, encoding another σ factor (Paget et al, 1999a), the function of which is poorly understood (Buttner et al, 1990; Strakova et al, 2014), and the 12-gene cwg operon, predicted to be involved in the biosynthesis of a cell wall glycan (Hong et al, 2002).

Results

Conclusion