Defining The Regulon Of Genes Controlled By Sigma(E), A Key Regulator Of The Cell Envelope Stress Response In Streptomyces Coelicolor

The extracytoplasmic function (ECF) sigma factor, sigma(E), 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 sigma(E) 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 sigma(E)-binding consensus. Subsequently, we used bioinformatic analysis to look for conservation of the sigma(E) target promoters identified in S. coelicolor across 19 Streptomyces species. Key proteins under sigma(E) 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 sigma(E)-mediated cell envelope stress response in the genus Streptomyces.