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

The extracytoplasmic function (ECF) sigma factor, sigmaE 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 sigmaE regulon. Approximately half of the genes identified encode proteins implicated in cell envelope function. 17 novel targets were validated by S1 nuclease mapping or in vitro transcription, establishing a sigmaE binding consensus. Subsequently, we used bioinformatic analysis to look for conservation of the sigmaE target promoters identified in S. coelicolor across 19 Streptomyces species. Key proteins under sigmaE 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 sigmaE-mediated cell envelope stress response in the genus Streptomyces.