Characterization of the Escherichia coli σS core regulon by Chromatin Immunoprecipitation-sequencing (ChIP-seq) analysis

In bacteria, selective promoter recognition by RNA polymerase is achieved by its association with sigma factors, accessory subunits able to direct RNA polymerase core enzyme (E) to different promoter sequences. Using Chromatin Immunoprecipitation-sequencing (ChIP-seq), we searched for promoters bound by the sigma(S)-associated RNA polymerase form (E sigma(S)) during transition from exponential to stationary phase. We identified 63 binding sites for E sigma(S) overlapping known or putative promoters, often located upstream of genes (encoding either ORFs or non-coding RNAs) showing at least some degree of dependence on the sigma(S)-encoding rpoS gene. E sigma(S) binding did not always correlate with an increase in transcription level, suggesting that, at some sigma(S)-dependent promoters, E sigma(S) might remain poised in a pre-initiation state upon binding. A large fraction of E sigma(S)-binding sites corresponded to promoters recognized by RNA polymerase associated with s 70 or other sigma factors, suggesting a considerable overlap in promoter recognition between different forms of RNA polymerase. In particular, E sigma(S) appears to contribute significantly to transcription of genes encoding proteins involved in LPS biosynthesis and in cell surface composition. Finally, our results highlight a direct role of E sigma(S) in the regulation of non coding RNAs, such as OmrA/B, RyeA/B and SibC.