Identification of sigma factors for growth phase-related promoter selectivity of RNA polymerases from Streptomyces coelicolor A3(2)

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Abstract
We examined the promoter selectivity of RNA polymerase (RNAP) from Streptomyces coelicolor at two growth phases by in vitro transcription. Distinct sets of promoters were preferentially recognized by either exponential or stationary phase RNAP. No change in molecular weight or net charge of the core subunits was observed, suggesting that the associated specificity factors determined phase-specific promoter selectivity of the holoenzyme. Five different specificity factors and their cognate promoters were identified by in vitro holoenzyme reconstitution and transcription assays. σ66 (σhrdB) and σ46 (σhrdD) recognized promoters (rrnDp2 and dagAp4 for σ66, actIIorf4p and whiBp2 for σ46) preferentially transcribed by the exponential phase RNAP. σ52 recognized promoters (dagAp3 and actIIIpx1) preferentially transcribed by the stationary phase RNAP. σ28 (σsigE) recognized promoters (hrdDp1, whiBp1 and dagAp2) transcribed equally by both RNAPs. A novel 31 kDa specificity factor recognized actIIIpx2, glnRp2 and hrdDp2 promoters preferentially transcribed by the stationary phase RNAP. This factor was isolated from the stationary phase RNAP and reconstituted holoenzyme in vitro as a sigma factor. The N-terminal sequence suggests that it is a novel factor. By examining phase-specific promoter recognition pattern we can predict that holoenzyme Eσ52 and Eσ31 activities are higher in the stationary phase, whereas Eσ66 and Eσ46 activities are higher in the exponential phase. Possible promoter sequences recognized by some of these sigma factors were suggested.