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

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. sigma66 (sigma hrdB) and sigma46 (sigma hrdD) recognized promoters (rrnD p2 and dagA p4 for sigma66, actII-orf4 p and whiB p2 for sigma46) preferentially transcribed by the exponential phase RNAP. sigma52 recognized promoters (dagA p3 and actIII px1) preferentially transcribed by the stationary phase RNAP. Sigma28 (sigma sigE) recognized promoters (hrdD p1, whiB p1 and dagA p2) transcribed equally by both RNAPs. A novel 31 kDa specificity factor recognized actIII px2, glnR p2 and hrdD p2 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 Esigma52 and Esigma31 activities are higher in the stationary phase, whereas Esigma66 and Esigma46activities are higher in the exponential phase. Possible promoter sequences recognized by some of these sigma factors were suggested.