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Previous studies have come to conflicting conclusions about the requirement for the ω subunit of RNA polymerase in bacterial transcription regulation. We demonstrate here that purified RNAP lacking ω does not respond in vitro to the effector of the stringent response, ppGpp. DksA, a transcription factor that works in concert with ppGpp to regulate rRNA expression in vivo and in vitro, fully rescues the ppGpp-unresponsiveness of RNAP lacking ω, likely explaining why strains lacking ω display a stringent response in vivo. These results demonstrate that ω plays a role in RNAP function (in addition to its previously reported role in RNAP assembly) and highlight the importance of inclusion of ω in RNAP purification protocols. Furthermore, these results suggest that either one or both of two short segments in the β′ subunit that physically link ω to the ppGpp-binding region of the enzyme may play crucial roles in ppGpp and DksA function.

Response of RNA polymerase to ppGpp: requirement for the ω subunit and relief of this requirement by DksA