Function of E. coli RNA polymerase sigma factor sigma 70 in promoter-proximal pausing.

The sigma factor sigma 70 of E. coli RNA polymerase acts not only in initiation, but also at an early stage of elongation to induce a transcription pause, and simultaneously to allow the phage lambda gene Q transcription antiterminator to act. We identify the signal in DNA that induces early pausing to be a version of the sigma 70 -10 promoter consensus, and we show that sigma 70 is both necessary for pausing and present in the paused transcription complex. Regions 2 and 3 of sigma 70 suffice to induce pausing. Since pausing is induced by the nontemplate DNA strand of the open transcription bubble, we conclude that RNA polymerase containing sigma 70 carries out base-specific recognition of the nontemplate strand as single stranded DNA. We suggest that sigma 70 remains bound to core RNA polymerase when the -10 promoter contacts are broken, and then moves to the pause-inducing sequence.