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.