Two transcription pause elements underlie a σ70-dependent pause cycle

The movement of RNA polymerase (RNAP) during transcription elongation is modulated by DNA-encoded elements that cause the elongation complex to pause. One of the best-characterized pause sequences is a binding site for the σ(70) initiation factor that induces pausing at a site near lambdoid phage late-gene promoters. An essential component of this σ(70)-dependent pause is the elemental pause site (EPS), a sequence that itself induces transcription pausing throughout the Escherichia coli genome and underlies other complex regulatory pause elements, such as the ops and his operon pauses. Here, we identify and provide a detailed kinetic analysis of a transcription cycle analogous to abortive cycling that underlies the σ(70)-dependent pause. We show that, in σ(70)-dependent pausing, the elemental pause acts primarily to modulate the rate at which complexes attempt to disengage the σ(70):DNA interaction. Our findings establish the σ(70)-dependent pause-encoding region as a multipartite element in which several pause-inducing components make distinct mechanistic contributions to the induction and maintenance of a regulatory transcription pause.