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Two transcription pause elements underlie a σ70-dependent pause cycle

Significance During transcription, RNA polymerase encounters DNA-encoded signals that interrupt RNA synthesis and cause the transcription elongation complex to pause. An important function of transcription pausing in gene regulation is the halting of transcription to facilitate assembly of regulatory factors into complex with RNA polymerase. An example of this function is found in the bacteriophage λ late-gene transcription, in which the initiation factor σ70 induces a pause that mediates recruitment of the antitermination factor Qλ, thereby allowing the expression of genes downstream of an intrinsic terminator. In this study, we characterize the contributions of two pause signals to σ70-dependent pause kinetics and propose a comprehensive model for σ70-dependent pausing. 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 σ70 initiation factor that induces pausing at a site near lambdoid phage late-gene promoters. An essential component of this σ70-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 σ70-dependent pause. We show that, in σ70-dependent pausing, the elemental pause acts primarily to modulate the rate at which complexes attempt to disengage the σ70:DNA interaction. Our findings establish the σ70-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.