The bacteriophage λ Q antiterminator protein contacts the β-flap domain of RNA polymerase

The multisubunit RNA polymerase (RNAP) in bacteria consists of a catalytically active core enzyme (alpha(2)beta beta'omega) complexed with a sigma factor that is required for promoter-specific transcription initiation. During early elongation the stability of interactions between (rand core decreases, in part because of the nascent RNA-mediated destabilization of an interaction between region 4 of sigma and the flap domain of the beta-subunit (beta-flap). The nascent RNA-mediated destabilization of the or region 4/beta-flap interaction is required for the bacteriophage lambda Q antiterminator protein (lambda Q) to engage the RNAP holoenzyme. Here, we provide an explanation for this requirement by showing that lambda Q establishes direct contact with the beta-flap during the engagement process, thus competing with sigma(70) region 4 for access to the beta-flap. We also show that lambda Q's affinity for the beta-flap is calibrated to ensure that lambda Q activity is restricted to the lambda late promoter P-R. Specifically, we find that strengthening the lambda Q/beta-flap interaction allows lambda Q to bypass the requirement for specific cis-acting sequence elements, a lambda Q-DNA binding site and a RNAP pause-inducing element, that normally ensure lambda Q is recruited exclusively to transcription complexes associated with P-R. Our findings demonstrate that the beta-flap can serve as a direct target for regulators of elongation.