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

Abstract

The multisubunit RNA polymerase (RNAP) in bacteria consists of a catalytically active core enzyme (α2ββ′ω) complexed with a σ factor that is required for promoter-specific transcription initiation. During early elongation the stability of interactions between σ and core decreases, in part because of the nascent RNA-mediated destabilization of an interaction between region 4 of σ and the flap domain of the β-subunit (β-flap). The nascent RNA-mediated destabilization of the σ region 4/β-flap interaction is required for the bacteriophage λ Q antiterminator protein (λQ) to engage the RNAP holoenzyme. Here, we provide an explanation for this requirement by showing that λQ establishes direct contact with the β-flap during the engagement process, thus competing with σ70 region 4 for access to the β-flap. We also show that λQ's affinity for the β-flap is calibrated to ensure that λQ activity is restricted to the λ late promoter PR′. Specifically, we find that strengthening the λQ/β-flap interaction allows λQ to bypass the requirement for specific cis-acting sequence elements, a λQ-DNA binding site and a RNAP pause-inducing element, that normally ensure λQ is recruited exclusively to transcription complexes associated with PR′. Our findings demonstrate that the β-flap can serve as a direct target for regulators of elongation.