Restructuring of an RNA polymerase holoenzyme elongation complex by lambdoid phage Q proteins

Abstract

The structure of an intermediate in the initiation to elongation transition of Escherichia coli RNA polymerase has been visualized through region-specific DNA cleavage by the hydroxyl radical reagent FeBABE. FeBABE was tethered to specific sites of the σ70 subunit and incorporated into two specialized paused elongation complexes that obligatorily retain the σ70 initiation subunit and are targets for modification by lambdoid phage late gene antiterminators. The FeBABE cleavage pattern reveals structures similar to open complex, except for notable changes to region 3 of σ70 that might reflect the presence of stably bound transcript. Binding of the antiterminator protein Q displaces the reactivity of FeBABE conjugated to region 4 of σ70, suggesting that σ70 subunit rearrangement is a step in conversion of RNAP to the antiterminating form.