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

The structure of an intermediate in the initiation to elongation transition of Escherichia coli RNA polymerase has been visualized through region-spec ific DNA cleavage by the hydroxyl radical reagent FeBABE. FeBABE was tether ed to specific sites of the sigma (70) subunit and incorporated into two sp ecialized paused elongation complexes that obligatorily retain the sigma (7 0) initiation subunit and are targets for modification by lambdoid phage la te gene antiterminators. The FeBABE cleavage pattern reveals structures sim ilar to open complex, except for notable changes to region 3 of sigma (70) that might reflect the presence of stably bound transcript. Binding of the antiterminator protein Q displaces the reactivity of FeBABE conjugated to r egion 4 of sigma (70), suggesting that a sigma (70) subunit rearrangement i s a step in conversion of RNAP to the antiterminating form.