Conformational switching of Escherichia coli RNA polymerase-promoter binary complex is facilitated elongation factor GreA and GreB

Background: The initiation arrest at a modified lambdaP(R) promoter is caus ed by irreversible divergence of the reaction pathway into productive and a rrested branches. Escherichia coli GreA and GreB induce cleavage of the nas cent transcript and relieve arrest in elongation. They also reduce abortive synthesis at several promoters and relieve initiation arrest. Their mechan ism of action during initiation, and its relationship to the branched initi ation pathway are unknown. Results: The Gre factors mitigated initiation arrest only when they were ad ded to the binary complex of the holoenzyme bound to the lambdaP(R) promote r, prior to RNA synthesis. They exerted little effect when they were added to ternary initiation complexes. They accelerated the exchange of the binar y complex with its free components by 6-9-fold. When they are present, a hi gh concentration of the initiating nucleotide increased yield of the full-l ength transcript, whereas a low concentration did not. Conclusions: All the results presented above can be explained by a model wh ere the productive and arrested pathways diverge at the binary complex stag e. The Gre factors relieve the initiation arrest by introducing reversibili ty between subspecies of the binary complex that are precursors of the two pathways. RNA cleavage is unlikely to cause relief of initiation arrest.