Mapping interactions of Escherichia coli GreB with RNA polymerase and ternary elongation complexes

Escherichia coli GreA and GreB modulate transcription elongation by interacting with the ternary elongation complex (containing RNA polymerase, DNA template, and RNA transcript) to induce hydrolytic cleavage of the transcript and release of the 3'-terminal fragment. Hydroxyl radical protein footprinting and alanine-scanning mutagenesis were used to investigate the interactions of GreB with RNA polymerase alone and in a ternary elongation complex. A major determinant for binding GreB to both RNA polymerase and the ternary elongation complex was identified. In addition, the hydroxyl radical footprinting indicated major conformational changes of GreB, in terms of reorientations of the N- and C-terminal domains with respect to each other, particularly upon interactions with the ternary elongation complex.