Altering the interaction between σ 70 and RNA polymerase generates complexes with distinct transcription-elongation properties

We compare the elongation behavior of native Escherichia coli RNA polymerase holoenzyme assembled in vivo, holoenzyme reconstituted from sigma70 and RNA polymerase in vitro, and holoenzyme with a specific alteration in the interface between sigma70 and RNA polymerase. Elongating RNA polymerase from each holoenzyme has distinguishable properties, some of which cannot be explained by differential retention or rebinding of sigma70 during elongation, or by differential presence of elongation factors. We suggest that interactions between RNA polymerase and sigma70 may influence the ensemble of conformational states adopted by RNA polymerase during initiation. These states, in turn, may affect the conformational states adopted by the elongating enzyme, thereby physically and functionally imprinting RNA polymerase.