Utilization of variably spaced promoter-like elements by the bacterial RNA polymerase holoenzyme during early elongation.

The bacterial RNA polymeras holoenzyme consists of a catalytic core enzyme in complex with a σ factor that is required for promoter-specific transcription initiation. During initiation, members of the σ70 family of σ factors contact two conserved promoter elements, the −10 and −35 elements, which are separated by ∼17 base pairs (bp). σ70 family members contain four flexibly linked domains. Two of these domains, σ2 and σ4, contain determinants for interactions with the promoter −10 and −35 elements respectively. σ2 and σ4 also contain core-binding determinants. When bound to core the inter-domain distance between σ2 and σ4 matches the distance between promoter elements separated by ∼17 bp. Prior work indicates that during early elongation the nascent RNA-assisted displacement of σ4 from core can enable the holoenzyme to adopt a configuration in which σ2 and σ4 are bound to ‘promoter-like’ DNA elements separated by a single base pair. Here we demonstrate that holoenzyme can also adopt configurations in which σ2 and σ4 are bound to ‘promoter-like’ DNA elements separated by 0, 2 or 3 bp. Thus, our findings suggest that displacement of σ4 from core enables the RNA polymerase holoenzyme to adopt a broad range of ‘elongation-specific’ configurations. [ABSTRACT FROM AUTHOR]