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The subunit of eubacterial RNA polymerase is required throughout initiation, but how it communicates with core polymerase (␣ 2 ␤␤) is poorly understood. The present work addresses the location and function of the interface of with core. Our studies suggest that this interface is extensive as mutations in six conserved regions of 70 hinder the ability of to bind core. Direct binding of one of these regions to core can be demonstrated using a peptide-based approach. The same regions, and even equivalent residues, in 32 and 70 alter core interaction, suggesting that 70 family members use homologous residues, at least in part, to interact with core. Finally, the regions of that we identify perform specialized functions, suggesting that different portions of the interface perform discrete roles during transcription initiation.

A central enigma of transcriptional regulation is how the normally efficient transcription elongation complex stops at pause and termination signals. One possibility, raised by the discovery that RNA polymerase sometimes contracts its DNA footprint, is that discontinuous movements contribute to recognizing these signals. We report that E. coli RNA polymerase responds to sequences immediately downstream and upstream from the his leader pause site by changing neither its downstream DNA contact nor its upstream RNA contact for 8 bp preceding the pause. This compressed complex isomerizes to a paused conformation by an approximately 10 bp jump of its downstream DNA contact and simultaneous extrusion of an RNA hairpin that stabilizes the paused conformation. We suggest pausing and termination could be alternative outcomes of a similar isomerization that depend on the strength of contacts to 3'-proximal RNA remaining after the jump.

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