The interface of σ with core RNA polymerase is extensive, conserved, and functionally specialized

Abstract

The σ subunit of eubacterial RNA polymerase is required throughout initiation, but how it communicates with core polymerase (α2ββ') is poorly understood. The present work addresses the location and function of the interface of σ with core. Our studies suggest that this interface is extensive as mutations in six conserved regions of σ70 hinder the ability of σ 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 σ32 and σ70 alter core interaction, suggesting that σ70 family members use homologous residues, at least in part, to interact with core. Finally, the regions of σ that we identify perform specialized functions, suggesting that different portions of the interface perform discrete roles during transcription initiation.