The interface of sigma 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.