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

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