Crystal structure ofAquifex aeolicusσNbound to promoter DNA and the structure of σN-holoenzyme

Abstract

The bacterial σ factors confer promoter specificity to the RNA polymerase (RNAP). One alternative σ factor, σN, is unique in its structure and functional mechanism, forming transcriptionally inactive promoter complexes that require activation by specialized AAA+ATPases. We report a 3.4-Å resolution X-ray crystal structure of a σNfragment in complex with its cognate promoter DNA, revealing the molecular details of promoter recognition by σN. The structure allowed us to build and refine an improved σN-holoenzyme model based on previously published 3.8-Å resolution X-ray data. The improved σN-holoenzyme model reveals a conserved interdomain interface within σNthat, when disrupted by mutations, leads to transcription activity without activator intervention (so-called bypass mutants). Thus, the structure and stability of this interdomain interface are crucial for the role of σNin blocking transcription activity and in maintaining the activator sensitivity of σN.