Structural Basis for Promoter −10 Element Recognition by the Bacterial RNA Polymerase σ Subunit

The key step in bacterial promoter opening is recognition of the −10 promoter element (T−12A−11T−10A−9A−8T−7 consensus sequence) by the RNA polymerase σ subunit. We determined crystal structures of σ domain 2 bound to single-stranded DNA bearing −10 element sequences. Extensive interactions occur between the protein and the DNA backbone of every −10 element nucleotide. Base-specific interactions occur primarily with A−11 and T−7, which are flipped out of the single-stranded DNA base stack and buried deep in protein pockets. The structures, along with biochemical data, support a model where the recognition of the −10 element sequence drives initial promoter opening as the bases of the nontemplate strand are extruded from the DNA double-helix and captured by σ. These results provide a detailed structural basis for the critical roles of A−11 and T−7 in promoter melting and reveal important insights into the initiation of transcription bubble formation.