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

SummaryThe 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.

Graphical AbstractFigure optionsDownload high-quality image (179 K)Download as PowerPoint slideHighlights
► Structure of the bacterial RNA polymerase σ subunit/promoter −10 element DNA complex
► Base-specific interactions occur with two highly conserved bases flipped out of the DNA
► Results suggest that −10 element recognition and melting are coupled