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(-12)A(-11)T(-10)A(-9) A(-8)T(-7) consensus sequence) by the RNA polymerase sigma subunit. We determined crystal structures of sigma 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 sigma. 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.