Structural basis for promoter-10 element recognition by the bacterial RNA polymerase σ subunit.

Publication Type:

Journal Article


Cell, Volume 147, Issue 6, p.1257-69 (2011)


Bacterial Proteins, Base Pairing, Base Sequence, Crystallography, X-Ray, DNA, Single-Stranded, DNA-Directed RNA Polymerases, Escherichia coli, Escherichia coli Proteins, Hydrophobic and Hydrophilic Interactions, Models, Molecular, Promoter Regions, Genetic, Sigma Factor, Thermus


<p>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 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.</p>