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A Role for Interaction of the RNA Polymerase Flap Domain with the σ Subunit in Promoter Recognition

In bacteria, promoter recognition depends on the RNA polymerase σ subunit, which combines with the catalytically proficient RNA polymerase core to form the holoenzyme. The major class of bacterial promoters is defined by two conserved elements (the –10 and –35 elements, which are 10 and 35 nucleotides upstream of the initiation point, respectively) that are contacted by σ in the holoenzyme. We show that recognition of promoters of this class depends on the “flexible flap” domain of the RNA polymerase β subunit. The flap interacts with conserved region 4 of σ and triggers a conformational change that moves region 4 into the correct position for interaction with the –35 element. Because the flexible flap is evolutionarily conserved, this domain may facilitate promoter recognition by specificity factors in eukaryotes as well.