Structural Basis of DNA Recognition by the Alternative Sigma-factor, σ54

The σ subunit of bacterial RNA polymerase (RNAP) regulates gene expression by directing RNAP to specific promoters. Unlike σ70-type proteins, the alternative σ factor, σ54, requires interaction with an ATPase to open DNA. We present the solution structure of the C-terminal domain of σ54 bound to the −24 promoter element, in which the conserved RpoN box motif inserts into the major groove of the DNA. This structure elucidates the basis for sequence specific recognition of the −24 element, orients σ54 on the promoter, and suggests how the C-terminal domain of σ54 interacts with RNAP.