A general mechanism for transcription bubble nucleation in bacteria

Bacterial transcription initiation requires σ factors for nucleation of the transcription bubble. The canonical housekeeping σ factor, σ(70), nucleates DNA melting via recognition of conserved bases of the promoter −10 motif, which are unstacked and captured in pockets of σ(70). By contrast, the mechanism of transcription bubble nucleation and formation during the unrelated σ(N)-mediated transcription initiation is poorly understood. Herein, we combine structural and biochemical approaches to establish that σ(N), like σ(70), captures a flipped, unstacked base in a pocket formed between its N-terminal region I (RI) and extra-long helix features. Strikingly, RI inserts into the nascent bubble to stabilize the nucleated bubble prior to engagement of the obligate ATPase activator. Our data suggest a general paradigm of transcription initiation that requires σ factors to nucleate an early melted intermediate prior to productive RNA synthesis.