Structural basis for transcription initiation by bacterial ECF σ factors

Bacterial RNA polymerase employs extra-cytoplasmic function (ECF) σ factors to regulate context-specific gene expression programs. Despite being the most abundant and divergent σ factor class, the structural basis of ECF σ factor-mediated transcription initiation remains unknown. Here, we determine a crystal structure of Mycobacterium tuberculosis (Mtb) RNAP holoenzyme comprising an RNAP core enzyme and the ECF σ factor σ(H) (σ(H)-RNAP) at 2.7 Å, and solve another crystal structure of a transcription initiation complex of Mtb σ(H)-RNAP (σ(H)-RPo) comprising promoter DNA and an RNA primer at 2.8 Å. The two structures together reveal the interactions between σ(H) and RNAP that are essential for σ(H)-RNAP holoenzyme assembly as well as the interactions between σ(H)-RNAP and promoter DNA responsible for stringent promoter recognition and for promoter unwinding. Our study establishes that ECF σ factors and primary σ factors employ distinct mechanisms for promoter recognition and for promoter unwinding.