Structural basis for transcription initiation by bacterial ECF σ factors

Abstract

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