A phage transcription factor displaces the host σ factor and stabilizes its own σ factor

Phages are the most abundant self-replicating entities on earth, and understanding their transcriptional regulation can provide insights into bacterial gene expression mechanisms. The bacterial RNA polymerase core enzyme interacts with various σ factors to recognize and unwind promoter DNA. Gp79, a protein from Escherichia coli phage phiEco32, inhibits host σ70-mediated transcription while simultaneously activating transcription through its own σ factor, gp36. The underlying mechanism of this unusual dual regulatory role has remained unclear. In this study, we present cryo-EM structures of E. coli RNA polymerase (RNAP) in complex with gp79, and of RNAP in complex with gp79, gp36, and a cognate promoter. Structural and biochemical analyses reveal the basis for σ displacement by gp79 and promoter recognition by gp36. Our findings show that the N-terminus of gp79 invades the RNA channel, effectively displacing σ4. Upon encountering gp36, the N-terminus of gp79 adopts a new conformation, binds to gp36, and stabilizes the RNAP-promoter open complex. These findings advance our understanding of phage transcriptional regulation and suggest potential applications for synthetic biology.