Crl activates transcription by stabilizing the active conformation of the master stress factor σ^S

Abstract

σ S is a master transcription initiation factor that protects bacterial cells from various harmful environmental stresses and antibiotic pressure. Although its mechanism remains unclear, it is known that full activation of σ S -mediated transcription requires a σ S -specific activator, Crl. In this study, we determined a 3.80 Å cryo-EM structure of an E. coli transcription activation complex (E. coli Crl-TAC) comprising E. coli σ S -RNAP holoenzyme, Crl, and a nucleic-acid scaffold. The structure reveals that Crl interacts with the domain 2 of σ S (σ S 2 ), sharing no interaction with promoter DNA. Subsequent hydrogen-deuterium exchange mass spectrometry (HDX-MS) results indicate that Crl stabilizes key structural motifs of σ S 2 to promote the assembly of σ S -RNAP holoenzyme and also to facilitate formation of the RNA polymerase-promoter DNA open complex (RPo). Our study demonstrates a unique DNA contact-independent mechanism of transcription activation, thereby defining a previously unrecognized mode of transcription activation in cells.