A classical paradigm of transcription activation was established by studies of the catabolite activator protein (CAP) in Escherichia coli ( Eco), the bacterium where much of our understanding of gene expression is rooted ( 1). Gene expression is orchestrated by transcription factors that activate or inhibit initiation by RNA polymerase (RNAP). Finally, we compare the architecture of the WhiA/B σ A-holoenzyme promoter complex with the unrelated but model CAP Class I and Class II complexes, showing that WhiA/WhiB represent a new mechanism in bacterial transcriptional activation. Structure-guided mutagenesis designed to disrupt these protein–DNA interactions reduces or abolishes developmental cell division in Sven, confirming their significance. Notably, the structure of the WhiA-CTD and its interactions with the WhiA motif are strikingly similar to those observed between σ A 4 housekeeping σ-factors and the −35 promoter element, suggesting an evolutionary relationship. The N-terminal homing endonuclease-like domain of WhiA interacts with WhiB, while the WhiA C-terminal domain (WhiA-CTD) makes base-specific contacts with the conserved WhiA GACAC motif. These structures reveal that WhiB binds to domain 4 of σ A (σ A 4) of the σ A-holoenzyme, bridging an interaction with WhiA while making non-specific contacts with the DNA upstream of the −35 core promoter element. Here we present cryoelectron microscopy structures of Sven transcriptional regulatory complexes comprising RNA polymerase (RNAP) σ A-holoenzyme and WhiA and WhiB, in complex with the WhiA/B target promoter sepX. However, how these factors cooperate at the molecular level is not understood. The WhiA/B regulons and binding sites have been elucidated in Streptomyces venezuelae ( Sven), where they coordinate to activate sporulation septation. The WhiA and WhiB factors are both required to express cell division genes in Actinobacteria and are essential in notable pathogens such as Mycobacterium tuberculosis. Studies of transcriptional initiation in different bacterial clades reveal diverse molecular mechanisms regulating this first step in gene expression.

Parallels 14 activation key