Unraveling the start element and regulatory divergence of core promoters across the domain Bacteria

Core promoters comprise multiple elements whose interaction with RNA polymerase initiates transcription. Despite decades of research, substantial sequence and length variation of promoter elements has hindered efforts to elucidate their function and the evolutionary diversity of transcriptional regulation. Combining massively parallel assays, biophysical modeling, and functional validation, we systematically dissected the promoter architecture upstream of experimentally determined transcription start sites in 49 phylogenetically diverse bacterial genomes (GC content: 27.8–72.1%). We identified a conserved 3-bp promoter element, termed ‘start,’ that dictates transcription start site selection and enhances transcription. We uncovered a four-region organization within the variable spacer element, whose sequence composition modulates transcription by up to 600-fold. We showed that the discriminator element is conserved in Terrabacteria but diverse in Gracilicutes, the two major bacterial clades. High discriminator sequence diversity in Gracilicutes likely reflects diversifying evolution, enabling promoter-encoded regulation to orchestrate global gene expression in response to growth rate changes. Together, our findings reveal broad conservation of bacterial promoter organization while highlighting regulatory divergence of promoter elements and RNA polymerase between Terrabacteria and Gracilicutes. Sequence and functional similarities between bacterial promoter elements and their archaeal and eukaryotic counterparts further suggest a shared evolutionary origin of promoter architecture.