Unravel the start element and promoter architecture across the domain Bacteria

Promoters comprise multiple elements to modulate transcription. Despite decades of research, significant sequence and length variation of promoter elements renders elucidation of promoter function and the evolutionary diversity of transcriptional regulation challenging. Combining massively parallel assays with biophysical modeling, we mapped each promoter element across 49 phylogenetically diverse bacterial genomes (GC%: 27.8-72.1). We discovered a conserved promoter element, ‘start,’ that dictates transcription start site selection. We uncovered broad sequence conservation in the underappreciated spacer element, affecting transcription by up to 600-fold. We showed the discriminator element conserved in major bacterial clades Terrabacteria but variable in Gracilicutes. High sequence variation in Gracilicutes’ discriminator element resulted from diversifying evolution, enabling coordination of global gene expression with cellular growth rate through differential regulation of individual promoters. Identifying sequence and functional similarity between bacterial promoter elements and their archaeal and eukaryotic counterparts strongly suggests a shared evolutionary origin of promoter architecture.