Core promoter sequences provide primary cues to direct RNA polymerase for transcription. Yet former studies of transcriptional regulation revolve around transcription factors and their binding sites, largely neglecting the role of core promoters. To better understand, my group performed high-throughput experiments to determine the comprehensive sequence-function relationship of two bacterial promoter elements, -35 and -10, in two constitutive promoters and three promoters regulated by distinct transcription factors. Using the sequence-function data of tens of millions of promoter variants, we constructed biophysical models to decipher the design principles of bacterial promoters and transcriptional regulation. Our results show the -10 element absolutely essential to transcription initiation. Though the -35 element is dispensable in this regard, its interaction with RNA polymerase and transcription factors contributes significantly to the dynamic range of regulated promoters (i.e., fold-change between the basal and induced states). Moreover, we find evolution has shaped the native -35 and -10 elements of three regulated promoters distinctively to attain nearly maximal dynamic ranges. Our work highlights the functional integration of core promoters in transcriptional regulation, yields computational tools to guide promoter design, and has profound implications for the evolution of cis-regulatory elements and transcription machinery.
Unraveling the Design Principles of Bacterial Promoters and Transcriptional Regulation