The Role of Binding Sequence, Position, and Promoter Strength on the Regulatory Modes of E. coli Transcription

Abstract

The activity of Transcription Factors (TFs) is essential to gene regulation, facilitating the transfer of information encoded in cis-regulatory elements into temporal and spatial control of gene expression. Despite progress in mapping the genomic binding sites of TFs, the regulatory role of TFs once bound is often convoluted. Here, we utilize a synthetic biology approach that allows for precise manipulation of TF concentration in vivo and interrogation of the role of promoter features on the regulatory function of E.coli TFs. Using thermodynamic models of gene regulation, we decouple TF occupancy from its maximal regulatory output and probe its regulation on two steps of the transcription process: stabilization of RNA polymerase (RNAP) binding and modulation of transcription initiation. Profiling the CpxR activator, we discover universal stabilization across regulated positions, with differences in strong and weak activation set primarily by regulation of the initiation rate. Formulating a high-throughput approach, we probe the regulation of 93 E.coli TFs to find that the relative contributions of binding sequence and position on the mode of action are decoupled, with position playing a dominant role for select factors. Building on this information, we assessed the interplay between binding position, TF identity, and basal promoter strength - uncovering a conserved mode of stabilizing regulation across TFs with diverse regulatory outcomes. Taken together, our work delineates the effect of promoter architecture on the quantitative regulatory activity of TFs, with implications for design of synthetic gene circuits and understanding natural promoters