A balancing act in transcription regulation by response regulators: titration of transcription factor activity by decoy DNA binding sites

Abstract

Studies of transcription regulation are often focused on binding of transcription factors (TFs) to a small number of promoters of interest. It is often assumed that TFs are in great excess to their binding sites (TFBSs) and competition for TFs between DNA sites is seldom considered. With increasing evidence that TFBSs are exceedingly abundant for many TFs and significant variations in TF and TFBS numbers occur during growth, the interplay between a TF and all TFBSs should not be ignored. Here, we use additional decoy DNA sites to quantitatively analyze how the relative abundance of a TF to its TFBSs impacts the steady-state level and onset time of gene expression for the auto-activated Escherichia coli PhoB response regulator. We show that increasing numbers of decoy sites progressively delayed transcription activation and lowered promoter activities. Perturbation of transcription regulation by additional TFBSs did not require extreme numbers of decoys, suggesting that PhoB is approximately at capacity for its DNA sites. Addition of decoys also converted a graded response to a bi-modal response. We developed a binding competition model that captures the major features of experimental observations, providing a quantitative framework to assess how variations in TFs and TFBSs influence transcriptional responses.

Loss of heterochromatin at endogenous retroviruses creates competition for transcription factor binding

“…Interestingly, previous studies have suggested that repetitive elements or even transgenes might serve as sinks for TF binding (31)(32)(33)(34)(35)(36). Studies in bacteria have been particularly important in exploring the stoichiometry between TF protein level and TF binding sites and suggest that certain TFs may be more susceptible to titration effects than others (35,36).…”

“…Interestingly, previous studies have suggested that repetitive elements or even transgenes might serve as sinks for TF binding (31)(32)(33)(34)(35)(36). Studies in bacteria have been particularly important in exploring the stoichiometry between TF protein level and TF binding sites and suggest that certain TFs may be more susceptible to titration effects than others (35,36). While these studies provide important conceptual advances in our understanding of the biophysical determinants of transcription at the level of transcription factor binding, they use exogenous cellular perturbations and do not always mimic molecular mechanisms relevant to eukaryotic cells.…”

“…While it is possible that ERVs are competing with genes for transcription machinery such as the Mediator complex or RNAPII, the specificity of this competition must be driven by transcription factors themselves. Additionally, our model requires that occupied TF binding sites are at equilibrium with the molecules of TF available for binding (35)(36)(37). It is welldocumented that not all predicted TF motifs in the genome are bound by TFs, and we still do not fully understand the "grammar" of regulatory elements that prefers binding at certain sites over others (38).…”

The regulon of Brucella abortus two-component system BvrR/BvrS reveals the coordination of metabolic pathways required for intracellular life

“…Global regulators are known to bind to a collection of sites, and the regulatory effect on each binding site would be dependent on the protein concentration at any given moment, its affinity, and additional transcription factors. Hence, they can be activators, repressors, have dual regulatory roles, or have no described regulatory function [103][104][105][106][107].…”

Development of a highly efficient LbCas12a CRISPR system in barley with additional utility in Brassica oleracea

“…Conversely V2 transcription of guide 1 may be less than in V1 due to local competition for transcription factors between the 4 closely linked TaU6/TaU3 promoters in V2. Reduced promoter activity resulting from the addition of decoy transcription factor binding sites has been reported (Gao et al, 2021). Knockout of both copies of HORVU.MOREX.r3.2HG0184740 is expected to result in the conversion of tworowed Golden Promise spikes into six row spikes (Komatsuda et al, 2007).…”