Quantitative influence of macromolecular crowding on gene regulation kinetics

Abstract

We introduce macromolecular crowding quantitatively into the model for kinetics of gene regulation in Escherichia coli. We analyse and compute the specific-site searching time for 180 known transcription factors (TFs) regulating 1300 operons. The time is between 160 s (e.g. for SoxS Mw = 12.91 kDa) and 1550 s (e.g. for PepA6 of Mw = 329.28 kDa). Diffusion coefficients for one-dimensional sliding are between for large proteins up to for small monomers or dimers. Three-dimensional diffusion coefficients in the cytoplasm are 2 orders of magnitude larger than 1D sliding coefficients, nevertheless the sliding enhances the binding rates of TF to specific sites by 1–2 orders of magnitude. The latter effect is due to ubiquitous non-specific binding. We compare the model to experimental data for LacI repressor and find that non-specific binding of the protein to DNA is activation- and not diffusion-limited. We show that the target location rate by LacI repressor is optimized with respect to microscopic rate constant for association to non-specific sites on DNA. We analyse the effect of oligomerization of TFs and DNA looping effects on searching kinetics. We show that optimal searching strategy depends on TF abundance.

Biochemical reactions in crowded environments: revisiting the effects of volume exclusion with simulations

“…Most efforts to study the impact of molecular crowding on gene expression have been devoted to the binding of transcription factors to their binding sites on the chromosome [14,15,41]. For most transcription factors, this is a typical case of equilibrium binding and indeed most models for gene regulation are based on the assumption of a binding equilibrium for transcription factors [42,43].…”

The effect of macromolecular crowding on mobility of biomolecules, association kinetics, and gene expression in living cells

“…On the basis of these experiments we calculated the impact of macromolecular crowding [15] inside E. coli cell on transcription factor binding rates to specific sites [114]. We considered multilevel impact of in vivo crowding on association rates to specific sites in the facilitated diffusion model: (1) reduction of the nucleoid volume due to the presence of nucleoid-associated proteins that modify persistence length of DNA and cross-link DNA chains, (2) reduction of transcription factor three-and onedimensional diffusion constants [15], (3) obstruction of transcription factor binding to non-specific DNA and its sliding due to presence of nucleoid-associated proteins [115][116][117][118][119].…”

“…The detailed picture of the regulation kinetics is available only for lac repressor in E. coli [104][105][106]. The existing models, taking intracellular crowding into account and all existing experimental data show that this transcription factor is nearly optimized for its function [105,114,116]. We look forward to studies of gene regulation kinetics of other transcription factors to check generalization of the predictions in prokaryotes and detailed models of facilitated diffusion in eukaryotes.…”

Effect of crowding on protein-protein association in diffusion-limited regime

“…Protein association is an important center for various cellular processes such as enzyme catalysis, regulation of immune response by cytokines as well as gene regulation, etc [1,2]. Understanding the physical principles governing association mechanisms and rate constants and furthermore, realistically modeling them, are crucial to study the relationship between the cellular structure and function.…”