Aspects of protein-DNA interactions: a review of quantitative thermodynamic theory for modelling synthetic circuits utilising LacI and CI repressors, IPTG and the reporter gene lacZ

A systematic survey of TF function in E. coli suggests RNAP stabilization is a prevalent strategy for both repressors and activators

Transcription factors (TFs) are often classified as activators or repressors, yet these context-dependent labels are inadequate to predict quantitative profiles that emerge across different promoters. A mechanistic understanding of how different regulatory sequences shape TF function is challenging due to the lack of systematic genetic control in endogenous genes. To address this, we use a library of Escherichia coli strains with precise control of TF copy number, measuring the quantitative regulatory input-output function of 90 TFs on synthetic promoters that isolate the contributions of TF binding sequence, location, and basal promoter strength to gene expression. We interpret the measured regulation of these TFs using a thermodynamic model of gene expression and uncover stabilization of RNA polymerase as a pervasive regulatory mechanism, common to both activating and repressing TFs. This property suggests ways to tune the dynamic range of gene expression through the interplay of stabilizing TF function and RNA polymerase basal occupancy, a phenomenon we confirm by measuring fold change for stabilizing TFs across synthetic promoter sequences spanning over 100-fold basal expression. Our work deconstructs TF function at a mechanistic level, providing foundational principles on how gene expression is realized across different promoter contexts, with implications for decoding the relationship between sequence and gene expression.

Governing principles of transcriptional logic out of equilibrium

To survive, adapt, and develop, cells respond to external and internal stimuli by tightly regulating transcription. Transcriptional regulation involves the combinatorial binding of a repertoire of transcription factors to DNA, which often results in switch-like binary outputs akin to Boolean logic gates. Recent experimental studies have demonstrated that in eukaryotes, transcription factor binding to DNA often involves energy expenditure, thereby driving the system out of equilibrium. The governing principles of transcriptional logic operations out of equilibrium remain unexplored. Here, we employ a simple two-input, single-locus model of transcription that can accommodate both equilibrium and nonequilibrium mechanisms. Using this model, we find that nonequilibrium regimes can give rise to all the logic operations accessible in equilibrium. Strikingly, energy expenditure alters the regulatory function of the two transcription factors in a mutually exclusive manner. This allows for the emergence of new logic operations that are inaccessible in equilibrium. Overall, our results show that energy expenditure can expand the range of cellular decision-making without the need for more complex promoter architectures.

Determining the Transcription Rates Yielding Steady-State Production of mRNA in the Lac Genetic Switch of Escherichia coli

To elucidate the regulatory dynamics of the gene expression activation and inactivation, an in silico biochemical model of the lac circuit in Escherichia coli was used to evaluate the transcription rates that yield the steady-state mRNA production in active and inactive states of the lac circuit. This result can be used in synthetic biology applications to understand the limits of the genetic synthesis. Since most genetic networks involve many interconnected components with positive and negative feedback control, intuitive understanding of their dynamics is often difficult to obtain. Although the kinetic model of the lac circuit considered involves only a single positive feedback, the developed computational framework can be used to evaluate supported ranges of other reaction rates in genetic circuits with more complex regulatory networks. More specifically, the inducible lac gene switch in E. coli is regulated by unbinding and binding of the inducer-repressor complexes to or from the DNA operator to switch the gene expression on and off. The dependency of mRNA production at steady state on different transcription rates and the repressor complexes has been studied by computer simulations in the Lattice Microbe software. Provided that the lac circuit is in active state, the transcription rate is independent of the inducer-repressor complexes present in the cell. In inactive state, the transcription rate is dependent on the specific inducer-repressor complex bound to the operator that inactivates the gene expression. We found that the repressor complex with the largest affinity to the operator yields the smallest range of the feasible transcription rates to yield the steady state while the lac circuit is in inactive state. In contrast, the steady state in active state can be obtained for any value of the transcription rate.

Foreword to 'Quantitative and analytical relations in biochemistry'-a special issue in honour of Donald J. Winzor's 80th birthday

The purpose of this special issue is to honour Professor Donald J. Winzor's long career as a researcher and scientific mentor, and to celebrate the milestone of his 80th birthday. Throughout his career, Don has been renowned for his development of clever approximations to difficult quantitative relations governing a range of biophysical measurements. The theme of this special issue, 'Quantitative and analytical relations in biochemistry', was chosen to reflect this aspect of Don's scientific approach.