Gene regulatory networks are based on simple building blocks such as promoters, transcription factors (TFs) and their binding sites on DNA. But how diverse are the functions that can be obtained by different arrangements of promoters and TF binding sites? In this work we constructed synthetic regulatory regions using promoter elements and binding sites of two noninteracting TFs, each sensing a single environmental input signal. We show that simply by combining these three kinds of elements, we can obtain 11 of the 16 Boolean logic gates that integrate two environmental signals in vivo. Further, we demonstrate how combination of logic gates can result in new logic functions. Our results suggest that simple elements of transcription regulation form a highly flexible toolbox that can generate diverse functions under natural selection.evolution | gene regulation | regulatory logic | signal integration
BackgroundThe p53 signalling pathway has hundreds of inputs and outputs. It can trigger cellular senescence, cell-cycle arrest and apoptosis in response to diverse stress conditions, including DNA damage, hypoxia and nutrient deprivation. Signals from all these inputs are channeled through a single node, the transcription factor p53. Yet, the pathway is flexible enough to produce different downstream gene expression patterns in response to different stresses.ResultsWe construct a mathematical model of the negative feedback loop involving p53 and its inhibitor, Mdm2, at the core of this pathway, and use it to examine the effect of different stresses that trigger p53. In response to DNA damage, hypoxia, etc., the model exhibits a wide variety of specific output behaviour - steady states with low or high levels of p53 and Mdm2, as well as spiky oscillations with low or high average p53 levels.ConclusionsWe show that even a simple negative feedback loop is capable of exhibiting the kind of flexible stress-specific response observed in the p53 system. Further, our model provides a framework for predicting the differences in p53 response to different stresses and single nucleotide polymorphisms.
In the natural environment, bacterial cells have to adjust their metabolism to alterations in the availability of food sources. The order and timing of gene expression are crucial in these situations to produce an appropriate response. We used the galactose regulation in Escherichia coli as a model system for understanding how cells integrate information about food availability and cAMP levels to adjust the timing and intensity of gene expression. We simulated the feast-famine cycle of bacterial growth by diluting stationary phase cells in fresh medium containing galactose as the sole carbon source. We followed the activities of six promoters of the galactose system as cells grew on and ran out of galactose. We found that the cell responds to a decreasing external galactose level by increasing the internal galactose level, which is achieved by limiting galactose metabolism and increasing the expression of transporters. We show that the cell alters gene expression based primarily on the current state of the cell and not on monitoring the level of extracellular galactose in real time. Some decisions have longer term effects; therefore, the current state does subtly encode the history of food availability. In summary, our measurements of timing of gene expression in the galactose system suggest that the system has evolved to respond to environments where future galactose levels are unpredictable rather than regular feast and famine cycles.Transport and metabolism of several sugars are controlled via two feedback loops connected by a common regulator that senses the intracellular concentration of the small molecule (1, 2). The simplest systems (e.g. the lactose utilization system in Escherichia coli) consist of two operons, a regulator gene and a regulated operon containing at least two cistrons, one encoding a transporter and the other encoding an enzyme that modifies/degrades the small molecule (3). In such systems, the genes encoding the sugar transporter (e.g. lacY) and the enzyme for sugar degradation (e.g. lacZ) are regulated simultaneously. However, many sugar utilization systems reached higher levels of complexity, e.g. having multiple transporters, regulators, or several enzymes of a metabolic pathway. For example, the gal system of E. coli contains genes involved in the transport (galP and mglBAC) and amphibolic utilization (galETKM) of the sugar D-galactose. Genes of the gal regulon belong to different operons (4). This setup allows differential regulation of functions when needed. Regulation of the gal system is governed by two similar regulators, GalR and GalS, which are regulated in different ways (5-7). Previous studies suggested that GalS plays only a minor role in steady-state conditions but becomes important transiently when a high level of extracellular galactose is quickly decreased (8). Besides sensing the intracellular sugar level, galactose utilization is also regulated by the cAMP-cAMP receptor protein (CRP) 2 complex. cAMP is a signal of carbon shortage and is sensed by CRP. cAMP is synthesi...
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