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Register a new userEfficiency and versatility of distal multisite transcription regulation
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Transcription regulation typically involves the binding of proteins over long distances on multiple DNA sites that are brought close to each other by the formation of DNA loops. The inherent complexity of the assembly of regulatory complexes on looped DNA challenges the understanding of even the simplest genetic systems, including the prototypical lac operon. Here we implement a scalable quantitative computational approach to analyze systems regulated through multiple DNA sites with looping. Our approach applied to the lac operon accurately predicts the transcription rate over five orders of magnitude for wild type and seven mutants accounting for all the combinations of deletions of the three operators. A quantitative analysis of the model reveals that the presence of three operators provides a mechanism to combine robust repression with sensitive induction, two seemingly mutually exclusive properties that are required for optimal functioning of metabolic switches.
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Recent years have witnessed an increasing interest in neuron-glia communication. This interest stems from the realization that glia participates in cognitive functions and information processing and is involved in many brain disorders and neurodegenerative diseases. An important process in neuron-glia communications is astrocyte encoding of synaptic information transfer: the modulation of intracellular calcium dynamics in astrocytes in response to synaptic activity. Here, we derive and investigate a concise mathematical model for glutamate-induced astrocytic intracellular Ca2+ dynamics that captures the essential biochemical features of the regulatory pathway of inositol 1,4,5-trisphosphate (IP3). Starting from the well-known two-state Li-Rinzel model for calcium-induced-calcium release, we incorporate the regulation of the IP3 production and phosphorylation. Doing so we extended it to a three-state model (referred as the G-ChI model), that could account for Ca2+ oscillations triggered by endogenous IP3 metabolism as well as by IP3 production by external glutamate signals. Compared to previous similar models, our three-state models include a more realistic description of the IP3 production and degradation pathways, lumping together their essential nonlinearities within a concise formulation. Using bifurcation analysis and time simulations, we demonstrate the existence of new putative dynamical features. The cross-couplings between IP3 and Ca2+ pathways endows the system with self-consistent oscillator properties and favor mixed frequency-amplitude encoding modes over pure amplitude modulation ones. These and additional results of our model are in general agreement with available experimental data and may have important implications on the role of astrocytes in the synaptic transfer of information.
Auto-regulatory feedback loops are one of the most common network motifs. A wide variety of stochastic models have been constructed to understand how the fluctuations in protein numbers in these loops are influenced by the kinetic parameters of the main biochemical steps. These models differ according to (i) which sub-cellular processes are explicitly modelled; (ii) the modelling methodology employed (discrete, continuous or hybrid); (iii) whether they can be analytically solved for the steady-state distribution of protein numbers. We discuss the assumptions and properties of the main models in the literature, summarize our current understanding of the relationship between them and highlight some of the insights gained through modelling.
Mutation is a critical mechanism by which evolution explores the functional landscape of proteins. Despite our ability to experimentally inflict mutations at will, it remains difficult to link sequence-level perturbations to systems-level responses. Here, we present a framework centered on measuring changes in the free energy of the system to link individual mutations in an allosteric transcriptional repressor to the parameters which govern its response. We find the energetic effects of the mutations can be categorized into several classes which have characteristic curves as a function of the inducer concentration. We experimentally test these diagnostic predictions using the well-characterized LacI repressor of Escherichia coli, probing several mutations in the DNA binding and inducer binding domains. We find that the change in gene expression due to a point mutation can be captured by modifying only a subset of the model parameters that describe the respective domain of the wild-type protein. These parameters appear to be insulated, with mutations in the DNA binding domain altering only the DNA affinity and those in the inducer binding domain altering only the allosteric parameters. Changing these subsets of parameters tunes the free energy of the system in a way that is concordant with theoretical expectations. Finally, we show that the induction profiles and resulting free energies associated with pairwise double mutants can be predicted with quantitative accuracy given knowledge of the single mutants, providing an avenue for identifying and quantifying epistatic interactions.
Rule-based modeling is a powerful way to model kinetic interactions in biochemical systems. Rules enable a precise encoding of biochemical interactions at the resolution of sites within molecules, but obtaining an integrated global view from sets of rules remains challenging. Current automated approaches to rule visualization fail to address the complexity of interactions between rules, limiting either the types of rules that are allowed or the set of interactions that can be visualized simultaneously. There is a need for scalable visualization approaches that present the information encoded in rules in an intuitive and useful manner at different levels of detail. We have developed new automated approaches for visualizing both individual rules and complete rule-based models. We find that a more compact representation of an individual rule promotes promotes understanding the model assumptions underlying each rule. For global visualization of rule interactions, we have developed a method to synthesize a network of interactions between sites and processes from a rule-based model and then use a combination of user-defined and automated approaches to compress this network into a readable form. The resulting diagrams enable modelers to identify signaling motifs such as cascades, feedback loops, and feed-forward loops in complex models, as we demonstrate using several large-scale models. These capabilities are implemented within the BioNetGen framework but the approach is equally applicable to rule-based models specified in other formats.
We study genetic networks that produce many species of non-coding RNA molecules that are present at a moderate density, as typically exists in the cell. The associations of the many species of these RNA are modeled physically, taking into account the equilibrium constants between bound and unbound states. By including the pair-wise binding of the many RNA species, the network becomes highly interconnected and shows different properties than the usual type of genetic network. It shows much more robustness to mutation, and also rapid evolutionary adaptation in an environment that oscillates in time. This provides a possible explanation for the weak evolutionary constraints seen in much of the non-coding RNA that has been studied.
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