Abstract
BackgroundGenetic switches are ubiquitous in nature, frequently associated with the control of cellular functions and developmental programs. In the realm of synthetic biology, it is of great interest to engineer genetic circuits that can change their mode of operation from monostable to bistable, or even to multistable, based on the experimental fine-tuning of readily accessible parameters. In order to successfully design robust, bistable synthetic circuits to be used as biomolecular probes, or understand modes of operation of such naturally occurring circuits, we must identify parameters that are key in determining their characteristics.ResultsHere, we analyze the bistability properties of a general, asymmetric genetic toggle switch based on a chemical-reaction kinetic description. By making appropriate approximations, we are able to reduce the system to two coupled differential equations. Their deterministic stability analysis and stochastic numerical simulations are in excellent agreement. Drawing upon this general framework, we develop a model of an experimentally realized asymmetric bistable genetic switch based on the LacI and TetR repressors. By varying the concentrations of two synthetic inducers, doxycycline and isopropyl β-D-1-thiogalactopyranoside, we predict that it will be possible to repeatedly fine-tune the mode of operation of this genetic switch from monostable to bistable, as well as the switching rates over many orders of magnitude, in an experimental setting. Furthermore, we find that the shape and size of the bistability region is closely connected with plasmid copy number.ConclusionsBased on our numerical calculations of the LacI-TetR asymmetric bistable switch phase diagram, we propose a generic work-flow for developing and applying biomolecular probes: Their initial state of operation should be specified by controlling inducer concentrations, and dilution due to cellular division would turn the probes into memory devices in which information could be preserved over multiple generations. Additionally, insights from our analysis of the LacI-TetR system suggest that this particular system is readily available to be employed in this kind of probe.Electronic supplementary materialThe online version of this article (doi:10.1186/s12918-016-0279-y) contains supplementary material, which is available to authorized users.
Highlights
Genetic switches are ubiquitous in nature, frequently associated with the control of cellular functions and developmental programs
Genetic switches and circuits are abundant in nature and control the regulation and genetic development programs that are at the basis of cellular function
We investigated the stability of our circuit as a function of [isopropyl β-D-1-thiogalactopyranoside (IPTG)] and [DOX], as well as of plasmid copy number
Summary
Genetic switches are ubiquitous in nature, frequently associated with the control of cellular functions and developmental programs. Among the early demonstrations of the engineering of synthetic circuits, Gardner et al used molecular genetic tools to construct a bistable toggle switch consisting of two genes coding for mutually repressing proteins [6] They implemented control of the toggle-switch state of operation by using an inducer that could affect transcription in the circuit, and affect its stability (monostable or bistable). For instance Deans et al combined tunability with robustness in a proteinRNA genetic switch [7], while Green et al combined robustness with unprecedented scalability using an RNA toehold system [8] While both protein and RNA switches are commonly used in scientific practice, the focus on robustness, being the lack of dynamics, has led to the fact that not many studies have investigated the dynamics of specific or generic genetic switches. This study was limited by the absence of reliable kinetic information concerning the circuit system in question and by the lack of stochastic analysis, both experimental and theoretical
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