Molecular switches in animal cells

Molecular switches are the fundamental building blocks in the field of synthetic biology. The majority of these switches is based on protein-protein, protein-DNA or protein-RNA interactions that are responsive towards endogenous metabolites or external stimuli like small molecules or light. By the rational and predictive reassembling of multiple compatible molecular switches, complex synthetic signaling networks can be engineered. Here we review how these switches were used for the regulation of important cellular processes at every level of the signaling cascade. In the second part we review how these switches can be assembled to open- and closed-loop control signaling networks and how these networks can be applied to facilitate cattle reproduction, to treat diabetes or to autonomously detect and cure disease states like gouty arthritis or cancer.     

Adaptive switches in midbrain circuits

In this issue of Neuron, Mysore and Knudsen (2012) describe a simple, anatomically supported circuit that can categorize stimuli into "strongest" and "others," regardless of their absolute strength. Such flexible categorization cannot be achieved by lateral inhibition alone but also requires that the inhibitory neurons reciprocally inhibit each other.     

Architectural switches in plant thylakoid membranes

Recent progress in elucidating the structure of higher plants photosynthetic membranes provides a wealth of information. It allows generation of architectural models that reveal well-organized and complex arrangements not only on whole membrane level, but also on the supramolecular level. These arrangements are not static but highly responsive to the environment. Knowledge about the interdependency between dynamic structural features of the photosynthetic machinery and the functionality of energy conversion is central to understanding the plasticity of photosynthesis in an ever-changing environment. This review summarizes the architectural switches that are realized in thylakoid membranes of green plants.     

Protein-responsive ribozyme switches in eukaryotic cells

Genetic devices that directly detect and respond to intracellular concentrations of proteins are important synthetic biology tools, supporting the design of biological systems that target, respond to or alter specific cellular states. Here, we develop ribozyme-based devices that respond to protein ligands in two eukaryotic hosts, yeast and mammalian cells, to regulate the expression of a gene of interest. Our devices allow for both gene-ON and gene-OFF response upon sensing the protein ligand. As part of our design process, we describe an in vitro characterization pipeline for prescreening device designs to identify promising candidates for in vivo testing. The in vivo gene-regulatory activities in the two types of eukaryotic cells correlate with in vitro cleavage activities determined at different physiologically relevant magnesium concentrations. Finally, localization studies with the ligand demonstrate that ribozyme switches respond to ligands present in the nucleus and/or cytoplasm, providing new insight into their mechanism of action. By extending the sensing capabilities of this important class of gene-regulatory device, our work supports the implementation of ribozyme-based devices in applications requiring the detection of protein biomarkers.     

Memory switches in chemical reaction space

Just as complex electronic circuits are built from simple Boolean gates, diverse biological functions, including signal transduction, differentiation, and stress response, frequently use biochemical switches as a functional module. A relatively small number of such switches have been described in the literature, and these exhibit considerable diversity in chemical topology. We asked if biochemical switches are indeed rare and if there are common chemical motifs and family relationships among such switches. We performed a systematic exploration of chemical reaction space by generating all possible stoichiometrically valid chemical configurations up to 3 molecules and 6 reactions and up to 4 molecules and 3 reactions. We used Monte Carlo sampling of parameter space for each such configuration to generate specific models and checked each model for switching properties. We found nearly 4,500 reaction topologies, or about 10% of our tested configurations, that demonstrate switching behavior. Commonly accepted topological features such as feedback were poor predictors of bistability, and we identified new reaction motifs that were likely to be found in switches. Furthermore, the discovered switches were related in that most of the larger configurations were derived from smaller ones by addition of one or more reactions. To explore even larger configurations, we developed two tools: the “bistabilizer,” which converts almost-bistable systems into bistable ones, and frequent motif mining, which helps rank untested configurations. Both of these tools increased the coverage of our library of bistable systems. Thus, our systematic exploration of chemical reaction space has produced a valuable resource for investigating the key signaling motif of bistability.     

Nucleic acid molecular switches

Natural and artificial ribozymes can catalyse a diverse range of chemical reactions. Through recent efforts in enzyme engineering, it has become possible to tailor the activity of ribozymes to respond allosterically to specific effector compounds. These allosteric ribozymes function as effector-dependent molecular switches that could find application as novel genetic-control elements, biosensor components or precision switches for use in nanotechnology.     

Candida albicans switches mates

The "asexual" human fungal pathogen Candida albicans has recently been engineered to be able to mate. A paper in the August 9, 2002 issue of Cell shows that mating competence is increased dramatically when mating partners are in a rare switch variant cell type that does not normally occur at body temperature.     

Reversible frequency-dependent switches in male mate choice

Current sexual-selection theories predict that mating should occur preferentially with the highest-quality partner, and assume that for distinguishing among potential mates the choosy sex applies an internal representation of the characteristics of the desired mate, i.e. a template. Binary choice experiments were performed to test male mate choice between two different female colour morphs in the damselfly Ischnura elegans. Choice experiments were conducted before and after an habituation period, during which males were exposed to only one female colour morph. Given the choice between the two female morphs, males did exhibit a choice for the most recently experienced female morph. This is the first evidence for a reversible switch in mate choice in a frequency-dependent way. In contrast with previous studies on mate choice, template formation in male I. elegans seems not to be based on quality. Switching mate choice in a frequency-dependent manner, choosing the most common morph, probably allows males to minimize their search efforts and to maximize fitness.     

Coupling oscillations and switches in genetic networks

Switches (bistability) and oscillations (limit cycle) are omnipresent in biological networks. Synthetic genetic networks producing bistability and oscillations have been designed and constructed experimentally. However, in real biological systems, regulatory circuits are usually interconnected and the dynamics of those complex networks is often richer than the dynamics of simple modules. Here we couple the genetic Toggle switch and the Repressilator, two prototypic systems exhibiting bistability and oscillations, respectively. We study two types of coupling. In the first type, the bistable switch is under the control of the oscillator. Numerical simulation of this system allows us to determine the conditions under which a periodic switch between the two stable steady states of the Toggle switch occurs. In addition we show how birhythmicity characterized by the coexistence of two stable small-amplitude limit cycles, can easily be obtained in the system. In the second type of coupling, the oscillator is placed under the control of the Toggleswitch. Numerical simulation of this system shows that this construction could for example be exploited to generate a permanent transition from a stable steady state to self-sustained oscillations (and vice versa) after a transient external perturbation. Those results thus describe qualitative dynamical behaviors that can be generated through the coupling of two simple network modules. These results differ from the dynamical properties resulting from interlocked feedback loops systems in which a given variable is involved at the same time in both positive and negative feedbacks. Finally the models described here may be of interest in synthetic biology, as they give hints on how the coupling should be designed to get the required properties.     

Toll-like receptors as molecular switches

Members of the Toll family of single-pass transmembrane receptors are key mediators of innate immunity in both vertebrates and invertebrates. They respond to various pathogen-associated stimuli and transduce the complex signalling responses that are required for inflammation and for the subsequent development of adaptive immunity. Here, we propose a molecular mechanism for signalling by the Toll and Toll-like receptors that involves a series of protein conformational changes initiated by dimerization of their extracellular domains. The initial dimerization event, which is triggered by the interaction of the receptor with its ligand, might disrupt a pre-formed but non-functional dimer. Formation of a stable receptor-ligand complex then relieves constitutive autoinhibition, enabling receptor-receptor association of the extracellular juxtamembrane regions and cytoplasmic signalling domains. This activation process constitutes a tightly regulated, unidirectional molecular switch.