Efforts to engineer synthetic gene networks that spontaneously produce patterning in multicellular ensembles have focused on Turing's original model and the “activator-inhibitor” models of Meinhardt and Gierer. Systems based on this model are notoriously difficult to engineer. We present the first demonstration that Turing pattern formation can arise in a new family of oscillator-driven gene network topologies, specifically when a second feedback loop is introduced which quenches oscillations and incorporates a diffusible molecule. We provide an analysis of the system that predicts the range of kinetic parameters over which patterning should emerge and demonstrate the system's viability using stochastic simulations of a field of cells using realistic parameters. The primary goal of this paper is to provide a circuit architecture which can be implemented with relative ease by practitioners and which could serve as a model system for pattern generation in synthetic multicellular systems. Given the wide range of oscillatory circuits in natural systems, our system supports the tantalizing possibility that Turing pattern formation in natural multicellular systems can arise from oscillator-driven mechanisms.
Synthetic zinc finger proteins (ZFPs) can be created to target promoter DNA sequences, repressing transcription. The binding of small RNA (sRNA) to ZFP mRNA creates an ultrasensitive response to generate higher effective Hill coefficients. Here we combined three “off the shelf” ZFPs and three sRNAs to create new modular inverters in E. coli and quantify their behavior using induction fold. We found a general ordering of the effects of the ZFPs and sRNAs on induction fold that mostly held true when combining these parts. We then attempted to construct a ring oscillator using our new inverters. Our chosen parts performed insufficiently to create oscillations, but we include future directions for improvement upon our work presented here.
Pattern formation and differential interactions are important for microbial consortia to divide labor and perform complex functions. To obtain further insight into such interactions, we present a computational method for simulating physically separated microbial colonies, each implementing different gene regulatory networks. We validate our theory by experimentally demonstrating control over gene expression patterns in a diffusion-mediated lateral inhibition circuit. We highlight the importance of spatial arrangement as a control knob for modulating system behavior. Our systematic approach provides a foundation for future applications that require understanding and engineering of multistrain microbial communities for sophisticated, synergistic functions.
Biologists have long searched for reaction networks that can spontaneously generate spatial patterns in the presence of diffusion. The studies so far closely follow Alan Turing's "activator-inhibitor" model, where diffusion destabilizes a spatially homogeneous steady state. In this paper, we propose a new type of Turing system based on an oscillator that destabilizes a spatially homogeneous steady state towards a spatio-temporal pattern. We develop a model based on current experimentally-viable systems and study its benefits and limitations.
In our search for a viable synthetic gene network that can spontaneously produce patterning, we previously identified a new class of networks that we call quenched oscillator systems. These systems consist of a primary feedback loop that serves as an oscillator and a secondary feedback loop that quenches the oscillations and incorporates a diffusible molecule. We demonstrated that quenched oscillator systems are capable of generating spatio-temporal patterning with appropriate parameter values. Here we take advantage of recent work with zinc finger proteins (ZFPs) and small RNAs (sRNAs) to propose a new implementation using a new oscillator subsystem and a modified quenching loop.
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