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Complex signal processing in synthetic gene circuits using cooperative regulatory assemblies

Published on May 10, 2019in Science41.063
· DOI :10.1126/science.aau8287
Caleb J. Bashor9
Estimated H-index: 9
(Rice University),
Nikit Patel5
Estimated H-index: 5
(BU: Boston University)
+ 4 AuthorsAhmad S. Khalil18
Estimated H-index: 18
(Wyss Institute for Biologically Inspired Engineering)
Sources
Abstract
Eukaryotic genes are regulated by multivalent transcription factor complexes. Through cooperative self-assembly, these complexes perform nonlinear regulatory operations involved in cellular decision-making and signal processing. In this study, we apply this design principle to synthetic networks, testing whether engineered cooperative assemblies can program nonlinear gene circuit behavior in yeast. Using a model-guided approach, we show that specifying the strength and number of assembly subunits enables predictive tuning between linear and nonlinear regulatory responses for single- and multi-input circuits. We demonstrate that assemblies can be adjusted to control circuit dynamics. We harness this capability to engineer circuits that perform dynamic filtering, enabling frequency-dependent decoding in cell populations. Programmable cooperative assembly provides a versatile way to tune the nonlinearity of network connections, markedly expanding the engineerable behaviors available to synthetic circuits.
  • References (55)
  • Citations (7)
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References55
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#1Delphine Aymoz (UNIL: University of Lausanne)H-Index: 4
#2Carme Solé (UPF: Pompeu Fabra University)H-Index: 15
Last. Serge Pelet (UNIL: University of Lausanne)H-Index: 18
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During development, morphogens provide extracellular cues allowing cells to select a specific fate by inducing complex transcriptional programs. The mating pathway in budding yeast offers simplified settings to understand this process. Pheromone secreted by the mating partner triggers the activity of a MAPK pathway, which results in the expression of hundreds of genes. Using a dynamic expression reporter, we quantified the kinetics of gene expression in single cells upon exogenous pheromone stim...
7 CitationsSource
#1Yaron E. Antebi (California Institute of Technology)H-Index: 13
#2James M. Linton (California Institute of Technology)H-Index: 3
Last. Michael B. Elowitz (California Institute of Technology)H-Index: 49
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The bone morphogenetic protein (BMP) signaling pathway comprises multiple ligands and receptors that interact promiscuously with one another and typically appear in combinations. This feature is often explained in terms of redundancy and regulatory flexibility, but it has remained unclear what signal-processing capabilities it provides. Here, we show that the BMP pathway processes multi-ligand inputs using a specific repertoire of computations, including ratiometric sensing, balance detection, a...
49 CitationsSource
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#2Krishna ShrinivasH-Index: 5
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#1Denes Hnisz (MIT: Massachusetts Institute of Technology)H-Index: 22
#2Krishna Shrinivas (MIT: Massachusetts Institute of Technology)H-Index: 5
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Phase-separated multi-molecular assemblies provide a general regulatory mechanism to compartmentalize biochemical reactions within cells. We propose that a phase separation model explains established and recently described features of transcriptional control. These features include the formation of super-enhancers, the sensitivity of super-enhancers to perturbation, the transcriptional bursting patterns of enhancers, and the ability of an enhancer to produce simultaneous activation at multiple g...
296 CitationsSource
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Summary The quantitative concepts used to reason about gene regulation largely derive from bacterial studies. We show that this bacterial paradigm cannot explain the sharp expression of a canonical developmental gene in response to a regulating transcription factor (TF). In the absence of energy expenditure, with regulatory DNA at thermodynamic equilibrium, information integration across multiple TF binding sites can generate the required sharpness, but with strong constraints on the resultant "...
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Membrane-associated guanylate kinases (MAGUKs) are synaptic scaffold proteins involved in organizing protein complexes that are required for synaptic development and plasticity. Placing their focus on recent biochemical and structural data, Zhang and colleagues review the role of MAGUKs in synaptic protein complex formation and regulation.
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Cells must interpret environmental information that often changes over time. In our experiment, we systematically monitored the growth of yeast cells under various frequencies of oscillating osmotic stress. Growth was severely inhibited at a particular resonance frequency, at which cells show hyperactivated transcriptional stress responses. This behavior represents a sensory misperception: The cells incorrectly interpret oscillations as a staircase of ever-increasing osmolarity. The misperceptio...
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Switch-like, ultrasensitive responses – responses that resemble those of cooperative enzymes but are not necessarily generated by cooperativity – are widespread in signal transduction. In the previous installments in this series, we reviewed several mechanisms for generating ultrasensitivity: zero-order ultrasensitivity; multistep ultrasensitivity; inhibitor ultrasensitivity; and positive feedback (or double negative feedback) loops. In this review, we focus on how ultrasensitive components can ...
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Summary The transcription of genomic information in eukaryotes is regulated in large part by chromatin. How a diverse array of chromatin regulator (CR) proteins with different functions and genomic localization patterns coordinates chromatin activity to control transcription remains unclear. Here, we take a synthetic biology approach to decipher the complexity of chromatin regulation by studying emergent transcriptional behaviors from engineered combinatorial, spatial, and temporal patterns of i...
81 CitationsSource
Cells are able to navigate environments, communicate, and build complex patterns by initiating gene expression in response to specific signals. Engineers need to harness this capability to program cells to perform tasks or build chemicals and materials that match the complexity seen in nature. This review describes new tools that aid the construction of genetic circuits. We show how circuit dynamics can be influenced by the choice of regulators and changed with expression “tuning knobs.” We coll...
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Yeast has been a robust platform to manufacture a broad range of biofuels, commodity chemicals, natural products and pharmaceuticals. The membrane-bound organelles in yeast provide us the means to access the specialized metabolism for various biosynthetic applications. The separation and compartmentalization of genetic and metabolic events presents us the opportunity to precisely control and program gene expression for higher order biological functions. To further advance yeast synthetic biology...
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Agricultural biotechnology strategies often require the precise regulation of multiple genes to effectively modify complex plant traits. However, most efforts are hindered by a lack of characterized tools that allow for reliable and targeted expression of transgenes. We have successfully engineered a library of synthetic transcriptional regulators that modulate expression strength in planta. By leveraging orthogonal regulatory systems from Saccharomyces spp., we have developed a strategy for the...
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