Genetic circuit engineering articles within Nature Communications

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  • Review Article
    | Open Access

    As synthetic biology permeates society, the signal processing circuits in engineered living systems must be customized to meet practical demands. In this review, the authors outline design strategies for the DNA, RNA, and protein-level circuits and the hybrid “multi-level” circuits.

    • Yuanli Gao
    • , Lei Wang
    •  & Baojun Wang

  • Article
    | Open Access

    The rational design and implementation of synthetic mammalian communication systems can unravel fundamental design principles of cell communication circuits and offer a framework for engineering of designer cell consortia with potential applications in cell therapeutics. Here the authors present a synthetic communication platform in mammalian cells based on diffusible dipeptide ligands and synthetic receptors, that is by design highly orthogonal, scalable, and programmable.

    • Anna-Maria Makri Pistikou
    • , Glenn A. O. Cremers
    •  & Tom F. A. de Greef

  • Article
    | Open Access

    Plastic pollution is rapidly increasing worldwide, causing adverse impacts on the environment, wildlife and human health. Here the authors present a synthetic microbial consortium that efficiently degrades polyethylene terephthalate hydrolysate and upcycles it to desired chemicals through cellular division of labor.

    • Teng Bao
    • , Yuanchao Qian
    •  & Ting Lu

  • Article
    | Open Access

    Memory is a basic tenet of intelligent biological systems. Here the authors engineered a programmable and expandable iteration of recombinase-based synthetic memory (interception) that functions post-translation, resulting in faster recombination.

    • Andrew E. Short
    • , Dowan Kim
    •  & Corey J. Wilson

  • Article
    | Open Access

    The ability to independently control the expression of different genes is important for quantitative biology. Here, the authors report kinetic parameters, noise scaling, impact on growth, and the fundamental leakiness of a wide range of inducible transcriptional systems, including a new, highly light sensitive LOV-transcription factor.

    • Vojislav Gligorovski
    • , Ahmad Sadeghi
    •  & Sahand Jamal Rahi

  • Article
    | Open Access

    The ability to externally control gene expression has been important for all areas of biological research, especially for synthetic biology. Here the authors present plasmid TULIP which offers DNA copy number control via chemical induction to accelerate the design, prototyping, and reuse of gene circuits in diverse contexts.

    • Shivang Hina-Nilesh Joshi
    • , Chentao Yong
    •  & Andras Gyorgy

  • Article
    | Open Access

    Site-specific recombination (SSR) is an important tool in synthetic biology, but its applications are limited by the inability to predictably tune SSR reaction rates. Here, using quantitative high-throughput experiments and machine learning, the authors achieve rational control of a DNA attachment site sequence to predictably modulate site-specific recombination rates both in vitro and in cells.

    • Qiuge Zhang
    • , Samira M. Azarin
    •  & Casim A. Sarkar

  • Article
    | Open Access

    Optimization of biological networks is often limited by wet lab labor and cost, and the lack of convenient computational tools. Here, aimed at democratization and standardization, the authors describe METIS, a modular and versatile active machine learning workflow with a simple online interface for the optimization of biological target functions with minimal experimental datasets.

    • Amir Pandi
    • , Christoph Diehl
    •  & Tobias J. Erb

  • Article
    | Open Access

    Gene expression noise can reduce fitness but analysis is hampered by a scaling relationship between noise and expression level. Here the authors show that gene expression mean and noise can be independently controlled by expressing two copies of a gene from separate inducible promoters in the same cell.

    • Karl P. Gerhardt
    • , Satyajit D. Rao
    •  & Jeffrey J. Tabor

  • Article
    | Open Access

    Biological systems are known to behave in optimal ways when poised close to critical points, right on the edge between order and disorder. Here the authors show how this state can be engineered in living cells.

    • Blai Vidiella
    • , Antoni Guillamon
    •  & Ricard Solé

  • Article
    | Open Access

    A promising strategy to increase product synthesis from bacteria uses inducible systems to switch metabolism to production. Here, the authors use models to show how engineering positive feedback loops into the genetic circuitry creates a switch that requires only temporary induction with a cheap nutrient to switch metabolism irreversibly, and so drastically reduce inducer use and cost.

    • Ahmad A. Mannan
    •  & Declan G. Bates

  • Article
    | Open Access

    Inducible gene expression systems should minimise leaky output and offer a large achievable range of expression. Here, the authors regulate transcription and translation together to suppress noise and create digital-like responses, while maintaining a large expression range in vivo and in vitro.

    • F. Veronica Greco
    • , Amir Pandi
    •  & Thomas E. Gorochowski

  • Article
    | Open Access

    Genetic circuits can be engineered to generate predefined outcomes, however host context is a crucial factor in performance. Here the authors characterise twenty NOT gates in seven different bacteria to understand and predict interoperability and portability across hosts.

    • Huseyin Tas
    • , Lewis Grozinger
    •  & Ángel Goñi-Moreno

  • Article
    | Open Access

    Accurately predicting the behaviour of a genetic circuit remains difficult due to the lack of modularity. Here the authors quantify the effects of resource loading in mammalian systems and develop an endoribonuclease-based feedfoward controller to adapt gene expression to the effects of resource loading.

    • Ross D. Jones
    • , Yili Qian
    •  & Domitilla Del Vecchio

  • Article
    | Open Access

    Synthetic circuits based on CRISPRi have not achieved multistable and dynamic behaviors. Here the authors build an oscillator, a toggle switch and an incoherent feed-forward loop using CRISPRi, and provide a mathematical model suggesting that unspecific binding in CRISPRi enables multistability.

    • Javier Santos-Moreno
    • , Eve Tasiudi
    •  & Yolanda Schaerli

  • Article
    | Open Access

    Synthetic genetic circuits are sensitive to their environment and host cell, requiring many rounds of physical reassembly to achieve a desired function. Here the authors use a multi-level regulatory motif to dynamically tune the function of genetic parts as a step towards robust adaptive circuits.

    • Vittorio Bartoli
    • , Grace A. Meaker
    •  & Thomas E. Gorochowski

  • Article
    | Open Access

    It is difficult to improve the efficacy of oncolytic virotherapy due to immune system responses and limited understanding of population dynamics. Here the authors use synthetic biology gene circuits to control adenoviral replication and release of immunomodulators in hepatocellular carcinoma cells.

    • Huiya Huang
    • , Yiqi Liu
    •  & Zhen Xie

  • Article
    | Open Access

    Crosstalk between genetic circuits is a major challenge for engineering sophisticated networks. Here the authors design networks that compensate for crosstalk by integrating, not insulating, pathways.

    • Isaak E. Müller
    • , Jacob R. Rubens
    •  & Timothy K. Lu

  • Article
    | Open Access

    Current flux rewiring technologies in metabolic engineering are mainly transcriptional regulation. Here, the authors build two sets of controllable protein units using engineered viral proteases and proteolytic signals, and utilize for increasing titers of shikimate and D-xylonate in E. coli.

    • Cong Gao
    • , Jianshen Hou
    •  & Liming Liu

  • Article
    | Open Access

    One method of controlling protein degradation is through the use of degrons. Here the authors present a toolbox of characterised degrons as a library to fine-tune biological gene-expression systems. Its application is demonstrated by a set of tunable synthetic pulse generators in mammalian cells.

    • Hélène Chassin
    • , Marius Müller
    •  & Martin Fussenegger

  • Article
    | Open Access

    The translation of heterologous proteins places a burden on host cell resources, affecting growth and productivity. Here the authors develop a cell-free assay to measure resource consumption and predict in vivo burden.

    • Olivier Borkowski
    • , Carlos Bricio
    •  & Tom Ellis

  • Article
    | Open Access

    Deactivated Cas9 fused to transactivation domains can be used to control gene expression, however its presence can prevent rapid switching between different regulatory states. Here the authors generate conditionally degradable dCas9 and Cpf1 proteins for multidimensional control of functional activity.

    • Dirk A. Kleinjan
    • , Caroline Wardrope
    •  & Susan J. Rosser

  • Article
    | Open Access

    Naturally evolved regulatory circuits have hierarchical layers of signal generation and processing. Here, the authors emulate these networks using feedback-controlled DNA circuits that convert upstream signaling to downstream enzyme activity in a switchable memories circuit.

    • Lenny H. H. Meijer
    • , Alex Joesaar
    •  & Tom F. A. de Greef

  • Article
    | Open Access

    Genetic isolation of a genetically modified organism represents a useful strategy for biocontainment. Here the authors use dCas9-VP64-driven gene expression to construct a ‘species-like’ barrier to reproduction between two otherwise compatible populations.

    • Maciej Maselko
    • , Stephen C. Heinsch
    •  & Michael J. Smanski

  • Article
    | Open Access

    Unwanted interactions between cellular components can complicate rational engineering of biological systems. Here the authors design insulated minimal promoters and operators that enable biophysical modeling of bacterial transcription without free parameters for precise circuit design.

    • Yeqing Zong
    • , Haoqian M. Zhang
    •  & Chunbo Lou

  • Article
    | Open Access

    The leakiness of commonly used genetic components can make the construction of complex synthetic circuits difficult. Here the authors construct NOR gate architecture, using dCas9 fused to the chromatin remodeller Mxi1, that can be wired together into complex circuits.

    • Miles W. Gander
    • , Justin D. Vrana
    •  & Eric Klavins

  • Article
    | Open Access

    Synthetic circuits in host cells compete with endogenous processes for limited resources. Here the authors use MazF to funnel cellular resources to a synthetic circuit to increase product production and demonstrate how resource allocation can be manipulated.

    • Ophelia S. Venturelli
    • , Mika Tei
    •  & Adam P Arkin

  • Article
    | Open Access

    Genetic circuits usually employ the same set of transcription factors which can act via repression or activation of the target promoter. Here the authors present dual activator-repressor switches, designed via directed evolution, for orthogonal logic gates and multi-input circuit architectures.

    • Andreas K. Brödel
    • , Alfonso Jaramillo
    •  & Mark Isalan

  • Article |

    Engineering gene expression systems that can be programmed to respond to specific environmental conditions is challenging. Here, the authors develop a synthetic bow-tie circuit that is able to sense signals from microRNA molecules and affect a change in protein dynamics in mammalian cells.

    • Laura Prochazka
    • , Bartolomeo Angelici
    •  & Yaakov Benenson

  • Article
    | Open Access

    Constructing gene circuits with predefined behaviours is typically done on a case-by-case basis. Schaerli et al.instead computationally explore the design space for 3-node networks that generate a stripe in response to a morphogen gradient, and build networks based on their simplest possible forms.

    • Yolanda Schaerli
    • , Andreea Munteanu
    •  & Mark Isalan

  • Article |

    Synthetic gene circuits can be programmed in living cells to perform diverse cellular functions. Here, the authors program a genetic circuit that performs a Pavlovian-like learning and recall function in E. coli, and demonstrate the dynamic nature of this conditioning process at a population level.

    • Haoqian Zhang
    • , Min Lin
    •  & Qi Ouyang

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