Synthetic biology articles within Nature Communications

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  • Article
    | Open Access

    Restoring lost excitability of injured tissue is a paramount of regenerative medicine. By using a combined expression of bacterial voltage-gated Na+ channel, Kir2.1, and connexin-43 in non-excitable human fibroblasts, here the authors generate excitable cells that rescue action potential conduction in an in vitromodel of cardiac fibrosis.

    • Hung X. Nguyen
    • , Robert D. Kirkton
    •  & Nenad Bursac

  • Article
    | Open Access

    Directed evolution is a powerful technique for generating improved biological systems through repeated rounds of mutagenesis and selection. Here the authors engineer the yeast retrotransposon Ty1 to enable the creation of large mutant libraries in vivoand use this system to generate improved variants of single enzymes and multigene pathways.

    • Nathan Crook
    • , Joseph Abatemarco
    •  & Hal S. Alper

  • Article
    | Open Access

    Assembling multiple biological components into synthetic lipid vesicles is a limiting step in the manufacture of biomimetic cell-like structures. Here the authors use fusogenic proteoliposomes of opposite charge for fast assembly of a minimal electron transport chain consisting of F1F0 ATP-synthase and the proton pump bo3-oxidase.

    • Robert R. Ishmukhametov
    • , Aidan N. Russell
    •  & Richard M. Berry

  • Article
    | Open Access

    In the construction of single fluorescent protein biosensors, selection of the insertion point of a fluorescent protein into a ligand-binding domain is a rate-limiting step. Here, the authors develop an unbiased, high-throughput approach, called domain insertion profiling with DNA sequencing (DIP-seq), to generate a novel trehalose biosensor.

    • Dana C. Nadler
    • , Stacy-Anne Morgan
    •  & David F. Savage

  • Article
    | Open Access

    Droplet-based optical polymerase sorting employs a fluorescent sensor to monitor polymerase activity inside the microenvironment of uniform water-in-oil emulsions. Here, the authors use this technique to select and isolate single cells for evolution of an unnatural nucleic acid polymerase.

    • Andrew C. Larsen
    • , Matthew R. Dunn
    •  & John C. Chaput

  • Article
    | Open Access

    Early cells likely consisted of fatty acid vesicles enclosing magnesium-dependent ribozymes. Here, the authors show that fatty acid derivatives can form vesicles that, unlike those formed from only unmodified fatty acids, are stable in the presence of magnesium and could support ribozyme catalysis.

    • Katarzyna P. Adamala
    • , Aaron E. Engelhart
    •  & Jack W. Szostak

  • Article
    | Open Access

    Photocaged inositol-pyrophosphates offer a tool to study cellular signalling, but their challenging synthesis has precluded any biological studies so far. Here, the authors report the synthesis and cellular delivery of a photocaged analogue, and show that it mediates protein translocation in cellulo.

    • Igor Pavlovic
    • , Divyeshsinh T. Thakor
    •  & Henning J. Jessen

  • Article
    | Open Access

    Mussels use strong filaments to adhere to rocks, preventing them from being swept away in strong currents. Here, the authors borrow and simplify chemistries from the mussel foot to create a one component adhesive system which holds potential for employment in nanofabrication protocols.

    • B. Kollbe Ahn
    • , Saurabh Das
    •  & J. Herbert Waite

  • Article
    | Open Access

    Endogenous fungal gene promoters can be hundreds of base pairs long, limiting their use in synthetic biology and biotechnology. Here Redden and Alper screen a library of synthetic promoter elements to generate compact DNA sequences of ∼100 base pairs able to drive high levels of gene expression.

    • Heidi Redden
    •  & Hal S. Alper

  • Article
    | Open Access

    Synthetic engineering of complex pathways is often hindered by pathway branching and generation of non-target compounds. Here, the authors show that by judicious combination of moderately selective enzyme variants, a non-natural C50 carotenoid can be generated in bacteria with minimal production of unwanted compounds.

    • Maiko Furubayashi
    • , Mayu Ikezumi
    •  & Daisuke Umeno

  • Article
    | Open Access

    Phosphatidylinositol mannosides are cell envelope components vital for the survival of M. tuberculosis. Here, the authors report an elegant and convergent total synthesis of the complex glycolipid tetraacylated phosphatidylinositol hexamannoside (Ac2PIM6) and study the immunological effects in mice.

    • Pratap S. Patil
    • , Ting-Jen Rachel Cheng
    •  & Shang-Cheng Hung

  • Article
    | Open Access

    Spider webs have some intriguing mechanical properties, but understanding of the properties is limited to individual silk fibres. Here, the authors create mimics of spider web using 3D techniques, which enables them to acquire knowledge of mechanical strength of the entire synthetic web.

    • Zhao Qin
    • , Brett G. Compton
    •  & Markus J. Buehler

  • Article
    | Open Access

    Brain–machine interfaces offer the possibility of controlling prosthetic devices using changes in brain activity. Folcher et al.couple such a system wirelessly to an optogenetic implant in mice to control expression of a transgene, demonstrating its potential for mind-controlled drug delivery.

    • Marc Folcher
    • , Sabine Oesterle
    •  & Martin Fussenegger

  • 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
    | Open Access

    The advancement of sensitive, accurate and non-invasive methods to identify the allergen that drives allergic disease in an individual remains a challenge. Here, the authors develop a synthetic biology approach using human designer cells to profile allergic reactions against an array of allergens measuring histamine release from whole blood.

    • David Ausländer
    • , Benjamin Eggerschwiler
    •  & Martin Fussenegger

  • Article
    | Open Access

    The ability to control antibody binding could have important medical implications. Here, the authors present a method to engineer phosphatase-controllable antibodies that bind to a specific recognition site in the presence of two biomarker inputs.

    • Smita B. Gunnoo
    • , Helene M. Finney
    •  & Benjamin G. Davis

  • Article
    | Open Access

    Neural circuits are functional ensembles of neurons that are selectively interconnected by chemical or electrical synapses. Here the authors describe an approach to the study of neural circuits in C. eleganswhereby electrical synapses are introduced between previously unconnected neurons to reprogram behaviour.

    • Ithai Rabinowitch
    • , Marios Chatzigeorgiou
    •  & William R. Schafer

  • Article |

    In vitro biochemical pathways could provide the high yields required for economical commodity chemical production, but require circuitry development to regulate high-energy cofactors. Here, the authors design and test a simple purge valve system to maintain NADP+/NADPH balance in E. coli.

    • Paul H. Opgenorth
    • , Tyler P. Korman
    •  & James U. Bowie

  • Article |

    Model-based part design is a key step in synthetic biology. Here, the authors report a method for tuning nucleosome architecture in order to strengthen native promoters and facilitate synthetic promoter design in yeast.

    • Kathleen A. Curran
    • , Nathan C. Crook
    •  & Hal S. Alper

  • Article
    | Open Access

    Designer gene circuits allow the controlled expression of proteins in response to specific stimuli. Here, Rössger et al.use synthetic biology approaches to create a fatty-acid biosensor that controls the production of a satiety hormone and use it to control diet-induced obesity in mice.

    • Katrin Rössger
    • , Ghislaine Charpin-El-Hamri
    •  & Martin Fussenegger

  • Article |

    The ability to induce metabolic pathways in response to a changing environment is an important component of bacterial fitness. Bartl et al. identify optimal programmes for metabolic pathway activation depending on protein synthesis capacity constraints, and demonstrate their impact on operonic organization.

    • Martin Bartl
    • , Martin Kötzing
    •  & Christoph Kaleta

  • Article |

    While small molecules that destabilize actin filaments are readily available, artificially stimulating actin polymerization in cells typically involves genetic manipulation. Here, the authors design cell-permeable branched polyamines that promote lamellipodium formation by stimulating actin polymerization.

    • Iliana Nedeva
    • , Girish Koripelly
    •  & Daniel Riveline

  • Article |

    An important challenge in the bottom-up fabrication of artificial tissues is communication between compartments bounded by lipid bilayers. Mantri et al. engineer a dimeric transmembrane pore that, like eukaryotic gap junctions, can form a conductive pathway between adjacent bilayers.

    • Shiksha Mantri
    • , K. Tanuj Sapra
    •  & Hagan Bayley

  • Article |

    Gene circuits created by synthetic biologists working in one system may not be functional when transferred to a different organism. Using computational modelling to identify factors underlying such differences, the authors successfully adapt a yeast ‘linearizer’ circuit so that it functions in mammalian cells.

    • Dmitry Nevozhay
    • , Tomasz Zal
    •  & Gábor Balázsi

  • Article |

    Genome-wide variation in the directed evolution of metabolite-overproducing microbes requires high-throughput screening platforms. Yang et al.show that synthetic RNA devices can sense target metabolites, enrich pathway optimisation, and expedite the evolution of metabolite-producing microbes.

    • Jina Yang
    • , Sang Woo Seo
    •  & Gyoo Yeol Jung

  • Article |

    Protein encapsulation in molecular cages has the potential to alter protein function and aid crystallization. Here, ubiquitin is encapsulated within a giant coordination cage; the protein is attached to a bidentate ligand, and the cage self-assembles upon addition of capping ligands and Pd(II) ions.

    • Daishi Fujita
    • , Kosuke Suzuki
    •  & Makoto Fujita

  • Article
    | Open Access

    Secondary metabolites are widely used in human health and nutrition, but extraction yields from plants are often low. Nakagawaet al. have engineered the metabolism of Escherichia colito develop a fermentation system that produces plant alkaloids from simple carbon sources.

    • Akira Nakagawa
    • , Hiromichi Minami
    •  & Hidehiko Kumagai

  • Article
    | Open Access

    The control of cell fate and apoptosis is a continuing challenge in synthetic biology. In this study, systems are developed in which an intracellularly expressed genome-encoded protein simultaneously achieves up- and downregulation of two distinct apoptosis pathways.

    • Hirohide Saito
    • , Yoshihiko Fujita
    •  & Tan Inoue

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