Synthetic biology articles within Nature Communications

Featured

  • Article
    | Open Access

    Addition of fluorine to organic structures is a unique strategy for tuning molecular properties, but approaches to integrate fluorometabolites into the biochemistry of living cells are scarce. Here, the authors develop a fluoride-responsive genetic circuit to enable in vivo biofluorination in engineered Pseudomonas putida.

    • Patricia Calero
    • , Daniel C. Volke
    •  & Pablo I. Nikel
  • Article
    | Open Access

    RNA can be used as a programmable tool for detection of biological analytes. Here the authors use deep neural networks to predict toehold switch functionality in synthetic biology applications.

    • Nicolaas M. Angenent-Mari
    • , Alexander S. Garruss
    •  & James J. Collins
  • Article
    | Open Access

    The design of synthetic biology circuits remains challenging due to poorly understood design rules. Here the authors introduce STORM and NuSpeak, two deep-learning architectures to characterize and optimize toehold switches.

    • Jacqueline A. Valeri
    • , Katherine M. Collins
    •  & Diogo M. Camacho
  • Article
    | Open Access

    The chemical stability of DNA makes complete erasure of DNA-encoded data difficult. Here the authors mix true and false messages, differentiated by whether a truth marker oligo is bound to it, and show that brief exposure to elevated temperatures randomizes the binding of truth markers preventing data recovery.

    • Jangwon Kim
    • , Jin H. Bae
    •  & David Yu Zhang
  • Article
    | Open Access

    In contrast to genetic circuits, here the authors develop protein biocircuits based on proteases. They show these activity-based circuits can execute Boolean logic for programmable drug delivery and perform fuzzy logic to solve a mathematical oracle problem, Learning Parity with Noise.

    • Brandon Alexander Holt
    •  & Gabriel A. Kwong
  • Article
    | Open Access

    Current gene drive strategies are restricted to sexually reproducing species. Here the authors develop a gene drive in herpesviruses that allows the spread of an engineered trait through a viral population.

    • Marius Walter
    •  & Eric Verdin
  • Article
    | Open Access

    In metabolic engineering, mechanistic models require prior metabolism knowledge of the chassis strain, whereas machine learning models need ample training data. Here, the authors combine the mechanistic and machine learning models to improve prediction performance of tryptophan metabolism in baker’s yeast.

    • Jie Zhang
    • , Søren D. Petersen
    •  & Michael K. Jensen
  • Article
    | Open Access

    Synthetic Biology often lacks the predictive power needed for efficient bioengineering. Here the authors present ART, a machine learning and probabilistic predictive tool to guide synthetic biology design in a systematic fashion.

    • Tijana Radivojević
    • , Zak Costello
    •  & Hector Garcia Martin
  • Article
    | Open Access

    Transcriptional biosensors represent powerful tools for the screening of vast strain libraries, but the broad ligand specificity of some transcriptional regulators (TRs) can prohibit such applications. Here authors present the engineering of a LysG-based biosensor with a focused ligand specificity to isolate L-histidine-producing strains.

    • Dennis Della Corte
    • , Hugo L. van Beek
    •  & Jan Marienhagen
  • Article
    | Open Access

    Short hairpin RNAs can be used to modulate and regulate gene expression. Here the authors generate chimeric RNAs that interact with the photoreceptor PAL, allowing for optoribogenetic control of cell physiology.

    • Sebastian Pilsl
    • , Charles Morgan
    •  & Günter Mayer
  • Article
    | Open Access

    Non-ribosomal peptide synthases are multimodular enzymes comprised of adenylation (A), condensation (C) and thiolation domains. Here, the authors show that non-ribosomal peptides can be generated solely by A domain substitutions, providing evidence that the postulated substrate specifying role of C-domains may be rare in nature.

    • Mark J. Calcott
    • , Jeremy G. Owen
    •  & David F. Ackerley
  • Article
    | Open Access

    Natural speciation can be driven by pre-zygotic and post-zygotic barriers. Here the authors use a dominant lethal transgene coupled to a recessive resistance allele to engineer species-like barriers in Drosophila.

    • Maciej Maselko
    • , Nathan Feltman
    •  & Michael J. Smanski
  • Article
    | Open Access

    Controlled membrane synthesis in liposomes is a prerequisite for synthetic systems emulating the fundamental properties of living cells. Here authors present that a de novo synthesized metabolic pathway converts precursors into a variety of lipids, including the constituents of the parental liposome.

    • Duco Blanken
    • , David Foschepoth
    •  & Christophe Danelon
  • Article
    | Open Access

    Self-propagating drives allow for non-Mendelian inheritance. Here the authors use CRISPR to build a chromosome drive, showing elimination of entire chromosomes, endoreduplication of desired chromosomes and enabling preferential transmissions of complex genetic traits on a chromosomal scale in yeast.

    • Hui Xu
    • , Mingzhe Han
    •  & Ying-Jin Yuan
  • Article
    | Open Access

    Backbone extended monomers are poorly compatible with the natural ribosomes, impeding their polymerization into polypeptides. Here the authors design non-canonical amino acid analogs with cyclic structures or extended carbon chains and used an engineered ribosome to improve tRNA-charging and incorporation into peptides.

    • Joongoo Lee
    • , Kevin J. Schwarz
    •  & Michael C. Jewett
  • Article
    | Open Access

    A cell free or synthetic biochemistry approach offers a way to circumvent the many constraints of living cells. Here, the authors demonstrate, via enzyme and process enhancements, the production of isobutanol with the metrics exceeding highly developed ethanol fermentation.

    • Saken Sherkhanov
    • , Tyler P. Korman
    •  & James U. Bowie
  • Article
    | Open Access

    Biosynthetic gene clusters (BGCs) make small molecules with fitness-enhancing activities that drive BGC evolution. Here, the authors show that synthetic biology can leverage bioactivity to achieve continuous evolution of an antibiotic BGC in the lab and improve antibiotic production in a new host.

    • Chad W. Johnston
    • , Ahmed H. Badran
    •  & James J. Collins
  • Article
    | Open Access

    The ability to regulate nanobody affinity with light would expand the applications toolbox for these reagents. Here the authors insert an optimised photoswitchable AsLOV2 domain into multiple nanobodies and demonstrate photoswitchable binding to fluorescent proteins and endogenous proteins in cells.

    • Agnieszka A. Gil
    • , César Carrasco-López
    •  & Jared E. Toettcher
  • Article
    | Open Access

    Cas9 fusions partners are often limited to natural polypeptide chains at the Cas9 termni. Here the authors present a platform for site-specific and multiple-site conjugation to both termini and internal sites of Cas9, and they apply this platform to efficiently engineer insulin-producing β cells.

    • Donghyun Lim
    • , Vedagopuram Sreekanth
    •  & Amit Choudhary
  • Article
    | Open Access

    Regulatory networks respond to environmental and genetic perturbations by reprogramming metabolism. Here the authors screen a library of 82 regulators with 110,120 mutations to map the regulatory network of 4000 genes.

    • Rongming Liu
    • , Liya Liang
    •  & Ryan T. Gill
  • Article
    | Open Access

    Designing distributed circuits that respond predictably to variation in bacterial populations remains difficult. Here the authors develop a two-strain circuit that senses and responds to the majority strain.

    • Razan N. Alnahhas
    • , Mehdi Sadeghpour
    •  & Matthew R. Bennett
  • Article
    | Open Access

    Current methods to generate sequence-function data at large scale are either technically complex or limited to specific applications. Here the authors introduce DNA-based phenotypic recording to overcome these limitations and enable deep learning for accurate prediction of function from sequence.

    • Simon Höllerer
    • , Laetitia Papaxanthos
    •  & Markus Jeschek
  • Article
    | Open Access

    DNA is an attractive digital data storing medium due to high information density and longevity. Here the authors use millions of sequences to investigate inherent biases in DNA synthesis and PCR amplification.

    • Yuan-Jyue Chen
    • , Christopher N. Takahashi
    •  & Karin Strauss
  • Article
    | Open Access

    Insect population control using conditional lethal systems could break down due to spontaneous mutations that render the system ineffective. Here the authors analyse the structure and frequency of such mutations in Drosophila and suggest the use of dual lethality systems to mitigate their survival.

    • Yang Zhao
    • , Marc F. Schetelig
    •  & Alfred M. Handler
  • Article
    | Open Access

    Control over splicing could be used for both therapeutic and engineering applications. Here the authors create artificial splicing factors using RNA-targeting CRISPR systems under small molecule control.

    • Menghan Du
    • , Nathaniel Jillette
    •  & Albert Wu Cheng
  • Article
    | Open Access

    The physical architectures of information storage dictate how data is encoded, organised and accessed. Here the authors use DNA with a single-strand overhang as a physical address to access specific data and do in-storage file operations in a scalable and reusuable manner.

    • Kevin N. Lin
    • , Kevin Volkel
    •  & Albert J. Keung
  • Article
    | Open Access

    Previous design strategies for pH sensitive aptamers were not readily tunable across pH ranges. Here the authors present a general method to convert aptamers into pH-responsive switches using two orthogonal motifs.

    • Ian A. P. Thompson
    • , Liwei Zheng
    •  & H. Tom Soh
  • 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

    While organisms like squid can adaptively modulate the optical properties of their tissues, human cells lack analogous abilities. Here the authors engineer human cells to produce protein architectures with tunable light scattering functionalities.

    • Atrouli Chatterjee
    • , Juana Alejandra Cerna Sanchez
    •  & Alon A. Gorodetsky
  • Article
    | Open Access

    Protospacer adjacent motif (PAM) requirements limit the target range of CRISPR endonucleases. Here, the authors graft the 5\(^{\prime}\)-NAAN-3\(^{\prime}\) PAM-interacting domain of SmacCas9 onto SpyCas9 to create adenine dinucleotide targeting chimeras.

    • Pranam Chatterjee
    • , Jooyoung Lee
    •  & Noah Jakimo
  • Review Article
    | Open Access

    Our efforts to build complex synthetic biology circuits are impeded by limited knowledge of optimal combinations. In this review, the authors consider current combinatorial methods and look to emerging technologies.

    • Gita Naseri
    •  & Mattheos A. G. Koffas
  • Article
    | Open Access

    The spatial organisation of microbial communities is caused by the interplay of biotic and abiotic factors. Here the authors design a microfluidic platform to quantify the spatiotemporal parameters influencing diffusion-mediated interactions, and use this device to investigate information transmission and metabolic cross-feeding in synthetic microbial consortia.

    • Sonali Gupta
    • , Tyler D. Ross
    •  & Ophelia S. Venturelli