Synthetic biology articles within Nature Communications

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  • Article
    | Open Access

    Full traceability and transparency are important to establish trust in engineered cell lines. Here the authors argue that version control for cell engineering marks a significant step toward more open, reproducible, traceable and ultimately more trustworthy engineering biology.

    • Jonathan Tellechea-Luzardo
    • , Leanne Hobbs
    •  & Natalio Krasnogor

  • Article
    | Open Access

    The ergot alkaloids are a class of natural products known for their pharmacologically privileged molecular structure that are used in the treatment of neurological ailments. Here the authors report on the production of the ergot (fungus)-derived therapeutic precursor, D-lysergic acid (DLA), in baker’s yeast.

    • Garrett Wong
    • , Li Rong Lim
    •  & Wen Shan Yew

  • Article
    | Open Access

    Biocontainment is a key to developing safe genetically-engineered microbes (GEMs). Here the authors demonstrate genetically stable CRISPR-based kill switches that control GEMs’ viability in animal hosts, enabling their safe biomedical applications.

    • Austin G. Rottinghaus
    • , Aura Ferreiro
    •  & Tae Seok Moon

  • Article
    | Open Access

    Site-specific labelling of proteins can be performed with unnatural amino acids combined with bioorthogonal click chemistry. Here the authors establish this in living neurons, using neurofilament light chain; they show combination with CRISPR/Cas9 engineering to tag the endogenous protein.

    • Aleksandra Arsić
    • , Cathleen Hagemann
    •  & Ivana Nikić-Spiegel

  • Article
    | Open Access

    There are a lack of eukaryotic biosensors specific for branched-chain amino acid (BCAA)-derived products. Here the authors report a genetically encoded biosensor for BCAA metabolism based on the Leu3p transcriptional regulator; they use this to monitor yeast production of isobutanol and isopentanol.

    • Yanfei Zhang
    • , Jeremy D. Cortez
    •  & José L. Avalos

  • Article
    | Open Access

    Generic approach for rapid prototyping is essential for the progress of synthetic biology. Here the authors modify the cell-free translation system to control protein aggregation and folding and validate the approach by using single conditions for prototyping of various disulfide-constrained polypeptides.

    • Yue Wu
    • , Zhenling Cui
    •  & Sergey Mureev

  • Article
    | Open Access

    Genome editing methods are limited by the inability to selectively edit repetitive sequences. Here the authors demonstrate precise editing of a repetitive genetic element, a ribosome, while avoiding edits to native sites sharing identical sequence.

    • Felix Radford
    • , Shane D. Elliott
    •  & Farren J. Isaacs

  • Article
    | Open Access

    CRISPR-based engineering can be used to bias sex ratios. Here the authors develop a transgenic line of Drosophila melanogaster expressing Cas9 from the Y chromosome and functionally characterize the utility of this strain for both sex selection and gene drive.

    • Stephanie Gamez
    • , Duverney Chaverra-Rodriguez
    •  & Omar S. Akbari

  • 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

    Engineering biosynthetic assembly lines is a powerful path to new natural products but is challenging with current methods. Here the authors use CRISPR-Cas9 to exchange subdomains within NRPS to alter substrate selectivity.

    • Wei Li Thong
    • , Yingxin Zhang
    •  & Jason Micklefield

  • Article
    | Open Access

    Rational design of enzymes with new or improved properties is rarely straightforward, and artificial selection pressure approaches that link an improvement in the target to cell growth are an alternative. Here, the authors show that diverse enzymes sharing the ubiquitous cofactor NAD(P)+ can substitute for defective NAD+ regeneration, representing a very broadly-applicable artificial selection.

    • Lara Sellés Vidal
    • , James W. Murray
    •  & John T. Heap

  • Comment
    | Open Access

    Developing more productive and sustainable crops will be essential to achieving food security in coming decades. A core process in plant evolution has been the transfer of chloroplast-encoded genes to the nuclear genome. We propose reverting this process as a new approach to improve plant disease resistance and photosynthesis in future crops.

    • Briardo Llorente
    • , María Eugenia Segretin
    •  & Nicolás E. Blanco

  • Article
    | Open Access

    Traditional synthetic biology tools operate by complex re-programming of DNA, requiring significant amount of ‘nucleotide-based code’ to implement instructions that are transcribed at the protein level. Here the authors demonstrate the direct regulation of cellular phenotype at the single-protein level by creating a two-input logic gate for biological computation using ‘allosteric wiring’.

    • Yashavantha L. Vishweshwaraiah
    • , Jiaxing Chen
    •  & Nikolay V. Dokholyan

  • Article
    | Open Access

    Morphogens disperse to pattern tissues and control their growth during development, allowing for the specification of multiple fates across space. Here the authors block dispersal of a morphogen Dpp (BMP2/4) and show that the requirement for Dpp dispersal is much lower than previously thought.

    • Shinya Matsuda
    • , Jonas V. Schaefer
    •  & Markus Affolter

  • Article
    | Open Access

    Peptide secondary metabolites have a diverse range of functions. Here the authors present a method to design and screen a large library of modified peptides in E. coli against a target of interest.

    • Andrew M. King
    • , Daniel A. Anderson
    •  & Christopher A. Voigt

  • Article
    | Open Access

    Cell-based transcriptional reporters are an invaluable part of highthroughput screening, but many such reporters have weak or transient responses. Here, the authors describe a digitizer circuit for amplifying reporter activity, increasing sensitivity, and retaining memory of pathway activation.

    • Nicole M. Wong
    • , Elizabeth Frias
    •  & Wilson W. Wong

  • Article
    | Open Access

    Isoflavonoids are a class of industrially important plant natural products, but their low abundance and structural complexity limits their availability. Here, the authors engineer Saccharomyces cerevisiae metabolism to become a platform for efficient production of daidzein which is core chemical scaffold for isoflavonoid biosynthesis, and show its application for production of bioactive glucosides from glucose.

    • Quanli Liu
    • , Yi Liu
    •  & Jens Nielsen

  • Article
    | Open Access

    Heterologous expression of recombinant proteins often results in misfolding, aggregation and degradation. Here, we show an in vivo dual-biosensor system that simultaneously assesses protein translation and protein folding, thereby enabling rapid screening of expression strains as well as mutant libraries.

    • Ariane Zutz
    • , Louise Hamborg
    •  & Alex Toftgaard Nielsen

  • Article
    | Open Access

    The directed evolution of antibodies yields important tools for research and therapy. Here the authors develop a periplasmic phage-assisted continuous evolution platform for improvement of protein-protein interactions in the disulfidecompatible E. coli periplasm.

    • Mary S. Morrison
    • , Tina Wang
    •  & David R. Liu

  • Article
    | Open Access

    Genome engineering is challenging compared to plasmid DNA manipulation. Here the authors create a simple methodology called SEGA that enables genome engineering by combining DNA and bacterial cells followed by identification of recombinant clones by a change in colour when grown on agar plates.

    • Carolyn N. Bayer
    • , Maja Rennig
    •  & Morten H. H. Nørholm

  • Article
    | Open Access

    Fatty acyl reductases (FARs) are critical enzymes in the biosynthesis of fatty alcohols and have the ability to directly acces acyl-ACP substrates. Here, authors couple machine learning-based protein engineering framework with gene shuffling to optimize a FAR for the activity on acyl-ACP and improve fatty alcohol production.

    • Jonathan C. Greenhalgh
    • , Sarah A. Fahlberg
    •  & Philip A. Romero

  • Article
    | Open Access

    Small-molecule responsive protein switches are crucial components to control synthetic cellular activities. Here, we present a computational protein design strategy to repurpose drug-inhibited protein-protein interactions into OFF- and ON-switches active in cells.

    • Sailan Shui
    • , Pablo Gainza
    •  & Bruno E. Correia

  • Article
    | Open Access

    Genetic code expansion strategies are limited to specific codons that can be reassigned to new amino acids. Here the authors show that quadruplet-decoding tRNAs (qtRNAs) can be rapidly discovered and evolved to decode new quadruplet codons, enabling four independent decoding events in a single protein in living cells.

    • Erika A. DeBenedictis
    • , Gavriela D. Carver
    •  & Ahmed H. Badran

  • Article
    | Open Access

    Simultaneous detection of multiple analytes from a sample is currently difficult. Here the authors present protocell arrays in a customisable platform integrating cell-free expression with a polymer-based aqueous two-phase system; they use this for detection of chemically diverse targets from biofluids.

    • Yan Zhang
    • , Taisuke Kojima
    •  & Mark P. Styczynski

  • Article
    | Open Access

    Practical implementation of genetic circuits is difficult due to low predictability and time-intensive troubleshooting. Here the authors present Cyberloop, which interfaces a computer with single cells to enable cell-in-the-loop testing and optimization of circuit designs before they are built.

    • Sant Kumar
    • , Marc Rullan
    •  & Mustafa Khammash

  • Article
    | Open Access

    Complex biomolecular networks are fundamental to the functioning of living systems, both at the cellular level and beyond. In this paper, the authors develop a systems framework to elucidate the interplay of networks and the spatial localisation of network components.

    • Govind Menon
    •  & J. Krishnan

  • Comment
    | Open Access

    Synthetic biology has brought about a conceptual shift in our ability to redesign microbial metabolic networks. Combining metabolic pathway-modularization with growth-coupled selection schemes is a powerful tool that enables deep rewiring of the cell factories’ biochemistry for rational bioproduction.

    • Enrico Orsi
    • , Nico J. Claassens
    •  & Steffen N. Lindner

  • Article
    | Open Access

    Here, the authors engineer microbial production of muscle titin fibers with highly desirable mechanical properties and provide structural analyses that explain the molecular mechanisms underlying high performance of this polymer with potential uses in biomedicine and textile industries, among others.

    • Christopher H. Bowen
    • , Cameron J. Sargent
    •  & Fuzhong Zhang

  • Article
    | Open Access

    The use of synthetic organisms could provide opportunities for discovery and advanced manufacturing of medical drugs. Here the authors use a semi-synthetic organism with an expanded genetic code to generate site-specific chemical modifications in human IL-2.

    • Jerod L. Ptacin
    • , Carolina E. Caffaro
    •  & Marcos E. Milla

  • Perspective
    | Open Access

    A key feature of living cells is the cell cycle. In this Perspective, the authors explore attempts to recreate this process and what is still required for an integrated synthetic cell cycle.

    • Lorenzo Olivi
    • , Mareike Berger
    •  & John van der Oost

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