Synthetic biology articles within Nature Communications

Featured

  • 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

  • Article
    | Open Access

    A small set of promoters is used for most genetic construct design in S. cerevisiae. Here, the authors develop a predictive model of promoter activity trained on a data set of over one million sequences and use it to design large sets of high-activity promoters.

    • Benjamin J. Kotopka
    •  & Christina D. Smolke

  • Article
    | Open Access

    Many industrial organisms are the result of recent or ancient allopolypoidy events. Here the authors iteratively combine the genomes of six yeast species to generate a viable hybrid.

    • David Peris
    • , William G. Alexander
    •  & Chris Todd Hittinger

  • 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

    Antibodies conjugated to bioactive compounds can allow targeted delivery of therapeutics. Here the authors present a strategy for fusing nanobodies to suboptimal GPCR peptide ligands to potently and selectively activate receptors.

    • Ross W. Cheloha
    • , Fabian A. Fischer
    •  & Hidde L. Ploegh

  • Article
    | Open Access

    Cell-free lysates are a major platform for in vitro protein production but batch-to-batch variation makes production difficult to predict. Here the authors develop an active learning approach to optimising buffer conditions to bring homemade lysates up to commercial production potential.

    • Olivier Borkowski
    • , Mathilde Koch
    •  & Jean-Loup Faulon

  • Article
    | Open Access

    Ribosome engineering is an emerging powerful approach for synthetic protein synthesis. Here the authors invert the Ribo-T system, using the engineered ribosome to translate the proteome while the native ribosome translates specific mRNA.

    • Nikolay A. Aleksashin
    • , Teresa Szal
    •  & Alexander S. Mankin

  • Article
    | Open Access

    Current synthetic DNA-based data storage systems have high recording costs, read-write latency and error-rates that make them uncompetitive compared to traditional digital storage. The authors use nicks in native DNA to encode data in parallel and create access sites for in-memory computations.

    • S. Kasra Tabatabaei
    • , Boya Wang
    •  & Olgica Milenkovic

  • Article
    | Open Access

    The spectra of light used by photosynthetic organisms are determined by their pigmentation colour palettes. Here Liu et al. show that a genetically-encoded chimera of light-harvesting proteins from plants and reaction centres from purple bacteria allows for polychromatic solar energy harvesting.

    • Juntai Liu
    • , Vincent M. Friebe
    •  & Michael R. Jones

  • Article
    | Open Access

    Granadaene, produced by Group B Streptococcus (GBS), is a long polyene lipid involved in cellular toxicity and hemolytic activity. Here, the authors synthesize and characterize granadaene-like compounds and show that a non-toxic analog diminishes GBS infection in mice when incorporated into a vaccine formulation.

    • Blair Armistead
    • , Pilar Herrero-Foncubierta
    •  & Lakshmi Rajagopal

  • Article
    | Open Access

    Genetic variation in natural populations could represent gene drive resistant alleles, preventing successful application for population management. Here the authors survey 1280 genomes from three mosquito species and concludes natural variation will not be detrimental to deploying gene drive technology.

    • Hanno Schmidt
    • , Travis C. Collier
    •  & Gregory C. Lanzaro

  • Article
    | Open Access

    Cell surface proteins mediate the interactions between cells and their extracellular environment. Here the authors design synthetic biomemetic receptor-like sensors that facilitate programmable interactions between bacteria and their target.

    • Naama Lahav-Mankovski
    • , Pragati Kishore Prasad
    •  & David Margulies

  • Review Article
    | Open Access

    Multiplexed CRISPR technologies have recently emerged as powerful approaches for genetic editing and transcriptional regulation. Here the authors review this emerging technology and discuss challenges and considerations for future studies.

    • Nicholas S. McCarty
    • , Alicia E. Graham
    •  & Rodrigo Ledesma-Amaro

  • Article
    | Open Access

    Bacteria represent an unexploited reservoir of biosensing proteins. Here the authors use genomic screens and functional assays to isolate a progesterone sensing allosteric transcription factor and use a FRET-based method to develop an optical progesterone sensor.

    • Chloé Grazon
    • , R C. Baer
    •  & James E. Galagan

  • Article
    | Open Access

    Directed evolution of the ribosome is challenging because the requirement of cell viability limits the mutations that can be made. Here the authors develop a platform for in vitro ribosome synthesis and evolution (RISE) to overcome these constraints.

    • Michael J. Hammerling
    • , Brian R. Fritz
    •  & Michael C. Jewett

  • Article
    | Open Access

    Optogenetic tools have been used to control cellular behaviours but their use to probe structure-function relations of signalling proteins are underexplored. Here the authors engineer optogenetic modules into STIM1 to dissect molecular details of STIM1-mediated signalling and control various cellular events.

    • Guolin Ma
    • , Lian He
    •  & Yubin Zhou

  • Article
    | Open Access

    Genome engineering will one day benefit from computational tools that can design genomes with desired functions. Here the authors develop computational design-simulate-test algorithms to design minimal genomes based on the whole-cell model of Mycoplasma genitalium.

    • Joshua Rees-Garbutt
    • , Oliver Chalkley
    •  & Claire Grierson

  • Article
    | Open Access

    Protein tyrosine phosphatases regulate many cellular processes but are difficult to study in their native context. Here the authors develop an approach for using light to control the activity of a disease-relevant phosphatase without interfering with its native cellular organization.

    • Akarawin Hongdusit
    • , Peter H. Zwart
    •  & Jerome M. Fox

  • Article
    | Open Access

    Engineering mammalian cellular functions requires a toolkit of orthogonal and well-characterized genetic components. Here the authors develop COMET: an ensemble of transcription factors, promoters, and accompanying models for the design and construction of genetic programs.

    • Patrick S. Donahue
    • , Joseph W. Draut
    •  & Joshua N. Leonard

  • Perspective
    | Open Access

    Genome-scale engineering requires the integration of a wide range of in silico and in vivo technologies, as well data management procedures and legal infrastructure. Here the authors provide a list of recommendations to address these challenges.

    • Bryan A. Bartley
    • , Jacob Beal
    •  & Elizabeth A. Strychalski

  • Article
    | Open Access

    Current cellular rewiring designs are typically tailored to detect single inputs. Here the authors present GEARs that function independently of engineered receptor/reporter systems and directly reroute endogenous signaling pathways to alternative genomic loci using dCas9-directed gene expression.

    • Krzysztof Krawczyk
    • , Leo Scheller
    •  & Martin Fussenegger

  • Article
    | Open Access

    Optogenetic approaches to control protein-protein interactions usually require overexpression of the target proteins. Here the authors integrate intrabodies into near-infrared- and blue-light activatable optogenetic tools to control endogenous proteins in mammalian cells.

    • Taras A. Redchuk
    • , Maksim M. Karasev
    •  & Vladislav V. Verkhusha

  • Article
    | Open Access

    Cellular interactions are a major driver of microbial communities and shown highly variable in strength. Here the authors construct synthetic consortia and mathematical models to elucidate the role of interaction variability in driving ecosystem succession.

    • Feng Liu
    • , Junwen Mao
    •  & Ting Lu

  • Article
    | Open Access

    DNA strand displacement reactions can be difficult to scale up for computational tasks. Here the authors develop DNA switching circuits that achieve high-speed computing with fewer molecules.

    • Fei Wang
    • , Hui Lv
    •  & Chunhai Fan

  • Article
    | Open Access

    Feedback mechanisms for synthetic gene circuits are necessary to provide robustness to external perturbations. Here the authors validate a biomolecular controller based on a sigma and anti-sigma factor to achieve stable gene expression in the face of external disturbances in an in vitro synthetic gene circuit.

    • Deepak K. Agrawal
    • , Ryan Marshall
    •  & Eduardo D Sontag

  • Article
    | Open Access

    Tightly controlling cell output is challenging, which has limited development and applications of bacterial sensors. Here the authors develop tunable, fast-responding sensors to control production of metabolic pigments and use them to assess zinc deficiency in a low-cost, minimal equipment fashion.

    • Monica P. McNerney
    • , Cirstyn L. Michel
    •  & Mark P. Styczynski

  • Article
    | Open Access

    CRISPR-Cas systems have well characterized, modular structures. Here the authors use that architecture to design a Cas12a library of 560 synthetic chimeras, with altered PAM preferences and specificities.

    • R. M. Liu
    • , L. L. Liang
    •  & R. T. Gill

  • Article
    | Open Access

    Constructing biosynthetic pathways to study and engineer glycoprotein structures is difficult. Here, the authors use GlycoPRIME, a cell-free workflow for mixing-and-matching glycosylation enzymes, to evaluate 37 putative glycosylation pathways and discover routes to 18 new glycoprotein structures

    • Weston Kightlinger
    • , Katherine E. Duncker
    •  & Michael C. Jewett

Browse broader subjects

Browse Synthetic biology across other nature.com journals