Featured
-
-
Article
| Open AccessA fluoride-responsive genetic circuit enables in vivo biofluorination in engineered Pseudomonas putida
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 AccessA deep learning approach to programmable RNA switches
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 AccessSequence-to-function deep learning frameworks for engineered riboregulators
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 AccessMetastable hybridization-based DNA information storage to allow rapid and permanent erasure
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 AccessProtease circuits for processing biological information
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 AccessGenetic circuit characterization by inferring RNA polymerase movement and ribosome usage
Debugging a genetic circuit is frustrated by the inability to characterize parts in the context of the circuit. Here the authors use RNA-seq and ribosome profiling to take ‘snapshots’ of a large circuit in different states.
- Amin Espah Borujeni
- , Jing Zhang
- & Christopher A. Voigt
-
Article
| Open AccessViral gene drive in herpesviruses
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 AccessCombining mechanistic and machine learning models for predictive engineering and optimization of tryptophan metabolism
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 AccessA machine learning Automated Recommendation Tool for synthetic biology
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 AccessEngineering and application of a biosensor with focused ligand specificity
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 AccessOptoribogenetic control of regulatory RNA molecules
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 AccessA possible universal role for mRNA secondary structure in bacterial translation revealed using a synthetic operon
The mechanisms for regulating translation re-initiation in bacteria remain poorly understood. Here, the authors screened a library of synthetic operons and identified a ribosome termination structure that modulates re-initiation efficiency and which is conserved across bacteria.
- Yonatan Chemla
- , Michael Peeri
- & Lital Alfonta
-
Article
| Open AccessRational programming of history-dependent logic in cellular populations
Automated frameworks to systematically implement robust history-dependent genetic programs in cellular populations.
- Ana Zúñiga
- , Sarah Guiziou
- & Jerome Bonnet
-
Article
| Open AccessCharacterization and mitigation of gene expression burden in mammalian cells
The design of genetic networks in mammalian cells is still slow and often fails. Here the authors show that miRNA-based incoherent feedforward loop circuits can be used to alleviate cellular burden.
- Timothy Frei
- , Federica Cella
- & Velia Siciliano
-
Article
| Open AccessEfficient rational modification of non-ribosomal peptides by adenylation domain substitution
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 AccessA role for Biofoundries in rapid development and validation of automated SARS-CoV-2 clinical diagnostics
The SARS-CoV-2 pandemic has created large demand on global testing capability. Here the authors use the London Biofoundry, an automated synthetic biology platform, and develop an open-source virus-like particle to implement high-throughput diagnostics.
- Michael A. Crone
- , Miles Priestman
- & Paul S. Freemont
-
Article
| Open AccessEngineering multiple species-like genetic incompatibilities in insects
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 AccessEngineered systems of inducible anti-repressors for the next generation of biological programming
Transcriptional anti-repressors have been largely absent in the design of regulated genetic circuits. Here, the authors present a workflow of the engineering of non-natural anti-reperssors that can be built into NOT oriented logic gates.
- Thomas M. Groseclose
- , Ronald E. Rondon
- & Corey J. Wilson
-
Article
| Open AccessGenetically controlled membrane synthesis in liposomes
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 AccessChromosome drives via CRISPR-Cas9 in yeast
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 AccessRibosome-mediated polymerization of long chain carbon and cyclic amino acids into peptides in vitro
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 AccessIsobutanol production freed from biological limits using synthetic biochemistry
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 AccessDe novo design of an intercellular signaling toolbox for multi-channel cell–cell communication and biological computation
Intercellular signalling is fundamental for the formation of complex structures from single cells. Here the authors design six orthogonal cell–cell signalling channels for cell consortia communication and bio-computation.
- Pei Du
- , Huiwei Zhao
- & Chunbo Lou
-
Article
| Open AccessContinuous bioactivity-dependent evolution of an antibiotic biosynthetic pathway
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 AccessEngineering AvidCARs for combinatorial antigen recognition and reversible control of CAR function
The lack of tumour-specific antigens and control over T-cell activity limits the development of CAR-T cell therapies for solid tumours. Here the authors present an avidity-controlled CAR platform with inducible logic control functions.
- Benjamin Salzer
- , Christina M. Schueller
- & Manfred Lehner
-
Article
| Open AccessOptogenetic control of protein binding using light-switchable nanobodies
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 AccessEngineering designer beta cells with a CRISPR-Cas9 conjugation platform
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 AccessEngineering regulatory networks for complex phenotypes in E. coli
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 AccessExploiting natural chemical photosensitivity of anhydrotetracycline and tetracycline for dynamic and setpoint chemo-optogenetic control
Anhydrotetracycline and tetracycline are commonly used chemicals to regulate transcription and translation, respectively. Here the authors exploit the natural photosensitivity of these molecules to place their activity under optical control.
- Armin Baumschlager
- , Marc Rullan
- & Mustafa Khammash
-
Article
| Open AccessA non-invasive far-red light-induced split-Cre recombinase system for controllable genome engineering in mice
Current light-inducible Cre-loxP systems have minimal capacity for deep tissue penetration. Here, the authors present a far-red light-induced split Cre-loxP system for in vivo genome engineering.
- Jiali Wu
- , Meiyan Wang
- & Haifeng Ye
-
Article
| Open AccessMajority sensing in synthetic microbial consortia
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 AccessLarge-scale DNA-based phenotypic recording and deep learning enable highly accurate sequence-function mapping
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 AccessAccessing unexplored regions of sequence space in directed enzyme evolution via insertion/deletion mutagenesis
Insertions/Deletions (InDels) remain an untapped source of protein diversity in laboratory evolution. The method TRIAD generates libraries of random variants with short in-frame InDels using transposons, allowing a comparison of their evolutionary potential with widely-used point mutant libraries.
- Stephane Emond
- , Maya Petek
- & Florian Hollfelder
-
Article
| Open AccessQuantifying molecular bias in DNA data storage
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 AccessChimeric design of pyrrolysyl-tRNA synthetase/tRNA pairs and canonical synthetase/tRNA pairs for genetic code expansion
Orthogonal aminoacyl-tRNA synthetase/tRNA pairs are crucial for the incorporation of unnatural amino acids in a site-specific manner. Here the authors use rational chimera design to create multiple efficient pairs that function in bacterial and mammalian systems for genetic code expansion.
- Wenlong Ding
- , Hongxia Zhao
- & Shixian Lin
-
Article
| Open AccessHolistic engineering of cell-free systems through proteome-reprogramming synthetic circuits
Synthetic biological modules can be used to reprogram host proteomes, which in turn enhance the function of the synthetic modules. The authors use this holistic synthetic biology approach to engineer a more favorable environment for cell-free protein synthesis.
- Luis E. Contreras-Llano
- , Conary Meyer
- & Cheemeng Tan
-
Article
| Open AccessGenetic breakdown of a Tet-off conditional lethality system for insect population control
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 AccessPhosphoregulated orthogonal signal transduction in mammalian cells
Phosphoregulation is a key mechanism of signal processing. Here the authors build a phosphoregulated relay system in mammalian cells for orthogonal signal transduction.
- Leo Scheller
- , Marc Schmollack
- & Martin Fussenegger
-
Article
| Open AccessCRISPR artificial splicing factors
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 AccessDynamic and scalable DNA-based information storage
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 AccessRational design of aptamer switches with programmable pH response
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 AccessMultistable and dynamic CRISPRi-based synthetic circuits
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 AccessCephalopod-inspired optical engineering of human cells
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 AccessImmunotherapy with engineered bacteria by targeting the STING pathway for anti-tumor immunity
Synthetic biology can be used to create rationally designed living therapeutics. Here the authors engineer E. coli Nissle to target STING activation in antigen presenting cells for the treatment of solid tumors and demonstrate preclinical activity in murine models.
- Daniel S. Leventhal
- , Anna Sokolovska
- & Jose M. Lora
-
Article
| Open AccessImproving the safety of human pluripotent stem cell therapies using genome-edited orthogonal safeguards
Human pluripotent stem cell derived therapies can have serious safety risks. Here the authors design two drug inducible genetic safeguards to deplete undifferentiated hPSCs and hPSC-derived cell types.
- Renata M. Martin
- , Jonas L. Fowler
- & Kyle M. Loh
-
Article
| Open AccessA Cas9 with PAM recognition for adenine dinucleotides
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 AccessApplication of combinatorial optimization strategies in synthetic biology
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 AccessA redox-based electrogenetic CRISPR system to connect with and control biological information networks
Redox-responsive transcriptional regulators can enable user-specified electronic control over biological functions. Here the authors demonstrate electronic control of CRISPRa and CRISPRi using redox signalling.
- Narendranath Bhokisham
- , Eric VanArsdale
- & William E. Bentley
-
Article
| Open AccessInvestigating the dynamics of microbial consortia in spatially structured environments
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