Featured
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Article
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Proton gradients from light-harvesting E. coli control DNA assemblies for synthetic cells
Controlled actuation is an important aspect of synthetic cellular systems. Here, the authors combine pH responsive DNA origami structures with light triggered proton pump engineered E. coli to trigger a change in pH and control the deformation of giant unilamellar vesicles by simple illumination.
- Kevin Jahnke
- , Noah Ritzmann
- & Kerstin Göpfrich
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Article
| Open Access
A genetically encoded anti-CRISPR protein constrains gene drive spread and prevents population suppression
Technologies that can halt the spread of gene drives would be highly useful in controlling or reverting their effect. Here the authors use the anti-CRISPR protein AcrIIA4 to inactivate drives in A. gambiae.
- Chrysanthi Taxiarchi
- , Andrea Beaghton
- & Andrea Crisanti
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Article
| Open Access
Improved pyrrolysine biosynthesis through phage assisted non-continuous directed evolution of the complete pathway
Pyrrolysine (Pyl) exists in nature as the 22nd proteinogenic amino acid, but studies of Pyl have been hindered by the difficulty and inefficiency of both its chemical and biological syntheses. Here, the authors developed an improved PANCE approach to evolve the pylBCD pathway for increased production of Pyl proteins in E. coli.
- Joanne M. L. Ho
- , Corwin A. Miller
- & Matthew R. Bennett
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Article
| Open Access
Single-component near-infrared optogenetic systems for gene transcription regulation
Current near-IR optogenetic systems to regulate transcription consist of a number of large protein components. Here the authors report a smaller single-component near-IR system, iLight, developed from a bacterial phytochrome that they use to control gene transcription in bacterial and mammalian cells.
- Andrii A. Kaberniuk
- , Mikhail Baloban
- & Vladislav V. Verkhusha
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Article
| Open Access
Dynamic self-assembly of compartmentalized DNA nanotubes
A major goal in Engineering Biology and Materials Science is the development of active, autonomous scaffolds that mimic those present in biological cells. Here the authors report a toolkit for programming the dynamic behaviour of nucleic acid scaffolds in minimal cell-like compartments.
- Siddharth Agarwal
- , Melissa A. Klocke
- & Elisa Franco
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Article
| Open Access
Promiscuous molecules for smarter file operations in DNA-based data storage
The molecular architecture of DNA data storage opens up interesting possibilities and functionalities. Here the authors leverage thermodynamics to control the access of different subsets of data in a file.
- Kyle J. Tomek
- , Kevin Volkel
- & Albert J. Keung
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Article
| Open Access
Living fabrication of functional semi-interpenetrating polymeric materials
Cell based materials production has potential for generating diverse materials with a range of functions. Here, the authors report development of living fabrication of biohybrid semi interpenetrating polymer networks by encapsulating protein producing bacteria within polymer microcapsules.
- Zhuojun Dai
- , Xiaoyu Yang
- & Lingchong You
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Article
| Open Access
Designing an irreversible metabolic switch for scalable induction of microbial chemical production
A promising strategy to increase product synthesis from bacteria uses inducible systems to switch metabolism to production. Here, the authors use models to show how engineering positive feedback loops into the genetic circuitry creates a switch that requires only temporary induction with a cheap nutrient to switch metabolism irreversibly, and so drastically reduce inducer use and cost.
- Ahmad A. Mannan
- & Declan G. Bates
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Perspective
| Open Access
Towards an engineering theory of evolution
Effective biological engineering requires the acknowledgement of evolution and its consideration during the design process. In this perspective, the authors present the concept of the evotype to reason about and shape the evolutionary potential of natural and engineered biosystems.
- Simeon D. Castle
- , Claire S. Grierson
- & Thomas E. Gorochowski
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Article
| Open Access
Smart-watch-programmed green-light-operated percutaneous control of therapeutic transgenes
Wearable smart devices often have green light diodes to monitor health. Here the authors use this to control a light-activated genetic switch for GLP1 production in diabetic mice.
- Maysam Mansouri
- , Marie-Didiée Hussherr
- & Martin Fussenegger
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Article
| Open Access
Engineered reproductively isolated species drive reversible population replacement
There exist only a handful of methods to engineer reproductive barriers in eukaryotes. Here the authors use CRISPR to engineer multiple barriers in D. melanogaster and model their spread.
- Anna Buchman
- , Isaiah Shriner
- & Omar S. Akbari
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Article
| Open Access
Design of synthetic human gut microbiome assembly and butyrate production
Microbiomes designed with predictable functions could enable broad applications in health, agriculture and bioprocessing. Here the authors use a model-guided approach to design diverse synthetic human gut communities for production of the health-relevant metabolite butyrate.
- Ryan L. Clark
- , Bryce M. Connors
- & Ophelia S. Venturelli
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Comment
| Open Access
Strengthening the United Nations Secretary-General’s Mechanism to an alleged use of bioweapons through a quality-assured laboratory response
The cascade of innovations in biotechnology opens new pathways for biological warfare. The international laboratory network being developed under the UN Secretary-General’s Mechanism could provide vital evidence in case of an alleged biological attack.
- Sandra Appelt
- , Anna-Maria Rohleder
- & Roland Grunow
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Article
| Open Access
Synthetic neural-like computing in microbial consortia for pattern recognition
Complex biological systems have individual cells acting collectively to solve complex tasks. Here the authors implement neural network-like computing in a bacterial consortia to recognise patterns.
- Ximing Li
- , Luna Rizik
- & Ramez Daniel
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Article
| Open Access
The transcriptional landscape of a rewritten bacterial genome reveals control elements and genome design principles
Rewriting genomes allows for complete annotation of gene regulatory elements. Here the authors compare endogenous and rewritten segments of a genome and find extensive transcriptional changes, based on which they formulate design principles that aid in the programming of biological systems.
- Mariëlle J. F. M. van Kooten
- , Clio A. Scheidegger
- & Beat Christen
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Article
| Open Access
Optimized CRISPR tools and site-directed transgenesis towards gene drive development in Culex quinquefasciatus mosquitoes
Culex mosquitoes are a global vector for insect-borne diseases, though progress with genetic tools lags behind other mosquito species. Here the authors present a Cas9-based toolkit and methods that could support future gene drive development in these mosquitoes.
- Xuechun Feng
- , Víctor López Del Amo
- & Valentino M. Gantz
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Article
| Open Access
Characterization of an engineered live bacterial therapeutic for the treatment of phenylketonuria in a human gut-on-a-chip
Engineered live bacteria could represent a new class of therapeutic treatment for human disease. Here, the authors use a human gut-on-a-chip microfluidics system to characterize an engineered live bacterial therapeutic, designed for the treatment of phenylketonuria, and to construct mathematical models that predict therapeutic strain function in non-human primates.
- M. Tyler Nelson
- , Mark R. Charbonneau
- & Camilla A. Mauzy
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Article
| Open Access
Programming gene expression in multicellular organisms for physiology modulation through engineered bacteria
Manipulating animal physiology can be difficult because of the complexity of multicellular systems. Here the authors use engineered bacteria to modulate Caenorhabditis elegans gene expression through genetic circuit controlled RNAi.
- Baizhen Gao
- & Qing Sun
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Article
| Open Access
Scalable recombinase-based gene expression cascades
There are few robust circuit architectures for sequential gene perturbations. Here, the authors use a modular recombinase-based design that sequentially edits loci, synchronizes cells, and deletes itself.
- Tackhoon Kim
- , Benjamin Weinberg
- & Timothy K. Lu
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Article
| Open Access
CopyCatchers are versatile active genetic elements that detect and quantify inter-homolog somatic gene conversion
CRISPR-based genetic elements can copy themselves across host genomes. Here the authors introduce CopyCatcher, a gene-drive related system for detecting and quantifying somatic gene conversion events.
- Zhiqian Li
- , Nimi Marcel
- & Ethan Bier
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Comment
| Open Access
A call for caution in analysing mammalian co-transfection experiments and implications of resource competition in data misinterpretation
Transient transfections are routinely used in basic and synthetic biology studies to unravel pathway regulation and to probe and characterise circuit designs. As each experiment has a component of intrinsic variability, reporter gene expression is usually normalized with co-delivered genes that act as transfection controls. Recent reports in mammalian cells highlight how resource competition for gene expression leads to biases in data interpretation, with a direct impact on co-transfection experiments. Here we define the connection between resource competition and transient transfection experiments and discuss possible alternatives. Our aim is to raise awareness within the community and stimulate discussion to include such considerations in future experimental designs, for the development of better transfection controls.
- Roberto Di Blasi
- , Masue M. Marbiah
- & Francesca Ceroni
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Article
| Open Access
Automatic synchronisation of the cell cycle in budding yeast through closed-loop feedback control
It is difficult to synchronize the cell cycle in a population of yeast cells for extended periods of time. Here the authors use a cybergenetic system with inbuilt feedback to synchronize a population of modified yeast.
- Giansimone Perrino
- , Sara Napolitano
- & Diego di Bernardo
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Article
| Open Access
Improving cell-free glycoprotein synthesis by characterizing and enriching native membrane vesicles
Cell-free gene expression systems are an attractive platform for biomanufacturing and synthetic biology. Here the authors characterize native membrane vesicles in E. coli extracts for improved glycoengineering.
- Jasmine M. Hershewe
- , Katherine F. Warfel
- & Michael C. Jewett
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Article
| Open Access
Biased cytochrome P450-mediated metabolism via small-molecule ligands binding P450 oxidoreductase
P450 oxidoreductase (POR) selectively activates numerous cytochromes P450 (CYP), crucial for metabolism of drugs, steroids and xenobiotics and natural product biosynthesis. Here, the authors identify ligands that bind POR and bias its specificity towards CYP redox partners, activating distinct metabolic cascades in cells.
- Simon Bo Jensen
- , Sara Thodberg
- & Nikos S. Hatzakis
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Article
| Open Access
A systematic approach to inserting split inteins for Boolean logic gate engineering and basal activity reduction
Split inteins are powerful tools for designing synthetic split proteins. Here the authors use a mini-Mu transposon screen to map split sites, enabling the development of protein-based logic gates and fine control of protein activity.
- Trevor Y. H. Ho
- , Alexander Shao
- & Baojun Wang
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Article
| Open Access
Creating enzymes and self-sufficient cells for biosynthesis of the non-natural cofactor nicotinamide cytosine dinucleotide
Nicotinamide cytosine dinucleotide is an NAD mimic that can be used to mediate redox reactions. Here the authors design an NCD synthetase for the intracellular production of NCD.
- Xueying Wang
- , Yanbin Feng
- & Zongbao K. Zhao
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Article
| Open Access
Single strain control of microbial consortia
Engineered microbial communities can divide labour between their members and interface with natural microbiomes. Here the authors demonstrate how a single toxin producing engineered strain can tune the composition of a two-strain community.
- Alex J. H. Fedorec
- , Behzad D. Karkaria
- & Chris P. Barnes
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Article
| Open Access
A rationally engineered decoder of transient intracellular signals
Cells encode information by modulating signal dynamics. Here the authors developed a rapid prototyping tool, TopoDesign, to engineer a synthetic short-pulse decoder in yeast.
- Claude Lormeau
- , Fabian Rudolf
- & Jörg Stelling
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Article
| Open Access
Robust and flexible platform for directed evolution of yeast genetic switches
Eukaryotic genetic switches are more complex than prokaryotic ones, complicating their design. Here the authors present a workflow for parallel screening, selection and evolution of yeast genetic switches.
- Masahiro Tominaga
- , Kenta Nozaki
- & Akihiko Kondo
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Article
| Open Access
A modular tool to query and inducibly disrupt biomolecular condensates
Here, the authors present DisCo (Disassembly of Condensates), a method that allows the fast, inducible, and specific disruption of tagged condensates in mammalian cells. DisCo uses chemical dimerizers to induce the recruitment of a ligand into condensates leading to condensate disassembly.
- Carmen N. Hernández-Candia
- , Sarah Pearce
- & Chandra L. Tucker
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Article
| Open Access
Harnessing the central dogma for stringent multi-level control of gene expression
Inducible gene expression systems should minimise leaky output and offer a large achievable range of expression. Here, the authors regulate transcription and translation together to suppress noise and create digital-like responses, while maintaining a large expression range in vivo and in vitro.
- F. Veronica Greco
- , Amir Pandi
- & Thomas E. Gorochowski
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Article
| Open Access
dCas9 regulator to neutralize competition in CRISPRi circuits
CRISPRi allows for the simultaneous control of many genes, however the sgRNAs compete for binding to dCas9. Here the authors design a dCas9 concentration regulator to allow independent regulation of multiple genes.
- Hsin-Ho Huang
- , Massimo Bellato
- & Domitilla Del Vecchio
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Article
| Open Access
2D printed multicellular devices performing digital and analogue computation
Synthetic biology circuits are finding application in a wide range of computational devices, such as contaminant detection. Here, the authors design 2D paper circuits in which the spatial orientation of the cellular components specifies function.
- Sira Mogas-Díez
- , Eva Gonzalez-Flo
- & Javier Macía
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Comment
| Open Access
Seeding the idea of encapsulating a representative synthetic metagenome in a single yeast cell
Synthetic metagenomics could potentially unravel the complexities of microbial ecosystems by revealing the simplicity of microbial communities captured in a single cell. Conceptionally, a yeast cell carrying a representative synthetic metagenome could uncover the complexity of multi-species interactions, illustrated here with wine ferments.
- Ignacio Belda
- , Thomas C. Williams
- & Isak S. Pretorius
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Article
| Open Access
Overcoming the design, build, test bottleneck for synthesis of nonrepetitive protein-RNA cassettes
Phage-coat proteins can be used to build synthetic biology parts. Here the authors use an oligo library and machine learning to predict and verify sequences based on binding scores.
- Noa Katz
- , Eitamar Tripto
- & Roee Amit
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Article
| Open Access
Polymerase-guided base editing enables in vivo mutagenesis and rapid protein engineering
Existing in vivo mutagenesis tools are limited by low mutation diversity and mutation rates. Here the authors present TRIDENT for targeted, continual and inducible diversification of genes of interest using deaminases fused to T7 RNA polymerase.
- Aaron Cravens
- , Osman K. Jamil
- & Christina D. Smolke
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Article
| Open Access
A self-organized synthetic morphogenic liposome responds with shape changes to local light cues
The authors generated a Synthetic Morphogenic Membrane System by encapsulating a dynamic microtubule aster and a light-inducible signaling system driven by GTP/ATP chemical potential into cell-sized liposomes. This reconstitution of artificial proto-cells reveals how non-equilibrium phenomena affect cellular information processing in morphogenesis.
- Konstantin Gavriljuk
- , Bruno Scocozza
- & Philippe I. H. Bastiaens
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Article
| Open Access
De novo design of a reversible phosphorylation-dependent switch for membrane targeting
The ability to dynamically control protein-protein interactions and localization of proteins is critical in synthetic biological systems. Here the authors develop a peptide-based molecular switch that regulates dimer formation and lipid membrane targeting via reversible phosphorylation.
- Leon Harrington
- , Jordan M. Fletcher
- & Petra Schwille
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Article
| Open Access
Inherently confinable split-drive systems in Drosophila
NHEJ alleles and Cas9 remnants after a gene drive introduction are scientific and public concerns. Here, the authors use split drives with recoded rescue elements to target essential genes and minimize the appearance of NHEJ alleles while also leaving no trace of Cas9.
- Gerard Terradas
- , Anna B. Buchman
- & Ethan Bier
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Article
| Open Access
Engineered yeast genomes accurately assembled from pure and mixed samples
The cost and complexity of whole genome sequencing limits its use in identifying and validating sequences used for genetic engineering and synthetic biology. Here the authors present Prymetime, an integrated workflow to sequence engineered strains and identify engineering in metagenomes.
- Joseph H. Collins
- , Kevin W. Keating
- & Eric M. Young
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Article
| Open Access
Single-cell measurement of plasmid copy number and promoter activity
A quantitative assessment of promoter function can improve the precision of cellular engineering. Here the authors develop a method to simultaneously count plasmid DNA, RNA transcripts and protein expression in single living bacteria.
- Bin Shao
- , Jayan Rammohan
- & Christopher A. Voigt
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Article
| Open Access
A multiplexed, automated evolution pipeline enables scalable discovery and characterization of biosensors
Biosensors are key to engineered biological systems. Here the authors demonstrate rapid de novo in vitro evolution of RNA biosensors of small molecules in a fully automated system.
- Brent Townshend
- , Joy S. Xiang
- & Christina D. Smolke
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Article
| Open Access
Reversible thermal regulation for bifunctional dynamic control of gene expression in Escherichia coli
Genetic circuits can be built with bifunctional dynamic regulation of gene expression. Here the authors design a thermosensitive switch for spatial and temporal control of colony pattern, cell shape and polymer production.
- Xuan Wang
- , Jia-Ning Han
- & Guo-Qiang Chen
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Article
| Open Access
Programmable C:G to G:C genome editing with CRISPR-Cas9-directed base excision repair proteins
Many diseases are caused by single-nucleotide polymorphisms. Here, the authors present CRISPR base editors that use the base excision machinery for single-base transversions.
- Liwei Chen
- , Jung Eun Park
- & Wei Leong Chew
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Perspective
| Open Access
Applications, challenges, and needs for employing synthetic biology beyond the lab
Current developments in synthetic biology are not immediately applicable outside of the controlled laboratory environment. In this Perspective, the authors outline the advances and challenges the field faces in operating in resource limited and off-the-grid scenarios.
- Sierra M. Brooks
- & Hal S. Alper
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Review Article
| Open Access
DNA stability: a central design consideration for DNA data storage systems
DNA has the potential to store vast amounts of data but it is subject to physical decay. In this Perspective, the authors propose that the stability of DNA should be a key consideration in how it is used for data storage.
- Karishma Matange
- , James M. Tuck
- & Albert J. Keung
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Article
| Open Access
Chemogenetic ON and OFF switches for RNA virus replication
Therapeutic application of RNA viruses requires tight control over viral activity. Here the authors design a regulatory switch that enables control over activity with clinically approved HIV protease inhibitors.
- E. Heilmann
- , J. Kimpel
- & D. von Laer
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Article
| Open Access
PlasmidHawk improves lab of origin prediction of engineered plasmids using sequence alignment
Advances in synthetic biology and genome engineering raise awareness of potential misuse. Here, the authors present PlasmidHawk, a sequence alignment based method for lab-of-origin prediction.
- Qi Wang
- , Bryce Kille
- & Todd J. Treangen
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Article
| Open Access
Cas12a-assisted precise targeted cloning using in vivo Cre-lox recombination
Direct cloning of biosynthetic gene clusters is difficult due to their size and repetitive nature. Here, the authors present CAPTURE, which uses Cas12a and in vivo Cre-lox recombination for efficient cloning of gene clusters up to 113 kb, and demonstrate how this method can be used for large-scale discovery of novel natural products.
- Behnam Enghiad
- , Chunshuai Huang
- & Huimin Zhao
Synchronization of gene expression across eukaryotic communities through chemical rhythms