Article
|
Open Access
Featured
-
-
Article
| Open AccessGeneration of a more efficient prime editor 2 by addition of the Rad51 DNA-binding domain
While prime editing is a promising technology, PE2 systems often have low efficiency. Here the authors fuse a Rad51 DNA-binding domain to create hyPE2 with improved editing efficiency.
- Myungjae Song
- , Jung Min Lim
- & Hyongbum Henry Kim
-
Article
| Open AccessCoevolutionary methods enable robust design of modular repressors by reestablishing intra-protein interactions
Genetic sensors can be created by mix and matching DNA-binding modules with ligand-binding modules. Here the authors use a computational model to overcome module incompatibilities and restore function by rescuing key interactions.
- Xian-Li Jiang
- , Rey P. Dimas
- & Faruck Morcos
-
Article
| Open AccessOne-step construction of circularized nanodiscs using SpyCatcher-SpyTag
Circularised nanodiscs (cNDs) are able to stabilise large lipid bilayer patches and are used for structural and functional studies. Current techniques to build cNDs have numerous steps and low yields; here the authors report a single step construction method using the SpyCatcher-SpyTag system.
- Shanwen Zhang
- , Qian Ren
- & Huan Bao
-
Article
| Open AccessA versatile genetic engineering toolkit for E. coli based on CRISPR-prime editing
CRISPR prime editing enables double-strand break free engineering of the genome. Here the authors present a toolkit for prime editing in E. coli.
- Yaojun Tong
- , Tue S. Jørgensen
- & Sang Yup Lee
-
Article
| Open AccessProgrammable receptors enable bacterial biosensors to detect pathological biomarkers in clinical samples
Bacterial biosensors have promising applications in medical and environmental diagnostics. Here the authors use EMeRALD synthetic receptors to design bile salt sensors for use in liver transplant patient serum.
- Hung-Ju Chang
- , Ana Zúñiga
- & Jerome Bonnet
-
Article
| Open AccessIntegration of FRET and sequencing to engineer kinase biosensors from mammalian cell libraries
Existing Förster Resonance Energy Transfer (FRET) biosensors are often limited in their sensitivity. Here the authors report FRET-seq which they use to identify Fyn and ZAP70 kinase biosensors with enhanced performance, and use them to image T-cell activation and screen drugs.
- Longwei Liu
- , Praopim Limsakul
- & Yingxiao Wang
-
Article
| Open AccessMetabolome and proteome analyses reveal transcriptional misregulation in glycolysis of engineered E. coli
Synthetic pathways represent a metabolic burden on host cells. Here the authors engineer Cra-binding sites to prevent misregulation in glycerol and carotenoid overproducing E. coli strains.
- Chun-Ying Wang
- , Martin Lempp
- & Hannes Link
-
Article
| Open AccessAn engineered IL-2 reprogrammed for anti-tumor therapy using a semi-synthetic organism
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
-
Article
| Open AccessGene-drive suppression of mosquito populations in large cages as a bridge between lab and field
Experimental analysis of gene drive population dynamics has mostly been limited to small cage trials. Here the authors, to fill the gap between lab based studies and field studies, use large indoor cages and see population suppression without the emergence of resistant alleles
- Andrew Hammond
- , Paola Pollegioni
- & Andrea Crisanti
-
Perspective
| Open AccessTowards a synthetic cell cycle
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
-
Article
| Open AccessRational construction of genome-reduced Burkholderiales chassis facilitates efficient heterologous production of natural products from proteobacteria
An efficient chassis for heterologous expression of biosynthetic gene clusters (BGCs) from Gram-negative bacteria is still unavailable. Here, the authors report rational construction of genome-reduced Burkholderials chassis to facilitate production of a class of new compounds by expressing BGC from Chitinimonas koreensis.
- Jiaqi Liu
- , Haibo Zhou
- & Xiaoying Bian
-
Article
| Open AccessReprogrammed CRISPR-Cas13b suppresses SARS-CoV-2 replication and circumvents its mutational escape through mismatch tolerance
Cas13b can be harnessed to target and degrade RNA transcripts inside a cellular environment. Here the authors reprogram Cas13b to target SARSCoV-2 transcripts in infected mammalian cells and reveal its resilience to variants thanks to single mismatch tolerance.
- Mohamed Fareh
- , Wei Zhao
- & Joseph A. Trapani
-
Article
| Open AccessEnhanced regulation of prokaryotic gene expression by a eukaryotic transcriptional activator
Expanded toolkits for prokaryotic synthetic biology can enhance the dynamic range of gene expression. Here the authors move the eukaryotic transcription factor QF into E. coli and integrate it into genetic devices.
- I. Cody MacDonald
- , Travis R. Seamons
- & Tara L. Deans
-
Article
| Open AccessA 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
-
Article
| Open AccessImproved 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
-
Article
| Open AccessSingle-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
-
Article
| Open AccessRepurposing tRNAs for nonsense suppression
Here, the authors report de novo design, optimization and characterization of tRNAs that decode UGA stop codons in E. coli. The structure of the ribosome in a complex with the designed tRNA bound to a UGA stop codon suggests that distinct A-site ligands (tRNAs versus release factors) induce distinct conformation of the stop codon within the mRNA in the decoding center.
- Suki Albers
- , Bertrand Beckert
- & Zoya Ignatova
-
Article
| Open AccessHigh-throughput screening and rational design of biofunctionalized surfaces with optimized biocompatibility and antimicrobial activity
Optimizing the concentration of different functional peptides on a surface can be a complex process. Here, the authors report on the use of a click immobilization strategy to create gradients of two different functional peptides on a surface to screen different density functions for rapid optimization.
- Zhou Fang
- , Junjian Chen
- & Chuanbin Mao
-
Article
| Open AccessEngineering an anti-HER2 biparatopic antibody with a multimodal mechanism of action
HER2 acts an oncogenic driver in numerous cancers. Here, the authors design an anti-HER2 biparatopic and tetravalent IgG fusion with inhibitory effects in a xenograft model.
- Florian Kast
- , Martin Schwill
- & Andreas Plückthun
-
Article
| Open AccessEngineering the protein dynamics of an ancestral luciferase
Directed evolution commonly relies on point mutations but InDels frequently occur in evolution. Here the authors report a protein-engineering framework based on InDel mutagenesis and fragment transplantation resulting in greater catalysis and longer glow-type bioluminescence of the ancestral luciferase.
- Andrea Schenkmayerova
- , Gaspar P. Pinto
- & Jiri Damborsky
-
Article
| Open AccessPromiscuous 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
-
Article
| Open AccessIntracellular artificial supramolecules based on de novo designed Y15 peptides
Self-assembling peptides (SAPs) can be used to build biomaterials, but genetically encoded SAPs have rarely been used as building blocks in cells. Here, the authors design a SAP that can be genetically fused to target proteins to induce their intracellular clustering and modulate their signaling functions.
- Takayuki Miki
- , Taichi Nakai
- & Hisakazu Mihara
-
Article
| Open AccessEngineered 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
-
Comment
| Open AccessStrengthening 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
-
Article
| Open AccessOptimized 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
-
Article
| Open AccessCharacterization 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
-
Article
| Open AccessTissue-specific activation of gene expression by the Synergistic Activation Mediator (SAM) CRISPRa system in mice
CRISPR-Cas9 is a gene editing tool that can be used to modulate gene expression. Here, the authors report the generation of a mouse model that express all components of the CRISPR-Cas9 guide directed Synergistic Activation Mediator (SAM), demonstrate that gene activation can be achieved with various delivery methods and include generation of a disease model of hypercholesterolemia
- Charleen Hunt
- , Suzanne A. Hartford
- & Guochun Gong
-
Article
| Open AccessScalable 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
-
Article
| Open AccessCopyCatchers 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
-
Article
| Open AccessProgramming 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
-
Comment
| Open AccessA 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
-
Article
| Open AccessMachine learning guided aptamer refinement and discovery
Current aptamer discovery approaches are unable to probe the complete space of possible sequences. Here, the authors use machine learning to facilitate the development of DNA aptamers with improved binding affinities, and truncate them without significantly compromising binding affinity.
- Ali Bashir
- , Qin Yang
- & B. Scott Ferguson
-
Article
| Open AccessStructure-guided engineering of adenine base editor with minimized RNA off-targeting activity
Base editors can induce transcriptome-wide RNA off-target editing independent of gRNA. Here, the authors engineer ABEmax variants with minimized RNA off-target activities.
- Jianan Li
- , Wenxia Yu
- & Yunbo Qiao
-
Article
| Open AccessA designer FG-Nup that reconstitutes the selective transport barrier of the nuclear pore complex
Intrinsically disordered FG-Nups line the Nuclear Pore Complex (NPC) lumen and form a selective barrier where transport of most proteins is inhibited, whereas specific transporter proteins are able to pass. Here, the authors reconstitute the selective behaviour of the NPC by introducing a rationally designed artificial FG-Nup that demonstrates that no specific spacer sequence nor a spatial segregation of different FG-motif types are needed to create selective NPCs.
- Alessio Fragasso
- , Hendrik W. de Vries
- & Cees Dekker
-
Article
| Open AccessRobust 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
-
Article
| Open AccessA 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
-
Article
| Open Access2D 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
-
Article
| Open AccessPolymerase-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
-
Article
| Open AccessLasso-grafting of macrocyclic peptide pharmacophores yields multi-functional proteins
RaPID (Random non-standard Peptides Integrated Discovery) enables discovery of small macrocyclic peptides binding desired targets. Here, the authors propose lasso-grafting: the RaPID-derived peptides are implanted onto diverse proteins and maintain both the binding properties of the cyclic peptide and the host protein function.
- Emiko Mihara
- , Satoshi Watanabe
- & Junichi Takagi
-
Article
| Open AccessInherently 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
-
Article
| Open AccessA 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
-
Article
| Open AccessProgrammable 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
-
Perspective
| Open AccessApplications, 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
-
Review Article
| Open AccessDNA 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
-
Article
| Open AccessChemogenetic 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
-
Article
| Open AccessPlasmidHawk 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
-
Article
| Open AccessCas12a-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
-
Article
| Open AccessCre-Controlled CRISPR mutagenesis provides fast and easy conditional gene inactivation in zebrafish
Targeting a gene with two loxP sites is both time and labour intensive. Here the authors present Cre-Controlled CRISPR allowing conditional mutagenesis of a gene of interest and simultaneously labelling the putative mutant cells fluorescently.
- Stefan Hans
- , Daniela Zöller
- & Michael Brand
-
Article
| Open AccessAuxin-mediated protein depletion for metabolic engineering in terpene-producing yeast
Loss-of-function experiments are used in metabolic engineering to understand and optimise metabolism. Here, the authors apply auxin inducible protein degradation to test different metabolic engineering strategies for improved terpenoid production in yeast.
- Zeyu Lu
- , Bingyin Peng
- & Claudia E. Vickers