2,315 results match your criteria ACS Synthetic Biology[Journal]

Temporal Expression of Transcription Factor Improves Natural Killer Cell Differentiation from Human Pluripotent Stem Cells.

ACS Synth Biol 2022 May 24. Epub 2022 May 24.

Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907, United States.

Natural killer (NK) cells are one type of innate lymphoid cells, and NK cell-based immunotherapy serves as a potentially curative therapy for cancers. However, the lack of reliable resources for a large amount of NK cells required for clinical infusion has limited the broader application of NK cells in targeted immunotherapy. Substantial effort has thus been made to generate NK-like cells from human pluripotent stem cells (hPSCs), but detailed molecular mechanisms regulating NK cell differentiation remain elusive, preventing us from developing robust strategies for NK cell production. Read More

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CRISPR/dCas9-RpoD-Mediated Simultaneous Transcriptional Activation and Repression in MR-1.

ACS Synth Biol 2022 May 24. Epub 2022 May 24.

Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.

Extracellular electron transfer (EET) of electroactive microorganisms (EAMs) is the dominating factor for versatile applications of bio-electrochemical systems. MR-1 is one of the model EAMs for the study of EET, which is associated with a variety of cellular activities. However, due to the lack of a transcriptional activation tool, regulation of multiple genes is labor-intensive and time-consuming, which hampers the advancement of improving the EET efficiency in . Read More

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Functional Nanopore Screen: A Versatile High-Throughput Assay to Study and Engineer Protein Nanopores in .

ACS Synth Biol 2022 May 23. Epub 2022 May 23.

Department of Biology, TU Darmstadt, 64287 Darmstadt, Germany.

Nanopores comprise a versatile class of membrane proteins that carry out a range of key physiological functions and are increasingly developed for different biotechnological applications. Yet, a capacity to study and engineer protein nanopores by combinatorial means has so far been hampered by a lack of suitable assays that combine sufficient experimental resolution with throughput. Addressing this technological gap, the functional nanopore (FuN) screen now provides a quantitative and dynamic readout of nanopore assembly and function in the context of the inner membrane of . Read More

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Engineering of a TrpR-Based Biosensor for Altered Dynamic Range and Ligand Preference.

ACS Synth Biol 2022 May 20. Epub 2022 May 20.

School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, 302 East Campus Road, Athens, Georgia 30602, United States.

Transcriptional factors play a crucial role in regulating cellular functions. Understanding and altering the dynamic behavior of the transcriptional factor-based biosensors will expand our knowledge in investigating biomolecular interactions and facilitating biosynthetic applications. In this study, we characterized and engineered a TrpR-based tryptophan repressor system in . Read More

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Efficient Single-Nucleotide Microbial Genome Editing Achieved Using CRISPR/Cpf1 with Maximally 3'-End-Truncated crRNAs.

ACS Synth Biol 2022 May 18. Epub 2022 May 18.

Department of Systems Biotechnology and Institute of Microbiomics, Chung-Ang University, Anseong 17546, Republic of Korea.

Mismatch tolerance, a cause of the off-target effect, impedes accurate genome editing with the CRISPR/Cas system. Herein, we observed that oligonucleotide-directed single-base substitutions could be rarely introduced in the microbial genome using CRISPR/Cpf1-mediated negative selection. Because crRNAs have the ability to recognize and discriminate among specific target DNA sequences, we systematically compared the effects of modified crRNAs with 3'-end nucleotide truncations and a single mismatch on the genomic cleavage activity of FnCpf1 in. Read More

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Efficient Synthesis of Phycocyanobilin by Combinatorial Metabolic Engineering in .

ACS Synth Biol 2022 May 17. Epub 2022 May 17.

Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.

Phycocyanobilin (PCB) is a kind of light-harvesting pigment which naturally exists in algae and plays important roles in absorbing and transferring energy. Based on its antioxidant and optical properties, PCB has been applied in food, medicine, and cosmetics. Currently, PCB is mainly extracted from through complicated steps; thus, the biosynthesis of PCB in has attracted more attention. Read More

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Construction of an l-Tyrosine Chassis in Enhances Aromatic Secondary Metabolite Production from Glycerol.

ACS Synth Biol 2022 May 16. Epub 2022 May 16.

Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan.

Bioactive plant-based secondary metabolites such as stilbenoids, flavonoids, and benzylisoquinoline alkaloids (BIAs) are produced from l-tyrosine (l-Tyr) and have a wide variety of commercial applications. Therefore, building a microorganism with high l-Tyr productivity (l-Tyr chassis) is of immense value for large-scale production of various aromatic compounds. The aim of this study was to develop an l-Tyr chassis in the nonconventional yeast () to produce various aromatic secondary metabolites (resveratrol, naringenin, norcoclaurine, and reticuline). Read More

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Whole-Cell Biosensor and Producer Co-cultivation-Based Microfludic Platform for Screening with Hyper Erythromycin Production.

ACS Synth Biol 2022 May 13. Epub 2022 May 13.

Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China.

Actinomycetes are versatile secondary metabolite producers with great application potential in industries. However, industrial strain engineering has long been limited by the inefficient and labor-consuming plate/flask-based screening process, resulting in an urgent need for product-driven high-throughput screening methods for actinomycetes. Here, we combine a whole-cell biosensor and microfluidic platform to establish the hole-cl biosensor and producer -cultivation-based icrofluidic platform for screning actinomycetes (WELCOME). Read More

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DNA Memristors and Their Application to Reservoir Computing.

ACS Synth Biol 2022 May 13. Epub 2022 May 13.

Department of Electrical and Computer Engineering, University of Minnesota, Minneapolis, Minnesota55455, United States.

This paper introduces memristors realized by molecular and DNA reactions. Molecular memristors process one input molecule, generate two output molecules, and are realized using two molecular reactions with two different rate constants. The DNA memristors are realized using five DNA strand displacement (DSD) reactions with two effective rate constants. Read More

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Hyperaccurate Ribosomes for Improved Genetic Code Reprogramming.

ACS Synth Biol 2022 May 12. Epub 2022 May 12.

Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23220, United States.

The reprogramming of the genetic code through the introduction of noncanonical amino acids (ncAAs) has enabled exciting advances in synthetic biology and peptide drug discovery. Ribosomes that function with high efficiency and fidelity are necessary for all of these efforts, but for challenging ncAAs, the competing processes of near-cognate readthrough and peptidyl-tRNA dropoff can be issues. Here we uncover the surprising extent of these competing pathways in the PURE translation system using mRNAs encoding peptides with affinity tags at the N- and C-termini. Read More

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Generation of Allogeneic CAR T Cells through Specific Degradation of the T Cell Antigen Receptor by E3 Ubiquitin Ligase Fusion Proteins.

ACS Synth Biol 2022 May 13. Epub 2022 May 13.

Boan Boston LLC, 19 Presidential Way, Suite 304, Woburn, Massachusetts 01801, United States.

Receptor downregulation is instrumental for many therapeutic interventions. Receptor knockout through gene-editing technologies is efficient but can introduce off-target mutations and chromothripsis. Regulation of gene expression at the protein level is a promising alternative. Read More

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Pathway Engineering, Re-targeting, and Synthetic Scaffolding Improve the Production of Squalene in Plants.

ACS Synth Biol 2022 May 13. Epub 2022 May 13.

Cell and Molecular Biology Program, Michigan State University, East Lansing, Michigan 48824, United States.

Plants are increasingly becoming an option for sustainable bioproduction of chemicals and complex molecules like terpenoids. The triterpene squalene has a variety of biotechnological uses and is the precursor to a diverse array of triterpenoids, but we currently lack a sustainable strategy to produce large quantities for industrial applications. Here, we further establish engineered plants as a platform for production of squalene through pathway re-targeting and membrane scaffolding. Read More

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High-Throughput Regulatory Part Prototyping and Analysis by Cell-Free Protein Synthesis and Droplet Microfluidics.

ACS Synth Biol 2022 May 12. Epub 2022 May 12.

Broad Institute of MIT and Harvard, Cambridge, 415 Main Street, Cambridge, Massachusetts 02142, United States.

Engineering regulatory parts for improved performance in genetic programs has played a pivotal role in the development of the synthetic biology cell programming toolbox. Here, we report the development of a novel high-throughput platform for regulatory part prototyping and analysis that leverages the advantages of engineered DNA libraries, cell-free protein synthesis (CFPS), high-throughput emulsion droplet microfluidics, standard flow sorting adapted to screen droplet reactions, and next-generation sequencing (NGS). With this integrated platform, we screened the activity of millions of genetic parts within hours, followed by NGS retrieval of the improved designs. Read More

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Automated Leak Analysis of Nucleic Acid Circuits.

ACS Synth Biol 2022 May 11;11(5):1931-1948. Epub 2022 May 11.

Microsoft Research, Cambridge, CB1 2FB, U.K.

Nucleic acids are a powerful engineering material that can be used to implement a broad range of computational circuits at the nanoscale, with potential applications in high-precision biosensing, diagnostics, and therapeutics. However, nucleic acid circuits are prone to leaks, which result from unintended displacement interactions between nucleic acid strands. Such leaks can grow combinatorially with circuit size, are challenging to mitigate, and can significantly compromise circuit behavior. Read More

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Design, Analysis, and Implementation of a Novel Biochemical Pathway for Ethylene Glycol Production in .

ACS Synth Biol 2022 May 11;11(5):1790-1800. Epub 2022 May 11.

Department of Chemical Engineering, Loughborough University, Loughborough LE11 3TU, U.K.

The platform chemical ethylene glycol (EG) is used to manufacture various commodity chemicals of industrial importance, but largely remains synthesized from fossil fuels. Although several novel metabolic pathways have been reported for its bioproduction in model organisms, none has been reported for gas-fermenting, non-model acetogenic chassis organisms. Here, we describe a novel, synthetic biochemical pathway to convert acetate into EG in the industrially important gas-fermenting acetogen,. Read More

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Engineering the Entrance of a Flavonoid Glycosyltransferase Promotes the Glycosylation of Etoposide Aglycone.

ACS Synth Biol 2022 May 6;11(5):1874-1880. Epub 2022 May 6.

Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratory of Industrial Microbiology, Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei University of Technology, Wuhan 430068, China.

Enzyme entrances, which function as the first molecular filters, influence substrate selectivity and enzymatic activity. Because of low binding affinities, engineering enzyme entrances that recognize non-natural substrates is a major challenge for artificial biocatalyst design. Here, the entrance of flavonoid glycosyltransferase UGT78D2 was engineered to promote the recognition of the aglycone of etoposide, a chemotherapeutic agent. Read More

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Genome Engineering of the Fast-Growing toward a Live Vaccine Chassis.

ACS Synth Biol 2022 May 5;11(5):1919-1930. Epub 2022 May 5.

University of Bordeaux, INRAE, UMR BFP, F-33882 Villenave d'Ornon, France.

Development of a new generation of vaccines is a key challenge for the control of infectious diseases affecting both humans and animals. Synthetic biology methods offer new ways to engineer bacterial chassis that can be used as vectors to present heterologous antigens and train the immune system against pathogens. Here, we describe the construction of a bacterial chassis based on the fast-growing , and the first steps toward its application as a live vaccine against contagious caprine pleuropneumonia (CCPP). Read More

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"Multiagent" Screening Improves Directed Enzyme Evolution by Identifying Epistatic Mutations.

ACS Synth Biol 2022 May 4;11(5):1971-1983. Epub 2022 May 4.

Department of Biomedical Engineering, Duke University, Durham, North Carolina 27701, United States.

Enzyme evolution has enabled numerous advances in biotechnology and synthetic biology, yet still requires many iterative rounds of screening to identify optimal mutant sequences. This is due to the sparsity of the fitness landscape, which is caused by epistatic mutations that only offer improvements when combined with other mutations. We report an approach that incorporates diverse substrate analogues in the screening process, where multiple substrates act like multiple agents navigating the fitness landscape, identifying epistatic mutant residues without a need for testing the entire combinatorial search space. Read More

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Systems Metabolic Engineering of Coculture for Production of Genistein.

ACS Synth Biol 2022 May 4;11(5):1746-1757. Epub 2022 May 4.

Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, China.

Genistein is a plant-derived isoflavone possessing various bioactivities to prevent aging, carcinogenesis, and neurodegenerative and inflammation diseases. As a typical complex flavonoid, its microbial production from sugar remains to be completed. Here, we use systems metabolic engineering stategies to design and develop a three-strain commensalistic coculture that for the first time realized the production of genistein. Read More

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LOICA: Integrating Models with Data for Genetic Network Design Automation.

ACS Synth Biol 2022 May 4;11(5):1984-1990. Epub 2022 May 4.

Interdisciplinary Computing and Complex BioSystems (ICOS) Research Group, School of Computing, Newcastle University, Newcastle upon Tyne NE1 7RU, U.K.

Genetic design automation tools are necessary to expand the scale and complexity of possible synthetic genetic networks. These tools are enabled by abstraction of a hierarchy of standardized components and devices. Abstracted elements must be parametrized from data derived from relevant experiments, and these experiments must be related to the part composition of the abstract components. Read More

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Tuning Geraniol Biosynthesis via a Novel Decane-Responsive Promoter in .

ACS Synth Biol 2022 May 4;11(5):1835-1844. Epub 2022 May 4.

The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China.

Geraniol is a rose-scented monoterpene with significant commercial and industrial value in medicine, condiments, cosmetics, and bioenergy. Here, we first targeted geraniol as a reporter metabolite and explored the suitability and potential of as a heterologous host for monoterpenoid production. Subsequently, dual-pathway engineering was employed to improve the production of geraniol with a geraniol titer of 858. Read More

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Mutational Studies of the Mersacidin Leader Reveal the Function of Its Unique Two-Step Leader Processing Mechanism.

ACS Synth Biol 2022 May 3;11(5):1949-1957. Epub 2022 May 3.

Department of Molecular Genetics, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.

The class II lanthipeptide mersacidin, a ribosomally synthesized and post-translationally modified peptide (RiPP), displays unique intramolecular structures, including a very small lanthionine ring. When applied in the growing field of RiPP engineering, these can add unique features to new-to-nature compounds with novel properties. Recently, a heterologous expression system for mersacidin in was developed to add its modification enzymes to the RiPP engineering toolbox and further explore mersacidin biosynthesis and leader-processing. Read More

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AbSE Workflow: Rapid Identification of the Coding Sequence and Linear Epitope of the Monoclonal Antibody at the Single-cell Level.

ACS Synth Biol 2022 May 3;11(5):1856-1864. Epub 2022 May 3.

Key Lab for Zoonoses Research, Ministry of Education, Animal Genome Editing Technology Innovation Center, Jilin Province, College of Animal Sciences, Jilin University, Changchun 130062, China.

Monoclonal antibody (mAb) has been widely used in immunity research and disease diagnosis and therapy. Antibody sequence and epitope are the prerequisites and basis of mAb applications, which determine the properties of antibodies and make the preparation of antibody-based molecules controllable and reliable. Here, we present the antibody sequence and epitope identification (AbSE) workflow, a time-saving and cost-effective route for rapid determination of antibody sequence and linear epitope of mAb even at the single-cell level. Read More

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DeepTESR: A Deep Learning Framework to Predict the Degree of Translational Elongation Short Ramp for Gene Expression Control.

ACS Synth Biol 2022 May 3;11(5):1719-1726. Epub 2022 May 3.

Controlling translational elongation is essential for efficient protein synthesis. Ribosome profiling has revealed that the speed of ribosome movement is correlated with translational efficiency in the translational elongation ramp. In this work, we present a new deep learning model, called DeepTESR, to predict the degree of translational elongation short ramp (TESR) from mRNA sequence. Read More

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Catalytically Active Inclusion Bodies─Benchmarking and Application in Flow Chemistry.

ACS Synth Biol 2022 May 2;11(5):1881-1896. Epub 2022 May 2.

Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, Wilhelm Johnen Strasse, D-52425 Jülich, Germany.

In industries, enzymes are often immobilized to obtain stable preparations that can be utilized in batch and flow processes. In contrast to traditional immobilization methods that rely on carrier binding, various immobilization strategies have been recently presented that enable the simultaneous production and in vivo immobilization of enzymes. Catalytically active inclusion bodies (CatIBs) are a promising example for such in vivo enzyme immobilizates. Read More

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CRISPR-Cas Assisted Shotgun Mutagenesis Method for Evolutionary Genome Engineering.

ACS Synth Biol 2022 May 2;11(5):1958-1970. Epub 2022 May 2.

State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.

Genome mutagenesis drives the evolution of organisms. Here, we developed a RISPR-Cas ssisted andom utation (CARM) technique for whole-genome mutagenesis. The method leverages an entirely random gRNA library and SpCas9-NG to randomly damage genomes in a controllable shotgunlike manner that then triggers diverse and abundant mutations via low-fidelity repair. Read More

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Detection of Major SARS-CoV-2 Variants of Concern in Clinical Samples via CRISPR-Cas12a-Mediated Mutation-Specific Assay.

ACS Synth Biol 2022 May 28;11(5):1811-1823. Epub 2022 Apr 28.

Department of Epidemiology, School of Public Health, Southern Medical University, Guangzhou 510515, China.

: Emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants pose a great threat and burden to global public health. Here, we evaluated a clustered regularly interspaced short palindromic repeat-associated enzyme 12a (CRISPR-Cas12a)-based method for detecting major SARS-CoV-2 variants of concern (VOCs) in SARS-CoV-2 positive clinical samples. : Allele-specific CRISPR RNAs (crRNAs) targeting the signature mutations in the spike protein of SARS-CoV-2 are designed. Read More

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Rerouting Fluxes of the Central Carbon Metabolism and Relieving Mechanism-Based Inactivation of l-Aspartate-α-decarboxylase for Fermentative Production of β-Alanine in .

ACS Synth Biol 2022 May 27;11(5):1908-1918. Epub 2022 Apr 27.

Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou 310014, P. R. China.

β-Alanine, with the amino group at the β-position, is an important platform chemical that has been widely applied in pharmaceuticals and feed and food additives. However, the current modest titer and productivity, increased fermentation cost, and complicated operation are the challenges for producing β-alanine by microbial fermentation. In this study, a high-yield β-alanine-producing strain was constructed by combining metabolic engineering, protein engineering, and fed-batch bioprocess optimization strategies. Read More

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RPA/CRISPR/Cas12a-Based On-Site and Rapid Nucleic Acid Detection of in the Environment.

ACS Synth Biol 2022 May 26;11(5):1772-1781. Epub 2022 Apr 26.

School of Life Science and Biotechnology, Dalian University, Dalian, Liaoning116622, China.

is an opportunistic pathogen widely distributed within the world, poses a huge threat to human health, and causes significant economic losses to the livestock industry. Herein, we developed a portable one-pot detection of by combining recombinase polymerase amplification (RPA) and a clustered regularly interspaced short palindromic repeats (CRISPR)/Cas12a system. A glass microfiber filter device used for the first step can efficiently extract from low-concentration samples. Read More

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