1
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Meyer C, Arizzi A, Henson T, Aviran S, Longo ML, Wang A, Tan C. Designer artificial environments for membrane protein synthesis. Nat Commun 2025; 16:4363. [PMID: 40348791 PMCID: PMC12065789 DOI: 10.1038/s41467-025-59471-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 04/22/2025] [Indexed: 05/14/2025] Open
Abstract
Protein synthesis in natural cells involves intricate interactions between chemical environments, protein-protein interactions, and protein machinery. Replicating such interactions in artificial and cell-free environments can control the precision of protein synthesis, elucidate complex cellular mechanisms, create synthetic cells, and discover new therapeutics. Yet, creating artificial synthesis environments, particularly for membrane proteins, is challenging due to the poorly defined chemical-protein-lipid interactions. Here, we introduce MEMPLEX (Membrane Protein Learning and Expression), which utilizes machine learning and a fluorescent reporter to rapidly design artificial synthesis environments of membrane proteins. MEMPLEX generates over 20,000 different artificial chemical-protein environments spanning 28 membrane proteins. It captures the interdependent impact of lipid types, chemical environments, chaperone proteins, and protein structures on membrane protein synthesis. As a result, MEMPLEX creates new artificial environments that successfully synthesize membrane proteins of broad interest but previously intractable. In addition, we identify a quantitative metric, based on the hydrophobicity of the membrane-contacting amino acids, that predicts membrane protein synthesis in artificial environments. Our work allows others to rapidly study and resolve the "dark" proteome using predictive generation of artificial chemical-protein environments. Furthermore, the results represent a new frontier in artificial intelligence-guided approaches to creating synthetic environments for protein synthesis.
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Affiliation(s)
- Conary Meyer
- Department of Biomedical Engineering, University of California, Davis, Davis, CA, 95616, USA
| | - Alessandra Arizzi
- Department of Biomedical Engineering, University of California, Davis, Davis, CA, 95616, USA
| | - Tanner Henson
- Department of Biomedical Engineering, University of California, Davis, Davis, CA, 95616, USA
- Center for Surgical Bioengineering, Department of Surgery, University of California Davis School of Medicine, Davis, USA
- Institute for Pediatric Regenerative Medicine (IPRM), Shriners Children's Northern, California, USA
| | - Sharon Aviran
- Department of Biomedical Engineering, University of California, Davis, Davis, CA, 95616, USA
- Genome Center, University of California, Davis, Davis, CA, 95616, USA
| | - Marjorie L Longo
- Department of Chemical Engineering, University of California, Davis, Davis, CA, 95616, USA
| | - Aijun Wang
- Department of Biomedical Engineering, University of California, Davis, Davis, CA, 95616, USA
- Center for Surgical Bioengineering, Department of Surgery, University of California Davis School of Medicine, Davis, USA
- Institute for Pediatric Regenerative Medicine (IPRM), Shriners Children's Northern, California, USA
| | - Cheemeng Tan
- Department of Biomedical Engineering, University of California, Davis, Davis, CA, 95616, USA.
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2
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Chen Y, Xia W, Lu F, Chen Z, Liu Y, Cao M, He N. Cell-free synthesis system: An accessible platform from biosensing to biomanufacturing. Microbiol Res 2025; 293:128079. [PMID: 39908944 DOI: 10.1016/j.micres.2025.128079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2024] [Revised: 01/06/2025] [Accepted: 01/22/2025] [Indexed: 02/07/2025]
Abstract
The fundamental aspect of cell-free synthesis systems is the in vitro transcription-translation process. By artificially providing the components required for protein expression, in vitro protein production alleviates various limitations tied to in vivo production, such as oxygen supply and nutrient constraints, thus showcasing substantial potential in engineering applications. This article presents a comprehensive review of cell-free synthesis systems, with a primary focus on biosensing and biomanufacturing. In terms of biosensing, it summarizes the recognition-response mechanisms and key advantages of cell-free biosensors. Moreover, it examines the strategies for the cell-free production of intricate proteins, including membrane proteins and glycoproteins. Additionally, the integration of cell-free metabolic engineering approaches with cell-free synthesis systems in biomanufacturing is thoroughly discussed, with the expectation that biotechnology will embrace greater prosperity.
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Affiliation(s)
- Yongbin Chen
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; The Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen 361005, China
| | - Wenhao Xia
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; The Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen 361005, China
| | - Fuping Lu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zhen Chen
- College of Life Science, Xinyang Normal University, Xinyang 464000, China
| | - Yihan Liu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, The College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China.
| | - Mingfeng Cao
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; The Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen 361005, China.
| | - Ning He
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China; The Key Laboratory for Synthetic Biotechnology of Xiamen City, Xiamen 361005, China.
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3
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Mansour A, Kipper K, Pulk A. Optimizing Human Cell-Free System for Efficient Protein Production. J Microbiol Biotechnol 2025; 35:e2410026. [PMID: 40016147 PMCID: PMC11896798 DOI: 10.4014/jmb.2410.10026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2024] [Revised: 12/13/2024] [Accepted: 01/06/2025] [Indexed: 03/01/2025]
Abstract
We present a highly efficient human HEK293-based cell-free protein synthesis (CFPS) system capable of producing up to 300 μg/ml reporter protein. One of the limitations of the CFPS systems with respect to protein yield has been the decline of the protein-synthesizing activity of the system upon prolonged incubation. Though factors contributing to this decline in activity have been investigated in yeast, little is known about the factors in mammalian systems. We find that a rapid depletion of the components of the energy-regeneration system is a major factor behind the decreasing protein-synthesis activity in the HEK293-derived system. In addition, we demonstrate that a functional CFPS system can be prepared from other mammalian cell lines as evidenced by our use of a human neuroblastoma SH-SY5Y-derived CFPS system. We also find that exogenous creatine kinase (CK) is dispensable for the functionality of the energy-regeneration system in HEK293 due to the presence of a sufficiently high endogenous CK activity in an HEK293 cell-free extract.
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Affiliation(s)
- Abbas Mansour
- Structural Biology Unit, Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - Kalle Kipper
- Structural Biology Unit, Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - Arto Pulk
- Structural Biology Unit, Institute of Technology, University of Tartu, Tartu 50411, Estonia
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4
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Hunt A, Rasor BJ, Seki K, Ekas HM, Warfel KF, Karim AS, Jewett MC. Cell-Free Gene Expression: Methods and Applications. Chem Rev 2025; 125:91-149. [PMID: 39700225 PMCID: PMC11719329 DOI: 10.1021/acs.chemrev.4c00116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 07/29/2024] [Accepted: 10/21/2024] [Indexed: 12/21/2024]
Abstract
Cell-free gene expression (CFE) systems empower synthetic biologists to build biological molecules and processes outside of living intact cells. The foundational principle is that precise, complex biomolecular transformations can be conducted in purified enzyme or crude cell lysate systems. This concept circumvents mechanisms that have evolved to facilitate species survival, bypasses limitations on molecular transport across the cell wall, and provides a significant departure from traditional, cell-based processes that rely on microscopic cellular "reactors." In addition, cell-free systems are inherently distributable through freeze-drying, which allows simple distribution before rehydration at the point-of-use. Furthermore, as cell-free systems are nonliving, they provide built-in safeguards for biocontainment without the constraints attendant on genetically modified organisms. These features have led to a significant increase in the development and use of CFE systems over the past two decades. Here, we discuss recent advances in CFE systems and highlight how they are transforming efforts to build cells, control genetic networks, and manufacture biobased products.
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Affiliation(s)
- Andrew
C. Hunt
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Blake J. Rasor
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Kosuke Seki
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Holly M. Ekas
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Katherine F. Warfel
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Ashty S. Karim
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael C. Jewett
- Department
of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry
of Life Processes Institute, Northwestern
University, Evanston, Illinois 60208, United States
- Robert
H. Lurie Comprehensive Cancer Center, Northwestern
University, Chicago, Illinois 60611, United States
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
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5
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Chowdhury S, Westenberg R, Wennerholm K, Cardiff RAL, Beliaev AS, Noireaux V, Carothers JM, Peralta-Yahya P. Carbon Negative Synthesis of Amino Acids Using a Cell-Free-Based Biocatalyst. ACS Synth Biol 2024; 13:3961-3975. [PMID: 39570279 DOI: 10.1021/acssynbio.4c00359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2024]
Abstract
Biological systems can directly upgrade carbon dioxide (CO2) into chemicals. The CO2 fixation rate of autotrophic organisms, however, is too slow for industrial utility, and the breadth of engineered metabolic pathways for the synthesis of value-added chemicals is too limited. Biotechnology workhorse organisms with extensively engineered metabolic pathways have recently been engineered for CO2 fixation. Yet, their low carbon fixation rate, compounded by the fact that living organisms split their carbon between cell growth and chemical synthesis, has led to only cell growth with no chemical synthesis achieved to date. Here, we engineer a lysate-based cell-free expression (CFE)-based multienzyme biocatalyst for the carbon negative synthesis of the industrially relevant amino acids glycine and serine from CO2 equivalents─formate and bicarbonate─and ammonia. The formate-to-serine biocatalyst leverages tetrahydrofolate (THF)-dependent formate fixation, reductive glycine synthesis, serine synthesis, and phosphite dehydrogenase-dependent NAD(P)H regeneration to convert 30% of formate into serine and glycine, surpassing the previous 22% conversion using a purified enzyme system. We find that (1) the CFE-based biocatalyst is active even after 200-fold dilution, enabling higher substrate loading and product synthesis without incurring additional cell lysate cost, (2) NAD(P)H regeneration is pivotal to driving forward reactions close to thermodynamic equilibrium, (3) balancing the ratio of the formate-to-serine pathway genes added to the CFE is key to improving amino acid synthesis, and (4) efficient THF recycling enables lowering the loading of this cofactor, reducing the cost of the CFE-based biocatalyst. To our knowledge, this is the first synthesis of amino acids that can capture CO2 equivalents for the carbon negative synthesis of amino acids using a CFE-based biocatalyst. Looking ahead, the CFE-based biocatalyst process could be extended beyond serine to pyruvate, a key intermediate, to access a variety of chemicals from aromatics and terpenes to alcohols and polymers.
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Affiliation(s)
- Shaafique Chowdhury
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ray Westenberg
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Bioengineering Program, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Kimberly Wennerholm
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ryan A L Cardiff
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington 98195, United States
| | - Alexander S Beliaev
- Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
- Centre for Agriculture and the Bioeconomy, School of Biological and Environmental Sciences, Queensland University of Technology, Gardens Point Campus, P.O. Box 2434, Brisbane 4001, Queensland, Australia
| | - Vincent Noireaux
- School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - James M Carothers
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington 98195, United States
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Pamela Peralta-Yahya
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- Bioengineering Program, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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6
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Burbano DA, Kiattisewee C, Karanjia AV, Cardiff RAL, Faulkner ID, Sugianto W, Carothers JM. CRISPR Tools for Engineering Prokaryotic Systems: Recent Advances and New Applications. Annu Rev Chem Biomol Eng 2024; 15:389-430. [PMID: 38598861 DOI: 10.1146/annurev-chembioeng-100522-114706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
In the past decades, the broad selection of CRISPR-Cas systems has revolutionized biotechnology by enabling multimodal genetic manipulation in diverse organisms. Rooted in a molecular engineering perspective, we recapitulate the different CRISPR components and how they can be designed for specific genetic engineering applications. We first introduce the repertoire of Cas proteins and tethered effectors used to program new biological functions through gene editing and gene regulation. We review current guide RNA (gRNA) design strategies and computational tools and how CRISPR-based genetic circuits can be constructed through regulated gRNA expression. Then, we present recent advances in CRISPR-based biosensing, bioproduction, and biotherapeutics across in vitro and in vivo prokaryotic systems. Finally, we discuss forthcoming applications in prokaryotic CRISPR technology that will transform synthetic biology principles in the near future.
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Affiliation(s)
- Diego Alba Burbano
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Cholpisit Kiattisewee
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ava V Karanjia
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ryan A L Cardiff
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Ian D Faulkner
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - Widianti Sugianto
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
| | - James M Carothers
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA
- Molecular Engineering & Sciences Institute and Center for Synthetic Biology, University of Washington, Seattle, Washington, USA;
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7
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Downey ML, Peralta-Yahya P. Technologies for the discovery of G protein-coupled receptor-targeting biologics. Curr Opin Biotechnol 2024; 87:103138. [PMID: 38728825 PMCID: PMC11250939 DOI: 10.1016/j.copbio.2024.103138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 04/13/2024] [Indexed: 05/12/2024]
Abstract
G protein-coupled receptors (GPCRs) are important pharmaceutical targets, working as entry points for signaling pathways involved in metabolic, neurological, and cardiovascular diseases. Although small molecules remain the major GPCR drug type, biologic therapeutics, such as peptides and antibodies, are increasingly found among clinical trials and Food and Drug Administration (FDA)-approved drugs. Here, we review state-of-the-art technologies for the engineering of biologics that target GPCRs, as well as proof-of-principle technologies that are ripe for this application. Looking ahead, inexpensive DNA synthesis will enable the routine generation of computationally predesigned libraries for use in display assays for the rapid discovery of GPCR binders. Advances in synthetic biology are enabling the increased throughput of functional GPCR assays to the point that they can be used to directly identify biologics that modulate GPCR activity. Finally, we give an overview of adjacent technologies that are ripe for application to discover biologics that target human GPCRs.
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Affiliation(s)
- McKenna L Downey
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Pamela Peralta-Yahya
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA.
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8
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Steinkühler J, Peruzzi JA, Krüger A, Villaseñor CG, Jacobs ML, Jewett MC, Kamat NP. Improving Cell-Free Expression of Model Membrane Proteins by Tuning Ribosome Cotranslational Membrane Association and Nascent Chain Aggregation. ACS Synth Biol 2024; 13:129-140. [PMID: 38150067 DOI: 10.1021/acssynbio.3c00357] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
Cell-free gene expression (CFE) systems are powerful tools for transcribing and translating genes outside of a living cell. Synthesis of membrane proteins is of particular interest, but their yield in CFE is substantially lower than that for soluble proteins. In this paper, we study the CFE of membrane proteins and develop a quantitative kinetic model. We identify that ribosome stalling during the translation of membrane proteins is a strong predictor of membrane protein synthesis due to aggregation between the ribosome nascent chains. Synthesis can be improved by the addition of lipid membranes, which incorporate protein nascent chains and, therefore, kinetically compete with aggregation. We show that the balance between peptide-membrane association and peptide aggregation rates determines the yield of the synthesized membrane protein. We define a membrane protein expression score that can be used to rationalize the engineering of lipid composition and the N-terminal domain of a native and computationally designed membrane proteins produced through CFE.
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Affiliation(s)
- Jan Steinkühler
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Bio-Inspired Computation, Kiel University, Kaiserstraße 2, 24143 Kiel, Germany
- Kiel Nano, Surface and Interface Science KiNSIS, Kiel University, Christian-Albrechts-Platz 4, 24118 Kiel, Germany
| | - Justin A Peruzzi
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Antje Krüger
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Citlayi G Villaseñor
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Miranda L Jacobs
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Department of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Neha P Kamat
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
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9
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Alba Burbano D, Cardiff RAL, Tickman BI, Kiattisewee C, Maranas CJ, Zalatan JG, Carothers JM. Engineering activatable promoters for scalable and multi-input CRISPRa/i circuits. Proc Natl Acad Sci U S A 2023; 120:e2220358120. [PMID: 37463216 PMCID: PMC10374173 DOI: 10.1073/pnas.2220358120] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 06/13/2023] [Indexed: 07/20/2023] Open
Abstract
Dynamic, multi-input gene regulatory networks (GRNs) are ubiquitous in nature. Multilayer CRISPR-based genetic circuits hold great promise for building GRNs akin to those found in naturally occurring biological systems. We develop an approach for creating high-performing activatable promoters that can be assembled into deep, wide, and multi-input CRISPR-activation and -interference (CRISPRa/i) GRNs. By integrating sequence-based design and in vivo screening, we engineer activatable promoters that achieve up to 1,000-fold dynamic range in an Escherichia coli-based cell-free system. These components enable CRISPRa GRNs that are six layers deep and four branches wide. We show the generalizability of the promoter engineering workflow by improving the dynamic range of the light-dependent EL222 optogenetic system from 6-fold to 34-fold. Additionally, high dynamic range promoters enable CRISPRa systems mediated by small molecules and protein-protein interactions. We apply these tools to build input-responsive CRISPRa/i GRNs, including feedback loops, logic gates, multilayer cascades, and dynamic pulse modulators. Our work provides a generalizable approach for the design of high dynamic range activatable promoters and enables classes of gene regulatory functions in cell-free systems.
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Affiliation(s)
- Diego Alba Burbano
- Department of Chemical Engineering, University of Washington, Seattle, WA98195
- Center for Synthetic Biology, University of Washington, Seattle, WA98195
| | - Ryan A. L. Cardiff
- Center for Synthetic Biology, University of Washington, Seattle, WA98195
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA98195
| | - Benjamin I. Tickman
- Center for Synthetic Biology, University of Washington, Seattle, WA98195
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA98195
| | - Cholpisit Kiattisewee
- Center for Synthetic Biology, University of Washington, Seattle, WA98195
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA98195
| | - Cassandra J. Maranas
- Center for Synthetic Biology, University of Washington, Seattle, WA98195
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA98195
| | - Jesse G. Zalatan
- Center for Synthetic Biology, University of Washington, Seattle, WA98195
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA98195
- Department of Chemistry, University of Washington, Seattle, WA98195
| | - James M. Carothers
- Department of Chemical Engineering, University of Washington, Seattle, WA98195
- Center for Synthetic Biology, University of Washington, Seattle, WA98195
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA98195
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10
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Stano P, Gentili PL, Damiano L, Magarini M. A Role for Bottom-Up Synthetic Cells in the Internet of Bio-Nano Things? Molecules 2023; 28:5564. [PMID: 37513436 PMCID: PMC10385758 DOI: 10.3390/molecules28145564] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/29/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
The potential role of bottom-up Synthetic Cells (SCs) in the Internet of Bio-Nano Things (IoBNT) is discussed. In particular, this perspective paper focuses on the growing interest in networks of biological and/or artificial objects at the micro- and nanoscale (cells and subcellular parts, microelectrodes, microvessels, etc.), whereby communication takes place in an unconventional manner, i.e., via chemical signaling. The resulting "molecular communication" (MC) scenario paves the way to the development of innovative technologies that have the potential to impact biotechnology, nanomedicine, and related fields. The scenario that relies on the interconnection of natural and artificial entities is briefly introduced, highlighting how Synthetic Biology (SB) plays a central role. SB allows the construction of various types of SCs that can be designed, tailored, and programmed according to specific predefined requirements. In particular, "bottom-up" SCs are briefly described by commenting on the principles of their design and fabrication and their features (in particular, the capacity to exchange chemicals with other SCs or with natural biological cells). Although bottom-up SCs still have low complexity and thus basic functionalities, here, we introduce their potential role in the IoBNT. This perspective paper aims to stimulate interest in and discussion on the presented topics. The article also includes commentaries on MC, semantic information, minimal cognition, wetware neuromorphic engineering, and chemical social robotics, with the specific potential they can bring to the IoBNT.
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Affiliation(s)
- Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, 73100 Lecce, Italy
| | - Pier Luigi Gentili
- Dipartimento di Chimica, Biologia e Biotecnologie, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Luisa Damiano
- Department of Communication, Arts and Media, IULM University, 20143 Milan, Italy
| | - Maurizio Magarini
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, 20133 Milan, Italy
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11
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Manzer ZA, Selivanovitch E, Ostwalt AR, Daniel S. Membrane protein synthesis: no cells required. Trends Biochem Sci 2023; 48:642-654. [PMID: 37087310 DOI: 10.1016/j.tibs.2023.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/20/2023] [Accepted: 03/22/2023] [Indexed: 04/24/2023]
Abstract
Despite advances in membrane protein (MP) structural biology and a growing interest in their applications, these proteins remain challenging to study. Progress has been hindered by the complex nature of MPs and innovative methods will be required to circumvent technical hurdles. Cell-free protein synthesis (CFPS) is a burgeoning technique for synthesizing MPs directly into a membrane environment using reconstituted components of the cellular transcription and translation machinery in vitro. We provide an overview of CFPS and how this technique can be applied to the synthesis and study of MPs. We highlight numerous strategies including synthesis methods and folding environments, each with advantages and limitations, to provide a survey of how CFPS techniques can advance the study of MPs.
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Affiliation(s)
- Zachary A Manzer
- R.F. School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Ekaterina Selivanovitch
- R.F. School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Alexis R Ostwalt
- R.F. School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Susan Daniel
- R.F. School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA.
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12
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Peruzzi JA, Galvez NR, Kamat NP. Engineering transmembrane signal transduction in synthetic membranes using two-component systems. Proc Natl Acad Sci U S A 2023; 120:e2218610120. [PMID: 37126679 PMCID: PMC10175788 DOI: 10.1073/pnas.2218610120] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/27/2023] [Indexed: 05/03/2023] Open
Abstract
Cells use signal transduction across their membranes to sense and respond to a wide array of chemical and physical signals. Creating synthetic systems which can harness cellular signaling modalities promises to provide a powerful platform for biosensing and therapeutic applications. As a first step toward this goal, we investigated how bacterial two-component systems (TCSs) can be leveraged to enable transmembrane-signaling with synthetic membranes. Specifically, we demonstrate that a bacterial two-component nitrate-sensing system (NarX-NarL) can be reproduced outside of a cell using synthetic membranes and cell-free protein expression systems. We find that performance and sensitivity of the TCS can be tuned by altering the biophysical properties of the membrane in which the histidine kinase (NarX) is integrated. Through protein engineering efforts, we modify the sensing domain of NarX to generate sensors capable of detecting an array of ligands. Finally, we demonstrate that these systems can sense ligands in relevant sample environments. By leveraging membrane and protein design, this work helps reveal how transmembrane sensing can be recapitulated outside of the cell, adding to the arsenal of deployable cell-free systems primed for real world biosensing.
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Affiliation(s)
- Justin A. Peruzzi
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL60208
- Center for Synthetic Biology, Northwestern University, Evanston, IL60208
| | - Nina R. Galvez
- Center for Synthetic Biology, Northwestern University, Evanston, IL60208
- Department of Biomedical Engineering, Northwestern University, Evanston, IL60208
| | - Neha P. Kamat
- Center for Synthetic Biology, Northwestern University, Evanston, IL60208
- Department of Biomedical Engineering, Northwestern University, Evanston, IL60208
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL60208
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13
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Kelwick RJR, Webb AJ, Heliot A, Segura CT, Freemont PS. Opportunities to accelerate extracellular vesicle research with cell-free synthetic biology. JOURNAL OF EXTRACELLULAR BIOLOGY 2023; 2:e90. [PMID: 38938277 PMCID: PMC11080881 DOI: 10.1002/jex2.90] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 04/03/2023] [Accepted: 05/05/2023] [Indexed: 06/29/2024]
Abstract
Extracellular vesicles (EVs) are lipid-membrane nanoparticles that are shed or secreted by many different cell types. The EV research community has rapidly expanded in recent years and is leading efforts to deepen our understanding of EV biological functions in human physiology and pathology. These insights are also providing a foundation on which future EV-based diagnostics and therapeutics are poised to positively impact human health. However, current limitations in our understanding of EV heterogeneity, cargo loading mechanisms and the nascent development of EV metrology are all areas that have been identified as important scientific challenges. The field of synthetic biology is also contending with the challenge of understanding biological complexity as it seeks to combine multidisciplinary scientific knowledge with engineering principles, to build useful and robust biotechnologies in a responsible manner. Within this context, cell-free systems have emerged as a powerful suite of in vitro biotechnologies that can be employed to interrogate fundamental biological mechanisms, including the study of aspects of EV biogenesis, or to act as a platform technology for medical biosensors and therapeutic biomanufacturing. Cell-free gene expression (CFE) systems also enable in vitro protein production, including membrane proteins, and could conceivably be exploited to rationally engineer, or manufacture, EVs loaded with bespoke molecular cargoes for use in foundational or translational EV research. Our pilot data herein, also demonstrates the feasibility of cell-free EV engineering. In this perspective, we discuss the opportunities and challenges for accelerating EV research and healthcare applications with cell-free synthetic biology.
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Affiliation(s)
- Richard J. R. Kelwick
- Section of Structural and Synthetic BiologyDepartment of Infectious DiseaseImperial College LondonLondonUK
| | - Alexander J. Webb
- Section of Structural and Synthetic BiologyDepartment of Infectious DiseaseImperial College LondonLondonUK
| | - Amelie Heliot
- Section of Structural and Synthetic BiologyDepartment of Infectious DiseaseImperial College LondonLondonUK
| | | | - Paul S. Freemont
- Section of Structural and Synthetic BiologyDepartment of Infectious DiseaseImperial College LondonLondonUK
- The London BiofoundryImperial College Translation & Innovation HubLondonUK
- UK Dementia Research Institute Care Research and Technology CentreImperial College London, Hammersmith CampusLondonUK
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14
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Wang T, Lin X, Li Y, Lu Y. Artificial Lipid Biomembranes for Full-Length SARS-CoV-2 Receptor. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023:e2300575. [PMID: 36932971 DOI: 10.1002/adma.202300575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/08/2023] [Indexed: 06/18/2023]
Abstract
The angiotensin-converting enzyme 2 (ACE2), as a functional receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is essential for assessing potential hosts and treatments. However, many studies are based on its truncated version but not full-length structure. Indeed, a single transmembrane (TM) helix presents in the full-length ACE2, influencing its interaction with SARS-CoV-2. Therefore, synthesis of the full-length ACE2 is an urgent requirement. Here, cell-free membrane protein synthesis systems (CFMPSs) are constructed for full-length membrane proteins. MscL is screened as a model among ten membrane proteins based on their expression and solubility. Next, CFMPSs are constructed and optimized based on natural vesicles, vesicles with four membrane proteins removed or two chaperonins added, and 37 types of nanodiscs. They all increase membrane protein solubility to over 50%. Finally, the full-length ACE2 of 21 species are successfully expressed with yields between 0.4 and 0.9 mg mL-1 . The definite functional differences from the truncated version suggest that the TM region affects ACE2's structure and function. CFMPSs can be extended to more membrane proteins, paving the way for further applications.
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Affiliation(s)
- Ting Wang
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, China
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Xiaomei Lin
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, China
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Yuting Li
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, China
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, China
- Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
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15
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Manzer ZA, Ghosh S, Roy A, Jacobs ML, Carten J, Kamat NP, Daniel S. Cell-Free Synthesis Goes Electric: Dual Optical and Electronic Biosensor via Direct Channel Integration into a Supported Membrane Electrode. ACS Synth Biol 2023; 12:502-510. [PMID: 36651574 PMCID: PMC11364431 DOI: 10.1021/acssynbio.2c00531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Assembling transmembrane proteins on organic electronic materials is one promising approach to couple biological functions to electrical readouts. A biosensing device produced in such a way would enable both the monitoring and regulation of physiological processes and the development of new analytical tools to identify drug targets and new protein functionalities. While transmembrane proteins can be interfaced with bioelectronics through supported lipid bilayers (SLBs), incorporating functional and oriented transmembrane proteins into these structures remains challenging. Here, we demonstrate that cell-free expression systems allow for the one-step integration of an ion channel into SLBs assembled on an organic conducting polymer, poly(3,4-ethylenedioxythiophene) polystyrenesulfonate (PEDOT:PSS). Using the large conductance mechanosensitive channel (MscL) as a model ion channel, we demonstrate that MscL adopts the correct orientation, remains mobile in the SLB, and is active on the polyelectrolyte surface using optical and electrical readouts. This work serves as an important illustration of a rapidly assembled bioelectronic platform with a diverse array of downstream applications, including electrochemical sensing, physiological regulation, and screening of transmembrane protein modulators.
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Affiliation(s)
- Zachary A Manzer
- R.F. School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Surajit Ghosh
- R.F. School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Arpita Roy
- R.F. School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Miranda L Jacobs
- Department of Biomedical Engineering and Interdisciplinary Biological Sciences Program, Northwestern University, Evanston, Illinois 60208, United States
| | - Juliana Carten
- R.F. School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Neha P Kamat
- Department of Biomedical Engineering, Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Susan Daniel
- R.F. School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
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16
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Cell-free protein synthesis systems for vaccine design and production. Curr Opin Biotechnol 2023; 79:102888. [PMID: 36641905 DOI: 10.1016/j.copbio.2022.102888] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 12/14/2022] [Indexed: 01/15/2023]
Abstract
Vaccines are vital for protection against existing and emergent diseases. Current vaccine production strategies are limited by long production times, risky viral material, weak immunogenicity, and poor stability, ultimately restricting the safe or rapid production of vaccines for widespread utilization. Cell-free protein synthesis (CFPS) systems, which use extracted transcriptional and translational machinery from cells, are promising tools for vaccine production because they can rapidly produce proteins without the constraints of living cells, have a highly optimizable open system, and can be used for on-demand biomanufacturing. Here, we review how CFPS systems have been explored for the production of subunit, conjugate, virus-like particle (VLP), and membrane-augmented vaccines and as a tool in vaccine design. We also discuss efforts to address potential limitations with CFPS such as the presence of endotoxins, poor protein folding, reaction stability, and glycosylation to enable promising future vaccine design and production.
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17
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Egan M, Kuscu M, Barros MT, Booth M, Llopis-Lorente A, Magarini M, Martins DP, Schäfer M, Stano P. Toward Interdisciplinary Synergies in Molecular Communications: Perspectives from Synthetic Biology, Nanotechnology, Communications Engineering and Philosophy of Science. Life (Basel) 2023; 13:208. [PMID: 36676156 PMCID: PMC9861838 DOI: 10.3390/life13010208] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/18/2022] [Accepted: 12/30/2022] [Indexed: 01/12/2023] Open
Abstract
Within many chemical and biological systems, both synthetic and natural, communication via chemical messengers is widely viewed as a key feature. Often known as molecular communication, such communication has been a concern in the fields of synthetic biologists, nanotechnologists, communications engineers, and philosophers of science. However, interactions between these fields are currently limited. Nevertheless, the fact that the same basic phenomenon is studied by all of these fields raises the question of whether there are unexploited interdisciplinary synergies. In this paper, we summarize the perspectives of each field on molecular communications, highlight potential synergies, discuss ongoing challenges to exploit these synergies, and present future perspectives for interdisciplinary efforts in this area.
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Affiliation(s)
- Malcolm Egan
- Univ Lyon, INSA Lyon, INRIA, CITI, 69621 Villeurbanne, France
| | - Murat Kuscu
- Department of Electrical and Electronics Engineering, Koç University, Istanbul 34450, Turkey
| | - Michael Taynnan Barros
- School of Computer Science and Electronic Engineering, University of Essex, Colchester CO4 3SQ, UK
| | - Michael Booth
- Department of Chemistry, University College London (UCL), London WC1H 0AJ, UK
| | - Antoni Llopis-Lorente
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Universitat Politècnica de València, Camino de Vera, 46022 València, Spain
| | - Maurizio Magarini
- Department of Electronics, Information and Bioengineering (DEIB), Politecnico di Milano, 20133 Milan, Italy
| | - Daniel P. Martins
- Walton Institute for Information and Communication Systems Science, South East Technological University (SETU), X91 P20H Waterford, Ireland
| | - Maximilian Schäfer
- Institute for Digital Communications, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | - Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, 73100 Lecce, Italy
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18
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Boyd MA, Thavarajah W, Lucks JB, Kamat NP. Robust and tunable performance of a cell-free biosensor encapsulated in lipid vesicles. SCIENCE ADVANCES 2023; 9:eadd6605. [PMID: 36598992 PMCID: PMC9812392 DOI: 10.1126/sciadv.add6605] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 11/23/2022] [Indexed: 05/21/2023]
Abstract
Cell-free systems have enabled the development of genetically encoded biosensors to detect a range of environmental and biological targets. Encapsulation of these systems in synthetic membranes to form artificial cells can reintroduce features of the cellular membrane, including molecular containment and selective permeability, to modulate cell-free sensing capabilities. Here, we demonstrate robust and tunable performance of a transcriptionally regulated, cell-free riboswitch encapsulated in lipid membranes, allowing the detection of fluoride, an environmentally important molecule. Sensor response can be tuned by varying membrane composition, and encapsulation protects from sensor degradation, facilitating detection in real-world samples. These sensors can detect fluoride using two types of genetically encoded outputs, enabling detection of fluoride at the Environmental Protection Agency maximum contaminant level of 0.2 millimolars. This work demonstrates the capacity of bilayer membranes to confer tunable permeability to encapsulated, genetically encoded sensors and establishes the feasibility of artificial cell platforms to detect environmentally relevant small molecules.
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Affiliation(s)
- Margrethe A. Boyd
- Department of Biomedical Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Walter Thavarajah
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, USA
- Center for Water Research, Northwestern University, Evanston, IL, USA
| | - Julius B. Lucks
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, USA
- Center for Water Research, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- Corresponding author. (N.P.K.); (J.B.L.)
| | - Neha P. Kamat
- Department of Biomedical Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- Corresponding author. (N.P.K.); (J.B.L.)
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19
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Chien PJ, Shih YL, Cheng CT, Tu HL. Chip assisted formation of phase-separated liposomes for reconstituting spatial protein-lipid interactions. LAB ON A CHIP 2022; 22:2540-2548. [PMID: 35667105 DOI: 10.1039/d2lc00089j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Spatially organized molecular interactions are fundamental features underlying many biochemical processes in cells. These spatially defined reactions are essential to ensure high signaling specificity and are indispensable for maintaining cell functions. The construction of synthetic cell models that can resemble such properties is thus important yet less investigated. In this study, we present a reliable method for the rapid production of highly uniform phase-separated liposomes as synthetic cell models. Specifically, a microfluidics-based strategy coupled with custom reagents for generating size-tunable liposomes with various lipid compositions is presented. In addition, an important cell signaling interacting pair, the pleckstrin homology (PH) domain and PIP2 lipid, is used to demonstrate the controlled molecular assembly inside these liposomes. The result shows that PIP2 on phase-separated domains successfully recruits the PH domains to realize spatially defined molecular interactions. Such a system is versatile and can be expanded to synthesize other proteins for realizing multiplexed molecular interactions in the same liposome. Phase-separated lipid domains can also be used to recruit targeted proteins to initiate localized reactions, thus paving the way for organizing a complex signaling cascade in the synthetic cell.
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Affiliation(s)
- Po-Jen Chien
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan.
| | - Yi-Lun Shih
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan.
- Department of Chemical Engineering, National Taiwan University of Science and Technology, Taipei 10607, Taiwan
| | - Chieh-Teng Cheng
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan.
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taiwan
| | - Hsiung-Lin Tu
- Institute of Chemistry, Academia Sinica, Taipei 115, Taiwan.
- Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taiwan
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20
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Danchin A. In vivo, in vitro and in silico: an open space for the development of microbe-based applications of synthetic biology. Microb Biotechnol 2022; 15:42-64. [PMID: 34570957 PMCID: PMC8719824 DOI: 10.1111/1751-7915.13937] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 12/24/2022] Open
Abstract
Living systems are studied using three complementary approaches: living cells, cell-free systems and computer-mediated modelling. Progresses in understanding, allowing researchers to create novel chassis and industrial processes rest on a cycle that combines in vivo, in vitro and in silico studies. This design-build-test-learn iteration loop cycle between experiments and analyses combines together physiology, genetics, biochemistry and bioinformatics in a way that keeps going forward. Because computer-aided approaches are not directly constrained by the material nature of the entities of interest, we illustrate here how this virtuous cycle allows researchers to explore chemistry which is foreign to that present in extant life, from whole chassis to novel metabolic cycles. Particular emphasis is placed on the importance of evolution.
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Affiliation(s)
- Antoine Danchin
- Kodikos LabsInstitut Cochin24 rue du Faubourg Saint‐JacquesParis75014France
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21
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Altamura E, Albanese P, Mavelli F, Stano P. The Rise of the Nested Multicompartment Model in Synthetic Cell Research. Front Mol Biosci 2021; 8:750576. [PMID: 34540903 PMCID: PMC8446550 DOI: 10.3389/fmolb.2021.750576] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 08/19/2021] [Indexed: 11/19/2022] Open
Affiliation(s)
| | - Paola Albanese
- Department of Chemistry, University of Bari Aldo Moro, Bari, Italy
| | - Fabio Mavelli
- Department of Chemistry, University of Bari Aldo Moro, Bari, Italy
| | - Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy
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