1
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Huang J, Xue S, Buchmann P, Teixeira AP, Fussenegger M. An electrogenetic interface to program mammalian gene expression by direct current. Nat Metab 2023; 5:1395-1407. [PMID: 37524785 PMCID: PMC10447240 DOI: 10.1038/s42255-023-00850-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/23/2023] [Indexed: 08/02/2023]
Abstract
Wearable electronic devices are playing a rapidly expanding role in the acquisition of individuals' health data for personalized medical interventions; however, wearables cannot yet directly program gene-based therapies because of the lack of a direct electrogenetic interface. Here we provide the missing link by developing an electrogenetic interface that we call direct current (DC)-actuated regulation technology (DART), which enables electrode-mediated, time- and voltage-dependent transgene expression in human cells using DC from batteries. DART utilizes a DC supply to generate non-toxic levels of reactive oxygen species that act via a biosensor to reversibly fine-tune synthetic promoters. In a proof-of-concept study in a type 1 diabetic male mouse model, a once-daily transdermal stimulation of subcutaneously implanted microencapsulated engineered human cells by energized acupuncture needles (4.5 V DC for 10 s) stimulated insulin release and restored normoglycemia. We believe this technology will enable wearable electronic devices to directly program metabolic interventions.
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Affiliation(s)
- Jinbo Huang
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Shuai Xue
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Peter Buchmann
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Ana Palma Teixeira
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
- Faculty of Science, University of Basel, Basel, Switzerland.
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2
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Liu Y, Kim E, Lei M, Wu S, Yan K, Shen J, Bentley WE, Shi X, Qu X, Payne GF. Electro-Biofabrication. Coupling Electrochemical and Biomolecular Methods to Create Functional Bio-Based Hydrogels. Biomacromolecules 2023. [PMID: 37155361 DOI: 10.1021/acs.biomac.3c00132] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Twenty years ago, this journal published a review entitled "Biofabrication with Chitosan" based on the observations that (i) chitosan could be electrodeposited using low voltage electrical inputs (typically less than 5 V) and (ii) the enzyme tyrosinase could be used to graft proteins (via accessible tyrosine residues) to chitosan. Here, we provide a progress report on the coupling of electronic inputs with advanced biological methods for the fabrication of biopolymer-based hydrogel films. In many cases, the initial observations of chitosan's electrodeposition have been extended and generalized: mechanisms have been established for the electrodeposition of various other biological polymers (proteins and polysaccharides), and electrodeposition has been shown to allow the precise control of the hydrogel's emergent microstructure. In addition, the use of biotechnological methods to confer function has been extended from tyrosinase conjugation to the use of protein engineering to create genetically fused assembly tags (short sequences of accessible amino acid residues) that facilitate the attachment of function-conferring proteins to electrodeposited films using alternative enzymes (e.g., transglutaminase), metal chelation, and electrochemically induced oxidative mechanisms. Over these 20 years, the contributions from numerous groups have also identified exciting opportunities. First, electrochemistry provides unique capabilities to impose chemical and electrical cues that can induce assembly while controlling the emergent microstructure. Second, it is clear that the detailed mechanisms of biopolymer self-assembly (i.e., chitosan gel formation) are far more complex than anticipated, and this provides a rich opportunity both for fundamental inquiry and for the creation of high performance and sustainable material systems. Third, the mild conditions used for electrodeposition allow cells to be co-deposited for the fabrication of living materials. Finally, the applications have been expanded from biosensing and lab-on-a-chip systems to bioelectronic and medical materials. We suggest that electro-biofabrication is poised to emerge as an enabling additive manufacturing method especially suited for life science applications and to bridge communication between our biological and technological worlds.
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Affiliation(s)
- Yi Liu
- Institute for Bioscience and Biotechnology Research and Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland 20742, United States
| | - Eunkyoung Kim
- Institute for Bioscience and Biotechnology Research and Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland 20742, United States
| | - Miao Lei
- Key Laboratory for Ultrafine Materials of Ministry of Education Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Si Wu
- College of Resources and Environmental Engineering, Hubei Key Laboratory for Efficient Utilization and Agglomeration of Metallurgic Mineral Resources, Wuhan University of Science and Technology, Wuhan 430081, P. R. China
| | - Kun Yan
- Hubei Key Laboratory of Advanced Textile Materials & Application, Wuhan Textile University, Wuhan 430200, P. R. China
| | - Jana Shen
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
| | - William E Bentley
- Institute for Bioscience and Biotechnology Research and Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland 20742, United States
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Xiaowen Shi
- School of Resource and Environmental Science, Hubei International Scientific and Technological Cooperation Base of Sustainable Resource and Energy, Hubei Engineering Center of Natural Polymers-Based Medical Materials, Hubei Biomass-Resource Chemistry and Environmental Biotechnology Key Laboratory, Wuhan University, Wuhan 430079, P. R. China
| | - Xue Qu
- Key Laboratory for Ultrafine Materials of Ministry of Education Frontiers Science Center for Materiobiology and Dynamic Chemistry, School of Materials Science and Engineering, Shanghai Frontier Science Research Base of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai 200237, P. R. China
| | - Gregory F Payne
- Institute for Bioscience and Biotechnology Research and Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland 20742, United States
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3
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Atkinson JT, Chavez MS, Niman CM, El-Naggar MY. Living electronics: A catalogue of engineered living electronic components. Microb Biotechnol 2023; 16:507-533. [PMID: 36519191 PMCID: PMC9948233 DOI: 10.1111/1751-7915.14171] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/26/2022] [Accepted: 11/01/2022] [Indexed: 12/23/2022] Open
Abstract
Biology leverages a range of electrical phenomena to extract and store energy, control molecular reactions and enable multicellular communication. Microbes, in particular, have evolved genetically encoded machinery enabling them to utilize the abundant redox-active molecules and minerals available on Earth, which in turn drive global-scale biogeochemical cycles. Recently, the microbial machinery enabling these redox reactions have been leveraged for interfacing cells and biomolecules with electrical circuits for biotechnological applications. Synthetic biology is allowing for the use of these machinery as components of engineered living materials with tuneable electrical properties. Herein, we review the state of such living electronic components including wires, capacitors, transistors, diodes, optoelectronic components, spin filters, sensors, logic processors, bioactuators, information storage media and methods for assembling these components into living electronic circuits.
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Affiliation(s)
- Joshua T Atkinson
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA
| | - Marko S Chavez
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA
| | - Christina M Niman
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA
| | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA.,Department of Biological Sciences, University of Southern California, Los Angeles, California, USA.,Department of Chemistry, University of Southern California, Los Angeles, California, USA
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4
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Mansouri M, Fussenegger M. Electrogenetics: Bridging synthetic biology and electronics to remotely control the behavior of mammalian designer cells. Curr Opin Chem Biol 2022; 68:102151. [PMID: 35483127 DOI: 10.1016/j.cbpa.2022.102151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/21/2022] [Accepted: 03/24/2022] [Indexed: 11/03/2022]
Abstract
Electrogenetics, the combination of electronics and genetics, is an emerging field of mammalian synthetic biology in which electrostimulation is used to remotely program user-designed genetic elements within designer cells to generate desired outputs. Here, we describe recent advances in electro-induced therapeutic gene expression and therapeutic protein secretion in engineered mammalian cells. We also review available tools and strategies to engineer electro-sensitive therapeutic designer cells that are able to sense electrical pulses and produce appropriate clinically relevant outputs in response. We highlight current limitations facing mammalian electrogenetics and suggest potential future directions for research.
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Affiliation(s)
- Maysam Mansouri
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel, CH-4058, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel, CH-4058, Switzerland; Faculty of Science, University of Basel, Mattenstrasse 26, Basel, CH-4058, Switzerland.
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5
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VanArsdale E, Pitzer J, Wang S, Stephens K, Chen CY, Payne GF, Bentley WE. Electrogenetic Signal Transmission and Propagation in Coculture to Guide Production of a Small Molecule, Tyrosine. ACS Synth Biol 2022; 11:877-887. [PMID: 35113532 DOI: 10.1021/acssynbio.1c00522] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
There are many strategies to actuate and control genetic circuits, including providing stimuli like exogenous chemical inducers, light, magnetic fields, and even applied voltage, that are orthogonal to metabolic activity. Their use enables actuation of gene expression for the production of small molecules and proteins in many contexts. Additionally, there are a growing number of reports wherein cocultures, consortia, or even complex microbiomes are employed for the production of biologics, taking advantage of an expanded array of biological function. Combining stimuli-responsive engineered cell populations enhances design space but increases complexity. In this work, we co-opt nature's redox networks and electrogenetically route control signals into a consortium of microbial cells engineered to produce a model small molecule, tyrosine. In particular, we show how electronically programmed short-lived signals (i.e., hydrogen peroxide) can be transformed by one population and propagated into sustained longer-distance signals that, in turn, guide tyrosine production in a second population building on bacterial quorum sensing that coordinates their collective behavior. Two design methodologies are demonstrated. First, we use electrogenetics to transform redox signals into the quorum sensing autoinducer, AI-1, that, in turn, induces a tyrosine biosynthesis pathway transformed into a second population. Second, we use the electrogenetically stimulated AI-1 to actuate expression of ptsH, boosting the growth rate of tyrosine-producing cells, augmenting both their number and metabolic activity. In both cases, we show how signal propagation within the coculture helps to ensure tyrosine production. We suggest that this work lays a foundation for employing electrochemical stimuli and engineered cocultures for production of molecular products in biomanufacturing environments.
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Affiliation(s)
- Eric VanArsdale
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland 20742, United States
| | - Juliana Pitzer
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Sally Wang
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland 20742, United States
| | - Kristina Stephens
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland 20742, United States
| | - Chen-yu Chen
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland 20742, United States
| | - Gregory F. Payne
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland 20742, United States
| | - William E. Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
- Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland 20742, United States
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6
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Sundaram S, Chen CS. Next-generation engineered microsystems for cell biology: a systems-level roadmap. Trends Cell Biol 2022; 32:490-500. [DOI: 10.1016/j.tcb.2022.01.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/05/2022] [Accepted: 01/07/2022] [Indexed: 12/16/2022]
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7
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Zhao Z, Ozcan EE, VanArsdale E, Li J, Kim E, Sandler AD, Kelly DL, Bentley WE, Payne GF. Mediated Electrochemical Probing: A Systems-Level Tool for Redox Biology. ACS Chem Biol 2021; 16:1099-1110. [PMID: 34156828 DOI: 10.1021/acschembio.1c00267] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Biology uses well-known redox mechanisms for energy harvesting (e.g., respiration), biosynthesis, and immune defense (e.g., oxidative burst), and now we know biology uses redox for systems-level communication. Currently, we have limited abilities to "eavesdrop" on this redox modality, which can be contrasted with our abilities to observe and actuate biology through its more familiar ionic electrical modality. In this Perspective, we argue that the coupling of electrochemistry with diffusible mediators (electron shuttles) provides a unique opportunity to access the redox communication modality through its electrical features. We highlight previous studies showing that mediated electrochemical probing (MEP) can "communicate" with biology to acquire information and even to actuate specific biological responses (i.e., targeted gene expression). We suggest that MEP may reveal an extent of redox-based communication that has remained underappreciated in nature and that MEP could provide new technological approaches for redox biology, bioelectronics, clinical care, and environmental sciences.
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Affiliation(s)
- Zhiling Zhao
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
- Robert E. Fischell Biomedical Device Institute, University of Maryland, College Park, Maryland 20742, United States
| | - Evrim E. Ozcan
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
| | - Eric VanArsdale
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
- Robert E. Fischell Biomedical Device Institute, University of Maryland, College Park, Maryland 20742, United States
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Jinyang Li
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
- Robert E. Fischell Biomedical Device Institute, University of Maryland, College Park, Maryland 20742, United States
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Eunkyoung Kim
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
- Robert E. Fischell Biomedical Device Institute, University of Maryland, College Park, Maryland 20742, United States
| | - Anthony D. Sandler
- Department of General and Thoracic Surgery, Children’s National Hospital, Washington, D.C. 20010, United States
| | - Deanna L. Kelly
- Maryland Psychiatric Research Center, University of Maryland School of Medicine, Baltimore, Maryland 21228, United States
| | - William E. Bentley
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
- Robert E. Fischell Biomedical Device Institute, University of Maryland, College Park, Maryland 20742, United States
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, United States
| | - Gregory F. Payne
- Institute for Bioscience & Biotechnology Research, University of Maryland, College Park, Maryland 20742, United States
- Robert E. Fischell Biomedical Device Institute, University of Maryland, College Park, Maryland 20742, United States
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8
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Stephens K, Zakaria FR, VanArsdale E, Payne GF, Bentley WE. Electronic signals are electrogenetically relayed to control cell growth and co-culture composition. Metab Eng Commun 2021; 13:e00176. [PMID: 34194997 PMCID: PMC8233222 DOI: 10.1016/j.mec.2021.e00176] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/20/2021] [Accepted: 05/31/2021] [Indexed: 01/17/2023] Open
Abstract
There is much to be gained by enabling electronic interrogation and control of biological function. While the benefits of bioelectronics that rely on potential-driven ionic flows are well known (electrocardiograms, defibrillators, neural prostheses, etc) there are relatively few advances targeting nonionic molecular networks, including genetic circuits. Redox activities combine connectivity to electronics with the potential for specific genetic control in cells. Here, electrode-generated hydrogen peroxide is used to actuate an electrogenetic "relay" cell population, which interprets the redox cue and synthesizes a bacterial signaling molecule (quorum sensing autoinducer AI-1) that, in turn, signals increased growth rate in a second population. The dramatically increased growth rate of the second population is enabled by expression of a phosphotransferase system protein, HPr, which is important for glucose transport. The potential to electronically modulate cell growth via direct genetic control will enable new opportunities in the treatment of disease and manufacture of biological therapeutics and other molecules.
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Affiliation(s)
- Kristina Stephens
- Fischell Department of Bioengineering, University of Maryland, College Park, USA.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, USA.,Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, USA
| | - Fauziah Rahma Zakaria
- Fischell Department of Bioengineering, University of Maryland, College Park, USA.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, USA.,Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, USA
| | - Eric VanArsdale
- Fischell Department of Bioengineering, University of Maryland, College Park, USA.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, USA.,Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, USA
| | - Gregory F Payne
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, USA.,Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, USA
| | - William E Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, USA.,Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, USA.,Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, USA
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9
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Burgos-Morales O, Gueye M, Lacombe L, Nowak C, Schmachtenberg R, Hörner M, Jerez-Longres C, Mohsenin H, Wagner H, Weber W. Synthetic biology as driver for the biologization of materials sciences. Mater Today Bio 2021; 11:100115. [PMID: 34195591 PMCID: PMC8237365 DOI: 10.1016/j.mtbio.2021.100115] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/16/2021] [Accepted: 05/18/2021] [Indexed: 01/16/2023] Open
Abstract
Materials in nature have fascinating properties that serve as a continuous source of inspiration for materials scientists. Accordingly, bio-mimetic and bio-inspired approaches have yielded remarkable structural and functional materials for a plethora of applications. Despite these advances, many properties of natural materials remain challenging or yet impossible to incorporate into synthetic materials. Natural materials are produced by living cells, which sense and process environmental cues and conditions by means of signaling and genetic programs, thereby controlling the biosynthesis, remodeling, functionalization, or degradation of the natural material. In this context, synthetic biology offers unique opportunities in materials sciences by providing direct access to the rational engineering of how a cell senses and processes environmental information and translates them into the properties and functions of materials. Here, we identify and review two main directions by which synthetic biology can be harnessed to provide new impulses for the biologization of the materials sciences: first, the engineering of cells to produce precursors for the subsequent synthesis of materials. This includes materials that are otherwise produced from petrochemical resources, but also materials where the bio-produced substances contribute unique properties and functions not existing in traditional materials. Second, engineered living materials that are formed or assembled by cells or in which cells contribute specific functions while remaining an integral part of the living composite material. We finally provide a perspective of future scientific directions of this promising area of research and discuss science policy that would be required to support research and development in this field.
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Affiliation(s)
- O. Burgos-Morales
- École Supérieure de Biotechnologie de Strasbourg - ESBS, University of Strasbourg, Illkirch, 67412, France
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - M. Gueye
- École Supérieure de Biotechnologie de Strasbourg - ESBS, University of Strasbourg, Illkirch, 67412, France
| | - L. Lacombe
- École Supérieure de Biotechnologie de Strasbourg - ESBS, University of Strasbourg, Illkirch, 67412, France
| | - C. Nowak
- École Supérieure de Biotechnologie de Strasbourg - ESBS, University of Strasbourg, Illkirch, 67412, France
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - R. Schmachtenberg
- École Supérieure de Biotechnologie de Strasbourg - ESBS, University of Strasbourg, Illkirch, 67412, France
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - M. Hörner
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, 79104, Germany
| | - C. Jerez-Longres
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, 79104, Germany
- Spemann Graduate School of Biology and Medicine - SGBM, University of Freiburg, Freiburg, 79104, Germany
| | - H. Mohsenin
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, 79104, Germany
| | - H.J. Wagner
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, 79104, Germany
- Department of Biosystems Science and Engineering - D-BSSE, ETH Zurich, Basel, 4058, Switzerland
| | - W. Weber
- Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, 79104, Germany
- Spemann Graduate School of Biology and Medicine - SGBM, University of Freiburg, Freiburg, 79104, Germany
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10
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Yim SS, McBee RM, Song AM, Huang Y, Sheth RU, Wang HH. Robust direct digital-to-biological data storage in living cells. Nat Chem Biol 2021; 17:246-253. [PMID: 33432236 PMCID: PMC7904632 DOI: 10.1038/s41589-020-00711-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 10/30/2020] [Accepted: 11/12/2020] [Indexed: 02/06/2023]
Abstract
DNA has been the predominant information storage medium for biology and holds great promise as a next-generation high-density data medium in the digital era. Currently, the vast majority of DNA-based data storage approaches rely on in vitro DNA synthesis. As such, there are limited methods to encode digital data into the chromosomes of living cells in a single step. Here, we describe a new electrogenetic framework for direct storage of digital data in living cells. Using an engineered redox-responsive CRISPR adaptation system, we encoded binary data in 3-bit units into CRISPR arrays of bacterial cells by electrical stimulation. We demonstrate multiplex data encoding into barcoded cell populations to yield meaningful information storage and capacity up to 72 bits, which can be maintained over many generations in natural open environments. This work establishes a direct digital-to-biological data storage framework and advances our capacity for information exchange between silicon- and carbon-based entities.
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Affiliation(s)
- Sung Sun Yim
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Ross M McBee
- Department of Systems Biology, Columbia University, New York, NY, USA
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Alan M Song
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Yiming Huang
- Department of Systems Biology, Columbia University, New York, NY, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY, USA
| | - Ravi U Sheth
- Department of Systems Biology, Columbia University, New York, NY, USA
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY, USA
| | - Harris H Wang
- Department of Systems Biology, Columbia University, New York, NY, USA.
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA.
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11
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Tan X, Letendre JH, Collins JJ, Wong WW. Synthetic biology in the clinic: engineering vaccines, diagnostics, and therapeutics. Cell 2021; 184:881-898. [PMID: 33571426 PMCID: PMC7897318 DOI: 10.1016/j.cell.2021.01.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 12/17/2022]
Abstract
Synthetic biology is a design-driven discipline centered on engineering novel biological functions through the discovery, characterization, and repurposing of molecular parts. Several synthetic biological solutions to critical biomedical problems are on the verge of widespread adoption and demonstrate the burgeoning maturation of the field. Here, we highlight applications of synthetic biology in vaccine development, molecular diagnostics, and cell-based therapeutics, emphasizing technologies approved for clinical use or in active clinical trials. We conclude by drawing attention to recent innovations in synthetic biology that are likely to have a significant impact on future applications in biomedicine.
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Affiliation(s)
- Xiao Tan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Division of Gastroenterology, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA; Harvard Medical School, 25 Shattuck St., Boston, MA 02115, USA; Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA
| | - Justin H Letendre
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Biological Design Center, Boston University, Boston, MA 02215, USA
| | - James J Collins
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA; Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Synthetic Biology Center, MIT, 77 Massachusetts Ave., Cambridge, MA 02139, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA.
| | - Wilson W Wong
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Biological Design Center, Boston University, Boston, MA 02215, USA.
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12
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VanArsdale E, Pitzer J, Payne GF, Bentley WE. Redox Electrochemistry to Interrogate and Control Biomolecular Communication. iScience 2020; 23:101545. [PMID: 33083771 PMCID: PMC7516135 DOI: 10.1016/j.isci.2020.101545] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cells often communicate by the secretion, transport, and perception of molecules. Information conveyed by molecules is encoded, transmitted, and decoded by cells within the context of the prevailing microenvironments. Conversely, in electronics, transmission reliability and message validation are predictable, robust, and less context dependent. In turn, many transformative advances have resulted by the formal consideration of information transfer. One way to explore this potential for biological systems is to create bio-device interfaces that facilitate bidirectional information transfer between biology and electronics. Redox reactions enable this linkage because reduction and oxidation mediate communication within biology and can be coupled with electronics. By manipulating redox reactions, one is able to combine the programmable features of electronics with the ability to interrogate and modulate biological function. In this review, we examine methods to electrochemically interrogate the various components of molecular communication using redox chemistry and to electronically control cell communication using redox electrogenetics.
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Affiliation(s)
- Eric VanArsdale
- Fischell Department of Bioengineering, University of Maryland, 3102 A. James Clark Hall 8278 Paint Branch Drive, College Park, MD 20742, USA.,Institute of Bioscience and Biotechnology Research, University of Maryland, 5115 Plant Sciences Building, College Park, MD 20742, USA.,Robert E. Fischell Institute for Biomedical Devices, University of Maryland, Room 5102, A. James Clark Hall, College Park, MD 20742, USA
| | - Juliana Pitzer
- Fischell Department of Bioengineering, University of Maryland, 3102 A. James Clark Hall 8278 Paint Branch Drive, College Park, MD 20742, USA
| | - Gregory F Payne
- Institute of Bioscience and Biotechnology Research, University of Maryland, 5115 Plant Sciences Building, College Park, MD 20742, USA.,Robert E. Fischell Institute for Biomedical Devices, University of Maryland, Room 5102, A. James Clark Hall, College Park, MD 20742, USA
| | - William E Bentley
- Fischell Department of Bioengineering, University of Maryland, 3102 A. James Clark Hall 8278 Paint Branch Drive, College Park, MD 20742, USA.,Institute of Bioscience and Biotechnology Research, University of Maryland, 5115 Plant Sciences Building, College Park, MD 20742, USA.,Robert E. Fischell Institute for Biomedical Devices, University of Maryland, Room 5102, A. James Clark Hall, College Park, MD 20742, USA
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13
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Zajdel TJ, Shim G, Wang L, Rossello-Martinez A, Cohen DJ. SCHEEPDOG: Programming Electric Cues to Dynamically Herd Large-Scale Cell Migration. Cell Syst 2020; 10:506-514.e3. [PMID: 32684277 PMCID: PMC7779114 DOI: 10.1016/j.cels.2020.05.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 05/06/2020] [Accepted: 05/19/2020] [Indexed: 10/24/2022]
Abstract
Directed cell migration is critical across biological processes spanning healing to cancer invasion, yet no existing tools allow real-time interactive guidance over such migration. We present a new bioreactor that harnesses electrotaxis-directed cell migration along electric field gradients-by integrating four independent electrodes under computer control to dynamically program electric field patterns, and hence steer cell migration. Using this platform, we programmed and characterized multiple precise, two-dimensional collective migration maneuvers in renal epithelia and primary skin keratinocyte ensembles. First, we demonstrated on-demand, 90-degree collective turning. Next, we developed a universal electrical stimulation scheme capable of programming arbitrary 2D migration maneuvers such as precise angular turns and migration in a complete circle. Our stimulation scheme proves that cells effectively time-average electric field cues, helping to elucidate the transduction timescales in electrotaxis. Together, this work represents an enabling platform for controlling cell migration with broad utility across many cell types.
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Affiliation(s)
- Tom J Zajdel
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Gawoon Shim
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Linus Wang
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ 08544, USA
| | - Alejandro Rossello-Martinez
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ 08544, USA; Department of Aeronautics, Imperial College London, London SW7 2AZ, UK
| | - Daniel J Cohen
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ 08544, USA.
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14
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Krawczyk K, Xue S, Buchmann P, Charpin-El-Hamri G, Saxena P, Hussherr MD, Shao J, Ye H, Xie M, Fussenegger M. Electrogenetic cellular insulin release for real-time glycemic control in type 1 diabetic mice. Science 2020; 368:993-1001. [DOI: 10.1126/science.aau7187] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 02/11/2020] [Accepted: 04/03/2020] [Indexed: 12/11/2022]
Abstract
Sophisticated devices for remote-controlled medical interventions require an electrogenetic interface that uses digital electronic input to directly program cellular behavior. We present a cofactor-free bioelectronic interface that directly links wireless-powered electrical stimulation of human cells to either synthetic promoter–driven transgene expression or rapid secretion of constitutively expressed protein therapeutics from vesicular stores. Electrogenetic control was achieved by coupling ectopic expression of the L-type voltage-gated channel CaV1.2 and the inwardly rectifying potassium channel Kir2.1 to the desired output through endogenous calcium signaling. Focusing on type 1 diabetes, we engineered electrosensitive human β cells (Electroβ cells). Wireless electrical stimulation of Electroβ cells inside a custom-built bioelectronic device provided real-time control of vesicular insulin release; insulin levels peaked within 10 minutes. When subcutaneously implanted, this electrotriggered vesicular release system restored normoglycemia in type 1 diabetic mice.
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Affiliation(s)
- Krzysztof Krawczyk
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland
| | - Shuai Xue
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, People’s Republic of China
| | - Peter Buchmann
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland
| | - Ghislaine Charpin-El-Hamri
- Département Génie Biologique, Institut Universitaire de Technologie Lyon 1, F-69622 Villeurbanne Cedex, France
| | - Pratik Saxena
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland
| | - Marie-Didiée Hussherr
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland
| | - Jiawei Shao
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, People’s Republic of China
- Key Laboratory of Growth Regulation and Transformation Research of Zheijang Province, School of Life Sciences, Westlake University, Hangzhou, People’s Republic of China
| | - Haifeng Ye
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, People’s Republic of China
| | - Mingqi Xie
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland
- Key Laboratory of Growth Regulation and Transformation Research of Zheijang Province, School of Life Sciences, Westlake University, Hangzhou, People’s Republic of China
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, CH-4058 Basel, Switzerland
- Faculty of Science, University of Basel, CH-4058 Basel, Switzerland
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15
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VanArsdale E, Hörnström D, Sjöberg G, Järbur I, Pitzer J, Payne GF, van Maris AJA, Bentley WE. A Coculture Based Tyrosine-Tyrosinase Electrochemical Gene Circuit for Connecting Cellular Communication with Electronic Networks. ACS Synth Biol 2020; 9:1117-1128. [PMID: 32208720 DOI: 10.1021/acssynbio.9b00469] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
There is a growing interest in mediating information transfer between biology and electronics. By the addition of redox mediators to various samples and cells, one can both electronically obtain a redox "portrait" of a biological system and, conversely, program gene expression. Here, we have created a cell-based synthetic biology-electrochemical axis in which engineered cells process molecular cues, producing an output that can be directly recorded via electronics-but without the need for added redox mediators. The process is robust; two key components must act together to provide a valid signal. The system builds on the tyrosinase-mediated conversion of tyrosine to L-DOPA and L-DOPAquinone, which are both redox active. "Catalytic" transducer cells provide for signal-mediated surface expression of tyrosinase. Additionally, "reagent" transducer cells synthesize and export tyrosine, a substrate for tyrosinase. In cocultures, this system enables real-time electrochemical transduction of cell activating molecular cues. To demonstrate, we eavesdrop on quorum sensing signaling molecules that are secreted by Pseudomonas aeruginosa, N-(3-oxododecanoyl)-l-homoserine lactone and pyocyanin.
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Affiliation(s)
- Eric VanArsdale
- Fischell Department of Bioengineering, University of Maryland, 3102 A. James Clark Hall, 8278 Paint Branch Drive, College Park, Maryland 20742, United States
| | - David Hörnström
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, SE 10691 Stockholm, Sweden
| | - Gustav Sjöberg
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, SE 10691 Stockholm, Sweden
| | - Ida Järbur
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, SE 10691 Stockholm, Sweden
| | - Juliana Pitzer
- Fischell Department of Bioengineering, University of Maryland, 3102 A. James Clark Hall, 8278 Paint Branch Drive, College Park, Maryland 20742, United States
| | - Gregory F. Payne
- Fischell Department of Bioengineering, University of Maryland, 3102 A. James Clark Hall, 8278 Paint Branch Drive, College Park, Maryland 20742, United States
| | - Antonius J. A. van Maris
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, SE 10691 Stockholm, Sweden
| | - William E. Bentley
- Fischell Department of Bioengineering, University of Maryland, 3102 A. James Clark Hall, 8278 Paint Branch Drive, College Park, Maryland 20742, United States
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16
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Weisenberger MS, Deans TL. Bottom-up approaches in synthetic biology and biomaterials for tissue engineering applications. J Ind Microbiol Biotechnol 2018; 45:599-614. [PMID: 29552703 PMCID: PMC6041164 DOI: 10.1007/s10295-018-2027-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Accepted: 03/11/2018] [Indexed: 12/30/2022]
Abstract
Synthetic biologists use engineering principles to design and construct genetic circuits for programming cells with novel functions. A bottom-up approach is commonly used to design and construct genetic circuits by piecing together functional modules that are capable of reprogramming cells with novel behavior. While genetic circuits control cell operations through the tight regulation of gene expression, a diverse array of environmental factors within the extracellular space also has a significant impact on cell behavior. This extracellular space offers an addition route for synthetic biologists to apply their engineering principles to program cell-responsive modules within the extracellular space using biomaterials. In this review, we discuss how taking a bottom-up approach to build genetic circuits using DNA modules can be applied to biomaterials for controlling cell behavior from the extracellular milieu. We suggest that, by collectively controlling intrinsic and extrinsic signals in synthetic biology and biomaterials, tissue engineering outcomes can be improved.
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Affiliation(s)
| | - Tara L Deans
- Department of Bioengineering, University of Utah, Salt Lake City, UT, 84112, USA.
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17
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Electronic control of gene expression and cell behaviour in Escherichia coli through redox signalling. Nat Commun 2017; 8:14030. [PMID: 28094788 PMCID: PMC5247576 DOI: 10.1038/ncomms14030] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 11/21/2016] [Indexed: 12/18/2022] Open
Abstract
The ability to interconvert information between electronic and ionic modalities has transformed our ability to record and actuate biological function. Synthetic biology offers the potential to expand communication ‘bandwidth' by using biomolecules and providing electrochemical access to redox-based cell signals and behaviours. While engineered cells have transmitted molecular information to electronic devices, the potential for bidirectional communication stands largely untapped. Here we present a simple electrogenetic device that uses redox biomolecules to carry electronic information to engineered bacterial cells in order to control transcription from a simple synthetic gene circuit. Electronic actuation of the native transcriptional regulator SoxR and transcription from the PsoxS promoter allows cell response that is quick, reversible and dependent on the amplitude and frequency of the imposed electronic signals. Further, induction of bacterial motility and population based cell-to-cell communication demonstrates the versatility of our approach and potential to drive intricate biological behaviours. Synthetic biology offers the ability to explore new ways of manipulating gene expression and function. Here the authors demonstrate an electrogenetic device that allows control of transcription by an exogenous electrical signal.
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18
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Kis Z, Pereira HS, Homma T, Pedrigi RM, Krams R. Mammalian synthetic biology: emerging medical applications. J R Soc Interface 2016; 12:rsif.2014.1000. [PMID: 25808341 DOI: 10.1098/rsif.2014.1000] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
In this review, we discuss new emerging medical applications of the rapidly evolving field of mammalian synthetic biology. We start with simple mammalian synthetic biological components and move towards more complex and therapy-oriented gene circuits. A comprehensive list of ON-OFF switches, categorized into transcriptional, post-transcriptional, translational and post-translational, is presented in the first sections. Subsequently, Boolean logic gates, synthetic mammalian oscillators and toggle switches will be described. Several synthetic gene networks are further reviewed in the medical applications section, including cancer therapy gene circuits, immuno-regulatory networks, among others. The final sections focus on the applicability of synthetic gene networks to drug discovery, drug delivery, receptor-activating gene circuits and mammalian biomanufacturing processes.
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Affiliation(s)
- Zoltán Kis
- Department of Bioengineering, Imperial College London, London, UK
| | | | - Takayuki Homma
- Department of Bioengineering, Imperial College London, London, UK
| | - Ryan M Pedrigi
- Department of Bioengineering, Imperial College London, London, UK
| | - Rob Krams
- Department of Bioengineering, Imperial College London, London, UK
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19
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Ciechonska M, Grob A, Isalan M. From noise to synthetic nucleoli: can synthetic biology achieve new insights? Integr Biol (Camb) 2016; 8:383-93. [PMID: 26751735 DOI: 10.1039/c5ib00271k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Synthetic biology aims to re-organise and control biological components to make functional devices. Along the way, the iterative process of designing and testing gene circuits has the potential to yield many insights into the functioning of the underlying chassis of cells. Thus, synthetic biology is converging with disciplines such as systems biology and even classical cell biology, to give a new level of predictability to gene expression, cell metabolism and cellular signalling networks. This review gives an overview of the contributions that synthetic biology has made in understanding gene expression, in terms of cell heterogeneity (noise), the coupling of growth and energy usage to expression, and spatiotemporal considerations. We mainly compare progress in bacterial and mammalian systems, which have some of the most-developed engineering frameworks. Overall, one view of synthetic biology can be neatly summarised as "creating in order to understand."
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Affiliation(s)
- Marta Ciechonska
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
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20
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Characterizing Synthetic Biology Through Its Novel and Enhanced Functionalities. Synth Biol (Oxf) 2015. [DOI: 10.1007/978-3-319-02783-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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21
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Mol M, Raj Bejugam P, Singh S. Synthetic biology at the interface of functional genomics. Brief Funct Genomics 2014; 14:180-8. [PMID: 25212484 DOI: 10.1093/bfgp/elu031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Functional genomics is considered a powerful tool that helps understand the relation between an organism's genotype and possible phenotypes. Volumes of data generated on several 'omics' platforms have revealed the network complexities underlying biological processes. Systems and synthetic biology have garnered much attention because of the ability to infer and comprehend the uncertainties associated with such complexities. Also, part-wise characterization of the network components (e.g. DNA, RNA, protein) has rendered an engineering perspective in life sciences to build modular and functional devices. This approach can be used to combat one of the many concerns of the world, i.e. in the area of biomedical translational research by designing and constructing novel therapeutic devices to intervene network perturbation in a diseased state to transform to a healthy state.
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22
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Heng BC, Aubel D, Fussenegger M. G protein-coupled receptors revisited: therapeutic applications inspired by synthetic biology. Annu Rev Pharmacol Toxicol 2013; 54:227-49. [PMID: 24160705 DOI: 10.1146/annurev-pharmtox-011613-135921] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
G protein-coupled receptors (GPCRs) mediate the majority of cellular responses to hormones and neurotransmitters within the human body. They have much potential in the emerging field of synthetic biology, which is the rational, systematic design of biological systems with desired functionality. The responsiveness of GPCRs to a plethora of endogenous and exogenous ligands and stimuli make them ideal sensory receptor modules of synthetic gene networks. Such networks can activate target gene expression in response to a specific stimulus. Additionally, because GPCRs are important pharmacological targets of various human diseases, genes encoding their protein/peptide ligands can also be incorporated as target genes of the response output elements of synthetic gene networks. This review aims to critically examine the potential role of GPCRs in constructing therapeutic synthetic gene networks and to discuss various challenges in utilizing GPCRs for synthetic biology applications.
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Affiliation(s)
- Boon Chin Heng
- Department of Biosystems Science and Engineering, ETH Zürich, CH-4058 Basel, Switzerland;
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23
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Liba BD, Kim E, Martin AN, Liu Y, Bentley WE, Payne GF. Biofabricated film with enzymatic and redox-capacitor functionalities to harvest and store electrons. Biofabrication 2013; 5:015008. [DOI: 10.1088/1758-5082/5/1/015008] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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24
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Müller K, Weber W. Optogenetic tools for mammalian systems. MOLECULAR BIOSYSTEMS 2013; 9:596-608. [DOI: 10.1039/c3mb25590e] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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25
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Design and Application of Synthetic Biology Devices for Therapy. Synth Biol (Oxf) 2013. [DOI: 10.1016/b978-0-12-394430-6.00009-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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26
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Synthetic signaling networks for therapeutic applications. Curr Opin Biotechnol 2012; 23:773-9. [DOI: 10.1016/j.copbio.2012.01.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 01/03/2012] [Accepted: 01/08/2012] [Indexed: 01/02/2023]
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27
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Folcher M, Fussenegger M. Synthetic biology advancing clinical applications. Curr Opin Chem Biol 2012; 16:345-54. [DOI: 10.1016/j.cbpa.2012.06.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Revised: 05/31/2012] [Accepted: 06/20/2012] [Indexed: 10/28/2022]
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28
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Wieland M, Fussenegger M. Engineering Molecular Circuits Using Synthetic Biology in Mammalian Cells. Annu Rev Chem Biomol Eng 2012; 3:209-34. [DOI: 10.1146/annurev-chembioeng-061010-114145] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Markus Wieland
- Department of Biosystems Science and Bioengineering, ETH Zurich, CH-4058 Basel, Switzerland; ,
| | - Martin Fussenegger
- Department of Biosystems Science and Bioengineering, ETH Zurich, CH-4058 Basel, Switzerland; ,
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29
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Ausländer S, Wieland M, Fussenegger M. Smart medication through combination of synthetic biology and cell microencapsulation. Metab Eng 2012; 14:252-60. [DOI: 10.1016/j.ymben.2011.06.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 05/11/2011] [Accepted: 06/09/2011] [Indexed: 01/05/2023]
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30
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Synthetic Biology: Its Applications in Biotechnology*. PROG BIOCHEM BIOPHYS 2012. [DOI: 10.3724/sp.j.1206.2011.00583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Botezatu L, Sievers S, Gama-Norton L, Schucht R, Hauser H, Wirth D. Genetic aspects of cell line development from a synthetic biology perspective. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2012; 127:251-284. [PMID: 22068842 DOI: 10.1007/10_2011_117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Animal cells can be regarded as factories for the production of relevant proteins. The advances described in this chapter towards the development of cell lines with higher productivity capacities, certain metabolic and proliferation properties, reduced apoptosis and other features must be regarded in an integrative perspective. The systematic application of systems biology approaches in combination with a synthetic arsenal for targeted modification of endogenous networks are proposed to lead towards the achievement of a predictable and technologically advanced cell system with high biotechnological impact.
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Affiliation(s)
- L Botezatu
- Helmholtz Centre for Infection Research, Braunschweig, Germany
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33
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Bhomkar P, Materi W, Wishart DS. The bacterial nanorecorder: engineering E. coli to function as a chemical recording device. PLoS One 2011; 6:e27559. [PMID: 22132112 PMCID: PMC3223186 DOI: 10.1371/journal.pone.0027559] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 10/19/2011] [Indexed: 02/02/2023] Open
Abstract
Synthetic biology is an emerging branch of molecular biology that uses synthetic genetic constructs to create man-made cells or organisms that are capable of performing novel and/or useful applications. Using a synthetic chemically sensitive genetic toggle switch to activate appropriate fluorescent protein indicators (GFP, RFP) and a cell division inhibitor (minC), we have created a novel E. coli strain that can be used as a highly specific, yet simple and inexpensive chemical recording device. This biological "nanorecorder" can be used to determine both the type and the time at which a brief chemical exposure event has occurred. In particular, we show that the short-term exposure (15-30 min) of cells harboring this synthetic genetic circuit to small molecule signals (anhydrotetracycline or IPTG) triggered long-term and uniform cell elongation, with cell length being directly proportional to the time elapsed following a brief chemical exposure. This work demonstrates that facile modification of an existing genetic toggle switch can be exploited to generate a robust, biologically-based "nanorecorder" that could potentially be adapted to detect, respond and record a wide range of chemical stimuli that may vary over time and space.
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Affiliation(s)
- Prasanna Bhomkar
- National Institute for Nanotechnology, Edmonton, Alberta, Canada.
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34
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Agapakis CM, Silver PA. Modular electron transfer circuits for synthetic biology: insulation of an engineered biohydrogen pathway. Bioeng Bugs 2011; 1:413-8. [PMID: 21468209 DOI: 10.4161/bbug.1.6.12462] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Revised: 05/24/2010] [Accepted: 05/26/2010] [Indexed: 11/19/2022] Open
Abstract
Electron transfer is central to a wide range of essential metabolic pathways, from photosynthesis to fermentation. The evolutionary diversity and conservation of proteins that transfer electrons makes these pathways a valuable platform for engineered metabolic circuits in synthetic biology. Rational engineering of electron transfer pathways containing hydrogenases has the potential to lead to industrial scale production of hydrogen as an alternative source of clean fuel and experimental assays for understanding the complex interactions of multiple electron transfer proteins in vivo. We designed and implemented a synthetic hydrogen metabolism circuit in Escherichia coli that creates an electron transfer pathway both orthogonal to and integrated within existing metabolism. The design of such modular electron transfer circuits allows for facile characterization of in vivo system parameters with applications toward further engineering for alternative energy production.
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35
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Abstract
Early synthetic biology designs, namely the genetic toggle switch and repressilator, showed that regulatory components can be characterized and assembled to bring about complex, electronics-inspired behaviours in living systems (for example, memory storage and timekeeping). Through the characterization and assembly of genetic parts and biological building blocks, many more devices have been constructed, including switches, memory elements, oscillators, pulse generators, digital logic gates, filters and communication modules. Advances in the field are now allowing expansion beyond small gene networks to the realm of larger biological programs, which hold promise for a wide range of applications, including biosensing, therapeutics and the production of biofuels, pharmaceuticals and biomaterials. Synthetic biosensing circuits consist of sensitive elements that bind analytes and transducer modules that mobilize cellular responses. Balancing these two modules involves engineering modularity and specificity into the various circuits. Biosensor sensitive elements include environment-responsive promoters (transcriptional), RNA aptamers (translational) and protein receptors (post-translational). Biosensor transducer modules include engineered gene networks (transcriptional), non-coding regulatory RNAs (translational) and protein signal-transduction circuits (post-translational). The contributions of synthetic biology to therapeutics include: engineered networks and organisms for disease-mechanism elucidation, drug-target identification, drug-discovery platforms, therapeutic treatment, therapeutic delivery, and drug production and access. In the microbial production of biofuels and pharmaceuticals, synthetic biology has supplemented traditional genetic and metabolic engineering efforts by aiding the construction of optimized biosynthetic pathways. Optimizing metabolic flux through biosynthetic pathways is traditionally accomplished by driving the expression of pathway enzymes with strong, inducible promoters. New synthetic approaches include the rapid diversification of various pathway components, the rational and model-guided assembly of pathway components, and hybrid solutions.
Advances in the synthetic biology field are allowing an expansion beyond small gene networks towards larger biological programs that hold promise for a wide range of applications, including biosensing, therapeutics and the production of biofuels, pharmaceuticals and biomaterials. Synthetic biology is bringing together engineers and biologists to design and build novel biomolecular components, networks and pathways, and to use these constructs to rewire and reprogram organisms. These re-engineered organisms will change our lives over the coming years, leading to cheaper drugs, 'green' means to fuel our cars and targeted therapies for attacking 'superbugs' and diseases, such as cancer. The de novo engineering of genetic circuits, biological modules and synthetic pathways is beginning to address these crucial problems and is being used in related practical applications.
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Affiliation(s)
- Ahmad S Khalil
- Howard Hughes Medical Institute, Department of Biomedical Engineering, Center for BioDynamics and Center for Advanced Biotechnology, Boston University, Boston, Massachusetts 02215, USA
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Kämpf MM, Weber W. Synthetic biology in the analysis and engineering of signaling processes. Integr Biol (Camb) 2010; 2:12-24. [DOI: 10.1039/b913490e] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Tigges M, Fussenegger M. Recent advances in mammalian synthetic biology-design of synthetic transgene control networks. Curr Opin Biotechnol 2009; 20:449-60. [PMID: 19762224 DOI: 10.1016/j.copbio.2009.07.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2009] [Revised: 07/30/2009] [Accepted: 07/31/2009] [Indexed: 10/20/2022]
Abstract
Capitalizing on an era of functional genomic research, systems biology offers a systematic quantitative analysis of existing biological systems thereby providing the molecular inventory of biological parts that are currently being used for rational synthesis and engineering of complex biological systems with novel and potentially useful functions-an emerging discipline known as synthetic biology. During the past decade synthetic biology has rapidly developed from simple control devices fine-tuning the activity of single genes and proteins to multi-gene/protein-based transcription and signaling networks providing new insight into global control and molecular reaction dynamics, thereby enabling the design of novel drug-synthesis pathways as well as genetic devices with unmatched biological functions. While pioneering synthetic devices have first been designed as test, toy, and teaser systems for use in prokaryotes and lower eukaryotes, first examples of a systematic assembly of synthetic gene networks in mammalian cells has sketched the full potential of synthetic biology: foster novel therapeutic opportunities in gene and cell-based therapies. Here we provide a concise overview on the latest advances in mammalian synthetic biology.
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Affiliation(s)
- Marcel Tigges
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel CH-4058, Switzerland
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Agapakis CM, Silver PA. Synthetic biology: exploring and exploiting genetic modularity through the design of novel biological networks. MOLECULAR BIOSYSTEMS 2009; 5:704-13. [PMID: 19562109 DOI: 10.1039/b901484e] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Synthetic biology has been used to describe many biological endeavors over the past thirty years--from designing enzymes and in vitro systems, to manipulating existing metabolisms and gene expression, to creating entirely synthetic replicating life forms. What separates the current incarnation of synthetic biology from the recombinant DNA technology or metabolic engineering of the past is an emphasis on principles from engineering such as modularity, standardization, and rigorously predictive models. As such, synthetic biology represents a new paradigm for learning about and using biological molecules and data, with applications in basic science, biotechnology, and medicine. This review covers the canonical examples as well as some recent advances in synthetic biology in terms of what we know and what we can learn about the networks underlying biology, and how this endeavor may shape our understanding of living systems.
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