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Jones EM, Marken JP, Silver PA. Synthetic microbiology in sustainability applications. Nat Rev Microbiol 2024; 22:345-359. [PMID: 38253793 DOI: 10.1038/s41579-023-01007-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2023] [Indexed: 01/24/2024]
Abstract
Microorganisms are a promising means to address many societal sustainability challenges owing to their ability to thrive in diverse environments and interface with the microscale chemical world via diverse metabolic capacities. Synthetic biology can engineer microorganisms by rewiring their regulatory networks or introducing new functionalities, enhancing their utility for target applications. In this Review, we provide a broad, high-level overview of various research efforts addressing sustainability challenges through synthetic biology, emphasizing foundational microbiological research questions that can accelerate the development of these efforts. We introduce an organizational framework that categorizes these efforts along three domains - factory, farm and field - that are defined by the extent to which the engineered microorganisms interface with the natural external environment. Different application areas within the same domain share many fundamental challenges, highlighting productive opportunities for cross-disciplinary collaborations between researchers working in historically disparate fields.
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Affiliation(s)
- Ethan M Jones
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - John P Marken
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Resnick Sustainability Institute, California Institute of Technology, Pasadena, CA, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA.
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2
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Benman W, Iyengar P, Mumford T, Huang Z, Bugaj LJ. Multiplexed dynamic control of temperature to probe and observe mammalian cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.18.580877. [PMID: 38562729 PMCID: PMC10983861 DOI: 10.1101/2024.02.18.580877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Temperature is a critical parameter for biological function, yet there is a lack of approaches to modulate the temperature of biological specimens in a dynamic and high-throughput manner. We present the thermoPlate, a device for programmable control of temperature in each well of a 96-well plate, in a manner compatible with mammalian cell culture and live cell imaging. The thermoPlate maintains precise feedback control of temperature patterns independently in each well, with minutes-scale heating and cooling through ΔT ~15-20°C. A computational model that predicts thermal diffusion guides optimal design of heating protocols. The thermoPlate allowed systematic characterization of both synthetic and natural thermo-responsive systems. We first used the thermoPlate in conjunction with live-cell microscopy to characterize the rapid temperature-dependent phase separation of a synthetic elastin-like polypeptide (ELP53). We then measured stress granule (SG) formation in response to heat stress, observing differences in SG dynamics with each increasing degree of stress. We observed adaptive formation of SGs, whereby SGs formed but then dissolved in response to persistent heat stress (≥ 42°C). SG adaptation revealed a biochemical memory of stress that depended on both the time and temperature of heat shock. Stress memories continued to form even after the removal of heat and persisted for 6-9 hours before dissipating. The capabilities and open-source nature of the thermoPlate will empower the study and engineering of a wide range of thermoresponsive phenomena.
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Affiliation(s)
- William Benman
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Pavan Iyengar
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Thomas Mumford
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Zikang Huang
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Lukasz J. Bugaj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Institute of Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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3
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Fang Z, Zhu YJ, Qian ZG, Xia XX. Designer protein compartments for microbial metabolic engineering. Curr Opin Biotechnol 2024; 85:103062. [PMID: 38199036 DOI: 10.1016/j.copbio.2023.103062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/16/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024]
Abstract
Protein compartments are distinct structures assembled in living cells via self-assembly or phase separation of specific proteins. Significant efforts have been made to discover their molecular structures and formation mechanisms, as well as their fundamental roles in spatiotemporal control of cellular metabolism. Here, we review the design and construction of synthetic protein compartments for spatial organization of target metabolic pathways toward increased efficiency and specificity. In particular, we highlight the compartmentalization strategies and recent examples to speed up desirable metabolic reactions, to reduce the accumulation of toxic metabolic intermediates, and to switch competing metabolic pathways. We also identify the most important challenges that need to be addressed for exploitation of these designer compartments as a versatile toolkit in metabolic reprogramming.
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Affiliation(s)
- Zhen Fang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China
| | - Ya-Jiao Zhu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China
| | - Zhi-Gang Qian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China.
| | - Xiao-Xia Xia
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, People's Republic of China.
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4
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Qian W, Good MC. Peeking under the hood of early embryogenesis: Using tools and synthetic biology to understand native control systems and sculpt tissues. Semin Cell Dev Biol 2023; 141:43-49. [PMID: 35525819 PMCID: PMC9633583 DOI: 10.1016/j.semcdb.2022.04.016] [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: 02/27/2022] [Accepted: 04/13/2022] [Indexed: 10/18/2022]
Abstract
Early embryogenesis requires rapid division of pluripotent blastomeres, regulated genome activation, precise spatiotemporal signaling to pattern cell fate, and morphogenesis to shape primitive tissue architectures. The complexity of this process has inspired researchers to move beyond simple genetic perturbation into engineered devices and synthetic biology tools to permit temporal and spatial manipulation of the control systems guiding development. By precise alteration of embryo organization, it is now possible to advance beyond basic analytical strategies and directly test the sufficiency of models for developmental regulation. Separately, advances in micropatterning and embryoid culture have facilitated the bottom-up construction of complex embryo tissues allowing ex vivo systems to recapitulate even later stages of development. Embryos fertilized and grown ex vivo offer an excellent opportunity to exogenously perturb fundamental pathways governing embryogenesis. Here we review the technologies developed to thermally modulate the embryo cell cycle, and optically regulate morphogen and signaling pathways in space and time, specifically in the blastula embryo. Additionally, we highlight recent advances in cell patterning in two and three dimensions that have helped reveal the self-organizing properties and gene regulatory networks guiding early embryo organization.
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Affiliation(s)
- Wenchao Qian
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Cell and Molecular Biology Graduate Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew C. Good
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Department of Bioengineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA,Cell and Molecular Biology Graduate Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA,Lead Contact,Correspondence: (M.C.G), Address: 421 Curie Blvd, 1151 Biomedical Research Building, Philadelphia PA 19104
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5
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Qian ZG, Huang SC, Xia XX. Synthetic protein condensates for cellular and metabolic engineering. Nat Chem Biol 2022; 18:1330-1340. [DOI: 10.1038/s41589-022-01203-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/07/2022] [Indexed: 11/20/2022]
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6
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Greeson EM, Madsen CS, Makela AV, Contag CH. Magnetothermal Control of Temperature-Sensitive Repressors in Superparamagnetic Iron Nanoparticle-Coated Bacillus subtilis. ACS NANO 2022; 16:16699-16712. [PMID: 36200984 DOI: 10.1021/acsnano.2c06239] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Superparamagnetic iron oxide nanoparticles (SPIONs) are used as contrast agents in magnetic resonance imaging (MRI) and magnetic particle imaging (MPI), and resulting images can be used to guide magnetothermal heating. Alternating magnetic fields (AMF) cause local temperature increases in regions with SPIONs, and we investigated the ability of magnetic hyperthermia to regulate temperature-sensitive repressors (TSRs) of bacterial transcription. The TSR, TlpA39, was derived from a Gram-negative bacterium and used here for thermal control of reporter gene expression in Gram-positive, Bacillus subtilis. In vitro heating of B. subtilis with TlpA39 controlling bacterial luciferase expression resulted in a 14.6-fold (12 hours; h) and 1.8-fold (1 h) increase in reporter transcripts with a 10.0-fold (12 h) and 12.1-fold (1 h) increase in bioluminescence. To develop magnetothermal control, B. subtilis cells were coated with three SPION variations. Electron microscopy coupled with energy dispersive X-ray spectroscopy revealed an external association with, and retention of, SPIONs on B. subtilis. Furthermore, using long duration AMF we demonstrated magnetothermal induction of the TSRs in SPION-coated B. subtilis with a maximum of 5.6-fold increases in bioluminescence. After intramuscular injections of SPION-coated B. subtilis, histology revealed that SPIONs remained in the same locations as the bacteria. For in vivo studies, 1 h of AMF is the maximum exposure due to anesthesia constraints. Both in vitro and in vivo, there was no change in bioluminescence after 1 h of AMF treatment. Pairing TSRs with magnetothermal energy using SPIONs for localized heating with AMF can lead to transcriptional control that expands options for targeted bacteriotherapies.
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Affiliation(s)
- Emily M Greeson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, United States
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan 48824, United States
| | - Cody S Madsen
- Department of Biomedical Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan 48824, United States
| | - Ashley V Makela
- Department of Biomedical Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan 48824, United States
| | - Christopher H Contag
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Biomedical Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, Michigan 48824, United States
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7
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Lee TA, Steel H. Cybergenetic control of microbial community composition. Front Bioeng Biotechnol 2022; 10:957140. [PMID: 36277404 PMCID: PMC9582452 DOI: 10.3389/fbioe.2022.957140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
The use of bacterial communities in bioproduction instead of monocultures has potential advantages including increased productivity through division of labour, ability to utilise cheaper substrates, and robustness against perturbations. A key challenge in the application of engineered bacterial communities is the ability to reliably control the composition of the community in terms of its constituent species. This is crucial to prevent faster growing species from outcompeting others with a lower relative fitness, and to ensure that all species are present at an optimal ratio during different steps in a biotechnological process. In contrast to purely biological approaches such as synthetic quorum sensing circuits or paired auxotrophies, cybergenetic control techniques - those in which computers interface with living cells-are emerging as an alternative approach with many advantages. The community composition is measured through methods such as fluorescence intensity or flow cytometry, with measured data fed real-time into a computer. A control action is computed using a variety of possible control algorithms and then applied to the system, with actuation taking the form of chemical (e.g., inducers, nutrients) or physical (e.g., optogenetic, mechanical) inputs. Subsequent changes in composition are then measured and the cycle repeated, maintaining or driving the system to a desired state. This review discusses recent and future developments in methods for implementing cybergenetic control systems, contrasts their capabilities with those of traditional biological methods of population control, and discusses future directions and outstanding challenges for the field.
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Lu K, Wazawa T, Sakamoto J, Vu CQ, Nakano M, Kamei Y, Nagai T. Intracellular Heat Transfer and Thermal Property Revealed by Kilohertz Temperature Imaging with a Genetically Encoded Nanothermometer. NANO LETTERS 2022; 22:5698-5707. [PMID: 35792763 PMCID: PMC9335883 DOI: 10.1021/acs.nanolett.2c00608] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Despite improved sensitivity of nanothermometers, direct observation of heat transport inside single cells has remained challenging for the lack of high-speed temperature imaging techniques. Here, we identified insufficient temperature resolution under short signal integration time and slow sensor kinetics as two major bottlenecks. To overcome the limitations, we developed B-gTEMP, a nanothermometer based on the tandem fusion of mNeonGreen and tdTomato fluorescent proteins. We visualized the propagation of heat inside intracellular space by tracking the temporal variation of local temperature at a time resolution of 155 μs and a temperature resolution 0.042 °C. By comparing the fast in situ temperature dynamics with computer-simulated heat diffusion, we estimated the thermal diffusivity of live HeLa cells. The present thermal diffusivity in cells was about 1/5.3 of that of water and much smaller than the values reported for bulk tissues, which may account for observations of heterogeneous intracellular temperature distributions.
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Affiliation(s)
- Kai Lu
- SANKEN
(The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Tetsuichi Wazawa
- SANKEN
(The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Joe Sakamoto
- National
Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Cong Quang Vu
- SANKEN
(The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
- Graduate
School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masahiro Nakano
- SANKEN
(The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Yasuhiro Kamei
- National
Institute for Basic Biology, Nishigonaka 38, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Takeharu Nagai
- SANKEN
(The Institute of Scientific and Industrial Research), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
- Graduate
School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan
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9
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Chee WKD, Yeoh JW, Dao VL, Poh CL. Highly Reversible Tunable Thermal-Repressible Split-T7 RNA Polymerases (Thermal-T7RNAPs) for Dynamic Gene Regulation. ACS Synth Biol 2022; 11:921-937. [PMID: 35089710 DOI: 10.1021/acssynbio.1c00545] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Temperature is a physical cue that is easy to apply, allowing cellular behaviors to be controlled in a contactless and dynamic manner via heat-inducible/repressible systems. However, existing heat-repressible systems are limited in number, rely on thermal sensitive mRNA or transcription factors that function at low temperatures, lack tunability, suffer delays, and are overly complex. To provide an alternative mode of thermal regulation, we developed a library of compact, reversible, and tunable thermal-repressible split-T7 RNA polymerase systems (Thermal-T7RNAPs), which fused temperature-sensitive domains of Tlpa protein with split-T7RNAP to enable direct thermal control of the T7RNAP activity between 30 and 42 °C. We generated a large mutant library with varying thermal performances via an automated screening framework to extend temperature tunability. Lastly, using the mutants, novel thermal logic circuitry was implemented to regulate cell growth and achieve active thermal control of the cell proportions within co-cultures. Overall, this technology expanded avenues for thermal control in biotechnology applications.
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Affiliation(s)
- Wai Kit David Chee
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, 4 Engineering Drive 3, 117583 Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, 117456 Singapore
| | - Jing Wui Yeoh
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, 4 Engineering Drive 3, 117583 Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, 117456 Singapore
| | - Viet Linh Dao
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, 4 Engineering Drive 3, 117583 Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, 117456 Singapore
| | - Chueh Loo Poh
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, 4 Engineering Drive 3, 117583 Singapore
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, 117456 Singapore
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10
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Ronda C, Wang HH. Engineering temporal dynamics in microbial communities. Curr Opin Microbiol 2022; 65:47-55. [PMID: 34739926 PMCID: PMC10659046 DOI: 10.1016/j.mib.2021.10.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 09/05/2021] [Accepted: 10/08/2021] [Indexed: 12/20/2022]
Abstract
Microbial communities are a key part to tackling global challenges in human health, environmental conservation, and sustainable agriculture in the coming decade. Recent advances in synthetic biology to study and modify microbial communities have led to important insights into their physiology and ecology. Understanding how targeted changes to microbial communities result in reproducible alterations of the community's intrinsic fluctuations and function is important for mechanistic reconstruction of microbiomes. Studies of synthetic microbial consortia and comparative analysis of communities in normal and disrupted states have revealed ecological principles that can be leveraged to engineer communities towards desired functions. Tools enabling temporal modulation and sensing of the community dynamics offer precise spatiotemporal control of functions, help to dissect microbial interaction networks, and improve predictions of population temporal dynamics. Here we discuss recent advances to manipulate microbiome dynamics through control of specific strain engraftment and abundance, modulation of cell-cell signaling for tuning population dynamics, infiltration of new functions in the existing community with in situ engineering, and in silico modeling of microbial consortia to predict community function and ecology.
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Affiliation(s)
- Carlotta Ronda
- Department of Systems Biology, 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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Chee WKD, Yeoh JW, Dao VL, Poh CL. Thermogenetics: Applications come of age. Biotechnol Adv 2022; 55:107907. [PMID: 35041863 DOI: 10.1016/j.biotechadv.2022.107907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/13/2021] [Accepted: 01/09/2022] [Indexed: 12/20/2022]
Abstract
Temperature is a ubiquitous physical cue that is non-invasive, penetrative and easy to apply. In the growing field of thermogenetics, through beneficial repurposing of natural thermosensing mechanisms, synthetic biology is bringing new opportunities to design and build robust temperature-sensitive (TS) sensors which forms a thermogenetic toolbox of well characterised biological parts. Recent advancements in technological platforms available have expedited the discovery of novel or de novo thermosensors which are increasingly deployed in many practical temperature-dependent biomedical, industrial and biosafety applications. In all, the review aims to convey both the exhilarating recent technological developments underlying the advancement of thermosensors and the exciting opportunities the nascent thermogenetic field holds for biomedical and biotechnology applications.
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Affiliation(s)
- Wai Kit David Chee
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Jing Wui Yeoh
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Viet Linh Dao
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore
| | - Chueh Loo Poh
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 4 Engineering Drive 3, Singapore 117583, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Life Sciences Institute, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore.
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12
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Thermodynamic and structural basis of temperature-dependent gating in TRP channels. Biochem Soc Trans 2021; 49:2211-2219. [PMID: 34623379 DOI: 10.1042/bst20210301] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 09/16/2021] [Accepted: 09/21/2021] [Indexed: 11/17/2022]
Abstract
Living organisms require detecting the environmental thermal clues for survival, allowing them to avoid noxious stimuli or find prey moving in the dark. In mammals, the Transient Receptor Potential ion channels superfamily is constituted by 27 polymodal receptors whose activity is controlled by small ligands, peptide toxins, protons and voltage. The thermoTRP channels subgroup exhibits unparalleled temperature dependence -behaving as heat and cold sensors. Functional studies have dissected their biophysical features in detail, and the advances of single-particle Cryogenic Electron microscopy provided the structural framework required to propose detailed channel gating mechanisms. However, merging structural and functional evidence for temperature-driven gating of thermoTRP channels has been a hard nut to crack, remaining an open question nowadays. Here we revisit the highlights on the study of heat and cold sensing in thermoTRP channels in the light of the structural data that has emerged during recent years.
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13
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Stefanov B, Teixeira AP, Mansouri M, Bertschi A, Krawczyk K, Hamri GC, Xue S, Fussenegger M. Genetically Encoded Protein Thermometer Enables Precise Electrothermal Control of Transgene Expression. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2101813. [PMID: 34496151 PMCID: PMC8564464 DOI: 10.1002/advs.202101813] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/05/2021] [Indexed: 05/25/2023]
Abstract
Body temperature is maintained at around 37 °C in humans, but may rise to 40 °C or more during high-grade fever, which occurs in most adults who are seriously ill. However, endogenous temperature sensors, such as ion channels and heat-shock promoters, are fully activated only at noxious temperatures above this range, making them unsuitable for medical applications. Here, a genetically encoded protein thermometer (human enhanced gene activation thermometer; HEAT) is designed that can trigger transgene expression in the range of 37-40 °C by linking a mutant coiled-coil temperature-responsive protein sensor to a synthetic transcription factor. To validate the construct, a HEAT-transgenic monoclonal human cell line, FeverSense, is generated and it is confirmed that it works as a fever sensor that can temperature- and exposure-time-dependently trigger reporter gene expression in vitro and in vivo. For translational proof of concept, microencapsulated designer cells stably expressing a HEAT-controlled insulin production cassette in a mouse model of type-1 diabetes are subcutaneously implanted and topical heating patches are used to apply heat corresponding to a warm sensation in humans. Insulin release is induced, restoring normoglycemia. Thus, HEAT appears to be suitable for practical electrothermal control of cell-based therapy, and may also have potential for next-generation treatment of fever-associated medical conditions.
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Affiliation(s)
| | - Ana P. Teixeira
- ETH ZürichDepartment of Biosystems Science and EngineeringMattenstrasse 26Basel4058Switzerland
| | - Maysam Mansouri
- ETH ZürichDepartment of Biosystems Science and EngineeringMattenstrasse 26Basel4058Switzerland
| | - Adrian Bertschi
- ETH ZürichDepartment of Biosystems Science and EngineeringMattenstrasse 26Basel4058Switzerland
| | - Krzysztof Krawczyk
- ETH ZürichDepartment of Biosystems Science and EngineeringMattenstrasse 26Basel4058Switzerland
| | | | - Shuai Xue
- ETH ZürichDepartment of Biosystems Science and EngineeringMattenstrasse 26Basel4058Switzerland
| | - Martin Fussenegger
- ETH ZürichDepartment of Biosystems Science and EngineeringMattenstrasse 26Basel4058Switzerland
- University of BaselFaculty of Life ScienceBasel4056Switzerland
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14
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Vennettilli M, Saha S, Roy U, Mugler A. Precision of Protein Thermometry. PHYSICAL REVIEW LETTERS 2021; 127:098102. [PMID: 34506193 DOI: 10.1103/physrevlett.127.098102] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 08/06/2021] [Indexed: 05/23/2023]
Abstract
Temperature sensing is a ubiquitous cell behavior, but the fundamental limits to the precision of temperature sensing are poorly understood. Unlike in chemical concentration sensing, the precision of temperature sensing is not limited by extrinsic fluctuations in the temperature field itself. Instead, we find that precision is limited by the intrinsic copy number, turnover, and binding kinetics of temperature-sensitive proteins. Developing a model based on the canonical TlpA protein, we find that a cell can estimate temperature to within 2%. We compare this prediction with in vivo data on temperature sensing in bacteria.
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Affiliation(s)
- Michael Vennettilli
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907, USA
| | - Soutick Saha
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907, USA
| | - Ushasi Roy
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907, USA
- Centre for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Andrew Mugler
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47907, USA
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15
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Garabedian MV, Wang W, Dabdoub JB, Tong M, Caldwell RM, Benman W, Schuster BS, Deiters A, Good MC. Designer membraneless organelles sequester native factors for control of cell behavior. Nat Chem Biol 2021; 17:998-1007. [PMID: 34341589 PMCID: PMC8387445 DOI: 10.1038/s41589-021-00840-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 06/24/2021] [Indexed: 02/08/2023]
Abstract
Subcellular compartmentalization of macromolecules increases flux and prevents inhibitory interactions to control biochemical reactions. Inspired by this functionality, we sought to build designer compartments that function as hubs to regulate the flow of information through cellular control systems. We report a synthetic membraneless organelle platform to control endogenous cellular activities through sequestration and insulation of native proteins. We engineer and express a disordered protein scaffold to assemble micron size condensates and recruit endogenous clients via genomic tagging with high-affinity dimerization motifs. By relocalizing up to ninety percent of a targeted enzymes to synthetic condensates, we efficiently control cellular behaviors, including proliferation, division, and cytoskeletal organization. Further, we demonstrate multiple strategies for controlled cargo release from condensates to switch cells between functional states. These synthetic organelles offer a powerful and generalizable approach to modularly control cell decision-making in a variety of model systems with broad applications for cellular engineering.
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Affiliation(s)
- Mikael V Garabedian
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Wentao Wang
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Jorge B Dabdoub
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Michelle Tong
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Reese M Caldwell
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - William Benman
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin S Schuster
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Matthew C Good
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, USA. .,Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA.
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16
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Lacroix JJ. Dichotomy between heterotypic and homotypic interactions by a common chemical law. Phys Chem Chem Phys 2021; 23:17761-17765. [PMID: 34241615 DOI: 10.1039/d1cp02171k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
It is now well established that chemical systems evolve as a function of the frequency at which their individual chemical components interact. This notion is seemingly embedded into a ubiquitous chemical law which proposes that the rate of elementary chemical interactions is proportional to the Product of Interactant Concentrations (PIC) by a rate constant. Here, it is shown that, while the PIC is always proportional to the frequency at which interactants simultaneously collide (Interactant Collision Frequency, or ICF), the coefficient of proportionality between PIC and ICF diverges as a function of the number of identical interactants, a property hereby defined as "homo-molecularity". To eliminate the divergence between heterotypic and homotypic chemical interactions, the PIC must be divided by the factorial of homo-molecularity. Although this correction may not be practically essential for studies in which the homo-molecularity of chemical interactions is unchanged, it becomes critical when the goal is to compare interaction rates between similar chemical systems differing by their homo-molecularity, such as when interactants are purposefully modified for de novo design of heterotypic interactions, or when the goal is to compare theoretically-predicted rates of homotypic interactions with those that are empirically-determined by varying interactant concentrations.
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Affiliation(s)
- Jérôme J Lacroix
- Graduate College of Biomedical Sciences, Western University of Health Sciences, 309 E 2nd St, Pomona, CA 91709, USA.
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17
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Wang X, Han JN, Zhang X, Ma YY, Lin Y, Wang H, Li DJ, Zheng TR, Wu FQ, Ye JW, Chen GQ. Reversible thermal regulation for bifunctional dynamic control of gene expression in Escherichia coli. Nat Commun 2021; 12:1411. [PMID: 33658500 PMCID: PMC7930084 DOI: 10.1038/s41467-021-21654-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/03/2021] [Indexed: 11/08/2022] Open
Abstract
Genetically programmed circuits allowing bifunctional dynamic regulation of enzyme expression have far-reaching significances for various bio-manufactural purposes. However, building a bio-switch with a post log-phase response and reversibility during scale-up bioprocesses is still a challenge in metabolic engineering due to the lack of robustness. Here, we report a robust thermosensitive bio-switch that enables stringent bidirectional control of gene expression over time and levels in living cells. Based on the bio-switch, we obtain tree ring-like colonies with spatially distributed patterns and transformer cells shifting among spherical-, rod- and fiber-shapes of the engineered Escherichia coli. Moreover, fed-batch fermentations of recombinant E. coli are conducted to obtain ordered assembly of tailor-made biopolymers polyhydroxyalkanoates including diblock- and random-copolymer, composed of 3-hydroxybutyrate and 4-hydroxybutyrate with controllable monomer molar fraction. This study demonstrates the possibility of well-organized, chemosynthesis-like block polymerization on a molecular scale by reprogrammed microbes, exemplifying the versatility of thermo-response control for various practical uses.
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Affiliation(s)
- Xuan Wang
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Jia-Ning Han
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xu Zhang
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yue-Yuan Ma
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yina Lin
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Huan Wang
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Dian-Jie Li
- School of Physics, Peking University, Beijing, China
| | - Tao-Ran Zheng
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Fu-Qing Wu
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- MOE Key Lab of Industrial Biocatalysts, Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Jian-Wen Ye
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China.
- MOE Key Lab of Industrial Biocatalysts, Department of Chemical Engineering, Tsinghua University, Beijing, China.
- Center for Materials Synthetic Biology, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
| | - Guo-Qiang Chen
- Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
- MOE Key Lab of Industrial Biocatalysts, Department of Chemical Engineering, Tsinghua University, Beijing, China.
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18
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Ling B, Lee J, Maresca D, Lee-Gosselin A, Malounda D, Swift MB, Shapiro MG. Biomolecular Ultrasound Imaging of Phagolysosomal Function. ACS NANO 2020; 14:12210-12221. [PMID: 32902951 PMCID: PMC7685203 DOI: 10.1021/acsnano.0c05912] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Phagocytic clearance and lysosomal processing of pathogens and debris are essential functions of the innate immune system. However, the assessment of these functions in vivo is challenging because most nanoscale contrast agents compatible with noninvasive imaging techniques are made from nonbiodegradable synthetic materials that do not undergo regular lysosomal degradation. To overcome this challenge, we describe the use of an all-protein contrast agent to directly visualize and quantify phagocytic and lysosomal activities in vivo by ultrasound imaging. This contrast agent is based on gas vesicles (GVs), a class of air-filled protein nanostructures naturally expressed by buoyant microbes. Using a combination of ultrasound imaging, pharmacology, immunohistology, and live-cell optical microscopy, we show that after intravenous injection, GVs are cleared from circulation by liver-resident macrophages. Once internalized, the GVs undergo lysosomal degradation, resulting in the elimination of their ultrasound contrast. By noninvasively monitoring the temporal dynamics of GV-generated ultrasound signal in circulation and in the liver and fitting them with a pharmacokinetic model, we can quantify the rates of phagocytosis and lysosomal degradation in living animals. We demonstrate the utility of this method by showing how these rates are perturbed in two models of liver dysfunction: phagocyte deficiency and nonalcoholic fatty liver disease. The combination of proteolytically degradable nanoscale contrast agents and quantitative ultrasound imaging thus enables noninvasive functional imaging of cellular degradative processes.
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Affiliation(s)
- Bill Ling
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, 91125, United States
| | - Justin Lee
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, California, 91125, United States
| | - David Maresca
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, 91125, United States
| | - Audrey Lee-Gosselin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, 91125, United States
| | - Dina Malounda
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, 91125, United States
| | - Margaret B. Swift
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, 91125, United States
| | - Mikhail G. Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, 91125, United States
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19
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Abstract
Genetically engineered T-cells are being developed to perform a variety of therapeutic functions. However, no robust mechanisms exist to externally control the activity of T-cells at specific locations within the body. Such spatiotemporal control could help mitigate potential off-target toxicity due to incomplete molecular specificity in applications such as T-cell immunotherapy against solid tumors. Temperature is a versatile external control signal that can be delivered to target tissues in vivo using techniques such as focused ultrasound and magnetic hyperthermia. Here, we test the ability of heat shock promoters to mediate thermal actuation of genetic circuits in primary human T-cells in the well-tolerated temperature range of 37-42 °C, and introduce genetic architectures enabling the tuning of the amplitude and duration of thermal activation. We demonstrate the use of these circuits to control the expression of chimeric antigen receptors and cytokines, and the killing of target tumor cells. This technology provides a critical tool to direct the activity of T-cells after they are deployed inside the body.
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20
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A folding reaction at the C-terminal domain drives temperature sensing in TRPM8 channels. Proc Natl Acad Sci U S A 2020; 117:20298-20304. [PMID: 32747539 DOI: 10.1073/pnas.2004303117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In mammals, temperature-sensitive TRP channels make membrane conductance of cells extremely temperature dependent, allowing the detection of temperature ranging from noxious cold to noxious heat. We progressively deleted the distal carboxyl terminus domain (CTD) of the cold-activated melastatin receptor channel, TRPM8. We found that the enthalpy change associated with channel gating is proportional to the length of the CTD. Deletion of the last 36 amino acids of the CTD transforms TRPM8 into a reduced temperature-sensitivity channel (Q10 ∼4). Exposing the intracellular domain to a denaturing agent increases the energy required to open the channel indicating that cold drives channel gating by stabilizing the folded state of the CTD. Experiments in the presence of an osmoticant agent suggest that channel gating involves a change in solute-inaccessible volume in the CTD of ∼1,900 Å3 This volume matches the void space inside the coiled coil according to the cryogenic electron microscopy structure of TRPM8. The results indicate that a folding-unfolding reaction of a specialized temperature-sensitive structure is coupled to TRPM8 gating.
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