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Caliari A, Hanczyc MM, Imai M, Xu J, Yomo T. Quantification of Giant Unilamellar Vesicle Fusion Products by High-Throughput Image Analysis. Int J Mol Sci 2023; 24:ijms24098241. [PMID: 37175944 PMCID: PMC10179211 DOI: 10.3390/ijms24098241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/29/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
Artificial cells are based on dynamic compartmentalized systems. Thus, remodeling of membrane-bound systems, such as giant unilamellar vesicles, is finding applications beyond biological studies, to engineer cell-mimicking structures. Giant unilamellar vesicle fusion is rapidly becoming an essential experimental step as artificial cells gain prominence in synthetic biology. Several techniques have been developed to accomplish this step, with varying efficiency and selectivity. To date, characterization of vesicle fusion has relied on small samples of giant vesicles, examined either manually or by fluorometric assays on suspensions of small and large unilamellar vesicles. Automation of the detection and characterization of fusion products is now necessary for the screening and optimization of these fusion protocols. To this end, we implemented a fusion assay based on fluorophore colocalization on the membranes and in the lumen of vesicles. Fluorescence colocalization was evaluated within single compartments by image segmentation with minimal user input, allowing the application of the technique to high-throughput screenings. After detection, statistical information on vesicle fluorescence and morphological properties can be summarized and visualized, assessing lipid and content transfer for each object by the correlation coefficient of different fluorescence channels. Using this tool, we report and characterize the unexpected fusogenic activity of sodium chloride on phosphatidylcholine giant vesicles. Lipid transfer in most of the vesicles could be detected after 20 h of incubation, while content exchange only occurred with additional stimuli in around 8% of vesicles.
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Affiliation(s)
- Adriano Caliari
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, China
- Laboratory for Artificial Biology, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Polo Scientifico e Tecnologico Fabio Ferrari, Polo B, Via Sommarive 9, 38123 Povo, Italy
| | - Martin M Hanczyc
- Laboratory for Artificial Biology, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Polo Scientifico e Tecnologico Fabio Ferrari, Polo B, Via Sommarive 9, 38123 Povo, Italy
| | - Masayuki Imai
- Department of Physics, Graduate School of Science, Tohoku University, 6-3 Aramaki, Aoba, Sendai 980-8578, Japan
| | - Jian Xu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, China
| | - Tetsuya Yomo
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, China
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2
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Herianto S, Chien PJ, Ho JAA, Tu HL. Liposome-based artificial cells: From gene expression to reconstitution of cellular functions and phenotypes. BIOMATERIALS ADVANCES 2022; 142:213156. [PMID: 36302330 DOI: 10.1016/j.bioadv.2022.213156] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Bottom-up approaches in creating artificial cells that can mimic natural cells have significant implications for both basic research and translational application. Among various artificial cell models, liposome is one of the most sophisticated systems. By encapsulating proteins and associated biomolecules, they can functionally reconstitute foundational features of biological cells, such as the ability to divide, communicate, and undergo shape deformation. Yet constructing liposome artificial cells from the genetic level, which is central to generate self-sustained systems remains highly challenging. Indeed, many studies have successfully established the expression of gene-coded proteins inside liposomes. Further, recent endeavors to build a direct integration of gene-expressed proteins for reconstituting molecular functions and phenotypes in liposomes have also significantly increased. Thus, this review presents the development of liposome-based artificial cells to demonstrate the process of gene-expressed proteins and their reconstitution to perform desired molecular and cell-like functions. The molecular and cellular phenotypes discussed here include the self-production of membrane phospholipids, division, shape deformation, self-DNA/RNA replication, fusion, and intercellular communication. Together, this review gives a comprehensive overview of gene-expressing liposomes that can stimulate further research of this technology and achieve artificial cells with superior properties in the future.
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Affiliation(s)
- Samuel Herianto
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan; Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan; Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Po-Jen Chien
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Ja-An Annie Ho
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan; BioAnalytical Chemistry and Nanobiomedicine Laboratory, Department of Biochemical Science and Technology, National Taiwan University, Taipei 10617, Taiwan
| | - Hsiung-Lin Tu
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan; Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan.
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3
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Paez-Perez M, Russell IA, Cicuta P, Di Michele L. Modulating membrane fusion through the design of fusogenic DNA circuits and bilayer composition. SOFT MATTER 2022; 18:7035-7044. [PMID: 36000473 PMCID: PMC9516350 DOI: 10.1039/d2sm00863g] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Membrane fusion is a ubiquitous phenomenon linked to many biological processes, and represents a crucial step in liposome-based drug delivery strategies. The ability to control, ever more precisely, membrane fusion pathways would thus be highly valuable for next generation nano-medical solutions and, more generally, the design of advanced biomimetic systems such as synthetic cells. In this article, we present fusogenic nanostructures constructed from synthetic DNA which, different from previous solutions, unlock routes for modulating the rate of fusion and making it conditional to the presence of soluble DNA molecules, thus demonstrating how membrane fusion can be controlled through simple DNA-based molecular circuits. We then systematically explore the relationship between lipid-membrane composition, its biophysical properties, and measured fusion efficiency, linking our observations to the stability of transition states in the fusion pathway. Finally, we observe that specific lipid compositions lead to the emergence of complex bilayer architectures in the fusion products, such as nested morphologies, which are accompanied by alterations in biophysical behaviour. Our findings provide multiple, orthogonal strategies to program lipid-membrane fusion, which leverage the design of either the fusogenic DNA constructs or the physico/chemical properties of the membranes, and could thus be valuable in applications where some design parameters are constrained by other factors such as material cost and biocompatibility, as it is often the case in biotechnological applications.
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Affiliation(s)
- Miguel Paez-Perez
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, Wood Lane, London, W12 0BZ, UK.
- fabriCELL, Imperial College London, Wood Lane, London, W12 0BZ, UK
| | - I Alasdair Russell
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, UK
| | - Pietro Cicuta
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK.
| | - Lorenzo Di Michele
- Molecular Sciences Research Hub, Department of Chemistry, Imperial College London, Wood Lane, London, W12 0BZ, UK.
- fabriCELL, Imperial College London, Wood Lane, London, W12 0BZ, UK
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, UK.
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4
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Xu B, Ding J, Caliari A, Lu N, Han F, Xia Y, Xu J, Yomo T. Photoinducible Azobenzene trimethylammonium bromide (AzoTAB)-mediated giant vesicle fusion compatible with synthetic protein translation reactions. Biochem Biophys Res Commun 2022; 618:113-118. [PMID: 35717905 DOI: 10.1016/j.bbrc.2022.06.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/21/2022] [Accepted: 06/10/2022] [Indexed: 11/18/2022]
Abstract
Lipid giant vesicles represent a versatile minimal model system to study the physicochemical basis of lipid membrane fusion. Membrane fusion processes are also of interest in synthetic cell research, where cell-mimicking behavior often requires dynamically interacting compartments. For these applications, triggered fusion compatible with transcription-translation systems is key in achieving complexity. Recently, a photosensitive surfactant, azobenzene trimethylammonium bromide (AzoTAB), has been reported to induce membrane fusion by a photoinduced conformational change. Using imaging flow cytometer (IFC) and confocal microscopy we quantitatively investigated photoinduced AzoTAB-mediated fusion of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine vesicles. The IFC analysis result showed that the fusion rate could reach about 40% following AzoTAB addition and UV irradiation in optimized conditions. We confirmed the compatibility between AzoTAB-induced vesicle fusion and a synthetic cell-free protein translation system using green fluorescent protein as reporter. With the techniques presented, cell-sized vesicle fusion can be quantitatively analyzed and optimized, paving the way to controllable synthetic cells with fundamental biological functions like the ability to express proteins from encapsulated plasmids.
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Affiliation(s)
- Boying Xu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai, 200062, PR China; Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, PR China
| | - Jinquan Ding
- School of Software Engineering, East China Normal University, Shanghai, 200062, PR China
| | - Adriano Caliari
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai, 200062, PR China
| | - Nan Lu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai, 200062, PR China
| | - Fuhai Han
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai, 200062, PR China
| | - Yang Xia
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai, 200062, PR China
| | - Jian Xu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai, 200062, PR China.
| | - Tetsuya Yomo
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai, 200062, PR China.
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5
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Zhao J, Zhang Y, Zhang X, Li C, Du H, Sønderskov SM, Mu W, Dong M, Han X. Mimicking Cellular Metabolism in Artificial Cells: Universal Molecule Transport across the Membrane through Vesicle Fusion. Anal Chem 2022; 94:3811-3818. [PMID: 35189059 DOI: 10.1021/acs.analchem.1c04696] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Mass transport across cell membranes is a primary process for cellular metabolism. For this purpose, electrostatically mediated membrane fusion is exploited to transport various small molecules including glucose-6-phosphate, isopropyl β-D-thiogalactoside, and macromolecules such as DNA plasmids from negatively charged large unilamellar vesicles (LUVs) to positively charged giant unilamellar vesicles (GUVs). After membrane fusion between these oppositely charged vesicles, molecules are transported into GUVs to trigger the NAD+ involved enzyme reaction, bacterial gene expression, and in vitro gene expression of green fluorescent protein from a DNA plasmid. The optimized charged lipid percentages are 10% for both positively charged GUVs and negatively charged LUVs to ensure the fusion process. The experimental results demonstrate a universal way for mass transport into the artificial cells through vesicle fusions, which paves a crucial step for the investigation of complicated cellular metabolism.
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Affiliation(s)
- Jingjing Zhao
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin 150001, China
| | - Ying Zhang
- College of Materials and Chemical Engineering, Heilongjiang Institute of Technology, 999 Hongqi Street, Harbin 150050, China
| | - Xiangxiang Zhang
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin 150001, China
| | - Chao Li
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin 150001, China
| | - Hang Du
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin 150001, China
| | | | - Wei Mu
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin 150001, China
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus DK-8000, Denmark
| | - Xiaojun Han
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin 150001, China
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6
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Gaut NJ, Gomez-Garcia J, Heili JM, Cash B, Han Q, Engelhart AE, Adamala KP. Programmable Fusion and Differentiation of Synthetic Minimal Cells. ACS Synth Biol 2022; 11:855-866. [PMID: 35089706 DOI: 10.1021/acssynbio.1c00519] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Synthetic cells can mimic the intricate complexities of live cells, while mitigating the level of noise that is present natural systems; however, many crucial processes still need to be demonstrated in synthetic cells to use them to comprehensively study and engineer biology. Here we demonstrate key functionalities of synthetic cells previously available only to natural life: differentiation and mating. This work presents a toolset for engineering combinatorial genetic circuits in synthetic cells. We demonstrate how progenitor populations can differentiate into new lineages in response to small molecule stimuli or as a result of fusion, and we provide practical demonstration of utility for metabolic engineering. This work provides a tool for bioengineering and for natural pathway studies, as well as paving the way toward the construction of live artificial cells.
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Affiliation(s)
- Nathaniel J. Gaut
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55407 United States
| | - Jose Gomez-Garcia
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55407 United States
| | - Joseph M. Heili
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55407 United States
| | - Brock Cash
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55407 United States
| | - Qiyuan Han
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55407 United States
| | - Aaron E. Engelhart
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55407 United States
| | - Katarzyna P. Adamala
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55407 United States
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7
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Uwaguchi Y, Fujiwara K, Doi N. Switching ON of Transcription-Translation System Using GUV Fusion by Co-supplementation of Calcium with Long-Chain Polyethylene Glycol. Chembiochem 2021; 22:2319-2324. [PMID: 33971077 DOI: 10.1002/cbic.202100100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/28/2021] [Indexed: 11/09/2022]
Abstract
Giant unilamellar vesicles (GUVs) have been used as a material for bottom-up synthetic biology. However, due to the semi-permeability of the membrane, the need for methods to fuse GUVs has increased. To this aim, methods that are simple and show low leakage during fusion are important. In this study, we report a method of GUV fusion by a divalent cation (Ca2+ ) enhanced with a long chain polyethylene glycol (PEG20k). The methods showed significant GUV fusion without leakage of internal components of GUVs and maintained cell-free transcription-translation ability inside the GUVs without external supplementation of macromolecules. We demonstrate that the Ca-PEG method can be applied for switching ON of transcription-translation in GUVs in a fusion-dependent manner. The method developed here can be applied to extend bottom-up synthetic biology and molecular robotics that use GUVs as a chassis.
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Affiliation(s)
- Yusuke Uwaguchi
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
| | - Kei Fujiwara
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
| | - Nobuhide Doi
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
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8
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Cho E, Lu Y. Compartmentalizing Cell-Free Systems: Toward Creating Life-Like Artificial Cells and Beyond. ACS Synth Biol 2020; 9:2881-2901. [PMID: 33095011 DOI: 10.1021/acssynbio.0c00433] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Building an artificial cell is a research area that is rigorously studied in the field of synthetic biology. It has brought about much attention with the aim of ultimately constructing a natural cell-like structure. In particular, with the more mature cell-free platforms and various compartmentalization methods becoming available, achieving this aim seems not far away. In this review, we discuss the various types of artificial cells capable of hosting several cellular functions. Different compartmental boundaries and the mature and evolving technologies that are used for compartmentalization are examined, and exciting recent advances that overcome or have the potential to address current challenges are discussed. Ultimately, we show how compartmentalization and cell-free systems have, and will, come together to fulfill the goal to assemble a fully synthetic cell that displays functionality and complexity as advanced as that in nature. The development of such artificial cell systems will offer insight into the fundamental study of evolutionary biology and the sea of applications as a result. Although several challenges remain, emerging technologies such as artificial intelligence also appear to help pave the way to address them and achieve the ultimate goal.
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Affiliation(s)
- Eunhee Cho
- Key Lab of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Yuan Lu
- Key Lab of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
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9
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Fusing Artificial Cell Compartments and Lipid Domains Using Optical Traps: A Tool to Modulate Membrane Composition and Phase Behaviour. MICROMACHINES 2020; 11:mi11040388. [PMID: 32272670 PMCID: PMC7230983 DOI: 10.3390/mi11040388] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/25/2020] [Accepted: 03/28/2020] [Indexed: 01/26/2023]
Abstract
New technologies for manipulating biomembranes have vast potential to aid the understanding of biological phenomena, and as tools to sculpt novel artificial cell architectures for synthetic biology. The manipulation and fusion of vesicles using optical traps is amongst the most promising due to the level of spatiotemporal control it affords. Herein, we conduct a suite of feasibility studies to show the potential of optical trapping technologies to (i) modulate the lipid composition of a vesicle by delivering new membrane material through fusion events and (ii) manipulate and controllably fuse coexisting membrane domains for the first time. We also outline some noteworthy morphologies and transitions that the vesicle undergoes during fusion, which gives us insight into the mechanisms at play. These results will guide future exploitation of laser-assisted membrane manipulation methods and feed into a technology roadmap for this emerging technology.
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10
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A protocell with fusion and division. Biochem Soc Trans 2019; 47:1909-1919. [PMID: 31819942 DOI: 10.1042/bst20190576] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/12/2019] [Accepted: 11/25/2019] [Indexed: 11/17/2022]
Abstract
A protocell is a synthetic form of cellular life that is constructed from phospholipid vesicles and used to understand the emergence of life from a nonliving chemical network. To be considered 'living', a protocell should be capable of self-proliferation, which includes successive growth and division processes. The growth of protocells can be achieved via vesicle fusion approaches. In this review, we provide a brief overview of recent research on the formation of a protocell, fusion and division processes of the protocell, and encapsulation of a defined chemical network such as the genetic material. We also provide some perspectives on the challenges and future developments of synthetic protocell research.
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11
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Peruzzi JA, Jacobs ML, Vu TQ, Wang KS, Kamat NP. Barcoding Biological Reactions with DNA-Functionalized Vesicles. Angew Chem Int Ed Engl 2019; 58:18683-18690. [PMID: 31596992 PMCID: PMC6901749 DOI: 10.1002/anie.201911544] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Indexed: 11/08/2022]
Abstract
Targeted vesicle fusion is a promising approach to selectively control interactions between vesicle compartments and would enable the initiation of biological reactions in complex aqueous environments. Here, we explore how two features of vesicle membranes, DNA tethers and phase-segregated membranes, promote fusion between specific vesicle populations. Membrane phase-segregation provides an energetic driver for membrane fusion that increases the efficiency of DNA-mediated fusion events. The orthogonality provided by DNA tethers allows us to direct fusion and delivery of DNA cargo to specific vesicle populations. Vesicle fusion between DNA-tethered vesicles can be used to initiate in vitro protein expression to produce model soluble and membrane proteins. Engineering orthogonal fusion events between DNA-tethered vesicles provides a new strategy to control the spatiotemporal dynamics of cell-free reactions, expanding opportunities to engineer artificial cellular systems.
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Affiliation(s)
- Justin A Peruzzi
- Department of Chemical and Biological Engineering, Northwestern University, USA
| | - Miranda L Jacobs
- Department of Biomedical Engineering, Northwestern University, McCormick School of Engineering, Technological Institute, 2145 Sheridan Road, Evanston, Il, 60208, USA
| | - Timothy Q Vu
- Department of Biomedical Engineering, Northwestern University, McCormick School of Engineering, Technological Institute, 2145 Sheridan Road, Evanston, Il, 60208, USA
| | - Kenneth S Wang
- Department of Biomedical Engineering, Northwestern University, McCormick School of Engineering, Technological Institute, 2145 Sheridan Road, Evanston, Il, 60208, USA
| | - Neha P Kamat
- Department of Biomedical Engineering, Northwestern University, McCormick School of Engineering, Technological Institute, 2145 Sheridan Road, Evanston, Il, 60208, USA
- Center for Synthetic Biology, Northwestern University, USA
- Chemistry of Life Processes Institute, Northwestern University, USA
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12
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Peruzzi JA, Jacobs ML, Vu TQ, Wang KS, Kamat NP. Barcoding Biological Reactions with DNA‐Functionalized Vesicles. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201911544] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Justin A. Peruzzi
- Department of Chemical and Biological Engineering Northwestern University USA
| | - Miranda L. Jacobs
- Department of Biomedical Engineering Northwestern University McCormick School of Engineering Technological Institute 2145 Sheridan Road Evanston Il 60208 USA
| | - Timothy Q. Vu
- Department of Biomedical Engineering Northwestern University McCormick School of Engineering Technological Institute 2145 Sheridan Road Evanston Il 60208 USA
| | - Kenneth S. Wang
- Department of Biomedical Engineering Northwestern University McCormick School of Engineering Technological Institute 2145 Sheridan Road Evanston Il 60208 USA
| | - Neha P. Kamat
- Department of Biomedical Engineering Northwestern University McCormick School of Engineering Technological Institute 2145 Sheridan Road Evanston Il 60208 USA
- Center for Synthetic Biology Northwestern University USA
- Chemistry of Life Processes Institute Northwestern University USA
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13
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Katsuta S, Okano T, Koiwai K, Suzuki H. Ejection of Large Particulate Materials from Giant Unilamellar Vesicles Induced by Electropulsation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:13196-13204. [PMID: 31498647 DOI: 10.1021/acs.langmuir.9b01617] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Electroporation or electropermealization is a technique to open pores in the lipid bilayer membrane of cells and vesicles transiently to increase its permeability to otherwise impermeable molecules. However, the upper size limit of the materials permeable through this operation has not been studied in the past. Here, we investigate the size of the material that can be released (ejected) from giant unilamellar vesicles (GUVs) upon electrical pulsation. We confirm that the volume of GUV shrinks in a stepwise manner upon periodical pulsation, in accordance with previous studies. When the same operation is applied to GUVs that encapsulate microbeads, we find that beads as large as 20 μm can be ejected across the membrane without rupturing the whole GUV structure. We also demonstrate that functional bioactive particulate materials, such as gel balls, vesicles, and cells can be encapsulated in and ejected from GUVs. We foresee that this phenomenon can be applied to precisely regulate the time and location of release of these particulate materials in the microenvironment.
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Affiliation(s)
- Shota Katsuta
- Dept. Precision Mechanics, Faculty of Science and Engineering , Chuo University , 1-13-27 Kasuga , Bunkyo-ku , Tokyo 112-8551 , Japan
| | - Taiji Okano
- Dept. Precision Mechanics, Faculty of Science and Engineering , Chuo University , 1-13-27 Kasuga , Bunkyo-ku , Tokyo 112-8551 , Japan
| | - Keiichiro Koiwai
- Dept. Precision Mechanics, Faculty of Science and Engineering , Chuo University , 1-13-27 Kasuga , Bunkyo-ku , Tokyo 112-8551 , Japan
- Japan Society for the Promotion of Science (JSPS) , 5-3-1 Kojimachi , Chiyoda-ku , Tokyo 102-0083 , Japan
| | - Hiroaki Suzuki
- Dept. Precision Mechanics, Faculty of Science and Engineering , Chuo University , 1-13-27 Kasuga , Bunkyo-ku , Tokyo 112-8551 , Japan
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14
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Affiliation(s)
- Kilian Vogele
- Physik-DepartmentTechnische Universitat Munchen, TU München Garching Germany
| | - Tobias Pirzer
- Physik-DepartmentTechnische Universitat Munchen, TU München Garching Germany
| | - Friedrich C. Simmel
- Physik-DepartmentTechnische Universitat Munchen, TU München Garching Germany
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15
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Ivanov I, Lira RB, Tang TYD, Franzmann T, Klosin A, da Silva LC, Hyman A, Landfester K, Lipowsky R, Sundmacher K, Dimova R. Directed Growth of Biomimetic Microcompartments. ACTA ACUST UNITED AC 2019; 3:e1800314. [PMID: 32648704 DOI: 10.1002/adbi.201800314] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/15/2019] [Indexed: 01/04/2023]
Abstract
Contemporary biological cells are sophisticated and highly compartmentalized. Compartmentalization is an essential principle of prebiotic life as well as a key feature in bottom-up synthetic biology research. In this review, the dynamic growth of compartments as an essential prerequisite for enabling self-reproduction as a fundamental life process is discussed. The micrometer-sized compartments are focused on due to their cellular dimensions. Two types of compartments are considered, membraneless droplets and membrane-bound microcompartments. Growth mechanisms of aqueous droplets such as protein (condensates) or macromolecule-rich droplets (aqueous two phase systems) and coacervates are discussed, for which growth occurs via Ostwald ripening or coalescence. For membrane-bound compartments, vesicles are considered, which are composed of fatty acids, lipids, or polymers, where directed growth can occur via fusion or uptake of material from the surrounding. The development of novel approaches for growth of biomimetic microcompartments can eventually be utilized to construct new synthetic cells.
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Affiliation(s)
- Ivan Ivanov
- Max Planck Institute for Dynamics of Complex Technical Systems, Process Systems Engineering, Sandtorstrasse 1, 39106, Magdeburg, Germany
| | - Rafael B Lira
- Max Planck Institute of Colloids and Interfaces, Theory and Bio-Systems, Science Park Golm, 14424, Potsdam, Germany
| | - T-Y Dora Tang
- Max Planck Institute of Molecular Cell Biology and Genetics, Organization of Cytoplasm & Dynamic Protocellular Systems, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Titus Franzmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Organization of Cytoplasm & Dynamic Protocellular Systems, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Adam Klosin
- Max Planck Institute of Molecular Cell Biology and Genetics, Organization of Cytoplasm & Dynamic Protocellular Systems, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Lucas Caire da Silva
- Max Planck Institute for Polymer Research, Physical Chemistry of Polymers, Ackermannweg 10, 55128, Mainz, Germany
| | - Anthony Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Organization of Cytoplasm & Dynamic Protocellular Systems, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Katharina Landfester
- Max Planck Institute for Polymer Research, Physical Chemistry of Polymers, Ackermannweg 10, 55128, Mainz, Germany
| | - Reinhard Lipowsky
- Max Planck Institute of Colloids and Interfaces, Theory and Bio-Systems, Science Park Golm, 14424, Potsdam, Germany
| | - Kai Sundmacher
- Max Planck Institute for Dynamics of Complex Technical Systems, Process Systems Engineering, Sandtorstrasse 1, 39106, Magdeburg, Germany
| | - Rumiana Dimova
- Max Planck Institute of Colloids and Interfaces, Theory and Bio-Systems, Science Park Golm, 14424, Potsdam, Germany
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16
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Uda RM, Yoshikawa Y, Kitaba M, Nishimoto N. Irradiation-induced fusion between giant vesicles and photoresponsive large unilamellar vesicles containing malachite green derivative. Colloids Surf B Biointerfaces 2018; 167:544-549. [DOI: 10.1016/j.colsurfb.2018.04.061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 03/22/2018] [Accepted: 04/29/2018] [Indexed: 10/17/2022]
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17
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Progress in programming spatiotemporal patterns and machine-assembly in cell-free protein expression systems. Curr Opin Chem Biol 2017. [DOI: 10.1016/j.cbpa.2017.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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18
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Caschera F. Bacterial cell-free expression technology to in vitro systems engineering and optimization. Synth Syst Biotechnol 2017; 2:97-104. [PMID: 29062966 PMCID: PMC5637228 DOI: 10.1016/j.synbio.2017.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 07/25/2017] [Accepted: 07/25/2017] [Indexed: 12/26/2022] Open
Abstract
Cell-free expression system is a technology for the synthesis of proteins in vitro. The system is a platform for several bioengineering projects, e.g. cell-free metabolic engineering, evolutionary design of experiments, and synthetic minimal cell construction. Bacterial cell-free protein synthesis system (CFPS) is a robust tool for synthetic biology. The bacteria lysate, the DNA, and the energy module, which are the three optimized sub-systems for in vitro protein synthesis, compose the integrated system. Currently, an optimized E. coli cell-free expression system can produce up to ∼2.3 mg/mL of a fluorescent reporter protein. Herein, I will describe the features of ATP-regeneration systems for in vitro protein synthesis, and I will present a machine-learning experiment for optimizing the protein yield of E. coli cell-free protein synthesis systems. Moreover, I will introduce experiments on the synthesis of a minimal cell using liposomes as dynamic containers, and E. coli cell-free expression system as biochemical platform for metabolism and gene expression. CFPS can be further integrated with other technologies for novel applications in environmental, medical and material science.
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19
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Adamala KP, Martin-Alarcon DA, Guthrie-Honea KR, Boyden ES. Engineering genetic circuit interactions within and between synthetic minimal cells. Nat Chem 2017; 9:431-439. [PMID: 28430194 PMCID: PMC5407321 DOI: 10.1038/nchem.2644] [Citation(s) in RCA: 219] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 09/12/2016] [Indexed: 12/14/2022]
Abstract
Genetic circuits and reaction cascades are of great importance for synthetic biology, biochemistry and bioengineering. An open question is how to maximize the modularity of their design to enable the integration of different reaction networks and to optimize their scalability and flexibility. One option is encapsulation within liposomes, which enables chemical reactions to proceed in well-isolated environments. Here we adapt liposome encapsulation to enable the modular, controlled compartmentalization of genetic circuits and cascades. We demonstrate that it is possible to engineer genetic circuit-containing synthetic minimal cells (synells) to contain multiple-part genetic cascades, and that these cascades can be controlled by external signals as well as inter-liposomal communication without crosstalk. We also show that liposomes that contain different cascades can be fused in a controlled way so that the products of incompatible reactions can be brought together. Synells thus enable a more modular creation of synthetic biology cascades, an essential step towards their ultimate programmability.
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Affiliation(s)
| | - Daniel A. Martin-Alarcon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | | | - Edward S. Boyden
- Media Lab, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
- McGovern Institute for Brain Research, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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20
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Bhaskara RM, Linker SM, Vögele M, Köfinger J, Hummer G. Carbon Nanotubes Mediate Fusion of Lipid Vesicles. ACS NANO 2017; 11:1273-1280. [PMID: 28103440 DOI: 10.1021/acsnano.6b05434] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The fusion of lipid membranes is opposed by high energetic barriers. In living organisms, complex protein machineries carry out this biologically essential process. Here we show that membrane-spanning carbon nanotubes (CNTs) can trigger spontaneous fusion of small lipid vesicles. In coarse-grained molecular dynamics simulations, we find that a CNT bridging between two vesicles locally perturbs their lipid structure. Their outer leaflets merge as the CNT pulls lipids out of the membranes, creating an hourglass-shaped fusion intermediate with still intact inner leaflets. As the CNT moves away from the symmetry axis connecting the vesicle centers, the inner leaflets merge, forming a pore that completes fusion. The distinct mechanism of CNT-mediated membrane fusion may be transferable, providing guidance in the development of fusion agents, e.g., for the targeted delivery of drugs or nucleic acids.
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Affiliation(s)
- Ramachandra M Bhaskara
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Stephanie M Linker
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Martin Vögele
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Jürgen Köfinger
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany
- Institute for Biophysics, Goethe University Frankfurt , 60438 Frankfurt am Main, Germany
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21
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de Souza TP, Bossa GV, Stano P, Steiniger F, May S, Luisi PL, Fahr A. Vesicle aggregates as a model for primitive cellular assemblies. Phys Chem Chem Phys 2017; 19:20082-20092. [DOI: 10.1039/c7cp03751a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Primitive cell models help to understand the role that compartmentalization plays in origin of life scenarios.
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Affiliation(s)
- Tereza Pereira de Souza
- Institut für Pharmazie
- Friedrich Schiller Universität Jena
- Lessingstrasse 8
- D-07743 Jena
- Germany
| | | | - Pasquale Stano
- Science Department
- Roma Tre University
- Viale G. Marconi 446
- I-00146 Rome
- Italy
| | - Frank Steiniger
- Elektronenmikroskopisches Zentrum
- Friedrich Schiller Universität Jena
- D-07743 Jena
- Germany
| | - Sylvio May
- Department of Physics
- North Dakota State University
- Fargo North Dakota 58108-6050
- USA
| | - Pier Luigi Luisi
- Science Department
- Roma Tre University
- Viale G. Marconi 446
- I-00146 Rome
- Italy
| | - Alfred Fahr
- Institut für Pharmazie
- Friedrich Schiller Universität Jena
- Lessingstrasse 8
- D-07743 Jena
- Germany
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22
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Caschera F, Lee JW, Ho KKY, Liu AP, Jewett MC. Cell-free compartmentalized protein synthesis inside double emulsion templated liposomes with in vitro synthesized and assembled ribosomes. Chem Commun (Camb) 2016; 52:5467-9. [PMID: 27019994 DOI: 10.1039/c6cc00223d] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A cell-free expression platform for making bacterial ribosomes encapsulated within giant liposomes was capable of synthesizing sfGFP. The liposomes were prepared using a double emulsion template, and compartmentalized in vitro protein synthesis was analysed using spinning disk confocal microscopy. Two different liposome phospholipid formulations were investigated to characterize their effects on the compartmentalized reaction kinetics. This study was performed as a necessary step towards the synthesis of minimal cells.
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Affiliation(s)
- Filippo Caschera
- Department of Chemical and Biochemical Engineering, Chemistry of Life Processes Institute, Simpson Querrey Institute for BioNanotechnology, Northwestern University, Evanston, 60208, Illinois, USA.
| | - Jin Woo Lee
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, 48109, Michigan, USA.
| | - Kenneth K Y Ho
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, 48109, Michigan, USA.
| | - Allen P Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, 48109, Michigan, USA.
| | - Michael C Jewett
- Department of Chemical and Biochemical Engineering, Chemistry of Life Processes Institute, Simpson Querrey Institute for BioNanotechnology, Northwestern University, Evanston, 60208, Illinois, USA.
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23
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Sunami T, Ichihashi N, Nishikawa T, Kazuta Y, Yomo T. Effect of Liposome Size on Internal RNA Replication Coupled with Replicase Translation. Chembiochem 2016; 17:1282-9. [DOI: 10.1002/cbic.201500662] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Takeshi Sunami
- Institute for Academic Initiatives; Osaka University; 1-5 Yamadaoka Suita Osaka 565-0871 Japan
- Exploratory Research for Advanced Technology (ERATO); Japan Science and Technology Agency (JST); 1-5 Yamadaoka Suita Osaka 565-0871 Japan
| | - Norikazu Ichihashi
- Exploratory Research for Advanced Technology (ERATO); Japan Science and Technology Agency (JST); 1-5 Yamadaoka Suita Osaka 565-0871 Japan
- Department of Bioinformatics Engineering; Graduate School of Information Science and Technology; Osaka University; 1-5 Yamadaoka Suita Osaka 565-0871 Japan
| | - Takehiro Nishikawa
- Exploratory Research for Advanced Technology (ERATO); Japan Science and Technology Agency (JST); 1-5 Yamadaoka Suita Osaka 565-0871 Japan
| | - Yasuaki Kazuta
- Exploratory Research for Advanced Technology (ERATO); Japan Science and Technology Agency (JST); 1-5 Yamadaoka Suita Osaka 565-0871 Japan
| | - Tetsuya Yomo
- Exploratory Research for Advanced Technology (ERATO); Japan Science and Technology Agency (JST); 1-5 Yamadaoka Suita Osaka 565-0871 Japan
- Department of Bioinformatics Engineering; Graduate School of Information Science and Technology; Osaka University; 1-5 Yamadaoka Suita Osaka 565-0871 Japan
- Graduate School of Frontier Biosciences; Osaka University; 1-5 Yamadaoka Suita Osaka 565-0871 Japan
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24
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Caschera F, Noireaux V. Compartmentalization of an all-E. coli Cell-Free Expression System for the Construction of a Minimal Cell. ARTIFICIAL LIFE 2016; 22:185-195. [PMID: 26934095 DOI: 10.1162/artl_a_00198] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Cell-free expression is a technology used to synthesize minimal biological cells from natural molecular components. We have developed a versatile and powerful all-E. coli cell-free transcription-translation system energized by a robust metabolism, with the far objective of constructing a synthetic cell capable of self-reproduction. Inorganic phosphate (iP), a byproduct of protein synthesis, is recycled through polysugar catabolism to regenerate ATP (adenosine triphosphate) and thus supports long-lived and highly efficient protein synthesis in vitro. This cell-free TX-TL system is encapsulated into cell-sized unilamellar liposomes to express synthetic DNA programs. In this work, we study the compartmentalization of cell-free TX-TL reactions, one of the aspects of minimal cell module integration. We analyze the signals of various liposome populations by fluorescence microscopy for one and for two reporter genes, and for an inducible genetic circuit. We show that small nutrient molecules and proteins are encapsulated uniformly in the liposomes with small fluctuations. However, cell-free expression displays large fluctuations in signals among the same population, which are due to heterogeneous encapsulation of the DNA template. Consequently, the correlations of gene expression with the compartment dimension are difficult to predict accurately. Larger vesicles can have either low or high protein yields.
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25
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Kurihara K, Okura Y, Matsuo M, Toyota T, Suzuki K, Sugawara T. A recursive vesicle-based model protocell with a primitive model cell cycle. Nat Commun 2015; 6:8352. [PMID: 26418735 PMCID: PMC4598553 DOI: 10.1038/ncomms9352] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 08/13/2015] [Indexed: 12/19/2022] Open
Abstract
Self-organized lipid structures (protocells) have been proposed as an intermediate between nonliving material and cellular life. Synthetic production of model protocells can demonstrate the potential processes by which living cells first arose. While we have previously described a giant vesicle (GV)-based model protocell in which amplification of DNA was linked to self-reproduction, the ability of a protocell to recursively self-proliferate for multiple generations has not been demonstrated. Here we show that newborn daughter GVs can be restored to the status of their parental GVs by pH-induced vesicular fusion of daughter GVs with conveyer GVs filled with depleted substrates. We describe a primitive model cell cycle comprising four discrete phases (ingestion, replication, maturity and division), each of which is selectively activated by a specific external stimulus. The production of recursive self-proliferating model protocells represents a step towards eventual production of model protocells that are able to mimic evolution.
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Affiliation(s)
- Kensuke Kurihara
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
- Research Center for Complex Systems Biology, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Yusaku Okura
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Muneyuki Matsuo
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Taro Toyota
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
- Research Center for Complex Systems Biology, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Kentaro Suzuki
- Research Center for Complex Systems Biology, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
- Department of Chemistry, Faculty of Science, Kanagawa University, Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan
| | - Tadashi Sugawara
- Research Center for Complex Systems Biology, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
- Department of Chemistry, Faculty of Science, Kanagawa University, Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan
- Toyota Physical and Chemical Research Institute, Nagakute, Aichi 480-1192, Japan
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26
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de la Escosura A, Briones C, Ruiz-Mirazo K. The systems perspective at the crossroads between chemistry and biology. J Theor Biol 2015; 381:11-22. [DOI: 10.1016/j.jtbi.2015.04.036] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 04/26/2015] [Indexed: 01/21/2023]
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27
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Tsuda S, Sakakura T, Fujii S, Suzuki H, Yomo T. Shape Transformations of Lipid Vesicles by Insertion of Bulky-Head Lipids. PLoS One 2015; 10:e0132963. [PMID: 26176953 PMCID: PMC4503622 DOI: 10.1371/journal.pone.0132963] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 06/20/2015] [Indexed: 11/26/2022] Open
Abstract
Lipid vesicles, in particular Giant Unilamellar Vesicles (GUVs), have been increasingly important as compartments of artificial cells to reconstruct living cell-like systems in a bottom-up fashion. Here, we report shape transformations of lipid vesicles induced by polyethylene glycol-lipid conjugate (PEG lipids). Statistical analysis of deformed vesicle shapes revealed that shapes vesicles tend to deform into depended on the concentration of the PEG lipids. When compared with theoretically simulated vesicle shapes, those shapes were found to be more energetically favorable, with lower membrane bending energies than other shapes. This result suggests that the vesicle shape transformations can be controlled by externally added membrane molecules, which can serve as a potential method to control the replications of artificial cells.
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Affiliation(s)
- Soichiro Tsuda
- Yomo Dynamical Micro-scale Reaction Environment Project, ERATO, Japan Science and Technology Agency, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tatsuya Sakakura
- Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Satoshi Fujii
- Yomo Dynamical Micro-scale Reaction Environment Project, ERATO, Japan Science and Technology Agency, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hiroaki Suzuki
- Yomo Dynamical Micro-scale Reaction Environment Project, ERATO, Japan Science and Technology Agency, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tetsuya Yomo
- Yomo Dynamical Micro-scale Reaction Environment Project, ERATO, Japan Science and Technology Agency, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
- Graduate School of Frontier Biosciences, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
- * E-mail:
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28
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Elani Y, Law RV, Ces O. Protein synthesis in artificial cells: using compartmentalisation for spatial organisation in vesicle bioreactors. Phys Chem Chem Phys 2015; 17:15534-7. [DOI: 10.1039/c4cp05933f] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Spatially segregated in vitro protein expression in a vesicle-based artificial cell, with different proteins synthesised in defined vesicle regions.
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Affiliation(s)
- Yuval Elani
- Department of Chemistry
- Imperial College London
- UK
- Institute of Chemical Biology
- Imperial College London
| | - Robert V. Law
- Department of Chemistry
- Imperial College London
- UK
- Institute of Chemical Biology
- Imperial College London
| | - Oscar Ces
- Department of Chemistry
- Imperial College London
- UK
- Institute of Chemical Biology
- Imperial College London
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29
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de Souza TP, Fahr A, Luisi PL, Stano P. Spontaneous Encapsulation and Concentration of Biological Macromolecules in Liposomes: An Intriguing Phenomenon and Its Relevance in Origins of Life. J Mol Evol 2014; 79:179-92. [DOI: 10.1007/s00239-014-9655-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 11/10/2014] [Indexed: 12/31/2022]
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30
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Fellermann H, Cardelli L. Programming chemistry in DNA-addressable bioreactors. J R Soc Interface 2014; 11:rsif.2013.0987. [PMID: 25121647 DOI: 10.1098/rsif.2013.0987] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We present a formal calculus, termed the chemtainer calculus, able to capture the complexity of compartmentalized reaction systems such as populations of possibly nested vesicular compartments. Compartments contain molecular cargo as well as surface markers in the form of DNA single strands. These markers serve as compartment addresses and allow for their targeted transport and fusion, thereby enabling reactions of previously separated chemicals. The overall system organization allows for the set-up of programmable chemistry in microfluidic or other automated environments. We introduce a simple sequential programming language whose instructions are motivated by state-of-the-art microfluidic technology. Our approach integrates electronic control, chemical computing and material production in a unified formal framework that is able to mimic the integrated computational and constructive capabilities of the subcellular matrix. We provide a non-deterministic semantics of our programming language that enables us to analytically derive the computational and constructive power of our machinery. This semantics is used to derive the sets of all constructable chemicals and supermolecular structures that emerge from different underlying instruction sets. Because our proofs are constructive, they can be used to automatically infer control programs for the construction of target structures from a limited set of resource molecules. Finally, we present an example of our framework from the area of oligosaccharide synthesis.
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Affiliation(s)
- Harold Fellermann
- School of Computing Science, Newcastle University, King's Gate, Newcastle upon Tyne NE1 7RU, UK Center for Fundamental Living Technology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Luca Cardelli
- Microsoft Research Cambridge, 21 Station Road, Cambridge CB1 2FB, UK
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31
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Integration of biological parts toward the synthesis of a minimal cell. Curr Opin Chem Biol 2014; 22:85-91. [DOI: 10.1016/j.cbpa.2014.09.028] [Citation(s) in RCA: 94] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 09/19/2014] [Accepted: 09/22/2014] [Indexed: 11/21/2022]
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32
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Shiomi H, Tsuda S, Suzuki H, Yomo T. Liposome-based liquid handling platform featuring addition, mixing, and aliquoting of femtoliter volumes. PLoS One 2014; 9:e101820. [PMID: 24991878 PMCID: PMC4081812 DOI: 10.1371/journal.pone.0101820] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 06/10/2014] [Indexed: 11/18/2022] Open
Abstract
This paper describes the utilization of giant unilamellar vesicles (GUVs) as a platform for handling chemical and biochemical reagents. GUVs with diameters of 5 to 10 µm and containing chemical/biochemical reagents together with inert polymers were fused with electric pulses (electrofusion). After reagent mixing, the fused GUVs spontaneously deformed to a budding shape, separating the mixed solution into sub-volumes. We utilized a microfluidic channel and optical tweezers to select GUVs of interest, bring them into contact, and fuse them together to mix and aliquot the reaction product. We also show that, by lowering the ambient temperature close to the phase transition temperature Tm of the lipid used, daughter GUVs completely detached (fission). This process performs all the liquid-handing features used in bench-top biochemistry using the GUV, which could be advantageous for the membrane-related biochemical assays.
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Affiliation(s)
- Hideaki Shiomi
- Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Soichiro Tsuda
- School of Chemistry, University of Glasgow, Glasgow, United Kingdom
- ERATO, JST, Tokyo, Japan
| | - Hiroaki Suzuki
- ERATO, JST, Tokyo, Japan
- Faculty of Science and Engineering, Chuo University, Tokyo, Japan
| | - Tetsuya Yomo
- Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
- ERATO, JST, Tokyo, Japan
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
- * E-mail:
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33
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Cao J, Seekell R, Li Y, Wang X, Zhan S, Li Y. High Yield of Supergiant Vesicles on Glyoxylic Acid Modified Aluminum Electrode. J DISPER SCI TECHNOL 2014. [DOI: 10.1080/01932691.2013.825568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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34
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Wu F, Tan C. The engineering of artificial cellular nanosystems using synthetic biology approaches. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2014; 6:369-83. [PMID: 24668724 DOI: 10.1002/wnan.1265] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Revised: 02/05/2014] [Accepted: 02/08/2014] [Indexed: 12/26/2022]
Abstract
Artificial cellular systems are minimal systems that mimic certain properties of natural cells, including signaling pathways, membranes, and metabolic pathways. These artificial cells (or protocells) can be constructed following a synthetic biology approach by assembling biomembranes, synthetic gene circuits, and cell-free expression systems. As artificial cells are built from bottom-up using minimal and a defined number of components, they are more amenable to predictive mathematical modeling and engineered controls when compared with natural cells. Indeed, artificial cells have been implemented as drug delivery machineries and in situ protein expression systems. Furthermore, artificial cells have been used as biomimetic systems to unveil new insights into functions of natural cells, which are otherwise difficult to investigate owing to their inherent complexity. It is our vision that the development of artificial cells would bring forth parallel advancements in synthetic biology, cell-free systems, and in vitro systems biology. For further resources related to this article, please visit the WIREs website. Conflict of interests: The authors declare that they have no competing financial interests.
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Affiliation(s)
- Fan Wu
- Department of Biomedical Engineering, University of California Davis, Davis, CA, USA
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35
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Hosta-Rigau L, Schattling P, Teo BM, Lynge ME, Städler B. Recent progress of liposomes in nanomedicine. J Mater Chem B 2014; 2:6686-6691. [DOI: 10.1039/c4tb00825a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Liposome formulations are highlighted focusing on their chemical modification, interaction with cells, and use in substrate-mediated drug delivery and cell mimicry.
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Affiliation(s)
- Leticia Hosta-Rigau
- Interdisciplinary Nanoscience Centre (iNANO)
- Aarhus University
- Aarhus, Denmark
| | - Philipp Schattling
- Interdisciplinary Nanoscience Centre (iNANO)
- Aarhus University
- Aarhus, Denmark
| | - Boon M. Teo
- Interdisciplinary Nanoscience Centre (iNANO)
- Aarhus University
- Aarhus, Denmark
| | - Martin E. Lynge
- Interdisciplinary Nanoscience Centre (iNANO)
- Aarhus University
- Aarhus, Denmark
| | - Brigitte Städler
- Interdisciplinary Nanoscience Centre (iNANO)
- Aarhus University
- Aarhus, Denmark
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36
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The MATCHIT automaton: exploiting compartmentalization for the synthesis of branched polymers. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2013; 2013:467428. [PMID: 24489601 PMCID: PMC3893812 DOI: 10.1155/2013/467428] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 12/08/2013] [Indexed: 11/18/2022]
Abstract
We propose an automaton, a theoretical framework that demonstrates how to improve the yield of the synthesis of branched chemical polymer reactions. This is achieved by separating substeps of the path of synthesis into compartments. We use chemical containers (chemtainers) to carry the substances through a sequence of fixed successive compartments. We describe the automaton in mathematical terms and show how it can be configured automatically in order to synthesize a given branched polymer target. The algorithm we present finds an optimal path of synthesis in linear time. We discuss how the automaton models compartmentalized structures found in cells, such as the endoplasmic reticulum and the Golgi apparatus, and we show how this compartmentalization can be exploited for the synthesis of branched polymers such as oligosaccharides. Lastly, we show examples of artificial branched polymers and discuss how the automaton can be configured to synthesize them with maximal yield.
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37
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Ruiz-Mirazo K, Briones C, de la Escosura A. Prebiotic Systems Chemistry: New Perspectives for the Origins of Life. Chem Rev 2013; 114:285-366. [DOI: 10.1021/cr2004844] [Citation(s) in RCA: 563] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kepa Ruiz-Mirazo
- Biophysics
Unit (CSIC-UPV/EHU), Leioa, and Department of Logic and Philosophy
of Science, University of the Basque Country, Avenida de Tolosa 70, 20080 Donostia−San Sebastián, Spain
| | - Carlos Briones
- Department
of Molecular Evolution, Centro de Astrobiología (CSIC−INTA, associated to the NASA Astrobiology Institute), Carretera de Ajalvir, Km 4, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Andrés de la Escosura
- Organic
Chemistry Department, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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38
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Stano P, Luisi PL. Semi-synthetic minimal cells: origin and recent developments. Curr Opin Biotechnol 2013; 24:633-8. [PMID: 23374484 DOI: 10.1016/j.copbio.2013.01.002] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 12/19/2012] [Accepted: 01/03/2013] [Indexed: 10/27/2022]
Abstract
The notion of minimal cells refers to cellular structures that contain the minimal and sufficient complexity to still be defined as living, or at least capable to display the most important features of biological cells. Here we briefly describe the laboratory construction of minimal cells, a project within the broader field of synthetic biology. In particular we discuss the advancements in the preparation of semi-synthetic cells based on the encapsulation of biochemicals inside liposomes, illustrating from the one hand the origin of this research and the most recent developments; and from the other the difficulties and limits of the approach. The role of physicochemical understandings is greatly emphasized.
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Affiliation(s)
- Pasquale Stano
- Biology Department, University of Roma Tre, Viale G. Marconi 446, I-00146 Rome, Italy
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39
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Great application prospect in vivo: Efficient electroformation of giant vesicles on novel carbon fiber microelectrode. Electrochem commun 2012. [DOI: 10.1016/j.elecom.2012.10.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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40
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Suzuki K, Aboshi R, Kurihara K, Sugawara T. Adhesion and Fusion of Two Kinds of Phospholipid Hybrid Vesicles Controlled by Surface Charges of Vesicular Membranes. CHEM LETT 2012. [DOI: 10.1246/cl.2012.789] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kentaro Suzuki
- Research Center of Life Science as Complex Systems, The University of Tokyo
| | - Ryo Aboshi
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo
| | - Kensuke Kurihara
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo
| | - Tadashi Sugawara
- Research Center of Life Science as Complex Systems, The University of Tokyo
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41
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Nishimura K, Matsuura T, Nishimura K, Sunami T, Suzuki H, Yomo T. Cell-free protein synthesis inside giant unilamellar vesicles analyzed by flow cytometry. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:8426-8432. [PMID: 22578080 DOI: 10.1021/la3001703] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Lipid vesicles have been used as model cell systems, in which an in-vitro transcription-translation system (IVTT) is encapsulated to carry out intravesicular protein synthesis. Despite a large number of previous studies, a quantitative understanding of how protein synthesis inside the vesicles is affected by the lipid membrane remains elusive. This is mainly because of the heterogeneity in structural properties of the lipid vesicles used in the experiments. We investigated the effects of the phospholipid membrane on green fluorescent protein (GFP) synthesis occurring inside cell-sized giant unilamellar vesicles (GUV), which have a defined quantity of lipids relative to the reaction volume. We first developed a method to distinguish GUV from multilamellar vesicles using flow cytometry (FCM). Using this method, we investigated the time course of GFP synthesis using one of the IVTT, the PURE system, and found that phospholipid in the form of GUV has little effect on GFP synthesis based on three lines of investigation. (1) GFP synthesis inside the GUV was not dependent on the size of GUV (2) or on the fraction of cholesterol or anionic phospholipid constituting the GUV, and (3) GFP synthesis proceeded similarly in GUV and in the test tube. The present results suggest that GUV provides an ideal reaction environment that does not affect the internal biochemical reaction. On the other hand, we also found that internal GFP synthesis is strongly dependent on the chemical composition of the outer solution.
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Affiliation(s)
- Koji Nishimura
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
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42
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Coupling of the fusion and budding of giant phospholipid vesicles containing macromolecules. Proc Natl Acad Sci U S A 2012; 109:5942-7. [PMID: 22474340 DOI: 10.1073/pnas.1120327109] [Citation(s) in RCA: 128] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mechanisms that enabled primitive cell membranes to self-reproduce have been discussed based on the physicochemical properties of fatty acids; however, there must be a transition to modern cell membranes composed of phospholipids [Budin I, Szostak JW (2011) Proc Natl Acad Sci USA 108:5249-5254]. Thus, a growth-division mechanism of membranes that does not depend on the chemical nature of amphiphilic molecules must have existed. Here, we show that giant unilamellar vesicles composed of phospholipids can undergo the coupled process of fusion and budding transformation, which mimics cell growth and division. After gaining excess membrane by electrofusion, giant vesicles spontaneously transform into the budded shape only when they contain macromolecules (polymers) inside their aqueous core. This process is a result of the vesicle maximizing the translational entropy of the encapsulated polymers (depletion volume effect). Because the cell is a lipid membrane bag containing highly concentrated biopolymers, this coupling process that is induced by physical and nonspecific interactions may have a general importance in the self-reproduction of the early cellular compartments.
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