1
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Ben Trad F, Delacotte J, Lemaître F, Guille-Collignon M, Arbault S, Sojic N, Labbé E, Buriez O. Shadow electrochemiluminescence imaging of giant liposomes opening at polarized electrodes. Analyst 2024; 149:3317-3324. [PMID: 38742381 DOI: 10.1039/d4an00470a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
In this work, the release of giant liposome (∼100 μm in diameter) content was imaged by shadow electrochemiluminescence (ECL) microscopy. Giant unilamellar liposomes were pre-loaded with a sucrose solution and allowed to sediment at an ITO electrode surface immersed in a solution containing a luminophore ([Ru(bpy)3]2+) and a sacrificial co-reactant (tri-n-propylamine). Upon polarization, the electrode exhibited illumination over its entire surface thanks to the oxidation of ECL reagents. However, as soon as liposomes reached the electrode surface, dark spots appeared and then spread over time on the surface. This observation reflected a blockage of the electrode surface at the contact point between the liposome and the electrode surface, followed by the dilution of ECL reagents after the rupture of the liposome membrane and release of its internal ECL-inactive solution. Interestingly, ECL reappeared in areas where it initially faded, indicating back-diffusion of ECL reagents towards the previously diluted area and thus confirming liposome permeabilization. The whole process was analyzed qualitatively and quantitatively within the defined region of interest. Two mass transport regimes were identified: a gravity-driven spreading process when the liposome releases its content leading to ECL vanishing and a diffusive regime when ECL recovers. The reported shadow ECL microscopy should find promising applications for the imaging of transient events such as molecular species released by artificial or biological vesicles.
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Affiliation(s)
- Fatma Ben Trad
- PASTEUR, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Jérôme Delacotte
- PASTEUR, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Frédéric Lemaître
- PASTEUR, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Manon Guille-Collignon
- PASTEUR, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Stéphane Arbault
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600 Pessac, France
| | - Neso Sojic
- Univ. Bordeaux, CNRS, Bordeaux INP, ISM, UMR 5255 CNRS, 33400 Talence, France.
| | - Eric Labbé
- PASTEUR, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
| | - Olivier Buriez
- PASTEUR, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France.
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2
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Izumi K, Ji J, Koiwai K, Kawano R. Long-Term Stable Liposome Modified by PEG-Lipid in Natural Seawater. ACS OMEGA 2024; 9:10958-10966. [PMID: 38463291 PMCID: PMC10918668 DOI: 10.1021/acsomega.3c10346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 01/10/2024] [Indexed: 03/12/2024]
Abstract
This paper describes the stabilization of liposomes using a PEGylated lipid, N-(methylpolyoxyethylene oxycarbonyl)-1,2-distearoyl-sn-glycero-3-phosphoethanolamine sodium salt (DSPE-PEGs), and the evaluation of the survival rate in natural seawater for future environmental applications. Liposomes in natural seawater were first monitored by confocal microscopy, and the stability was compared among different lengths and the introduction ratio of DSPE-PEGs. The survival rate increased with an increase in the PEG ratio. In addition, the survival rate in different cationic solutions (Na+, K+, Mg2+, and Ca2+ solutions) was studied to estimate the effects of the DSPE-PEG introduction. We propose that these variations in liposome stability are due to the cations, specifically the interaction between the poly(ethylene glycol) (PEG) chains and divalent ions, which contribute to making it difficult for cations to access the lipid membrane. Our studies provide insights into the use of PEG lipids and may offer a promising approach to the fabrication of liposomal molecular robots using different natural environments.
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Affiliation(s)
- Kayano Izumi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Jiajue Ji
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Keiichiro Koiwai
- Laboratory of Genome Science, Tokyo University of Marine Science and Technology, Tokyo 108-8477, Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
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3
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Miwa A, Wakamori M, Ariyoshi T, Okada Y, Shirouzu M, Umehara T, Kamiya K. Efficiency of transcription and translation of cell-free protein synthesis systems in cell-sized lipid vesicles with changing lipid composition determined by fluorescence measurements. Sci Rep 2024; 14:2852. [PMID: 38310141 PMCID: PMC10838264 DOI: 10.1038/s41598-024-53135-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 01/29/2024] [Indexed: 02/05/2024] Open
Abstract
To develop artificial cell models that mimic living cells, cell-sized lipid vesicles encapsulating cell-free protein synthesis (CFPS) systems are useful for protein expressions or artificial gene circuits for vesicle-vesicle communications. Therefore, investigating the transcriptional and translational properties of CFPS systems in lipid vesicles is important for maximizing the synthesis and functions of proteins. Although transcription and translation using CFPS systems inside lipid vesicles are more important than that outside lipid vesicles, the former processes are not investigated by changing the lipid composition of lipid vesicles. Herein, we investigated changes in transcription and translation using CFPS systems inside giant lipid vesicles (approximately 5-20 μm in diameter) caused by changing the lipid composition of lipid vesicles containing neutral, positively, and negatively charged lipids. After incubating for 30 min, 1 h, 2 h, and 4 h, the transcriptional and translational activities in these lipid vesicles were determined by detecting the fluorescence intensities of the fluorogenic RNA aptamer on the 3'-untranslated region of mRNA (transcription) and the fluorescent protein sfCherry (translation), respectively. The results revealed that transcriptional and translational activities in a lipid vesicle containing positively charged lipids were high when the protein was synthesized using the CFPS system inside the lipid vesicle. Thus, the present study provides an experimental basis for constructing complex artificial cell models using bottom-up approaches.
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Affiliation(s)
- Akari Miwa
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-Cho, Kiryu, Gunma, 376-8515, Japan
| | - Masatoshi Wakamori
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-Cho, Tsurumi-Ku, Yokohama, 230-0045, Japan
| | - Tetsuro Ariyoshi
- Laboratory for Cell Polarity Regulation, RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furue-Dai, Suita, Osaka, 565-0874, Japan
- Department of Cell Biology, Graduate School of Medicine, and International Research Center for Neurointelligence (WPI-IRCN), the University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | - Yasushi Okada
- Laboratory for Cell Polarity Regulation, RIKEN Center for Biosystems Dynamics Research, 6-2-3 Furue-Dai, Suita, Osaka, 565-0874, Japan
- Department of Cell Biology, Graduate School of Medicine, and International Research Center for Neurointelligence (WPI-IRCN), the University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
- Department of Physics and Universal Biology Institute (UBI), Graduate School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo, 113-0033, Japan
| | - Mikako Shirouzu
- Laboratory for Protein Functional and Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-Cho, Tsurumi-Ku, Yokohama, 230-0045, Japan
| | - Takashi Umehara
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-Cho, Tsurumi-Ku, Yokohama, 230-0045, Japan
| | - Koki Kamiya
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-Cho, Kiryu, Gunma, 376-8515, Japan.
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4
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Herianto S, Subramani B, Chen BR, Chen CS. Recent advances in liposome development for studying protein-lipid interactions. Crit Rev Biotechnol 2024; 44:1-14. [PMID: 36170980 DOI: 10.1080/07388551.2022.2111294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 05/12/2022] [Accepted: 05/29/2022] [Indexed: 11/03/2022]
Abstract
Protein-lipid interactions are crucial for various cellular biological processes like intracellular signaling, membrane transport, and cytoskeletal dynamics. Therefore, studying these interactions is essential to understand and unravel their specific functions. Nevertheless, the interacting proteins of many lipids are poorly understood and still require systematic study. Liposomes are the most well-known and familiar biomimetic systems used to study protein-lipid interactions. Although liposomes have been widely used for studying protein-lipid interactions in classical methods such as the co-flotation assay (CFA), co-sedimentation assay (CSA), and flow cytometric assay (FCA), an overview of their current applications and developments in high-throughput methods is not yet available. Here, we summarize the liposome development in low and high-throughput methods to study protein-lipid interactions. Besides, a constructive comment for each platform is presented to stimulate the advancement of these technologies in the future.
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Affiliation(s)
- Samuel Herianto
- Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program (TIGP), Academia Sinica, Taipei, Taiwan
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Department of Chemistry (Chemical Biology Division), College of Science, National Taiwan University, Taipei, Taiwan
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Boopathi Subramani
- Institute of Food Science and Technology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Bo-Ruei Chen
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chien-Sheng Chen
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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5
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Godino E, Restrepo Sierra AM, Danelon C. Imaging Flow Cytometry for High-Throughput Phenotyping of Synthetic Cells. ACS Synth Biol 2023. [PMID: 37155828 PMCID: PMC10367129 DOI: 10.1021/acssynbio.3c00074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The reconstitution of basic cellular functions in micrometer-sized liposomes has led to a surge of interest in the construction of synthetic cells. Microscopy and flow cytometry are powerful tools for characterizing biological processes in liposomes with fluorescence readouts. However, applying each method separately leads to a compromise between information-rich imaging by microscopy and statistical population analysis by flow cytometry. To address this shortcoming, we here introduce imaging flow cytometry (IFC) for high-throughput, microscopy-based screening of gene-expressing liposomes in laminar flow. We developed a comprehensive pipeline and analysis toolset based on a commercial IFC instrument and software. About 60 thousands of liposome events were collected per run starting from one microliter of the stock liposome solution. Robust population statistics from individual liposome images was performed based on fluorescence and morphological parameters. This allowed us to quantify complex phenotypes covering a wide range of liposomal states that are relevant for building a synthetic cell. The general applicability, current workflow limitations, and future prospects of IFC in synthetic cell research are finally discussed.
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Affiliation(s)
- Elisa Godino
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629HZ Delft, The Netherlands
| | - Ana Maria Restrepo Sierra
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629HZ Delft, The Netherlands
| | - Christophe Danelon
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629HZ Delft, The Netherlands
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
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6
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Supramaniam P, Wang Z, Chatzimichail S, Parperis C, Kumar A, Ho V, Ces O, Salehi-Reyhani A. Measuring Encapsulation Efficiency in Cell-Mimicking Giant Unilamellar Vesicles. ACS Synth Biol 2023; 12:1227-1238. [PMID: 36977193 PMCID: PMC10127275 DOI: 10.1021/acssynbio.2c00684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
One of the main drivers within the field of bottom-up synthetic biology is to develop artificial chemical machines, perhaps even living systems, that have programmable functionality. Numerous toolkits exist to generate giant unilamellar vesicle-based artificial cells. However, methods able to quantitatively measure their molecular constituents upon formation is an underdeveloped area. We report an artificial cell quality control (AC/QC) protocol using a microfluidic-based single-molecule approach, enabling the absolute quantification of encapsulated biomolecules. While the measured average encapsulation efficiency was 11.4 ± 6.8%, the AC/QC method allowed us to determine encapsulation efficiencies per vesicle, which varied significantly from 2.4 to 41%. We show that it is possible to achieve a desired concentration of biomolecule within each vesicle by commensurate compensation of its concentration in the seed emulsion. However, the variability in encapsulation efficiency suggests caution is necessary when using such vesicles as simplified biological models or standards.
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Affiliation(s)
| | - Zibo Wang
- Department of Surgery & Cancer, Imperial College London, London W12 0HS, U.K
- Department of Chemistry, King's College London, London SE1 1DB, U.K
| | | | - Christopher Parperis
- Department of Chemistry, Imperial College London, London W12 0BZ, U.K
- Department of Chemistry, King's College London, London SE1 1DB, U.K
| | - Aditi Kumar
- Department of Chemistry, Imperial College London, London W12 0BZ, U.K
| | - Vanessa Ho
- Department of Chemistry, Imperial College London, London W12 0BZ, U.K
| | - Oscar Ces
- Department of Chemistry, Imperial College London, London W12 0BZ, U.K
- fabriCELL, Imperial College London, London SW7 2AZ, U.K
| | - Ali Salehi-Reyhani
- Department of Surgery & Cancer, Imperial College London, London W12 0HS, U.K
- fabriCELL, Imperial College London, London SW7 2AZ, U.K
- Institute for Molecular Science and Engineering, Imperial College London, London SW7 2AZ, U.K
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7
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Boyd MA, Thavarajah W, Lucks JB, Kamat NP. Robust and tunable performance of a cell-free biosensor encapsulated in lipid vesicles. SCIENCE ADVANCES 2023; 9:eadd6605. [PMID: 36598992 PMCID: PMC9812392 DOI: 10.1126/sciadv.add6605] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 11/23/2022] [Indexed: 05/21/2023]
Abstract
Cell-free systems have enabled the development of genetically encoded biosensors to detect a range of environmental and biological targets. Encapsulation of these systems in synthetic membranes to form artificial cells can reintroduce features of the cellular membrane, including molecular containment and selective permeability, to modulate cell-free sensing capabilities. Here, we demonstrate robust and tunable performance of a transcriptionally regulated, cell-free riboswitch encapsulated in lipid membranes, allowing the detection of fluoride, an environmentally important molecule. Sensor response can be tuned by varying membrane composition, and encapsulation protects from sensor degradation, facilitating detection in real-world samples. These sensors can detect fluoride using two types of genetically encoded outputs, enabling detection of fluoride at the Environmental Protection Agency maximum contaminant level of 0.2 millimolars. This work demonstrates the capacity of bilayer membranes to confer tunable permeability to encapsulated, genetically encoded sensors and establishes the feasibility of artificial cell platforms to detect environmentally relevant small molecules.
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Affiliation(s)
- Margrethe A. Boyd
- Department of Biomedical Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Walter Thavarajah
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, USA
- Center for Water Research, Northwestern University, Evanston, IL, USA
| | - Julius B. Lucks
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Department of Chemical and Biological Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, USA
- Center for Water Research, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- Corresponding author. (N.P.K.); (J.B.L.)
| | - Neha P. Kamat
- Department of Biomedical Engineering, McCormick School of Engineering and Applied Science, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA
- Corresponding author. (N.P.K.); (J.B.L.)
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8
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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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9
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Miele Y, Jones SJ, Rossi F, Beales PA, Taylor AF. Collective Behavior of Urease pH Clocks in Nano- and Microvesicles Controlled by Fast Ammonia Transport. J Phys Chem Lett 2022; 13:1979-1984. [PMID: 35188399 PMCID: PMC9007528 DOI: 10.1021/acs.jpclett.2c00069] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
The transmission of chemical signals via an extracellular solution plays a vital role in collective behavior in cellular biological systems and may be exploited in applications of lipid vesicles such as drug delivery. Here, we investigated chemical communication in synthetic micro- and nanovesicles containing urease in a solution of urea and acid. We combined experiments with simulations to demonstrate that the fast transport of ammonia to the external solution governs the pH-time profile and synchronizes the timing of the pH clock reaction in a heterogeneous population of vesicles. This study shows how the rate of production and emission of a small basic product controls pH changes in active vesicles with a distribution of sizes and enzyme amounts, which may be useful in bioreactor or healthcare applications.
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Affiliation(s)
- Ylenia Miele
- Department
of Chemistry and Biology, University of
Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Salerno, Italy
| | - Stephen J. Jones
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Federico Rossi
- Department
of Earth, Environmental and Physical Sciences, University of Siena, Pian dei Mantellini 44, 53100 Siena, Italy
| | - Paul A. Beales
- School
of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, U.K.
| | - Annette F. Taylor
- Chemical
and Biological Engineering, University of
Sheffield, Sheffield S1 3JD, U.K.
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10
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Gonzales D, Yandrapalli N, Robinson T, Zechner C, Tang TYD. Cell-Free Gene Expression Dynamics in Synthetic Cell Populations. ACS Synth Biol 2022; 11:205-215. [PMID: 35057626 PMCID: PMC8787815 DOI: 10.1021/acssynbio.1c00376] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Indexed: 11/29/2022]
Abstract
The ability to build synthetic cellular populations from the bottom-up provides the groundwork to realize minimal living tissues comprising single cells which can communicate and bridge scales into multicellular systems. Engineered systems made of synthetic micron-sized compartments and integrated reaction networks coupled with mathematical modeling can facilitate the design and construction of complex and multiscale chemical systems from the bottom-up. Toward this goal, we generated populations of monodisperse liposomes encapsulating cell-free expression systems (CFESs) using double-emulsion microfluidics and quantified transcription and translation dynamics within individual synthetic cells of the population using a fluorescent Broccoli RNA aptamer and mCherry protein reporter. CFE dynamics in bulk reactions were used to test different coarse-grained resource-limited gene expression models using model selection to obtain transcription and translation rate parameters by likelihood-based parameter estimation. The selected model was then applied to quantify cell-free gene expression dynamics in populations of synthetic cells. In combination, our experimental and theoretical approaches provide a statistically robust analysis of CFE dynamics in bulk and monodisperse synthetic cell populations. We demonstrate that compartmentalization of CFESs leads to different transcription and translation rates compared to bulk CFE and show that this is due to the semipermeable lipid membrane that allows the exchange of materials between the synthetic cells and the external environment.
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Affiliation(s)
- David
T. Gonzales
- Max
Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Center
for Systems Biology Dresden, 01307 Dresden, Germany
| | | | - Tom Robinson
- Max
Planck Institute of Colloids and Interfaces, 14476 Potsdam, Germany
| | - Christoph Zechner
- Max
Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Center
for Systems Biology Dresden, 01307 Dresden, Germany
- Physics
of Life, Cluster of Excellence, TU Dresden, 01603 Dresden, Germany
| | - T-Y. Dora Tang
- Max
Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Center
for Systems Biology Dresden, 01307 Dresden, Germany
- Physics
of Life, Cluster of Excellence, TU Dresden, 01603 Dresden, Germany
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11
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Ben Trad F, Wieczny V, Delacotte J, Morel M, Guille-Collignon M, Arbault S, Lemaître F, Sojic N, Labbé E, Buriez O. Dynamic Electrochemiluminescence Imaging of Single Giant Liposome Opening at Polarized Electrodes. Anal Chem 2022; 94:1686-1696. [DOI: 10.1021/acs.analchem.1c04238] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Fatma Ben Trad
- PASTEUR, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Vincent Wieczny
- PASTEUR, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Jérôme Delacotte
- PASTEUR, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Mathieu Morel
- PASTEUR, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Manon Guille-Collignon
- PASTEUR, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Stéphane Arbault
- University of Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248 CNRS, F-33600 Pessac, France
| | - Frédéric Lemaître
- PASTEUR, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Neso Sojic
- University of Bordeaux, CNRS, Bordeaux INP, ISM, UMR CNRS 5255, 33607 Pessac, France
| | - Eric Labbé
- PASTEUR, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Olivier Buriez
- PASTEUR, Département de Chimie, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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12
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Van de Cauter L, Fanalista F, van Buren L, De Franceschi N, Godino E, Bouw S, Danelon C, Dekker C, Koenderink GH, Ganzinger KA. Optimized cDICE for Efficient Reconstitution of Biological Systems in Giant Unilamellar Vesicles. ACS Synth Biol 2021. [PMID: 34185516 DOI: 10.1101/2021.02.24.432456] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
Giant unilamellar vesicles (GUVs) are often used to mimic biological membranes in reconstitution experiments. They are also widely used in research on synthetic cells, as they provide a mechanically responsive reaction compartment that allows for controlled exchange of reactants with the environment. However, while many methods exist to encapsulate functional biomolecules in GUVs, there is no one-size-fits-all solution and reliable GUV fabrication still remains a major experimental hurdle in the field. Here, we show that defect-free GUVs containing complex biochemical systems can be generated by optimizing a double-emulsion method for GUV formation called continuous droplet interface crossing encapsulation (cDICE). By tightly controlling environmental conditions and tuning the lipid-in-oil dispersion, we show that it is possible to significantly improve the reproducibility of high-quality GUV formation as well as the encapsulation efficiency. We demonstrate efficient encapsulation for a range of biological systems including a minimal actin cytoskeleton, membrane-anchored DNA nanostructures, and a functional PURE (protein synthesis using recombinant elements) system. Our optimized cDICE method displays promising potential to become a standard method in biophysics and bottom-up synthetic biology.
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Affiliation(s)
| | - Federico Fanalista
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Lennard van Buren
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Nicola De Franceschi
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Elisa Godino
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Sharon Bouw
- Department of Living Matter, AMOLF, 1098 XG Amsterdam, The Netherlands
| | - Christophe Danelon
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Gijsje H Koenderink
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
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13
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Van de Cauter L, Fanalista F, van Buren L, De Franceschi N, Godino E, Bouw S, Danelon C, Dekker C, Koenderink GH, Ganzinger KA. Optimized cDICE for Efficient Reconstitution of Biological Systems in Giant Unilamellar Vesicles. ACS Synth Biol 2021; 10:1690-1702. [PMID: 34185516 PMCID: PMC8291763 DOI: 10.1021/acssynbio.1c00068] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Indexed: 12/17/2022]
Abstract
Giant unilamellar vesicles (GUVs) are often used to mimic biological membranes in reconstitution experiments. They are also widely used in research on synthetic cells, as they provide a mechanically responsive reaction compartment that allows for controlled exchange of reactants with the environment. However, while many methods exist to encapsulate functional biomolecules in GUVs, there is no one-size-fits-all solution and reliable GUV fabrication still remains a major experimental hurdle in the field. Here, we show that defect-free GUVs containing complex biochemical systems can be generated by optimizing a double-emulsion method for GUV formation called continuous droplet interface crossing encapsulation (cDICE). By tightly controlling environmental conditions and tuning the lipid-in-oil dispersion, we show that it is possible to significantly improve the reproducibility of high-quality GUV formation as well as the encapsulation efficiency. We demonstrate efficient encapsulation for a range of biological systems including a minimal actin cytoskeleton, membrane-anchored DNA nanostructures, and a functional PURE (protein synthesis using recombinant elements) system. Our optimized cDICE method displays promising potential to become a standard method in biophysics and bottom-up synthetic biology.
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Affiliation(s)
| | - Federico Fanalista
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Lennard van Buren
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Nicola De Franceschi
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Elisa Godino
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Sharon Bouw
- Department
of Living Matter, AMOLF, 1098 XG Amsterdam, The Netherlands
| | - Christophe Danelon
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Cees Dekker
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Gijsje H. Koenderink
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
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14
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Wang X, Du H, Wang Z, Mu W, Han X. Versatile Phospholipid Assemblies for Functional Synthetic Cells and Artificial Tissues. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2002635. [PMID: 32830387 DOI: 10.1002/adma.202002635] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/09/2020] [Indexed: 06/11/2023]
Abstract
The bottom-up construction of a synthetic cell from nonliving building blocks capable of mimicking cellular properties and behaviors helps to understand the particular biophysical properties and working mechanisms of a cell. A synthetic cell built in this way possesses defined chemical composition and structure. Since phospholipids are native biomembrane components, their assemblies are widely used to mimic cellular structures. Here, recent developments in the formation of versatile phospholipid assemblies are described, together with the applications of these assemblies for functional membranes (protein reconstituted giant unilamellar vesicles), spherical and nonspherical protoorganelles, and functional synthetic cells, as well as the high-order hierarchical structures of artificial tissues. Their biomedical applications are also briefly summarized. Finally, the challenges and future directions in the field of synthetic cells and artificial tissues based on phospholipid assemblies are proposed.
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Affiliation(s)
- Xuejing Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Hang Du
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
- Marine Antifouling Engineering Technology Center of Shangdong Province, Harbin Institute of Technology, Weihai, 264209, China
| | - Zhao Wang
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Wei Mu
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Xiaojun Han
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
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15
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Blanken D, Foschepoth D, Serrão AC, Danelon C. Genetically controlled membrane synthesis in liposomes. Nat Commun 2020; 11:4317. [PMID: 32859896 PMCID: PMC7455746 DOI: 10.1038/s41467-020-17863-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 07/19/2020] [Indexed: 12/21/2022] Open
Abstract
Lipid membranes, nucleic acids, proteins, and metabolism are essential for modern cellular life. Synthetic systems emulating the fundamental properties of living cells must therefore be built upon these functional elements. In this work, phospholipid-producing enzymes encoded in a synthetic minigenome are cell-free expressed within liposome compartments. The de novo synthesized metabolic pathway converts precursors into a variety of lipids, including the constituents of the parental liposome. Balanced production of phosphatidylethanolamine and phosphatidylglycerol is realized, owing to transcriptional regulation of the activity of specific genes combined with a metabolic feedback mechanism. Fluorescence-based methods are developed to image the synthesis and membrane incorporation of phosphatidylserine at the single liposome level. Our results provide experimental evidence for DNA-programmed membrane synthesis in a minimal cell model. Strategies are discussed to alleviate current limitations toward effective liposome growth and self-reproduction.
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Affiliation(s)
- Duco Blanken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - David Foschepoth
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Adriana Calaça Serrão
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Christophe Danelon
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
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16
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Takahashi H, Ogawa A. Preparation of a Millimeter-Sized Supergiant Liposome That Allows for Efficient, Eukaryotic Cell-Free Translation in the Interior by Spontaneous Emulsion Transfer. ACS Synth Biol 2020; 9:1608-1614. [PMID: 32559381 DOI: 10.1021/acssynbio.0c00173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We sought to prepare millimeter-sized supergiant unilamellar vesicles (SGUVs) by spontaneous emulsion transfer for efficient, eukaryotic cell-free translation in the interior. Although the conventional protocols require that a considerably high concentration of sucrose be encapsulated into the SGUVs for their efficient formation, such high amounts of sucrose severely inhibited cell-free translation based on wheat germ extract (WGE). We thus optimized the preparation conditions to permit SGUV formation at a much lower concentration of sucrose that has almost no effect on WGE translation. Under the optimized conditions, we successfully prepared WGE translation system-encapsulating SGUVs that allow for protein synthesis with a high efficiency comparable to that outside a liposome. The optimization also resulted in a high rate of successful SGUV formation (>90%) and a decent stability of the formed SGUVs (>60 min). These SGUVs are expected to serve as research tools in cell-free synthetic biology and as foundations for artificial cell-based biosensors.
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Affiliation(s)
- Hajime Takahashi
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Atsushi Ogawa
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
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17
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Blanken D, van Nies P, Danelon C. Quantitative imaging of gene-expressing liposomes reveals rare favorable phenotypes. Phys Biol 2019; 16:045002. [PMID: 30978176 DOI: 10.1088/1478-3975/ab0c62] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The biosynthesis of proteins from genomic DNA is a universal process in every living organism. Building a synthetic cell using separate biological parts hence implies to reconstitute a minimal gene expression apparatus and to compartmentalize it in a cell-mimicking environment. Previous studies have demonstrated that the PURE (Protein synthesis Using Recombinant Elements) system could be functionally encapsulated inside lipid vesicles. However, quantitative insights on functional consequences of spatial confinement of PURE system reactions remain scarce, which has hampered the full exploitation of gene-expressing liposomes as the fundamental unit to build an artificial cell. We report on direct imaging of tens of thousands of gene-expressing liposomes per sample allowing us to assess sub-population features in a statistically relevant manner. Both the vesicle size (diameter <10 μm) and lipid composition (mixture of phospholipids with zwitterionic and negatively charged headgroups, including cardiolipin) are compatible with the properties of bacterial cells. Therefore, our liposomes provide a suitable chassis to host the Escherichia coli-derived PURE translation machinery and other bacterial processes in future developments. The potential of high-content imaging to identify rare phenotypes is demonstrated by the fact that a subset of the liposome population exhibits a remarkably high yield of synthesized protein or a prolonged expression lifespan that surpasses the performance of ensemble liposome-averaged and bulk reactions. Among the three commercial PURE systems tested, PUREfrex2.0 offers the most favorable phenotypes displaying both high yield and long protein synthesis lifespan. Moreover, probing membrane permeability reveals a large heterogeneity amongst liposomes. In situ expression and membrane embedding of the pore-forming connexin leads to a characteristic permeability time profile, while increasing the fraction of permeable liposomes in the population. We see diversity in gene expression dynamics and membrane permeability as an opportunity to complement a rational design approach aiming at further implementing biological functions in liposome-based synthetic cells.
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Affiliation(s)
- Duco Blanken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
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18
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Tsuji G, Sunami T, Ichihashi N. Production of giant unilamellar vesicles by the water-in-oil emulsion-transfer method without high internal concentrations of sugars. J Biosci Bioeng 2018; 126:540-545. [DOI: 10.1016/j.jbiosc.2018.04.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 04/24/2018] [Accepted: 04/26/2018] [Indexed: 10/16/2022]
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19
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Trantidou T, Friddin MS, Salehi-Reyhani A, Ces O, Elani Y. Droplet microfluidics for the construction of compartmentalised model membranes. LAB ON A CHIP 2018; 18:2488-2509. [PMID: 30066008 DOI: 10.1039/c8lc00028j] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The design of membrane-based constructs with multiple compartments is of increasing importance given their potential applications as microreactors, as artificial cells in synthetic-biology, as simplified cell models, and as drug delivery vehicles. The emergence of droplet microfluidics as a tool for their construction has allowed rapid scale-up in generation throughput, scale-down of size, and control over gross membrane architecture. This is true on several levels: size, level of compartmentalisation and connectivity of compartments can all be programmed to various degrees. This tutorial review explains and explores the reasons behind this. We discuss microfluidic strategies for the generation of a family of compartmentalised systems that have lipid membranes as the basic structural motifs, where droplets are either the fundamental building blocks, or are precursors to the membrane-bound compartments. We examine the key properties associated with these systems (including stability, yield, encapsulation efficiency), discuss relevant device fabrication technologies, and outline the technical challenges. In doing so, we critically review the state-of-play in this rapidly advancing field.
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Affiliation(s)
- T Trantidou
- Department of Chemistry, Imperial College London, London, SW7 2AZ, UK.
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20
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Altamura E, Carrara P, D'Angelo F, Mavelli F, Stano P. Extrinsic stochastic factors (solute partition) in gene expression inside lipid vesicles and lipid-stabilized water-in-oil droplets: a review. Synth Biol (Oxf) 2018; 3:ysy011. [PMID: 32995519 PMCID: PMC7445889 DOI: 10.1093/synbio/ysy011] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 06/18/2018] [Accepted: 06/21/2018] [Indexed: 11/13/2022] Open
Abstract
The encapsulation of transcription-translation (TX-TL) machinery inside lipid vesicles and water-in-oil droplets leads to the construction of cytomimetic systems (often called 'synthetic cells') for synthetic biology and origins-of-life research. A number of recent reports have shown that protein synthesis inside these microcompartments is highly diverse in terms of rate and amount of synthesized protein. Here, we discuss the role of extrinsic stochastic effects (i.e. solute partition phenomena) as relevant factors contributing to this pattern. We evidence and discuss cases where between-compartment diversity seems to exceed the expected theoretical values. The need of accurate determination of solute content inside individual vesicles or droplets is emphasized, aiming at validating or rejecting the predictions calculated from the standard fluctuations theory. At the same time, we promote the integration of experiments and stochastic modeling to reveal the details of solute encapsulation and intra-compartment reactions.
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Affiliation(s)
- Emiliano Altamura
- Chemistry Department, University of Bari, Via E. Orabona 4, I-70126, Bari, Italy
| | - Paolo Carrara
- Department of Sciences, Roma Tre University, Viale G. Marconi 446, I-00146, Rome, Italy
| | - Francesca D'Angelo
- Department of Sciences, Roma Tre University, Viale G. Marconi 446, I-00146, Rome, Italy
| | - Fabio Mavelli
- Chemistry Department, University of Bari, Via E. Orabona 4, I-70126, Bari, Italy
| | - Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Ecotekne, I-73100, Lecce, Italy
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21
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Bolognesi G, Friddin MS, Salehi-Reyhani A, Barlow NE, Brooks NJ, Ces O, Elani Y. Sculpting and fusing biomimetic vesicle networks using optical tweezers. Nat Commun 2018; 9:1882. [PMID: 29760422 PMCID: PMC5951844 DOI: 10.1038/s41467-018-04282-w] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 04/10/2018] [Indexed: 11/16/2022] Open
Abstract
Constructing higher-order vesicle assemblies has discipline-spanning potential from responsive soft-matter materials to artificial cell networks in synthetic biology. This potential is ultimately derived from the ability to compartmentalise and order chemical species in space. To unlock such applications, spatial organisation of vesicles in relation to one another must be controlled, and techniques to deliver cargo to compartments developed. Herein, we use optical tweezers to assemble, reconfigure and dismantle networks of cell-sized vesicles that, in different experimental scenarios, we engineer to exhibit several interesting properties. Vesicles are connected through double-bilayer junctions formed via electrostatically controlled adhesion. Chemically distinct vesicles are linked across length scales, from several nanometres to hundreds of micrometres, by axon-like tethers. In the former regime, patterning membranes with proteins and nanoparticles facilitates material exchange between compartments and enables laser-triggered vesicle merging. This allows us to mix and dilute content, and to initiate protein expression by delivering biomolecular reaction components. Assembly of higher-order artificial vesicles can unlock new applications. Here, the authors use optical tweezers to construct user-defined 2D and 3D architectures of chemically distinct vesicles and demonstrate inter-vesicle communication and light-enabled compartment merging.
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Affiliation(s)
- Guido Bolognesi
- Department of Chemical Engineering, Loughborough University, Loughborough, LE11 3TU, UK
| | - Mark S Friddin
- Department of Chemistry, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - Ali Salehi-Reyhani
- Department of Chemistry, Imperial College London, Exhibition Road, London, SW7 2AZ, UK.,Institute of Chemical Biology, Imperial College London, Exhibition Road, London, SW7 2AZ, UK.,FABRICELL, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - Nathan E Barlow
- Department of Chemistry, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - Nicholas J Brooks
- Department of Chemistry, Imperial College London, Exhibition Road, London, SW7 2AZ, UK.,Institute of Chemical Biology, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - Oscar Ces
- Department of Chemistry, Imperial College London, Exhibition Road, London, SW7 2AZ, UK. .,Institute of Chemical Biology, Imperial College London, Exhibition Road, London, SW7 2AZ, UK. .,FABRICELL, Imperial College London, Exhibition Road, London, SW7 2AZ, UK.
| | - Yuval Elani
- Department of Chemistry, Imperial College London, Exhibition Road, London, SW7 2AZ, UK. .,Institute of Chemical Biology, Imperial College London, Exhibition Road, London, SW7 2AZ, UK. .,FABRICELL, Imperial College London, Exhibition Road, London, SW7 2AZ, UK.
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22
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Natsume Y, Wen HI, Zhu T, Itoh K, Sheng L, Kurihara K. Preparation of Giant Vesicles Encapsulating Microspheres by Centrifugation of a Water-in-oil Emulsion. J Vis Exp 2017:55282. [PMID: 28190062 PMCID: PMC5352288 DOI: 10.3791/55282] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The constructive biology and the synthetic biology approach to creating artificial life involve the bottom-up assembly of biological or nonbiological materials. Such approaches have received considerable attention in research on the boundary between living and nonliving matter and have been used to construct artificial cells over the past two decades. In particular, Giant Vesicles (GVs) have often been used as artificial cell membranes. In this paper, we describe the preparation of GVs encapsulating highly packed microspheres as a model of cells containing highly condensed biomolecules. The GVs were prepared by means of a simple water-in-oil emulsion centrifugation method. Specifically, a homogenizer was used to emulsify an aqueous solution containing the materials to be encapsulated and an oil containing dissolved phospholipids, and the resulting emulsion was layered carefully on the surface of another aqueous solution. The layered system was then centrifuged to generate the GVs. This powerful method was used to encapsulate materials ranging from small molecules to microspheres.
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Affiliation(s)
- Yuno Natsume
- Department of Mathematical and Physical Sciences, Faculty of Science, Japan Women's University;
| | - Hsin-I Wen
- Department of Bioorganization Research, Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences
| | - Tong Zhu
- Department of Bioorganization Research, Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences
| | - Kazumi Itoh
- Department of Mathematical and Physical Sciences, Faculty of Science, Japan Women's University
| | - Li Sheng
- Department of Bioorganization Research, Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences
| | - Kensuke Kurihara
- Department of Bioorganization Research, Okazaki Institute for Integrative Bioscience, National Institutes of Natural Sciences; Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, National Institutes of Natural Sciences; Research Center for Complex Systems Biology, The University of Tokyo;
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23
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Deng NN, Yelleswarapu M, Huck WTS. Monodisperse Uni- and Multicompartment Liposomes. J Am Chem Soc 2016; 138:7584-91. [DOI: 10.1021/jacs.6b02107] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Nan-Nan Deng
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Maaruthy Yelleswarapu
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Wilhelm T. S. Huck
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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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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Schoonen L, van Hest JCM. Compartmentalization Approaches in Soft Matter Science: From Nanoreactor Development to Organelle Mimics. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2016; 28:1109-28. [PMID: 26509964 DOI: 10.1002/adma.201502389] [Citation(s) in RCA: 216] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 08/14/2015] [Indexed: 05/19/2023]
Abstract
Compartmentalization is an essential feature found in living cells to ensure that biological processes occur without being affected by undesired external influences. Over the years many scientists have designed self-assembled soft matter structures that mimic these natural catalytic compartments. The rationale behind this research is threefold. First of all, compartmentalization leads to the creation of a secluded environment for the catalytic species, which solves compatibility issues and which can improve catalyst efficiency and selectivity. Secondly, nano- and micro-compartments are constructed with the aim to obtain microenvironments that more closely mimic the cellular architecture. These biomimetic platforms are used to attain a better understanding of how cellular processes are executed. Thirdly, natural design rules are applied to create biomolecular assemblies with unusual functionality, which for example are used as artificial organelles. Here, recent developments will be discussed regarding these compartmentalized catalytic systems, with a selected number of illustrative examples to demonstrate which strategies have been followed, and to show to what extent the ambitious goals of this field of science have been reached. The focus here is on the field of soft matter science, covering the wide spectrum from polymeric assemblies to protein nanocages.
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Affiliation(s)
- Lise Schoonen
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands
| | - Jan C M van Hest
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525, AJ, Nijmegen, The Netherlands
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26
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Chan V, Novakowski SK, Law S, Klein-Bosgoed C, Kastrup CJ. Controlled Transcription of Exogenous mRNA in Platelets Using Protocells. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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27
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Chan V, Novakowski SK, Law S, Klein-Bosgoed C, Kastrup CJ. Controlled Transcription of Exogenous mRNA in Platelets Using Protocells. Angew Chem Int Ed Engl 2015; 54:13590-3. [PMID: 26368852 DOI: 10.1002/anie.201506500] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Indexed: 12/15/2022]
Abstract
Transcribing exogenous RNA in eukaryotic cells requires delivering DNA to their nuclei and changing their genome. Nuclear delivery is often inefficient, limiting the potential scope of gene therapy and synthetic biology. These challenges may be overcome by techniques that allow for extranucleate transcription within eukaryotic cells. Protocells have been developed that enable transcription inside of liposomes; however, it has not yet been demonstrated whether this technology can be extended for use within eukaryotic cells. Here we show RNA-synthesizing nanoliposomes allow transcription of exogenous RNA inside anucleate cells. To accomplish this, components of transcription were encapsulated into liposomes and delivered to platelets. These liposomes were capable of light-induced transcription in platelets, providing proof-of-concept that protocell technology can be adapted for use within mammalian cells.
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Affiliation(s)
- Vivienne Chan
- Michael Smith Laboratories, University of British Columbia (Canada).,Biochemistry and Molecular Biology, University of British Columbia (Canada).,Centre for Blood Research, University of British Columbia (Canada)
| | - Stefanie K Novakowski
- Michael Smith Laboratories, University of British Columbia (Canada).,Biochemistry and Molecular Biology, University of British Columbia (Canada).,Centre for Blood Research, University of British Columbia (Canada)
| | - Simon Law
- Biochemistry and Molecular Biology, University of British Columbia (Canada).,Centre for Blood Research, University of British Columbia (Canada)
| | - Christa Klein-Bosgoed
- Centre for Blood Research, University of British Columbia (Canada).,Pathology and Laboratory Medicine, University of British Columbia (Canada)
| | - Christian J Kastrup
- Michael Smith Laboratories, University of British Columbia (Canada). .,Biochemistry and Molecular Biology, University of British Columbia (Canada). .,Centre for Blood Research, University of British Columbia (Canada).
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28
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Morita M, Onoe H, Yanagisawa M, Ito H, Ichikawa M, Fujiwara K, Saito H, Takinoue M. Droplet-Shooting and Size-Filtration (DSSF) Method for Synthesis of Cell-Sized Liposomes with Controlled Lipid Compositions. Chembiochem 2015. [DOI: 10.1002/cbic.201500354] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Masamune Morita
- Department of Computational Intelligence and Systems Science; Tokyo Institute of Technology; Kanagawa 226-8502 Japan
| | - Hiroaki Onoe
- Department of Mechanical Engineering; Keio University; Kanagawa 223-8522 Japan
| | - Miho Yanagisawa
- Department of Applied Physics; Tokyo University of Agriculture and Technology; Tokyo 184-8588 Japan
| | - Hiroaki Ito
- Department of Physics; Kyoto University; Kyoto 606-8502 Japan
| | | | - Kei Fujiwara
- Department of Bioscience and Informatics; Keio University; Kanagawa 223-8522 Japan
| | - Hirohide Saito
- Center for iPS Cell Research and Application (CiRA); Kyoto University; Kyoto 606-8507 Japan
| | - Masahiro Takinoue
- Department of Computational Intelligence and Systems Science; Tokyo Institute of Technology; Kanagawa 226-8502 Japan
- PRESTO; Japan Science and Technology Agency; Saitama 332-0012 Japan
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29
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Shohda K, Takahashi K, Suyama A. A method of gentle hydration to prepare oil-free giant unilamellar vesicles that can confine enzymatic reactions. Biochem Biophys Rep 2015; 3:76-82. [PMID: 29124169 PMCID: PMC5668676 DOI: 10.1016/j.bbrep.2015.07.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 06/23/2015] [Accepted: 07/07/2015] [Indexed: 12/04/2022] Open
Abstract
We report a new and improved method to prepare, by gentle hydration of lipid films, oil-free giant unilamellar vesicles (GUVs), in which enzymatic reactions can be encapsulated. The traditional method of gentle hydration requires very low concentrations of metal ions, whereas enzymatic reactions generally require mono- and divalent metal ions at physiological concentrations. In order to improve the production of oil-free GUVs that can confine enzymatic reactions, we developed a novel method also based on gentle hydration, but in which the precursor lipid film was doped with both 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)-2000] (PEGylated lipid) and sugar. Close examination of the size, shape, and lamellarity of vesicles prepared in this manner demonstrated that the process improves the production of oil-free GUVs even at low temperatures and physiological salt concentrations. PEGylated lipid and sugar were found to synergistically improve GUV formation. Finally, we demonstrate the successful enzymatic synthesis of RNA within oil-free GUVs that were prepared on ice. Preparation of oil-free GUVs at physiological metal ion concentrations on ice. Synergistic effects of PEGylated lipid and sugar on improvement in GUV formation. Enzymatic RNA synthesis with RNA polymerase in oil-free GUVs prepared on ice.
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Affiliation(s)
- K Shohda
- Department of Life Sciences and Institute of Physics, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - K Takahashi
- Department of Life Sciences and Institute of Physics, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - A Suyama
- Department of Life Sciences and Institute of Physics, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
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30
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Nishimura K, Tsuru S, Suzuki H, Yomo T. Stochasticity in gene expression in a cell-sized compartment. ACS Synth Biol 2015; 4:566-76. [PMID: 25280237 DOI: 10.1021/sb500249g] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The gene expression in a clonal cell population fluctuates significantly, and its relevance to various cellular functions is under intensive debate. A fundamental question is whether the fluctuation is a consequence of the complexity and redundancy in living cells or an inevitable attribute of the minute microreactor nature of cells. To answer this question, we constructed an artificial cell, which consists of only necessary components for the gene expression (in vitro transcription and translation system) and its boundary as a microreactor (cell-sized lipid vesicle), and investigated the gene expression noise. The variation in the expression of two fluorescent proteins was decomposed into the components that were correlated and uncorrelated between the two proteins using a method similar to the one used by Elowitz and co-workers to analyze the expression noise in E. coli. The observed fluctuation was compared with a theoretical model that expresses the amplitude of noise as a function of the average number of intermediate molecules and products. With the assumption that the transcripts are partly active, the theoretical model was able to well describe the noise in the artificial system. Furthermore, the same measurement for E. coli cells harboring an identical plasmid revealed that the E. coli exhibited a similar level of expression noise. Our results demonstrated that the level of fluctuation found in bacterial cells is mostly an intrinsic property that arises even in a primitive form of the cell.
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Affiliation(s)
- Kazuya Nishimura
- Department
of Bioinformatic Engineering, Graduate School of Information Science
and Technology, Osaka University, Yamadaoka 1-5, Suita, Osaka 565-0871, Japan
- Quantitative Biology
Center (QBiC), Riken, Fuedai 6-2-3, Suita, Osaka 565-0874, Japan
| | - Saburo Tsuru
- Department
of Bioinformatic Engineering, Graduate School of Information Science
and Technology, Osaka University, Yamadaoka 1-5, Suita, Osaka 565-0871, Japan
| | - Hiroaki Suzuki
- Faculty
of Science and Engineering, Chuo University, Kasuga 1-13-27, Bunkyo-ku, Tokyo 112-8551, Japan
- Exploratory
Research for Advanced Technology (ERATO), Japan Science and Technology Agency, Yamadaoka 1-5, Suita, Osaka 565-0871, Japan
| | - Tetsuya Yomo
- Department
of Bioinformatic Engineering, Graduate School of Information Science
and Technology, Osaka University, Yamadaoka 1-5, Suita, Osaka 565-0871, Japan
- Exploratory
Research for Advanced Technology (ERATO), Japan Science and Technology Agency, Yamadaoka 1-5, Suita, Osaka 565-0871, Japan
- Department
of Frontier Biosciences, Graduate School of Frontier Biosciences, Osaka University, Yamadaoka 1-5, Suita, Osaka 565-0871, Japan
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31
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Mavelli F, Marangoni R, Stano P. A Simple Protein Synthesis Model for the PURE System Operation. Bull Math Biol 2015; 77:1185-212. [PMID: 25911591 DOI: 10.1007/s11538-015-0082-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 04/07/2015] [Indexed: 11/24/2022]
Abstract
The encapsulation of transcription-translation (TX-TL) cell-free machinery inside lipid vesicles (liposomes) is a key element in synthetic cell technology. The PURE system is a TX-TL kit composed of well-characterized parts, whose concentrations are fine tunable, which works according to a modular architecture. For these reasons, the PURE system perfectly fulfils the requirements of synthetic biology and is widely used for constructing synthetic cells. In this work, we present a simplified mathematical model to simulate the PURE system operations. Based on Michaelis-Menten kinetics and differential equations, the model describes protein synthesis dynamics by using 9 chemical species, 6 reactions and 16 kinetic parameters. The model correctly predicts the time course for messenger RNA and protein production and allows quantitative predictions. By means of this model, it is possible to foresee how the PURE system species affect the mechanism of proteins synthesis and therefore help in understanding scenarios where the concentration of the PURE system components has been modified purposely or as a result of stochastic fluctuations (for example after random encapsulation inside vesicles). The model also makes the determination of response coefficients for all species involved in the TX-TL mechanism possible and allows for scrutiny on how chemical energy is consumed by the three PURE system modules (transcription, translation and aminoacylation).
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Affiliation(s)
- Fabio Mavelli
- Chemistry Department, University of Bari, Via Orabona 4, Bari, Italy,
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32
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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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33
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Soga H, Fujii S, Yomo T, Kato Y, Watanabe H, Matsuura T. In vitro membrane protein synthesis inside cell-sized vesicles reveals the dependence of membrane protein integration on vesicle volume. ACS Synth Biol 2014; 3:372-9. [PMID: 24328098 DOI: 10.1021/sb400094c] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Giant unilamellar vesicles (GUVs) are vesicles>1 μm in diameter that provide an environment in which the effect of a confined reaction volume on intravesicular reactions can be investigated. By synthesizing EmrE, a multidrug transporter from Escherichia coli, as a model membrane protein using a reconstituted in vitro transcription-translation system inside GUVs, we investigated the effect of a confined volume on the synthesis and membrane integration of EmrE. Flow cytometry was used to analyze multiple properties of the vesicles and to quantify EmrE synthesis inside GUVs composed of only 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine. We found that EmrE was synthesized and integrated into the GUV membrane in its active form. We also found that the ratio of membrane-integrated EmrE to total synthesized EmrE increased with decreasing vesicle volume; this finding is explained by the effect of an increased surface-area-to-volume ratio in smaller vesicles. In vitro membrane synthesis inside GUVs is a useful approach to study quantitatively the properties of membrane proteins and their interaction with the membrane under cell-mimicking environments.
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Affiliation(s)
- Haruka Soga
- Department
of Biotechnology, Graduate School of Engineering, Osaka University, 2-1
Yamadaoka, Suita, Osaka, Japan
| | - Satoshi Fujii
- Exploratory
Research for Advanced Technology, Japan Science and Technology Agency, 1-5 Yamadaoka, Suita, Osaka, Japan
| | - Tetsuya Yomo
- Exploratory
Research for Advanced Technology, Japan Science and Technology Agency, 1-5 Yamadaoka, Suita, Osaka, Japan
- Department
of Bioinformatic Engineering, Graduate School of Information Science
and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, Japan
| | - Yasuhiko Kato
- Department
of Biotechnology, Graduate School of Engineering, Osaka University, 2-1
Yamadaoka, Suita, Osaka, Japan
| | - Hajime Watanabe
- Department
of Biotechnology, Graduate School of Engineering, Osaka University, 2-1
Yamadaoka, Suita, Osaka, Japan
| | - Tomoaki Matsuura
- Department
of Biotechnology, Graduate School of Engineering, Osaka University, 2-1
Yamadaoka, Suita, Osaka, Japan
- Exploratory
Research for Advanced Technology, Japan Science and Technology Agency, 1-5 Yamadaoka, Suita, Osaka, Japan
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34
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Yanagisawa M, Sakaue T, Yoshikawa K. Characteristic Behavior of Crowding Macromolecules Confined in Cell-Sized Droplets. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 307:175-204. [DOI: 10.1016/b978-0-12-800046-5.00007-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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35
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Toyota T, Banno T, Nitta S, Takinoue M, Nomoto T, Natsume Y, Matsumura S, Fujinami M. Molecular Building Blocks and Their Architecture in Biologically/Environmentally Compatible Soft Matter Chemical Machinery. J Oleo Sci 2014; 63:1085-98. [DOI: 10.5650/jos.ess14190] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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36
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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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37
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van Nies P, Nourian Z, Kok M, van Wijk R, Moeskops J, Westerlaken I, Poolman JM, Eelkema R, van Esch JH, Kuruma Y, Ueda T, Danelon C. Unbiased Tracking of the Progression of mRNA and Protein Synthesis in Bulk and in Liposome-Confined Reactions. Chembiochem 2013; 14:1963-6. [DOI: 10.1002/cbic.201300449] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Indexed: 12/18/2022]
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38
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Grotzky A, Altamura E, Adamcik J, Carrara P, Stano P, Mavelli F, Nauser T, Mezzenga R, Schlüter AD, Walde P. Structure and enzymatic properties of molecular dendronized polymer-enzyme conjugates and their entrapment inside giant vesicles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:10831-10840. [PMID: 23895383 DOI: 10.1021/la401867c] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Macromolecular hybrid structures were prepared in which two types of enzymes, horseradish peroxidase (HRP) and bovine erythrocytes Cu,Zn-superoxide dismutase (SOD), were linked to a fluorescently labeled, polycationic, dendronized polymer (denpol). Two homologous denpols of first and second generation were used and compared, and the activities of HRP and SOD of the conjugates were measured in aqueous solution separately and in combination. In the latter case the efficiency of the two enzymes in catalyzing a two-step cascade reaction was evaluated. Both enzymes in the two types of conjugates were highly active and comparable to free enzymes, although the efficiency of the enzymes bound to the second-generation denpol was significantly lower (up to a factor of 2) than the efficiency of HRP and SOD linked to the first-generation denpol. Both conjugates were analyzed by atomic force microscopy (AFM), confirming the expected increase in object size compared to free denpols and demonstrating the presence of enzyme molecules localized along the denpol chains. Finally, giant phospholipid vesicles with diameters of up to about 20 μm containing in their aqueous interior pool a first-generation denpol-HRP conjugate were prepared. The HRP of the entrapped conjugate was shown to remain active toward externally added, membrane-permeable substrates, an important prerequisite for the development of vesicular multienzyme reaction systems.
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Affiliation(s)
- Andrea Grotzky
- Laboratory of Polymer Chemistry, Department of Materials, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
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39
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Calviello L, Stano P, Mavelli F, Luisi PL, Marangoni R. Quasi-cellular systems: stochastic simulation analysis at nanoscale range. BMC Bioinformatics 2013; 14 Suppl 7:S7. [PMID: 23815522 PMCID: PMC3633058 DOI: 10.1186/1471-2105-14-s7-s7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The wet-lab synthesis of the simplest forms of life (minimal cells) is a challenging aspect in modern synthetic biology. Quasi-cellular systems able to produce proteins directly from DNA can be obtained by encapsulating the cell-free transcription/translation system PURESYSTEM(PS) in liposomes. It is possible to detect the intra-vesicle protein production using DNA encoding for GFP and monitoring the fluorescence emission over time. The entrapment of solutes in small-volume liposomes is a fundamental open problem. Stochastic simulation is a valuable tool in the study of biochemical reaction at nanoscale range. QDC (Quick Direct-Method Controlled), a stochastic simulation software based on the well-known Gillespie's SSA algorithm, was used. A suitable model formally describing the PS reactions network was developed, to predict, from inner species concentrations (very difficult to measure in small-volumes), the resulting fluorescence signal (experimentally observable). RESULTS Thanks to suitable features specific of QDC, we successfully formalized the dynamical coupling between the transcription and translation processes that occurs in the real PS, thus bypassing the concurrent-only environment of Gillespie's algorithm. Simulations were firstly performed for large liposomes (2.67µm of diameter) entrapping the PS to synthetize GFP. By varying the initial concentrations of the three main classes of molecules involved in the PS (DNA, enzymes, consumables), we were able to stochastically simulate the time-course of GFP-production. The sigmoid fit of the GFP-production curves allowed us to extract three quantitative parameters which are significantly dependent on the various initial states. Then we extended this study for small-volume liposomes (575 nm of diameter), where it is more complex to infer the intra-vesicle composition, due to the expected anomalous entrapment phenomena. We identified almost two extreme states that are forecasted to give rise to significantly different experimental observables. CONCLUSIONS The present work is the first one describing in the detail the stochastic behavior of the PS. Thanks to our results, an experimental approach is now possible, aimed at recording the GFP production kinetics in very small micro-emulsion droplets or liposomes, and inferring, by using the simulation as a reverse-engineering procedure, the internal solutes distribution, and shed light on the still unknown forces driving the entrapment phenomenon.
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Affiliation(s)
- Lorenzo Calviello
- Dipartimento di Informatica, Università di Pisa, L.go B. Pontecorvo 3, 56127 Pisa, Italy
| | - Pasquale Stano
- Dipartimento di Biologia, Università di Roma III, Via G. Marconi 446, 00146 Roma, Italy
| | - Fabio Mavelli
- Dipartimento di Chimica, Università di Bari, Via E. Orabona 4, 70121 Bari, Italy
| | - Pier Luigi Luisi
- Dipartimento di Biologia, Università di Roma III, Via G. Marconi 446, 00146 Roma, Italy
| | - Roberto Marangoni
- Dipartimento di Informatica, Università di Pisa, L.go B. Pontecorvo 3, 56127 Pisa, Italy
- Istituto di Biofisica del CNR, Via G. Moruzzi 1, 56124 Pisa, Italy
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40
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Nourian Z, Danelon C. Linking genotype and phenotype in protein synthesizing liposomes with external supply of resources. ACS Synth Biol 2013; 2:186-93. [PMID: 23656477 DOI: 10.1021/sb300125z] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reconstituting an elementary gene expression system inside self-assembled lipid vesicles to mimic the cellular synthesis machinery is at the core of the development of a minimal cell following a bottom-up synthetic biology approach. The ability to operate the expression of multiple genes in a controlled manner and to generate the output proteins with predictable dynamics in liposomes relies on the link between genotype and phenotype. Here, we established this link in surface-tethered liposomes producing proteins from a linear DNA template using a reconstituted transcription/translation/aminoacylation apparatus fuelled by external supply of feedstock. The amounts of entrapped DNA molecules and synthesized proteins were visualized by fluorescence confocal microscopy in individual vesicles. We showed that there exists no linear correlation between the amount of encapsulated genes and the level of output proteins, which is a consequence of the compositional heterogeneity between liposomes due to the low-copy number of some constituents, as well as interfacing differences with the nutrient-containing environment. In order to decouple gene activity from those sources of variability and, thus, infer the probabilistic occupancy of transcriptionally active genes in protein synthesizing liposomes, we developed a dual gene expression assay consisting of the production of two fluorescent reporter proteins of distinguishable colors from two different DNA templates. The stochastic color-coding of the vesicles was analyzed and compared to the color pattern expected from a Poisson distribution of encapsulated genes. Unexpectedly, we found that the apparent number of transcriptionally active DNA molecules in liposomes corresponds only to ca. 10% of the bulk concentration. We believe that our study provides new insights about the relationship between the genotype and phenotype in protein synthesizing liposomes, which is of primary importance toward the construction of a programmable artificial cell implemented with regulatory gene networks of predictable dynamics.
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Affiliation(s)
- Zohreh Nourian
- Department of Bionanoscience,
Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628
CJ, Delft, The Netherlands
| | - Christophe Danelon
- Department of Bionanoscience,
Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628
CJ, Delft, The Netherlands
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41
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Patil YP, Ahluwalia AK, Jadhav S. Isolation of giant unilamellar vesicles from electroformed vesicle suspensions and their extrusion through nano-pores. Chem Phys Lipids 2013; 167-168:1-8. [DOI: 10.1016/j.chemphyslip.2013.01.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2012] [Revised: 01/05/2013] [Accepted: 01/07/2013] [Indexed: 12/16/2022]
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42
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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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43
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Kuroiwa T, Fujita R, Kobayashi I, Uemura K, Nakajima M, Sato S, Walde P, Ichikawa S. Efficient Preparation of Giant Vesicles as Biomimetic Compartment Systems with High Entrapment Yields for Biomacromolecules. Chem Biodivers 2012; 9:2453-72. [DOI: 10.1002/cbdv.201200274] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Indexed: 11/09/2022]
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44
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Stano P, Rampioni G, Carrara P, Damiano L, Leoni L, Luisi PL. Semi-synthetic minimal cells as a tool for biochemical ICT. Biosystems 2012; 109:24-34. [DOI: 10.1016/j.biosystems.2012.01.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2011] [Accepted: 01/04/2012] [Indexed: 11/25/2022]
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45
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Malinova V, Nallani M, Meier W, Sinner E. Synthetic biology, inspired by synthetic chemistry. FEBS Lett 2012; 586:2146-56. [DOI: 10.1016/j.febslet.2012.05.033] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 05/14/2012] [Accepted: 05/16/2012] [Indexed: 12/12/2022]
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46
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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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Nishimura K, Suzuki H, Toyota T, Yomo T. Size control of giant unilamellar vesicles prepared from inverted emulsion droplets. J Colloid Interface Sci 2012; 376:119-25. [DOI: 10.1016/j.jcis.2012.02.029] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 02/14/2012] [Accepted: 02/15/2012] [Indexed: 10/28/2022]
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Abstract
BACKGROUND The process of solutes entrapment during liposomes formation is interesting for the investigation of the relationship between the formation of compartments and the distribution of molecules inside them; a relevant issue in the studies of the origin of life. Theoretically, when no interactions are supposed among the chemical species to be entrapped, the entrapment is described by a standard Poisson process. But very recent experimental findings show that, for small liposomes (100 nm diameter), the distribution of entrapped molecules is best described by a power-law function. This is of a great importance, as the two random processes give rise to two completely different scenarios. Here we present an in silico stochastic simulation of the encapsulation of a cell-free molecular translation system (the PURE system), obtained following two different entrapment models: a pure Poisson process, and a power-law. The protein synthesis inside the liposomes has been studied in both cases, with the aim to highlight experimental observables that could be measured to assess which model gives a better representation of the real process. RESULTS Firstly, a minimal model for in vitro protein synthesis, based on the PURE system molecular composition, has been formalized. Then, we have designed a reliable experimental simulation where stochastic factors affect the reaction course inside the compartment. To this end, 24 solutes, which represent the PURE system components, have been stochastically distributed among vesicles by following either a Poisson or a power-law distribution. The course of the protein synthesis within each vesicle has been consequently calculated, as a function of vesicle size. Our study can predict translation yield in a population of small liposomes down to the attoliter (10(-18) L) range. Our results show that the efficiency of protein synthesis peaks at approximately 3 · 10(-16) L (840 nm diam.) with a Poisson distribution of solutes, while a relative optimum is found at around 10(-17) L (275 nm diam.) for the power-law statistics. CONCLUSIONS Our simulation clearly shows that the wet-lab measurement of an effective protein synthesis at smaller volumes than 10(-17) L would rule out, according to our models, a Poisson distribution of solutes.
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Diguet A, Yanagisawa M, Liu YJ, Brun E, Abadie S, Rudiuk S, Baigl D. UV-induced bursting of cell-sized multicomponent lipid vesicles in a photosensitive surfactant solution. J Am Chem Soc 2012; 134:4898-904. [PMID: 22316240 PMCID: PMC3303198 DOI: 10.1021/ja211664f] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We study the behavior of multicomponent giant unilamellar vesicles (GUVs) in the presence of AzoTAB, a photosensitive surfactant. GUVs are made of an equimolar ratio of dioleoylphosphatidylcholine (DOPC) and dipalmitoylphosphatidylcholine (DPPC) and various amounts of cholesterol (Chol), where the lipid membrane shows a phase separation into a DPPC-rich liquid-ordered (L(o)) phase and a DOPC-rich liquid-disordered (L(d)) phase. We find that UV illumination at 365 nm for 1 s induces the bursting of a significant fraction of the GUV population. The percentage of UV-induced disrupted vesicles, called bursting rate (Y(burst)), increases with an increase in [AzoTAB] and depends on [Chol] in a non-monotonous manner. Y(burst) decreases when [Chol] increases from 0 to 10 mol % and then increases with a further increase in [Chol], which can be correlated with the phase composition of the membrane. We show that Y(burst) increases with the appearance of solid domains ([Chol] = 0) or with an increase in area fraction of L(o) phase (with increasing [Chol] ≥ 10 mol %). Under our conditions (UV illumination at 365 nm for 1 s), maximal bursting efficiency (Y(burst) = 53%) is obtained for [AzoTAB] = 1 mM and [Chol] = 40 mol %. Finally, by restricting the illumination area, we demonstrate the first selective UV-induced bursting of individual target GUVs. These results show a new method to probe biomembrane mechanical properties using light as well as pave the way for novel strategies of light-induced drug delivery.
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Affiliation(s)
- Antoine Diguet
- Department of Chemistry, Ecole Normale Supérieure, 24 rue Lhomond, 75005 Paris, France
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Cell-Sized confinement in microspheres accelerates the reaction of gene expression. Sci Rep 2012; 2:283. [PMID: 22359735 PMCID: PMC3283880 DOI: 10.1038/srep00283] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 02/02/2012] [Indexed: 11/08/2022] Open
Abstract
Cell-sized water-in-oil droplet covered by a lipid layer was used to understand how lipid membranes affect biochemical systems in living cells. Here, we report a remarkable acceleration of gene expression in a cell-sized water-in-oil droplet entrapping a cell-free translation system to synthesize GFP (green fluorescent protein). The production rate of GFP (V(GFP)) in each droplet remained almost constant at least for on the order of a day, which implies 0(th)-order reaction kinetics. Interestingly, V(GFP) was inversely proportional to radius of droplets (R) when R is under 50 μm, and V(GFP) in droplets with R ∼ 10 μm was more than 10 times higher than that in the bulk. The acceleration rates of GFP production in cell-sized droplets strongly depended on the lipid types. These results demonstrate that the membrane surface has the significant effect to facilitate protein production, especially when the scale of confinement is on the order of cell-size.
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