51
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de Matos MBC, Miranda BS, Rizky Nuari Y, Storm G, Leneweit G, Schiffelers RM, Kok RJ. Liposomes with asymmetric bilayers produced from inverse emulsions for nucleic acid delivery. J Drug Target 2019; 27:681-689. [DOI: 10.1080/1061186x.2019.1579819] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Maria B. C. de Matos
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | | | - Yudha Rizky Nuari
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | - Gert Storm
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
| | | | - Raymond M. Schiffelers
- Laboratory Clinical Chemistry & Haematology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Robbert J. Kok
- Department of Pharmaceutics, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands
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52
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Rampioni G, D'Angelo F, Leoni L, Stano P. Gene-Expressing Liposomes as Synthetic Cells for Molecular Communication Studies. Front Bioeng Biotechnol 2019; 7:1. [PMID: 30705882 PMCID: PMC6344414 DOI: 10.3389/fbioe.2019.00001] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 01/02/2019] [Indexed: 11/13/2022] Open
Abstract
The bottom-up branch of synthetic biology includes-among others-innovative studies that combine cell-free protein synthesis with liposome technology to generate cell-like systems of minimal complexity, often referred to as synthetic cells. The functions of this type of synthetic cell derive from gene expression, hence they can be programmed in a modular, progressive and customizable manner by means of ad hoc designed genetic circuits. This experimental scenario is rapidly expanding and synthetic cell research already counts numerous successes. Here, we present a review focused on the exchange of chemical signals between liposome-based synthetic cells (operating by gene expression) and biological cells, as well as between two populations of synthetic cells. The review includes a short presentation of the "molecular communication technologies," briefly discussing their promises and challenges.
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Affiliation(s)
| | | | - Livia Leoni
- Department of Science, University Roma Tre, Rome, Italy
| | - Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy
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53
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Rampioni G, Leoni L, Stano P. Molecular Communications in the Context of “Synthetic Cells” Research. IEEE Trans Nanobioscience 2019; 18:43-50. [DOI: 10.1109/tnb.2018.2882543] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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54
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Stano P. Is Research on "Synthetic Cells" Moving to the Next Level? Life (Basel) 2018; 9:E3. [PMID: 30587790 PMCID: PMC6463193 DOI: 10.3390/life9010003] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 12/20/2018] [Accepted: 12/21/2018] [Indexed: 12/15/2022] Open
Abstract
"Synthetic cells" research focuses on the construction of cell-like models by using solute-filled artificial microcompartments with a biomimetic structure. In recent years this bottom-up synthetic biology area has considerably progressed, and the field is currently experiencing a rapid expansion. Here we summarize some technical and theoretical aspects of synthetic cells based on gene expression and other enzymatic reactions inside liposomes, and comment on the most recent trends. Such a tour will be an occasion for asking whether times are ripe for a sort of qualitative jump toward novel SC prototypes: is research on "synthetic cells" moving to a next level?
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Affiliation(s)
- Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento; Ecotekne-S.P. Lecce-Monteroni, I-73100 Lecce, Italy.
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55
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G-Protein Coupled Receptor Protein Synthesis on a Lipid Bilayer Using a Reconstituted Cell-Free Protein Synthesis System. Life (Basel) 2018; 8:life8040054. [PMID: 30400226 PMCID: PMC6316570 DOI: 10.3390/life8040054] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/23/2018] [Accepted: 10/30/2018] [Indexed: 12/31/2022] Open
Abstract
Membrane proteins are important drug targets which play a pivotal role in various cellular activities. However, unlike cytosolic proteins, most of them are difficult-to-express proteins. In this study, to synthesize and produce sufficient quantities of membrane proteins for functional and structural analysis, we used a bottom-up approach in a reconstituted cell-free synthesis system, the PURE system, supplemented with artificial lipid mimetics or micelles. Membrane proteins were synthesized by the cell-free system and integrated into lipid bilayers co-translationally. Membrane proteins such as the G-protein coupled receptors were expressed in the PURE system and a productivity ranging from 0.04 to 0.1 mg per mL of reaction was achieved with a correct secondary structure as predicted by circular dichroism spectrum. In addition, a ligand binding constant of 27.8 nM in lipid nanodisc and 39.4 nM in micelle was obtained by surface plasmon resonance and the membrane protein localization was confirmed by confocal microscopy in giant unilamellar vesicles. We found that our method is a promising approach to study the different classes of membrane proteins in their native-like artificial lipid bilayer environment for functional and structural studies.
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56
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Sugiyama H, Toyota T. Toward Experimental Evolution with Giant Vesicles. Life (Basel) 2018; 8:life8040053. [PMID: 30384503 PMCID: PMC6316375 DOI: 10.3390/life8040053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/30/2018] [Accepted: 10/30/2018] [Indexed: 01/19/2023] Open
Abstract
Experimental evolution in chemical models of cells could reveal the fundamental mechanisms of cells today. Various chemical cell models, water-in-oil emulsions, oil-on-water droplets, and vesicles have been constructed in order to conduct research on experimental evolution. In this review, firstly, recent studies with these candidate models are introduced and discussed with regards to the two hierarchical directions of experimental evolution (chemical evolution and evolution of a molecular self-assembly). Secondly, we suggest giant vesicles (GVs), which have diameters larger than 1 µm, as promising chemical cell models for studying experimental evolution. Thirdly, since technical difficulties still exist in conventional GV experiments, recent developments of microfluidic devices to deal with GVs are reviewed with regards to the realization of open-ended evolution in GVs. Finally, as a future perspective, we link the concept of messy chemistry to the promising, unexplored direction of experimental evolution in GVs.
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Affiliation(s)
- Hironori Sugiyama
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.
| | - Taro Toyota
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.
- Universal Biology Institute, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.
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57
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Trantidou T, Dekker L, Polizzi K, Ces O, Elani Y. Functionalizing cell-mimetic giant vesicles with encapsulated bacterial biosensors. Interface Focus 2018; 8:20180024. [PMID: 30443325 PMCID: PMC6227772 DOI: 10.1098/rsfs.2018.0024] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2018] [Indexed: 12/15/2022] Open
Abstract
The design of vesicle microsystems as artificial cells (bottom-up synthetic biology) has traditionally relied on the incorporation of molecular components to impart functionality. These cell mimics have reduced capabilities compared with their engineered biological counterparts (top-down synthetic biology), as they lack the powerful metabolic and regulatory pathways associated with living systems. There is increasing scope for using whole intact cellular components as functional modules within artificial cells, as a route to increase the capabilities of artificial cells. In this feasibility study, we design and embed genetically engineered microbes (Escherichia coli) in a vesicle-based cell mimic and use them as biosensing modules for real-time monitoring of lactate in the external environment. Using this conceptual framework, the functionality of other microbial devices can be conferred into vesicle microsystems in the future, bridging the gap between bottom-up and top-down synthetic biology.
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Affiliation(s)
- Tatiana Trantidou
- Department of Chemistry, Imperial College London, London SW7 2AZ, UK
| | - Linda Dekker
- Department of Life Sciences and Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, UK
| | - Karen Polizzi
- Department of Life Sciences and Centre for Synthetic Biology and Innovation, Imperial College London, London SW7 2AZ, UK
| | - Oscar Ces
- Department of Chemistry, Imperial College London, London SW7 2AZ, UK
- Institute of Chemical Biology, Imperial College London, London SW7 2AZ, UK
- fabriCELL, Imperial College London, London SW7 2AZ, UK
| | - Yuval Elani
- Department of Chemistry, Imperial College London, London SW7 2AZ, UK
- Institute of Chemical Biology, Imperial College London, London SW7 2AZ, UK
- fabriCELL, Imperial College London, London SW7 2AZ, UK
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58
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Sharma K, Hongo A, Nishigaki K, Takamura Y, Biyani M. 'Head-to-Head' mRNA display for the translation of multi-copied proteins with a free C-terminus. Anal Biochem 2018; 557:77-83. [PMID: 30031739 DOI: 10.1016/j.ab.2018.07.015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/14/2018] [Accepted: 07/17/2018] [Indexed: 12/01/2022]
Abstract
With the development of various methods for affinity-based selection of proteins such as phage display, ribosomal display, and mRNA display, the progress in this field has been gradually shifting to function-based selection, such as through single-molecule observation, genetic selection, and compartmentalization technologies. In this vein, we present an opposite link mode of mRNA display termed as a 'Head-to-Head' (H2H) link. The key technique in H2H, formation of a covalent bond between O6-benzylguanine (BG) and O6-alkylguanine-DNA alkyltransferase (AGT), was demonstrated to be workable in H2H ligation, where mRNA is linked to a nascent AGT via a BG-DNA linker, resulting in a "(C-terminus) protein-BG-DNA linker-mRNA (5'-terminus)" conjugate. Thus, a head (N-terminus) to head (5'-terminus) linkage is formed. Among the advantages of H2H, the generation of multi-copied proteins is the most promising and was proven to be possible owing to the restored stop codon, which had been intentionally removed in the conventional mRNA display. Another advantage is obviously having a free C-terminus of the protein, which can be used for modifications such as C-terminal methylation, α-amidation, and others, which occur in nature. A superior merit of H2H is that it makes it possible to use a single construct commonly in mRNA display (affinity-based) and compartmentalization technologies (function-based) without requiring complicated construct changes.
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Affiliation(s)
- Kirti Sharma
- Department of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi city, Ishikawa 923-1292, Japan
| | - Aya Hongo
- Graduate School of Science and Technology, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama city, Saitama 338-8570, Japan
| | - Koichi Nishigaki
- Graduate School of Science and Technology, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama city, Saitama 338-8570, Japan; Center for Single Nanoscale Innovative Devices, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi city, Ishikawa 923-1292, Japan; BioSeeds Corporation, JAIST venture business laboratory, 1-1 Asahidai, Nomi city, Ishikawa 923-1292, Japan
| | - Yuzuru Takamura
- Department of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi city, Ishikawa 923-1292, Japan; Center for Single Nanoscale Innovative Devices, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi city, Ishikawa 923-1292, Japan
| | - Manish Biyani
- Department of Bioscience and Biotechnology, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi city, Ishikawa 923-1292, Japan; Center for Single Nanoscale Innovative Devices, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi city, Ishikawa 923-1292, Japan; BioSeeds Corporation, JAIST venture business laboratory, 1-1 Asahidai, Nomi city, Ishikawa 923-1292, Japan.
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59
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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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60
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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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61
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Contreras-Llano LE, Tan C. High-throughput screening of biomolecules using cell-free gene expression systems. Synth Biol (Oxf) 2018; 3:ysy012. [PMID: 32995520 PMCID: PMC7445777 DOI: 10.1093/synbio/ysy012] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 05/31/2018] [Accepted: 06/25/2018] [Indexed: 01/13/2023] Open
Abstract
The incorporation of cell-free transcription and translation systems into high-throughput screening applications enables the in situ and on-demand expression of peptides and proteins. Coupled with modern microfluidic technology, the cell-free methods allow the screening, directed evolution and selection of desired biomolecules in minimal volumes within a short timescale. Cell-free high-throughput screening applications are classified broadly into in vitro display and on-chip technologies. In this review, we outline the development of cell-free high-throughput screening methods. We further discuss operating principles and representative applications of each screening method. The cell-free high-throughput screening methods may be advanced by the future development of new cell-free systems, miniaturization approaches, and automation technologies.
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Affiliation(s)
| | - Cheemeng Tan
- Department of Biomedical Engineering, University of California Davis, Davis, CA, USA
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62
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Abraham T, Mao M, Tan C. Engineering approaches of smart, bio-inspired vesicles for biomedical applications. Phys Biol 2018; 15:061001. [DOI: 10.1088/1478-3975/aac7a2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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63
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Tsugane M, Suzuki H. Reverse Transcription Polymerase Chain Reaction in Giant Unilamellar Vesicles. Sci Rep 2018; 8:9214. [PMID: 29907779 PMCID: PMC6003926 DOI: 10.1038/s41598-018-27547-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 06/04/2018] [Indexed: 02/07/2023] Open
Abstract
We assessed the applicability of giant unilamellar vesicles (GUVs) for RNA detection using in vesicle reverse transcription polymerase chain reaction (RT-PCR). We prepared GUVs that encapsulated one-pot RT-PCR reaction mixture including template RNA, primers, and Taqman probe, using water-in-oil emulsion transfer method. After thermal cycling, we analysed the GUVs that exhibited intense fluorescence signals, which represented the cDNA amplification. The detailed analysis of flow cytometry data demonstrated that rRNA and mRNA in the total RNA can be amplified from 10–100 copies in the GUVs with 5–10 μm diameter, although the fraction of reactable GUV was approximately 60% at most. Moreover, we report that the target RNA, which was directly transferred into the GUV reactors via membrane fusion, can be amplified and detected using in vesicle RT-PCR. These results suggest that the GUVs can be used as biomimetic reactors capable of performing PCR and RT-PCR, which are important in analytical and diagnostic applications with additional functions.
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Affiliation(s)
- Mamiko Tsugane
- Department of Precision Mechanics, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, Japan.,Japan Society for the Promotion of Science (JSPS), 5-3-1 Kojimachi, Chiyoda-ku, Tokyo, Japan
| | - Hiroaki Suzuki
- Department of Precision Mechanics, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, Japan.
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64
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Uyeda A, Watanabe T, Hohsaka T, Matsuura T. Different protein localizations on the inner and outer leaflet of cell-sized liposomes using cell-free protein synthesis. Synth Biol (Oxf) 2018; 3:ysy007. [PMID: 32995515 PMCID: PMC7445883 DOI: 10.1093/synbio/ysy007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/07/2018] [Accepted: 05/09/2018] [Indexed: 12/02/2022] Open
Abstract
Membranes of living cells possess asymmetry. The inner and outer leaflets of the membrane consist of different phospholipid compositions, which are known to affect the function of membrane proteins, and the loss of the asymmetry has been reported to lead to cell apoptosis. In addition, different proteins are found on the inner and outer leaflets of the membrane, and they are essential for various biochemical reactions, including those related to signal transduction and cell morphology. While in vitro lipid bilayer reconstitution with asymmetric phospholipid compositions has been reported, the reconstitution of lipid bilayer where different proteins are localized in the inner and outer leaflet, thereby enables asymmetric protein localizations, has remained difficult. Herein, we developed a simple method to achieve this asymmetry using an in vitro transcription–translation system (IVTT). The method used a benzylguanine (BG) derivative-modified phospholipid, which forms a covalent bond with a snap-tag sequence. We show that purified snap-tagged protein can be localized to the cell-sized liposome surface via an interaction between BG and the snap-tag. We then show that IVTT-synthesized proteins can be located at the lipid membrane and that different proteins can be asymmetrically localized on the outer and inner leaflets of liposomes.
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Affiliation(s)
- Atsuko Uyeda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takayoshi Watanabe
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Takahiro Hohsaka
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Tomoaki Matsuura
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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65
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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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66
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Karamdad K, Hindley JW, Bolognesi G, Friddin MS, Law RV, Brooks NJ, Ces O, Elani Y. Engineering thermoresponsive phase separated vesicles formed via emulsion phase transfer as a content-release platform. Chem Sci 2018; 9:4851-4858. [PMID: 29910937 PMCID: PMC5982195 DOI: 10.1039/c7sc04309k] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 04/22/2018] [Indexed: 01/20/2023] Open
Abstract
Elucidation of cholesterol insertion efficiency into phase-transfer vesicles enables the rational design of phase-separated membranes as thermally-responsive platforms for artificial cell construction.
Giant unilamellar vesicles (GUVs) are a well-established tool for the study of membrane biophysics and are increasingly used as artificial cell models and functional units in biotechnology. This trend is driven by the development of emulsion-based generation methods such as Emulsion Phase Transfer (EPT), which facilitates the encapsulation of almost any water-soluble compounds (including biomolecules) regardless of size or charge, is compatible with droplet microfluidics, and allows GUVs with asymmetric bilayers to be assembled. However, the ability to control the composition of membranes formed via EPT remains an open question; this is key as composition gives rise to an array of biophysical phenomena which can be used to add functionality to membranes. Here, we evaluate the use of GUVs constructed via this method as a platform for phase behaviour studies and take advantage of composition-dependent features to engineer thermally-responsive GUVs. For the first time, we generate ternary GUVs (DOPC/DPPC/cholesterol) using EPT, and by compensating for the lower cholesterol incorporation efficiencies, show that these possess the full range of phase behaviour displayed by electroformed GUVs. As a demonstration of the fine control afforded by this approach, we demonstrate release of dye and peptide cargo when ternary GUVs are heated through the immiscibility transition temperature, and show that release temperature can be tuned by changing vesicle composition. We show that GUVs can be individually addressed and release triggered using a laser beam. Our findings validate EPT as a suitable method for generating phase separated vesicles and provide a valuable proof-of-concept for engineering content release functionality into individually addressable vesicles, which could have a host of applications in the development of smart synthetic biosystems.
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Affiliation(s)
- Kaiser Karamdad
- 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
| | - James W Hindley
- 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
| | - 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 . ;
| | - Robert V Law
- 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
| | - 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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67
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Krinsky N, Kaduri M, Zinger A, Shainsky-Roitman J, Goldfeder M, Benhar I, Hershkovitz D, Schroeder A. Synthetic Cells Synthesize Therapeutic Proteins inside Tumors. Adv Healthc Mater 2018; 7:e1701163. [PMID: 29283226 PMCID: PMC6684359 DOI: 10.1002/adhm.201701163] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 11/11/2017] [Indexed: 12/14/2022]
Abstract
Synthetic cells, artificial cell-like particles, capable of autonomously synthesizing RNA and proteins based on a DNA template, are emerging platforms for studying cellular functions and for revealing the origins-of-life. Here, it is shown for the first time that artificial lipid-based vesicles, containing the molecular machinery necessary for transcription and translation, can be used to synthesize anticancer proteins inside tumors. The synthetic cells are engineered as stand-alone systems, sourcing nutrients from their biological microenvironment to trigger protein synthesis. When pre-loaded with template DNA, amino acids and energy-supplying molecules, up to 2 × 107 copies of green fluorescent protein are synthesized in each synthetic cell. A variety of proteins, having molecular weights reaching 66 kDa and with diagnostic and therapeutic activities, are synthesized inside the particles. Incubating synthetic cells, encoded to secrete Pseudomonas exotoxin A (PE) with 4T1 breast cancer cells in culture, resulted in killing of most of the malignant cells. In mice bearing 4T1 tumors, histological evaluation of the tumor tissue after a local injection of PE-producing particles indicates robust apoptosis. Synthetic cells are new platforms for synthesizing therapeutic proteins on-demand in diseased tissues.
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Affiliation(s)
- Nitzan Krinsky
- Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 32000, Israel
- The Interdisciplinary Programs for Biotechnology, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Maya Kaduri
- Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Assaf Zinger
- Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Janna Shainsky-Roitman
- Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Mor Goldfeder
- Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - Itai Benhar
- Department of Molecular Microbiology and Biotechnology, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, 6997801, Israel
| | - Dov Hershkovitz
- Department of Pathology, Tel-Aviv Sourasky Medical Center, Tel Aviv, 6423906, Israel
| | - Avi Schroeder
- Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 32000, Israel
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68
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Furusato T, Horie F, Matsubayashi HT, Amikura K, Kuruma Y, Ueda T. De Novo Synthesis of Basal Bacterial Cell Division Proteins FtsZ, FtsA, and ZipA Inside Giant Vesicles. ACS Synth Biol 2018; 7:953-961. [PMID: 29510621 DOI: 10.1021/acssynbio.7b00350] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cell division is the most dynamic event in the cell cycle. Recently, efforts have been made to reconstruct it using the individual component proteins to obtain a better understanding of the process of self-reproduction of cells. However, such reconstruction studies are frequently hampered by difficulties in preparing membrane-associated proteins. Here we demonstrate a de novo synthesis approach based on a cell-free translation system. Genes for fundamental cell division proteins, FtsZ, FtsA, and ZipA, were expressed inside the lipid compartment of giant vesicles (GVs). The synthesized proteins showed polymerization, membrane localization, and eventually membrane deformation. Notably, we found that this morphological change of the vesicle is forced by only FtsZ and ZipA, which form clusters on the membrane at the vesicle interior. Our cell-free approach provides a platform for studying protein dynamics associated with lipid membrane and paves the way to create a synthetic cell that undergoes self-reproduction.
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Affiliation(s)
- Takumi Furusato
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bldg. FSB-401, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Fumihiro Horie
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bldg. FSB-401, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Hideaki T. Matsubayashi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bldg. FSB-401, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Kazuaki Amikura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bldg. FSB-401, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Yutetsu Kuruma
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Takuya Ueda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bldg. FSB-401, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
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69
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Majumder S, Garamella J, Wang YL, DeNies M, Noireaux V, Liu AP. Cell-sized mechanosensitive and biosensing compartment programmed with DNA. Chem Commun (Camb) 2018; 53:7349-7352. [PMID: 28524182 DOI: 10.1039/c7cc03455e] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The bottom-up construction of cell-sized compartments programmed with DNA that are capable of sensing the chemical and physical environment remains challenging in synthetic cell engineering. Here, we construct mechanosensitive liposomes with biosensing capability by expressing the E. coli channel MscL and a calcium biosensor using cell-free expression.
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Affiliation(s)
- Sagardip Majumder
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, Michigan, USA.
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70
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Rampioni G, D'Angelo F, Messina M, Zennaro A, Kuruma Y, Tofani D, Leoni L, Stano P. Synthetic cells produce a quorum sensing chemical signal perceived by Pseudomonas aeruginosa. Chem Commun (Camb) 2018; 54:2090-2093. [PMID: 29334092 DOI: 10.1039/c7cc09678j] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Recent developments in bottom-up synthetic biology (e.g., lipid vesicle technology integrated with cell-free protein expression systems) allow the generation of semi-synthetic minimal cells (in short, synthetic cells, SCs) endowed with some distinctive capacities of natural cells. In particular, such approaches provide technological tools and conceptual frameworks for the design and engineering of programmable SCs capable of communicating with natural cells by exchanging chemical signals. Here we describe the generation of giant vesicle-based SCs which, via gene expression, synthesize in their aqueous lumen an enzyme that in turn produces a chemical signal. The latter is a small molecule, which is passively released in the medium and then perceived by the bacterium Pseudomonas aeruginosa, demonstrating that SCs and bacteria can communicate chemically. The results pave the way to a novel basic and applied research area where synthetic cells can communicate with natural cells, for example for exploring minimal cognition, developing chemical information technologies, and producing smart and programmable drug-producing/drug-delivery systems.
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Affiliation(s)
- Giordano Rampioni
- Department of Sciences, Roma Tre University, Viale G. Marconi 446, I-00146 Rome, Italy
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71
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Light-triggered enzymatic reactions in nested vesicle reactors. Nat Commun 2018; 9:1093. [PMID: 29545566 PMCID: PMC5854585 DOI: 10.1038/s41467-018-03491-7] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 02/19/2018] [Indexed: 11/09/2022] Open
Abstract
Cell-sized vesicles have tremendous potential both as miniaturised pL reaction vessels and in bottom-up synthetic biology as chassis for artificial cells. In both these areas the introduction of light-responsive modules affords increased functionality, for example, to initiate enzymatic reactions in the vesicle interior with spatiotemporal control. Here we report a system composed of nested vesicles where the inner compartments act as phototransducers, responding to ultraviolet irradiation through diacetylene polymerisation-induced pore formation to initiate enzymatic reactions. The controlled release and hydrolysis of a fluorogenic β-galactosidase substrate in the external compartment is demonstrated, where the rate of reaction can be modulated by varying ultraviolet exposure time. Such cell-like nested microreactor structures could be utilised in fields from biocatalysis through to drug delivery.
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72
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Elani Y, Trantidou T, Wylie D, Dekker L, Polizzi K, Law RV, Ces O. Constructing vesicle-based artificial cells with embedded living cells as organelle-like modules. Sci Rep 2018. [PMID: 29540757 PMCID: PMC5852042 DOI: 10.1038/s41598-018-22263-3] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
There is increasing interest in constructing artificial cells by functionalising lipid vesicles with biological and synthetic machinery. Due to their reduced complexity and lack of evolved biochemical pathways, the capabilities of artificial cells are limited in comparison to their biological counterparts. We show that encapsulating living cells in vesicles provides a means for artificial cells to leverage cellular biochemistry, with the encapsulated cells serving organelle-like functions as living modules inside a larger synthetic cell assembly. Using microfluidic technologies to construct such hybrid cellular bionic systems, we demonstrate that the vesicle host and the encapsulated cell operate in concert. The external architecture of the vesicle shields the cell from toxic surroundings, while the cell acts as a bioreactor module that processes encapsulated feedstock which is further processed by a synthetic enzymatic metabolism co-encapsulated in the vesicle.
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Affiliation(s)
- 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.
| | - Tatiana Trantidou
- Department of Chemistry, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - Douglas Wylie
- 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
| | - Linda Dekker
- Department of Life Sciences, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - Karen Polizzi
- Department of Life Sciences, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - Robert V Law
- Department of Chemistry, 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.
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73
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Gupta K, Varadarajan R. Insights into protein structure, stability and function from saturation mutagenesis. Curr Opin Struct Biol 2018; 50:117-125. [PMID: 29505936 DOI: 10.1016/j.sbi.2018.02.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 02/09/2018] [Accepted: 02/17/2018] [Indexed: 12/20/2022]
Abstract
Where convenient phenotypic readouts are available, saturation mutagenesis coupled to deep sequencing provides a rapid and facile method to infer sequence determinants of protein structure, stability and function. We provide brief descriptions and currently available options for the various steps involved, and mention limitations of current implementations. We also highlight recent applications such as estimating relative stabilities and affinities of protein variants, mapping epitopes, protein model discrimination and prediction of mutant phenotypes. Most mutational scans have so far been applied to single genes and proteins. Additional methodological improvements are required to expand the scope to study intergenic epistasis and intermolecular interactions in macromolecular complexes.
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Affiliation(s)
- Kritika Gupta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Raghavan Varadarajan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India; Jawaharlal Nehru Center for Advanced Scientific Research, Jakkur P.O., Bangalore 560 004, India.
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74
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Machida K, Kanzawa K, Shigeta T, Yamamoto Y, Tsumoto K, Imataka H. Huntingtin Polyglutamine-Dependent Protein Aggregation in Reconstituted Cells. ACS Synth Biol 2018; 7:377-383. [PMID: 29232946 DOI: 10.1021/acssynbio.7b00372] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One of the aims of synthetic biology is bottom-up construction of reconstituted human cells for medical uses. To that end, we generated giant unilamellar vesicles (GUVs) that contained a HeLa cell extract, which comprises a cell-free protein synthesis (CFPS) system. Then we expressed Huntingtin protein fragments that contained polyglutamine (polyQ) sequences (Htt-polyQ), a hallmark of Huntington's disease. That system produced polyQ-dependent protein aggregates, as previously demonstrated in living cells. We next simplified the system by generating GUVs that contained purified human factors, which reconstituted a CFPS system. Htt-polyQ fragments expressed in these GUVs also formed protein aggregates. Moreover, an N-terminal deletion mutant, which had failed to form protein aggregates in living cells, also failed to form protein aggregates in the reconstituted GUVs. Thus, the GUV systems that encapsulated a human CFPS system could serve as reconstituted cells for studying neurological diseases.
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Affiliation(s)
- Kodai Machida
- Department
of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji 671-2201, Japan
- RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan
| | - Kuru Kanzawa
- Department
of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji 671-2201, Japan
| | - Tomoaki Shigeta
- Department
of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji 671-2201, Japan
| | - Yuki Yamamoto
- Department
of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji 671-2201, Japan
| | - Kanta Tsumoto
- Division
of Chemistry for Materials, Graduate School of Engineering, Mie University, Tsu 514-8507, Japan
| | - Hiroaki Imataka
- Department
of Applied Chemistry, Graduate School of Engineering, University of Hyogo, Himeji 671-2201, Japan
- RIKEN Center for Life Science Technologies, Yokohama 230-0045, Japan
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75
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Okano T, Inoue K, Koseki K, Suzuki H. Deformation Modes of Giant Unilamellar Vesicles Encapsulating Biopolymers. ACS Synth Biol 2018; 7:739-747. [PMID: 29382193 DOI: 10.1021/acssynbio.7b00460] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The shapes of giant unilamellar vesicles (GUVs) enclosing polymer molecules at relatively high concentration, used as a model cytoplasm, significantly differ from those containing only small molecules. Here, we investigated the effects of the molecular weights and concentrations of polymers such as polyethylene glycol (PEG), bovine serum albumin (BSA), and DNA on the morphology of GUVs deflated by osmotic pressure. Although small PEG (MW < 1000) does not alter the mode of shape transformation even at >10% (w/w), PEG with MW > 6000 induces budding and pearling transformation at above 1% (w/w). Larger PEG frequently induced small buddings and tubulation from the membrane of mother GUVs. A similar trend was observed with BSA, indicating that the effect is irrelevant to the chemical nature of polymers. More surprisingly, long strands of DNA (>105 bp) enclosed in GUVs induced budding transformation at concentrations as low as 0.01-0.1% (w/w). We expect that this molecular size dependency arises mainly from the depletion volume effect. Our results showed that curving, budding, and tubulation of lipid membranes, which are ubiquitous in living cells, can result from simple cell-mimics consisting of the membrane and cytosolic macromolecules, but without specific shape-determining proteins.
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Affiliation(s)
- Taiji Okano
- Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
| | - Koya Inoue
- Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
| | - Kaoru Koseki
- Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
| | - Hiroaki Suzuki
- Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
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76
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Arai R. Hierarchical design of artificial proteins and complexes toward synthetic structural biology. Biophys Rev 2017; 10:391-410. [PMID: 29243094 DOI: 10.1007/s12551-017-0376-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 11/23/2017] [Indexed: 12/14/2022] Open
Abstract
In multiscale structural biology, synthetic approaches are important to demonstrate biophysical principles and mechanisms underlying the structure, function, and action of bio-nanomachines. A central goal of "synthetic structural biology" is the design and construction of artificial proteins and protein complexes as desired. In this paper, I review recent remarkable progress of an array of approaches for hierarchical design of artificial proteins and complexes that signpost the path forward toward synthetic structural biology as an emerging interdisciplinary field. Topics covered include combinatorial and protein-engineering approaches for directed evolution of artificial binding proteins and membrane proteins, binary code strategy for structural and functional de novo proteins, protein nanobuilding block strategy for constructing nano-architectures, protein-metal-organic frameworks for 3D protein complex crystals, and rational and computational approaches for design/creation of artificial proteins and complexes, novel protein folds, ideal/optimized protein structures, novel binding proteins for targeted therapeutics, and self-assembling nanomaterials. Protein designers and engineers look toward a bright future in synthetic structural biology for the next generation of biophysics and biotechnology.
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Affiliation(s)
- Ryoichi Arai
- Department of Applied Biology, Faculty of Textile Science and Technology, Shinshu University, Ueda, Nagano 386-8567, Japan. .,Department of Supramolecular Complexes, Research Center for Fungal and Microbial Dynamism, Shinshu University, Minamiminowa, Nagano 399-4598, Japan. .,Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, Matsumoto, Nagano 390-8621, Japan. .,Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
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77
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Stano P, Altamura E, Mavelli F. Novel directions in molecular systems design: The case of light-transducing synthetic cells. Commun Integr Biol 2017; 10:e1365993. [PMID: 29260799 PMCID: PMC5731512 DOI: 10.1080/19420889.2017.1365993] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 08/04/2017] [Accepted: 08/04/2017] [Indexed: 12/01/2022] Open
Abstract
Important progresses have been achieved in the past years in the field of bottom-up synthetic biology, especially aiming at constructing cell-like systems based on lipid vesicles (liposomes) entrapping both biomolecules or synthetic compounds. These "synthetic cells" mimic the behaviour of biological cells but are constituted by a minimal number of components. One key aspect related to this research is the energetic needs of synthetic cells. Up to now, high-energy compounds have been given in order to drive biochemical reactions inside the vesicle lumen. In order to be autonomous, synthetic cells must produce their own biochemical energy from available energy sources. At this aim we started a long-term research program focused on the construction of photoautotrophic synthetic cells, starting with the reconstitution, in active and highly oriented form, of the photosynthetic reaction centre in giant lipid vesicles (Altamura et al., PNAS 2017, 114, 3837-3842). Here we comment this first milestone by showing the synthetic biology context wherein it is developed, the future steps, and the experimental approach that might allow such an achievement.
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Affiliation(s)
- Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Ecotekne, Lecce, Italy
| | | | - Fabio Mavelli
- Chemistry Department, University “Aldo Moro,” Bari, Italy
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78
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Katsura K, Matsuda T, Tomabechi Y, Yonemochi M, Hanada K, Ohsawa N, Sakamoto K, Takemoto C, Shirouzu M. A reproducible and scalable procedure for preparing bacterial extracts for cell-free protein synthesis. J Biochem 2017; 162:357-369. [PMID: 28992119 PMCID: PMC7109869 DOI: 10.1093/jb/mvx039] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 05/21/2017] [Indexed: 01/30/2023] Open
Abstract
Cell-free protein synthesis is a useful method for preparing proteins for functional or structural analyses. However, batch-to-batch variability with regard to protein synthesis activity remains a problem for large-scale production of cell extract in the laboratory. To address this issue, we have developed a novel procedure for large-scale preparation of bacterial cell extract with high protein synthesis activity. The developed procedure comprises cell cultivation using a fermentor, harvesting and washing of cells by tangential flow filtration, cell disruption with high-pressure homogenizer and continuous diafiltration. By optimizing and combining these methods, ∼100 ml of the cell extract was prepared from 150 g of Escherichia coli cells. The protein synthesis activities, defined as the yield of protein per unit of absorbance at 260 nm of the cell extract, were shown to be reproducible, and the average activity of several batches was twice that obtained using a previously reported method. In addition, combinatorial use of the high-pressure homogenizer and diafiltration increased the scalability, indicating that the cell concentration at disruption varies from 0.04 to 1 g/ml. Furthermore, addition of Gam protein and examinations of the N-terminal sequence rendered the extract prepared here useful for rapid screening with linear DNA templates.
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Affiliation(s)
- Kazushige Katsura
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takayoshi Matsuda
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yuri Tomabechi
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mayumi Yonemochi
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Kazuharu Hanada
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Noboru Ohsawa
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Kensaku Sakamoto
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Chie Takemoto
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Mikako Shirouzu
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technology, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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79
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Brödel AK, Jaramillo A, Isalan M. Intracellular directed evolution of proteins from combinatorial libraries based on conditional phage replication. Nat Protoc 2017; 12:1830-1843. [PMID: 28796233 DOI: 10.1038/nprot.2017.084] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Directed evolution is a powerful tool to improve the characteristics of biomolecules. Here we present a protocol for the intracellular evolution of proteins with distinct differences and advantages in comparison with established techniques. These include the ability to select for a particular function from a library of protein variants inside cells, minimizing undesired coevolution and propagation of nonfunctional library members, as well as allowing positive and negative selection logics using basally active promoters. A typical evolution experiment comprises the following stages: (i) preparation of a combinatorial M13 phagemid (PM) library expressing variants of the gene of interest (GOI) and preparation of the Escherichia coli host cells; (ii) multiple rounds of an intracellular selection process toward a desired activity; and (iii) the characterization of the evolved target proteins. The system has been developed for the selection of new orthogonal transcription factors (TFs) but is capable of evolving any gene-or gene circuit function-that can be linked to conditional M13 phage replication. Here we demonstrate our approach using as an example the directed evolution of the bacteriophage λ cI TF against two synthetic bidirectional promoters. The evolved TF variants enable simultaneous activation and repression against their engineered promoters and do not cross-react with the wild-type promoter, thus ensuring orthogonality. This protocol requires no special equipment, allowing synthetic biologists and general users to evolve improved biomolecules within ∼7 weeks.
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Affiliation(s)
- Andreas K Brödel
- Department of Life Sciences, Imperial College London, London, UK
| | - Alfonso Jaramillo
- Warwick Integrative Synthetic Biology Centre and School of Life Sciences, University of Warwick, Coventry, UK.,Laboratoire iSSB, UMR 8030, Université Paris-Saclay, Université d'Évry-Val d'Essonne, CNRS, CEA, IG/Genoscope, CEA DRF, Évry, France.,Institute for Integrative Systems Biology (I2SysBio), University of Valencia-CSIC, Paterna, Spain
| | - Mark Isalan
- Department of Life Sciences, Imperial College London, London, UK
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80
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Altamura E, Fiorentino R, Milano F, Trotta M, Palazzo G, Stano P, Mavelli F. First moves towards photoautotrophic synthetic cells: In vitro study of photosynthetic reaction centre and cytochrome bc1 complex interactions. Biophys Chem 2017; 229:46-56. [PMID: 28688734 DOI: 10.1016/j.bpc.2017.06.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 06/23/2017] [Accepted: 06/23/2017] [Indexed: 11/26/2022]
Abstract
Following a bottom-up synthetic biology approach it is shown that vesicle-based cell-like systems (shortly "synthetic cells") can be designed and assembled to perform specific function (for biotechnological applications) and for studies in the origin-of-life field. We recently focused on the construction of synthetic cells capable to converting light into chemical energy. Here we first present our approach, which has been realized so far by the reconstitution of photosynthetic reaction centre in the membrane of giant lipid vesicles. Next, the details of our ongoing research program are presented. It involves the use of the reaction centre, the coenzyme Q-cytochrome c oxidoreductase, and the ATP synthase for creating an autonomous synthetic cell. We show experimental results on the chemistry of the first two proteins showing that they can efficiently sustain light-driven chemical oscillations. Moreover, the cyclic pattern has been reproduced in silico by a minimal kinetic model.
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Affiliation(s)
- Emiliano Altamura
- Chemistry Department, University "Aldo Moro", Via Orabona 4, I-70126 Bari, Italy
| | - Rosa Fiorentino
- Chemistry Department, University "Aldo Moro", Via Orabona 4, I-70126 Bari, Italy
| | - Francesco Milano
- CNR-IPCF, Istituto per i Processi Chimico Fisici, Via Orabona 4, I-70126 Bari, Italy
| | - Massimo Trotta
- CNR-IPCF, Istituto per i Processi Chimico Fisici, Via Orabona 4, I-70126 Bari, Italy
| | - Gerardo Palazzo
- Chemistry Department, University "Aldo Moro", Via 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
| | - Fabio Mavelli
- Chemistry Department, University "Aldo Moro", Via Orabona 4, I-70126 Bari, Italy.
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81
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Highly oriented photosynthetic reaction centers generate a proton gradient in synthetic protocells. Proc Natl Acad Sci U S A 2017; 114:3837-3842. [PMID: 28320948 DOI: 10.1073/pnas.1617593114] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Photosynthesis is responsible for the photochemical conversion of light into the chemical energy that fuels the planet Earth. The photochemical core of this process in all photosynthetic organisms is a transmembrane protein called the reaction center. In purple photosynthetic bacteria a simple version of this photoenzyme catalyzes the reduction of a quinone molecule, accompanied by the uptake of two protons from the cytoplasm. This results in the establishment of a proton concentration gradient across the lipid membrane, which can be ultimately harnessed to synthesize ATP. Herein we show that synthetic protocells, based on giant lipid vesicles embedding an oriented population of reaction centers, are capable of generating a photoinduced proton gradient across the membrane. Under continuous illumination, the protocells generate a gradient of 0.061 pH units per min, equivalent to a proton motive force of 3.6 mV⋅min-1 Remarkably, the facile reconstitution of the photosynthetic reaction center in the artificial lipid membrane, obtained by the droplet transfer method, paves the way for the construction of novel and more functional protocells for synthetic biology.
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82
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Tagami S, Attwater J, Holliger P. Simple peptides derived from the ribosomal core potentiate RNA polymerase ribozyme function. Nat Chem 2017; 9:325-332. [PMID: 28338682 DOI: 10.1038/nchem.2739] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 01/20/2017] [Indexed: 11/09/2022]
Abstract
The emergence of functional interactions between nucleic acids and polypeptides was a key transition in the origin of life and remains at the heart of all biology. However, how and why simple non-coded peptides could have become critical for RNA function is unclear. Here, we show that putative ancient peptide segments from the cores of both ribosomal subunits enhance RNA polymerase ribozyme (RPR) function, as do derived homopolymeric peptides comprising lysine or the non-proteinogenic lysine analogues ornithine or, to a lesser extent, diaminobutyric acid, irrespective of chirality or chiral purity. Lysine decapeptides enhance RPR function by promoting holoenzyme assembly through primer-template docking, accelerate RPR evolution, and allow RPR-catalysed RNA synthesis at near physiological (≥1 mM) Mg2+ concentrations, enabling templated RNA synthesis within membranous protocells. Our results outline how compositionally simple, mixed-chirality peptides may have augmented the functional potential of early RNAs and promoted the emergence of the first protocells.
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Affiliation(s)
- Shunsuke Tagami
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - James Attwater
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
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83
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Sato Y, Hiratsuka Y, Kawamata I, Murata S, Nomura SIM. Micrometer-sized molecular robot changes its shape in response to signal molecules. Sci Robot 2017; 2:2/4/eaal3735. [DOI: 10.1126/scirobotics.aal3735] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 02/03/2017] [Indexed: 11/02/2022]
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84
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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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85
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Uyeda A, Nakayama S, Kato Y, Watanabe H, Matsuura T. Construction of an in Vitro Gene Screening System of the E. coli EmrE Transporter Using Liposome Display. Anal Chem 2016; 88:12028-12035. [DOI: 10.1021/acs.analchem.6b02308] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Atsuko Uyeda
- Department of Biotechnology,
Graduate School of Engineering, Osaka University, 2-1 Yamadaoka,
Suita, Osaka 565-0871, Japan
| | - Shintaro Nakayama
- Department of Biotechnology,
Graduate School of Engineering, Osaka University, 2-1 Yamadaoka,
Suita, Osaka 565-0871, Japan
| | - Yasuhiko Kato
- Department of Biotechnology,
Graduate School of Engineering, Osaka University, 2-1 Yamadaoka,
Suita, Osaka 565-0871, Japan
| | - Hajime Watanabe
- Department of Biotechnology,
Graduate School of Engineering, Osaka University, 2-1 Yamadaoka,
Suita, Osaka 565-0871, Japan
| | - Tomoaki Matsuura
- Department of Biotechnology,
Graduate School of Engineering, Osaka University, 2-1 Yamadaoka,
Suita, Osaka 565-0871, Japan
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86
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Ohta N, Kato Y, Watanabe H, Mori H, Matsuura T. In vitro membrane protein synthesis inside Sec translocon-reconstituted cell-sized liposomes. Sci Rep 2016; 6:36466. [PMID: 27808179 PMCID: PMC5093552 DOI: 10.1038/srep36466] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 10/17/2016] [Indexed: 12/24/2022] Open
Abstract
Protein synthesis using an in vitro transcription-translation system (IVTT) inside cell-sized liposomes has become a valuable tool to study the properties of biological systems under cell-mimicking conditions. However, previous liposome systems lacked the machinery for membrane protein translocation. Here, we reconstituted the translocon consisting of SecYEG from Escherichia coli inside cell-sized liposomes. The cell-sized liposomes also carry the reconstituted IVTT, thereby providing a cell-mimicking environment for membrane protein synthesis. By using EmrE, a multidrug transporter from E. coli, as a model membrane protein, we found that both the amount and activity of EmrE synthesized inside the liposome is increased approximately three-fold by incorporating the Sec translocon. The topological change of EmrE induced by the translocon was also identified. The membrane integration of 6 out of 9 E. coli inner membrane proteins that was tested was increased by incorporation of the translocon. By introducing the Sec translocon, the membrane integration efficiency of the membrane protein of interest was increased, and enabled the integration of membrane proteins that otherwise cannot be inserted. In addition, this work represents an essential step toward the construction of an artificial cell through a bottom-up approach.
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Affiliation(s)
- Naoki Ohta
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 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
| | - Hirotada Mori
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-tyou, Ikoma, Nara, Japan
| | - Tomoaki Matsuura
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, Japan
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87
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Xing H, Hwang K, Lu Y. Recent Developments of Liposomes as Nanocarriers for Theranostic Applications. Theranostics 2016; 6:1336-52. [PMID: 27375783 PMCID: PMC4924503 DOI: 10.7150/thno.15464] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 05/15/2016] [Indexed: 12/12/2022] Open
Abstract
Liposomes are nanocarriers comprised of lipid bilayers encapsulating an aqueous core. The ability of liposomes to encapsulate a wide variety of diagnostic and therapeutic agents has led to significant interest in utilizing liposomes as nanocarriers for theranostic applications. In this review, we highlight recent progress in developing liposomes as nanocarriers for a) diagnostic applications to detect proteins, DNA, and small molecule targets using fluorescence, magnetic resonance, ultrasound, and nuclear imaging; b) therapeutic applications based on small molecule-based therapy, gene therapy and immunotherapy; and c) theranostic applications for simultaneous detection and treatment of heavy metal toxicity and cancers. In addition, we summarize recent studies towards understanding of interactions between liposomes and biological components. Finally, perspectives on future directions in advancing the field for clinical translations are also discussed.
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Affiliation(s)
- Hang Xing
- 1. Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA, 61801
- 2. Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA, 61801
| | - Kevin Hwang
- 1. Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA, 61801
| | - Yi Lu
- 1. Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA, 61801
- 2. Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA, 61801
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88
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Sheng L, Kurihara K. Generation of Catalytic Amphiphiles in a Self-reproducing Giant Vesicle. CHEM LETT 2016. [DOI: 10.1246/cl.160107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Li Sheng
- 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
| | - 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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89
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Stickney Z, Losacco J, McDevitt S, Zhang Z, Lu B. Development of exosome surface display technology in living human cells. Biochem Biophys Res Commun 2016; 472:53-9. [PMID: 26902116 DOI: 10.1016/j.bbrc.2016.02.058] [Citation(s) in RCA: 123] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 02/15/2016] [Indexed: 12/20/2022]
Abstract
Surface display technology is an emerging key player in presenting functional proteins for targeted drug delivery and therapy. Although a number of technologies exist, a desirable mammalian surface display system is lacking. Exosomes are extracellular vesicles that facilitate cell-cell communication and can be engineered as nano-shuttles for cell-specific delivery. In this study, we report the development of a novel exosome surface display technology by exploiting mammalian cell secreted nano-vesicles and their trans-membrane protein tetraspanins. By constructing a set of fluorescent reporters for both the inner and outer surface display on exosomes at two selected sites of tetraspanins, we demonstrated the successful exosomal display via gene transfection and monitoring fluorescence in vivo. We subsequently validated our system by demonstrating the expected intracellular partitioning of reporter protein into sub-cellular compartments and secretion of exosomes from human HEK293 cells. Lastly, we established the stable engineered cells to harness the ability of this robust system for continuous production, secretion, and uptake of displayed exosomes with minimal impact on human cell biology. In sum, our work paved the way for potential applications of exosome, including exosome tracking and imaging, targeted drug delivery, as well as exosome-mediated vaccine and therapy.
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Affiliation(s)
- Zachary Stickney
- Department of Bioengineering, Santa Clara University, 500 El Camino Real, Santa Clara, CA CA95053, USA.
| | - Joseph Losacco
- Department of Bioengineering, Santa Clara University, 500 El Camino Real, Santa Clara, CA CA95053, USA.
| | - Sophie McDevitt
- Department of Bioengineering, Santa Clara University, 500 El Camino Real, Santa Clara, CA CA95053, USA.
| | - Zhiwen Zhang
- Department of Bioengineering, Santa Clara University, 500 El Camino Real, Santa Clara, CA CA95053, USA.
| | - Biao Lu
- Department of Bioengineering, Santa Clara University, 500 El Camino Real, Santa Clara, CA CA95053, USA.
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90
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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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91
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Sustainable proliferation of liposomes compatible with inner RNA replication. Proc Natl Acad Sci U S A 2015; 113:590-5. [PMID: 26711996 DOI: 10.1073/pnas.1516893113] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although challenging, the construction of a life-like compartment via a bottom-up approach can increase our understanding of life and protocells. The sustainable replication of genome information and the proliferation of phospholipid vesicles are requisites for reconstituting cell growth. However, although the replication of DNA or RNA has been developed in phospholipid vesicles, the sustainable proliferation of phospholipid vesicles has remained difficult to achieve. Here, we demonstrate the sustainable proliferation of liposomes that replicate RNA within them. Nutrients for RNA replication and membranes for liposome proliferation were combined by using a modified freeze-thaw technique. These liposomes showed fusion and fission compatible with RNA replication and distribution to daughter liposomes. The RNAs in daughter liposomes were repeatedly used as templates in the next RNA replication and were distributed to granddaughter liposomes. Liposome proliferation was achieved by 10 cycles of iterative culture operation. Therefore, we propose the use of culturable liposomes as an advanced protocell model with the implication that the concurrent supplement of both the membrane material and the nutrients of inner reactions might have enabled protocells to grow sustainably.
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92
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93
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High-Throughput Screening in Protein Engineering: Recent Advances and Future Perspectives. Int J Mol Sci 2015; 16:24918-45. [PMID: 26492240 PMCID: PMC4632782 DOI: 10.3390/ijms161024918] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 10/13/2015] [Accepted: 10/13/2015] [Indexed: 11/17/2022] Open
Abstract
Over the last three decades, protein engineering has established itself as an important tool for the development of enzymes and (therapeutic) proteins with improved characteristics. New mutagenesis techniques and computational design tools have greatly aided in the advancement of protein engineering. Yet, one of the pivotal components to further advance protein engineering strategies is the high-throughput screening of variants. Compartmentalization is one of the key features allowing miniaturization and acceleration of screening. This review focuses on novel screening technologies applied in protein engineering, highlighting flow cytometry- and microfluidics-based platforms.
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94
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Colin PY, Zinchenko A, Hollfelder F. Enzyme engineering in biomimetic compartments. Curr Opin Struct Biol 2015; 33:42-51. [PMID: 26311177 DOI: 10.1016/j.sbi.2015.06.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 05/12/2015] [Accepted: 06/04/2015] [Indexed: 12/25/2022]
Abstract
The success of a directed evolution approach to creating custom-made enzymes relies in no small part on screening as many clones as possible. The miniaturisation of assays into pico to femtoliter compartments (emulsion droplets, vesicles or gel-shell beads) makes directed evolution campaigns practically more straightforward than current large scale industrial screening that requires liquid handling equipment and much manpower. Several recent experimental formats have established protocols to screen more than 10 million compartments per day, representing unprecedented throughput at low cost. This review introduces the emerging approaches towards making biomimetic man-made compartments that are poised to be adapted by a wider circle of researchers. In addition to cost and time saving, control of selection pressures and conditions, the quantitative readout that reports on every library members and the ability to develop strategies based on these data will increase the degrees of freedom in designing and testing strategies for directed evolution experiments.
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Affiliation(s)
- Pierre-Yves Colin
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | | | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
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95
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Ying BW, Honda T, Tsuru S, Seno S, Matsuda H, Kazuta Y, Yomo T. Evolutionary Consequence of a Trade-Off between Growth and Maintenance along with Ribosomal Damages. PLoS One 2015; 10:e0135639. [PMID: 26292224 PMCID: PMC4546238 DOI: 10.1371/journal.pone.0135639] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 07/24/2015] [Indexed: 12/15/2022] Open
Abstract
Microorganisms in nature are constantly subjected to a limited availability of resources and experience repeated starvation and nutrition. Therefore, microbial life may evolve for both growth fitness and sustainability. By contrast, experimental evolution, as a powerful approach to investigate microbial evolutionary strategies, often targets the increased growth fitness in controlled, steady-state conditions. Here, we address evolutionary changes balanced between growth and maintenance while taking nutritional fluctuations into account. We performed a 290-day-long evolution experiment with a histidine-requiring Escherichia coli strain that encountered repeated histidine-rich and histidine-starved conditions. The cells that experienced seven rounds of starvation and re-feed grew more sustainably under prolonged starvation but dramatically lost growth fitness under rich conditions. The improved sustainability arose from the evolved capability to use a trace amount of histidine for cell propagation. The reduced growth rate was attributed to mutations genetically disturbing the translation machinery, that is, the ribosome, ultimately slowing protein translation. This study provides the experimental demonstration of slow growth accompanied by an enhanced affinity to resources as an evolutionary adaptation to oscillated environments and verifies that it is possible to evolve for reduced growth fitness. Growth economics favored for population increase under extreme resource limitations is most likely a common survival strategy adopted by natural microbes.
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Affiliation(s)
- Bei-Wen Ying
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305–8572, Japan
| | - Tomoya Honda
- Section of Molecular Biology, Division of Biological Sciences, University of California San Diego, La Jolla, California, 92093, United States of America
| | - Saburo Tsuru
- Graduate School of Information Science and Technology, Osaka University, 1–5 Yamadaoka, Suita, Osaka, 565–0871, Japan
| | - Shigeto Seno
- Graduate School of Information Science and Technology, Osaka University, 1–5 Yamadaoka, Suita, Osaka, 565–0871, Japan
| | - Hideo Matsuda
- Graduate School of Information Science and Technology, Osaka University, 1–5 Yamadaoka, Suita, Osaka, 565–0871, Japan
| | - Yasuaki Kazuta
- ERATO, JST, 1–5 Yamadaoka, Suita, Osaka, 565–0871, Japan
| | - Tetsuya Yomo
- Graduate School of Information Science and Technology, Osaka University, 1–5 Yamadaoka, Suita, Osaka, 565–0871, Japan
- ERATO, JST, 1–5 Yamadaoka, Suita, Osaka, 565–0871, Japan
- Graduate School of Frontier Biosciences, Osaka University, 1–5 Yamadaoka, Suita, Osaka, 565–0871, Japan
- * E-mail:
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96
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97
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Awai T, Ichihashi N, Yomo T. Activities of 20 aminoacyl-tRNA synthetases expressed in a reconstituted translation system in Escherichia coli. Biochem Biophys Rep 2015; 3:140-143. [PMID: 29124177 PMCID: PMC5668874 DOI: 10.1016/j.bbrep.2015.08.006] [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: 08/01/2015] [Revised: 08/06/2015] [Accepted: 08/06/2015] [Indexed: 01/18/2023] Open
Abstract
A significant challenge in the field of in vitro synthetic biology is the construction of a self-reproducing cell-free translation system, which reproduces its components, such as translation proteins, through translation and transcription by itself. As a first step for such construction, in this study we expressed and evaluated the activity of 20 aminoacyl-tRNA synthetases (aaRSs), a major component of a translation system, in a reconstituted translation system (PURE system). We found that 19 aaRS with the exception of phenylalanyl-tRNA synthetase (PheRS) are expressed as soluble proteins and their activities are comparable to those expressed in Escherichia coli . This study provides basic information on the properties of aaRSs expressed in the PURE system, which will be helpful for the future reconstitution of a self-reproducing translation system. We expressed 20 aminoacyl-tRNA synthetases in a reconstituted translation system. All aminoacyl-tRNA synthetases (aaRSs) are expressed as soluble proteins. All aaRSs with the exception of phenylalanyl-tRNA synthetase are active. Their activities are comparable to those expressed in E. coli.
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Affiliation(s)
- Takako Awai
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.,Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University, Japan
| | - Norikazu Ichihashi
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.,Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tetsuya Yomo
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.,Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.,Graduate School of Frontier Biosciences, Osaka University University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
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98
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Fujii S, Matsuura T, Yomo T. Membrane Curvature Affects the Formation of α-Hemolysin Nanopores. ACS Chem Biol 2015; 10:1694-701. [PMID: 25860290 DOI: 10.1021/acschembio.5b00107] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Membrane proteins perform their functions within or on the lipid membrane, and lipid compositions are known to affect membrane protein integration and activity. Recently, the geometric aspect of membrane curvature was shown to play an important role in membrane protein behavior. Certain membrane proteins are known to sense the curvature of the membrane and to preferentially bind to highly curved membranes. However, although numerous membrane proteins assemble to form homo- or heterocomplexes and perform their biological functions, the dependence of membrane protein assembly on membrane curvature remains elusive. In this study, we analyzed the effect of the membrane curvature on the nanopore formation of α-hemolysin (AH), which is a toxic membrane protein derived from Staphylococcus aureus. The AH protein binds to the membrane as a monomer, assembles to form a heptamer, and forms a nanopore. By simultaneously measuring the molecules bound to the membrane and the activities of the nanopore on the membrane, we determined the nanopore formation ratio of AH. We used various sizes of liposomes and analyzed the dependence on the membrane curvature by using flow cytometry. Combining the results for positive and negative curvature, we found that the nanopore formation ratio of AH was curvature sensitive and was higher in a flat membrane than in a curved membrane. Furthermore, the nanopore formation ratio was almost identical or relatively higher in membranes with negative curvature than those with positive curvature.
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Affiliation(s)
- Satoshi Fujii
- Japan Science and Technology (JST), ERATO, Yomo
Dynamical Micro-scale Reaction Environment Project, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tomoaki Matsuura
- Japan Science and Technology (JST), ERATO, Yomo
Dynamical Micro-scale Reaction Environment Project, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
- Graduate
School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tetsuya Yomo
- Japan Science and Technology (JST), ERATO, Yomo
Dynamical Micro-scale Reaction Environment Project, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
- Graduate
School of Information Science and Technology, Osaka University, 1-5
Yamadaoka, Suita, Osaka 565-0871, Japan
- Graduate
School of Frontier Biosciences, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
- Earth-Life
Science Institute, Tokyo Institute of Technology, Meguro, Tokyo, 152-8550, Japan
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Uyeda A, Watanabe T, Kato Y, Watanabe H, Yomo T, Hohsaka T, Matsuura T. Liposome-Based in Vitro Evolution of Aminoacyl-tRNA Synthetase for Enhanced Pyrrolysine Derivative Incorporation. Chembiochem 2015; 16:1797-802. [DOI: 10.1002/cbic.201500174] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Indexed: 11/09/2022]
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100
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Miller E, Sikes HD. Addressing Barriers to the Development and Adoption of Rapid Diagnostic Tests in Global Health. Nanobiomedicine (Rij) 2015; 2. [PMID: 26594252 PMCID: PMC4652944 DOI: 10.5772/61114] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Immunochromatographic rapid diagnostic tests (RDTs) have demonstrated significant potential for use as point-of-care diagnostic tests in resource-limited settings. Most notably, RDTs for malaria have reached an unparalleled level of technological maturity and market penetration, and are now considered an important complement to standard microscopic methods of malaria diagnosis. However, the technical development of RDTs for other infectious diseases, and their uptake within the global health community as a core diagnostic modality, has been hindered by a number of extant challenges. These range from technical and biological issues, such as the need for better affinity agents and biomarkers of disease, to social, infrastructural, regulatory and economic barriers, which have all served to slow their adoption and diminish their impact. In order for the immunochromatographic RDT format to be successfully adapted to other disease targets, to see widespread distribution, and to improve clinical outcomes for patients on a global scale, these challenges must be identified and addressed, and the global health community must be engaged in championing the broader use of RDTs.
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Affiliation(s)
- Eric Miller
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, USA
| | - Hadley D Sikes
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, USA
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