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Kohyama S, Frohn BP, Babl L, Schwille P. Machine learning-aided design and screening of an emergent protein function in synthetic cells. Nat Commun 2024; 15:2010. [PMID: 38443351 PMCID: PMC10914801 DOI: 10.1038/s41467-024-46203-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 02/16/2024] [Indexed: 03/07/2024] Open
Abstract
Recently, utilization of Machine Learning (ML) has led to astonishing progress in computational protein design, bringing into reach the targeted engineering of proteins for industrial and biomedical applications. However, the design of proteins for emergent functions of core relevance to cells, such as the ability to spatiotemporally self-organize and thereby structure the cellular space, is still extremely challenging. While on the generative side conditional generative models and multi-state design are on the rise, for emergent functions there is a lack of tailored screening methods as typically needed in a protein design project, both computational and experimental. Here we describe a proof-of-principle of how such screening, in silico and in vitro, can be achieved for ML-generated variants of a protein that forms intracellular spatiotemporal patterns. For computational screening we use a structure-based divide-and-conquer approach to find the most promising candidates, while for the subsequent in vitro screening we use synthetic cell-mimics as established by Bottom-Up Synthetic Biology. We then show that the best screened candidate can indeed completely substitute the wildtype gene in Escherichia coli. These results raise great hopes for the next level of synthetic biology, where ML-designed synthetic proteins will be used to engineer cellular functions.
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Affiliation(s)
- Shunshi Kohyama
- Dept. Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, D-82152, Germany
| | - Béla P Frohn
- Dept. Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, D-82152, Germany
| | - Leon Babl
- Dept. Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, D-82152, Germany
| | - Petra Schwille
- Dept. Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, D-82152, Germany.
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2
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Nishikawa S, Sato G, Takada S, Kohyama S, Honda G, Yanagisawa M, Hori Y, Doi N, Yoshinaga N, Fujiwara K. Multimolecular Competition Effect as a Modulator of Protein Localization and Biochemical Networks in Cell-Size Space. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308030. [PMID: 38054641 PMCID: PMC10853730 DOI: 10.1002/advs.202308030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/22/2023] [Indexed: 12/07/2023]
Abstract
Cells are small, closed spaces filled with various types of macromolecules. Although it is shown that the characteristics of biochemical reactions in vitro are quite different from those in living cells, the role of the co-existence of various macromolecules in cell-size space remains still elusive. Here, using a constructive approach, it is demonstrated that the co-existence of various macromolecules themselves has the ability to tune protein localization for spatiotemporal regulation and a biochemical reaction system in a cell-size space. Both experimental and theoretical analyses reveal that enhancement of interfacial effects by a large surface-area-to-volume ratio facilitates membrane localization of molecules in the cell-size space, and the interfacial effects are alleviated by competitive binding to lipid membranes among multiple proteins even if their membrane affinities are weak. These results indicate that competition for membrane binding among various macromolecules in the cell-size space plays a role in regulating the spatiotemporal molecular organization and biochemical reaction networks. These findings shed light on the importance of surrounding molecules for biochemical reactions using purified elements in small spaces.
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Affiliation(s)
- Saki Nishikawa
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
| | - Gaku Sato
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
| | - Sakura Takada
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
| | - Shunshi Kohyama
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
- Present address:
Department for Cellular and Molecular BiophysicsMax Planck Institute for BiochemistryAm Klopferspitz 18D‐82152MartinsriedGermany
| | - Gen Honda
- Komaba Institute for ScienceGraduate School of Arts and SciencesThe University of TokyoKomaba 3‐8‐1MeguroTokyo153‐8902Japan
| | - Miho Yanagisawa
- Komaba Institute for ScienceGraduate School of Arts and SciencesThe University of TokyoKomaba 3‐8‐1MeguroTokyo153‐8902Japan
- Graduate School of ScienceThe University of TokyoHongo 7‐3‐1BunkyoTokyo113‐0033Japan
- Center for Complex Systems BiologyUniversal Biology InstituteThe University of TokyoKomaba 3‐8‐1MeguroTokyo153‐8902Japan
| | - Yutaka Hori
- Department of Applied Physics and Physico‐informaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
| | - Nobuhide Doi
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
| | - Natsuhiko Yoshinaga
- WPI Advanced Institute for Materials Research (WPI‐AIMR)Tohoku UniversityKatahira 2‐1‐1, Aoba‐KuSendai980‐8577Japan
- MathAM‐OILAISTSendai980‐8577Japan
| | - Kei Fujiwara
- Department of Biosciences and InformaticsFaculty of Science and TechnologyKeio University3‐14‐1 Hiyoshi, Kohoku‐kuYokohamaKanagawa223‐8522Japan
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3
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Cameron TA, Margolin W. Insights into the assembly and regulation of the bacterial divisome. Nat Rev Microbiol 2024; 22:33-45. [PMID: 37524757 PMCID: PMC11102604 DOI: 10.1038/s41579-023-00942-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2023] [Indexed: 08/02/2023]
Abstract
The ability to split one cell into two is fundamental to all life, and many bacteria can accomplish this feat several times per hour with high accuracy. Most bacteria call on an ancient homologue of tubulin, called FtsZ, to localize and organize the cell division machinery, the divisome, into a ring-like structure at the cell midpoint. The divisome includes numerous other proteins, often including an actin homologue (FtsA), that interact with each other at the cytoplasmic membrane. Once assembled, the protein complexes that comprise the dynamic divisome coordinate membrane constriction with synthesis of a division septum, but only after overcoming checkpoints mediated by specialized protein-protein interactions. In this Review, we summarize the most recent evidence showing how the divisome proteins of Escherichia coli assemble at the cell midpoint, interact with each other and regulate activation of septum synthesis. We also briefly discuss the potential of divisome proteins as novel antibiotic targets.
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Affiliation(s)
- Todd A Cameron
- Department of Microbiology and Molecular Genetics, McGovern Medical School, Houston, TX, USA
| | - William Margolin
- Department of Microbiology and Molecular Genetics, McGovern Medical School, Houston, TX, USA.
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4
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Gao R, Yu X, Kumar BVVSP, Tian L. Hierarchical Structuration in Protocellular System. SMALL METHODS 2023; 7:e2300422. [PMID: 37438327 DOI: 10.1002/smtd.202300422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/12/2023] [Indexed: 07/14/2023]
Abstract
Spatial control is one of the ubiquitous features in biological systems and the key to the functional complexity of living cells. The strategies to achieve such precise spatial control in protocellular systems are crucial to constructing complex artificial living systems with functional collective behavior. Herein, the authors review recent advances in the spatial control within a single protocell or between different protocells and discuss how such hierarchical structured protocellular system can be used to understand complex living systems or to advance the development of functional microreactors with the programmable release of various biomacromolecular payloads, or smart protocell-biological cell hybrid system.
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Affiliation(s)
- Rui Gao
- Key Laboratory of Biomedical Engineering of Ministry of Education, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Xinran Yu
- Key Laboratory of Biomedical Engineering of Ministry of Education, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
| | | | - Liangfei Tian
- Key Laboratory of Biomedical Engineering of Ministry of Education, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China
- Department of Ultrasound, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310027, China
- Innovation Center for Smart Medical Technologies & Devices, Binjiang Institute of Zhejiang University, Hangzhou, 310053, China
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5
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Tror S, Jeon S, Nguyen HT, Huh E, Shin K. A Self-Regenerating Artificial Cell, that is One Step Closer to Living Cells: Challenges and Perspectives. SMALL METHODS 2023; 7:e2300182. [PMID: 37246263 DOI: 10.1002/smtd.202300182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 04/29/2023] [Indexed: 05/30/2023]
Abstract
Controllable, self-regenerating artificial cells (SRACs) can be a vital advancement in the field of synthetic biology, which seeks to create living cells by recombining various biological molecules in the lab. This represents, more importantly, the first step on a long journey toward creating reproductive cells from rather fragmentary biochemical mimics. However, it is still a difficult task to replicate the complex processes involved in cell regeneration, such as genetic material replication and cell membrane division, in artificially created spaces. This review highlights recent advances in the field of controllable, SRACs and the strategies to achieve the goal of creating such cells. Self-regenerating cells start by replicating DNA and transferring it to a location where proteins can be synthesized. Functional but essential proteins must be synthesized for sustained energy generation and survival needs and function in the same liposomal space. Finally, self-division and repeated cycling lead to autonomous, self-regenerating cells. The pursuit of controllable, SRACs will enable authors to make bold advances in understanding life at the cellular level, ultimately providing an opportunity to use this knowledge to understand the nature of life.
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Affiliation(s)
- Seangly Tror
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Republic of Korea
| | - SeonMin Jeon
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Republic of Korea
| | - Huong Thanh Nguyen
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Republic of Korea
| | - Eunjin Huh
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Republic of Korea
| | - Kwanwoo Shin
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Republic of Korea
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6
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Van de Cauter L, van Buren L, Koenderink GH, Ganzinger KA. Exploring Giant Unilamellar Vesicle Production for Artificial Cells - Current Challenges and Future Directions. SMALL METHODS 2023; 7:e2300416. [PMID: 37464561 DOI: 10.1002/smtd.202300416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/30/2023] [Indexed: 07/20/2023]
Abstract
Creating an artificial cell from the bottom up is a long-standing challenge and, while significant progress has been made, the full realization of this goal remains elusive. Arguably, one of the biggest hurdles that researchers are facing now is the assembly of different modules of cell function inside a single container. Giant unilamellar vesicles (GUVs) have emerged as a suitable container with many methods available for their production. Well-studied swelling-based methods offer a wide range of lipid compositions but at the expense of limited encapsulation efficiency. Emulsion-based methods, on the other hand, excel at encapsulation but are only effective with a limited set of membrane compositions and may entrap residual additives in the lipid bilayer. Since the ultimate artificial cell will need to comply with both specific membrane and encapsulation requirements, there is still no one-method-fits-all solution for GUV formation available today. This review discusses the state of the art in different GUV production methods and their compatibility with GUV requirements and operational requirements such as reproducibility and ease of use. It concludes by identifying the most pressing issues and proposes potential avenues for future research to bring us one step closer to turning artificial cells into a reality.
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Affiliation(s)
- Lori Van de Cauter
- Autonomous Matter Department, AMOLF, Amsterdam, 1098 XG, The Netherlands
| | - Lennard van Buren
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2629 HZ, The Netherlands
| | - Gijsje H Koenderink
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2629 HZ, The Netherlands
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7
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Kobayashi M, Noguchi H, Sato G, Watanabe C, Fujiwara K, Yanagisawa M. Phase-Separated Giant Liposomes for Stable Elevation of α-Hemolysin Concentration in Lipid Membranes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:11481-11489. [PMID: 37531551 DOI: 10.1021/acs.langmuir.3c02019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
Abstract
Staphylococcus aureus α-hemolysin (αHL) is one of the most popular proteins in nanopore experiments within lipid membranes. Higher concentrations of αHL within the lipid membrane are desirable to enhance the mass transport capacity through nanopores. However, the reconstitution of αHL at high concentrations is associated with the problem of membrane lytic disruption. In this study, we present a method that effectively increases αHL concentration while maintaining membrane stability. This method is achieved by using phase-separated giant liposomes, where coexisting liquid-disordered (Ld) and liquid-ordered phases (Lo) are enriched in unsaturated lipids and saturated lipids with cholesterol (Chol), respectively. Fluorescence observation of αHL in liposomes revealed that the presence of Chol facilitates αHL insertion into the membrane. Despite the preferential localization of αHL in the Ld phase rather than the Lo phase, the coexistence of both Lo and Ld phases prevents membrane disruption in the presence of concentrated αHL. We have explained this stabilization mechanism considering the lower membrane tension exhibited by phase-separated liposomes compared to homogeneous liposomes. Under hypertonic conditions, we have successfully increased the local concentration of αHL by invagination of the lipid-only region in the Ld phase, leaving αHL behind. This method exhibits potential for the reconstitution of various nanochannels and membrane proteins that prefer the Ld phase over the Lo phase, thus enabling the production of giant liposomes at high concentrations and the replication of the membrane-crowding condition observed in cells.
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Affiliation(s)
- Mizuki Kobayashi
- Department of Applied Physics, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
- Graduate School of Arts and Sciences, Komaba Institute for Science, The University of Tokyo, Komaba, Meguro, Tokyo 153-8902, Japan
| | - Hiroshi Noguchi
- Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba 277-8581, Japan
- Graduate School of Science, The University of Tokyo, Hongo, Bunkyo, Tokyo 113-0033, Japan
| | - Gaku Sato
- Department of Biosciences and Informatics, Keio University, Kohoku-ku, Yokohama 223-8522, Japan
| | - Chiho Watanabe
- Graduate School of Arts and Sciences, Komaba Institute for Science, The University of Tokyo, Komaba, Meguro, Tokyo 153-8902, Japan
- School of Integrated Arts and Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama, Higashi, Hiroshima 739-8521, Japan
| | - Kei Fujiwara
- Department of Biosciences and Informatics, Keio University, Kohoku-ku, Yokohama 223-8522, Japan
| | - Miho Yanagisawa
- Graduate School of Arts and Sciences, Komaba Institute for Science, The University of Tokyo, Komaba, Meguro, Tokyo 153-8902, Japan
- Graduate School of Science, The University of Tokyo, Hongo, Bunkyo, Tokyo 113-0033, Japan
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8
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Nakamura M, Fujiwara K, Doi N. Cytoplasmic delivery of siRNA using human-derived membrane penetration-enhancing peptide. J Nanobiotechnology 2022; 20:458. [PMID: 36303212 DOI: 10.1186/s12951-022-01667-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 10/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although protein-based methods using cell-penetrating peptides such as TAT have been expected to provide an alternative approach to siRNA delivery, the low efficiency of endosomal escape of siRNA/protein complexes taken up into cells by endocytosis remains a problem. Here, to overcome this problem, we adopted the membrane penetration-enhancing peptide S19 from human syncytin 1 previously identified in our laboratory. RESULTS We prepared fusion proteins in which the S19 and TAT peptides were fused to the viral RNA-binding domains (RBDs) as carrier proteins, added the RBD-S19-TAT/siRNA complex to human cultured cells, and investigated the cytoplasmic delivery of the complex and the knockdown efficiency of target genes. We found that the intracellular uptake of the RBD-S19-TAT/siRNA complex was increased compared to that of the RBD-TAT/siRNA complex, and the expression level of the target mRNA was decreased. Because siRNA must dissociate from RBD and bind to Argonaute 2 (Ago2) to form the RNA-induced silencing complex (RISC) after the protein/siRNA complex is delivered into the cytoplasm, a dilemma arises: stronger binding between RBD and siRNA increases intracellular uptake but makes RISC formation more difficult. Thus, we next prepared fusion proteins in which the S19 and TAT peptides were fused with Ago2 instead of RBD and found that the efficiencies of siRNA delivery and knockdown obtained using TAT-S19-Ago2 were higher than those using TAT-Ago2. In addition, we found that the smallest RISC delivery induced faster knockdown than traditional siRNA lipofection, probably due to the decreased time required for RISC formation in the cytoplasm. CONCLUSION These results indicated that S19 and TAT-fused siRNA-binding proteins, especially Ago2, should be useful for the rapid and efficient delivery of siRNA without the addition of any endosome-disrupting agent.
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Affiliation(s)
- Momoko Nakamura
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama, 223-8522, Japan
| | - Kei Fujiwara
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama, 223-8522, Japan
| | - Nobuhide Doi
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama, 223-8522, Japan.
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9
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Takada S, Yoshinaga N, Doi N, Fujiwara K. Controlling the Periodicity of a Reaction-Diffusion Wave in Artificial Cells by a Two-Way Energy Supplier. ACS NANO 2022; 16:16853-16861. [PMID: 36214379 DOI: 10.1021/acsnano.2c06756] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Reaction-diffusion (RD) waves, which are dynamic self-organization structures generated by nanosize molecules, are a fundamental mechanism from patterning in nano- and micromaterials to spatiotemporal regulations in living cells, such as cell division and motility. Although the periods of RD waves are the critical element for these functions, the development of a system to control their period is challenging because RD waves result from nonlinear physical dynamics under far-from-equilibrium conditions. Here, we developed an artificial cell system with tunable period of an RD-driven wave (Min protein wave), which determines a cell division site plane in living bacterial cells. The developed system is based on our finding that Min waves are generated by energy consumption of either ATP or dATP, and the period of the wave is different between these two energy suppliers. We showed that the Min-wave period was modulated linearly by the mixing ratio of ATP and dATP and that it was also possible to estimate the mixing ratio of ATP and dATP from the period. Our findings illuminated a previously unidentified principle to control the dissipative dynamics of biomolecules and, simultaneously, built an important framework to construct molecular robots with spatiotemporal units.
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Affiliation(s)
- Sakura Takada
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Natsuhiko Yoshinaga
- Mathematical Science Group, WPI Advanced Institute for Materials Research (WPI-AIMR), Tohoku University Katahira 2-1-1, Aoba-Ku, Sendai 9808577, Japan
- MathAM-OIL, AIST, Sendai 980-8577, Japan
| | - Nobuhide Doi
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Kei Fujiwara
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan
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10
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In vitro assembly, positioning and contraction of a division ring in minimal cells. Nat Commun 2022; 13:6098. [PMID: 36243816 PMCID: PMC9569390 DOI: 10.1038/s41467-022-33679-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 09/27/2022] [Indexed: 02/07/2023] Open
Abstract
Constructing a minimal machinery for autonomous self-division of synthetic cells is a major goal of bottom-up synthetic biology. One paradigm has been the E. coli divisome, with the MinCDE protein system guiding assembly and positioning of a presumably contractile ring based on FtsZ and its membrane adaptor FtsA. Here, we demonstrate the full in vitro reconstitution of this machinery consisting of five proteins within lipid vesicles, allowing to observe the following sequence of events in real time: 1) Assembly of an isotropic filamentous FtsZ network, 2) its condensation into a ring-like structure, along with pole-to-pole mode selection of Min oscillations resulting in equatorial positioning, and 3) onset of ring constriction, deforming the vesicles from spherical shape. Besides demonstrating these essential features, we highlight the importance of decisive experimental factors, such as macromolecular crowding. Our results provide an exceptional showcase of the emergence of cell division in a minimal system, and may represent a step towards developing a synthetic cell.
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11
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Yanagisawa M, Watanabe C, Yoshinaga N, Fujiwara K. Cell-Size Space Regulates the Behavior of Confined Polymers: From Nano- and Micromaterials Science to Biology. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:11811-11827. [PMID: 36125172 DOI: 10.1021/acs.langmuir.2c01397] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Polymer micromaterials in a liquid or gel phase covered with a surfactant membrane are widely used materials in pharmaceuticals, cosmetics, and foods. In particular, cell-sized micromaterials of biopolymer solutions covered with a lipid membrane have been studied as artificial cells to understand cells from a physicochemical perspective. The characteristics and phase transitions of polymers confined to a microscopic space often differ from those in bulk systems. The effect that causes this difference is referred to as the cell-size space effect (CSE), but the specific physicochemical factors remain unclear. This study introduces the analysis of CSE on molecular diffusion, nanostructure transition, and phase separation and presents their main factors, i.e., short- and long-range interactions with the membrane surface and small volume (finite element nature). This serves as a guide for determining the dominant factors of CSE. Furthermore, we also introduce other factors of CSE such as spatial closure and the relationships among space size, the characteristic length of periodicity, the structure size, and many others produced by biomolecular assemblies through the analysis of protein reaction-diffusion systems and biochemical reactions.
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Affiliation(s)
- Miho Yanagisawa
- Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo, Tokyo 113-0033, Japan
| | - Chiho Watanabe
- School of Integrated Arts and Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama 1-7-1, Higashi-Hiroshima 739-8521, Japan
| | - Natsuhiko Yoshinaga
- Mathematical Science Group, WPI Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, Katahira 2-1-1, Aoba-Ku, Sendai 9808577, Japan
- MathAM-OIL, National Institute of Advanced Industrial Science and Technology, Sendai 980-8577, Japan
| | - Kei Fujiwara
- Department of Biosciences & Informatics, Keio University, Yokohama 223-8522, Japan
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12
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Wagner AM, Eto H, Joseph A, Kohyama S, Haraszti T, Zamora RA, Vorobii M, Giannotti MI, Schwille P, Rodriguez-Emmenegger C. Dendrimersome Synthetic Cells Harbor Cell Division Machinery of Bacteria. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2202364. [PMID: 35579491 DOI: 10.1002/adma.202202364] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/11/2022] [Indexed: 06/15/2023]
Abstract
The integration of active cell machinery with synthetic building blocks is the bridge toward developing synthetic cells with biological functions and beyond. Self-replication is one of the most important tasks of living systems, and various complex machineries exist to execute it. In Escherichia coli, a contractile division ring is positioned to mid-cell by concentration oscillations of self-organizing proteins (MinCDE), where it severs membrane and cell wall. So far, the reconstitution of any cell division machinery has exclusively been tied to liposomes. Here, the reconstitution of a rudimentary bacterial divisome in fully synthetic bicomponent dendrimersomes is shown. By tuning the membrane composition, the interaction of biological machinery with synthetic membranes can be tailored to reproduce its dynamic behavior. This constitutes an important breakthrough in the assembly of synthetic cells with biological elements, as tuning of membrane-divisome interactions is the key to engineering emergent biological behavior from the bottom-up.
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Affiliation(s)
- Anna M Wagner
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074, Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Hiromune Eto
- Max Planck Institute of Biochemistry, Department of Cellular and Molecular Biophysics, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Anton Joseph
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074, Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
| | - Shunshi Kohyama
- Max Planck Institute of Biochemistry, Department of Cellular and Molecular Biophysics, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Tamás Haraszti
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074, Aachen, Germany
| | - Ricardo A Zamora
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Carrer de Baldiri Reixac 10-12, Barcelona, 08028, Spain
- Network Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, 28029, Spain
| | - Mariia Vorobii
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074, Aachen, Germany
| | - Marina I Giannotti
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Carrer de Baldiri Reixac 10-12, Barcelona, 08028, Spain
- Network Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, 28029, Spain
- University of Barcelona, Department of Materials Science and Physical Chemistry, Martí i Franquès 10, Barcelona, 08028, Spain
| | - Petra Schwille
- Max Planck Institute of Biochemistry, Department of Cellular and Molecular Biophysics, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Cesar Rodriguez-Emmenegger
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074, Aachen, Germany
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Carrer de Baldiri Reixac 10-12, Barcelona, 08028, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona, 08010, Spain
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13
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Takada S, Yoshinaga N, Doi N, Fujiwara K. Mode selection mechanism in traveling and standing waves revealed by Min wave reconstituted in artificial cells. SCIENCE ADVANCES 2022; 8:eabm8460. [PMID: 35675408 PMCID: PMC9177070 DOI: 10.1126/sciadv.abm8460] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Reaction-diffusion coupling (RDc) generates spatiotemporal patterns, including two dynamic wave modes: traveling and standing waves. Although mode selection plays a substantial role in the spatiotemporal organization of living cell molecules, the mechanism for selecting each wave mode remains elusive. Here, we investigated a wave mode selection mechanism using Min waves reconstituted in artificial cells, emerged by the RDc of MinD and MinE. Our experiments and theoretical analysis revealed that the balance of membrane binding and dissociation from the membrane of MinD determines the mode selection of the Min wave. We successfully demonstrated that the transition of the wave modes can be regulated by controlling this balance and found hysteresis characteristics in the wave mode transition. These findings highlight a previously unidentified role of the balance between activators and inhibitors as a determinant of the mode selection of waves by RDc and depict an unexplored mechanism in intracellular spatiotemporal pattern formations.
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Affiliation(s)
- Sakura Takada
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Natsuhiko Yoshinaga
- Mathematical Science Group, WPI Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, Katahira 2-1-1, Aoba-Ku, Sendai 980-8577, Japan
- MathAM-OIL, AIST, Sendai 980-8577, Japan
- Corresponding author. (N.Y.); (K.F.)
| | - Nobuhide Doi
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Kei Fujiwara
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
- Corresponding author. (N.Y.); (K.F.)
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14
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Shimane Y, Kuruma Y. Rapid and Facile Preparation of Giant Vesicles by the Droplet Transfer Method for Artificial Cell Construction. Front Bioeng Biotechnol 2022; 10:873854. [PMID: 35464723 PMCID: PMC9021372 DOI: 10.3389/fbioe.2022.873854] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/03/2022] [Indexed: 11/22/2022] Open
Abstract
Giant vesicles have been widely used for the bottom-up construction of artificial (or synthetic) cells and the physicochemical analysis of lipid membranes. Although methods for the formation of giant vesicles and the encapsulation of molecules within them have been established, a standardized protocol has not been shared among researchers including non-experts. Here we proposed a rapid and facile protocol that allows the formation of giant vesicles within 30 min. The quality of the giant vesicles encapsulating a cell-free protein expression system was comparable to that of the ones formed using a conventional method, in terms of the synthesis of both soluble and membrane proteins. We also performed protein synthesis in artificial cells using a lyophilized cell-free mixture and showed an equivalent level of protein synthesis. Our method could become a standard method for giant vesicle formation suited for artificial cell research.
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Affiliation(s)
- Yasuhiro Shimane
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- Research Institute of Industrial Technology, Toyo University, Saitama, Japan
| | - Yutetsu Kuruma
- Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
- PRESTO, Japan Science and Technology Agency (JST), Saitama, Japan
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Japan
- *Correspondence: Yutetsu Kuruma,
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15
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Sato Y, Takinoue M. Capsule-like DNA Hydrogels with Patterns Formed by Lateral Phase Separation of DNA Nanostructures. JACS AU 2022; 2:159-168. [PMID: 35098232 PMCID: PMC8790810 DOI: 10.1021/jacsau.1c00450] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Indexed: 05/03/2023]
Abstract
Phase separation is a key phenomenon in artificial cell construction. Recent studies have shown that the liquid-liquid phase separation of designed-DNA nanostructures induces the formation of liquid-like condensates that eventually become hydrogels by lowering the solution temperature. As a compartmental capsule is an essential artificial cell structure, many studies have focused on the lateral phase separation of artificial lipid vesicles. However, controlling phase separation using a molecular design approach remains challenging. Here, we present the lateral liquid-liquid phase separation of DNA nanostructures that leads to the formation of phase-separated capsule-like hydrogels. We designed three types of DNA nanostructures (two orthogonal and a linker nanostructure) that were adsorbed onto an interface of water-in-oil (W/O) droplets via electrostatic interactions. The phase separation of DNA nanostructures led to the formation of hydrogels with bicontinuous, patch, and mix patterns, due to the immiscibility of liquid-like DNA during the self-assembly process. The frequency of appearance of these patterns was altered by designing DNA sequences and altering the mixing ratio of the nanostructures. We constructed a phase diagram for the capsule-like DNA hydrogels by investigating pattern formation under various conditions. The phase-separated DNA hydrogels did not only form on the W/O droplet interface but also on the inner leaflet of lipid vesicles. Notably, the capsule-like hydrogels were extracted into an aqueous solution, maintaining the patterns formed by the lateral phase separation. In addition, the extracted hydrogels were successfully combined with enzymatic reactions, which induced their degradation. Our results provide a method for the design and control of phase-separated hydrogel capsules using sequence-designed DNAs. We envision that by incorporating various DNA nanodevices into DNA hydrogel capsules, the capsules will gain molecular sensing, chemical-information processing, and mechanochemical actuating functions, allowing the construction of functional molecular systems.
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Affiliation(s)
- Yusuke Sato
- Frontier
Research Institute for Interdisciplinary Sciences, Tohoku University, Miyagi 980-8579, Japan
- Department
of Computer Science, Tokyo Institute of
Technology, Kanagawa 226-8502, Japan
| | - Masahiro Takinoue
- Department
of Computer Science, Tokyo Institute of
Technology, Kanagawa 226-8502, Japan
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16
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Okauchi H, Ichihashi N. Continuous Cell-Free Replication and Evolution of Artificial Genomic DNA in a Compartmentalized Gene Expression System. ACS Synth Biol 2021; 10:3507-3517. [PMID: 34781676 DOI: 10.1021/acssynbio.1c00430] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
In all living organisms, genomic DNA continuously replicates by the proteins encoded in itself and undergoes evolution through many generations of replication. This continuous replication coupled with gene expression and the resultant evolution are fundamental functions of living things, but they have not previously been reconstituted in cell-free systems. In this study, we combined an artificial DNA replication scheme with a reconstituted gene expression system and microcompartmentalization to realize these functions. Circular DNA replicated through rolling-circle replication followed by homologous recombination catalyzed by the proteins, phi29 DNA polymerase, and Cre recombinase expressed from the DNA. We encapsulated the system in microscale water-in-oil droplets and performed serial dilution cycles. Isolated circular DNAs at Round 30 accumulated several common mutations, and the isolated DNA clones exhibited higher replication abilities than the original DNA due to its improved ability as a replication template, increased polymerase activity, and a reduced inhibitory effect of polymerization by the recombinase. The artificial genomic DNA, which continuously replicates using self-encoded proteins and autonomously improves its sequence, provides a useful starting point for the development of more complex artificial cells.
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Affiliation(s)
- Hiroki Okauchi
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Norikazu Ichihashi
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
- Komaba Institute for Science, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
- Research Center for Complex Systems Biology, Universal Biology Institute, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
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17
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Matsui Y, Akui T, Doi N, Fujiwara K. Activation of a diluted E. coli cell-free transcription-translation system within liposomes by hypertonic concentration. STAR Protoc 2021; 2:101003. [PMID: 34950885 PMCID: PMC8672043 DOI: 10.1016/j.xpro.2021.101003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We present a protocol for activating protein synthesis in liposomes encapsulating a diluted E. coli cell extract-based TX-TL (transcription-translation) system by hypertonic concentration. Protein expression is turned on in the liposome-encapsulated TX-TL system by simple treatment with a concentrated external solution. The expression of sfGFP is demonstrated here, but it can be applied to other proteins. This protocol can be applied to the development of artificial cells utilizing the switch-on mechanism to activate protein expression, responding to the outer environment. For complete details on the use and execution of this protocol, please refer to Akui et al. (2021). A diluted cell extract-based transcription translation system encapsulated in liposomes Protein synthesis is activated inside liposomes by hypertonic treatment Protocol can be applied to developing artificial cells utilizing the switch-on mechanism
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Affiliation(s)
- Yukino Matsui
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohokuku, Yokohama, Kanagawa 223-8522, Japan
| | - Toshiki Akui
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohokuku, Yokohama, Kanagawa 223-8522, Japan
| | - Nobuhide Doi
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohokuku, Yokohama, Kanagawa 223-8522, Japan
| | - Kei Fujiwara
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohokuku, Yokohama, Kanagawa 223-8522, Japan
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18
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Gondal MN, Chaudhary SU. Navigating Multi-Scale Cancer Systems Biology Towards Model-Driven Clinical Oncology and Its Applications in Personalized Therapeutics. Front Oncol 2021; 11:712505. [PMID: 34900668 PMCID: PMC8652070 DOI: 10.3389/fonc.2021.712505] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 10/26/2021] [Indexed: 12/19/2022] Open
Abstract
Rapid advancements in high-throughput omics technologies and experimental protocols have led to the generation of vast amounts of scale-specific biomolecular data on cancer that now populates several online databases and resources. Cancer systems biology models built using this data have the potential to provide specific insights into complex multifactorial aberrations underpinning tumor initiation, development, and metastasis. Furthermore, the annotation of these single- and multi-scale models with patient data can additionally assist in designing personalized therapeutic interventions as well as aid in clinical decision-making. Here, we have systematically reviewed the emergence and evolution of (i) repositories with scale-specific and multi-scale biomolecular cancer data, (ii) systems biology models developed using this data, (iii) associated simulation software for the development of personalized cancer therapeutics, and (iv) translational attempts to pipeline multi-scale panomics data for data-driven in silico clinical oncology. The review concludes that the absence of a generic, zero-code, panomics-based multi-scale modeling pipeline and associated software framework, impedes the development and seamless deployment of personalized in silico multi-scale models in clinical settings.
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Affiliation(s)
- Mahnoor Naseer Gondal
- Biomedical Informatics Research Laboratory, Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
| | - Safee Ullah Chaudhary
- Biomedical Informatics Research Laboratory, Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
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19
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Controlled metabolic cascades for protein synthesis in an artificial cell. Biochem Soc Trans 2021; 49:2143-2151. [PMID: 34623386 DOI: 10.1042/bst20210175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 09/04/2021] [Accepted: 09/07/2021] [Indexed: 11/17/2022]
Abstract
In recent years, researchers have been pursuing a method to design and to construct life forms from scratch - in other words, to create artificial cells. In many studies, artificial cellular membranes have been successfully fabricated, allowing the research field to grow by leaps and bounds. Moreover, in addition to lipid bilayer membranes, proteins are essential factors required to construct any cellular metabolic reaction; for that reason, different cell-free expression systems under various conditions to achieve the goal of controlling the synthetic cascades of proteins in a confined area have been reported. Thus, in this review, we will discuss recent issues and strategies, enabling to control protein synthesis cascades that are being used, particularly in research on artificial cells.
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20
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Deyama T, Matsui Y, Chadani Y, Sekine Y, Doi N, Fujiwara K. Transcription-translation of the Escherichia coli genome within artificial cells. Chem Commun (Camb) 2021; 57:10367-10370. [PMID: 34541593 DOI: 10.1039/d1cc04401j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we created artificial cells in which information of the genome of living cells is expressed by the elements encoded in the genome. We confirmed that the system works normally within artificial cells, which paves the way for reconstructing living cells from biomolecules.
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Affiliation(s)
- Tatsuki Deyama
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan.
| | - Yukino Matsui
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan.
| | - Yuhei Chadani
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, S2-19, 4259 Nagatsuta, Midori-ku, Yokohama 226-8503, Japan
| | - Yasuhiko Sekine
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Nobuhide Doi
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan.
| | - Kei Fujiwara
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan.
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21
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System concentration shift as a regulator of transcription-translation system within liposomes. iScience 2021; 24:102859. [PMID: 34386726 PMCID: PMC8346668 DOI: 10.1016/j.isci.2021.102859] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/09/2021] [Accepted: 07/12/2021] [Indexed: 11/21/2022] Open
Abstract
Biochemical systems in living cells have their optimum concentration ratio among each constituent element to maintain their functionality. However, in the case of the biochemical system with complex interactions and feedbacks among elements, their activity as a system greatly changes by the concentration shift of the entire system irrespective of the concentration ratio among elements. In this study, by using a transcription-translation (TX-TL) system as the subject, we illustrate the principle of the nonlinear relationship between the system concentration and the activity of the system. Our experiment and simulation showed that shifts of the system concentration of TX-TL by dilution and concentration works as a switch of activity and demonstrated its ability to induce a biochemical system to confer the permeability of small molecules to liposomes. These results contribute to the creation of artificial cells with the switch and provide an insight into the emergence of protocells.
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22
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Uwaguchi Y, Fujiwara K, Doi N. Switching ON of Transcription-Translation System Using GUV Fusion by Co-supplementation of Calcium with Long-Chain Polyethylene Glycol. Chembiochem 2021; 22:2319-2324. [PMID: 33971077 DOI: 10.1002/cbic.202100100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/28/2021] [Indexed: 11/09/2022]
Abstract
Giant unilamellar vesicles (GUVs) have been used as a material for bottom-up synthetic biology. However, due to the semi-permeability of the membrane, the need for methods to fuse GUVs has increased. To this aim, methods that are simple and show low leakage during fusion are important. In this study, we report a method of GUV fusion by a divalent cation (Ca2+ ) enhanced with a long chain polyethylene glycol (PEG20k). The methods showed significant GUV fusion without leakage of internal components of GUVs and maintained cell-free transcription-translation ability inside the GUVs without external supplementation of macromolecules. We demonstrate that the Ca-PEG method can be applied for switching ON of transcription-translation in GUVs in a fusion-dependent manner. The method developed here can be applied to extend bottom-up synthetic biology and molecular robotics that use GUVs as a chassis.
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Affiliation(s)
- Yusuke Uwaguchi
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
| | - Kei Fujiwara
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
| | - Nobuhide Doi
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, 223-8522, Japan
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23
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A Relationship between NTP and Cell Extract Concentration for Cell-Free Protein Expression. Life (Basel) 2021; 11:life11030237. [PMID: 33805612 PMCID: PMC7999496 DOI: 10.3390/life11030237] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/10/2021] [Accepted: 03/11/2021] [Indexed: 01/29/2023] Open
Abstract
The cell-free protein synthesis (CFPS) that synthesizes mRNA and protein from a template DNA has been featured as an important tool to emulate living systems in vitro. However, an obstacle to emulate living cells by CFPS is the loss of activity in the case of usage of high concentration cell extracts. In this study, we found that a high concentration of NTP which inhibits in the case of lower concentration cell extract restored the loss of CFPS activity using high concentration cell extracts. The NTP restoration was independent of the energy regeneration system used, and NTP derivatives also restored the levels of CFPS using a high concentration cell extract. Experiments using dialysis mode of CFPS showed that continuous exchange of small molecule reduced levels of NTP requirement and improved reaction speed of CFPS using the high concentration of cell extract. These findings contribute to the development of a method to understand the condition of living cells by in vitro emulation, and are expected to lead to the achievement of the reconstitution of living cells from biomolecule mixtures.
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24
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Kohyama S, Fujiwara K, Yoshinaga N, Doi N. Conformational equilibrium of MinE regulates the allowable concentration ranges of a protein wave for cell division. NANOSCALE 2020; 12:11960-11970. [PMID: 32458918 DOI: 10.1039/d0nr00242a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The Min system for determining the cell division position at the center in bacteria has a unique character that uses a protein wave (Min wave) that emerges from its components (MinD and MinE). The Min wave emerges under the coupling of chemical reactions and molecular diffusions of MinDE and appears when the concentrations of MinD and MinE are similar. However, the nanoscale mechanism to determine their concentration ranges has remained elusive. In this study, by using artificial cells as a mimic of cells, we showed that the dominant MinE conformations determined the allowable concentration ranges for the emergence of the Min wave. Furthermore, the deletion of the membrane-binding region of MinE indicated that the region was essential for limiting the concentration ranges to be narrower. These findings illustrate a parameter tuning mechanism underlying complex molecular systems at the nanoscale for spatiotemporal regulation in living cells and show a possibility that the regulation of the equilibrium among molecular conformations can work as a switch for cell division.
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Affiliation(s)
- Shunshi Kohyama
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan.
| | - Kei Fujiwara
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan.
| | - Natsuhiko Yoshinaga
- Mathematical Science Group, WPI Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, Katahira 2-1-1, Aoba-Ku, Sendai 9808577, Japan and MathAM-OIL, AIST, Sendai 980-8577, Japan
| | - Nobuhide Doi
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan.
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25
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Kohyama S, Fujiwara K, Yoshinaga N, Doi N. Self-organization Assay for Min Proteins of Escherichia coli in Micro-droplets Covered with Lipids. Bio Protoc 2020; 10:e3561. [PMID: 33659532 PMCID: PMC7842281 DOI: 10.21769/bioprotoc.3561] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 02/03/2020] [Accepted: 02/19/2020] [Indexed: 11/09/2022] Open
Abstract
The Min system determines the cell division plane of bacteria. As a cue of spatiotemporal regulation, the Min system uses wave propagation of MinD protein (Min wave). Therefore, the reconstitution of the Min wave in cell-sized closed space will lead to the creation of artificial cells capable of cell division. The Min waves emerge via coupling between the reactions among MinD, MinE, and ATP and the differences in diffusion rate on the cell membrane and in the cytoplasm. Because Min waves appear only under the balanced condition of the reaction-diffusion coupling, special attentions are needed towards several technical points for the reconstitution of Min waves in artificial cells. This protocol describes a technical method for stably generating Min waves in artificial cells.
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Affiliation(s)
- Shunshi Kohyama
- Department of Biosciences and Informatics, Keio University, Yokohama, Japan
| | - Kei Fujiwara
- Department of Biosciences and Informatics, Keio University, Yokohama, Japan
| | - Natsuhiko Yoshinaga
- Mathematical Science Group, WPI Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, Sendai, Japan.,MathAM-OIL, AIST, Sendai, Japan
| | - Nobuhide Doi
- Department of Biosciences and Informatics, Keio University, Yokohama, Japan
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26
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Goto H, Kanai Y, Yotsui A, Shimokihara S, Shitara S, Oyobiki R, Fujiwara K, Watanabe T, Einaga Y, Matsumoto Y, Miki N, Doi N. Microfluidic screening system based on boron-doped diamond electrodes and dielectrophoretic sorting for directed evolution of NAD(P)-dependent oxidoreductases. LAB ON A CHIP 2020; 20:852-861. [PMID: 31984406 DOI: 10.1039/c9lc01263j] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We report the development of a micro total analysis system (μTAS) based on electrochemical measurements and dielectrophoretic sorting for screening of NAD(P)-dependent oxidoreductases. In this system, the activity of enzymes immobilized on microbeads, together with their encoding DNA, can be measured with a boron-doped diamond (BDD) electrode in each compartment (∼30 nL) of the microfluidic system. The 30 nL droplets containing microbead-displayed genes of enzymes with higher activity can then be recovered by dielectrophoretic sorting. Previously, we developed the NAD(P)H-measuring device containing the BDD electrode for high-throughput measurement of the activity of NAD(P)-dependent oxidoreductases. In this study, we fabricated an encapsulating device and a droplet-sorting device for nanoliter-size droplets, for the first time, and then combined these three devices to construct a μTAS for directed evolution of NAD(P)-dependent oxidoreductases. We confirmed that this system works by proof-of-principle experiments and successfully applied this system for screening of randomized libraries of NAD-dependent dehydrogenases.
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Affiliation(s)
- Haruna Goto
- Department of Biosciences and Informatics, Keio University, Yokohama 223-8522, Japan.
| | - Yuki Kanai
- Department of Biosciences and Informatics, Keio University, Yokohama 223-8522, Japan.
| | - Arisa Yotsui
- Department of Biosciences and Informatics, Keio University, Yokohama 223-8522, Japan.
| | - Shota Shimokihara
- Department of Biosciences and Informatics, Keio University, Yokohama 223-8522, Japan.
| | - Shunya Shitara
- Department of Biosciences and Informatics, Keio University, Yokohama 223-8522, Japan.
| | - Ryo Oyobiki
- Department of Biosciences and Informatics, Keio University, Yokohama 223-8522, Japan.
| | - Kei Fujiwara
- Department of Biosciences and Informatics, Keio University, Yokohama 223-8522, Japan.
| | - Takeshi Watanabe
- Department of Electrical Engineering and Electronics, Aoyama Gakuin University, Sagamihara 252-5258, Japan
| | - Yasuaki Einaga
- Department of Chemistry, Keio University, Yokohama 223-8522, Japan
| | - Yoshinori Matsumoto
- Department of Applied Physics and Physico-Informatics, Keio University, Yokohama 223-8522, Japan
| | - Norihisa Miki
- Department of Mechanical Engineering, Keio University, Yokohama 223-8522, Japan
| | - Nobuhide Doi
- Department of Biosciences and Informatics, Keio University, Yokohama 223-8522, Japan.
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