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Ishida T. Emergence Simulation of Biological Cell-like Shapes Satisfying the Conditions of Life Using a Lattice-Type Multiset Chemical Model. LIFE (BASEL, SWITZERLAND) 2022; 12:life12101580. [PMID: 36295015 PMCID: PMC9605168 DOI: 10.3390/life12101580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/04/2022] [Accepted: 10/08/2022] [Indexed: 11/06/2022]
Abstract
Simple Summary One of the great challenges in science is determining when, where, why, and how life first arose as well as the form taken by this life. In the present study, life was assumed to be (1) bounded, (2) replicating, (3) able to inherit information, and (4) able to metabolize energy. The various existing hypotheses provide little explanation of how these four conditions for life were established. Indeed, “how” a chemical process that simultaneously satisfies all four conditions emerged after the materials for life were in place is not always clear. In this study, a multiset chemical lattice model, which allows for virtual molecules of multiple types to be placed in each cell on a two-dimensional space, was considered. Using only the processes of molecular diffusion, reaction, and polymerization and modeling the chemical reactions of 15 types of molecules and 2 types of polymerized molecules, as well as using the morphogenesis rule of the Turing model, the process of emergence of a cell-like form with all three conditions except evolution ability was modeled and demonstrated. Abstract Although numerous reports using methods such as molecular dynamics, cellular automata, and artificial chemistry have clarified the process connecting non-life and life on protocell simulations, none of the models could simultaneously explain the emergence of cell shape, continuous self-replication, and replication control solely from molecular reactions and diffusion. Herein, we developed a model to generate all three conditions, except evolution ability, from hypothetical chains of chemical and molecular polymerization reactions. The present model considers a 2D lattice cell space, where virtual molecules are placed in each cell, and molecular reactions in each cell are based on a multiset rewriting rule, indicating stochastic transition of molecular species. The reaction paths of virtual molecules were implemented by replacing the rules of cellular automata that generate Turing patterns with molecular reactions. The emergence of a cell-like form with all three conditions except evolution ability was modeled and demonstrated using only molecular diffusion, reaction, and polymerization for modeling the chemical reactions of 15 types of molecules and 2 types of polymerized molecules. Furthermore, controlling self-replication is possible by changing the initial arrangement of a specific molecule. In summary, the present model is capable of investigating and refining existing hypotheses on the emergence of life.
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Affiliation(s)
- Takeshi Ishida
- Department of Ocean Mechanical Engineering, National Fisheries University, Shimonoseki 759-6595, Japan
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Gözen I, Köksal ES, Põldsalu I, Xue L, Spustova K, Pedrueza-Villalmanzo E, Ryskulov R, Meng F, Jesorka A. Protocells: Milestones and Recent Advances. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2106624. [PMID: 35322554 DOI: 10.1002/smll.202106624] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 02/06/2022] [Indexed: 06/14/2023]
Abstract
The origin of life is still one of humankind's great mysteries. At the transition between nonliving and living matter, protocells, initially featureless aggregates of abiotic matter, gain the structure and functions necessary to fulfill the criteria of life. Research addressing protocells as a central element in this transition is diverse and increasingly interdisciplinary. The authors review current protocell concepts and research directions, address milestones, challenges and existing hypotheses in the context of conditions on the early Earth, and provide a concise overview of current protocell research methods.
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Affiliation(s)
- Irep Gözen
- Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, Oslo, 0318, Norway
| | - Elif Senem Köksal
- Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, Oslo, 0318, Norway
| | - Inga Põldsalu
- Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, Oslo, 0318, Norway
| | - Lin Xue
- Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, Oslo, 0318, Norway
| | - Karolina Spustova
- Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, Oslo, 0318, Norway
| | - Esteban Pedrueza-Villalmanzo
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Göteborg, SE-412 96, Sweden
- Department of Physics, University of Gothenburg, Universitetsplatsen 1, Gothenburg, 40530, Sweden
| | - Ruslan Ryskulov
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Göteborg, SE-412 96, Sweden
| | - Fanda Meng
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Göteborg, SE-412 96, Sweden
- School of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, 250000, China
| | - Aldo Jesorka
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Göteborg, SE-412 96, Sweden
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Wang C, Yang J, Lu Y. Modularize and Unite: Toward Creating a Functional Artificial Cell. Front Mol Biosci 2021; 8:781986. [PMID: 34912849 PMCID: PMC8667554 DOI: 10.3389/fmolb.2021.781986] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/17/2021] [Indexed: 11/17/2022] Open
Abstract
An artificial cell is a simplified model of a living system, bringing breakthroughs into both basic life science and applied research. The bottom-up strategy instructs the construction of an artificial cell from nonliving materials, which could be complicated and interdisciplinary considering the inherent complexity of living cells. Although significant progress has been achieved in the past 2 decades, the area is still facing some problems, such as poor compatibility with complex bio-systems, instability, and low standardization of the construction method. In this review, we propose creating artificial cells through the integration of different functional modules. Furthermore, we divide the function requirements of an artificial cell into four essential parts (metabolism, energy supplement, proliferation, and communication) and discuss the present researches. Then we propose that the compartment and the reestablishment of the communication system would be essential for the reasonable integration of functional modules. Although enormous challenges remain, the modular construction would facilitate the simplification and standardization of an artificial cell toward a natural living system. This function-based strategy would also broaden the application of artificial cells and represent the steps of imitating and surpassing nature.
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Affiliation(s)
- Chen Wang
- Key Laboratory of Industrial Biocatalysis, Department of Chemical Engineering, Ministry of Education, Tsinghua University, Beijing, China
| | - Junzhu Yang
- Key Laboratory of Industrial Biocatalysis, Department of Chemical Engineering, Ministry of Education, Tsinghua University, Beijing, China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Department of Chemical Engineering, Ministry of Education, Tsinghua University, Beijing, China
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Wölfer C, Mangold M, Flassig RJ. Towards Design of Self-Organizing Biomimetic Systems. ACTA ACUST UNITED AC 2020; 3:e1800320. [PMID: 32648706 DOI: 10.1002/adbi.201800320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 02/28/2019] [Indexed: 11/08/2022]
Abstract
The ability of designing biosynthetic systems with well-defined functional biomodules from scratch is an ambitious and revolutionary goal to deliver innovative, engineered solutions to future challenges in biotechnology and process systems engineering. In this work, several key challenges including modularization, functional biomodule identification, and assembly are discussed. In addition, an in silico protocell modeling approach is presented as a foundation for a computational model-based toolkit for rational analysis and modular design of biomimetic systems.
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Affiliation(s)
- Christian Wölfer
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany
| | - Michael Mangold
- University of Applied Sciences Bingen, Berlinstraße 109, 55411, Bingen am Rhein, Germany
| | - Robert J Flassig
- Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstr. 1, 39106, Magdeburg, Germany.,University of Applied Sciences Brandenburg, Magdeburger Str. 50, 14770, Brandenburg an der Havel, Germany
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Schwille P, Spatz J, Landfester K, Bodenschatz E, Herminghaus S, Sourjik V, Erb TJ, Bastiaens P, Lipowsky R, Hyman A, Dabrock P, Baret JC, Vidakovic-Koch T, Bieling P, Dimova R, Mutschler H, Robinson T, Tang TYD, Wegner S, Sundmacher K. MaxSynBio: Wege zur Synthese einer Zelle aus nicht lebenden Komponenten. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802288] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Petra Schwille
- Zelluläre und molekulare Biophysik; MPI für Biochemie; Am Klopferspitz 18 82152 Martinsried Deutschland
| | - Joachim Spatz
- MPI für medizinische Forschung; Jahnstraße 29 69120 Heidelberg Deutschland
| | | | - Eberhard Bodenschatz
- MPI für Dynamik und Selbstorganisation; Am Fassberg 17 37077 Göttingen Deutschland
| | - Stephan Herminghaus
- MPI für Dynamik und Selbstorganisation; Am Fassberg 17 37077 Göttingen Deutschland
| | - Victor Sourjik
- MPI für terrestrische Mikrobiologie; Karl-von-Frisch-Str. 16 35043 Marburg Deutschland
| | - Tobias J. Erb
- MPI für terrestrische Mikrobiologie; Karl-von-Frisch-Str. 16 35043 Marburg Deutschland
| | - Philippe Bastiaens
- MPI für molekulare Physiologie; Otto-Hahn-Str. 11 44227 Dortmund Deutschland
| | - Reinhard Lipowsky
- MPI für Kolloide und Grenzflächen; Wissenschaftspark Golm 14424 Potsdam Deutschland
| | - Anthony Hyman
- MPI für molekulare Zellbiologie und Genetik; Pfotenhauerstraße 108 01307 Dresden Deutschland
| | - Peter Dabrock
- Friedrich-Alexander-Universität Erlangen-Nürnberg; Fachbereich Theologie; Kochstraße 6 91054 Erlangen Deutschland
| | - Jean-Christophe Baret
- University of Bordeaux - Centre de Recherches Paul Pascal; 115 Avenue Schweitze 33600 Pessac Frankreich
| | - Tanja Vidakovic-Koch
- MPI für Dynamik komplexer technischer Systeme; Sandtorstraße 1 39106 Magdeburg Deutschland
| | - Peter Bieling
- MPI für molekulare Physiologie; Otto-Hahn-Str. 11 44227 Dortmund Deutschland
| | - Rumiana Dimova
- MPI für Kolloide und Grenzflächen; Wissenschaftspark Golm 14424 Potsdam Deutschland
| | - Hannes Mutschler
- Zelluläre und molekulare Biophysik; MPI für Biochemie; Am Klopferspitz 18 82152 Martinsried Deutschland
| | - Tom Robinson
- MPI für Kolloide und Grenzflächen; Wissenschaftspark Golm 14424 Potsdam Deutschland
| | - T.-Y. Dora Tang
- MPI für molekulare Zellbiologie und Genetik; Pfotenhauerstraße 108 01307 Dresden Deutschland
| | - Seraphine Wegner
- MPI für Polymerforschung; Ackermannweg 10 55128 Mainz Deutschland
| | - Kai Sundmacher
- MPI für Dynamik komplexer technischer Systeme; Sandtorstraße 1 39106 Magdeburg Deutschland
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Schwille P, Spatz J, Landfester K, Bodenschatz E, Herminghaus S, Sourjik V, Erb TJ, Bastiaens P, Lipowsky R, Hyman A, Dabrock P, Baret JC, Vidakovic-Koch T, Bieling P, Dimova R, Mutschler H, Robinson T, Tang TYD, Wegner S, Sundmacher K. MaxSynBio: Avenues Towards Creating Cells from the Bottom Up. Angew Chem Int Ed Engl 2018; 57:13382-13392. [PMID: 29749673 DOI: 10.1002/anie.201802288] [Citation(s) in RCA: 189] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/03/2018] [Indexed: 12/18/2022]
Abstract
A large German research consortium mainly within the Max Planck Society ("MaxSynBio") was formed to investigate living systems from a fundamental perspective. The research program of MaxSynBio relies solely on the bottom-up approach to synthetic biology. MaxSynBio focuses on the detailed analysis and understanding of essential processes of life through modular reconstitution in minimal synthetic systems. The ultimate goal is to construct a basic living unit entirely from non-living components. The fundamental insights gained from the activities in MaxSynBio could eventually be utilized for establishing a new generation of biotechnological processes, which would be based on synthetic cell constructs that replace the natural cells currently used in conventional biotechnology.
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Affiliation(s)
- Petra Schwille
- Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Joachim Spatz
- MPI for Medical Research, Jahnstraße 29, 69120, Heidelberg, Germany
| | | | - Eberhard Bodenschatz
- MPI for Dynamics and Self-Organization, Am Fassberg 17, 37077, Göttingen, Germany
| | - Stephan Herminghaus
- MPI for Dynamics and Self-Organization, Am Fassberg 17, 37077, Göttingen, Germany
| | - Victor Sourjik
- MPI for Terrestrial Microbiology, Karl-von-Frisch-Str. 16, 35043, Marburg, Germany
| | - Tobias J Erb
- MPI for Terrestrial Microbiology, Karl-von-Frisch-Str. 16, 35043, Marburg, Germany
| | - Philippe Bastiaens
- MPI for Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
| | - Reinhard Lipowsky
- MPI of Colloids and Interfaces, Wissenschaftspark Golm, 14424, Potsdam, Germany
| | - Anthony Hyman
- MPI of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Peter Dabrock
- Friedrich-Alexander University Erlangen-Nuremberg, Department of Theology, Kochstraße 6, 91054, Erlangen, Germany
| | - Jean-Christophe Baret
- University of Bordeaux -Centre de Recherches Paul Pascal, 115 Avenue Schweitze, 33600, Pessac, France
| | - Tanja Vidakovic-Koch
- Process Systems Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106, Magdeburg, Germany
| | - Peter Bieling
- MPI for Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany
| | - Rumiana Dimova
- MPI of Colloids and Interfaces, Wissenschaftspark Golm, 14424, Potsdam, Germany
| | - Hannes Mutschler
- Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Tom Robinson
- MPI of Colloids and Interfaces, Wissenschaftspark Golm, 14424, Potsdam, Germany
| | - T-Y Dora Tang
- MPI of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Seraphine Wegner
- MPI for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - Kai Sundmacher
- Process Systems Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstraße 1, 39106, Magdeburg, Germany
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