101
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Mason A, Yewdall NA, Welzen PLW, Shao J, van Stevendaal M, van Hest JCM, Williams DS, Abdelmohsen LKEA. Mimicking Cellular Compartmentalization in a Hierarchical Protocell through Spontaneous Spatial Organization. ACS CENTRAL SCIENCE 2019; 5:1360-1365. [PMID: 31482118 PMCID: PMC6716124 DOI: 10.1021/acscentsci.9b00345] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Indexed: 05/19/2023]
Abstract
A systemic feature of eukaryotic cells is the spatial organization of functional components through compartmentalization. Developing protocells with compartmentalized synthetic organelles is, therefore, a critical milestone toward emulating one of the core characteristics of cellular life. Here we demonstrate the bottom-up, multistep, noncovalent, assembly of rudimentary subcompartmentalized protocells through the spontaneous encapsulation of semipermeable, polymersome proto-organelles inside cell-sized coacervates. The coacervate microdroplets are membranized using tailor-made terpolymers, to complete the hierarchical self-assembly of protocells, a system that mimics both the condensed cytosol and the structure of a cell membrane. In this way, the spatial organization of enzymes can be finely tuned, leading to an enhancement of functionality. Moreover, incompatible components can be sequestered in the same microenvironments without detrimental effect. The robust stability of the subcompartmentalized coacervate protocells in biocompatible milieu, such as in PBS or cell culture media, makes it a versatile platform to be extended toward studies in vitro, and perhaps, in vivo.
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Affiliation(s)
- Alexander
F. Mason
- Department
of Biomedical Engineering & Department of Chemical Engineering
and Chemistry, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - N. Amy Yewdall
- Department
of Biomedical Engineering & Department of Chemical Engineering
and Chemistry, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Pascal L. W. Welzen
- Department
of Biomedical Engineering & Department of Chemical Engineering
and Chemistry, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Jingxin Shao
- Department
of Biomedical Engineering & Department of Chemical Engineering
and Chemistry, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Marleen van Stevendaal
- Department
of Biomedical Engineering & Department of Chemical Engineering
and Chemistry, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Jan C. M. van Hest
- Department
of Biomedical Engineering & Department of Chemical Engineering
and Chemistry, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - David S. Williams
- Department
of Chemistry, College of Science, Swansea
University, Singleton Campus, Swansea, Wales SA2 8PP, United Kingdom
| | - Loai K. E. A. Abdelmohsen
- Department
of Biomedical Engineering & Department of Chemical Engineering
and Chemistry, Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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102
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Martin N. Dynamic Synthetic Cells Based on Liquid-Liquid Phase Separation. Chembiochem 2019; 20:2553-2568. [PMID: 31039282 DOI: 10.1002/cbic.201900183] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Indexed: 12/16/2022]
Abstract
Living cells have long been a source of inspiration for chemists. Their capacity of performing complex tasks relies on the spatiotemporal coordination of matter and energy fluxes. Recent years have witnessed growing interest in the bottom-up construction of cell-like models capable of reproducing aspects of such dynamic organisation. Liquid-liquid phase-separation (LLPS) processes in water are increasingly recognised as representing a viable compartmentalisation strategy through which to produce dynamic synthetic cells. Herein, we highlight examples of the dynamic properties of LLPS used to assemble synthetic cells, including their biocatalytic activity, reversible condensation and dissolution, growth and division, and recent directions towards the design of higher-order structures and behaviour.
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Affiliation(s)
- Nicolas Martin
- Université de Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR 5031, 115 Avenue du Dr. Albert Schweitzer, 33600, Pessac, France
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103
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Perro A, Giraud L, Coudon N, Shanmugathasan S, Lapeyre V, Goudeau B, Douliez JP, Ravaine V. Self-coacervation of ampholyte polymer chains as an efficient encapsulation strategy. J Colloid Interface Sci 2019; 548:275-283. [DOI: 10.1016/j.jcis.2019.04.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/09/2019] [Accepted: 04/10/2019] [Indexed: 01/09/2023]
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104
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Deshpande S, Brandenburg F, Lau A, Last MGF, Spoelstra WK, Reese L, Wunnava S, Dogterom M, Dekker C. Spatiotemporal control of coacervate formation within liposomes. Nat Commun 2019; 10:1800. [PMID: 30996302 PMCID: PMC6470218 DOI: 10.1038/s41467-019-09855-x] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 03/26/2019] [Indexed: 12/22/2022] Open
Abstract
Liquid-liquid phase separation (LLPS), especially coacervation, plays a crucial role in cell biology, as it forms numerous membraneless organelles in cells. Coacervates play an indispensable role in regulating intracellular biochemistry, and their dysfunction is associated with several diseases. Understanding of the LLPS dynamics would greatly benefit from controlled in vitro assays that mimic cells. Here, we use a microfluidics-based methodology to form coacervates inside cell-sized (~10 µm) liposomes, allowing control over the dynamics. Protein-pore-mediated permeation of small molecules into liposomes triggers LLPS passively or via active mechanisms like enzymatic polymerization of nucleic acids. We demonstrate sequestration of proteins (FtsZ) and supramolecular assemblies (lipid vesicles), as well as the possibility to host metabolic reactions (β-galactosidase activity) inside coacervates. This coacervate-in-liposome platform provides a versatile tool to understand intracellular phase behavior, and these hybrid systems will allow engineering complex pathways to reconstitute cellular functions and facilitate bottom-up creation of synthetic cells. The understanding of liquid-liquid phase separation is crucial to cell biology and benefits from cell-mimicking in vitro assays. Here, the authors develop a microfluidic platform to study coacervate formation inside liposomes and show the potential of these hybrid systems to create synthetic cells.
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Affiliation(s)
- Siddharth Deshpande
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Frank Brandenburg
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Anson Lau
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Mart G F Last
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Willem Kasper Spoelstra
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Louis Reese
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Sreekar Wunnava
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Marileen Dogterom
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
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105
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Matveev VV. Cell theory, intrinsically disordered proteins, and the physics of the origin of life. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 149:114-130. [PMID: 30965040 DOI: 10.1016/j.pbiomolbio.2019.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/01/2019] [Accepted: 04/05/2019] [Indexed: 12/30/2022]
Abstract
Cell theory, as formulated by Theodor Schwann in 1839, introduced the idea that the cell is the main structural unit of living nature. Later, in solving the problem of cell multiplication, Rudolf Virchow expanded the cell theory with a postulate: all cells only arise from pre-existing cells. But what did the very first cell arise from? This paper proposes extending the Virchow's law by the assumption that between the nonliving protocell and the first living cell the continuity of fundamental physical properties (the principle of invariance of physical properties) is preserved. The protocell is understood here as a cell-shaped physical system on the basis of the self-organized biologically significant prebiotic macromolecules, primarily peptides, having a potential to transform into the living cell. Biophase is considered as the physical basis of the membraneless protocell, the internal environment of which is separated from the external environment due to the phase of adsorbed water. The evidence is given that the first protocells may have been formed on the basis of intrinsically disordered peptides. Data on the similarity of the physical properties of living cells and the following model systems are given: protein and artificial polymer solutions, coacervate droplets, and ion-exchange resin granules. Available data on the similarity of the physical properties of cell models and living cells allow us to rephrase the Virchow's postulate as follows: the physical properties of a living cell could only arise from pre-existing physical properties of the protocell.
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Affiliation(s)
- Vladimir V Matveev
- Laboratory of Cell Physiology, Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave 4, St. Petersburg, 194064, Russia.
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106
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Nakashima KK, Vibhute MA, Spruijt E. Biomolecular Chemistry in Liquid Phase Separated Compartments. Front Mol Biosci 2019; 6:21. [PMID: 31001538 PMCID: PMC6456709 DOI: 10.3389/fmolb.2019.00021] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 03/11/2019] [Indexed: 12/11/2022] Open
Abstract
Biochemical processes inside the cell take place in a complex environment that is highly crowded, heterogeneous, and replete with interfaces. The recently recognized importance of biomolecular condensates in cellular organization has added new elements of complexity to our understanding of chemistry in the cell. Many of these condensates are formed by liquid-liquid phase separation (LLPS) and behave like liquid droplets. Such droplet organelles can be reproduced and studied in vitro by using coacervates and have some remarkable features, including regulated assembly, differential partitioning of macromolecules, permeability to small molecules, and a uniquely crowded environment. Here, we review the main principles of biochemical organization in model membraneless compartments. We focus on some promising in vitro coacervate model systems that aptly mimic part of the compartmentalized cellular environment. We address the physicochemical characteristics of these liquid phase separated compartments, and their impact on biomolecular chemistry and assembly. These model systems enable a systematic investigation of the role of spatiotemporal organization of biomolecules in controlling biochemical processes in the cell, and they provide crucial insights for the development of functional artificial organelles and cells.
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Affiliation(s)
| | | | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Nijmegen, Netherlands
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107
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Ivanov I, Lira RB, Tang TYD, Franzmann T, Klosin A, da Silva LC, Hyman A, Landfester K, Lipowsky R, Sundmacher K, Dimova R. Directed Growth of Biomimetic Microcompartments. ACTA ACUST UNITED AC 2019; 3:e1800314. [PMID: 32648704 DOI: 10.1002/adbi.201800314] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/15/2019] [Indexed: 01/04/2023]
Abstract
Contemporary biological cells are sophisticated and highly compartmentalized. Compartmentalization is an essential principle of prebiotic life as well as a key feature in bottom-up synthetic biology research. In this review, the dynamic growth of compartments as an essential prerequisite for enabling self-reproduction as a fundamental life process is discussed. The micrometer-sized compartments are focused on due to their cellular dimensions. Two types of compartments are considered, membraneless droplets and membrane-bound microcompartments. Growth mechanisms of aqueous droplets such as protein (condensates) or macromolecule-rich droplets (aqueous two phase systems) and coacervates are discussed, for which growth occurs via Ostwald ripening or coalescence. For membrane-bound compartments, vesicles are considered, which are composed of fatty acids, lipids, or polymers, where directed growth can occur via fusion or uptake of material from the surrounding. The development of novel approaches for growth of biomimetic microcompartments can eventually be utilized to construct new synthetic cells.
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Affiliation(s)
- Ivan Ivanov
- Max Planck Institute for Dynamics of Complex Technical Systems, Process Systems Engineering, Sandtorstrasse 1, 39106, Magdeburg, Germany
| | - Rafael B Lira
- Max Planck Institute of Colloids and Interfaces, Theory and Bio-Systems, Science Park Golm, 14424, Potsdam, Germany
| | - T-Y Dora Tang
- Max Planck Institute of Molecular Cell Biology and Genetics, Organization of Cytoplasm & Dynamic Protocellular Systems, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Titus Franzmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Organization of Cytoplasm & Dynamic Protocellular Systems, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Adam Klosin
- Max Planck Institute of Molecular Cell Biology and Genetics, Organization of Cytoplasm & Dynamic Protocellular Systems, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Lucas Caire da Silva
- Max Planck Institute for Polymer Research, Physical Chemistry of Polymers, Ackermannweg 10, 55128, Mainz, Germany
| | - Anthony Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Organization of Cytoplasm & Dynamic Protocellular Systems, Pfotenhauerstrasse 108, 01307, Dresden, Germany
| | - Katharina Landfester
- Max Planck Institute for Polymer Research, Physical Chemistry of Polymers, Ackermannweg 10, 55128, Mainz, Germany
| | - Reinhard Lipowsky
- Max Planck Institute of Colloids and Interfaces, Theory and Bio-Systems, Science Park Golm, 14424, Potsdam, Germany
| | - Kai Sundmacher
- Max Planck Institute for Dynamics of Complex Technical Systems, Process Systems Engineering, Sandtorstrasse 1, 39106, Magdeburg, Germany
| | - Rumiana Dimova
- Max Planck Institute of Colloids and Interfaces, Theory and Bio-Systems, Science Park Golm, 14424, Potsdam, Germany
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108
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Poudyal RR, Guth-Metzler RM, Veenis AJ, Frankel EA, Keating CD, Bevilacqua PC. Template-directed RNA polymerization and enhanced ribozyme catalysis inside membraneless compartments formed by coacervates. Nat Commun 2019; 10:490. [PMID: 30700721 PMCID: PMC6353945 DOI: 10.1038/s41467-019-08353-4] [Citation(s) in RCA: 159] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 01/02/2019] [Indexed: 11/17/2022] Open
Abstract
Membraneless compartments, such as complex coacervates, have been hypothesized as plausible prebiotic micro-compartments due to their ability to sequester RNA; however, their compatibility with essential RNA World chemistries is unclear. We show that such compartments can enhance key prebiotically-relevant RNA chemistries. We demonstrate that template-directed RNA polymerization is sensitive to polycation identity, with polydiallyldimethylammonium chloride (PDAC) outperforming poly(allylamine), poly(lysine), and poly(arginine) in polycation/RNA coacervates. Differences in RNA diffusion rates between PDAC/RNA and oligoarginine/RNA coacervates imply distinct biophysical environments. Template-directed RNA polymerization is relatively insensitive to Mg2+ concentration when performed in PDAC/RNA coacervates as compared to buffer, even enabling partial rescue of the reaction in the absence of magnesium. Finally, we show enhanced activities of multiple nucleic acid enzymes including two ribozymes and a deoxyribozyme, underscoring the generality of this approach, in which functional nucleic acids like aptamers and ribozymes, and in some cases key cosolutes localize within the coacervate microenvironments. Membraneless compartments have been theorized to be prebiotic micro-compartments as they spontaneously encapsulate RNA and proteins. Here, the authors report membraneless compartments can enhance RNA chemistries, affecting template directed RNA polymerization and stimulating nucleic acid enzymes.
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Affiliation(s)
- Raghav R Poudyal
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA. .,Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - Rebecca M Guth-Metzler
- Department of Biochemistry, Microbiology, and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.,School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Andrew J Veenis
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA.,Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Erica A Frankel
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA.,Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.,The Dow Chemical Company, 400 Arcola Road, Collegeville, PA, 19426, USA
| | - Christine D Keating
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA.
| | - Philip C Bevilacqua
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA. .,Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA. .,Department of Biochemistry, Microbiology, and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.
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109
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Tian L, Li M, Liu J, Patil AJ, Drinkwater BW, Mann S. Nonequilibrium Spatiotemporal Sensing within Acoustically Patterned Two-Dimensional Protocell Arrays. ACS CENTRAL SCIENCE 2018; 4:1551-1558. [PMID: 30555908 PMCID: PMC6276052 DOI: 10.1021/acscentsci.8b00555] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Indexed: 05/03/2023]
Abstract
Acoustically trapped periodic arrays of horseradish peroxidase (HRP)-loaded poly(diallydimethylammonium chloride) / adenosine 5'-triphosphate coacervate microdroplet-based protocells exhibit a spatiotemporal biochemical response when exposed to a codiffusing mixture of substrate molecules (o-phenylenediamine (o-PD) and hydrogen peroxide (H2O2)) under nonequilibrium conditions. Unidirectional propagation of the chemical concentration gradients gives rise to time- and position-dependent fluorescence signal outputs from individual coacervate microdroplets, indicating that the organized protocell assembly can dynamically sense encoded information in the advancing reaction-diffusion front. The methodology is extended to arrays comprising spatially separated binary populations of HRP- or glucose oxidase-containing coacervate microdroplets to internally generate a H2O2 signal that chemically connects the two protocell communities via a concerted biochemical cascade reaction. Our results provide a step toward establishing a systematic approach to study dynamic interactions between organized protocell consortia and propagating reaction-diffusion gradients, and offer a new methodology for exploring the complexity of protocellular communication networks operating under nonequilibrium conditions.
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Affiliation(s)
- Liangfei Tian
- Centre
for Protolife Research and Centre for Organized Matter Chemistry,
School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Mei Li
- Centre
for Protolife Research and Centre for Organized Matter Chemistry,
School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Juntai Liu
- School
of Biochemistry, Medical Sciences Building, University of Bristol, Bristol BS8 1TD, U.K.
| | - Avinash J. Patil
- Centre
for Protolife Research and Centre for Organized Matter Chemistry,
School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
| | - Bruce W. Drinkwater
- Faculty
of Engineering, Queens Building, University
of Bristol, Bristol BS8 1TR, U.K.
| | - Stephen Mann
- Centre
for Protolife Research and Centre for Organized Matter Chemistry,
School of Chemistry, University of Bristol, Bristol BS8 1TS, U.K.
- E-mail:
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110
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Crowe CD, Keating CD. Liquid-liquid phase separation in artificial cells. Interface Focus 2018; 8:20180032. [PMID: 30443328 PMCID: PMC6227770 DOI: 10.1098/rsfs.2018.0032] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2018] [Indexed: 12/25/2022] Open
Abstract
Liquid-liquid phase separation (LLPS) in biology is a recently appreciated means of intracellular compartmentalization. Because the mechanisms driving phase separations are grounded in physical interactions, they can be recreated within less complex systems consisting of only a few simple components, to serve as artificial microcompartments. Within these simple systems, the effect of compartmentalization and microenvironments upon biological reactions and processes can be studied. This review will explore several approaches to incorporating LLPS as artificial cytoplasms and in artificial cells, including both segregative and associative phase separation.
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Affiliation(s)
| | - Christine D. Keating
- Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA
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111
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Helwig B, van Sluijs B, Pogodaev AA, Postma SGJ, Huck WTS. Bottom-Up Construction of an Adaptive Enzymatic Reaction Network. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201806944] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Britta Helwig
- Radboud University; Institute for Molecules and Materials; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Bob van Sluijs
- Radboud University; Institute for Molecules and Materials; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Aleksandr A. Pogodaev
- Radboud University; Institute for Molecules and Materials; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Sjoerd G. J. Postma
- Radboud University; Institute for Molecules and Materials; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Wilhelm T. S. Huck
- Radboud University; Institute for Molecules and Materials; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
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112
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Helwig B, van Sluijs B, Pogodaev AA, Postma SGJ, Huck WTS. Bottom-Up Construction of an Adaptive Enzymatic Reaction Network. Angew Chem Int Ed Engl 2018; 57:14065-14069. [DOI: 10.1002/anie.201806944] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/13/2018] [Indexed: 01/23/2023]
Affiliation(s)
- Britta Helwig
- Radboud University; Institute for Molecules and Materials; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Bob van Sluijs
- Radboud University; Institute for Molecules and Materials; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Aleksandr A. Pogodaev
- Radboud University; Institute for Molecules and Materials; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Sjoerd G. J. Postma
- Radboud University; Institute for Molecules and Materials; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Wilhelm T. S. Huck
- Radboud University; Institute for Molecules and Materials; Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
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113
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Fanalista F, Deshpande S, Lau A, Pawlik G, Dekker C. FtsZ-Induced Shape Transformation of Coacervates. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/adbi.201800136] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Federico Fanalista
- Department of Bionanoscience; Kavli Institute of Nanoscience Delft; Delft University of Technology; Van der Maasweg 9 2629 HZ Delft The Netherlands
| | - Siddharth Deshpande
- Department of Bionanoscience; Kavli Institute of Nanoscience Delft; Delft University of Technology; Van der Maasweg 9 2629 HZ Delft The Netherlands
| | - Anson Lau
- Department of Bionanoscience; Kavli Institute of Nanoscience Delft; Delft University of Technology; Van der Maasweg 9 2629 HZ Delft The Netherlands
| | - Grzegorz Pawlik
- Department of Bionanoscience; Kavli Institute of Nanoscience Delft; Delft University of Technology; Van der Maasweg 9 2629 HZ Delft The Netherlands
| | - Cees Dekker
- Department of Bionanoscience; Kavli Institute of Nanoscience Delft; Delft University of Technology; Van der Maasweg 9 2629 HZ Delft The Netherlands
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114
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Poudyal R, Cakmak FP, Keating CD, Bevilacqua PC. Physical Principles and Extant Biology Reveal Roles for RNA-Containing Membraneless Compartments in Origins of Life Chemistry. Biochemistry 2018; 57:2509-2519. [PMID: 29560725 PMCID: PMC7276092 DOI: 10.1021/acs.biochem.8b00081] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
This Perspective focuses on RNA in biological and nonbiological compartments resulting from liquid-liquid phase separation (LLPS), with an emphasis on origins of life. In extant cells, intracellular liquid condensates, many of which are rich in RNAs and intrinsically disordered proteins, provide spatial regulation of biomolecular interactions that can result in altered gene expression. Given the diversity of biogenic and abiogenic molecules that undergo LLPS, such membraneless compartments may have also played key roles in prebiotic chemistries relevant to the origins of life. The RNA World hypothesis posits that RNA may have served as both a genetic information carrier and a catalyst during the origin of life. Because of its polyanionic backbone, RNA can undergo LLPS by complex coacervation in the presence of polycations. Phase separation could provide a mechanism for concentrating monomers for RNA synthesis and selectively partition longer RNAs with enzymatic functions, thus driving prebiotic evolution. We introduce several types of LLPS that could lead to compartmentalization and discuss potential roles in template-mediated non-enzymatic polymerization of RNA and other related biomolecules, functions of ribozymes and aptamers, and benefits or penalties imparted by liquid demixing. We conclude that tiny liquid droplets may have concentrated precious biomolecules and acted as bioreactors in the RNA World.
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Affiliation(s)
- Raghav Poudyal
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Fatma Pir Cakmak
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Christine D. Keating
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Philip C. Bevilacqua
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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