1
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Huster D, Maiti S, Herrmann A. Phospholipid Membranes as Chemically and Functionally Tunable Materials. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2312898. [PMID: 38456771 DOI: 10.1002/adma.202312898] [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: 11/29/2023] [Revised: 02/12/2024] [Indexed: 03/09/2024]
Abstract
The sheet-like lipid bilayer is the fundamental structural component of all cell membranes. Its building blocks are phospholipids and cholesterol. Their amphiphilic structure spontaneously leads to the formation of a bilayer in aqueous environment. Lipids are not just structural elements. Individual lipid species, the lipid membrane structure, and lipid dynamics influence and regulate membrane protein function. An exciting field is emerging where the membrane-associated material properties of different bilayer systems are used in designing innovative solutions for widespread applications across various fields, such as the food industry, cosmetics, nano- and biomedicine, drug storage and delivery, biotechnology, nano- and biosensors, and computing. Here, the authors summarize what is known about how lipids determine the properties and functions of biological membranes and how this has been or can be translated into innovative applications. Based on recent progress in the understanding of membrane structure, dynamics, and physical properties, a perspective is provided on how membrane-controlled regulation of protein functions can extend current applications and even offer new applications.
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Affiliation(s)
- Daniel Huster
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, D-04107, Leipzig, Germany
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai, 400 005, India
| | - Andreas Herrmann
- Freie Universität Berlin, Department Chemistry and Biochemistry, SupraFAB, Altensteinstr. 23a, D-14195, Berlin, Germany
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2
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Rothschild LJ, Averesch NJH, Strychalski EA, Moser F, Glass JI, Cruz Perez R, Yekinni IO, Rothschild-Mancinelli B, Roberts Kingman GA, Wu F, Waeterschoot J, Ioannou IA, Jewett MC, Liu AP, Noireaux V, Sorenson C, Adamala KP. Building Synthetic Cells─From the Technology Infrastructure to Cellular Entities. ACS Synth Biol 2024; 13:974-997. [PMID: 38530077 PMCID: PMC11037263 DOI: 10.1021/acssynbio.3c00724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 03/27/2024]
Abstract
The de novo construction of a living organism is a compelling vision. Despite the astonishing technologies developed to modify living cells, building a functioning cell "from scratch" has yet to be accomplished. The pursuit of this goal alone has─and will─yield scientific insights affecting fields as diverse as cell biology, biotechnology, medicine, and astrobiology. Multiple approaches have aimed to create biochemical systems manifesting common characteristics of life, such as compartmentalization, metabolism, and replication and the derived features, evolution, responsiveness to stimuli, and directed movement. Significant achievements in synthesizing each of these criteria have been made, individually and in limited combinations. Here, we review these efforts, distinguish different approaches, and highlight bottlenecks in the current research. We look ahead at what work remains to be accomplished and propose a "roadmap" with key milestones to achieve the vision of building cells from molecular parts.
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Affiliation(s)
- Lynn J. Rothschild
- Space Science
& Astrobiology Division, NASA Ames Research
Center, Moffett
Field, California 94035-1000, United States
- Department
of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Nils J. H. Averesch
- Department
of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | | | - Felix Moser
- Synlife, One Kendall Square, Cambridge, Massachusetts 02139-1661, United States
| | - John I. Glass
- J.
Craig
Venter Institute, La Jolla, California 92037, United States
| | - Rolando Cruz Perez
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
- Blue
Marble
Space Institute of Science at NASA Ames Research Center, Moffett Field, California 94035-1000, United
States
| | - Ibrahim O. Yekinni
- Department
of Biomedical Engineering, University of
Minnesota, Minneapolis, Minnesota 55455, United States
| | - Brooke Rothschild-Mancinelli
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332-0150, United States
| | | | - Feilun Wu
- J. Craig
Venter Institute, Rockville, Maryland 20850, United States
| | - Jorik Waeterschoot
- Mechatronics,
Biostatistics and Sensors (MeBioS), KU Leuven, 3000 Leuven Belgium
| | - Ion A. Ioannou
- Department
of Chemistry, MSRH, Imperial College London, London W12 0BZ, U.K.
| | - Michael C. Jewett
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Allen P. Liu
- Mechanical
Engineering & Biomedical Engineering, Cellular and Molecular Biology,
Biophysics, Applied Physics, University
of Michigan, Ann Arbor, Michigan 48109, United States
| | - Vincent Noireaux
- Physics
and Nanotechnology, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Carlise Sorenson
- Department
of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Katarzyna P. Adamala
- Department
of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, United States
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3
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Vashistha H, Jammal-Touma J, Singh K, Rabin Y, Salman H. Bacterial cell-size changes resulting from altering the relative expression of Min proteins. Nat Commun 2023; 14:5710. [PMID: 37714867 PMCID: PMC10504268 DOI: 10.1038/s41467-023-41487-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 09/06/2023] [Indexed: 09/17/2023] Open
Abstract
The timing of cell division, and thus cell size in bacteria, is determined in part by the accumulation dynamics of the protein FtsZ, which forms the septal ring. FtsZ localization depends on membrane-associated Min proteins, which inhibit FtsZ binding to the cell pole membrane. Changes in the relative concentrations of Min proteins can disrupt FtsZ binding to the membrane, which in turn can delay cell division until a certain cell size is reached, in which the dynamics of Min proteins frees the cell membrane long enough to allow FtsZ ring formation. Here, we study the effect of Min proteins relative expression on the dynamics of FtsZ ring formation and cell size in individual Escherichia coli bacteria. Upon inducing overexpression of minE, cell size increases gradually to a new steady-state value. Concurrently, the time required to initiate FtsZ ring formation grows as the size approaches the new steady-state, at which point the ring formation initiates as early as before induction. These results highlight the contribution of Min proteins to cell size control, which may be partially responsible for the size fluctuations observed in bacterial populations, and may clarify how the size difference acquired during asymmetric cell division is offset.
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Affiliation(s)
- Harsh Vashistha
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Joanna Jammal-Touma
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kulveer Singh
- Department of Physics and Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, Israel
| | - Yitzhak Rabin
- Department of Physics and Institute for Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat-Gan, Israel
| | - Hanna Salman
- Department of Physics and Astronomy, University of Pittsburgh, Pittsburgh, PA, USA.
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4
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Walczak M, Mancini L, Xu J, Raguseo F, Kotar J, Cicuta P, Di Michele L. A Synthetic Signaling Network Imitating the Action of Immune Cells in Response to Bacterial Metabolism. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2301562. [PMID: 37156014 DOI: 10.1002/adma.202301562] [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: 02/17/2023] [Revised: 04/16/2023] [Indexed: 05/10/2023]
Abstract
State-of-the-art bottom-up synthetic biology allows to replicate many basic biological functions in artificial-cell-like devices. To mimic more complex behaviors, however, artificial cells would need to perform many of these functions in a synergistic and coordinated fashion, which remains elusive. Here, a sophisticated biological response is considered, namely the capture and deactivation of pathogens by neutrophil immune cells, through the process of netosis. A consortium consisting of two synthetic agents is designed-responsive DNA-based particles and antibiotic-loaded lipid vesicles-whose coordinated action mimics the sought immune-like response when triggered by bacterial metabolism. The artificial netosis-like response emerges from a series of interlinked sensing and communication pathways between the live and synthetic agents, and translates into both physical and chemical antimicrobial actions, namely bacteria immobilization and exposure to antibiotics. The results demonstrate how advanced life-like responses can be prescribed with a relatively small number of synthetic molecular components, and outlines a new strategy for artificial-cell-based antimicrobial solutions.
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Affiliation(s)
- Michal Walczak
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Leonardo Mancini
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Jiayi Xu
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Federica Raguseo
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, Wood Lane, London, W12 0BZ, UK
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, Wood Lane, London, W12 0BZ, UK
| | - Jurij Kotar
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Pietro Cicuta
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
| | - Lorenzo Di Michele
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, Wood Lane, London, W12 0BZ, UK
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, Wood Lane, London, W12 0BZ, UK
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5
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Lin AJ, Sihorwala AZ, Belardi B. Engineering Tissue-Scale Properties with Synthetic Cells: Forging One from Many. ACS Synth Biol 2023; 12:1889-1907. [PMID: 37417657 PMCID: PMC11017731 DOI: 10.1021/acssynbio.3c00061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
In metazoans, living cells achieve capabilities beyond individual cell functionality by assembling into multicellular tissue structures. These higher-order structures represent dynamic, heterogeneous, and responsive systems that have evolved to regenerate and coordinate their actions over large distances. Recent advances in constructing micrometer-sized vesicles, or synthetic cells, now point to a future where construction of synthetic tissue can be pursued, a boon to pressing material needs in biomedical implants, drug delivery systems, adhesives, filters, and storage devices, among others. To fully realize the potential of synthetic tissue, inspiration has been and will continue to be drawn from new molecular findings on its natural counterpart. In this review, we describe advances in introducing tissue-scale features into synthetic cell assemblies. Beyond mere complexation, synthetic cells have been fashioned with a variety of natural and engineered molecular components that serve as initial steps toward morphological control and patterning, intercellular communication, replication, and responsiveness in synthetic tissue. Particular attention has been paid to the dynamics, spatial constraints, and mechanical strengths of interactions that drive the synthesis of this next-generation material, describing how multiple synthetic cells can act as one.
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Affiliation(s)
- Alexander J Lin
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Ahmed Z Sihorwala
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
| | - Brian Belardi
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, United States
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6
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Yang J, Jahnke K, Xin L, Jing X, Zhan P, Peil A, Griffo A, Škugor M, Yang D, Fan S, Göpfrich K, Yan H, Wang P, Liu N. Modulating Lipid Membrane Morphology by Dynamic DNA Origami Networks. NANO LETTERS 2023. [PMID: 37440701 DOI: 10.1021/acs.nanolett.3c00750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
Membrane morphology and its dynamic adaptation regulate many cellular functions, which are often mediated by membrane proteins. Advances in DNA nanotechnology have enabled the realization of various protein-inspired structures and functions with precise control at the nanometer level, suggesting a viable tool to artificially engineer membrane morphology. In this work, we demonstrate a DNA origami cross (DOC) structure that can be anchored onto giant unilamellar vesicles (GUVs) and subsequently polymerized into micrometer-scale reconfigurable one-dimensional (1D) chains or two-dimensional (2D) lattices. Such DNA origami-based networks can be switched between left-handed (LH) and right-handed (RH) conformations by DNA fuels and exhibit potent efficacy in remodeling the membrane curvatures of GUVs. This work sheds light on designing hierarchically assembled dynamic DNA systems for the programmable modulation of synthetic cells for useful applications.
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Affiliation(s)
- Juanjuan Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai 200127, People's Republic of China
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - Kevin Jahnke
- Biophysical Engineering Group, Max Planck Institute for Medical Research Heidelberg, Jahnstr. 29, 69120 Heidelberg, Germany
| | - Ling Xin
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - Xinxin Jing
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - Pengfei Zhan
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - Andreas Peil
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - Alessandra Griffo
- Biophysical Engineering Group, Max Planck Institute for Medical Research Heidelberg, Jahnstr. 29, 69120 Heidelberg, Germany
| | - Marko Škugor
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - Donglei Yang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai 200127, People's Republic of China
| | - Sisi Fan
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
| | - Kerstin Göpfrich
- Biophysical Engineering Group, Max Planck Institute for Medical Research Heidelberg, Jahnstr. 29, 69120 Heidelberg, Germany
- Center for Molecular Biology of Heidelberg University (ZMBH), Im Neuenheime Feld 329, 69120 Heidelberg, Germany
| | - Hao Yan
- School of Molecular Sciences and Center for Molecular Design and Biomimetics at Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Pengfei Wang
- Institute of Molecular Medicine, Department of Laboratory Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University Shanghai 200127, People's Republic of China
| | - Na Liu
- 2. Physics Institute, University of Stuttgart, Pfaffenwaldring 57, 70569, Stuttgart, Germany
- Max Planck Institute for Solid State Research, Heisenbergstrasse 1, D-70569 Stuttgart, Germany
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7
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Rubio-Sánchez R, Mognetti BM, Cicuta P, Di Michele L. DNA-Origami Line-Actants Control Domain Organization and Fission in Synthetic Membranes. J Am Chem Soc 2023; 145:11265-11275. [PMID: 37163977 DOI: 10.1021/jacs.3c01493] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Cells can precisely program the shape and lateral organization of their membranes using protein machinery. Aiming to replicate a comparable degree of control, here we introduce DNA-origami line-actants (DOLAs) as synthetic analogues of membrane-sculpting proteins. DOLAs are designed to selectively accumulate at the line-interface between coexisting domains in phase-separated lipid membranes, modulating the tendency of the domains to coalesce. With experiments and coarse-grained simulations, we demonstrate that DOLAs can reversibly stabilize two-dimensional analogues of Pickering emulsions on synthetic giant liposomes, enabling dynamic programming of membrane lateral organization. The control afforded over membrane structure by DOLAs extends to three-dimensional morphology, as exemplified by a proof-of-concept synthetic pathway leading to vesicle fission. With DOLAs we lay the foundations for mimicking, in synthetic systems, some of the critical membrane-hosted functionalities of biological cells, including signaling, trafficking, sensing, and division.
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Affiliation(s)
- Roger Rubio-Sánchez
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, United Kingdom
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, United Kingdom
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Bortolo Matteo Mognetti
- Interdisciplinary Center for Nonlinear Phenomena and Complex Systems, Université Libre de Bruxelles (ULB), Campus Plaine, CP 231, Boulevard du Triomphe, B-1050 Brussels, Belgium
| | - Pietro Cicuta
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Lorenzo Di Michele
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, United Kingdom
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, United Kingdom
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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8
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Jin Z, Vighi A, Dong Y, Bureau JA, Ignea C. Engineering membrane architecture for biotechnological applications. Biotechnol Adv 2023; 64:108118. [PMID: 36773706 DOI: 10.1016/j.biotechadv.2023.108118] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023]
Abstract
Cellular membranes, predominantly described as a dynamic bilayer, are composed of different lipids, transmembrane proteins, and carbohydrates. Most research on biological membranes focuses on the identification, characterization, and mechanistic aspects of their different components. These studies provide a fundamental understanding of membrane structure, function, and dynamics, establishing a basis for the development of membrane engineering strategies. To date, approaches in this field concentrate on membrane adaptation to harsh conditions during industrial fermentation, which can be caused by temperature, osmotic, or organic solvent stress. With advances in the field of metabolic engineering and synthetic biology, recent breakthroughs include proof of concept microbial production of essential medicines, such as cannabinoids and vinblastine. However, long pathways, low yields, and host adaptation continue to pose challenges to the efficient scale up production of many important compounds. The lipid bilayer is profoundly linked to the activity of heterologous membrane-bound enzymes and transport of metabolites. Therefore, strategies for improving enzyme performance, facilitating pathway reconstruction, and enabling storage of products to increase the yields directly involve cellular membranes. At the forefront of membrane engineering research are re-emerging approaches in lipid research and synthetic biology that manipulate membrane size and composition and target lipid profiles across species. This review summarizes engineering strategies applied to cellular membranes and discusses the challenges and future perspectives, particularly with regards to their applications in host engineering and bioproduction.
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Affiliation(s)
- Zimo Jin
- Department of Bioengineering, McGill University, Montreal, Quebec H3A 0E9, Canada
| | - Asia Vighi
- Department of Bioengineering, McGill University, Montreal, Quebec H3A 0E9, Canada
| | - Yueming Dong
- Department of Bioengineering, McGill University, Montreal, Quebec H3A 0E9, Canada
| | | | - Codruta Ignea
- Department of Bioengineering, McGill University, Montreal, Quebec H3A 0E9, Canada.
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9
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Hartmann D, Chowdhry R, Smith JM, Booth MJ. Orthogonal Light-Activated DNA for Patterned Biocomputing within Synthetic Cells. J Am Chem Soc 2023; 145:9471-9480. [PMID: 37125650 PMCID: PMC10161232 DOI: 10.1021/jacs.3c02350] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Cell-free gene expression is a vital research tool to study biological systems in defined minimal environments and has promising applications in biotechnology. Developing methods to control DNA templates for cell-free expression will be important for precise regulation of complex biological pathways and use with synthetic cells, particularly using remote, nondamaging stimuli such as visible light. Here, we have synthesized blue light-activatable DNA parts that tightly regulate cell-free RNA and protein synthesis. We found that this blue light-activated DNA could initiate expression orthogonally to our previously generated ultraviolet (UV) light-activated DNA, which we used to generate a dual-wavelength light-controlled cell-free AND-gate. By encapsulating these orthogonal light-activated DNAs into synthetic cells, we used two overlapping patterns of blue and UV light to provide precise spatiotemporal control over the logic gate. Our blue and UV orthogonal light-activated DNAs will open the door for precise control of cell-free systems in biology and medicine.
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Affiliation(s)
- Denis Hartmann
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Razia Chowdhry
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Jefferson M Smith
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Michael J Booth
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
- Department of Chemistry, University College London, 20 Gordon Street, London WC1H 0AJ, U.K
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10
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Uchida N, Ryu Y, Takagi Y, Yoshizawa K, Suzuki K, Anraku Y, Ajioka I, Shimokawa N, Takagi M, Hoshino N, Akutagawa T, Matsubara T, Sato T, Higuchi Y, Ito H, Morita M, Muraoka T. Endocytosis-Like Vesicle Fission Mediated by a Membrane-Expanding Molecular Machine Enables Virus Encapsulation for In Vivo Delivery. J Am Chem Soc 2023; 145:6210-6220. [PMID: 36853954 PMCID: PMC10037323 DOI: 10.1021/jacs.2c12348] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Biological membranes are functionalized by membrane-associated protein machinery. Membrane-associated transport processes, such as endocytosis, represent a fundamental and universal function mediated by membrane-deforming protein machines, by which small biomolecules and even micrometer-size substances can be transported via encapsulation into membrane vesicles. Although synthetic molecules that induce dynamic membrane deformation have been reported, a molecular approach enabling membrane transport in which membrane deformation is coupled with substance binding and transport remains critically lacking. Here, we developed an amphiphilic molecular machine containing a photoresponsive diazocine core (AzoMEx) that localizes in a phospholipid membrane. Upon photoirradiation, AzoMEx expands the liposomal membrane to bias vesicles toward outside-in fission in the membrane deformation process. Cargo components, including micrometer-size M13 bacteriophages that interact with AzoMEx, are efficiently incorporated into the vesicles through the outside-in fission. Encapsulated M13 bacteriophages are transiently protected from the external environment and therefore retain biological activity during distribution throughout the body via the blood following administration. This research developed a molecular approach using synthetic molecular machinery for membrane functionalization to transport micrometer-size substances and objects via vesicle encapsulation. The molecular design demonstrated in this study to expand the membrane for deformation and binding to a cargo component can lead to the development of drug delivery materials and chemical tools for controlling cellular activities.
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Affiliation(s)
- Noriyuki Uchida
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Yunosuke Ryu
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Yuichiro Takagi
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Ken Yoshizawa
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Kotono Suzuki
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Yasutaka Anraku
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Itsuki Ajioka
- Center for Brain Integration Research Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
- Kanagawa Institute of Industrial Science and Technology, 705-1 Shimoimaizumi, Ebina, Kanagawa 243-0435, Japan
| | - Naofumi Shimokawa
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Masahiro Takagi
- School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan
| | - Norihisa Hoshino
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Tomoyuki Akutagawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
| | - Teruhiko Matsubara
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Toshinori Sato
- Department of Biosciences and Informatics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama, Kanagawa 223-8522, Japan
| | - Yuji Higuchi
- Institute for Solid State Physics, The University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba 277-8581, Japan
| | - Hiroaki Ito
- Department of Physics, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage-ku, Chiba 263-8522, Japan
| | - Masamune Morita
- National Institute of Advanced Industrial Science and Technology, Center 6, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Takahiro Muraoka
- Department of Applied Chemistry, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
- Kanagawa Institute of Industrial Science and Technology, 705-1 Shimoimaizumi, Ebina, Kanagawa 243-0435, Japan
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 3-8-1 Harumi-cho, Fuchu, Tokyo 183-8538, Japan
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11
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Meindlhumer S, Brauns F, Finžgar JR, Kerssemakers J, Dekker C, Frey E. Directing Min protein patterns with advective bulk flow. Nat Commun 2023; 14:450. [PMID: 36707506 PMCID: PMC9883515 DOI: 10.1038/s41467-023-35997-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 01/10/2023] [Indexed: 01/29/2023] Open
Abstract
The Min proteins constitute the best-studied model system for pattern formation in cell biology. We theoretically predict and experimentally show that the propagation direction of in vitro Min protein patterns can be controlled by a hydrodynamic flow of the bulk solution. We find downstream propagation of Min wave patterns for low MinE:MinD concentration ratios, upstream propagation for large ratios, but multistability of both propagation directions in between. Whereas downstream propagation can be described by a minimal model that disregards MinE conformational switching, upstream propagation can be reproduced by a reduced switch model, where increased MinD bulk concentrations on the upstream side promote protein attachment. Our study demonstrates that a differential flow, where bulk flow advects protein concentrations in the bulk, but not on the surface, can control surface-pattern propagation. This suggests that flow can be used to probe molecular features and to constrain mathematical models for pattern-forming systems.
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Affiliation(s)
- Sabrina Meindlhumer
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Fridtjof Brauns
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Munich, Germany
- Kavli Institute for Theoretical Physics, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Jernej Rudi Finžgar
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jacob Kerssemakers
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, the Netherlands
| | - Erwin Frey
- Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Department of Physics, Ludwig-Maximilians-Universität München, Munich, Germany.
- Max Planck School Matter to Life, Hofgartenstraße 8, 80539, Munich, Germany.
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12
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Khmelinskaia A, Schwille P, Franquelim HG. Binding and Characterization of DNA Origami Nanostructures on Lipid Membranes. Methods Mol Biol 2023; 2639:231-255. [PMID: 37166721 DOI: 10.1007/978-1-0716-3028-0_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
DNA origami is an extremely versatile nanoengineering tool with widespread applicability in various fields of research, including membrane physiology and biophysics. The possibility to easily modify DNA strands with lipophilic moieties enabled the recent development of a variety of membrane-active DNA origami devices. Biological membranes, as the core barriers of the cells, display vital structural and functional roles. Therefore, lipid bilayers are widely popular targets of DNA origami nanotechnology for synthetic biology and biomedical applications. In this chapter, we summarize the typical experimental methods used to investigate the interaction of DNA origami with synthetic membrane models. Herein, we present detailed protocols for the production of lipid model membranes and characterization of membrane-targeted DNA origami nanostructures using different microscopy approaches.
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Affiliation(s)
- Alena Khmelinskaia
- Max Planck Institute of Biochemistry, Munich, Germany
- Institute of Protein Design, University of Washington, Seattle, WA, USA
- Life & Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | | | - Henri G Franquelim
- Max Planck Institute of Biochemistry, Munich, Germany.
- Interfaculty Centre for Bioactive Matter (b-ACTmatter), Leipzig University, Leipzig, Germany.
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13
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Avalos-Padilla Y, Georgiev VN, Ewins E, Robinson T, Orozco E, Lipowsky R, Dimova R. Stepwise remodeling and subcompartment formation in individual vesicles by three ESCRT-III proteins. iScience 2022; 26:105765. [PMID: 36590172 PMCID: PMC9800321 DOI: 10.1016/j.isci.2022.105765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/21/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
The endosomal sorting complex required for transport (ESCRT) is a multi-protein machinery involved in several membrane remodeling processes. Different approaches have been used to resolve how ESCRT proteins scission membranes. However, the underlying mechanisms generating membrane deformations are still a matter of debate. Here, giant unilamellar vesicles, microfluidic technology, and micropipette aspiration are combined to continuously follow the ESCRT-III-mediated membrane remodeling on the single-vesicle level for the first time. With this approach, we identify different mechanisms by which a minimal set of three ESCRT-III proteins from Entamoeba histolytica reshape the membrane. These proteins modulate the membrane stiffness and spontaneous curvature to regulate bud size and generate intraluminal vesicles even in the absence of ATP. We demonstrate that the bud stability depends on the protein concentration and membrane tension. The approaches introduced here should open the road to diverse applications in synthetic biology for establishing artificial cells with several membrane compartments.
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Affiliation(s)
- Yunuen Avalos-Padilla
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476 Potsdam, Germany,Nanomalaria Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, ES-08028 Barcelona, Spain,Barcelona Institute for Global Health (ISGlobal, Hospital Clínic-Universitat de Barcelona), Rosselló 149-153, ES-08036 Barcelona, Spain
| | - Vasil N. Georgiev
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476 Potsdam, Germany
| | - Eleanor Ewins
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476 Potsdam, Germany
| | - Tom Robinson
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476 Potsdam, Germany
| | - Esther Orozco
- Departamento de Infectómica y Patogénesis Molecular, CINVESTAV IPN, 07360 Ciudad de México, México
| | - Reinhard Lipowsky
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476 Potsdam, Germany
| | - Rumiana Dimova
- Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14476 Potsdam, Germany,Corresponding author
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14
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Abstract
One of the major challenges of bottom-up synthetic biology is rebuilding a minimal cell division machinery. From a reconstitution perspective, the animal cell division apparatus is mechanically the simplest and therefore attractive to rebuild. An actin-based ring produces contractile force to constrict the membrane. By contrast, microbes and plant cells have a cell wall, so division requires concerted membrane constriction and cell wall synthesis. Furthermore, reconstitution of the actin division machinery helps in understanding the physical and molecular mechanisms of cytokinesis in animal cells and thus our own cells. In this review, we describe the state-of-the-art research on reconstitution of minimal actin-mediated cytokinetic machineries. Based on the conceptual requirements that we obtained from the physics of the shape changes involved in cell division, we propose two major routes for building a minimal actin apparatus capable of division. Importantly, we acknowledge both the passive and active roles that the confining lipid membrane can play in synthetic cytokinesis. We conclude this review by identifying the most pressing challenges for future reconstitution work, thereby laying out a roadmap for building a synthetic cell equipped with a minimal actin division machinery.
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15
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Hirschi S, Ward TR, Meier WP, Müller DJ, Fotiadis D. Synthetic Biology: Bottom-Up Assembly of Molecular Systems. Chem Rev 2022; 122:16294-16328. [PMID: 36179355 DOI: 10.1021/acs.chemrev.2c00339] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bottom-up assembly of biological and chemical components opens exciting opportunities to engineer artificial vesicular systems for applications with previously unmet requirements. The modular combination of scaffolds and functional building blocks enables the engineering of complex systems with biomimetic or new-to-nature functionalities. Inspired by the compartmentalized organization of cells and organelles, lipid or polymer vesicles are widely used as model membrane systems to investigate the translocation of solutes and the transduction of signals by membrane proteins. The bottom-up assembly and functionalization of such artificial compartments enables full control over their composition and can thus provide specifically optimized environments for synthetic biological processes. This review aims to inspire future endeavors by providing a diverse toolbox of molecular modules, engineering methodologies, and different approaches to assemble artificial vesicular systems. Important technical and practical aspects are addressed and selected applications are presented, highlighting particular achievements and limitations of the bottom-up approach. Complementing the cutting-edge technological achievements, fundamental aspects are also discussed to cater to the inherently diverse background of the target audience, which results from the interdisciplinary nature of synthetic biology. The engineering of proteins as functional modules and the use of lipids and block copolymers as scaffold modules for the assembly of functionalized vesicular systems are explored in detail. Particular emphasis is placed on ensuring the controlled assembly of these components into increasingly complex vesicular systems. Finally, all descriptions are presented in the greater context of engineering valuable synthetic biological systems for applications in biocatalysis, biosensing, bioremediation, or targeted drug delivery.
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Affiliation(s)
- Stephan Hirschi
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Thomas R Ward
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Wolfgang P Meier
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, ETH Zürich, Mattenstrasse 26, 4058 Basel, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.,Molecular Systems Engineering, National Centre of Competence in Research (NCCR), 4002 Basel, Switzerland
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16
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Ganar KA, Leijten L, Deshpande S. Actinosomes: Condensate-Templated Containers for Engineering Synthetic Cells. ACS Synth Biol 2022; 11:2869-2879. [PMID: 35948429 PMCID: PMC9396703 DOI: 10.1021/acssynbio.2c00290] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Engineering synthetic cells has a broad appeal, from
understanding
living cells to designing novel biomaterials for therapeutics, biosensing,
and hybrid interfaces. A key prerequisite to creating synthetic cells
is a three-dimensional container capable of orchestrating biochemical
reactions. In this study, we present an easy and effective technique
to make cell-sized porous containers, coined actinosomes, using the
interactions between biomolecular condensates and the actin cytoskeleton.
This approach uses polypeptide/nucleoside triphosphate condensates
and localizes actin monomers on their surface. By triggering actin
polymerization and using osmotic gradients, the condensates are transformed
into containers, with the boundary made up of actin filaments and
polylysine polymers. We show that the guanosine triphosphate (GTP)-to-adenosine
triphosphate (ATP) ratio is a crucial parameter for forming actinosomes:
insufficient ATP prevents condensate dissolution, while excess ATP
leads to undesired crumpling. Permeability studies reveal the porous
surface of actinosomes, allowing small molecules to pass through while
restricting bigger macromolecules within the interior. We show the
functionality of actinosomes as bioreactors by carrying out in vitro protein translation within them. Actinosomes are
a handy addition to the synthetic cell platform, with appealing properties
like ease of production, inherent encapsulation capacity, and a potentially
active surface to trigger signaling cascades and form multicellular
assemblies, conceivably useful for biotechnological applications.
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Affiliation(s)
- Ketan A Ganar
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Liza Leijten
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
| | - Siddharth Deshpande
- Laboratory of Physical Chemistry and Soft Matter, Wageningen University and Research, Stippeneng 4, 6708 WE Wageningen, The Netherlands
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17
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Miele Y, Holló G, Lagzi I, Rossi F. Shape Deformation, Budding and Division of Giant Vesicles and Artificial Cells: A Review. Life (Basel) 2022; 12:841. [PMID: 35743872 PMCID: PMC9224789 DOI: 10.3390/life12060841] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/23/2022] [Accepted: 05/30/2022] [Indexed: 11/17/2022] Open
Abstract
The understanding of the shape-change dynamics leading to the budding and division of artificial cells has gained much attention in the past few decades due to an increased interest in designing stimuli-responsive synthetic systems and minimal models of biological self-reproduction. In this respect, membranes and their composition play a fundamental role in many aspects related to the stability of the vesicles: permeability, elasticity, rigidity, tunability and response to external changes. In this review, we summarise recent experimental and theoretical work dealing with shape deformation and division of (giant) vesicles made of phospholipids and/or fatty acids membranes. Following a classic approach, we divide the strategies used to destabilise the membranes into two different types, physical (osmotic stress, temperature and light) and chemical (addition of amphiphiles, the addition of reactive molecules and pH changes) even though they often act in synergy when leading to a complete division process. Finally, we review the most important theoretical methods employed to describe the equilibrium shapes of giant vesicles and how they provide ways to explain and control the morphological changes leading from one equilibrium structure to another.
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Affiliation(s)
- Ylenia Miele
- Department of Chemistry and Biology “A. Zambelli”, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy;
| | - Gábor Holló
- MTA-BME Condensed Matter Research Group, Budapest University of Technology and Economics, Muegyetem rkp. 3, 1111 Budapest, Hungary;
| | - István Lagzi
- MTA-BME Condensed Matter Research Group, Budapest University of Technology and Economics, Muegyetem rkp. 3, 1111 Budapest, Hungary;
- Department of Physics, Institute of Physics, Budapest University of Technology and Economics, Muegyetem rkp. 3, 1111 Budapest, Hungary
| | - Federico Rossi
- Department of Earth, Environmental and Physical Sciences—DEEP Sciences, University of Siena, Pian dei Mantellini 44, 53100 Siena, Italy
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18
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Kretschmer S, Kortemme T. Advances in the Computational Design of Small-Molecule-Controlled Protein-Based Circuits for Synthetic Biology. PROCEEDINGS OF THE IEEE. INSTITUTE OF ELECTRICAL AND ELECTRONICS ENGINEERS 2022; 110:659-674. [PMID: 36531560 PMCID: PMC9754107 DOI: 10.1109/jproc.2022.3157898] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Synthetic biology approaches living systems with an engineering perspective and promises to deliver solutions to global challenges in healthcare and sustainability. A critical component is the design of biomolecular circuits with programmable input-output behaviors. Such circuits typically rely on a sensor module that recognizes molecular inputs, which is coupled to a functional output via protein-level circuits or regulating the expression of a target gene. While gene expression outputs can be customized relatively easily by exchanging the target genes, sensing new inputs is a major limitation. There is a limited repertoire of sensors found in nature, and there are often difficulties with interfacing them with engineered circuits. Computational protein design could be a key enabling technology to address these challenges, as it allows for the engineering of modular and tunable sensors that can be tailored to the circuit's application. In this article, we review recent computational approaches to design protein-based sensors for small-molecule inputs with particular focus on those based on the widely used Rosetta software suite. Furthermore, we review mechanisms that have been harnessed to couple ligand inputs to functional outputs. Based on recent literature, we illustrate how the combination of protein design and synthetic biology enables new sensors for diverse applications ranging from biomedicine to metabolic engineering. We conclude with a perspective on how strategies to address frontiers in protein design and cellular circuit design may enable the next generation of sense-response networks, which may increasingly be assembled from de novo components to display diverse and engineerable input-output behaviors.
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Affiliation(s)
- Simon Kretschmer
- Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, CA 94158 USA, and affiliated with the California Quantitative Biosciences Institute (QBI) at UCSF, San Francisco, CA 94158 USA
| | - Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, University of California at San Francisco, San Francisco, CA 94158 USA, and affiliated with the California Quantitative Biosciences Institute (QBI) at UCSF, San Francisco, CA 94158 USA
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19
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Hernandez Bücher JE, Staufer O, Ostertag L, Mersdorf U, Platzman I, Spatz JP. Bottom-up assembly of target-specific cytotoxic synthetic cells. Biomaterials 2022; 285:121522. [DOI: 10.1016/j.biomaterials.2022.121522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 03/31/2022] [Accepted: 04/10/2022] [Indexed: 12/23/2022]
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20
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Smith JM, Chowdhry R, Booth MJ. Controlling Synthetic Cell-Cell Communication. Front Mol Biosci 2022; 8:809945. [PMID: 35071327 PMCID: PMC8766733 DOI: 10.3389/fmolb.2021.809945] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/13/2021] [Indexed: 11/28/2022] Open
Abstract
Synthetic cells, which mimic cellular function within a minimal compartment, are finding wide application, for instance in studying cellular communication and as delivery devices to living cells. However, to fully realise the potential of synthetic cells, control of their function is vital. An array of tools has already been developed to control the communication of synthetic cells to neighbouring synthetic cells or living cells. These tools use either chemical inputs, such as small molecules, or physical inputs, such as light. Here, we examine these current methods of controlling synthetic cell communication and consider alternative mechanisms for future use.
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Affiliation(s)
| | | | - Michael J. Booth
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
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21
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Arribas Perez M, Beales PA. Biomimetic Curvature and Tension-Driven Membrane Fusion Induced by Silica Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:13917-13931. [PMID: 34788054 DOI: 10.1021/acs.langmuir.1c02492] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Fusion events in living cells are intricate phenomena that require the coordinate action of multicomponent protein complexes. However, simpler synthetic tools to control membrane fusion in artificial cells are highly desirable. Native membrane fusion machinery mediates fusion, driving a delicate balance of membrane curvature and tension between two closely apposed membranes. Here, we show that silica nanoparticles (SiO2 NPs) at a size close to the cross-over between tension-driven and curvature-driven interaction regimes initiate efficient fusion of biomimetic model membranes. Fusion efficiency and mechanisms are studied by Förster resonance energy transfer and confocal fluorescence microscopy. SiO2 NPs induce a slight increase in lipid packing likely to increase the lateral tension of the membrane. We observe a connection between membrane tension and fusion efficiency. Finally, real-time confocal fluorescence microscopy reveals three distinct mechanistic pathways for membrane fusion. SiO2 NPs show significant potential for inclusion in the synthetic biology toolkit for membrane remodeling and fusion in artificial cells.
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Affiliation(s)
- Marcos Arribas Perez
- Astbury Centre for Structural Molecular Biology and School of Chemistry, University of Leeds, Leeds LS2 9JT, U.K
| | - Paul A Beales
- Astbury Centre for Structural Molecular Biology and School of Chemistry, University of Leeds, Leeds LS2 9JT, U.K
- Bragg Centre for Materials Research, University of Leeds, Leeds LS2 9JT, U.K
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22
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Abstract
A major goal of synthetic biology is to understand the transition between non-living matter and life. The bottom-up development of an artificial cell would provide a minimal system with which to study the border between chemistry and biology. So far, a fully synthetic cell has remained elusive, but chemists are progressing towards this goal by reconstructing cellular subsystems. Cell boundaries, likely in the form of lipid membranes, were necessary for the emergence of life. In addition to providing a protective barrier between cellular cargo and the external environment, lipid compartments maintain homeostasis with other subsystems to regulate cellular processes. In this Review, we examine different chemical approaches to making cell-mimetic compartments. Synthetic strategies to drive membrane formation and function, including bioorthogonal ligations, dissipative self-assembly and reconstitution of biochemical pathways, are discussed. Chemical strategies aim to recreate the interactions between lipid membranes, the external environment and internal biomolecules, and will clarify our understanding of life at the interface of chemistry and biology.
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23
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Abstract
Lipid membranes in cells are fluid structures that undergo constant synthesis, remodeling, fission, and fusion. The dynamic nature of lipid membranes enables their use as adaptive compartments, making them indispensable for all life on Earth. Efforts to create life-like artificial cells will likely involve mimicking the structure and function of lipid membranes to recapitulate fundamental cellular processes such as growth and division. As such, there is considerable interest in chemistry that mimics the functional properties of membranes, with the express intent of recapitulating biological phenomena. We suggest expanding the definition of membrane mimetic chemistry to capture these efforts. In this Perspective, we discuss how membrane mimetic chemistry serves the development of artificial cells. By leveraging recent advances in chemical biology and systems chemistry, we have an opportunity to use simplified chemical and biochemical systems to mimic the remarkable properties of living membranes.
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Affiliation(s)
- Jacob A Vance
- Chemistry and Biochemistry, University of California San Diego, California 92093, United States
| | - Neal K Devaraj
- Chemistry and Biochemistry, University of California San Diego, California 92093, United States
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24
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Casas-Ferrer L, Brisson A, Massiera G, Casanellas L. Design of vesicle prototissues as a model for cellular tissues. SOFT MATTER 2021; 17:5061-5072. [PMID: 33929482 DOI: 10.1039/d1sm00336d] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Synthesizing biomimetic prototissues with predictable physical properties is a promising tool for the study of cellular tissues, as they would enable to test systematically the role of individual physical mechanisms on complex biological processes. The aim of this study is to design a biomimetic cohesive tissue with tunable mechanical properties by the controlled assembly of giant unillamelar vesicles (GUV). GUV-GUV specific adhesion is mediated by the inclusion of the streptavidin-biotin pair, or DNA complementary strands. Using a simple assembly protocol, we are capable of synthesizing vesicle prototissues of spheroidal or sheet-like morphologies, with predictable cell-cell adhesion strengths, typical sizes, and degree of compaction.
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Affiliation(s)
- Laura Casas-Ferrer
- Laboratoire Charles Coulomb (L2C), UMR 5221 CNRS-Université de Montpellier. Place Eugène Bataillon, 34095 Montpellier, France.
| | - Amaury Brisson
- Laboratoire Charles Coulomb (L2C), UMR 5221 CNRS-Université de Montpellier. Place Eugène Bataillon, 34095 Montpellier, France.
| | - Gladys Massiera
- Laboratoire Charles Coulomb (L2C), UMR 5221 CNRS-Université de Montpellier. Place Eugène Bataillon, 34095 Montpellier, France.
| | - Laura Casanellas
- Laboratoire Charles Coulomb (L2C), UMR 5221 CNRS-Université de Montpellier. Place Eugène Bataillon, 34095 Montpellier, France.
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25
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Litschel T, Kelley CF, Holz D, Adeli Koudehi M, Vogel SK, Burbaum L, Mizuno N, Vavylonis D, Schwille P. Reconstitution of contractile actomyosin rings in vesicles. Nat Commun 2021; 12:2254. [PMID: 33859190 PMCID: PMC8050101 DOI: 10.1038/s41467-021-22422-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 03/04/2021] [Indexed: 12/31/2022] Open
Abstract
One of the grand challenges of bottom-up synthetic biology is the development of minimal machineries for cell division. The mechanical transformation of large-scale compartments, such as Giant Unilamellar Vesicles (GUVs), requires the geometry-specific coordination of active elements, several orders of magnitude larger than the molecular scale. Of all cytoskeletal structures, large-scale actomyosin rings appear to be the most promising cellular elements to accomplish this task. Here, we have adopted advanced encapsulation methods to study bundled actin filaments in GUVs and compare our results with theoretical modeling. By changing few key parameters, actin polymerization can be differentiated to resemble various types of networks in living cells. Importantly, we find membrane binding to be crucial for the robust condensation into a single actin ring in spherical vesicles, as predicted by theoretical considerations. Upon force generation by ATP-driven myosin motors, these ring-like actin structures contract and locally constrict the vesicle, forming furrow-like deformations. On the other hand, cortex-like actin networks are shown to induce and stabilize deformations from spherical shapes. Cytoskeletal networks support and direct cell shape and guide intercellular transport, but relatively little is understood about the self-organization of cytoskeletal components on the scale of an entire cell. Here, authors use an in vitro system and observe the assembly of different types of actin networks and the condensation of membrane-bound actin into single rings.
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Affiliation(s)
- Thomas Litschel
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Charlotte F Kelley
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany.,Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Danielle Holz
- Department of Physics, Lehigh University, Bethlehem, PA, USA
| | | | - Sven K Vogel
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Laura Burbaum
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Naoko Mizuno
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | | | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, Martinsried, Germany.
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26
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Piao J, Yuan W, Dong Y. Recent Progress of DNA Nanostructures on Amphiphilic Membranes. Macromol Biosci 2021; 21:e2000440. [PMID: 33759366 DOI: 10.1002/mabi.202000440] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/24/2021] [Indexed: 11/11/2022]
Abstract
Employing DNA nanostructures mimicking membrane proteins on artificial amphiphilic membranes have been widely developed to understand the structures and functions of the natural membrane systems. In this review, the recent developments in artificial systems constructed by amphiphilic membranes and DNA nanostructures are summarized. First, the preparations and properties of the amphipathic bilayer models are introduced. Second, the interactions are discussed between the membrane and the DNA nanostructures, as well as their coassembly behaviors. Next, the alternative systems related to membrane protein-mediated signal transmission, selective distribution, transmembrane channels, and membrane fusion are also introduced. Moreover, the constructions of membrane skeleton protein-mimicking DNA nanostructures are also highlighted.
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Affiliation(s)
- Jiafang Piao
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Chinese Academy of Sciences, Institute of Chemistry, Beijing, 100190, China.,Beijing National Laboratory for Molecular Sciences, Chinese Academy of Sciences, Institute of Chemistry, Beijing, 100190, China
| | - Wei Yuan
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Chinese Academy of Sciences, Institute of Chemistry, Beijing, 100190, China.,Beijing National Laboratory for Molecular Sciences, Chinese Academy of Sciences, Institute of Chemistry, Beijing, 100190, China
| | - Yuanchen Dong
- CAS Key Laboratory of Colloid, Interface and Chemical Thermodynamics, Chinese Academy of Sciences, Institute of Chemistry, Beijing, 100190, China.,Beijing National Laboratory for Molecular Sciences, Chinese Academy of Sciences, Institute of Chemistry, Beijing, 100190, China
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27
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Zorrilla S, Monterroso B, Robles-Ramos MÁ, Margolin W, Rivas G. FtsZ Interactions and Biomolecular Condensates as Potential Targets for New Antibiotics. Antibiotics (Basel) 2021; 10:antibiotics10030254. [PMID: 33806332 PMCID: PMC7999717 DOI: 10.3390/antibiotics10030254] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 12/18/2022] Open
Abstract
FtsZ is an essential and central protein for cell division in most bacteria. Because of its ability to organize into dynamic polymers at the cell membrane and recruit other protein partners to form a “divisome”, FtsZ is a leading target in the quest for new antibacterial compounds. Strategies to potentially arrest the essential and tightly regulated cell division process include perturbing FtsZ’s ability to interact with itself and other divisome proteins. Here, we discuss the available methodologies to screen for and characterize those interactions. In addition to assays that measure protein-ligand interactions in solution, we also discuss the use of minimal membrane systems and cell-like compartments to better approximate the native bacterial cell environment and hence provide a more accurate assessment of a candidate compound’s potential in vivo effect. We particularly focus on ways to measure and inhibit under-explored interactions between FtsZ and partner proteins. Finally, we discuss recent evidence that FtsZ forms biomolecular condensates in vitro, and the potential implications of these assemblies in bacterial resistance to antibiotic treatment.
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Affiliation(s)
- Silvia Zorrilla
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain; (M.-Á.R.-R.); (G.R.)
- Correspondence: (S.Z.); (B.M.); Tel.: +34-91-837-3112 (S.Z. & B.M.)
| | - Begoña Monterroso
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain; (M.-Á.R.-R.); (G.R.)
- Correspondence: (S.Z.); (B.M.); Tel.: +34-91-837-3112 (S.Z. & B.M.)
| | - Miguel-Ángel Robles-Ramos
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain; (M.-Á.R.-R.); (G.R.)
| | - William Margolin
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas, Houston, TX 77030, USA;
| | - Germán Rivas
- Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CSIC), 28040 Madrid, Spain; (M.-Á.R.-R.); (G.R.)
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28
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van Tatenhove-Pel RJ, Rijavec T, Lapanje A, van Swam I, Zwering E, Hernandez-Valdes JA, Kuipers OP, Picioreanu C, Teusink B, Bachmann H. Microbial competition reduces metabolic interaction distances to the low µm-range. THE ISME JOURNAL 2021; 15:688-701. [PMID: 33077887 PMCID: PMC8027890 DOI: 10.1038/s41396-020-00806-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 09/21/2020] [Accepted: 10/02/2020] [Indexed: 01/12/2023]
Abstract
Metabolic interactions between cells affect microbial community compositions and hence their function in ecosystems. It is well-known that under competition for the exchanged metabolite, concentration gradients constrain the distances over which interactions can occur. However, interaction distances are typically quantified in two-dimensional systems or without accounting for competition or other metabolite-removal, conditions which may not very often match natural ecosystems. We here analyze the impact of cell-to-cell distance on unidirectional cross-feeding in a three-dimensional aqueous system with competition for the exchanged metabolite. Effective interaction distances were computed with a reaction-diffusion model and experimentally verified by growing a synthetic consortium of 1 µm-sized metabolite producer, receiver, and competitor cells in different spatial structures. We show that receivers cannot interact with producers located on average 15 µm away from them, as product concentration gradients flatten close to producer cells. We developed an aggregation protocol and varied the receiver cells' product affinity, to show that within producer-receiver aggregates even low-affinity receiver cells could interact with producers. These results show that competition or other metabolite-removal of a public good in a three-dimensional system reduces metabolic interaction distances to the low µm-range, highlighting the importance of concentration gradients as physical constraint for cellular interactions.
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Affiliation(s)
- Rinke J van Tatenhove-Pel
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, 1081HV, Amsterdam, The Netherlands
| | - Tomaž Rijavec
- Department of Environmental Sciences, Jožef Stefan Institute, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Aleš Lapanje
- Department of Environmental Sciences, Jožef Stefan Institute, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Iris van Swam
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, 1081HV, Amsterdam, The Netherlands
| | - Emile Zwering
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, 1081HV, Amsterdam, The Netherlands
| | - Jhonatan A Hernandez-Valdes
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG, Groningen, The Netherlands
| | - Cristian Picioreanu
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ, Delft, The Netherlands
| | - Bas Teusink
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, 1081HV, Amsterdam, The Netherlands
| | - Herwig Bachmann
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, VU University Amsterdam, de Boelelaan 1108, 1081HV, Amsterdam, The Netherlands.
- NIZO Food Research, Kernhemseweg 2, 6718ZB, Ede, The Netherlands.
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29
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Aden S, Snoj T, Anderluh G. The use of giant unilamellar vesicles to study functional properties of pore-forming toxins. Methods Enzymol 2021; 649:219-251. [PMID: 33712188 DOI: 10.1016/bs.mie.2021.01.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Pore-forming toxins (PFTs) act upon lipid membranes and appropriate model systems are of great importance in researching these proteins. Giant unilamellar vesicles (GUVs) are an excellent model membrane system to study interactions between lipids and proteins. Their main advantage is the size comparable to cells, which means that GUVs can be observed directly under the light microscope. Many PFTs properties can be studied by using GUVs, such as binding specificity, membrane reorganization upon protein binding and oligomerization, pore properties and mechanism of pore formation. GUVs also represent a good model for biotechnological approaches, e.g., in applications in synthetic biology and medicine. Each research area has its own demands for GUVs properties, so several different approaches for GUVs preparations have been developed and will be discussed in this chapter.
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Affiliation(s)
- Saša Aden
- Department for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Tina Snoj
- Department for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Gregor Anderluh
- Department for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Ljubljana, Slovenia.
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30
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Gaut NJ, Adamala KP. Reconstituting Natural Cell Elements in Synthetic Cells. Adv Biol (Weinh) 2021; 5:e2000188. [DOI: 10.1002/adbi.202000188] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 01/05/2021] [Indexed: 02/06/2023]
Affiliation(s)
- Nathaniel J. Gaut
- Department of Genetics Cell Biology and Development University of Minnesota 420 Washington Ave SE Minneapolis MN 55455 USA
| | - Katarzyna P. Adamala
- Department of Genetics Cell Biology and Development University of Minnesota 420 Washington Ave SE Minneapolis MN 55455 USA
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31
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Franquelim HG, Dietz H, Schwille P. Reversible membrane deformations by straight DNA origami filaments. SOFT MATTER 2021; 17:276-287. [PMID: 32406895 DOI: 10.1039/d0sm00150c] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Membrane-active cytoskeletal elements, such as FtsZ, septin or actin, form filamentous polymers able to induce and stabilize curvature on cellular membranes. In order to emulate the characteristic dynamic self-assembly properties of cytoskeletal subunits in vitro, biomimetic synthetic scaffolds were here developed using DNA origami. In contrast to our earlier work with pre-curved scaffolds, we specifically assessed the potential of origami mimicking straight filaments, such as actin and microtubules, by origami presenting cholesteryl anchors for membrane binding and additional blunt end stacking interactions for controllable polymerization into linear filaments. By assessing the interaction of our DNA nanostructures with model membranes using fluorescence microscopy, we show that filaments can be formed, upon increasing MgCl2 in solution, for structures displaying blunt ends; and can subsequently depolymerize, by decreasing the concentration of MgCl2. Distinctive spike-like membrane protrusions were generated on giant unilamellar vesicles at high membrane-bound filament densities, and the presence of such deformations was reversible and shown to correlate with the MgCl2-triggered polymerization of DNA origami subunits into filamentous aggregates. In the end, our approach reveals the formation of membrane-bound filaments as a minimal requirement for membrane shaping by straight cytoskeletal-like objects.
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Affiliation(s)
| | - Hendrik Dietz
- Technical University of Munich, Garching Near Munich, Germany
| | - Petra Schwille
- Max Planck Institute of Biochemistry, Martinsried near Munich, Germany.
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32
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Kostina NY, Wagner AM, Haraszti T, Rahimi K, Xiao Q, Klein ML, Percec V, Rodriguez-Emmenegger C. Unraveling topology-induced shape transformations in dendrimersomes. SOFT MATTER 2021; 17:254-267. [PMID: 32789415 DOI: 10.1039/d0sm01097a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The vital functions of cell membranes require their ability to quickly change shape to perform complex tasks such as motion, division, endocytosis, and apoptosis. Membrane curvature in cells is modulated by very complex processes such as changes in lipid composition, the oligomerization of curvature-scaffolding proteins, and the reversible insertion of protein regions that act like wedges in the membrane. But, could much simpler mechanisms support membrane shape transformation? In this work, we demonstrate how the change of amphiphile topology in the bilayer can drive shape transformations of cell membrane models. To tackle this, we have designed and synthesized new types of amphiphiles-Janus dendrimers-that self-assemble into uni-, multilamellar, or smectic-ordered vesicles, named dendrimersomes. We synthesized Janus dendrimers containing a photo-labile bond that upon UV-Vis irradiation cleavage lose a part of the hydrophilic dendron. This leads to a change from a cylindrically to a wedge-shaped amphiphile. The high mobility of these dendrimers allows for the concentration of the wedge-shaped amphiphiles and the generation of transmembrane asymmetries. The concentration of the wedges and their rate of segregation allowed control of the budding and generation of structures such as tubules and high genus vesicles.
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Affiliation(s)
- Nina Yu Kostina
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany.
| | - Anna M Wagner
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany.
| | - Tamás Haraszti
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany.
| | - Khosrow Rahimi
- DWI-Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany.
| | - Qi Xiao
- Roy & Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA and Institute of Computational Molecular Science, Temple University, Philadelphia, PA 19122, USA
| | - Michael L Klein
- Institute of Computational Molecular Science, Temple University, Philadelphia, PA 19122, USA
| | - Virgil Percec
- Roy & Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
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Ganzinger KA, Merino‐Salomón A, García‐Soriano DA, Butterfield AN, Litschel T, Siedler F, Schwille P. FtsZ Reorganization Facilitates Deformation of Giant Vesicles in Microfluidic Traps**. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001928] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Kristina A. Ganzinger
- Department of Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
- Living Matter AMOLF P.O. Box 41883-1009 DB Amsterdam The Netherlands
| | - Adrián Merino‐Salomón
- Department of Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | - Daniela A. García‐Soriano
- Department of Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | - A. Nelson Butterfield
- Department of Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | - Thomas Litschel
- Department of Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | - Frank Siedler
- Department of Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
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34
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Ganzinger KA, Merino‐Salomón A, García‐Soriano DA, Butterfield AN, Litschel T, Siedler F, Schwille P. FtsZ Reorganization Facilitates Deformation of Giant Vesicles in Microfluidic Traps*. Angew Chem Int Ed Engl 2020; 59:21372-21376. [PMID: 32735732 PMCID: PMC7756778 DOI: 10.1002/anie.202001928] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/27/2020] [Indexed: 12/23/2022]
Abstract
The geometry of reaction compartments can affect the local outcome of interface-restricted reactions. Giant unilamellar vesicles (GUVs) are commonly used to generate cell-sized, membrane-bound reaction compartments, which are, however, always spherical. Herein, we report the development of a microfluidic chip to trap and reversibly deform GUVs into cigar-like shapes. When trapping and elongating GUVs that contain the primary protein of the bacterial Z ring, FtsZ, we find that membrane-bound FtsZ filaments align preferentially with the short GUV axis. When GUVs are released from this confinement and membrane tension is relaxed, FtsZ reorganizes reversibly from filaments into dynamic rings that stabilize membrane protrusions; a process that allows reversible GUV deformation. We conclude that microfluidic traps are useful for manipulating both geometry and tension of GUVs, and for investigating how both affect the outcome of spatially-sensitive reactions inside them, such as that of protein self-organization.
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Affiliation(s)
- Kristina A. Ganzinger
- Department of Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
- Living MatterAMOLFP.O. Box 41883-1009 DBAmsterdamThe Netherlands
| | - Adrián Merino‐Salomón
- Department of Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Daniela A. García‐Soriano
- Department of Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - A. Nelson Butterfield
- Department of Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Thomas Litschel
- Department of Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Frank Siedler
- Department of Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Petra Schwille
- Department of Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
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35
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Royes J, Biou V, Dautin N, Tribet C, Miroux B. Inducible intracellular membranes: molecular aspects and emerging applications. Microb Cell Fact 2020; 19:176. [PMID: 32887610 PMCID: PMC7650269 DOI: 10.1186/s12934-020-01433-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 08/27/2020] [Indexed: 02/08/2023] Open
Abstract
Membrane remodeling and phospholipid biosynthesis are normally tightly regulated to maintain the shape and function of cells. Indeed, different physiological mechanisms ensure a precise coordination between de novo phospholipid biosynthesis and modulation of membrane morphology. Interestingly, the overproduction of certain membrane proteins hijack these regulation networks, leading to the formation of impressive intracellular membrane structures in both prokaryotic and eukaryotic cells. The proteins triggering an abnormal accumulation of membrane structures inside the cells (or membrane proliferation) share two major common features: (1) they promote the formation of highly curved membrane domains and (2) they lead to an enrichment in anionic, cone-shaped phospholipids (cardiolipin or phosphatidic acid) in the newly formed membranes. Taking into account the available examples of membrane proliferation upon protein overproduction, together with the latest biochemical, biophysical and structural data, we explore the relationship between protein synthesis and membrane biogenesis. We propose a mechanism for the formation of these non-physiological intracellular membranes that shares similarities with natural inner membrane structures found in α-proteobacteria, mitochondria and some viruses-infected cells, pointing towards a conserved feature through evolution. We hope that the information discussed in this review will give a better grasp of the biophysical mechanisms behind physiological and induced intracellular membrane proliferation, and inspire new applications, either for academia (high-yield membrane protein production and nanovesicle production) or industry (biofuel production and vaccine preparation).
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Affiliation(s)
- Jorge Royes
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université de Paris, LBPC-PM, CNRS, UMR7099, 75005, Paris, France. .,Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le Développement de la Recherche Scientifique, 75005, Paris, France. .,Département de Chimie, École Normale Supérieure, PASTEUR, PSL University, CNRS, Sorbonne Université, 24 Rue Lhomond, 75005, Paris, France.
| | - Valérie Biou
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université de Paris, LBPC-PM, CNRS, UMR7099, 75005, Paris, France.,Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le Développement de la Recherche Scientifique, 75005, Paris, France
| | - Nathalie Dautin
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université de Paris, LBPC-PM, CNRS, UMR7099, 75005, Paris, France.,Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le Développement de la Recherche Scientifique, 75005, Paris, France
| | - Christophe Tribet
- Département de Chimie, École Normale Supérieure, PASTEUR, PSL University, CNRS, Sorbonne Université, 24 Rue Lhomond, 75005, Paris, France
| | - Bruno Miroux
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université de Paris, LBPC-PM, CNRS, UMR7099, 75005, Paris, France. .,Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le Développement de la Recherche Scientifique, 75005, Paris, France.
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36
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Pezeshkian W, König M, Wassenaar TA, Marrink SJ. Backmapping triangulated surfaces to coarse-grained membrane models. Nat Commun 2020; 11:2296. [PMID: 32385270 PMCID: PMC7210967 DOI: 10.1038/s41467-020-16094-y] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/07/2020] [Indexed: 12/14/2022] Open
Abstract
Many biological processes involve large-scale changes in membrane shape. Computer simulations of these processes are challenging since they occur across a wide range of spatiotemporal scales that cannot be investigated in full by any single current simulation technique. A potential solution is to combine different levels of resolution through a multiscale scheme. Here, we present a multiscale algorithm that backmaps a continuum membrane model represented as a dynamically triangulated surface (DTS) to its corresponding molecular model based on the coarse-grained (CG) Martini force field. Thus, we can use DTS simulations to equilibrate slow large-scale membrane conformational changes and then explore the local properties at CG resolution. We demonstrate the power of our method by backmapping a vesicular bud induced by binding of Shiga toxin and by transforming the membranes of an entire mitochondrion to near-atomic resolution. Our approach opens the way to whole cell simulations at molecular detail. Computer simulations of large-scale changes in membrane shape are challenging since they occur across a wide range of spatiotemporal scales. Here, authors present a multiscale algorithm that backmaps a continuum membrane model represented as a dynamically triangulated surface to its corresponding molecular model based on the coarse-grained Martini force field.
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Affiliation(s)
- Weria Pezeshkian
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands.
| | - Melanie König
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Tsjerk A Wassenaar
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, Netherlands.
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37
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Hindley JW, Law RV, Ces O. Membrane functionalization in artificial cell engineering. SN APPLIED SCIENCES 2020. [DOI: 10.1007/s42452-020-2357-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
AbstractBottom-up synthetic biology aims to construct mimics of cellular structure and behaviour known as artificial cells from a small number of molecular components. The development of this nascent field has coupled new insights in molecular biology with large translational potential for application in fields such as drug delivery and biosensing. Multiple approaches have been applied to create cell mimics, with many efforts focusing on phospholipid-based systems. This mini-review focuses on different approaches to incorporating molecular motifs as tools for lipid membrane functionalization in artificial cell construction. Such motifs range from synthetic chemical functional groups to components from extant biology that can be arranged in a ‘plug-and-play’ approach which is hard to replicate in living systems. Rationally designed artificial cells possess the promise of complex biomimetic behaviour from minimal, highly engineered chemical networks.
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38
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Controlled division of cell-sized vesicles by low densities of membrane-bound proteins. Nat Commun 2020; 11:905. [PMID: 32060284 PMCID: PMC7021675 DOI: 10.1038/s41467-020-14696-0] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 01/24/2020] [Indexed: 11/12/2022] Open
Abstract
The proliferation of life on earth is based on the ability of single cells to divide into two daughter cells. During cell division, the plasma membrane undergoes a series of morphological transformations which ultimately lead to membrane fission. Here, we show that analogous remodeling processes can be induced by low densities of proteins bound to the membranes of cell-sized lipid vesicles. Using His-tagged fluorescent proteins, we are able to precisely control the spontaneous curvature of the vesicle membranes. By fine-tuning this curvature, we obtain dumbbell-shaped vesicles with closed membrane necks as well as neck fission and complete vesicle division. Our results demonstrate that the spontaneous curvature generates constriction forces around the membrane necks and that these forces can easily cover the force range found in vivo. Our approach involves only one species of membrane-bound proteins at low densities, thereby providing a simple and extendible module for bottom-up synthetic biology. Membrane fission of a cell into two daughters is a core ability of cell-based life. Here the authors show that in artificial cells division can be controlled by regulating membrane curvature using low protein density.
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39
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Division in synthetic cells. Emerg Top Life Sci 2019; 3:551-558. [PMID: 33523162 DOI: 10.1042/etls20190023] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/06/2019] [Accepted: 08/07/2019] [Indexed: 12/13/2022]
Abstract
Cell division is one of the most fundamental processes of life, and so far the only known way of how living systems can come into existence at all. Consequently, its reconstitution in any artificial cell system that will have to be built from the bottom-up is a notoriously complex but an important task. In this short review, I discuss several approaches how to realize division of cell-like compartments, from simply relying on the physical principles of destabilization by growth, or applying external forces, to the design of self-assembling and self-organizing machineries that may autonomously accomplish this task in response to external or internal cues.
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