1
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Takahashi H, Fujikawa M, Ogawa A. Rational design of eukaryotic riboswitches that up-regulate IRES-mediated translation initiation with high switching efficiency through a kinetic trapping mechanism in vitro. RNA (NEW YORK, N.Y.) 2023; 29:1950-1959. [PMID: 37704221 PMCID: PMC10653380 DOI: 10.1261/rna.079778.123] [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: 07/20/2023] [Accepted: 09/05/2023] [Indexed: 09/15/2023]
Abstract
In general, riboswitches functioning through a cotranscriptional kinetic trapping mechanism (kt-riboswitches) show higher switching efficiencies in response to practical concentrations of their ligand molecules than eq-riboswitches, which function by an equilibrium mechanism. However, the former have been much more difficult to design due to their more complex mechanism. We here successfully developed a rational strategy for constructing eukaryotic kt-riboswitches that ligand-dependently enhance translation initiation mediated by an internal ribosome entry site (IRES). This was achieved both by utilizing some predicted structural features of a highly efficient bacterial kt-riboswitch identified through screening and by completely decoupling an aptamer domain from the IRES. Three kt-riboswitches optimized through this strategy, each responding to a different ligand, exhibited three- to sevenfold higher induction ratios (up to ∼90) than previously optimized eq-riboswitches regulating the same IRES-mediated translation in wheat germ extract. Because the IRES used functions well in various eukaryotic expression systems, these types of kt-riboswitches are expected to serve as major eukaryotic gene regulators based on RNA. In addition, the present strategy could be applied to the rational construction of other types of kt-riboswitches, including those functioning in bacterial expression systems.
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Affiliation(s)
- Hajime Takahashi
- Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Masahiro Fujikawa
- Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
| | - Atsushi Ogawa
- Proteo-Science Center, Ehime University, Matsuyama, Ehime 790-8577, Japan
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2
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Shin J, Jang Y. Rational design and engineering of polypeptide/protein vesicles for advanced biological applications. J Mater Chem B 2023; 11:8834-8847. [PMID: 37505198 DOI: 10.1039/d3tb01103h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Synthetic vesicles have gained considerable popularity in recent years for numerous biological and medical applications. Among the various types of synthetic vesicles, the utilization of polypeptides and/or proteins as fundamental constituents has garnered significant interest for vesicle construction owing to the unique bio-functionalities inherent in rationally designed amino acid sequences. Especially the incorporation of functional proteins onto the vesicle surface facilitates a wide range of advanced biological applications that are not easily attainable with traditional building blocks, such as lipids and polymers. The main goal of this review is to provide a comprehensive overview of the latest advancements in polypeptide/protein vesicles. Moreover, this review encompasses the rational design and engineering strategies employed in the creation of polypeptide/protein vesicles, including the synthesis of building blocks, the modulation of their self-assembly, as well as their diverse applications. Furthermore, this work includes an in-depth discussion of the key challenges and opportunities associated with polypeptide/protein vesicles, providing valuable insights for future research. By offering an up-to-date review of this burgeoning field of polypeptide/protein vesicle research, this review will shed light on the potential applications of these biomaterials.
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Affiliation(s)
- Jooyong Shin
- Department of Chemical Engineering, University of Florida, 1006 Center Drive, Gainesville, Florida 32611, USA.
| | - Yeongseon Jang
- Department of Chemical Engineering, University of Florida, 1006 Center Drive, Gainesville, Florida 32611, USA.
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3
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Turali-Emre ES, Emre AE, Vecchio DA, Kadiyala U, VanEpps JS, Kotov NA. Self-Organization of Iron Sulfide Nanoparticles into Complex Multicompartment Supraparticles. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2211244. [PMID: 36965166 PMCID: PMC10265277 DOI: 10.1002/adma.202211244] [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: 12/01/2022] [Revised: 03/02/2023] [Indexed: 06/09/2023]
Abstract
Self-assembled compartments from nanoscale components are found in all life forms. Their characteristic dimensions are in 50-1000 nm scale, typically assembled from a variety of bioorganic "building blocks". Among the various functions that these mesoscale compartments carry out, protection of the content from the environment is central. Finding synthetic pathways to similarly complex and functional particles from technologically friendly inorganic nanoparticles (NPs) is needed for a multitude of biomedical, biochemical, and biotechnological processes. Here, it is shown that FeS2 NPs stabilized by l-cysteine self-assemble into multicompartment supraparticles (mSPs). The NPs initially produce ≈55 nm concave assemblies that reconfigure into ≈75 nm closed mSPs with ≈340 interconnected compartments with an average size of ≈5 nm. The intercompartmental partitions and mSP surface are formed primarily from FeS2 and Fe2 O3 NPs, respectively. The intermediate formation of cup-like particles enables encapsulation of biological cargo. This capability is demonstrated by loading mSPs with DNA and subsequent transfection of mammalian cells. Also it is found that the temperature stability of the DNA cargo is enhanced compared to the traditional delivery vehicles. These findings demonstrate that biomimetic compartmentalized particles can be used to successfully encapsulate and enhance temperature stability of the nucleic acid cargo for a variety of bioapplications.
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Affiliation(s)
- E. Sumeyra Turali-Emre
- Biomedical Engineering Department, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute University of Michigan; University of Michigan; Ann Arbor, MI, 48109, USA
| | - Ahmet E. Emre
- Biomedical Engineering Department, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute University of Michigan; University of Michigan; Ann Arbor, MI, 48109, USA
| | - Drew A. Vecchio
- Chemical Engineering Department, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute University of Michigan; University of Michigan; Ann Arbor, MI, 48109, USA
| | - Usha Kadiyala
- Department of Emergency Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute University of Michigan; University of Michigan; Ann Arbor, MI, 48109, USA
| | - J. Scott VanEpps
- Department of Emergency Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
- Macromolecular Science and Engineering Department, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute University of Michigan; University of Michigan; Ann Arbor, MI, 48109, USA
| | - Nicholas A. Kotov
- Biomedical Engineering Department, University of Michigan, Ann Arbor, MI, 48109, USA
- Chemical Engineering Department, University of Michigan, Ann Arbor, MI, 48109, USA
- Materials Science and Engineering Department, University of Michigan Ann Arbor, MI, 48109, USA
- Macromolecular Science and Engineering Department, University of Michigan, Ann Arbor, MI, 48109, USA
- Biointerfaces Institute University of Michigan; University of Michigan; Ann Arbor, MI, 48109, USA
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4
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Rojas V, Larrondo LF. Coupling Cell Communication and Optogenetics: Implementation of a Light-Inducible Intercellular System in Yeast. ACS Synth Biol 2023; 12:71-82. [PMID: 36534043 PMCID: PMC9872819 DOI: 10.1021/acssynbio.2c00338] [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: 06/28/2022] [Indexed: 12/23/2022]
Abstract
Cell communication is a widespread mechanism in biology, allowing the transmission of information about environmental conditions. In order to understand how cell communication modulates relevant biological processes such as survival, division, differentiation, and apoptosis, different synthetic systems based on chemical induction have been successfully developed. In this work, we coupled cell communication and optogenetics in the budding yeast Saccharomyces cerevisiae. Our approach is based on two strains connected by the light-dependent production of α-factor pheromone in one cell type, which induces gene expression in the other type. After the individual characterization of the different variants of both strains, the optogenetic intercellular system was evaluated by combining the cells under contrasting illumination conditions. Using luciferase as a reporter gene, specific co-cultures at a 1:1 ratio displayed activation of the response upon constant blue light, which was not observed for the same cell mixtures grown in darkness. Then, the system was assessed at several dark/blue-light transitions, where the response level varies depending on the moment in which illumination was delivered. Furthermore, we observed that the amplitude of response can be tuned by modifying the initial ratio between both strains. Finally, the two-population system showed higher fold inductions in comparison with autonomous strains. Altogether, these results demonstrated that external light information is propagated through a diffusible signaling molecule to modulate gene expression in a synthetic system involving microbial cells, which will pave the road for studies allowing optogenetic control of population-level dynamics.
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Affiliation(s)
- Vicente Rojas
- Departamento
de Genética Molecular y Microbiología, Facultad de Ciencias
Biológicas, Pontificia Universidad
Católica de Chile, Santiago 8331150, Chile
- Millennium
Institute for Integrative Biology (iBio), Santiago 8331150, Chile
| | - Luis F. Larrondo
- Departamento
de Genética Molecular y Microbiología, Facultad de Ciencias
Biológicas, Pontificia Universidad
Católica de Chile, Santiago 8331150, Chile
- Millennium
Institute for Integrative Biology (iBio), Santiago 8331150, Chile
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5
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Ogawa A, Inoue H, Itoh Y, Takahashi H. Facile Expansion of the Variety of Orthogonal Ligand/Aptamer Pairs for Artificial Riboswitches. ACS Synth Biol 2023; 12:35-42. [PMID: 36566430 DOI: 10.1021/acssynbio.2c00475] [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] [Indexed: 12/26/2022]
Abstract
An RNA aptamer that induces suitable conformational changes upon binding to a user-defined ligand allows us to artificially construct a riboswitch, a ligand-dependent and cis-acting gene regulatory RNA. Although such an aptamer can be obtained through in vitro selection, it is still challenging to rationally expand the variety of orthogonal ligand/aptamer (ligand/riboswitch) pairs. To achieve this in a facile, selection-free way, we herein focused on a specific type of ligand, 6-nt nanosized DNA (nDNA) and its aptamer that was previously selected to construct a eukaryotic artificial riboswitch. Specifically, we merely mutated one or more possible Watson-Crick base pairs in the nDNA/aptamer (nDNA/riboswitch) interactions into another base pair or pairs. Using two sets that each had 16 comprehensive mutations, we obtained three groups of several orthogonal nDNA/riboswitch pairs. These pairs could be used to create complex gene circuits, including multiple simultaneous and/or multistep cascading regulations in synthetic biology.
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Affiliation(s)
- Atsushi Ogawa
- Proteo-Science Center, Ehime University, 3 Bunkyo, Matsuyama, Ehime 790-8577, Japan
| | - Honami Inoue
- Proteo-Science Center, Ehime University, 3 Bunkyo, Matsuyama, Ehime 790-8577, Japan
| | - Yu Itoh
- Proteo-Science Center, Ehime University, 3 Bunkyo, Matsuyama, Ehime 790-8577, Japan
| | - Hajime Takahashi
- Proteo-Science Center, Ehime University, 3 Bunkyo, Matsuyama, Ehime 790-8577, Japan
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6
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Leathers A, Walczak M, Brady RA, Al Samad A, Kotar J, Booth MJ, Cicuta P, Di Michele L. Reaction–Diffusion Patterning of DNA-Based Artificial Cells. J Am Chem Soc 2022; 144:17468-17476. [PMID: 36103297 PMCID: PMC9523701 DOI: 10.1021/jacs.2c06140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Biological cells display complex internal architectures
with distinct
micro environments that establish the chemical heterogeneity needed
to sustain cellular functions. The continued efforts to create advanced
cell mimics, namely, artificial cells, demands strategies for constructing
similarly heterogeneous structures with localized functionalities.
Here, we introduce a platform for constructing membraneless artificial
cells from the self-assembly of synthetic DNA nanostructures in which
internal domains can be established thanks to prescribed reaction–diffusion
waves. The method, rationalized through numerical modeling, enables
the formation of up to five distinct concentric environments in which
functional moieties can be localized. As a proof-of-concept, we apply
this platform to build DNA-based artificial cells in which a prototypical
nucleus synthesizes fluorescent RNA aptamers that then accumulate
in a surrounding storage shell, thus demonstrating the spatial segregation
of functionalities reminiscent of that observed in biological cells.
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Affiliation(s)
- Adrian Leathers
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, U.K
| | - Michal Walczak
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, U.K
| | - Ryan A. Brady
- Department of Chemistry, Faculty of Natural and Mathematical Sciences, King’s College London, London SE1 1DB, U.K
| | - Assala Al Samad
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
- Department of Chemistry, University College London, London WC1H 0AJ, U.K
| | - Jurij Kotar
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, U.K
| | - Michael J. Booth
- Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K
- Department of Chemistry, University College London, London WC1H 0AJ, U.K
| | - Pietro Cicuta
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, U.K
| | - Lorenzo Di Michele
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, U.K
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London W12 0BZ, U.K
- fabriCELL, Imperial College London, Molecular Sciences Research Hub, London W12 0BZ, U.K
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7
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Takahashi H, Okubo R, Ogawa A. Eukaryotic artificial ON-riboswitches that respond efficiently to mid-sized short peptides. Bioorg Med Chem Lett 2022; 71:128839. [PMID: 35654302 DOI: 10.1016/j.bmcl.2022.128839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/24/2022] [Accepted: 05/27/2022] [Indexed: 11/02/2022]
Abstract
We chose two types of mid-sized Arg-rich peptides (Rev-pep and Tat-pep) as ligands and used their aptamers to construct efficient eukaryotic ON-riboswitches (ligand-dependently upregulating riboswitches). Due to the aptamers' high affinities, the best Rev-pep-responsive and Tat-pep-responsive riboswitches obtained showed much higher switching efficiencies at low ligand concentrations than small ligand-responsive ON-riboswitches in the same mechanism. In addition, despite the high sequence similarity of Rev-pep and Tat-pep, the two best riboswitches were almost insensitive to each other's peptide ligand. Considering the high responsiveness and specificity along with the versatility of the expression platform used and the applicability of Arg-rich peptides, this orthogonal pair of riboswitches would be widely useful eukaryotic gene regulators or biosensors.
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Affiliation(s)
- Hajime Takahashi
- Proteo-Science Center, Ehime University, 3 Bunkyo, Matsuyama, Ehime 790-8577, Japan
| | - Ryo Okubo
- Proteo-Science Center, Ehime University, 3 Bunkyo, Matsuyama, Ehime 790-8577, Japan
| | - Atsushi Ogawa
- Proteo-Science Center, Ehime University, 3 Bunkyo, Matsuyama, Ehime 790-8577, Japan.
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8
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Cao S, da Silva LC, Landfester K. Light‐Activated Membrane Transport in Polymeric Cell‐Mimics. Angew Chem Int Ed Engl 2022; 61:e202205266. [PMID: 35759257 PMCID: PMC9542181 DOI: 10.1002/anie.202205266] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Indexed: 11/05/2022]
Affiliation(s)
- Shoupeng Cao
- Max Planck Institute for Polymer Research 55128 Mainz Germany
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9
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Cao S, da Silva LC, Landfester K. Light‐Activated Membrane Transport in Polymeric Cell‐Mimics. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202205266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Shoupeng Cao
- Max Planck Institute for Polymer Research 55128 Mainz Germany
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10
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Karoui H, Patwal PS, Pavan Kumar BVVS, Martin N. Chemical Communication in Artificial Cells: Basic Concepts, Design and Challenges. Front Mol Biosci 2022; 9:880525. [PMID: 35720123 PMCID: PMC9199989 DOI: 10.3389/fmolb.2022.880525] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/12/2022] [Indexed: 11/13/2022] Open
Abstract
In the past decade, the focus of bottom-up synthetic biology has shifted from the design of complex artificial cell architectures to the design of interactions between artificial cells mediated by physical and chemical cues. Engineering communication between artificial cells is crucial for the realization of coordinated dynamic behaviours in artificial cell populations, which would have implications for biotechnology, advanced colloidal materials and regenerative medicine. In this review, we focus our discussion on molecular communication between artificial cells. We cover basic concepts such as the importance of compartmentalization, the metabolic machinery driving signaling across cell boundaries and the different modes of communication used. The various studies in artificial cell signaling have been classified based on the distance between sender and receiver cells, just like in biology into autocrine, juxtacrine, paracrine and endocrine signaling. Emerging tools available for the design of dynamic and adaptive signaling are highlighted and some recent advances of signaling-enabled collective behaviours, such as quorum sensing, travelling pulses and predator-prey behaviour, are also discussed.
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Affiliation(s)
- Hedi Karoui
- Univ. Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR 5031, Pessac, France
| | - Pankaj Singh Patwal
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, India
| | - B. V. V. S. Pavan Kumar
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, India
- *Correspondence: B. V. V. S. Pavan Kumar, ; Nicolas Martin,
| | - Nicolas Martin
- Univ. Bordeaux, CNRS, Centre de Recherche Paul Pascal, UMR 5031, Pessac, France
- *Correspondence: B. V. V. S. Pavan Kumar, ; Nicolas Martin,
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11
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Synthetic cells with self-activating optogenetic proteins communicate with natural cells. Nat Commun 2022; 13:2328. [PMID: 35484097 PMCID: PMC9050678 DOI: 10.1038/s41467-022-29871-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 04/04/2022] [Indexed: 11/18/2022] Open
Abstract
Development of regulated cellular processes and signaling methods in synthetic cells is essential for their integration with living materials. Light is an attractive tool to achieve this, but the limited penetration depth into tissue of visible light restricts its usability for in-vivo applications. Here, we describe the design and implementation of bioluminescent intercellular and intracellular signaling mechanisms in synthetic cells, dismissing the need for an external light source. First, we engineer light generating SCs with an optimized lipid membrane and internal composition, to maximize luciferase expression levels and enable high-intensity emission. Next, we show these cells’ capacity to trigger bioprocesses in natural cells by initiating asexual sporulation of dark-grown mycelial cells of the fungus Trichoderma atroviride. Finally, we demonstrate regulated transcription and membrane recruitment in synthetic cells using bioluminescent intracellular signaling with self-activating fusion proteins. These functionalities pave the way for deploying synthetic cells as embeddable microscale light sources that are capable of controlling engineered processes inside tissues. Synthetic biology and engineering approaches are harnessed to incorporate new capabilities in synthetic cells. Here, the authors designed bioluminescent signaling mechanisms for intracellular and intercellular synthetic-to-natural cell communication.
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12
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Mashima T, van Stevendaal MHME, Cornelissens FRA, Mason AF, Rosier BJHM, Altenburg WJ, Oohora K, Hirayama S, Hayashi T, van Hest JCM, Brunsveld L. DNA-Mediated Protein Shuttling between Coacervate-Based Artificial Cells. Angew Chem Int Ed Engl 2022; 61:e202115041. [PMID: 35133040 PMCID: PMC9303767 DOI: 10.1002/anie.202115041] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Indexed: 11/30/2022]
Abstract
The regulation of protein uptake and secretion is crucial for (inter)cellular signaling. Mimicking these molecular events is essential when engineering synthetic cellular systems. A first step towards achieving this goal is obtaining control over the uptake and release of proteins from synthetic cells in response to an external trigger. Herein, we have developed an artificial cell that sequesters and releases proteinaceous cargo upon addition of a coded chemical signal: single‐stranded DNA oligos (ssDNA) were employed to independently control the localization of a set of three different ssDNA‐modified proteins. The molecular coded signal allows for multiple iterations of triggered uptake and release, regulation of the amount and rate of protein release and the sequential release of the three different proteins. This signaling concept was furthermore used to directionally transfer a protein between two artificial cell populations, providing novel directions for engineering lifelike communication pathways inside higher order (proto)cellular structures.
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Affiliation(s)
- Tsuyoshi Mashima
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB, Eindhoven, The Netherlands.,Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan
| | - Marleen H M E van Stevendaal
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB, Eindhoven, The Netherlands
| | - Femke R A Cornelissens
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB, Eindhoven, The Netherlands
| | - Alexander F Mason
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB, Eindhoven, The Netherlands
| | - Bas J H M Rosier
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB, Eindhoven, The Netherlands
| | - Wiggert J Altenburg
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB, Eindhoven, The Netherlands
| | - Koji Oohora
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan
| | - Shota Hirayama
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan
| | - Takashi Hayashi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan
| | - Jan C M van Hest
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB, Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB, Eindhoven, The Netherlands
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13
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Lu Y, Allegri G, Huskens J. Vesicle-based artificial cells: materials, construction methods and applications. MATERIALS HORIZONS 2022; 9:892-907. [PMID: 34908080 PMCID: PMC8900604 DOI: 10.1039/d1mh01431e] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/19/2021] [Indexed: 05/27/2023]
Abstract
The construction of artificial cells with specific cell-mimicking functions helps to explore complex biological processes and cell functions in natural cell systems and provides an insight into the origins of life. Bottom-up methods are widely used for engineering artificial cells based on vesicles by the in vitro assembly of biomimetic materials. In this review, the design of artificial cells with a specific function is discussed, by considering the selection of synthetic materials and construction technologies. First, a range of biomimetic materials for artificial cells is reviewed, including lipid, polymeric and hybrid lipid/copolymer materials. Biomaterials extracted from natural cells are also covered in this part. Then, the formation of microscale, giant unilamellar vesicles (GUVs) is reviewed based on different technologies, including gentle hydration, electro-formation, phase transfer and microfluidic methods. Subsequently, applications of artificial cells based on single vesicles or vesicle networks are addressed for mimicking cell behaviors and signaling processes. Microreactors for synthetic biology and cell-cell communication are highlighted here as well. Finally, current challenges and future trends for the development and applications of artificial cells are described.
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Affiliation(s)
- Yao Lu
- Molecular NanoFabrication Group, Department of Molecules & Materials, MESA+ Institute, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE, Enschede, The Netherlands.
| | - Giulia Allegri
- Molecular NanoFabrication Group, Department of Molecules & Materials, MESA+ Institute, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE, Enschede, The Netherlands.
| | - Jurriaan Huskens
- Molecular NanoFabrication Group, Department of Molecules & Materials, MESA+ Institute, Faculty of Science and Technology, University of Twente, P.O. Box 217, 7500 AE, Enschede, The Netherlands.
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14
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Mashima T, Stevendaal MHME, Cornelissens FRA, Mason AF, Rosier BJHM, Altenburg WJ, Oohora K, Hirayama S, Hayashi T, Hest JCM, Brunsveld L. DNA‐Mediated Protein Shuttling between Coacervate‐Based Artificial Cells. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202115041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Tsuyoshi Mashima
- Laboratory of Chemical Biology Department of Biomedical Engineering and Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 5600MB Eindhoven The Netherlands
- Department of Applied Chemistry Graduate School of Engineering Osaka University Suita 565-0871 Japan
| | - Marleen H. M. E. Stevendaal
- Laboratory of Chemical Biology Department of Biomedical Engineering and Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 5600MB Eindhoven The Netherlands
| | - Femke R. A. Cornelissens
- Laboratory of Chemical Biology Department of Biomedical Engineering and Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 5600MB Eindhoven The Netherlands
| | - Alexander F. Mason
- Laboratory of Chemical Biology Department of Biomedical Engineering and Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 5600MB Eindhoven The Netherlands
| | - Bas J. H. M. Rosier
- Laboratory of Chemical Biology Department of Biomedical Engineering and Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 5600MB Eindhoven The Netherlands
| | - Wiggert J. Altenburg
- Laboratory of Chemical Biology Department of Biomedical Engineering and Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 5600MB Eindhoven The Netherlands
| | - Koji Oohora
- Department of Applied Chemistry Graduate School of Engineering Osaka University Suita 565-0871 Japan
| | - Shota Hirayama
- Department of Applied Chemistry Graduate School of Engineering Osaka University Suita 565-0871 Japan
| | - Takashi Hayashi
- Department of Applied Chemistry Graduate School of Engineering Osaka University Suita 565-0871 Japan
| | - Jan C. M. Hest
- Laboratory of Chemical Biology Department of Biomedical Engineering and Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 5600MB Eindhoven The Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology Department of Biomedical Engineering and Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 5600MB Eindhoven The Netherlands
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15
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Rubio-Sánchez R, Fabrini G, Cicuta P, Di Michele L. Amphiphilic DNA nanostructures for bottom-up synthetic biology. Chem Commun (Camb) 2021; 57:12725-12740. [PMID: 34750602 PMCID: PMC8631003 DOI: 10.1039/d1cc04311k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/28/2021] [Indexed: 12/28/2022]
Abstract
DNA nanotechnology enables the construction of sophisticated biomimetic nanomachines that are increasingly central to the growing efforts of creating complex cell-like entities from the bottom-up. DNA nanostructures have been proposed as both structural and functional elements of these artificial cells, and in many instances are decorated with hydrophobic moieties to enable interfacing with synthetic lipid bilayers or regulating bulk self-organisation. In this feature article we review recent efforts to design biomimetic membrane-anchored DNA nanostructures capable of imparting complex functionalities to cell-like objects, such as regulated adhesion, tissue formation, communication and transport. We then discuss the ability of hydrophobic modifications to enable the self-assembly of DNA-based nanostructured frameworks with prescribed morphology and functionality, and explore the relevance of these novel materials for artificial cell science and beyond. Finally, we comment on the yet mostly unexpressed potential of amphiphilic DNA-nanotechnology as a complete toolbox for bottom-up synthetic biology - a figurative and literal scaffold upon which the next generation of synthetic cells could be built.
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Affiliation(s)
- Roger Rubio-Sánchez
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Giacomo Fabrini
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Pietro Cicuta
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
| | - Lorenzo Di Michele
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
- fabriCELL, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
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16
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Chen C, Wang X, Wang Y, Tian L, Cao J. Construction of protocell-based artificial signal transduction pathways. Chem Commun (Camb) 2021; 57:12754-12763. [PMID: 34755716 DOI: 10.1039/d1cc03775g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The maintenance of an orderly and controllable multicellular society depends on the communication and signal regulation between various types of biological cells. How to replicate complicated signal transduction pathways in synthetic protocellular communities remains a key challenge in bottom-up synthetic biology. Herein, we review recent advances in the design and construction of interactive protocell communities, or protocell communities and biological communities, and explore the ways of designing and constructing artificial paracrine-like signaling pathways and juxtacrine-like signaling pathways. Key molecules involved in the signaling pathways that can be used to connect two or more spatially separated communities, and diverse signal outputs generated by the communication are summarized. We also propose the limitations, challenges and opportunities in this field.
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Affiliation(s)
- Chong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China. .,Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, Ningbo University, Ningbo, 315211, China
| | - Xuejing Wang
- Key Laboratory of Biomedical Engineering of Ministry of Education, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China.
| | - Ying Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China. .,Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, Ningbo University, Ningbo, 315211, China
| | - Liangfei Tian
- Key Laboratory of Biomedical Engineering of Ministry of Education, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Department of Biomedical Engineering, Zhejiang University, Hangzhou, 310027, China. .,Department of Ultrasound, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,Binjiang Institute of Zhejiang University, 66 Dongxin Road, Hangzhou, 310053, China
| | - Jinxuan Cao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China. .,Key Laboratory of Animal Protein Food Processing Technology of Zhejiang Province, Ningbo University, Ningbo, 315211, China
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17
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Sharma B, Moghimianavval H, Hwang SW, Liu AP. Synthetic Cell as a Platform for Understanding Membrane-Membrane Interactions. MEMBRANES 2021; 11:912. [PMID: 34940413 PMCID: PMC8706075 DOI: 10.3390/membranes11120912] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/10/2021] [Accepted: 11/16/2021] [Indexed: 01/27/2023]
Abstract
In the pursuit of understanding life, model membranes made of phospholipids were envisaged decades ago as a platform for the bottom-up study of biological processes. Micron-sized lipid vesicles have gained great acceptance as their bilayer membrane resembles the natural cell membrane. Important biological events involving membranes, such as membrane protein insertion, membrane fusion, and intercellular communication, will be highlighted in this review with recent research updates. We will first review different lipid bilayer platforms used for incorporation of integral membrane proteins and challenges associated with their functional reconstitution. We next discuss different methods for reconstitution of membrane fusion and compare their fusion efficiency. Lastly, we will highlight the importance and challenges of intercellular communication between synthetic cells and synthetic cells-to-natural cells. We will summarize the review by highlighting the challenges and opportunities associated with studying membrane-membrane interactions and possible future research directions.
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Affiliation(s)
- Bineet Sharma
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; (B.S.); (H.M.)
| | - Hossein Moghimianavval
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; (B.S.); (H.M.)
| | - Sung-Won Hwang
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Allen P. Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; (B.S.); (H.M.)
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48105, USA
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48105, USA
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18
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Takahashi H, Ogawa A. Coupled in vitro transcription/translation based on wheat germ extract for efficient expression from PCR-generated templates in short-time batch reactions. Bioorg Med Chem Lett 2021; 52:128412. [PMID: 34634474 DOI: 10.1016/j.bmcl.2021.128412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 09/27/2021] [Accepted: 10/04/2021] [Indexed: 10/20/2022]
Abstract
We successfully constructed a coupled in vitro transcription/translation (cIVTT) system based on wheat germ extract (WGE) for efficient expression from PCR-generated DNA templates in short-time (∼3-h) batch reactions. The productivity of this system under optimized conditions was 85 μg (2.8 nmol) per 1 mL of reaction solution (corresponding to 425 μg per 1 mL of WGE), which was about 9-fold higher than that by the conventional batch method using mRNA as a template. The DNA template concentration required for efficient cIVTT was as low as 2.5 nM, which is much lower than those required for other eukaryotic cIVTT systems to maximize their productivity (30-50 nM). The productivity of the present system with a 2.5 nM template was 80-fold and 4-fold higher than that of a commercially available WGE-based cIVTT system with a 2.5 nM and a 40 nM template, respectively. In addition, the present system functioned well in a liposome (i.e., in an artificial cell) without a loss of productivity. Given that WGE-based systems have the advantage of being suitable for the expression of a broad range of proteins, the present cIVTT system is expected to be widely used in future cell-free synthetic biology.
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Affiliation(s)
- Hajime Takahashi
- Proteo-Science Center, Ehime University, 3 Bunkyo, Matsuyama, Ehime 790-8577, Japan
| | - Atsushi Ogawa
- Proteo-Science Center, Ehime University, 3 Bunkyo, Matsuyama, Ehime 790-8577, Japan.
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19
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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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20
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Yao Y, Zhang Y, Li L, Huang Y, Yang X, Peng Z, Wang K, Liu J. Photothermally Activated Coacervate Model Protocells as Signal Transducers Endow Mammalian Cells with Light Sensitivity. Adv Biol (Weinh) 2021; 5:e2100695. [PMID: 34160910 DOI: 10.1002/adbi.202100695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 06/03/2021] [Indexed: 11/08/2022]
Abstract
The development of a novel photothermally activated coacervate model protocell is reported as a signal transducer to endow mammalian cells with light sensitivity. In this system, near-infrared light irradiation triggers H2 S release in coacervate model protocells, leading to modulation of the behavior of living cells. The functional coacervate model protocells are prepared by loading metal-alloyed plasmonic nanoparticles and an H2 S donor into the liquid coacervate microdroplets. Upon light irradiation, the H2 S signal messenger is released through the photothermal effect of plasmonic nanoparticles and photothermal mediated pyrolysis of the H2 S donor. The H2 S signal is delivered to the mammalian cell community to trigger depletion of reactive oxygen species, reduce the activity of lactate dehydrogenase and improve cell viability. This study provides a new approach to the implementation of chemical signaling in artificial cell colonies and protocell/living cell consortia. The photothermal protocell system offers a powerful platform for light modulation of the behavior of mammalian cells and shows great promise for biomedical applications.
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Affiliation(s)
- Yu Yao
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, 410082, P. R. China
| | - Yanwen Zhang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, 410082, P. R. China
| | - Li Li
- Guangxi Scientific Research Center of Traditional Chinese Medicine, Guangxi University of Chinese Medicine, Nanning, 530000, P. R. China
| | - Yan Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, 410082, P. R. China
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, 410082, P. R. China
| | - Zhihong Peng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, 410082, P. R. China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, 410082, P. R. China
| | - Jianbo Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, 410082, P. R. China
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21
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Chakraborty T, Wegner SV. Cell to Cell Signaling through Light in Artificial Cell Communities: Glowing Predator Lures Prey. ACS NANO 2021; 15:9434-9444. [PMID: 34152740 DOI: 10.1021/acsnano.1c01600] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cells commonly communicate with each other through diffusible molecules but nonchemical communication remains elusive. While bioluminescent organisms communicate through light to find prey or attract mates, it is still under debate if signaling through light is possible at the cellular level. Here, we demonstrate that cell to cell signaling through light is possible in artificial cell communities derived from biomimetic vesicles. In our design, artificial sender cells produce an intracellular light signal, which triggers the adhesion to receiver cells. Unlike soluble molecules, the light signal propagates fast, independent of diffusion and without the need for a transporter across membranes. To obtain a predator-prey relationship, the luminescence predator cells is loaded with a secondary diffusible poison, which is transferred to the prey cell upon adhesion and leads to its lysis. This design provides a blueprint for light based intercellular communication, which can be used for programing artificial and natural cell communities.
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Affiliation(s)
- Taniya Chakraborty
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Waldeyerstr. 15, 48149 Münster, Germany
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Seraphine V Wegner
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Waldeyerstr. 15, 48149 Münster, Germany
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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22
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Zhao C, Li J, Wang S, Xu Z, Wang X, Liu X, Wang L, Huang X. Membranization of Coacervates into Artificial Phagocytes with Predation toward Bacteria. ACS NANO 2021; 15:10048-10057. [PMID: 34047543 DOI: 10.1021/acsnano.1c01694] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Coacervate-based membraneless organelles with diverse functionality as well as the capability of mimicking intracellular physiological environments are attracting researchers' great interest. However, the further studies focusing on functionalized membranization of coacervate as a step toward an advanced membrane-bound protocell are still rare. In this study, we develop a way to compartmentalize coacervate based on reconstitution with a natural cellular wall, which could then serve as a promising chassis for the development of protocells with selective sequestration of various biomacromolecules. Significantly, the compartmentalized protocell could behave like a phagocyte and selectively capture, engulf, and then kill Escherichia coli efficiently. Taken together, our studies present a strategy for advancing coacervate-based protocell design as well as the development of smart materials with on-demand functionalization.
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Affiliation(s)
- Chunyu Zhao
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
| | - Junbo Li
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
| | - Shengliang Wang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
| | - Zhijun Xu
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
| | - Xiaoliang Wang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
| | - Xiaoman Liu
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
| | - Lei Wang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
| | - Xin Huang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, P. R. China
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23
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Takahashi H, Ogawa A. A Detailed Protocol for Preparing Millimeter-sized Supergiant Liposomes that Permit Efficient Eukaryotic Cell-free Translation in the Interior. Bio Protoc 2021; 11:e4054. [PMID: 34262997 DOI: 10.21769/bioprotoc.4054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/29/2021] [Accepted: 03/29/2021] [Indexed: 11/02/2022] Open
Abstract
Liposomes have been used as a pseudo cell membrane for encapsulating biomolecules and creating an artificial cell in the interior where biochemical reactions can occur. Among the several methods used to prepare biomolecule-encapsulating liposomes, the spontaneous emulsion transfer method is superior to others in that it allows us to readily prepare relatively large liposomes whose sizes are controlled (from micrometer- to millimeter-sized liposomes) without special equipment. However, conventional protocols for this method require liposomes to contain a considerably high concentration of sucrose (high-density solute), which severely inhibits gene expression, one of the most important biochemical reactions. Thus, we optimized the preparation conditions to develop a wheat germ extract (WGE)-based protocol that requires a much lower concentration of sucrose and has almost no effect on eukaryotic cell-free translation. Our protocol allows us to successfully prepare millimeter-sized, moderately stable, WGE-encapsulating liposomes in which WGE translation takes place efficiently. Since a broad range of genes derived from various types of organisms can be efficiently translated in a WGE-based translation system, liposomes prepared using our protocol would be useful as a versatile research tool for artificial cells.
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Affiliation(s)
| | - Atsushi Ogawa
- Proteo-Science Center, Ehime University, Matsuyama, Japan
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24
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Stevendaal MHME, Hest JCM, Mason AF. Functional Interactions Between Bottom‐Up Synthetic Cells and Living Matter for Biomedical Applications. CHEMSYSTEMSCHEM 2021. [DOI: 10.1002/syst.202100009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Marleen H. M. E. Stevendaal
- Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 (STO 3.41) 5600MB Eindhoven (The Netherlands
| | - Jan C. M. Hest
- Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 (STO 3.41) 5600MB Eindhoven (The Netherlands
| | - Alexander F. Mason
- Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 (STO 3.41) 5600MB Eindhoven (The Netherlands
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25
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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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26
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Luan J, Wang D, Wilson DA. Leveraging synthetic particles for communication: from passive to active systems. NANOSCALE 2020; 12:21015-21033. [PMID: 33073819 DOI: 10.1039/d0nr05675h] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Communication is one of the most remarkable behaviors in the living world. It is an important prerequisite for building an artificial cell which can be considered as alive. Achieving complex communicative behaviors leveraging synthetic particles will likely fill the gap between artificial vesicles and natural counterpart of cells and allow for the discovery of new therapies in medicine. In this review, we highlight recent endeavors for constructing communication with synthetic particles by revealing the principles underlying the communicative behaviors. Emergent progress using active particles to achieve communication is also discussed, which resembles the dynamic and out-of-equilibrium properties of communication in nature.
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Affiliation(s)
- Jiabin Luan
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Danni Wang
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Daniela A Wilson
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
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27
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Groaz A, Galvan S, Valer L, Rossetto D, Benedetti F, Guella G, Toparlak ÖD, Mansy SS. Cell-Free Synthesis of Dopamine and Serotonin in Two Steps with Purified Enzymes. ACTA ACUST UNITED AC 2020; 4:e2000118. [PMID: 33107224 DOI: 10.1002/adbi.202000118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 10/14/2020] [Indexed: 01/05/2023]
Abstract
The synthesis of serotonin and dopamine with purified enzymes is described. Both pathways start from an amino acid substrate and synthesize the monoamine neurotransmitter in two enzymatic steps. The enzymes human tryptophan hydroxylase isoform 2, Rattus norvegicus tyrosine hydroxylase, Chlamydia pneumoniae Cpn1046, and aromatic amino acid decarboxylase from Drosophila melanogaster are recombinantly expressed, purified, and shown to be functional in vitro. The hydroxylases efficiently convert L-DOPA (L-dihydroxy-phenylalanine) and 5-HTP (5-hydroxytryptophan) from L-tyrosine and L-tryptophan, respectively. A single aromatic amino acid decarboxylase is capable of converting both hydroxylated intermediates into the final neurotransmitter. The platform described here may facilitate future efforts to generate medically useful artificial cells and nanofactories.
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Affiliation(s)
- Alessandro Groaz
- CIBIO, University of Trento, Via Sommarive 9, Trento, 38123, Italy
| | - Silvia Galvan
- CIBIO, University of Trento, Via Sommarive 9, Trento, 38123, Italy
| | - Luca Valer
- CIBIO, University of Trento, Via Sommarive 9, Trento, 38123, Italy
| | - Daniele Rossetto
- CIBIO, University of Trento, Via Sommarive 9, Trento, 38123, Italy
| | | | - Graziano Guella
- Department of Physics, University of Trento, Via Sommarive 14, Trento, 38123, Italy
| | | | - Sheref S Mansy
- CIBIO, University of Trento, Via Sommarive 9, Trento, 38123, Italy.,Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr, Edmonton, AB, T6G 2G2, Canada
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28
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Ogawa A, Itoh Y. In Vitro Selection of RNA Aptamers Binding to Nanosized DNA for Constructing Artificial Riboswitches. ACS Synth Biol 2020; 9:2648-2655. [PMID: 33017145 DOI: 10.1021/acssynbio.0c00384] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We here designed an in vitro selection scheme for obtaining an aptamer with which to rationally construct an artificial riboswitch as its component part. In fact, a nanosized DNA-binding aptamer obtained through this scheme allowed us to easily and successfully create eukaryotic riboswitches that upregulate internal ribosome entry site-mediated translation in response to the ligand (nanosized DNA) in wheat germ extract, a eukaryotic cell-free expression system. The induction ratio of the best riboswitch ligand-dose-dependently increased to 21 at 300 μM ligand. This switching efficiency is much higher than that of the same type of riboswitch with a widely used theophylline-binding aptamer, which was in vitro selected without considering its utility for constructing riboswitches. The selection scheme described here would facilitate obtaining various ligand/aptamer pairs suitable for constructing artificial riboswitches, which could serve as elements of synthetic gene circuits in synthetic biology.
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Affiliation(s)
- Atsushi Ogawa
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Yu Itoh
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
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29
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Liu Z, Zhou W, Qi C, Kong T. Interface Engineering in Multiphase Systems toward Synthetic Cells and Organelles: From Soft Matter Fundamentals to Biomedical Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e2002932. [PMID: 32954548 DOI: 10.1002/adma.202002932] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/19/2020] [Indexed: 06/11/2023]
Abstract
Synthetic cells have a major role in gaining insight into the complex biological processes of living cells; they also give rise to a range of emerging applications from gene delivery to enzymatic nanoreactors. Living cells rely on compartmentalization to orchestrate reaction networks for specialized and coordinated functions. Principally, the compartmentalization has been an essential engineering theme in constructing cell-mimicking systems. Here, efforts to engineer liquid-liquid interfaces of multiphase systems into membrane-bounded and membraneless compartments, which include lipid vesicles, polymer vesicles, colloidosomes, hybrids, and coacervate droplets, are summarized. Examples are provided of how these compartments are designed to imitate biological behaviors or machinery, including molecule trafficking, growth, fusion, energy conversion, intercellular communication, and adaptivity. Subsequently, the state-of-art applications of these cell-inspired synthetic compartments are discussed. Apart from being simplified and cell models for bridging the gap between nonliving matter and cellular life, synthetic compartments also are utilized as intracellular delivery vehicles for nuclei acids and nanoreactors for biochemical synthesis. Finally, key challenges and future directions for achieving the full potential of synthetic cells are highlighted.
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Affiliation(s)
- Zhou Liu
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, 518000, China
| | - Wen Zhou
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, 518000, China
| | - Cheng Qi
- College of Mechatronics and Control Engineering, Shenzhen University, Shenzhen, 518000, China
| | - Tiantian Kong
- Department of Biomedical Engineering, School of Medicine, Shenzhen University, Shenzhen, Guangdong, 518000, China
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30
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Takahashi H, Ogawa A. Preparation of a Millimeter-Sized Supergiant Liposome That Allows for Efficient, Eukaryotic Cell-Free Translation in the Interior by Spontaneous Emulsion Transfer. ACS Synth Biol 2020; 9:1608-1614. [PMID: 32559381 DOI: 10.1021/acssynbio.0c00173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We sought to prepare millimeter-sized supergiant unilamellar vesicles (SGUVs) by spontaneous emulsion transfer for efficient, eukaryotic cell-free translation in the interior. Although the conventional protocols require that a considerably high concentration of sucrose be encapsulated into the SGUVs for their efficient formation, such high amounts of sucrose severely inhibited cell-free translation based on wheat germ extract (WGE). We thus optimized the preparation conditions to permit SGUV formation at a much lower concentration of sucrose that has almost no effect on WGE translation. Under the optimized conditions, we successfully prepared WGE translation system-encapsulating SGUVs that allow for protein synthesis with a high efficiency comparable to that outside a liposome. The optimization also resulted in a high rate of successful SGUV formation (>90%) and a decent stability of the formed SGUVs (>60 min). These SGUVs are expected to serve as research tools in cell-free synthetic biology and as foundations for artificial cell-based biosensors.
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Affiliation(s)
- Hajime Takahashi
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
| | - Atsushi Ogawa
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan
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31
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Wang X, Liu X, Huang X. Bioinspired Protein-Based Assembling: Toward Advanced Life-Like Behaviors. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e2001436. [PMID: 32374501 DOI: 10.1002/adma.202001436] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 04/05/2020] [Accepted: 04/06/2020] [Indexed: 06/11/2023]
Abstract
The ability of living organisms to perform structure, energy, and information-related processes for molecular self-assembly through compartmentalization and chemical transformation can possibly be mimicked via artificial cell models. Recent progress in the development of various types of functional microcompartmentalized ensembles that can imitate rudimentary aspects of living cells has refocused attention on the important question of how inanimate systems can transition into living matter. Hence, herein, the most recent advances in the construction of protein-bounded microcompartments (proteinosomes), which have been exploited as a versatile synthetic chassis for integrating a wide range of functional components and biochemical machineries, are critically summarized. The techniques developed for fabricating various types of proteinosomes are discussed, focusing on the significance of how chemical information, substance transportation, enzymatic-reaction-based metabolism, and self-organization can be integrated and recursively exploited in constructed ensembles. Therefore, proteinosomes capable of exhibiting gene-directed protein synthesis, modulated membrane permeability, spatially confined membrane-gated catalytic reaction, internalized cytoskeletal-like matrix assembly, on-demand compartmentalization, and predatory-like chemical communication in artificial cell communities are specially highlighted. These developments are expected to bridge the gap between materials science and life science, and offer a theoretical foundation for developing life-inspired assembled materials toward various applications.
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Affiliation(s)
- Xiaoliang Wang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Xiaoman Liu
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
| | - Xin Huang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China
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32
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Zhou W, Šmidlehner T, Jerala R. Synthetic biology principles for the design of protein with novel structures and functions. FEBS Lett 2020; 594:2199-2212. [PMID: 32324903 DOI: 10.1002/1873-3468.13796] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/29/2020] [Accepted: 04/03/2020] [Indexed: 12/14/2022]
Abstract
Nature provides a large number of functional proteins that evolved during billions of years of evolution. The diversity of natural proteins encompasses versatile functions and more than a thousand different folds, which, however, represents only a tiny fraction of all possible folds and polypeptide sequences. Recent advances in the rational design of proteins demonstrate that it is possible to design de novo protein folds unseen in nature. Novel protein topologies have been designed based on similar principles as natural proteins using advanced computational modelling or modular construction principles, such as oligomerization domains. Designed proteins exhibit several interesting features such as extreme stability, designability of 3D topologies and folding pathways. Moreover, designed protein assemblies can implement symmetry similar to the viral capsids, while, on the other hand, single-chain pseudosymmetric designs can address each position independently. Recently, the design is expanding towards the introduction of new functions into designed proteins, and we may soon be able to design molecular machines.
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Affiliation(s)
- Weijun Zhou
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Tamara Šmidlehner
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Ljubljana, Slovenia
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33
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Peruzzi JA, Jacobs ML, Vu TQ, Wang KS, Kamat NP. Barcoding Biological Reactions with DNA-Functionalized Vesicles. Angew Chem Int Ed Engl 2019; 58:18683-18690. [PMID: 31596992 PMCID: PMC6901749 DOI: 10.1002/anie.201911544] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Indexed: 11/08/2022]
Abstract
Targeted vesicle fusion is a promising approach to selectively control interactions between vesicle compartments and would enable the initiation of biological reactions in complex aqueous environments. Here, we explore how two features of vesicle membranes, DNA tethers and phase-segregated membranes, promote fusion between specific vesicle populations. Membrane phase-segregation provides an energetic driver for membrane fusion that increases the efficiency of DNA-mediated fusion events. The orthogonality provided by DNA tethers allows us to direct fusion and delivery of DNA cargo to specific vesicle populations. Vesicle fusion between DNA-tethered vesicles can be used to initiate in vitro protein expression to produce model soluble and membrane proteins. Engineering orthogonal fusion events between DNA-tethered vesicles provides a new strategy to control the spatiotemporal dynamics of cell-free reactions, expanding opportunities to engineer artificial cellular systems.
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Affiliation(s)
- Justin A Peruzzi
- Department of Chemical and Biological Engineering, Northwestern University, USA
| | - Miranda L Jacobs
- Department of Biomedical Engineering, Northwestern University, McCormick School of Engineering, Technological Institute, 2145 Sheridan Road, Evanston, Il, 60208, USA
| | - Timothy Q Vu
- Department of Biomedical Engineering, Northwestern University, McCormick School of Engineering, Technological Institute, 2145 Sheridan Road, Evanston, Il, 60208, USA
| | - Kenneth S Wang
- Department of Biomedical Engineering, Northwestern University, McCormick School of Engineering, Technological Institute, 2145 Sheridan Road, Evanston, Il, 60208, USA
| | - Neha P Kamat
- Department of Biomedical Engineering, Northwestern University, McCormick School of Engineering, Technological Institute, 2145 Sheridan Road, Evanston, Il, 60208, USA
- Center for Synthetic Biology, Northwestern University, USA
- Chemistry of Life Processes Institute, Northwestern University, USA
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34
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Yeh Martín N, Valer L, Mansy SS. Toward long-lasting artificial cells that better mimic natural living cells. Emerg Top Life Sci 2019; 3:597-607. [PMID: 33523164 PMCID: PMC7288992 DOI: 10.1042/etls20190026] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/09/2019] [Accepted: 08/13/2019] [Indexed: 01/01/2023]
Abstract
Chemical communication is ubiquitous in biology, and so efforts in building convincing cellular mimics must consider how cells behave on a population level. Simple model systems have been built in the laboratory that show communication between different artificial cells and artificial cells with natural, living cells. Examples include artificial cells that depend on purely abiological components and artificial cells built from biological components and are driven by biological mechanisms. However, an artificial cell solely built to communicate chemically without carrying the machinery needed for self-preservation cannot remain active for long periods of time. What is needed is to begin integrating the pathways required for chemical communication with metabolic-like chemistry so that robust artificial systems can be built that better inform biology and aid in the generation of new technologies.
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Affiliation(s)
- Noël Yeh Martín
- Systems Biophysics, Physics Department, Ludwig-Maximilians-Universität München, Amalienstraße 54, 80799 München, Germany
| | - Luca Valer
- Department CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
| | - Sheref S Mansy
- Department CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB, Canada T6G 2G2
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35
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Peruzzi JA, Jacobs ML, Vu TQ, Wang KS, Kamat NP. Barcoding Biological Reactions with DNA‐Functionalized Vesicles. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201911544] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Justin A. Peruzzi
- Department of Chemical and Biological Engineering Northwestern University USA
| | - Miranda L. Jacobs
- Department of Biomedical Engineering Northwestern University McCormick School of Engineering Technological Institute 2145 Sheridan Road Evanston Il 60208 USA
| | - Timothy Q. Vu
- Department of Biomedical Engineering Northwestern University McCormick School of Engineering Technological Institute 2145 Sheridan Road Evanston Il 60208 USA
| | - Kenneth S. Wang
- Department of Biomedical Engineering Northwestern University McCormick School of Engineering Technological Institute 2145 Sheridan Road Evanston Il 60208 USA
| | - Neha P. Kamat
- Department of Biomedical Engineering Northwestern University McCormick School of Engineering Technological Institute 2145 Sheridan Road Evanston Il 60208 USA
- Center for Synthetic Biology Northwestern University USA
- Chemistry of Life Processes Institute Northwestern University USA
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36
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Abstract
While significant advances have been achieved with non-living synthetic cells built from the bottom-up, less progress has been made with the fabrication of synthetic tissues built from such cells. Synthetic tissues comprise patterned three-dimensional (3D) collections of communicating compartments. They can include both biological and synthetic parts and may incorporate features that do more than merely mimic nature. 3D-printed materials based on droplet-interface bilayers are the basis of the most advanced synthetic tissues and are being developed for several applications, including the controlled release of therapeutic agents and the repair of damaged organs. Current goals include the ability to manipulate synthetic tissues by remote signaling and the formation of hybrid structures with fabricated or natural living tissues.
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37
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de Luis B, Llopis-Lorente A, Rincón P, Gadea J, Sancenón F, Aznar E, Villalonga R, Murguía JR, Martínez-Máñez R. An Interactive Model of Communication between Abiotic Nanodevices and Microorganisms. Angew Chem Int Ed Engl 2019; 58:14986-14990. [PMID: 31424153 DOI: 10.1002/anie.201908867] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Indexed: 11/06/2022]
Abstract
The construction of communication models at the micro-/nanoscale involving abiotic nanodevices and living organisms has the potential to open a wide range of applications in biomedical and communication technologies. However, this area remains almost unexplored. Herein, we report, as a proof of concept, a stimuli-responsive interactive paradigm of communication between yeasts (as a model microorganism) and enzyme-controlled Janus Au-mesoporous silica nanoparticles. In the presence of the stimulus, the information flows from the microorganism to the nanodevice, and then returns from the nanodevice to the microorganism as a feedback.
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Affiliation(s)
- Beatriz de Luis
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina, (CIBER-BBN), Spain
| | - Antoni Llopis-Lorente
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina, (CIBER-BBN), Spain
| | - Paola Rincón
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain
| | - José Gadea
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), Valencia, Spain
| | - Félix Sancenón
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina, (CIBER-BBN), Spain
| | - Elena Aznar
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina, (CIBER-BBN), Spain
| | - Reynaldo Villalonga
- Nanosensors & Nanomachines Group, Department of Analytical Chemistry, Faculty of Chemistry, Complutense University of Madrid, Madrid, Spain
| | - José Ramón Murguía
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina, (CIBER-BBN), Spain
| | - Ramón Martínez-Máñez
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022, Valencia, Spain.,CIBER de Bioingeniería, Biomateriales y Nanomedicina, (CIBER-BBN), Spain.,Unidad Mixta UPV-CIPF de Investigación en Mecanismos de Enfermedades y Nanomedicina, Universitat Politècnica de València, Centro de Investigación Príncipe Felipe, Valencia, Spain.,Unidad Mixta de Investigación en Nanomedicina y Sensores, Universitat Politècnica de València, Instituto de Investigación Sanitaria La Fe, Valencia, Spain
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38
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Luis B, Llopis‐Lorente A, Rincón P, Gadea J, Sancenón F, Aznar E, Villalonga R, Murguía JR, Martínez‐Máñez R. An Interactive Model of Communication between Abiotic Nanodevices and Microorganisms. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201908867] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Beatriz Luis
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM) Universitat Politècnica de València Universitat de València Camino de Vera s/n 46022 Valencia Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina, (CIBER-BBN) Spain
| | - Antoni Llopis‐Lorente
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM) Universitat Politècnica de València Universitat de València Camino de Vera s/n 46022 Valencia Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina, (CIBER-BBN) Spain
| | - Paola Rincón
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM) Universitat Politècnica de València Universitat de València Camino de Vera s/n 46022 Valencia Spain
| | - José Gadea
- Instituto de Biología Molecular y Celular de Plantas (IBMCP) Universitat Politècnica de València (UPV)-Consejo Superior de Investigaciones Científicas (CSIC) Valencia Spain
| | - Félix Sancenón
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM) Universitat Politècnica de València Universitat de València Camino de Vera s/n 46022 Valencia Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina, (CIBER-BBN) Spain
| | - Elena Aznar
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM) Universitat Politècnica de València Universitat de València Camino de Vera s/n 46022 Valencia Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina, (CIBER-BBN) Spain
| | - Reynaldo Villalonga
- Nanosensors & Nanomachines Group Department of Analytical Chemistry Faculty of Chemistry Complutense University of Madrid Madrid Spain
| | - José Ramón Murguía
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM) Universitat Politècnica de València Universitat de València Camino de Vera s/n 46022 Valencia Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina, (CIBER-BBN) Spain
| | - Ramón Martínez‐Máñez
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM) Universitat Politècnica de València Universitat de València Camino de Vera s/n 46022 Valencia Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina, (CIBER-BBN) Spain
- Unidad Mixta UPV-CIPF de Investigación en Mecanismos de Enfermedades y Nanomedicina Universitat Politècnica de València Centro de Investigación Príncipe Felipe Valencia Spain
- Unidad Mixta de Investigación en Nanomedicina y Sensores Universitat Politècnica de València Instituto de Investigación Sanitaria La Fe Valencia Spain
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39
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Aufinger L, Simmel FC. Establishing Communication Between Artificial Cells. Chemistry 2019; 25:12659-12670. [DOI: 10.1002/chem.201901726] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 06/23/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Lukas Aufinger
- Physics Department and ZNNTechnische Universität München Am Coulombwall 4a 85748 Garching Germany
| | - Friedrich C. Simmel
- Physics Department and ZNNTechnische Universität München Am Coulombwall 4a 85748 Garching Germany
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40
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Torre P, Xiao Q, Buzzacchera I, Sherman SE, Rahimi K, Kostina NY, Rodriguez-Emmenegger C, Möller M, Wilson CJ, Klein ML, Good MC, Percec V. Encapsulation of hydrophobic components in dendrimersomes and decoration of their surface with proteins and nucleic acids. Proc Natl Acad Sci U S A 2019; 116:15378-15385. [PMID: 31308223 PMCID: PMC6681758 DOI: 10.1073/pnas.1904868116] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Reconstructing the functions of living cells using nonnatural components is one of the great challenges of natural sciences. Compartmentalization, encapsulation, and surface decoration of globular assemblies, known as vesicles, represent key early steps in the reconstitution of synthetic cells. Here we report that vesicles self-assembled from amphiphilic Janus dendrimers, called dendrimersomes, encapsulate high concentrations of hydrophobic components and do so more efficiently than commercially available stealth liposomes assembled from phospholipid components. Multilayer onion-like dendrimersomes demonstrate a particularly high capacity for loading low-molecular weight compounds and even folded proteins. Coassembly of amphiphilic Janus dendrimers with metal-chelating ligands conjugated to amphiphilic Janus dendrimers generates dendrimersomes that selectively display folded proteins on their periphery in an oriented manner. A modular strategy for tethering nucleic acids to the surface of dendrimersomes is also demonstrated. These findings augment the functional capabilities of dendrimersomes to serve as versatile biological membrane mimics.
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Affiliation(s)
- Paola Torre
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058
| | - Qi Xiao
- Roy & Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323
- Institute of Computational Molecular Science, Temple University, Philadelphia, PA 19122
| | - Irene Buzzacchera
- Roy & Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323
- DWI-Leibniz Institute for Interactive Materials, 52074 Aachen, Germany
- NovioSense B.V., 6534 AT Nijmegen, The Netherlands
| | - Samuel E Sherman
- Roy & Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323
| | - Khosrow Rahimi
- DWI-Leibniz Institute for Interactive Materials, 52074 Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, 52074 Aachen, Germany
| | - Nina Yu Kostina
- DWI-Leibniz Institute for Interactive Materials, 52074 Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, 52074 Aachen, Germany
| | - Cesar Rodriguez-Emmenegger
- DWI-Leibniz Institute for Interactive Materials, 52074 Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, 52074 Aachen, Germany
| | - Martin Möller
- DWI-Leibniz Institute for Interactive Materials, 52074 Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, 52074 Aachen, Germany
| | | | - Michael L Klein
- Institute of Computational Molecular Science, Temple University, Philadelphia, PA 19122;
| | - Matthew C Good
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-6058;
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104-6321
| | - Virgil Percec
- Roy & Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323;
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41
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Dwidar M, Seike Y, Kobori S, Whitaker C, Matsuura T, Yokobayashi Y. Programmable Artificial Cells Using Histamine-Responsive Synthetic Riboswitch. J Am Chem Soc 2019; 141:11103-11114. [PMID: 31241330 DOI: 10.1021/jacs.9b03300] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Artificial cells that encapsulate DNA-programmable protein expression machinery are emerging as an attractive platform for studying fundamental cellular properties and applications in synthetic biology. However, interfacing these artificial cells with the complex and dynamic chemical environment remains a major and urgent challenge. We demonstrate that the repertoire of molecules that artificial cells respond to can be expanded by synthetic RNA-based gene switches, or riboswitches. We isolated an RNA aptamer that binds histamine with high affinity and specificity and used it to design robust riboswitches that activate protein expression in the presence of histamine. Finally, the riboswitches were incorporated in artificial cells to achieve controlled release of an encapsulated small molecule and to implement a self-destructive kill-switch. Synthetic riboswitches should serve as modular and versatile interfaces to link artificial cell phenotypes with the complex chemical environment.
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Affiliation(s)
- Mohammed Dwidar
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University , Onna , Okinawa 904-0495 , Japan
| | - Yusuke Seike
- Department of Biotechnology, Graduate School of Engineering , Osaka University , 2-1 Yamadaoka , Suita , Osaka 565-0871 , Japan
| | - Shungo Kobori
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University , Onna , Okinawa 904-0495 , Japan
| | - Charles Whitaker
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University , Onna , Okinawa 904-0495 , Japan
| | - Tomoaki Matsuura
- Department of Biotechnology, Graduate School of Engineering , Osaka University , 2-1 Yamadaoka , Suita , Osaka 565-0871 , Japan
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University , Onna , Okinawa 904-0495 , Japan
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42
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Hilburger CE, Jacobs ML, Lewis KR, Peruzzi JA, Kamat NP. Controlling Secretion in Artificial Cells with a Membrane AND Gate. ACS Synth Biol 2019; 8:1224-1230. [PMID: 31051071 DOI: 10.1021/acssynbio.8b00435] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The assembly of channel proteins into vesicle membranes is a useful strategy to control activities of vesicle-based systems. Here, we developed a membrane AND gate that responds to both a fatty acid and a pore-forming channel protein to induce the release of encapsulated cargo. We explored how membrane composition affects the functional assembly of α-hemolysin into phospholipid vesicles as a function of oleic acid content and α-hemolysin concentration. We then showed that we could induce α-hemolysin assembly when we added oleic acid micelles to a specific composition of phospholipid vesicles. Finally, we demonstrated that our membrane AND gate could be coupled to a gene expression system. Our study provides a new method to control the temporal dynamics of vesicle permeability by controlling when the functional assembly of a channel protein into synthetic vesicles occurs. Furthermore, a membrane AND gate that utilizes membrane-associating biomolecules introduces a new way to implement Boolean logic that should complement genetic logic circuits and ultimately enhance the capabilities of artificial cellular systems.
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43
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Lopez A, Fiore M. Investigating Prebiotic Protocells for A Comprehensive Understanding of the Origins of Life: A Prebiotic Systems Chemistry Perspective. Life (Basel) 2019; 9:E49. [PMID: 31181679 PMCID: PMC6616946 DOI: 10.3390/life9020049] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 05/21/2019] [Accepted: 06/06/2019] [Indexed: 01/06/2023] Open
Abstract
Protocells are supramolecular systems commonly used for numerous applications, such as the formation of self-evolvable systems, in systems chemistry and synthetic biology. Certain types of protocells imitate plausible prebiotic compartments, such as giant vesicles, that are formed with the hydration of thin films of amphiphiles. These constructs can be studied to address the emergence of life from a non-living chemical network. They are useful tools since they offer the possibility to understand the mechanisms underlying any living cellular system: Its formation, its metabolism, its replication and its evolution. Protocells allow the investigation of the synergies occurring in a web of chemical compounds. This cooperation can explain the transition between chemical (inanimate) and biological systems (living) due to the discoveries of emerging properties. The aim of this review is to provide an overview of relevant concept in prebiotic protocell research.
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Affiliation(s)
- Augustin Lopez
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Université de Lyon, Claude Bernard Lyon 1, 1 Rue Victor Grignard, Bâtiment Lederer, 69622 Villeurbanne CEDEX, France.
- Master de Biologie, École Normale Supérieure de Lyon, Université Claude Bernard Lyon I, Université de Lyon, 69342 Lyon CEDEX 07, France.
| | - Michele Fiore
- Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, Université de Lyon, Claude Bernard Lyon 1, 1 Rue Victor Grignard, Bâtiment Lederer, 69622 Villeurbanne CEDEX, France.
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44
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Joesaar A, Yang S, Bögels B, van der Linden A, Pieters P, Kumar BVVSP, Dalchau N, Phillips A, Mann S, de Greef TFA. DNA-based communication in populations of synthetic protocells. NATURE NANOTECHNOLOGY 2019; 14:369-378. [PMID: 30833694 PMCID: PMC6451639 DOI: 10.1038/s41565-019-0399-9] [Citation(s) in RCA: 186] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 01/22/2019] [Indexed: 05/20/2023]
Abstract
Developing molecular communication platforms based on orthogonal communication channels is a crucial step towards engineering artificial multicellular systems. Here, we present a general and scalable platform entitled 'biomolecular implementation of protocellular communication' (BIO-PC) to engineer distributed multichannel molecular communication between populations of non-lipid semipermeable microcapsules. Our method leverages the modularity and scalability of enzyme-free DNA strand-displacement circuits to develop protocellular consortia that can sense, process and respond to DNA-based messages. We engineer a rich variety of biochemical communication devices capable of cascaded amplification, bidirectional communication and distributed computational operations. Encapsulating DNA strand-displacement circuits further allows their use in concentrated serum where non-compartmentalized DNA circuits cannot operate. BIO-PC enables reliable execution of distributed DNA-based molecular programs in biologically relevant environments and opens new directions in DNA computing and minimal cell technology.
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Affiliation(s)
- Alex Joesaar
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Shuo Yang
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Bas Bögels
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Ardjan van der Linden
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Pascal Pieters
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - B V V S Pavan Kumar
- Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | | | | | - Stephen Mann
- Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Tom F A de Greef
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
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45
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Sato Y, Takinoue M. Creation of Artificial Cell-Like Structures Promoted by Microfluidics Technologies. MICROMACHINES 2019; 10:E216. [PMID: 30934758 PMCID: PMC6523379 DOI: 10.3390/mi10040216] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 03/21/2019] [Accepted: 03/22/2019] [Indexed: 02/06/2023]
Abstract
The creation of artificial cells is an immensely challenging task in science. Artificial cells contribute to revealing the mechanisms of biological systems and deepening our understanding of them. The progress of versatile biological research fields has clarified many biological phenomena, and various artificial cell models have been proposed in these fields. Microfluidics provides useful technologies for the study of artificial cells because it allows the fabrication of cell-like compartments, including water-in-oil emulsions and giant unilamellar vesicles. Furthermore, microfluidics also allows the mimicry of cellular functions with chip devices based on sophisticated chamber design. In this review, we describe contributions of microfluidics to the study of artificial cells. Although typical microfluidic methods are useful for the creation of artificial-cell compartments, recent methods provide further benefits, including low-cost fabrication and a reduction of the sample volume. Microfluidics also allows us to create multi-compartments, compartments with artificial organelles, and on-chip artificial cells. We discuss these topics and the future perspective of microfluidics for the study of artificial cells and molecular robotics.
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Affiliation(s)
- Yusuke Sato
- Department of Computer Science, Tokyo Institute of Technology, Kanagawa 226-8502, Japan
| | - Masahiro Takinoue
- Department of Computer Science, Tokyo Institute of Technology, Kanagawa 226-8502, Japan
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46
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Martin L, Gurnani P, Zhang J, Hartlieb M, Cameron NR, Eissa AM, Perrier S. Polydimethylsiloxane-Based Giant Glycosylated Polymersomes with Tunable Bacterial Affinity. Biomacromolecules 2019; 20:1297-1307. [PMID: 30694656 DOI: 10.1021/acs.biomac.8b01709] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A synthetic cell mimic in the form of giant glycosylated polymersomes (GGPs) comprised of a novel amphiphilic diblock copolymer is reported. A synthetic approach involving a poly(dimethylsiloxane) (PDMS) macro-chain transfer agent (macroCTA) and postpolymerization modification was used to marry the hydrophobic and highly flexible properties of PDMS with the biological activity of glycopolymers. 2-Bromoethyl acrylate (BEA) was first polymerized using a PDMS macroCTA ( Mn,th ≈ 4900 g·mol-1, Đ = 1.1) to prepare well-defined PDMS- b-pBEA diblock copolymers ( Đ = 1.1) that were then substituted with 1-thio-β-d-glucose or 1-thio-β-d-galactose under facile conditions to yield PDMS- b-glycopolymers. Compositions possessing ≈25% of the glycopolymer block (by mass) were able to adopt a vesicular morphology in aqueous solution (≈210 nm in diameter), as indicated by TEM and light scattering techniques. The resulting carbohydrate-decorated polymersomes exhibited selective binding with the lectin concanavalin A (Con A), as demonstrated by turbidimetric experiments. Self-assembly of the same diblock copolymer compositions using an electroformation method yielded GGPs (ranging from 2-20 μm in diameter). Interaction of these cell-sized polymersomes with fimH positive E. coli was then studied via confocal microscopy. The glucose-decorated GGPs were found to cluster upon addition of the bacteria, while galactose-decorated GGPs could successfully interact with (and possibly immobilize) the bacteria without the onset of clustering. This demonstrates an opportunity to modulate the response of these synthetic cell mimics (protocells) toward biological entities through exploitation of selective ligand-receptor interactions, which may be readily tuned through a considered choice of carbohydrate functionality.
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Affiliation(s)
| | | | | | | | - Neil R Cameron
- Department of Materials Science and Engineering , Monash University , Clayton , VIC 3800 , Australia
| | - Ahmed M Eissa
- Department of Polymers, Chemical Industries Research Division , National Research Centre (NRC) , El-Bohouth Street , Dokki , 12622 , Cairo , Egypt
| | - Sébastien Perrier
- Faculty of Pharmacy and Pharmaceutical Sciences , Monash University , Clayton , VIC 3052 , Australia
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Rampioni G, D'Angelo F, Leoni L, Stano P. Gene-Expressing Liposomes as Synthetic Cells for Molecular Communication Studies. Front Bioeng Biotechnol 2019; 7:1. [PMID: 30705882 PMCID: PMC6344414 DOI: 10.3389/fbioe.2019.00001] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Accepted: 01/02/2019] [Indexed: 11/13/2022] Open
Abstract
The bottom-up branch of synthetic biology includes-among others-innovative studies that combine cell-free protein synthesis with liposome technology to generate cell-like systems of minimal complexity, often referred to as synthetic cells. The functions of this type of synthetic cell derive from gene expression, hence they can be programmed in a modular, progressive and customizable manner by means of ad hoc designed genetic circuits. This experimental scenario is rapidly expanding and synthetic cell research already counts numerous successes. Here, we present a review focused on the exchange of chemical signals between liposome-based synthetic cells (operating by gene expression) and biological cells, as well as between two populations of synthetic cells. The review includes a short presentation of the "molecular communication technologies," briefly discussing their promises and challenges.
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Affiliation(s)
| | | | - Livia Leoni
- Department of Science, University Roma Tre, Rome, Italy
| | - Pasquale Stano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Lecce, Italy
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48
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Chakraborty T, Bartelt SM, Steinkühler J, Dimova R, Wegner SV. Light controlled cell-to-cell adhesion and chemical communication in minimal synthetic cells. Chem Commun (Camb) 2019; 55:9448-9451. [DOI: 10.1039/c9cc04768a] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Light controlled adhesions between sender and receiver GUVs, used as minimal synthetic cells, photoregulates their spatial proximity and chemical communication.
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Affiliation(s)
| | - S. M. Bartelt
- Max Planck Institute for Polymer Research
- Mainz
- Germany
| | - J. Steinkühler
- Department of Theory and Biosystems
- Max Planck Institute of Colloids and Interfaces
- Potsdam
- Germany
| | - R. Dimova
- Department of Theory and Biosystems
- Max Planck Institute of Colloids and Interfaces
- Potsdam
- Germany
| | - S. V. Wegner
- Max Planck Institute for Polymer Research
- Mainz
- Germany
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49
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Dubuc E, Pieters PA, van der Linden AJ, van Hest JC, Huck WT, de Greef TF. Cell-free microcompartmentalised transcription-translation for the prototyping of synthetic communication networks. Curr Opin Biotechnol 2018; 58:72-80. [PMID: 30594098 PMCID: PMC6723619 DOI: 10.1016/j.copbio.2018.10.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 10/14/2018] [Indexed: 12/21/2022]
Abstract
Recent efforts in synthetic biology have shown the possibility of engineering distributed functions in populations of living cells, which requires the development of highly orthogonal, genetically encoded communication pathways. Cell-free transcription-translation (TXTL) reactions encapsulated in microcompartments enable prototyping of molecular communication channels and their integration into engineered genetic circuits by mimicking critical cell features, such as gene expression, cell size, and cell individuality within a community. In this review, we discuss the uses of cell-free transcription-translation reactions for the development of synthetic genetic circuits, with a special focus on the use of microcompartments supporting this reaction. We highlight several studies where molecular communication between non-living microcompartments and living cells have been successfully engineered.
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Affiliation(s)
- Emilien Dubuc
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands; Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands; Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Pascal A Pieters
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands; Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands; Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Ardjan J van der Linden
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands; Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands; Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Jan Cm van Hest
- Department of Biomedical Engineering & Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Wilhelm Ts Huck
- Department of Physical Organic Chemistry, Institute for Molecules and Materials, Radboud University, Nijmegen 6525 HP, The Netherlands
| | - Tom Fa de Greef
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands; Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands; Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands; Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
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50
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Zhu C, Itel F, Chandrawati R, Han X, Städler B. Multicompartmentalized Microreactors Containing Nuclei and Catalase-Loaded Liposomes. Biomacromolecules 2018; 19:4379-4385. [PMID: 30231209 DOI: 10.1021/acs.biomac.8b01260] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chuntao Zhu
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering. Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin 150001, China
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
| | - Fabian Itel
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
| | - Rona Chandrawati
- School of Chemical Engineering and Australian Centre for Nanomedicine (ACN), The University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia
| | - Xiaojun Han
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering. Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin 150001, China
| | - Brigitte Städler
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
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