1
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Schmidt HN, Gaetjens TK, Leopin EE, Abel SM. Compartmental exchange regulates steady states and stochastic switching of a phosphorylation network. Biophys J 2024; 123:598-609. [PMID: 38317416 PMCID: PMC10938077 DOI: 10.1016/j.bpj.2024.01.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 01/24/2024] [Accepted: 01/31/2024] [Indexed: 02/07/2024] Open
Abstract
The phosphoregulation of proteins with multiple phosphorylation sites is governed by biochemical reaction networks that can exhibit multistable behavior. However, the behavior of such networks is typically studied in a single reaction volume, while cells are spatially organized into compartments that can exchange proteins. In this work, we use stochastic simulations to study the impact of compartmentalization on a two-site phosphorylation network. We characterize steady states and fluctuation-driven transitions between them as a function of the rate of protein exchange between two compartments. Surprisingly, the average time spent in a state before stochastically switching to another depends nonmonotonically on the protein exchange rate, with the most frequent switching occurring at intermediate exchange rates. At sufficiently small exchange rates, the state of the system and mean switching time are controlled largely by fluctuations in the balance of enzymes in each compartment. This leads to negatively correlated states in the compartments. For large exchange rates, the two compartments behave as a single effective compartment. However, when the compartmental volumes are unequal, the behavior differs from a single compartment with the same total volume. These results demonstrate that exchange of proteins between distinct compartments can regulate the emergent behavior of a common signaling motif.
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Affiliation(s)
- Hannah N Schmidt
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee
| | - Thomas K Gaetjens
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee
| | - Emily E Leopin
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee
| | - Steven M Abel
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee.
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2
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Hueso-Gil A, Calles B, de Lorenzo V. In Vivo Sampling of Intracellular Heterogeneity of Pseudomonas putida Enables Multiobjective Optimization of Genetic Devices. ACS Synth Biol 2023; 12:1667-1676. [PMID: 37196337 PMCID: PMC10278179 DOI: 10.1021/acssynbio.3c00009] [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: 01/06/2023] [Indexed: 05/19/2023]
Abstract
The inner physicochemical heterogeneity of bacterial cells generates three-dimensional (3D)-dependent variations of resources for effective expression of given chromosomally located genes. This fact has been exploited for adjusting the most favorable parameters for implanting a complex device for optogenetic control of biofilm formation in the soil bacterium Pseudomonas putida. To this end, a DNA segment encoding a superactive variant of the Caulobacter crescendus diguanylate cyclase PleD expressed under the control of the cyanobacterial light-responsive CcaSR system was placed in a mini-Tn5 transposon vector and randomly inserted through the chromosome of wild-type and biofilm-deficient variants of P. putida lacking the wsp gene cluster. This operation delivered a collection of clones covering a whole range of biofilm-building capacities and dynamic ranges in response to green light. Since the phenotypic output of the device depends on a large number of parameters (multiple promoters, RNA stability, translational efficacy, metabolic precursors, protein folding, etc.), we argue that random chromosomal insertions enable sampling the intracellular milieu for an optimal set of resources that deliver a preset phenotypic specification. Results thus support the notion that the context dependency can be exploited as a tool for multiobjective optimization, rather than a foe to be suppressed in Synthetic Biology constructs.
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Affiliation(s)
| | - Belén Calles
- Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Campus
de Cantoblanco, Madrid 28049, Spain
| | - Víctor de Lorenzo
- Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Campus
de Cantoblanco, Madrid 28049, Spain
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3
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Chauhan G, Norred SE, Dabbs RM, Caveney PM, George JKV, Collier CP, Simpson ML, Abel SM. Crowding-Induced Spatial Organization of Gene Expression in Cell-Sized Vesicles. ACS Synth Biol 2022; 11:3733-3742. [PMID: 36260840 DOI: 10.1021/acssynbio.2c00336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Cell-free protein synthesis is an important tool for studying gene expression and harnessing it for applications. In cells, gene expression is regulated in part by the spatial organization of transcription and translation. Unfortunately, current cell-free approaches are unable to control the organization of molecular components needed for gene expression, which limits the ability to probe and utilize its effects. Here, we show, using complementary computational and experimental approaches, that macromolecular crowding can be used to control the spatial organization and translational efficiency of gene expression in cell-sized vesicles. Computer simulations and imaging experiments reveal that, as crowding is increased, DNA plasmids become localized at the inner surface of vesicles. Ribosomes, in contrast, remain uniformly distributed, demonstrating that crowding can be used to differentially organize components of gene expression. We further carried out cell-free protein synthesis reactions in cell-sized vesicles and quantified mRNA and protein abundance. At sufficiently high levels of crowding, we observed localization of mRNA near vesicle surfaces, a decrease in translational efficiency and protein abundance, and anomalous scaling of protein abundance as a function of vesicle size. These results are consistent with high levels of crowding causing altered spatial organization and slower diffusion. Our work demonstrates a straightforward way to control the organization of gene expression in cell-sized vesicles and provides insight into the spatial regulation of gene expression in cells.
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Affiliation(s)
- Gaurav Chauhan
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Knoxville, Tennessee37996, United States
| | - S Elizabeth Norred
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, United States.,Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville and Oak Ridge National Laboratory, Knoxville, Tennessee37996, United States
| | - Rosemary M Dabbs
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville and Oak Ridge National Laboratory, Knoxville, Tennessee37996, United States
| | - Patrick M Caveney
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, United States.,Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville and Oak Ridge National Laboratory, Knoxville, Tennessee37996, United States
| | - John K Vincent George
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, United States.,Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville and Oak Ridge National Laboratory, Knoxville, Tennessee37996, United States
| | - C Patrick Collier
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, United States
| | - Michael L Simpson
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, United States.,Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville and Oak Ridge National Laboratory, Knoxville, Tennessee37996, United States
| | - Steven M Abel
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Knoxville, Tennessee37996, United States
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4
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Herianto S, Chien PJ, Ho JAA, Tu HL. Liposome-based artificial cells: From gene expression to reconstitution of cellular functions and phenotypes. BIOMATERIALS ADVANCES 2022; 142:213156. [PMID: 36302330 DOI: 10.1016/j.bioadv.2022.213156] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 10/12/2022] [Indexed: 06/16/2023]
Abstract
Bottom-up approaches in creating artificial cells that can mimic natural cells have significant implications for both basic research and translational application. Among various artificial cell models, liposome is one of the most sophisticated systems. By encapsulating proteins and associated biomolecules, they can functionally reconstitute foundational features of biological cells, such as the ability to divide, communicate, and undergo shape deformation. Yet constructing liposome artificial cells from the genetic level, which is central to generate self-sustained systems remains highly challenging. Indeed, many studies have successfully established the expression of gene-coded proteins inside liposomes. Further, recent endeavors to build a direct integration of gene-expressed proteins for reconstituting molecular functions and phenotypes in liposomes have also significantly increased. Thus, this review presents the development of liposome-based artificial cells to demonstrate the process of gene-expressed proteins and their reconstitution to perform desired molecular and cell-like functions. The molecular and cellular phenotypes discussed here include the self-production of membrane phospholipids, division, shape deformation, self-DNA/RNA replication, fusion, and intercellular communication. Together, this review gives a comprehensive overview of gene-expressing liposomes that can stimulate further research of this technology and achieve artificial cells with superior properties in the future.
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Affiliation(s)
- Samuel Herianto
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan; Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan; Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Po-Jen Chien
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Ja-An Annie Ho
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan; BioAnalytical Chemistry and Nanobiomedicine Laboratory, Department of Biochemical Science and Technology, National Taiwan University, Taipei 10617, Taiwan
| | - Hsiung-Lin Tu
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan; Chemical Biology and Molecular Biophysics, Taiwan International Graduate Program, Academia Sinica, Taipei 11529, Taiwan.
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5
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In vitro assembly, positioning and contraction of a division ring in minimal cells. Nat Commun 2022; 13:6098. [PMID: 36243816 PMCID: PMC9569390 DOI: 10.1038/s41467-022-33679-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 09/27/2022] [Indexed: 02/07/2023] Open
Abstract
Constructing a minimal machinery for autonomous self-division of synthetic cells is a major goal of bottom-up synthetic biology. One paradigm has been the E. coli divisome, with the MinCDE protein system guiding assembly and positioning of a presumably contractile ring based on FtsZ and its membrane adaptor FtsA. Here, we demonstrate the full in vitro reconstitution of this machinery consisting of five proteins within lipid vesicles, allowing to observe the following sequence of events in real time: 1) Assembly of an isotropic filamentous FtsZ network, 2) its condensation into a ring-like structure, along with pole-to-pole mode selection of Min oscillations resulting in equatorial positioning, and 3) onset of ring constriction, deforming the vesicles from spherical shape. Besides demonstrating these essential features, we highlight the importance of decisive experimental factors, such as macromolecular crowding. Our results provide an exceptional showcase of the emergence of cell division in a minimal system, and may represent a step towards developing a synthetic cell.
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6
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Maeda YT. Negative autoregulation controls size scaling in confined gene expression reactions. Sci Rep 2022; 12:10516. [PMID: 35732682 PMCID: PMC9217826 DOI: 10.1038/s41598-022-14719-4] [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] [Received: 11/02/2021] [Accepted: 06/10/2022] [Indexed: 11/09/2022] Open
Abstract
Gene expression via transcription-translation is the most fundamental reaction to sustain biological systems, and complex reactions occur in a small compartment of living cells. There is increasing evidence that physical effects, such as molecular crowding or excluded volume effects of transcriptional-translational machinery, affect the yield of reaction products. On the other hand, transcriptional feedback that controls gene expression during mRNA synthesis is also a vital mechanism that regulates protein synthesis in cells. However, the excluded volume effect of spatial constraints on feedback regulation is not well understood. Here, we study the confinement effect on transcriptional autoregulatory feedbacks of gene expression reactions using a theoretical model. The excluded volume effects between molecules and the membrane interface suppress the gene expression in a small cell-sized compartment. We find that negative feedback regulation at the transcription step mitigates this size-induced gene repression and alters the scaling relation of gene expression level on compartment volume, approaching the regular scaling relation without the steric effect. This recovery of regular size-scaling of gene expression does not appear in positive feedback regulation, suggesting that negative autoregulatory feedback is crucial for maintaining reaction products constant regardless of compartment size in heterogeneous cell populations.
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Affiliation(s)
- Yusuke T Maeda
- Department of Physics, Kyushu University, Motooka 744, Fukuoka, 819-0395, Japan.
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7
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Li C, Zhang X, Dong M, Han X. Progress on Crowding Effect in Cell-like Structures. MEMBRANES 2022; 12:membranes12060593. [PMID: 35736300 PMCID: PMC9228500 DOI: 10.3390/membranes12060593] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 12/10/2022]
Abstract
Several biological macromolecules, such as proteins, nucleic acids, and polysaccharides, occupy about 30% of the space in cells, resulting in a crowded macromolecule environment. The crowding effect within cells exerts an impact on the functions of biological components, the assembly behavior of biomacromolecules, and the thermodynamics and kinetics of metabolic reactions. Cell-like structures provide confined and independent compartments for studying the working mechanisms of cells, which can be used to study the physiological functions arising from the crowding effect of macromolecules in cells. This article mainly summarizes the progress of research on the macromolecular crowding effects in cell-like structures. It includes the effects of this crowding on actin assembly behavior, tubulin aggregation behavior, and gene expression. The challenges and future trends in this field are presented at the end of the paper.
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Affiliation(s)
- Chao Li
- 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; (C.L.); (X.Z.)
| | - Xiangxiang Zhang
- 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; (C.L.); (X.Z.)
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus, Denmark
- Correspondence: (M.D.); (X.H.)
| | - 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; (C.L.); (X.Z.)
- Correspondence: (M.D.); (X.H.)
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8
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Gonzales D, Yandrapalli N, Robinson T, Zechner C, Tang TYD. Cell-Free Gene Expression Dynamics in Synthetic Cell Populations. ACS Synth Biol 2022; 11:205-215. [PMID: 35057626 PMCID: PMC8787815 DOI: 10.1021/acssynbio.1c00376] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Indexed: 11/29/2022]
Abstract
The ability to build synthetic cellular populations from the bottom-up provides the groundwork to realize minimal living tissues comprising single cells which can communicate and bridge scales into multicellular systems. Engineered systems made of synthetic micron-sized compartments and integrated reaction networks coupled with mathematical modeling can facilitate the design and construction of complex and multiscale chemical systems from the bottom-up. Toward this goal, we generated populations of monodisperse liposomes encapsulating cell-free expression systems (CFESs) using double-emulsion microfluidics and quantified transcription and translation dynamics within individual synthetic cells of the population using a fluorescent Broccoli RNA aptamer and mCherry protein reporter. CFE dynamics in bulk reactions were used to test different coarse-grained resource-limited gene expression models using model selection to obtain transcription and translation rate parameters by likelihood-based parameter estimation. The selected model was then applied to quantify cell-free gene expression dynamics in populations of synthetic cells. In combination, our experimental and theoretical approaches provide a statistically robust analysis of CFE dynamics in bulk and monodisperse synthetic cell populations. We demonstrate that compartmentalization of CFESs leads to different transcription and translation rates compared to bulk CFE and show that this is due to the semipermeable lipid membrane that allows the exchange of materials between the synthetic cells and the external environment.
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Affiliation(s)
- David
T. Gonzales
- Max
Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Center
for Systems Biology Dresden, 01307 Dresden, Germany
| | | | - Tom Robinson
- Max
Planck Institute of Colloids and Interfaces, 14476 Potsdam, Germany
| | - Christoph Zechner
- Max
Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Center
for Systems Biology Dresden, 01307 Dresden, Germany
- Physics
of Life, Cluster of Excellence, TU Dresden, 01603 Dresden, Germany
| | - T-Y. Dora Tang
- Max
Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
- Center
for Systems Biology Dresden, 01307 Dresden, Germany
- Physics
of Life, Cluster of Excellence, TU Dresden, 01603 Dresden, Germany
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9
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Chauhan G, Simpson ML, Abel SM. Adsorption of semiflexible polymers in crowded environments. J Chem Phys 2021; 155:034904. [PMID: 34293868 DOI: 10.1063/5.0054797] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Macromolecular crowding is a feature of cellular and cell-free systems that, through depletion effects, can impact the interactions of semiflexible biopolymers with surfaces. In this work, we use computer simulations to study crowding-induced adsorption of semiflexible polymers on otherwise repulsive surfaces. Crowding particles are modeled explicitly, and we investigate the interplay between the bending stiffness of the polymer and the volume fraction and size of crowding particles. Adsorption to flat surfaces is promoted by stiffer polymers, smaller crowding particles, and larger volume fractions of crowders. We characterize transitions from non-adsorbed to partially and strongly adsorbed states as a function of bending stiffness. The crowding-induced transitions occur at smaller values of the bending stiffness as the volume fraction of crowders increases. Concomitant effects on the size and shape of the polymer are reflected by crowding- and stiffness-dependent changes to the radius of gyration. For various polymer lengths, we identify a critical crowding fraction for adsorption and analyze its scaling behavior in terms of polymer stiffness. We also consider crowding-induced adsorption in spherical confinement and identify a regime in which increasing the bending stiffness induces desorption. The results of our simulations shed light on the interplay of crowding and bending stiffness on the spatial organization of biopolymers in encapsulated cellular and cell-free systems.
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Affiliation(s)
- Gaurav Chauhan
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Knoxville, Tennessee 37996, USA
| | - Michael L Simpson
- Department of Materials Science and Engineering, University of Tennessee, Knoxville, Knoxville, Tennessee 37996, USA
| | - Steven M Abel
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Knoxville, Tennessee 37996, USA
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10
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Dashnaw CM, Koone JC, Abdolvahabi A, Shaw BF. Measuring how two proteins affect each other's net charge in a crowded environment. Protein Sci 2021; 30:1594-1605. [PMID: 33928693 DOI: 10.1002/pro.4092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/23/2021] [Indexed: 12/19/2022]
Abstract
Theory predicts that the net charge (Z) of a protein can be altered by the net charge of a neighboring protein as the two approach one another below the Debye length. This type of charge regulation suggests that a protein's charge and perhaps function might be affected by neighboring proteins without direct binding. Charge regulation during protein crowding has never been directly measured due to analytical challenges. Here, we show that lysine specific protein crosslinkers (NHS ester-Staudinger pairs) can be used to mimic crowding by linking two non-interacting proteins at a maximal distance of ~7.9 Å. The net charge of the regioisomeric dimers and preceding monomers can then be determined with lysine-acyl "protein charge ladders" and capillary electrophoresis. As a proof of concept, we covalently linked myoglobin (Zmonomer = -0.43 ± 0.01) and α-lactalbumin (Zmonomer = -4.63 ± 0.05). Amide hydrogen/deuterium exchange and circular dichroism spectroscopy demonstrated that crosslinking did not significantly alter the structure of either protein or result in direct binding (thus mimicking crowding). Ultimately, capillary electrophoretic analysis of the dimeric charge ladder detected a change in charge of ΔZ = -0.04 ± 0.09 upon crowding by this pair (Zdimer = -5.10 ± 0.07). These small values of ΔZ are not necessarily general to protein crowding (qualitatively or quantitatively) but will vary per protein size, charge, and solvent conditions.
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Affiliation(s)
- Chad M Dashnaw
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, USA
| | - Jordan C Koone
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, USA
| | - Alireza Abdolvahabi
- Mass Spectrometry Core Facility, School of Pharmacy, University of Southern California, Los Angeles, California, USA
| | - Bryan F Shaw
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, USA
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11
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Batista AC, Soudier P, Kushwaha M, Faulon J. Optimising protein synthesis in cell‐free systems, a review. ENGINEERING BIOLOGY 2021; 5:10-19. [PMID: 36968650 PMCID: PMC9996726 DOI: 10.1049/enb2.12004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/03/2020] [Accepted: 12/09/2020] [Indexed: 12/25/2022] Open
Abstract
Over the last decades, cell-free systems have been extensively used for in vitro protein expression. A vast range of protocols and cellular sources varying from prokaryotes and eukaryotes are now available for cell-free technology. However, exploiting the maximum capacity of cell free systems is not achieved by using traditional protocols. Here, what are the strategies and choices one can apply to optimise cell-free protein synthesis have been reviewed. These strategies provide robust and informative improvements regarding transcription, translation and protein folding which can later be used for the establishment of individual best cell-free reactions per lysate batch.
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Affiliation(s)
- Angelo C. Batista
- Université Paris‐Saclay INRAE AgroParisTech Micalis Institute Jouy‐en‐Josas France
| | - Paul Soudier
- Université Paris‐Saclay INRAE AgroParisTech Micalis Institute Jouy‐en‐Josas France
| | - Manish Kushwaha
- Université Paris‐Saclay INRAE AgroParisTech Micalis Institute Jouy‐en‐Josas France
| | - Jean‐Loup Faulon
- Université Paris‐Saclay INRAE AgroParisTech Micalis Institute Jouy‐en‐Josas France
- SYNBIOCHEM Center School of Chemistry Manchester Institute of Biotechnology The University of Manchester Manchester UK
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12
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Chauhan G, Simpson ML, Abel SM. Crowding-induced interactions of ring polymers. SOFT MATTER 2021; 17:16-23. [PMID: 33155586 DOI: 10.1039/d0sm01847c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Macromolecular crowding and the presence of surfaces can significantly impact the spatial organization of biopolymers. While the importance of crowding-induced depletion interactions in biology has been recognized, much remains to be understood about the effect of crowding on biopolymers such as DNA plasmids. A fundamental problem highlighted by recent experiments is to characterize the impact of crowding on polymer-polymer and polymer-surface interactions. Motivated by the need for quantitative insight, we studied flexible ring polymers in crowded environments using Langevin dynamics simulations. The simulations demonstrated that crowding can lead to compaction of isolated ring polymers and enhanced interactions between two otherwise repulsive polymers. Using umbrella sampling, we determined the potential of mean force (PMF) between two ring polymers as a function of their separation distance at different volume fractions of crowding particles, φ. An effective attraction emerged at φ≈ 0.4, which is similar to the degree of crowding in cells. Analogous simulations showed that crowding can lead to strong adsorption of a ring polymer to a wall, with an effective attraction to the wall emerging at a smaller volume fraction of crowders (φ≈ 0.2). Our results reveal the magnitude of depletion interactions in a biologically-inspired model and highlight how crowding can be used to tune interactions in both cellular and cell-free systems.
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Affiliation(s)
- Gaurav Chauhan
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, USA.
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13
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Vibhute MA, Schaap MH, Maas RJM, Nelissen FHT, Spruijt E, Heus HA, Hansen MMK, Huck WTS. Transcription and Translation in Cytomimetic Protocells Perform Most Efficiently at Distinct Macromolecular Crowding Conditions. ACS Synth Biol 2020; 9:2797-2807. [PMID: 32976714 PMCID: PMC7573978 DOI: 10.1021/acssynbio.0c00330] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
The formation of
cytomimetic protocells that capture the physicochemical
aspects of living cells is an important goal in bottom-up synthetic
biology. Here, we recreated the crowded cytoplasm in liposome-based
protocells and studied the kinetics of cell-free gene expression in
these crowded containers. We found that diffusion of key components
is affected not only by macromolecular crowding but also by enzymatic
activity in the protocell. Surprisingly, size-dependent diffusion
in crowded conditions yielded two distinct maxima for protein synthesis,
reflecting the differential impact of crowding on transcription and
translation. Our experimental data show, for the first time, that
macromolecular crowding induces a switch from reaction to diffusion
control and that this switch depends on the sizes of the macromolecules
involved. These results highlight the need to control the physical
environment in the design of synthetic cells.
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Affiliation(s)
- Mahesh A. Vibhute
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Mark H. Schaap
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Roel J. M. Maas
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Frank H. T. Nelissen
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Evan Spruijt
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Hans A. Heus
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Maike M. K. Hansen
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Wilhelm T. S. Huck
- Radboud University, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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14
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Lee MS, Hung CS, Phillips DA, Buck CC, Gupta MK, Lux MW. Silk fibroin as an additive for cell-free protein synthesis. Synth Syst Biotechnol 2020; 5:145-154. [PMID: 32637668 PMCID: PMC7320238 DOI: 10.1016/j.synbio.2020.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/15/2020] [Accepted: 06/15/2020] [Indexed: 01/06/2023] Open
Abstract
Cell-free systems contain many proteins and metabolites required for complex functions such as transcription and translation or multi-step metabolic conversions. Research into expanding the delivery of these systems by drying or by embedding into other materials is enabling new applications in sensing, point-of-need manufacturing, and responsive materials. Meanwhile, silk fibroin from the silk worm, Bombyx mori, has received attention as a protective additive for dried enzyme formulations and as a material to build biocompatible hydrogels for controlled localization or delivery of biomolecular cargoes. In this work, we explore the effects of silk fibroin as an additive in cell-free protein synthesis (CFPS) reactions. Impacts of silk fibroin on CFPS activity and stability after drying, as well as the potential for incorporation of CFPS into hydrogels of crosslinked silk fibroin are assessed. We find that simple addition of silk fibroin increased productivity of the CFPS reactions by up to 42%, which we attribute to macromolecular crowding effects. However, we did not find evidence that silk fibroin provides a protective effects after drying as previously described for purified enzymes. Further, the enzymatic crosslinking transformations of silk fibroin typically used to form hydrogels are inhibited in the presence of the CFPS reaction mixture. Crosslinking attempts did not impact CFPS activity, but did yield localized protein aggregates rather than a hydrogel. We discuss the mechanisms at play in these results and how the silk fibroin-CFPS system might be improved for the design of cell-free devices.
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Affiliation(s)
- Marilyn S. Lee
- US Army Combat Capabilities Development Command Chemical and Biological Center, 8567 Ricketts Point Road, Aberdeen Proving Ground, MD, 21010, USA
| | - Chia-Suei Hung
- US Air Force Research Laboratory, 2179 12th St., B652/R122 Wright-Patterson Air Force Base, OH, 45433, USA
| | - Daniel A. Phillips
- US Naval Research Laboratory Center for Bio/Molecular Science and Engineering, Bldg. 42, Room 303 4555 Overlook Ave. Washington, DC 20375, UES Inc., 4401 Dayton Xenia Rd., Beavercreek, OH 45432, USA
| | - Chelsea C. Buck
- US Air Force Research Laboratory, 2179 12th St., B652/R122 Wright-Patterson Air Force Base, OH, 45433, USA
- US Naval Research Laboratory Center for Bio/Molecular Science and Engineering, Bldg. 42, Room 303 4555 Overlook Ave. Washington, DC 20375, UES Inc., 4401 Dayton Xenia Rd., Beavercreek, OH 45432, USA
| | - Maneesh K. Gupta
- US Air Force Research Laboratory, 2179 12th St., B652/R122 Wright-Patterson Air Force Base, OH, 45433, USA
| | - Matthew W. Lux
- US Army Combat Capabilities Development Command Chemical and Biological Center, 8567 Ricketts Point Road, Aberdeen Proving Ground, MD, 21010, USA
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15
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Chen X, Sun Q, Lu Y. Creating a locally crowded environment with nanoclay hydrogels for cell-free biosynthesis. SOFT MATTER 2020; 16:5132-5138. [PMID: 32478769 DOI: 10.1039/d0sm00636j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In living cells, the exceptionally high local concentration of macromolecules, or "locally crowded environment," could affect many aspects of cellular function. Exploration of the locally crowded environment can improve the understanding of living cells and advance the study of artificial cells. In this paper, nanoclay combined with gene templates is used to simulate the locally crowded environment in a cell-free system, ultimately to explore its effects on protein expression. The adsorption effect can immobilize the plasmid on the nanoclay surface, thereby achieving a higher local concentration in the cell-free system. A closer proximity of genes could result in an increase in the protein production of cell-free systems by 1.75 times. Besides, the kinetics of the nanoclay in the cell-free system was analyzed, and the results showed that the genetic transcription level involved in cell-free reactions was significantly improved. This study confirms that a locally crowded environment created by the nanoclay can achieve high protein expression in a cell-free system and help promote the process of transcription and translation. Application of the nanoclay in the cell-free system demonstrates the significance of applying nanomaterials in biological and biomedical fields and provides technical support for the study of the locally crowded environment.
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Affiliation(s)
- Xinjie Chen
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China.
| | - Qi Sun
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China.
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China.
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16
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Laohakunakorn N, Grasemann L, Lavickova B, Michielin G, Shahein A, Swank Z, Maerkl SJ. Bottom-Up Construction of Complex Biomolecular Systems With Cell-Free Synthetic Biology. Front Bioeng Biotechnol 2020; 8:213. [PMID: 32266240 PMCID: PMC7105575 DOI: 10.3389/fbioe.2020.00213] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 03/03/2020] [Indexed: 12/16/2022] Open
Abstract
Cell-free systems offer a promising approach to engineer biology since their open nature allows for well-controlled and characterized reaction conditions. In this review, we discuss the history and recent developments in engineering recombinant and crude extract systems, as well as breakthroughs in enabling technologies, that have facilitated increased throughput, compartmentalization, and spatial control of cell-free protein synthesis reactions. Combined with a deeper understanding of the cell-free systems themselves, these advances improve our ability to address a range of scientific questions. By mastering control of the cell-free platform, we will be in a position to construct increasingly complex biomolecular systems, and approach natural biological complexity in a bottom-up manner.
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Affiliation(s)
- Nadanai Laohakunakorn
- School of Biological Sciences, Institute of Quantitative Biology, Biochemistry, and Biotechnology, University of Edinburgh, Edinburgh, United Kingdom
| | - Laura Grasemann
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Barbora Lavickova
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Grégoire Michielin
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Amir Shahein
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Zoe Swank
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Sebastian J. Maerkl
- School of Engineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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17
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Prangemeier T, Lehr FX, Schoeman RM, Koeppl H. Microfluidic platforms for the dynamic characterisation of synthetic circuitry. Curr Opin Biotechnol 2020; 63:167-176. [PMID: 32172160 DOI: 10.1016/j.copbio.2020.02.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 01/31/2020] [Accepted: 02/03/2020] [Indexed: 01/28/2023]
Abstract
Generating novel functionality from well characterised synthetic parts and modules lies at the heart of synthetic biology. Ideally, circuitry is rationally designed in silico with quantitatively predictive models to predetermined design specifications. Synthetic circuits are intrinsically stochastic, often dynamically modulated and set in a dynamic fluctuating environment within a living cell. To build more complex circuits and to gain insight into context effects, intrinsic noise and transient performance, characterisation techniques that resolve both heterogeneity and dynamics are required. Here we review recent advances in both in vitro and in vivo microfluidic technologies that are suitable for the characterisation of synthetic circuitry, modules and parts.
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Affiliation(s)
- Tim Prangemeier
- Centre for Synthetic Biology, Department of Electrical Engineering and Information Technology, Department of Biology, Technische Universität Darmstadt, Germany
| | - François-Xavier Lehr
- Centre for Synthetic Biology, Department of Electrical Engineering and Information Technology, Department of Biology, Technische Universität Darmstadt, Germany
| | - Rogier M Schoeman
- Centre for Synthetic Biology, Department of Electrical Engineering and Information Technology, Department of Biology, Technische Universität Darmstadt, Germany
| | - Heinz Koeppl
- Centre for Synthetic Biology, Department of Electrical Engineering and Information Technology, Department of Biology, Technische Universität Darmstadt, Germany.
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18
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Kumar P, Theeyancheri L, Chaki S, Chakrabarti R. Transport of probe particles in a polymer network: effects of probe size, network rigidity and probe-polymer interaction. SOFT MATTER 2019; 15:8992-9002. [PMID: 31681926 DOI: 10.1039/c9sm01822k] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Fundamental understanding of the effect of microscopic parameters on the dynamics of probe particles in different complex environments has wide implications. Examples include diffusion of proteins in biological hydrogels, porous media, polymer matrix, etc. Here, we use extensive molecular dynamics simulations to investigate the dynamics of the probe particle in a polymer network on a diamond lattice, which provides substantial crowding to mimic the cellular environment. Our simulations show that the dynamics of the probe increasingly becomes restricted, non-Gaussian and subdiffusive on increasing the network rigidity, binding affinity and probe size. In addition, the velocity autocorrelation functions show negative dips owing to the viscoelasticity and caging due to the surrounding network. These observations go with the general experimental findings. Importantly, for a probe particle of size comparable to the mesh size, unrestricted motion engulfing large length scales has been observed. This happens with a more flexible polymer network, which is easily pushed by the bigger probe. On increasing the rigidity of the network, the bigger probe can not efficiently push the network and as a result the long tail disappears. Our study gives a general qualitative picture of the transport of probes in a gel-like medium, as encountered in different contexts.
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Affiliation(s)
- Praveen Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
| | - Ligesh Theeyancheri
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
| | - Subhasish Chaki
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
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19
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Shim AR, Nap RJ, Huang K, Almassalha LM, Matusda H, Backman V, Szleifer I. Dynamic Crowding Regulates Transcription. Biophys J 2019; 118:2117-2129. [PMID: 31818468 DOI: 10.1016/j.bpj.2019.11.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 09/26/2019] [Accepted: 11/11/2019] [Indexed: 02/01/2023] Open
Abstract
The nuclear environment is highly crowded by biological macromolecules, including chromatin and mobile proteins, which alter the kinetics and efficiency of transcriptional machinery. These alterations have been described, both theoretically and experimentally, for steady-state crowding densities; however, temporal changes in crowding density ("dynamic crowding") have yet to be integrated with gene expression. Dynamic crowding is pertinent to nuclear biology because processes such as chromatin translocation and protein diffusion lend to highly mobile biological crowders. Therefore, to capture such dynamic crowding and investigate its influence on transcription, we employ a three-pronged, systems-molecular approach. A system of chemical reactions represents the transcription pathway, the rates of which are determined by molecular-scale simulations; Brownian dynamics and Monte Carlo simulations quantify protein diffusion and DNA-protein binding affinity, dependent on macromolecular density. Altogether, this approach shows that transcription depends critically on dynamic crowding as the gene expression resultant from dynamic crowding can be profoundly different than that of steady-state crowding. In fact, expression levels can display both amplification and suppression and are notably different for genes or gene populations with different chemical and structural properties. These properties can be exploited to impose circadian expression, which is asymmetric and varies in strength, or to explain expression in cells under biomechanical stress. Therefore, this work demonstrates that dynamic crowding nontrivially alters transcription kinetics and presents dynamic crowding within the bulk nuclear nanoenvironment as a novel regulatory framework for gene expression.
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Affiliation(s)
- Anne R Shim
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois; Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois
| | - Rikkert J Nap
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois; Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois
| | - Kai Huang
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois; Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois
| | - Luay M Almassalha
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois
| | - Hiroaki Matusda
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois
| | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois; Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois
| | - Igal Szleifer
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois; Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois; Department of Chemistry, Northwestern University, Evanston, Illinois.
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20
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Blanken D, van Nies P, Danelon C. Quantitative imaging of gene-expressing liposomes reveals rare favorable phenotypes. Phys Biol 2019; 16:045002. [PMID: 30978176 DOI: 10.1088/1478-3975/ab0c62] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The biosynthesis of proteins from genomic DNA is a universal process in every living organism. Building a synthetic cell using separate biological parts hence implies to reconstitute a minimal gene expression apparatus and to compartmentalize it in a cell-mimicking environment. Previous studies have demonstrated that the PURE (Protein synthesis Using Recombinant Elements) system could be functionally encapsulated inside lipid vesicles. However, quantitative insights on functional consequences of spatial confinement of PURE system reactions remain scarce, which has hampered the full exploitation of gene-expressing liposomes as the fundamental unit to build an artificial cell. We report on direct imaging of tens of thousands of gene-expressing liposomes per sample allowing us to assess sub-population features in a statistically relevant manner. Both the vesicle size (diameter <10 μm) and lipid composition (mixture of phospholipids with zwitterionic and negatively charged headgroups, including cardiolipin) are compatible with the properties of bacterial cells. Therefore, our liposomes provide a suitable chassis to host the Escherichia coli-derived PURE translation machinery and other bacterial processes in future developments. The potential of high-content imaging to identify rare phenotypes is demonstrated by the fact that a subset of the liposome population exhibits a remarkably high yield of synthesized protein or a prolonged expression lifespan that surpasses the performance of ensemble liposome-averaged and bulk reactions. Among the three commercial PURE systems tested, PUREfrex2.0 offers the most favorable phenotypes displaying both high yield and long protein synthesis lifespan. Moreover, probing membrane permeability reveals a large heterogeneity amongst liposomes. In situ expression and membrane embedding of the pore-forming connexin leads to a characteristic permeability time profile, while increasing the fraction of permeable liposomes in the population. We see diversity in gene expression dynamics and membrane permeability as an opportunity to complement a rational design approach aiming at further implementing biological functions in liposome-based synthetic cells.
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Affiliation(s)
- Duco Blanken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
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21
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Nandy A, Chakraborty S, Nandi S, Bhattacharyya K, Mukherjee S. Structure, Activity, and Dynamics of Human Serum Albumin in a Crowded Pluronic F127 Hydrogel. J Phys Chem B 2019; 123:3397-3408. [DOI: 10.1021/acs.jpcb.9b00219] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Atanu Nandy
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
| | - Subhajit Chakraborty
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
| | - Somen Nandi
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Kankan Bhattacharyya
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
| | - Saptarshi Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal 462066, Madhya Pradesh, India
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22
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Norouzi M, Pickford AR, Butt LE, Vincent HA, Callaghan AJ. Application of mRNA Arrays for the Production of mCherry Reporter-Protein Arrays for Quantitative Gene Expression Analysis. ACS Synth Biol 2019; 8:207-215. [PMID: 30682244 DOI: 10.1021/acssynbio.8b00266] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The development of programmable regulators that precisely and predictably control gene expression is a major goal of synthetic biology. Consequently, rapid high-throughput biochemical methods capable of quantitatively analyzing all components of gene expression would be of value in the characterization and optimization of regulator performance. In this study we demonstrate a novel application of RNA arrays, involving the production of reporter-protein arrays, to gene expression analysis. This method enables simultaneous quantification of both the transcription and post-transcription/translation components of gene expression, and it also allows the assessment of the orthogonality of multiple regulators. We use our method to directly compare the performance of a series of previously characterized synthetic post-transcriptional riboregulators, thus demonstrating its utility in the development of synthetic regulatory modules and evaluation of gene expression regulation in general.
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Affiliation(s)
- Masoud Norouzi
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - Andrew R. Pickford
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - Louise E. Butt
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - Helen A. Vincent
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
| | - Anastasia J. Callaghan
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth PO1 2DY, United Kingdom
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23
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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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