1
|
Rothschild LJ, Averesch NJH, Strychalski EA, Moser F, Glass JI, Cruz Perez R, Yekinni IO, Rothschild-Mancinelli B, Roberts Kingman GA, Wu F, Waeterschoot J, Ioannou IA, Jewett MC, Liu AP, Noireaux V, Sorenson C, Adamala KP. Building Synthetic Cells─From the Technology Infrastructure to Cellular Entities. ACS Synth Biol 2024; 13:974-997. [PMID: 38530077 PMCID: PMC11037263 DOI: 10.1021/acssynbio.3c00724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 03/27/2024]
Abstract
The de novo construction of a living organism is a compelling vision. Despite the astonishing technologies developed to modify living cells, building a functioning cell "from scratch" has yet to be accomplished. The pursuit of this goal alone has─and will─yield scientific insights affecting fields as diverse as cell biology, biotechnology, medicine, and astrobiology. Multiple approaches have aimed to create biochemical systems manifesting common characteristics of life, such as compartmentalization, metabolism, and replication and the derived features, evolution, responsiveness to stimuli, and directed movement. Significant achievements in synthesizing each of these criteria have been made, individually and in limited combinations. Here, we review these efforts, distinguish different approaches, and highlight bottlenecks in the current research. We look ahead at what work remains to be accomplished and propose a "roadmap" with key milestones to achieve the vision of building cells from molecular parts.
Collapse
Affiliation(s)
- Lynn J. Rothschild
- Space Science
& Astrobiology Division, NASA Ames Research
Center, Moffett
Field, California 94035-1000, United States
- Department
of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Nils J. H. Averesch
- Department
of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | | | - Felix Moser
- Synlife, One Kendall Square, Cambridge, Massachusetts 02139-1661, United States
| | - John I. Glass
- J.
Craig
Venter Institute, La Jolla, California 92037, United States
| | - Rolando Cruz Perez
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
- Blue
Marble
Space Institute of Science at NASA Ames Research Center, Moffett Field, California 94035-1000, United
States
| | - Ibrahim O. Yekinni
- Department
of Biomedical Engineering, University of
Minnesota, Minneapolis, Minnesota 55455, United States
| | - Brooke Rothschild-Mancinelli
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332-0150, United States
| | | | - Feilun Wu
- J. Craig
Venter Institute, Rockville, Maryland 20850, United States
| | - Jorik Waeterschoot
- Mechatronics,
Biostatistics and Sensors (MeBioS), KU Leuven, 3000 Leuven Belgium
| | - Ion A. Ioannou
- Department
of Chemistry, MSRH, Imperial College London, London W12 0BZ, U.K.
| | - Michael C. Jewett
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Allen P. Liu
- Mechanical
Engineering & Biomedical Engineering, Cellular and Molecular Biology,
Biophysics, Applied Physics, University
of Michigan, Ann Arbor, Michigan 48109, United States
| | - Vincent Noireaux
- Physics
and Nanotechnology, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Carlise Sorenson
- Department
of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Katarzyna P. Adamala
- Department
of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, United States
| |
Collapse
|
2
|
Van de Cauter L, van Buren L, Koenderink GH, Ganzinger KA. Exploring Giant Unilamellar Vesicle Production for Artificial Cells - Current Challenges and Future Directions. SMALL METHODS 2023; 7:e2300416. [PMID: 37464561 DOI: 10.1002/smtd.202300416] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/30/2023] [Indexed: 07/20/2023]
Abstract
Creating an artificial cell from the bottom up is a long-standing challenge and, while significant progress has been made, the full realization of this goal remains elusive. Arguably, one of the biggest hurdles that researchers are facing now is the assembly of different modules of cell function inside a single container. Giant unilamellar vesicles (GUVs) have emerged as a suitable container with many methods available for their production. Well-studied swelling-based methods offer a wide range of lipid compositions but at the expense of limited encapsulation efficiency. Emulsion-based methods, on the other hand, excel at encapsulation but are only effective with a limited set of membrane compositions and may entrap residual additives in the lipid bilayer. Since the ultimate artificial cell will need to comply with both specific membrane and encapsulation requirements, there is still no one-method-fits-all solution for GUV formation available today. This review discusses the state of the art in different GUV production methods and their compatibility with GUV requirements and operational requirements such as reproducibility and ease of use. It concludes by identifying the most pressing issues and proposes potential avenues for future research to bring us one step closer to turning artificial cells into a reality.
Collapse
Affiliation(s)
- Lori Van de Cauter
- Autonomous Matter Department, AMOLF, Amsterdam, 1098 XG, The Netherlands
| | - Lennard van Buren
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2629 HZ, The Netherlands
| | - Gijsje H Koenderink
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2629 HZ, The Netherlands
| | | |
Collapse
|
3
|
Bartelds MW, García-Blay Ó, Verhagen PGA, Wubbolts EJ, van Sluijs B, Heus HA, de Greef TFA, Huck WTS, Hansen MMK. Noise Minimization in Cell-Free Gene Expression. ACS Synth Biol 2023; 12:2217-2225. [PMID: 37478000 PMCID: PMC10443034 DOI: 10.1021/acssynbio.3c00174] [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: 03/24/2023] [Indexed: 07/23/2023]
Abstract
Biochemical reactions that involve small numbers of molecules are accompanied by a degree of inherent randomness that results in noisy reaction outcomes. In synthetic biology, the ability to minimize noise particularly during the reconstitution of future synthetic protocells is an outstanding challenge to secure robust and reproducible behavior. Here we show that by encapsulation of a bacterial cell-free gene expression system in water-in-oil droplets, in vitro-synthesized MazF reduces cell-free gene expression noise >2-fold. With stochastic simulations we identify that this noise minimization acts through both increased degradation and the autoregulatory feedback of MazF. Specifically, we find that the expression of MazF enhances the degradation rate of mRNA up to 18-fold in a sequence-dependent manner. This sequence specificity of MazF would allow targeted noise control, making it ideal to integrate into synthetic gene networks. Therefore, including MazF production in synthetic biology can significantly minimize gene expression noise, impacting future design principles of more complex cell-free gene circuits.
Collapse
Affiliation(s)
- Mart W. Bartelds
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Óscar García-Blay
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Pieter G. A. Verhagen
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Elise J. Wubbolts
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Bob van Sluijs
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Hans A. Heus
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Tom F. A. de Greef
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- Laboratory
of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
- Institute
for Complex Molecular Systems, Eindhoven
University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
- Computational
Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology,
P.O. Box 513, 5600 MB Eindhoven, The Netherlands
- Center
for Living Technologies, Eindhoven-Wageningen-Utrecht
Alliance, 5600 MB Eindhoven, The Netherlands
| | - Wilhelm T. S. Huck
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Maike M. K. Hansen
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| |
Collapse
|
4
|
Nair KS, Bajaj H. Advances in giant unilamellar vesicle preparation techniques and applications. Adv Colloid Interface Sci 2023; 318:102935. [PMID: 37320960 DOI: 10.1016/j.cis.2023.102935] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 05/23/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023]
Abstract
Giant unilamellar vesicles (GUVs) are versatile and promising cell-sized bio-membrane mimetic platforms. Their applications range from understanding and quantifying membrane biophysical processes to acting as elementary blocks in the bottom-up assembly of synthetic cells. Definite properties and requisite goals in GUVs are dictated by the preparation techniques critical to the success of their applications. Here, we review key advances in giant unilamellar vesicle preparation techniques and discuss their formation mechanisms. Developments in lipid hydration and emulsion techniques for GUV preparation are described. Novel microfluidic-based techniques involving lipid or surfactant-stabilized emulsions are outlined. GUV immobilization strategies are summarized, including gravity-based settling, covalent linking, and immobilization by microfluidic, electric, and magnetic barriers. Moreover, some of the key applications of GUVs as biomimetic and synthetic cell platforms during the last decade have been identified. Membrane interface processes like phase separation, membrane protein reconstitution, and membrane bending have been deciphered using GUVs. In addition, vesicles are also employed as building blocks to construct synthetic cells with defined cell-like functions comprising compartments, metabolic reactors, and abilities to grow and divide. We critically discuss the pros and cons of preparation technologies and the properties they confer to the GUVs and identify potential techniques for dedicated applications.
Collapse
Affiliation(s)
- Karthika S Nair
- Microbial Processes and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum 695019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre, Ghaziabad 201002, India
| | - Harsha Bajaj
- Microbial Processes and Technology Division, CSIR- National Institute for Interdisciplinary Science and Technology (NIIST), Trivandrum 695019, Kerala, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-Human Resource Development Centre, Ghaziabad 201002, India.
| |
Collapse
|
5
|
Godino E, Restrepo Sierra AM, Danelon C. Imaging Flow Cytometry for High-Throughput Phenotyping of Synthetic Cells. ACS Synth Biol 2023. [PMID: 37155828 PMCID: PMC10367129 DOI: 10.1021/acssynbio.3c00074] [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: 05/10/2023]
Abstract
The reconstitution of basic cellular functions in micrometer-sized liposomes has led to a surge of interest in the construction of synthetic cells. Microscopy and flow cytometry are powerful tools for characterizing biological processes in liposomes with fluorescence readouts. However, applying each method separately leads to a compromise between information-rich imaging by microscopy and statistical population analysis by flow cytometry. To address this shortcoming, we here introduce imaging flow cytometry (IFC) for high-throughput, microscopy-based screening of gene-expressing liposomes in laminar flow. We developed a comprehensive pipeline and analysis toolset based on a commercial IFC instrument and software. About 60 thousands of liposome events were collected per run starting from one microliter of the stock liposome solution. Robust population statistics from individual liposome images was performed based on fluorescence and morphological parameters. This allowed us to quantify complex phenotypes covering a wide range of liposomal states that are relevant for building a synthetic cell. The general applicability, current workflow limitations, and future prospects of IFC in synthetic cell research are finally discussed.
Collapse
Affiliation(s)
- Elisa Godino
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629HZ Delft, The Netherlands
| | - Ana Maria Restrepo Sierra
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629HZ Delft, The Netherlands
| | - Christophe Danelon
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629HZ Delft, The Netherlands
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 31077 Toulouse, France
| |
Collapse
|
6
|
Tapie P, Prevost AM, Montel L, Pontani LL, Wandersman E. A simple method to make, trap and deform a vesicle in a gel. Sci Rep 2023; 13:5375. [PMID: 37009808 PMCID: PMC10068607 DOI: 10.1038/s41598-023-31996-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 03/21/2023] [Indexed: 04/04/2023] Open
Abstract
We present a simple method to produce giant lipid pseudo-vesicles (vesicles with an oily cap on the top), trapped in an agarose gel. The method can be implemented using only a regular micropipette and relies on the formation of a water/oil/water double droplet in liquid agarose. We characterize the produced vesicle with fluorescence imaging and establish the presence and integrity of the lipid bilayer by the successful insertion of [Formula: see text]-Hemolysin transmembrane proteins. Finally, we show that the vesicle can be easily mechanically deformed, non-intrusively, by indenting the surface of the gel.
Collapse
Affiliation(s)
- Pierre Tapie
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 4 place Jussieu, 75005, Paris, France
| | - Alexis M Prevost
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 4 place Jussieu, 75005, Paris, France
| | - Lorraine Montel
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 4 place Jussieu, 75005, Paris, France
| | - Léa-Laetitia Pontani
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 4 place Jussieu, 75005, Paris, France.
| | - Elie Wandersman
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine (IBPS), Laboratoire Jean Perrin (LJP), 4 place Jussieu, 75005, Paris, France.
| |
Collapse
|
7
|
Godino E, Danelon C. Gene-Directed FtsZ Ring Assembly Generates Constricted Liposomes with Stable Membrane Necks. Adv Biol (Weinh) 2023; 7:e2200172. [PMID: 36593513 DOI: 10.1002/adbi.202200172] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/15/2022] [Indexed: 01/04/2023]
Abstract
Mimicking bacterial cell division in well-defined cell-free systems has the potential to elucidate the minimal set of proteins required for cytoskeletal formation, membrane constriction, and final abscission. Membrane-anchored FtsZ polymers are often regarded as a sufficient system to realize this chain of events. By using purified FtsZ and its membrane-binding protein FtsA or the gain-of-function mutant FtsA* expressed in PURE (Protein synthesis Using Reconstituted Elements) from a DNA template, it is shown in this study that cytoskeletal structures are formed, and yield constricted liposomes exhibiting various morphologies. However, the resulting buds remain attached to the parental liposome by a narrow membrane neck. No division events can be monitored even after long-time tracking by fluorescence microscopy, nor when the osmolarity of the external solution is increased. The results provide evidence that reconstituted FtsA-FtsZ proto-rings coating the membrane necks are too stable to enable abscission. The prospect of combining a DNA-encoded FtsZ system with assisting mechanisms to achieve synthetic cell division is discussed.
Collapse
Affiliation(s)
- Elisa Godino
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2629HZ, The Netherlands
| | - Christophe Danelon
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2629HZ, The Netherlands
| |
Collapse
|
8
|
van Buren L, Koenderink GH, Martinez-Torres C. DisGUVery: A Versatile Open-Source Software for High-Throughput Image Analysis of Giant Unilamellar Vesicles. ACS Synth Biol 2022; 12:120-135. [PMID: 36508359 PMCID: PMC9872171 DOI: 10.1021/acssynbio.2c00407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Giant unilamellar vesicles (GUVs) are cell-sized aqueous compartments enclosed by a phospholipid bilayer. Due to their cell-mimicking properties, GUVs have become a widespread experimental tool in synthetic biology to study membrane properties and cellular processes. In stark contrast to the experimental progress, quantitative analysis of GUV microscopy images has received much less attention. Currently, most analysis is performed either manually or with custom-made scripts, which makes analysis time-consuming and results difficult to compare across studies. To make quantitative GUV analysis accessible and fast, we present DisGUVery, an open-source, versatile software that encapsulates multiple algorithms for automated detection and analysis of GUVs in microscopy images. With a performance analysis, we demonstrate that DisGUVery's three vesicle detection modules successfully identify GUVs in images obtained with a wide range of imaging sources, in various typical GUV experiments. Multiple predefined analysis modules allow the user to extract properties such as membrane fluorescence, vesicle shape, and internal fluorescence from large populations. A new membrane segmentation algorithm facilitates spatial fluorescence analysis of nonspherical vesicles. Altogether, DisGUVery provides an accessible tool to enable high-throughput automated analysis of GUVs, and thereby to promote quantitative data analysis in synthetic cell research.
Collapse
Affiliation(s)
- Lennard van Buren
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZDelft, The Netherlands
| | - Gijsje Hendrika Koenderink
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZDelft, The Netherlands,
| | - Cristina Martinez-Torres
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZDelft, The Netherlands,
| |
Collapse
|
9
|
Han F, Xu B, Lu N, Caliari A, Lu H, Xia Y, Su'etsugu M, Xu J, Yomo T. Optimization and compartmentalization of a cell-free mixture of DNA amplification and protein translation. Appl Microbiol Biotechnol 2022; 106:8139-8149. [PMID: 36355086 DOI: 10.1007/s00253-022-12278-2] [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: 08/08/2022] [Revised: 10/30/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022]
Abstract
Recent studies have shown that the reconstituted cell-free DNA replisome and in vitro transcription and translation systems from Escherichia coli are highly important in applied and synthetic biology. To date, no attempt has been made to combine those two systems. Here, we study the performance of the mixed two separately exploited systems commercially available as RCR and PURE systems. Regarding the genetic information flow from DNA to proteins, mixtures with various ratios of RCR/PURE gave low protein expression, possibly due to the well-known conflict between replication and transcription or inappropriate buffer conditions. To further increase the compatibility of the two systems, rationally designed reaction buffers with a lower concentration of nucleoside triphosphates in 50 mM HEPES (pH7.6) were evaluated, showing increased performance from RCR/PURE (85%/15%) in a time-dependent manner. The compatibility was also validated in compartmentalized cell-sized droplets encapsulating the same RCR/PURE soup. Our findings can help to better fine-tune the reaction conditions of RCR-PURE systems and provide new avenues for rewiring the central dogma of molecular biology as self-sustaining systems in synthetic cell models. KEY POINTS: • Commercial reconstituted DNA amplification (RCR) and transcription and translation (PURE) systems hamper each other upon mixing. • A newly optimized buffer with a low bias for PURE was formulated in the RCR-PURE mixture. • The performance and dynamics of RCR-PURE were investigated in either bulk or compartmentalized droplets.
Collapse
Affiliation(s)
- Fuhai Han
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai, 200062, People's Republic of China
| | - Boying Xu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai, 200062, People's Republic of China.,Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Nan Lu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai, 200062, People's Republic of China
| | - Adriano Caliari
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai, 200062, People's Republic of China
| | - Hui Lu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai, 200062, People's Republic of China
| | - Yang Xia
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai, 200062, People's Republic of China
| | - Masayuki Su'etsugu
- Department of Life Science, College of Science, Rikkyo University, Tokyo, 171-8501, Japan
| | - Jian Xu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai, 200062, People's Republic of China.
| | - Tetsuya Yomo
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai, 200062, People's Republic of China.
| |
Collapse
|
10
|
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.
Collapse
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.
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Kattan J, Doerr A, Dogterom M, Danelon C. Shaping Liposomes by Cell-Free Expressed Bacterial Microtubules. ACS Synth Biol 2021; 10:2447-2455. [PMID: 34585918 PMCID: PMC8524656 DOI: 10.1021/acssynbio.1c00278] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Genetic control over
a cytoskeletal network inside lipid vesicles
offers a potential route to controlled shape changes and DNA segregation
in synthetic cell biology. Bacterial microtubules (bMTs) are protein
filaments found in bacteria of the genus Prosthecobacter. They are formed by the tubulins BtubA and BtubB, which polymerize
in the presence of GTP. Here, we show that the tubulins BtubA/B can
be functionally expressed from DNA templates in a reconstituted transcription-translation
system, thus providing a cytosol-like environment to study their biochemical
and biophysical properties. We found that bMTs spontaneously interact
with lipid membranes and display treadmilling. When compartmentalized
inside liposomes, de novo synthesized BtubA/B tubulins
self-organize into cytoskeletal structures of different morphologies.
Moreover, bMTs can exert a pushing force on the membrane and deform
liposomes, a phenomenon that can be reversed by a light-activated
disassembly of the filaments. Our work establishes bMTs as a new building
block in synthetic biology. In the context of creating a synthetic
cell, bMTs could help shape the lipid compartment, establish polarity
or directional transport, and assist the division machinery.
Collapse
Affiliation(s)
- Johannes Kattan
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Anne Doerr
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Marileen Dogterom
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Christophe Danelon
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, 2629 HZ Delft, The Netherlands
| |
Collapse
|
13
|
Van de Cauter L, Fanalista F, van Buren L, De Franceschi N, Godino E, Bouw S, Danelon C, Dekker C, Koenderink GH, Ganzinger KA. Optimized cDICE for Efficient Reconstitution of Biological Systems in Giant Unilamellar Vesicles. ACS Synth Biol 2021. [PMID: 34185516 DOI: 10.1101/2021.02.24.432456] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
Giant unilamellar vesicles (GUVs) are often used to mimic biological membranes in reconstitution experiments. They are also widely used in research on synthetic cells, as they provide a mechanically responsive reaction compartment that allows for controlled exchange of reactants with the environment. However, while many methods exist to encapsulate functional biomolecules in GUVs, there is no one-size-fits-all solution and reliable GUV fabrication still remains a major experimental hurdle in the field. Here, we show that defect-free GUVs containing complex biochemical systems can be generated by optimizing a double-emulsion method for GUV formation called continuous droplet interface crossing encapsulation (cDICE). By tightly controlling environmental conditions and tuning the lipid-in-oil dispersion, we show that it is possible to significantly improve the reproducibility of high-quality GUV formation as well as the encapsulation efficiency. We demonstrate efficient encapsulation for a range of biological systems including a minimal actin cytoskeleton, membrane-anchored DNA nanostructures, and a functional PURE (protein synthesis using recombinant elements) system. Our optimized cDICE method displays promising potential to become a standard method in biophysics and bottom-up synthetic biology.
Collapse
Affiliation(s)
| | - Federico Fanalista
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Lennard van Buren
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Nicola De Franceschi
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Elisa Godino
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Sharon Bouw
- Department of Living Matter, AMOLF, 1098 XG Amsterdam, The Netherlands
| | - Christophe Danelon
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Gijsje H Koenderink
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | | |
Collapse
|
14
|
Van de Cauter L, Fanalista F, van Buren L, De Franceschi N, Godino E, Bouw S, Danelon C, Dekker C, Koenderink GH, Ganzinger KA. Optimized cDICE for Efficient Reconstitution of Biological Systems in Giant Unilamellar Vesicles. ACS Synth Biol 2021; 10:1690-1702. [PMID: 34185516 PMCID: PMC8291763 DOI: 10.1021/acssynbio.1c00068] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Indexed: 12/17/2022]
Abstract
Giant unilamellar vesicles (GUVs) are often used to mimic biological membranes in reconstitution experiments. They are also widely used in research on synthetic cells, as they provide a mechanically responsive reaction compartment that allows for controlled exchange of reactants with the environment. However, while many methods exist to encapsulate functional biomolecules in GUVs, there is no one-size-fits-all solution and reliable GUV fabrication still remains a major experimental hurdle in the field. Here, we show that defect-free GUVs containing complex biochemical systems can be generated by optimizing a double-emulsion method for GUV formation called continuous droplet interface crossing encapsulation (cDICE). By tightly controlling environmental conditions and tuning the lipid-in-oil dispersion, we show that it is possible to significantly improve the reproducibility of high-quality GUV formation as well as the encapsulation efficiency. We demonstrate efficient encapsulation for a range of biological systems including a minimal actin cytoskeleton, membrane-anchored DNA nanostructures, and a functional PURE (protein synthesis using recombinant elements) system. Our optimized cDICE method displays promising potential to become a standard method in biophysics and bottom-up synthetic biology.
Collapse
Affiliation(s)
| | - Federico Fanalista
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Lennard van Buren
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Nicola De Franceschi
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Elisa Godino
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Sharon Bouw
- Department
of Living Matter, AMOLF, 1098 XG Amsterdam, The Netherlands
| | - Christophe Danelon
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Cees Dekker
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Gijsje H. Koenderink
- Department
of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | | |
Collapse
|
15
|
Cell-free biogenesis of bacterial division proto-rings that can constrict liposomes. Commun Biol 2020; 3:539. [PMID: 32999429 PMCID: PMC7527988 DOI: 10.1038/s42003-020-01258-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 09/01/2020] [Indexed: 01/01/2023] Open
Abstract
A major challenge towards the realization of an autonomous synthetic cell resides in the encoding of a division machinery in a genetic programme. In the bacterial cell cycle, the assembly of cytoskeletal proteins into a ring defines the division site. At the onset of the formation of the Escherichia coli divisome, a proto-ring consisting of FtsZ and its membrane-recruiting proteins takes place. Here, we show that FtsA-FtsZ ring-like structures driven by cell-free gene expression can be reconstituted on planar membranes and inside liposome compartments. Such cytoskeletal structures are found to constrict the liposome, generating elongated membrane necks and budding vesicles. Additional expression of the FtsZ cross-linker protein ZapA yields more rigid FtsZ bundles that attach to the membrane but fail to produce budding spots or necks in liposomes. These results demonstrate that gene-directed protein synthesis and assembly of membrane-constricting FtsZ-rings can be combined in a liposome-based artificial cell. Godino et al. show that FtsA-FtsZ ring-like structures driven by cell-free gene expression can be reconstituted on planar membranes and inside liposome compartments. These cytoskeletal structures constrict the liposome, generating elongated membrane necks and budding vesicles. This study represents a step forward to realizing genetic programming of synthetic cell division.
Collapse
|
16
|
Blanken D, Foschepoth D, Serrão AC, Danelon C. Genetically controlled membrane synthesis in liposomes. Nat Commun 2020; 11:4317. [PMID: 32859896 PMCID: PMC7455746 DOI: 10.1038/s41467-020-17863-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 07/19/2020] [Indexed: 12/21/2022] Open
Abstract
Lipid membranes, nucleic acids, proteins, and metabolism are essential for modern cellular life. Synthetic systems emulating the fundamental properties of living cells must therefore be built upon these functional elements. In this work, phospholipid-producing enzymes encoded in a synthetic minigenome are cell-free expressed within liposome compartments. The de novo synthesized metabolic pathway converts precursors into a variety of lipids, including the constituents of the parental liposome. Balanced production of phosphatidylethanolamine and phosphatidylglycerol is realized, owing to transcriptional regulation of the activity of specific genes combined with a metabolic feedback mechanism. Fluorescence-based methods are developed to image the synthesis and membrane incorporation of phosphatidylserine at the single liposome level. Our results provide experimental evidence for DNA-programmed membrane synthesis in a minimal cell model. Strategies are discussed to alleviate current limitations toward effective liposome growth and self-reproduction.
Collapse
Affiliation(s)
- Duco Blanken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - David Foschepoth
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Adriana Calaça Serrão
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Christophe Danelon
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
| |
Collapse
|
17
|
Isozaki A, Mikami H, Tezuka H, Matsumura H, Huang K, Akamine M, Hiramatsu K, Iino T, Ito T, Karakawa H, Kasai Y, Li Y, Nakagawa Y, Ohnuki S, Ota T, Qian Y, Sakuma S, Sekiya T, Shirasaki Y, Suzuki N, Tayyabi E, Wakamiya T, Xu M, Yamagishi M, Yan H, Yu Q, Yan S, Yuan D, Zhang W, Zhao Y, Arai F, Campbell RE, Danelon C, Di Carlo D, Hiraki K, Hoshino Y, Hosokawa Y, Inaba M, Nakagawa A, Ohya Y, Oikawa M, Uemura S, Ozeki Y, Sugimura T, Nitta N, Goda K. Intelligent image-activated cell sorting 2.0. LAB ON A CHIP 2020; 20:2263-2273. [PMID: 32459276 DOI: 10.1039/d0lc00080a] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The advent of intelligent image-activated cell sorting (iIACS) has enabled high-throughput intelligent image-based sorting of single live cells from heterogeneous populations. iIACS is an on-chip microfluidic technology that builds on a seamless integration of a high-throughput fluorescence microscope, cell focuser, cell sorter, and deep neural network on a hybrid software-hardware data management architecture, thereby providing the combined merits of optical microscopy, fluorescence-activated cell sorting (FACS), and deep learning. Here we report an iIACS machine that far surpasses the state-of-the-art iIACS machine in system performance in order to expand the range of applications and discoveries enabled by the technology. Specifically, it provides a high throughput of ∼2000 events per second and a high sensitivity of ∼50 molecules of equivalent soluble fluorophores (MESFs), both of which are 20 times superior to those achieved in previous reports. This is made possible by employing (i) an image-sensor-based optomechanical flow imaging method known as virtual-freezing fluorescence imaging and (ii) a real-time intelligent image processor on an 8-PC server equipped with 8 multi-core CPUs and GPUs for intelligent decision-making, in order to significantly boost the imaging performance and computational power of the iIACS machine. We characterize the iIACS machine with fluorescent particles and various cell types and show that the performance of the iIACS machine is close to its achievable design specification. Equipped with the improved capabilities, this new generation of the iIACS technology holds promise for diverse applications in immunology, microbiology, stem cell biology, cancer biology, pathology, and synthetic biology.
Collapse
Affiliation(s)
- Akihiro Isozaki
- Department of Chemistry, The University of Tokyo, Tokyo 113-0033, Japan.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Buddingh' BC, Elzinga J, van Hest JCM. Intercellular communication between artificial cells by allosteric amplification of a molecular signal. Nat Commun 2020; 11:1652. [PMID: 32246068 PMCID: PMC7125153 DOI: 10.1038/s41467-020-15482-8] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 03/13/2020] [Indexed: 11/13/2022] Open
Abstract
Multicellular organisms rely on intercellular communication to coordinate the behaviour of individual cells, which enables their differentiation and hierarchical organization. Various cell mimics have been developed to establish fundamental engineering principles for the construction of artificial cells displaying cell-like organization, behaviour and complexity. However, collective phenomena, although of great importance for a better understanding of life-like behaviour, are underexplored. Here, we construct collectives of giant vesicles that can communicate with each other through diffusing chemical signals that are recognized and processed by synthetic enzymatic cascades. Similar to biological cells, the Receiver vesicles can transduce a weak signal originating from Sender vesicles into a strong response by virtue of a signal amplification step, which facilitates the propagation of signals over long distances within the artificial cell consortia. This design advances the development of interconnected artificial cells that can exchange metabolic and positional information to coordinate their higher-order organization.
Collapse
Affiliation(s)
- Bastiaan C Buddingh'
- Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, the Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, the Netherlands
| | - Janneke Elzinga
- Radboud University, PO Box 9102, 6500 HC, Nijmegen, the Netherlands
| | - Jan C M van Hest
- Department of Chemical Engineering and Chemistry, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, the Netherlands.
- Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, the Netherlands.
- Department of Biomedical Engineering, Eindhoven University of Technology, PO Box 513, 5600 MB, Eindhoven, the Netherlands.
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
De novo synthesized Min proteins drive oscillatory liposome deformation and regulate FtsA-FtsZ cytoskeletal patterns. Nat Commun 2019; 10:4969. [PMID: 31672986 PMCID: PMC6823393 DOI: 10.1038/s41467-019-12932-w] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 10/10/2019] [Indexed: 12/11/2022] Open
Abstract
The Min biochemical network regulates bacterial cell division and is a prototypical example of self-organizing molecular systems. Cell-free assays relying on purified proteins have shown that MinE and MinD self-organize into surface waves and oscillatory patterns. In the context of developing a synthetic cell from elementary biological modules, harnessing Min oscillations might allow us to implement higher-order cellular functions. To convey hereditary information, the Min system must be encoded in a DNA molecule that can be copied, transcribed, and translated. Here, the MinD and MinE proteins are synthesized de novo from their genes inside liposomes. Dynamic protein patterns and accompanying liposome shape deformation are observed. When integrated with the cytoskeletal proteins FtsA and FtsZ, the synthetic Min system is able to dynamically regulate FtsZ patterns. By enabling genetic control over Min protein self-organization and membrane remodeling, our methodology offers unique opportunities towards directed evolution of bacterial division processes in vitro. The Min biochemical network regulates bacterial cell division and is a prototypical example of self-organizing molecular systems. Here authors synthesize Min proteins from their genes inside liposomes and observe dynamic protein patterns and liposome shape deformation.
Collapse
|
21
|
Affiliation(s)
- Allen P Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, United States of America. Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, United States of America. Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, United States of America. Biophysics Program, University of Michigan, Ann Arbor, MI, United States of America
| |
Collapse
|