1
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Tror S, Jeon S, Nguyen HT, Huh E, Shin K. A Self-Regenerating Artificial Cell, that is One Step Closer to Living Cells: Challenges and Perspectives. SMALL METHODS 2023; 7:e2300182. [PMID: 37246263 DOI: 10.1002/smtd.202300182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 04/29/2023] [Indexed: 05/30/2023]
Abstract
Controllable, self-regenerating artificial cells (SRACs) can be a vital advancement in the field of synthetic biology, which seeks to create living cells by recombining various biological molecules in the lab. This represents, more importantly, the first step on a long journey toward creating reproductive cells from rather fragmentary biochemical mimics. However, it is still a difficult task to replicate the complex processes involved in cell regeneration, such as genetic material replication and cell membrane division, in artificially created spaces. This review highlights recent advances in the field of controllable, SRACs and the strategies to achieve the goal of creating such cells. Self-regenerating cells start by replicating DNA and transferring it to a location where proteins can be synthesized. Functional but essential proteins must be synthesized for sustained energy generation and survival needs and function in the same liposomal space. Finally, self-division and repeated cycling lead to autonomous, self-regenerating cells. The pursuit of controllable, SRACs will enable authors to make bold advances in understanding life at the cellular level, ultimately providing an opportunity to use this knowledge to understand the nature of life.
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Affiliation(s)
- Seangly Tror
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Republic of Korea
| | - SeonMin Jeon
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Republic of Korea
| | - Huong Thanh Nguyen
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Republic of Korea
| | - Eunjin Huh
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Republic of Korea
| | - Kwanwoo Shin
- Department of Chemistry and Institute of Biological Interfaces, Sogang University, Seoul, 04107, Republic of Korea
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2
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Kumar S, Karmacharya M, Cho YK. Bridging the Gap between Nonliving Matter and Cellular Life. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2202962. [PMID: 35988151 DOI: 10.1002/smll.202202962] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/28/2022] [Indexed: 06/15/2023]
Abstract
A cell, the fundamental unit of life, contains the requisite blueprint information necessary to survive and to build tissues, organs, and systems, eventually forming a fully functional living creature. A slight structural alteration can result in data misprinting, throwing the entire life process off balance. Advances in synthetic biology and cell engineering enable the predictable redesign of biological systems to perform novel functions. Individual functions and fundamental processes at the core of the biology of cells can be investigated by employing a synthetically constrained micro or nanoreactor. However, constructing a life-like structure from nonliving building blocks remains a considerable challenge. Chemical compartments, cascade signaling, energy generation, growth, replication, and adaptation within micro or nanoreactors must be comparable with their biological counterparts. Although these reactors currently lack the power and behavioral sophistication of their biological equivalents, their interface with biological systems enables the development of hybrid solutions for real-world applications, such as therapeutic agents, biosensors, innovative materials, and biochemical microreactors. This review discusses the latest advances in cell membrane-engineered micro or nanoreactors, as well as the limitations associated with high-throughput preparation methods and biological applications for the real-time modulation of complex pathological states.
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Affiliation(s)
- Sumit Kumar
- Center for Soft and Living Matter, Institute for Basic Science (IBS), UNIST-gil 50, Ulsan, 44919, Republic of Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan, 44919, Republic of Korea
| | - Mamata Karmacharya
- Center for Soft and Living Matter, Institute for Basic Science (IBS), UNIST-gil 50, Ulsan, 44919, Republic of Korea
- Department of Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan, 44919, Republic of Korea
| | - Yoon-Kyoung Cho
- Center for Soft and Living Matter, Institute for Basic Science (IBS), UNIST-gil 50, Ulsan, 44919, Republic of Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan, 44919, Republic of Korea
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3
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Yue K, Li Y, Cao M, Shen L, Gu J, Kai L. Bottom-Up Synthetic Biology Using Cell-Free Protein Synthesis. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 185:1-20. [PMID: 37526707 DOI: 10.1007/10_2023_232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Technical advances in biotechnology have greatly accelerated the development of bottom-up synthetic biology. Unlike top-down approaches, bottom-up synthetic biology focuses on the construction of a minimal cell from scratch and the application of these principles to solve challenges. Cell-free protein synthesis (CFPS) systems provide minimal machinery for transcription and translation, from either a fractionated cell lysate or individual purified protein elements, thus speeding up the development of synthetic cell projects. In this review, we trace the history of the cell-free technique back to the first in vitro fermentation experiment using yeast cell lysate. Furthermore, we summarized progresses of individual cell mimicry modules, such as compartmentalization, gene expression regulation, energy regeneration and metabolism, growth and division, communication, and motility. Finally, current challenges and future perspectives on the field are outlined.
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Affiliation(s)
- Ke Yue
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Yingqiu Li
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Mengjiao Cao
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Lulu Shen
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Jingsheng Gu
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China
| | - Lei Kai
- School of Life Sciences, Jiangsu Normal University, Xuzhou, China.
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4
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Wu H, Zheng B. Hydrogel-Based Multi-enzymatic System for Biosynthesis. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 186:51-76. [PMID: 37306702 DOI: 10.1007/10_2023_220] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Biosynthesis involving multi-enzymatic reactions is usually an efficient and economic method to produce plentiful important molecules. To increase the product yield in biosynthesis, the involved enzymes can be immobilized to carriers for enhancing enzyme stability, increasing synthesis efficiency and improving enzyme recyclability. Hydrogels with three-dimensional porous structures and versatile functional groups are promising carriers for enzyme immobilization. Herein, we review the recent advances of the hydrogel-based multi-enzymatic system for biosynthesis. First, we introduce the strategies of enzyme immobilization in hydrogel, including the pros and cons of the strategies. Then we overview the recent applications of the multi-enzymatic system for biosynthesis, including cell-free protein synthesis (CFPS) and non-protein synthesis, especially high value-added molecules. In the last section, we discuss the future perspective of the hydrogel-based multi-enzymatic system for biosynthesis.
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Affiliation(s)
- Han Wu
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Bo Zheng
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China.
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5
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Sánchez-Costa M, López-Gallego F. Solid-Phase Cell-Free Protein Synthesis and Its Applications in Biotechnology. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 185:21-46. [PMID: 37306703 DOI: 10.1007/10_2023_226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Cell-free systems for the in vitro production of proteins have revolutionized the synthetic biology field. In the last decade, this technology is gaining momentum in molecular biology, biotechnology, biomedicine and even education. Materials science has burst into the field of in vitro protein synthesis to empower the value of existing tools and expand its applications. In this sense, the combination of solid materials (normally functionalized with different biomacromolecules) together with cell-free components has made this technology more versatile and robust. In this chapter, we discuss the combination of solid materials with DNA and transcription-translation machinery to synthesize proteins within compartments, to immobilize and purify in situ the nascent protein, to transcribe and transduce DNAs immobilized on solid surfaces, and the combination of all or some of these strategies.
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Affiliation(s)
- Mercedes Sánchez-Costa
- Heterogeneous Biocatalysis Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain
| | - Fernando López-Gallego
- Heterogeneous Biocatalysis Laboratory, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain.
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6
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Gonzales DT, Suraritdechachai S, Tang TYD. Compartmentalized Cell-Free Expression Systems for Building Synthetic Cells. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 186:77-101. [PMID: 37306700 DOI: 10.1007/10_2023_221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
One of the grand challenges in bottom-up synthetic biology is the design and construction of synthetic cellular systems. One strategy toward this goal is the systematic reconstitution of biological processes using purified or non-living molecular components to recreate specific cellular functions such as metabolism, intercellular communication, signal transduction, and growth and division. Cell-free expression systems (CFES) are in vitro reconstitutions of the transcription and translation machinery found in cells and are a key technology for bottom-up synthetic biology. The open and simplified reaction environment of CFES has helped researchers discover fundamental concepts in the molecular biology of the cell. In recent decades, there has been a drive to encapsulate CFES reactions into cell-like compartments with the aim of building synthetic cells and multicellular systems. In this chapter, we discuss recent progress in compartmentalizing CFES to build simple and minimal models of biological processes that can help provide a better understanding of the process of self-assembly in molecularly complex systems.
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Affiliation(s)
- David T Gonzales
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Center for Systems Biology Dresden, Dresden, Germany
| | | | - T -Y Dora Tang
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
- Center for Systems Biology Dresden, Dresden, Germany.
- Physics of Life, Cluster of Excellence, TU Dresden, Dresden, Germany.
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7
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Fryer T, Rogers JD, Mellor C, Kohler TN, Minter R, Hollfelder F. Gigavalent Display of Proteins on Monodisperse Polyacrylamide Hydrogels as a Versatile Modular Platform for Functional Assays and Protein Engineering. ACS CENTRAL SCIENCE 2022; 8:1182-1195. [PMID: 36032770 PMCID: PMC9413441 DOI: 10.1021/acscentsci.2c00576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Indexed: 06/15/2023]
Abstract
The assembly of robust, modular biological components into complex functional systems is central to synthetic biology. Here, we apply modular "plug and play" design principles to a solid-phase protein display system that facilitates protein purification and functional assays. Specifically, we capture proteins on polyacrylamide hydrogel display beads (PHD beads) made in microfluidic droplet generators. These monodisperse PHD beads are decorated with predefined amounts of anchors, methacrylate-PEG-benzylguanine (BG) and methacrylate-PEG-chloroalkane (CA), that react covalently with SNAP-/Halo-tag fusion proteins, respectively, in a specific, orthogonal, and stable fashion. Anchors, and thus proteins, are distributed throughout the entire bead volume, allowing attachment of ∼109 protein molecules per bead (⌀ 20 μm) -a higher density than achievable with commercial surface-modified beads. We showcase a diverse array of protein modules that enable the secondary capture of proteins, either noncovalently (IgG and SUMO-tag) or covalently (SpyCatcher, SpyTag, SnpCatcher, and SnpTag), in mono- and multivalent display formats. Solid-phase protein binding and enzymatic assays are carried out, and incorporating the photocleavable protein PhoCl enables the controlled release of modules via visible-light irradiation for functional assays in solution. We utilize photocleavage for valency engineering of an anti-TRAIL-R1 scFv, enhancing its apoptosis-inducing potency ∼50-fold through pentamerization.
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Affiliation(s)
- Thomas Fryer
- Department
of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
- Antibody
Discovery and Protein Engineering, R&D, AstraZeneca, Milstein
Building, Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Joel David Rogers
- Department
of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
- Antibody
Discovery and Protein Engineering, R&D, AstraZeneca, Milstein
Building, Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Christopher Mellor
- Department
of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Timo N. Kohler
- Department
of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Ralph Minter
- Antibody
Discovery and Protein Engineering, R&D, AstraZeneca, Milstein
Building, Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Florian Hollfelder
- Department
of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
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8
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Abstract
Recent years have seen substantial efforts aimed at constructing artificial cells from various molecular components with the aim of mimicking the processes, behaviours and architectures found in biological systems. Artificial cell development ultimately aims to produce model constructs that progress our understanding of biology, as well as forming the basis for functional bio-inspired devices that can be used in fields such as therapeutic delivery, biosensing, cell therapy and bioremediation. Typically, artificial cells rely on a bilayer membrane chassis and have fluid aqueous interiors to mimic biological cells. However, a desire to more accurately replicate the gel-like properties of intracellular and extracellular biological environments has driven increasing efforts to build cell mimics based on hydrogels. This has enabled researchers to exploit some of the unique functional properties of hydrogels that have seen them deployed in fields such as tissue engineering, biomaterials and drug delivery. In this Review, we explore how hydrogels can be leveraged in the context of artificial cell development. We also discuss how hydrogels can potentially be incorporated within the next generation of artificial cells to engineer improved biological mimics and functional microsystems.
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9
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Wang T, Lu Y. Advances, Challenges and Future Trends of Cell-Free Transcription-Translation Biosensors. BIOSENSORS 2022; 12:bios12050318. [PMID: 35624619 PMCID: PMC9138237 DOI: 10.3390/bios12050318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/07/2022] [Accepted: 05/08/2022] [Indexed: 11/16/2022]
Abstract
In recent years, the application of cell-free protein synthesis systems in biosensing has been developing rapidly. Cell-free synthetic biology, with its advantages of high biosafety, fast material transport, and high sensitivity, has overcome many defects of cell-based biosensors and provided an abiotic substitute for biosensors. In addition, the application of freeze-drying technology has improved the stability of such systems, making it possible to realize point-of-care application of field detection and broadening the application prospects of cell-free biosensors. However, despite these advancements, challenges such as the risk of sample interference due to the lack of physical barriers, maintenance of activity during storage, and poor robustness still need to be addressed before the full potential of cell-free biosensors can be realized on a larger scale. In this review, current strategies and research results for improving the performance of cell-free biosensors are summarized, including a comprehensive discussion of the existing challenges, future trends, and potential investments needed for improvement.
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10
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Wang C, Yang J, Lu Y. Modularize and Unite: Toward Creating a Functional Artificial Cell. Front Mol Biosci 2021; 8:781986. [PMID: 34912849 PMCID: PMC8667554 DOI: 10.3389/fmolb.2021.781986] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/17/2021] [Indexed: 11/17/2022] Open
Abstract
An artificial cell is a simplified model of a living system, bringing breakthroughs into both basic life science and applied research. The bottom-up strategy instructs the construction of an artificial cell from nonliving materials, which could be complicated and interdisciplinary considering the inherent complexity of living cells. Although significant progress has been achieved in the past 2 decades, the area is still facing some problems, such as poor compatibility with complex bio-systems, instability, and low standardization of the construction method. In this review, we propose creating artificial cells through the integration of different functional modules. Furthermore, we divide the function requirements of an artificial cell into four essential parts (metabolism, energy supplement, proliferation, and communication) and discuss the present researches. Then we propose that the compartment and the reestablishment of the communication system would be essential for the reasonable integration of functional modules. Although enormous challenges remain, the modular construction would facilitate the simplification and standardization of an artificial cell toward a natural living system. This function-based strategy would also broaden the application of artificial cells and represent the steps of imitating and surpassing nature.
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Affiliation(s)
- Chen Wang
- Key Laboratory of Industrial Biocatalysis, Department of Chemical Engineering, Ministry of Education, Tsinghua University, Beijing, China
| | - Junzhu Yang
- Key Laboratory of Industrial Biocatalysis, Department of Chemical Engineering, Ministry of Education, Tsinghua University, Beijing, China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Department of Chemical Engineering, Ministry of Education, Tsinghua University, Beijing, China
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11
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Zhao L, Li L, Yang G, Wei B, Ma Y, Qu F. Aptamer functionalized DNA hydrogels: Design, applications and kinetics. Biosens Bioelectron 2021; 194:113597. [PMID: 34534951 DOI: 10.1016/j.bios.2021.113597] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/16/2021] [Accepted: 08/26/2021] [Indexed: 01/07/2023]
Abstract
DNA hydrogels have received considerable attention in various promising applications due to their excellent biocompatibility, controlled biodegradability, adjustable mechanical properties, stability against proteases, self-healing ability, and stimuli responsiveness. To obtain the specific molecular recognition capability, aptamers and many other functional motifs are utilized. Aptamers are short single-stranded DNA or RNA selected through SELEX to bind with specific target with high affinity and specificity. With advantages of broad range of targets, good stability, easy modification, and low cost, aptamer functionalized DNA hydrogels become popular in a wide range of promising applications. In this review, the recent progress on aptamer functionalized DNA hydrogels including general design principles, applications and kinetics has been summarized. Finally, the current challenges and prospects are discussed.
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Affiliation(s)
- Liping Zhao
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Linsen Li
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Ge Yang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Bo Wei
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Yao Ma
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Feng Qu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China.
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12
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Qian X, Westensee IN, Fernandes CC, Städler B. Enzyme Mimic Facilitated Artificial Cell to Mammalian Cell Signal Transfer. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Xiaomin Qian
- Interdisciplinary Nanoscience Center (iNANO) Aarhus University Gustav Wieds Vej 14 8000 Aarhus Denmark
| | - Isabella Nymann Westensee
- Interdisciplinary Nanoscience Center (iNANO) Aarhus University Gustav Wieds Vej 14 8000 Aarhus Denmark
| | | | - Brigitte Städler
- Interdisciplinary Nanoscience Center (iNANO) Aarhus University Gustav Wieds Vej 14 8000 Aarhus Denmark
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13
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Qian X, Westensee IN, Fernandes CC, Städler B. Enzyme Mimic Facilitated Artificial Cell to Mammalian Cell Signal Transfer. Angew Chem Int Ed Engl 2021; 60:18704-18711. [PMID: 34096152 DOI: 10.1002/anie.202104904] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/25/2021] [Indexed: 11/10/2022]
Abstract
Catalyzing biochemical reactions with enzymes and communicating with neighboring cells via chemical signaling are two fundamental cellular features that play a critical role in maintaining the homeostasis of organisms. Herein, we present an artificial enzyme (AE) facilitated signal transfer between artificial cells (ACs) and mammalian HepG2 cells. We synthesize metalloporphyrins (MPs) based AEs that mimic cytochrome P450 enzymes (CYPs) to catalyze a dealkylation and a hydroxylation reaction, exemplified by the conversion of resorufin ethyl ether (REE) to resorufin and coumarin (COU) to 7-hydroxycoumarin (7-HC), respectively. The AEs are immobilized in hydrogels to produce ACs that generate the two diffusive fluorophores, which can diffuse into HepG2 cells and result in dual intracellular emissions. This work highlights the use of AEs to promote AC to mammalian signal transfer, which opens up new opportunities for integrating the synthetic and living world with a bottom-up strategy.
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Affiliation(s)
- Xiaomin Qian
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus, Denmark
| | - Isabella Nymann Westensee
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus, Denmark
| | | | - Brigitte Städler
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus, Denmark
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14
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Abstract
A novel cell free protein synthesis (CFPS) system utilizing layer-by-layer (LbL) polymer assembly was developed to reduce the operational cost of conventional CFPS. This yielded an encapsulated cell system, dubbed "eCells", that successfully performs in vitro CFPS and allows cost-effective incorporation of noncanonical amino acids into proteins. The use of eCells in CFPS circumvents the need for traditional cell lysate preparation and purification of amino acyl-tRNA synthetases (aaRS) while still retaining the small scale of an in vitro reaction. eCells were found to be 55% as productive as standard dialysis CFPS at 13% of the cost. The reaction was shown to be scalable over a large range of reaction volumes, and the crowding environment in eCells confers a stabilizing effect on marginally stable proteins, such as the pyrrolysl tRNA synthetase (PylRS), providing a means for their application in in vitro protein expression. Photocaged-cysteine (PCC) and Nε-(tert-butoxycarbonyl)-l-lysine (Boc-lysine) were incorporated into Peptidyl-prolyl cis-trans isomerase B (PpiB) using small amounts of ncAA with an adequate yield of protein. Fluorescent activated cell sorting (FACS) was used to demonstrate the partition of the lysate within the eCells in contrast to standard one pot cell lysate-based methods.
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Affiliation(s)
- Damian Van Raad
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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15
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Chen X, Lu Y. In silico Design of Linear DNA for Robust Cell-Free Gene Expression. Front Bioeng Biotechnol 2021; 9:670341. [PMID: 34095101 PMCID: PMC8169995 DOI: 10.3389/fbioe.2021.670341] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 04/06/2021] [Indexed: 12/25/2022] Open
Abstract
Cell-free gene expression systems with linear DNA expression templates (LDETs) have been widely applied in artificial cells, biochips, and high-throughput screening. However, due to the degradation caused by native nucleases in cell extracts, the transcription with linear DNA templates is weak, thereby resulting in low protein expression level, which greatly limits the development of cell-free systems using linear DNA templates. In this study, the protective sequences for stabilizing linear DNA and the transcribed mRNAs were rationally designed according to nucleases' action mechanism, whose effectiveness was evaluated through computer simulation and cell-free gene expression. The cell-free experiment results indicated that, with the combined protection of designed sequence and GamS protein, the protein expression of LDET-based cell-free systems could reach the same level as plasmid-based cell-free systems. This study would potentially promote the development of the LDET-based cell-free gene expression system for broader applications.
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Affiliation(s)
- Xinjie Chen
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
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16
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Ouyang X, Zhou X, Lai SN, Liu Q, Zheng B. Immobilization of Proteins of Cell Extract to Hydrogel Networks Enhances the Longevity of Cell-Free Protein Synthesis and Supports Gene Networks. ACS Synth Biol 2021; 10:749-755. [PMID: 33784075 DOI: 10.1021/acssynbio.0c00541] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Herein, we constructed a new type of hydrogel based artificial cells supporting long-lived protein synthesis, post-translational modification, and gene networks. We constructed the artificial cells by immobilizing the transcription and translation system from E. coli cytoplasmic extract onto the polyacrylamide hydrogel. With the continuous supply of energy and nutrition, the artificial cells were capable of stable protein expression for at least 30 days. Functional proteins which were difficult to produce in vivo, including colicin E1 and urokinase, were synthesized in the artificial cells with high bioactivity. Furthermore, we constructed a sigma factor based genetic oscillator in the artificial cells. The artificial cells not only provide a powerful platform for continuous protein synthesis and convenient design and testing of genetic networks, but also hold great promise for the development of metabolic engineering, drug delivery, and biosensors.
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Affiliation(s)
- Xiaofei Ouyang
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Xiaoyu Zhou
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Sze Nga Lai
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Qi Liu
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Bo Zheng
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong
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17
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Elani Y. Interfacing Living and Synthetic Cells as an Emerging Frontier in Synthetic Biology. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 133:5662-5671. [PMID: 38505493 PMCID: PMC10946473 DOI: 10.1002/ange.202006941] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Indexed: 12/15/2022]
Abstract
The construction of artificial cells from inanimate molecular building blocks is one of the grand challenges of our time. In addition to being used as simplified cell models to decipher the rules of life, artificial cells have the potential to be designed as micromachines deployed in a host of clinical and industrial applications. The attractions of engineering artificial cells from scratch, as opposed to re-engineering living biological cells, are varied. However, it is clear that artificial cells cannot currently match the power and behavioural sophistication of their biological counterparts. Given this, many in the synthetic biology community have started to ask: is it possible to interface biological and artificial cells together to create hybrid living/synthetic systems that leverage the advantages of both? This article will discuss the motivation behind this cellular bionics approach, in which the boundaries between living and non-living matter are blurred by bridging top-down and bottom-up synthetic biology. It details the state of play of this nascent field and introduces three generalised hybridisation modes that have emerged.
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Affiliation(s)
- Yuval Elani
- Department of Chemical EngineeringImperial College LondonExhibition RoadLondonUK
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Elani Y. Interfacing Living and Synthetic Cells as an Emerging Frontier in Synthetic Biology. Angew Chem Int Ed Engl 2021; 60:5602-5611. [PMID: 32909663 PMCID: PMC7983915 DOI: 10.1002/anie.202006941] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Indexed: 12/11/2022]
Abstract
The construction of artificial cells from inanimate molecular building blocks is one of the grand challenges of our time. In addition to being used as simplified cell models to decipher the rules of life, artificial cells have the potential to be designed as micromachines deployed in a host of clinical and industrial applications. The attractions of engineering artificial cells from scratch, as opposed to re-engineering living biological cells, are varied. However, it is clear that artificial cells cannot currently match the power and behavioural sophistication of their biological counterparts. Given this, many in the synthetic biology community have started to ask: is it possible to interface biological and artificial cells together to create hybrid living/synthetic systems that leverage the advantages of both? This article will discuss the motivation behind this cellular bionics approach, in which the boundaries between living and non-living matter are blurred by bridging top-down and bottom-up synthetic biology. It details the state of play of this nascent field and introduces three generalised hybridisation modes that have emerged.
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Affiliation(s)
- Yuval Elani
- Department of Chemical EngineeringImperial College LondonExhibition RoadLondonUK
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Pilkington CP, Seddon JM, Elani Y. Microfluidic technologies for the synthesis and manipulation of biomimetic membranous nano-assemblies. Phys Chem Chem Phys 2021; 23:3693-3706. [PMID: 33533338 DOI: 10.1039/d0cp06226j] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Microfluidics has been proposed as an attractive alternative to conventional bulk methods used in the generation of self-assembled biomimetic structures, particularly where there is a desire for more scalable production. The approach also allows for greater control over the self-assembly process, and parameters such as particle architecture, size, and composition can be finely tuned. Microfluidic techniques used in the generation of microscale assemblies (giant vesicles and higher-order multi-compartment assemblies) are fairly well established. These tend to rely on microdroplet templation, and the resulting structures have found use as comparmentalised motifs in artificial cells. Challenges in generating sub-micron droplets have meant that reconfiguring this approach to form nano-scale structures is not straightforward. This is beginning to change however, and recent technological advances have instigated the manufacture and manipulation of an increasingly diverse repertoire of biomimetic nano-assemblies, including liposomes, polymersomes, hybrid particles, multi-lamellar structures, cubosomes, hexosomes, nanodiscs, and virus-like particles. The following review will discuss these higher-order self-assembled nanostructures, including their biochemical and industrial applications, and techniques used in their production and analysis. We suggest ways in which existing technologies could be repurposed for the enhanced design, manufacture, and exploitation of these structures and discuss potential challenges and future research directions. By compiling recent advances in this area, it is hoped we will inspire future efforts toward establishing scalable microfluidic platforms for the generation of biomimetic nanoparticles of enhanced architectural and functional complexity.
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Affiliation(s)
- Colin P Pilkington
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, 82 Wood Lane, London, W12 0BZ, UK and Department of Chemical Engineering, Exhibition Road, Imperial College London, London, SW7 2AZ, UK.
| | - John M Seddon
- Department of Chemistry, Molecular Science Research Hub, Imperial College London, 82 Wood Lane, London, W12 0BZ, UK
| | - Yuval Elani
- Department of Chemical Engineering, Exhibition Road, Imperial College London, London, SW7 2AZ, UK.
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Boyd MA, Kamat NP. Designing Artificial Cells towards a New Generation of Biosensors. Trends Biotechnol 2020; 39:927-939. [PMID: 33388162 DOI: 10.1016/j.tibtech.2020.12.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/25/2020] [Accepted: 12/01/2020] [Indexed: 01/31/2023]
Abstract
The combination of biological and synthetic materials has great potential to generate new types of biosensors. Toward this goal, recent advances in artificial cell development have demonstrated the capacity to detect a variety of analytes and environmental changes by encapsulating genetically encoded sensors within bilayer membranes, expanding the contexts within which biologically based sensing can operate. This chassis not only acts as a container for cell-free sensors, but can also play an active role in artificial cell sensing by serving as an additional gate mediating the transfer of environmental information. Here, we focus on recent progress toward stimuli-responsive artificial cells and discuss strategies for membrane functionalization in order to expand cell-free biosensing capabilities and applications.
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Affiliation(s)
- Margrethe A Boyd
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Neha P Kamat
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA; Center for Synthetic Biology, Northwestern University, Evanston, IL, USA; Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, USA.
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Wang C, Geng Y, Sun Q, Xu J, Lu Y. A Sustainable and Efficient Artificial Microgel System: Toward Creating a Configurable Synthetic Cell. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2002313. [PMID: 33241606 DOI: 10.1002/smll.202002313] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 10/10/2020] [Indexed: 06/11/2023]
Abstract
Artificial cells are a powerful platform in the study of synthetic biology and other valuable fields. They share a great potential in defining and utilizing the superiority of the living system. Here, a protein synthesis system based on thermal responsive hydrogels with porous structure is reported. The hydrogels can immobilize plasmids on the surface inside their porous structure through a volume phase transition upon 34 °C, forming an aggregation state of DNAs as in nature conditions. The artificial microgels can carry out bioreactions in cell-free systems and exhibit a sustainable and efficient performance for protein translation. The protein synthesis level reaches a maximum of twice more than that in a conventional solution system when the plasmid concentration is 10-20 ng µL-1 , along with a doubled effective interval. This is perhaps attributed to confined transcription and translation processes in the near-surface area of hydrogels. Summarily, the research provides an easy-handling approach in fabricating effective microgels for cell-free synthesis and also inspirations for constructing a configurable artificial cell.
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Affiliation(s)
- Chen Wang
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Yuhao Geng
- The State Key Lab of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Qi Sun
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Jianhong Xu
- The State Key Lab of Chemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing, China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, China
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Cho E, Lu Y. Compartmentalizing Cell-Free Systems: Toward Creating Life-Like Artificial Cells and Beyond. ACS Synth Biol 2020; 9:2881-2901. [PMID: 33095011 DOI: 10.1021/acssynbio.0c00433] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Building an artificial cell is a research area that is rigorously studied in the field of synthetic biology. It has brought about much attention with the aim of ultimately constructing a natural cell-like structure. In particular, with the more mature cell-free platforms and various compartmentalization methods becoming available, achieving this aim seems not far away. In this review, we discuss the various types of artificial cells capable of hosting several cellular functions. Different compartmental boundaries and the mature and evolving technologies that are used for compartmentalization are examined, and exciting recent advances that overcome or have the potential to address current challenges are discussed. Ultimately, we show how compartmentalization and cell-free systems have, and will, come together to fulfill the goal to assemble a fully synthetic cell that displays functionality and complexity as advanced as that in nature. The development of such artificial cell systems will offer insight into the fundamental study of evolutionary biology and the sea of applications as a result. Although several challenges remain, emerging technologies such as artificial intelligence also appear to help pave the way to address them and achieve the ultimate goal.
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Affiliation(s)
- Eunhee Cho
- Key Lab of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Yuan Lu
- Key Lab of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
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Liu J, Guo Z, Li Y, Liang J, Xue J, Xu J, Whitelock JM, Xie L, Kong B, Liang K. pH‐Gated Activation of Gene Transcription and Translation in Biocatalytic Metal–Organic Framework Artificial Cells. ADVANCED NANOBIOMED RESEARCH 2020. [DOI: 10.1002/anbr.202000034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Jian Liu
- Department of Chemistry Laboratory of Advanced Materials Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials iChEM Fudan University Shanghai 200433 China
- School of Chemical Engineering and Australian Centre for NanoMedicine University of New South Wales Sydney NSW 2052 Australia
| | - Ziyi Guo
- School of Chemical Engineering and Australian Centre for NanoMedicine University of New South Wales Sydney NSW 2052 Australia
| | - Yong Li
- National Supercomputer Research Center of Advanced Materials Advanced Materials Institute Qilu University of Technology (Shandong Academy of Sciences) Jinan 250014 China
| | - Jieying Liang
- School of Chemical Engineering and Australian Centre for NanoMedicine University of New South Wales Sydney NSW 2052 Australia
| | - Jueyi Xue
- Graduate School of Biomedical Engineering University of New South Wales Sydney NSW 2052 Australia
| | - Jiangtao Xu
- School of Chemical Engineering and Australian Centre for NanoMedicine University of New South Wales Sydney NSW 2052 Australia
| | - John M. Whitelock
- Graduate School of Biomedical Engineering University of New South Wales Sydney NSW 2052 Australia
| | - Lei Xie
- Department of Chemistry Laboratory of Advanced Materials Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials iChEM Fudan University Shanghai 200433 China
| | - Biao Kong
- Department of Chemistry Laboratory of Advanced Materials Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials iChEM Fudan University Shanghai 200433 China
| | - Kang Liang
- School of Chemical Engineering and Australian Centre for NanoMedicine University of New South Wales Sydney NSW 2052 Australia
- Graduate School of Biomedical Engineering University of New South Wales Sydney NSW 2052 Australia
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Stress-Structure Relationship of the Reversible Associating Polymer Network under Start-up Shear Flow. CHINESE JOURNAL OF POLYMER SCIENCE 2020. [DOI: 10.1007/s10118-020-2487-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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25
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Okauchi H, Sakatani Y, Otsuka K, Ichihashi N. Minimization of Elements for Isothermal DNA Replication by an Evolutionary Approach. ACS Synth Biol 2020; 9:1771-1780. [PMID: 32674580 DOI: 10.1021/acssynbio.0c00137] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA replication is one of the central functions of the cell. The complexity of modern DNA replication systems raises a question: is it possible to achieve a simpler continuous isothermal DNA replication using fewer proteins? Here, we searched such replication using an evolutionary approach. Through a long-term serial dilution experiment with phi29 DNA polymerase, we found that large repetitive DNAs spontaneously appear and continuously replicate. The repetitive sequence is critical for replication. Arbitrary sequences can replicate if they contain many repeats. We also demonstrated continuous DNA replication using expressed polymerase from the DNA for 10 rounds. This study revealed that continuous isothermal DNA replication can be achieved in a scheme simpler than that employed by modern organisms, providing an alternative strategy for simpler artificial cell synthesis and a clue to possible primitive forms of DNA replication.
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Affiliation(s)
- Hiroki Okauchi
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Yoshihiro Sakatani
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kensuke Otsuka
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Norikazu Ichihashi
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
- Komaba Institute for Science, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
- Research Center for Complex Systems Biology, Universal Biology Institute, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
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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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