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Kim D, Kim J, Han J, Shin J, Park KS. Split T7 switch-mediated cell-free protein synthesis system for detecting target nucleic acids. Biosens Bioelectron 2024; 261:116517. [PMID: 38924814 DOI: 10.1016/j.bios.2024.116517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024]
Abstract
Cell-free protein synthesis (CFPS) reactions can be used to detect nucleic acids. However, most CFPS systems rely on a toehold switch and exhibit the following critical limitations: (i) off-target signals due to leaky translation in the absence of target nucleic acids, (ii) a suboptimal detection limit of approximately 30 nM without pre-amplification, and (iii) labor-intensive screening processes due to sequence constraints for the target nucleic acids. To overcome these shortcomings, we developed a new split T7 switch-mediated CFPS system in which the split T7 promoter was applied to a three-way junction structure to selectively initiate transcription-translation only in the presence of target nucleic acids. Both fluorescence and colorimetric detection systems were constructed by employing different reporter proteins. Notably, we introduced the self-complementation of split fluorescent proteins to streamline preparation of the proposed system, enabling versatile applications. Operation of this one-pot approach under isothermal conditions enabled the detection of target nucleic acids at concentrations as low as 10 pM, representing more than a thousand times improvement over previous toehold switch-based approaches. Furthermore, the proposed system demonstrated high specificity in detecting target nucleic acids and compatibility with various reporter proteins encoded in the expression region. By eliminating issues associated with the previous toehold switch system, our split T7 switch-mediated CFPS system could become a core platform for detecting various target nucleic acids.
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Affiliation(s)
- Doyeon Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Junhyeong Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Jinjoo Han
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Jiye Shin
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea
| | - Ki Soo Park
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, Republic of Korea.
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2
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Taguchi H, Niwa T. Reconstituted cell-free translation systems for exploring protein folding and aggregation. J Mol Biol 2024:168726. [PMID: 39074633 DOI: 10.1016/j.jmb.2024.168726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 07/18/2024] [Accepted: 07/24/2024] [Indexed: 07/31/2024]
Abstract
Protein folding is crucial for achieving functional three-dimensional structures. However, the process is often hampered by aggregate formation, necessitating the presence of chaperones and quality control systems within the cell to maintain protein homeostasis. Despite a long history of folding studies involving the denaturation and subsequent refolding of translation-completed purified proteins, numerous facets of cotranslational folding, wherein nascent polypeptides are synthesized by ribosomes and folded during translation, remain unexplored. Cell-free protein synthesis (CFPS) systems are invaluable tools for studying cotranslational folding, offering a platform not only for elucidating mechanisms but also for large-scale analyses to identify aggregation-prone proteins. This review provides an overview of the extensive use of CFPS in folding studies to date. In particular, we discuss a comprehensive aggregation formation assay of thousands of Escherichia coli proteins conducted under chaperone-free conditions using a reconstituted translation system, along with its derived studies.
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Affiliation(s)
- Hideki Taguchi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, S2-19, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan.
| | - Tatsuya Niwa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, S2-19, 4259 Nagatsuta, Midori-ku, Yokohama 226-8501, Japan
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3
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Okamura H, Yao T, Nagatsugi F. Reversible Control of Gene Expression by Guest-Modified Adenosines in a Cell-Free System via Host-Guest Interaction. J Am Chem Soc 2024; 146:18513-18523. [PMID: 38941287 PMCID: PMC11240562 DOI: 10.1021/jacs.4c04262] [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: 03/27/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 06/30/2024]
Abstract
Gene expression technology has become an indispensable tool for elucidating biological processes and developing biotechnology. Cell-free gene expression (CFE) systems offer a fundamental platform for gene expression-based technology, in which the reversible and programmable control of transcription can expand its use in synthetic biology and medicine. This study shows that CFE can be controlled via the host-guest interaction of cucurbit[7]uril (CB[7]) with N6-guest-modified adenosines. These adenosine derivatives were conveniently incorporated into the DNA strand using a post-synthetic approach and formed a selective and stable base pair with complementary thymidine in DNA. Meanwhile, alternate addition of CB[7] and the exchanging guest molecule induced the reversible formation of a duplex structure through the formation and dissociation of a bulky complex on DNA. The kinetics of the reversibility was fine-tuned by changing the size of the modified guest moieties. When incorporated into a specific region of the T7 promoter sequence, the guest-modified adenosines enabled tight and reversible control of in vitro transcription and protein expression in the CFE system. This study marks the first utility of the host-guest interaction for gene expression control in the CFE system, opening new avenues for developing DNA-based technology, particularly for precise gene therapy and DNA nanotechnology.
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Affiliation(s)
- Hidenori Okamura
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
- Department
of Chemistry, Graduate School of Science, Tohoku University, Miyagi 980-8578, Japan
| | - Takeyuki Yao
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
- Department
of Chemistry, Graduate School of Science, Tohoku University, Miyagi 980-8578, Japan
| | - Fumi Nagatsugi
- Institute
of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577, Japan
- Department
of Chemistry, Graduate School of Science, Tohoku University, Miyagi 980-8578, Japan
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4
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Ishii Y, Fukunaga K, Cooney A, Yokobayashi Y, Matsuura T. Switchable and orthogonal gene expression control inside artificial cells by synthetic riboswitches. Chem Commun (Camb) 2024; 60:5972-5975. [PMID: 38767578 DOI: 10.1039/d4cc00965g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Here we report two novel synthetic riboswitches that respond to ASP2905 and theophylline and function in reconstituted cell-free protein synthesis (CFPS) system. We encapsulated the CFPS system as well as DNA-templated encoding reporter genes regulated by these orthogonal riboswitches inside liposomes, and achieved switchable and orthogonal control over gene expression by external stimulation with the cognate ligands.
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Affiliation(s)
- Yuta Ishii
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-Ku, Tokyo 152-8550, Japan.
- School of Life Science and Technology, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-Ku, Tokyo 152-8550, Japan
| | - Keisuke Fukunaga
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-Ku, Tokyo 152-8550, Japan.
| | - Aileen Cooney
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-Ku, Tokyo 152-8550, Japan.
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK
| | - Yohei Yokobayashi
- Nucleic Acid Chemistry and Engineering Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan
| | - Tomoaki Matsuura
- Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama 2-12-1, Meguro-Ku, Tokyo 152-8550, Japan.
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Hiroshima Y, Kido JI, Kido R, Yoshida K, Bando M, Kajimoto K, Yumoto H, Shinohara Y. β-defensin 2 synthesized by a cell-free protein synthesis system and encapsulated in liposomes inhibits adhesion of Porphyromonas gingivalis to oral epithelial cells. Odontology 2023; 111:830-838. [PMID: 36745267 DOI: 10.1007/s10266-023-00789-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 01/29/2023] [Indexed: 02/07/2023]
Abstract
β-defensin 2 (BD-2), an antimicrobial peptide (AMP), is expressed by oral epithelial cells and plays an important role in innate immunity of the oral cavity. Cell-free protein synthesis (CFPS) systems have been studied for the synthesis of various proteins, however, the synthesis of BD-2 by a CFPS system has not been extensively explored. Liposomes have been developed as tools for drug delivery. A delivery of liposome-encapsulated AMP to oral epithelium may be useful to prevent oral infectious diseases. In the present study, we investigated the antimicrobial activity of the BD-2 protein, artificially synthesized using a CFPS system and encapsulated in liposomes. BD-2 protein was artificially synthesized using template DNA and a reconstituted CFPS system and was identified by western blotting. Bilayer liposomes were prepared using 1,2-dioleoyl-sn-glycero-3-phospho-choline and 3-sn-phosphatidylcholine from egg yolk. The artificially synthesized BD-2 was encapsulated in liposomes, collected by ultrafiltration, and detected by western blotting. Human oral epithelial cells were cultured with the liposome-encapsulated BD-2 and the concentration of BD-2 in the cell lysate of the culture with the synthesized BD-2 was higher than that of the control cultures. The antimicrobial activity of the synthesized BD-2 was investigated by an adhesion assay of Porphyromonas gingivalis to oral epithelial cells. The artificially synthesized BD-2 and its liposome significantly inhibited adhesion of P. gingivalis to oral epithelial cells. These results suggest that artificially synthesized BD-2 and liposome-encapsulated BD-2 show antimicrobial activity and can potentially play a role in oral healthcare for periodontal diseases.
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Affiliation(s)
- Yuka Hiroshima
- Department of Oral Microbiology, Tokushima University, 3-18-15, Kuramoto, Tokushima, 770-8504, Japan.
| | - Jun-Ichi Kido
- Department of Periodontology and Endodontology, Tokushima University, Tokushima, Japan
| | - Rie Kido
- Department of Periodontology and Endodontology, Tokushima University, Tokushima, Japan
| | - Kaya Yoshida
- Department of Oral Healthcare Education, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Mika Bando
- Department of Periodontology and Endodontology, Tokushima University, Tokushima, Japan
| | - Kazuaki Kajimoto
- Health and Medical Research Institute, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
| | - Hiromichi Yumoto
- Department of Periodontology and Endodontology, Tokushima University, Tokushima, Japan
| | - Yasuo Shinohara
- Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan
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6
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Maheshwari AJ, Calles J, Waterton SK, Endy D. Engineering tRNA abundances for synthetic cellular systems. Nat Commun 2023; 14:4594. [PMID: 37524714 PMCID: PMC10390467 DOI: 10.1038/s41467-023-40199-9] [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: 12/24/2022] [Accepted: 07/13/2023] [Indexed: 08/02/2023] Open
Abstract
Routinizing the engineering of synthetic cells requires specifying beforehand how many of each molecule are needed. Physics-based tools for estimating desired molecular abundances in whole-cell synthetic biology are missing. Here, we use a colloidal dynamics simulator to make predictions for how tRNA abundances impact protein synthesis rates. We use rational design and direct RNA synthesis to make 21 synthetic tRNA surrogates from scratch. We use evolutionary algorithms within a computer aided design framework to engineer translation systems predicted to work faster or slower depending on tRNA abundance differences. We build and test the so-specified synthetic systems and find qualitative agreement between expected and observed systems. First principles modeling combined with bottom-up experiments can help molecular-to-cellular scale synthetic biology realize design-build-work frameworks that transcend tinker-and-test.
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Affiliation(s)
| | - Jonathan Calles
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Sean K Waterton
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Drew Endy
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
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7
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Yue K, Chen J, Li Y, Kai L. Advancing synthetic biology through cell-free protein synthesis. Comput Struct Biotechnol J 2023; 21:2899-2908. [PMID: 37216017 PMCID: PMC10196276 DOI: 10.1016/j.csbj.2023.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023] Open
Abstract
The rapid development of synthetic biology has enabled the production of compounds with revolutionary improvements in biotechnology. DNA manipulation tools have expedited the engineering of cellular systems for this purpose. Nonetheless, the inherent constraints of cellular systems persist, imposing an upper limit on mass and energy conversion efficiencies. Cell-free protein synthesis (CFPS) has demonstrated its potential to overcome these inherent constraints and has been instrumental in the further advancement of synthetic biology. Via the removal of the cell membranes and redundant parts of cells, CFPS has provided flexibility in directly dissecting and manipulating the Central Dogma with rapid feedback. This mini-review summarizes recent achievements of the CFPS technique and its application to a wide range of synthetic biology projects, such as minimal cell assembly, metabolic engineering, and recombinant protein production for therapeutics, as well as biosensor development for in vitro diagnostics. In addition, current challenges and future perspectives in developing a generalized cell-free synthetic biology are outlined.
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Affiliation(s)
- Ke Yue
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Junyu Chen
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Yingqiu Li
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
| | - Lei Kai
- School of Life Sciences, Jiangsu Normal University, Xuzhou 22116, China
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8
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Kido JI, Hiroshima Y, Kido R, Yoshida K, Inagaki Y, Naruishi K, Kajimoto K, Kataoka M, Shinohara Y, Yumoto H. Lipocalin 2, synthesized using a cell-free protein synthesis system and encapsulated into liposomes, inhibits the adhesion of Porphyromonas gingivalis to human oral epithelial cells. J Periodontal Res 2023; 58:262-273. [PMID: 36579753 DOI: 10.1111/jre.13088] [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: 06/24/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND AND OBJECTIVE Lipocalin 2 (LCN2), a glycoprotein expressed in epithelial cells and leukocytes, has an antibacterial effect and plays a role in innate immunity. The delivery of LCN2 encapsulated in liposomes to oral epithelium may be useful to prevent oral infectious diseases. This study aimed to investigate the inhibitory effect of LCN2, artificially synthesized using a cell-free protein synthesis (CFPS) system, on the adhesion of Porphyromonas gingivalis to oral epithelial cells in order to approach oral healthcare using LCN2. METHODS LCN 2 was synthesized using a CFPS system and assayed by Western blotting, mass spectrometry and enzyme-linked immunosorbent assay (ELISA). The bilayer liposomes were prepared by the spontaneous transfer method using 1,2-dioleoyl-sn-glycero-3 phosphocholine (DOPC), 3-sn-phosphatidylcholine from Egg Yolk (Egg-PC), and 1,2-dioleoyl-sn-glycero-3 phosphoethanolamine (DOPE). The cellular and medium fractions derived from the culture of oral epithelial cells with liposome-encapsulated LCN2 were assayed by Western blotting and ELISA. The effect of the synthesized LCN2 on adhesion of the labeled P. gingivalis to oral epithelial cells was investigated as an evaluation of its antibacterial activity. RESULTS The synthesized LCN2 protein was identified by Western blotting; its amino acid sequence was similar to that of recombinant LCN2 protein. The additions of DOPE and octa-arginine in the outer lipid-layer components of liposome significantly increased the delivery of liposomes to epithelial cells. When oral epithelial cells were cultured with the synthesized and liposome-encapsulated LCN2, LCN2 was identified in the cellular and medium fractions by Western blotting and its concentration in the cellular fraction from the culture with the synthesized LCN2 was significantly higher than that of a template DNA-free protein. The synthesized LCN2 and liposome-encapsulated LCN2 significantly inhibited the adhesion of P. gingivalis to oral epithelial cells compared with template DNA-free protein. CONCLUSION LCN2 was artificially synthesized by a CFPS system, encapsulated in liposomes, and delivered to oral epithelial cells, and demonstrated an antibacterial action against P. gingivalis. This approach may become a useful model for oral healthcare.
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Affiliation(s)
- Jun-Ichi Kido
- Department of Periodontology and Endodontology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Yuka Hiroshima
- Department of Oral Microbiology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Rie Kido
- Department of Periodontology and Endodontology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Kaya Yoshida
- Department of Oral Healthcare Education, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Yuji Inagaki
- Department of Periodontology and Endodontology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Koji Naruishi
- Department of Periodontology and Endodontology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Kazuaki Kajimoto
- Health and Medical Research Institute, National Institute of Advanced Industrial, Science and Technology, Tokushima, Japan
| | - Masatoshi Kataoka
- Health and Medical Research Institute, National Institute of Advanced Industrial, Science and Technology, Tokushima, Japan
| | - Yasuo Shinohara
- Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan
| | - Hiromichi Yumoto
- Department of Periodontology and Endodontology, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
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De Capitani J, Mutschler H. The Long Road to a Synthetic Self-Replicating Central Dogma. Biochemistry 2023; 62:1221-1232. [PMID: 36944355 PMCID: PMC10077596 DOI: 10.1021/acs.biochem.3c00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
The construction of a biochemical system capable of self-replication is a key objective in bottom-up synthetic biology. Throughout the past two decades, a rapid progression in the design of in vitro cell-free systems has provided valuable insight into the requirements for the development of a minimal system capable of self-replication. The main limitations of current systems can be attributed to their macromolecular composition and how the individual macromolecules use the small molecules necessary to drive RNA and protein synthesis. In this Perspective, we discuss the recent steps that have been taken to generate a minimal cell-free system capable of regenerating its own macromolecular components and maintaining the homeostatic balance between macromolecular biogenesis and consumption of primary building blocks. By following the flow of biological information through the central dogma, we compare the current versions of these systems to date and propose potential alterations aimed at designing a model system for self-replicative synthetic cells.
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Affiliation(s)
- Jacopo De Capitani
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
| | - Hannes Mutschler
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
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Cui Y, Chen X, Wang Z, Lu Y. Cell-Free PURE System: Evolution and Achievements. BIODESIGN RESEARCH 2022; 2022:9847014. [PMID: 37850137 PMCID: PMC10521753 DOI: 10.34133/2022/9847014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 08/16/2022] [Indexed: 10/19/2023] Open
Abstract
The cell-free protein synthesis (CFPS) system, as a technical core of synthetic biology, can simulate the transcription and translation process in an in vitro open environment without a complete living cell. It has been widely used in basic and applied research fields because of its advanced engineering features in flexibility and controllability. Compared to a typical crude extract-based CFPS system, due to defined and customizable components and lacking protein-degrading enzymes, the protein synthesis using recombinant elements (PURE) system draws great attention. This review first discusses the elemental composition of the PURE system. Then, the design and preparation of functional proteins for the PURE system, especially the critical ribosome, were examined. Furthermore, we trace the evolving development of the PURE system in versatile areas, including prototyping, synthesis of unnatural proteins, peptides and complex proteins, and biosensors. Finally, as a state-of-the-art engineering strategy, this review analyzes the opportunities and challenges faced by the PURE system in future scientific research and diverse applications.
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Affiliation(s)
- Yi Cui
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- College of Life Sciences, Shenyang Normal University, Shenyang 110034, Liaoning, China
| | - Xinjie Chen
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Ze Wang
- College of Life Sciences, Shenyang Normal University, Shenyang 110034, Liaoning, China
| | - Yuan Lu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
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Li C, Zhang X, Dong M, Han X. Progress on Crowding Effect in Cell-like Structures. MEMBRANES 2022; 12:membranes12060593. [PMID: 35736300 PMCID: PMC9228500 DOI: 10.3390/membranes12060593] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 12/10/2022]
Abstract
Several biological macromolecules, such as proteins, nucleic acids, and polysaccharides, occupy about 30% of the space in cells, resulting in a crowded macromolecule environment. The crowding effect within cells exerts an impact on the functions of biological components, the assembly behavior of biomacromolecules, and the thermodynamics and kinetics of metabolic reactions. Cell-like structures provide confined and independent compartments for studying the working mechanisms of cells, which can be used to study the physiological functions arising from the crowding effect of macromolecules in cells. This article mainly summarizes the progress of research on the macromolecular crowding effects in cell-like structures. It includes the effects of this crowding on actin assembly behavior, tubulin aggregation behavior, and gene expression. The challenges and future trends in this field are presented at the end of the paper.
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Affiliation(s)
- Chao Li
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin 150001, China; (C.L.); (X.Z.)
| | - Xiangxiang Zhang
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin 150001, China; (C.L.); (X.Z.)
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus, Denmark
- Correspondence: (M.D.); (X.H.)
| | - Xiaojun Han
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin 150001, China; (C.L.); (X.Z.)
- Correspondence: (M.D.); (X.H.)
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12
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Sakai A, Deich CR, Nelissen FHT, Jonker AJ, Bittencourt DMDC, Kempes CP, Wise KS, Heus HA, Huck WTS, Adamala KP, Glass JI. Traditional Protocols and Optimization Methods Lead to Absent Expression in a Mycoplasma Cell-Free Gene Expression Platform. Synth Biol (Oxf) 2022; 7:ysac008. [PMID: 35774105 PMCID: PMC9239315 DOI: 10.1093/synbio/ysac008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 04/11/2022] [Accepted: 05/20/2022] [Indexed: 11/23/2022] Open
Abstract
Cell-free expression (CFE) systems are one of the main platforms for building synthetic cells. A major drawback is the orthogonality of cell-free systems across species. To generate a CFE system compatible with recently established minimal cell constructs, we attempted to optimize a Mycoplasma bacterium-based CFE system using lysates of the genome-minimized cell JCVI-syn3A (Syn3A) and its close phylogenetic relative Mycoplasma capricolum (Mcap). To produce mycoplasma-derived crude lysates, we systematically tested methods commonly used for bacteria, based on the S30 protocol of Escherichia coli. Unexpectedly, after numerous attempts to optimize lysate production methods or composition of feeding buffer, none of the Mcap or Syn3A lysates supported cell-free gene expression. Only modest levels of in vitro transcription of RNA aptamers were observed. While our experimental systems were intended to perform transcription and translation, our assays focused on RNA. Further investigations identified persistently high ribonuclease (RNase) activity in all lysates, despite removal of recognizable nucleases from the respective genomes and attempts to inhibit nuclease activities in assorted CFE preparations. An alternative method using digitonin to permeabilize the mycoplasma cell membrane produced a lysate with diminished RNase activity yet still was unable to support cell-free gene expression. We found that intact mycoplasma cells poisoned E. coli cell-free extracts by degrading ribosomal RNAs, indicating that the mycoplasma cells, even the minimal cell, have a surface-associated RNase activity. However, it is not clear which gene encodes the RNase. This work summarizes attempts to produce mycoplasma-based CFE and serves as a cautionary tale for researchers entering this field.
Graphical Abstract
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Affiliation(s)
- Andrei Sakai
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Christopher R Deich
- Department of Genetics, Cell Biology and Development, University of Minnesota, 420 Washington Avenue SE, Minneapolis, MN 55455, USA
| | - Frank H T Nelissen
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Aafke J Jonker
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Daniela M de C Bittencourt
- The J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA
- Embrapa Genetic Resources and Biotechnology/National Institute of Science and Technology - Synthetic Biology, Parque Estação Biológica, PqEB, Av. W5 Norte (final), Brasília, DF, 70770-917, Brazil, Norte (final), Brasília, DF, 70770-917, Brazil
| | | | - Kim S Wise
- The J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA
| | - Hans A Heus
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Wilhelm T S Huck
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands
| | - Katarzyna P Adamala
- Department of Genetics, Cell Biology and Development, University of Minnesota, 420 Washington Avenue SE, Minneapolis, MN 55455, USA
| | - John I Glass
- The J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA 92037, USA
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13
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Umezawa K, Kii I. Druggable Transient Pockets in Protein Kinases. Molecules 2021; 26:molecules26030651. [PMID: 33513739 PMCID: PMC7865889 DOI: 10.3390/molecules26030651] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/23/2021] [Accepted: 01/26/2021] [Indexed: 12/29/2022] Open
Abstract
Drug discovery using small molecule inhibitors is reaching a stalemate due to low selectivity, adverse off-target effects and inevitable failures in clinical trials. Conventional chemical screening methods may miss potent small molecules because of their use of simple but outdated kits composed of recombinant enzyme proteins. Non-canonical inhibitors targeting a hidden pocket in a protein have received considerable research attention. Kii and colleagues identified an inhibitor targeting a transient pocket in the kinase DYRK1A during its folding process and termed it FINDY. FINDY exhibits a unique inhibitory profile; that is, FINDY does not inhibit the fully folded form of DYRK1A, indicating that the FINDY-binding pocket is hidden in the folded form. This intriguing pocket opens during the folding process and then closes upon completion of folding. In this review, we discuss previously established kinase inhibitors and their inhibitory mechanisms in comparison with FINDY. We also compare the inhibitory mechanisms with the growing concept of “cryptic inhibitor-binding sites.” These sites are buried on the inhibitor-unbound surface but become apparent when the inhibitor is bound. In addition, an alternative method based on cell-free protein synthesis of protein kinases may allow the discovery of small molecules that occupy these mysterious binding sites. Transitional folding intermediates would become alternative targets in drug discovery, enabling the efficient development of potent kinase inhibitors.
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Affiliation(s)
- Koji Umezawa
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, 8304 Minami-Minowa, Kami-ina, Nagano 399-4598, Japan;
| | - Isao Kii
- Laboratory for Drug Target Research, Faculty & Graduate School of Agriculture, Shinshu University, 8304 Minami-Minowa, Kami-ina, Nagano 399-4598, Japan
- Correspondence: ; Tel.: +81-265-77-1521
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14
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Zhang W, Wu Q. Applications of phage-derived RNA-based technologies in synthetic biology. Synth Syst Biotechnol 2020; 5:343-360. [PMID: 33083579 PMCID: PMC7564126 DOI: 10.1016/j.synbio.2020.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 09/22/2020] [Accepted: 09/27/2020] [Indexed: 12/20/2022] Open
Abstract
As the most abundant biological entities with incredible diversity, bacteriophages (also known as phages) have been recognized as an important source of molecular machines for the development of genetic-engineering tools. At the same time, phages are crucial for establishing and improving basic theories of molecular biology. Studies on phages provide rich sources of essential elements for synthetic circuit design as well as powerful support for the improvement of directed evolution platforms. Therefore, phages play a vital role in the development of new technologies and central scientific concepts. After the RNA world hypothesis was proposed and developed, novel biological functions of RNA continue to be discovered. RNA and its related elements are widely used in many fields such as metabolic engineering and medical diagnosis, and their versatility led to a major role of RNA in synthetic biology. Further development of RNA-based technologies will advance synthetic biological tools as well as provide verification of the RNA world hypothesis. Most synthetic biology efforts are based on reconstructing existing biological systems, understanding fundamental biological processes, and developing new technologies. RNA-based technologies derived from phages will offer abundant sources for synthetic biological components. Moreover, phages as well as RNA have high impact on biological evolution, which is pivotal for understanding the origin of life, building artificial life-forms, and precisely reprogramming biological systems. This review discusses phage-derived RNA-based technologies terms of phage components, the phage lifecycle, and interactions between phages and bacteria. The significance of RNA-based technology derived from phages for synthetic biology and for understanding the earliest stages of biological evolution will be highlighted.
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Affiliation(s)
- Wenhui Zhang
- MOE Key Lab. Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Qiong Wu
- MOE Key Lab. Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing, 100084, China
- Corresponding author. MOE Key Lab. Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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15
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Levy M, Falkovich R, Daube SS, Bar-Ziv RH. Autonomous synthesis and assembly of a ribosomal subunit on a chip. SCIENCE ADVANCES 2020; 6:eaaz6020. [PMID: 32494616 PMCID: PMC7159907 DOI: 10.1126/sciadv.aaz6020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 01/22/2020] [Indexed: 05/03/2023]
Abstract
Ribosome biogenesis is an efficient and complex assembly process that has not been reconstructed outside a living cell so far, yet is the most critical step for establishing a self-replicating artificial cell. We recreated the biogenesis of Escherichia coli's small ribosomal subunit by synthesizing and capturing all its ribosomal proteins and RNA on a chip. Surface confinement provided favorable conditions for autonomous stepwise assembly of new subunits, spatially segregated from original intact ribosomes. Our real-time fluorescence measurements revealed hierarchal assembly, cooperative interactions, unstable intermediates, and specific binding to large ribosomal subunits. Using only synthetic genes, our methodology is a crucial step toward creation of a self-replicating artificial cell and a general strategy for the mechanistic investigation of diverse multicomponent macromolecular machines.
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16
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Shimojo M, Amikura K, Masuda K, Kanamori T, Ueda T, Shimizu Y. In vitro reconstitution of functional small ribosomal subunit assembly for comprehensive analysis of ribosomal elements in E. coli. Commun Biol 2020; 3:142. [PMID: 32214223 PMCID: PMC7096426 DOI: 10.1038/s42003-020-0874-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 03/03/2020] [Indexed: 11/25/2022] Open
Abstract
In vitro reconstitution is a powerful tool for investigating ribosome functions and biogenesis, as well as discovering new ribosomal features. In this study, we integrated all of the processes required for Escherichia coli small ribosomal subunit assembly. In our method, termed fully Recombinant-based integrated Synthesis, Assembly, and Translation (R-iSAT), assembly and evaluation of the small ribosomal subunits are coupled with ribosomal RNA (rRNA) synthesis in a reconstituted cell-free protein synthesis system. By changing the components of R-iSAT, including recombinant ribosomal protein composition, we coupled ribosomal assembly with ribosomal protein synthesis, enabling functional synthesis of ribosomal proteins and subsequent subunit assembly. In addition, we assembled and evaluated subunits with mutations in both rRNA and ribosomal proteins. The study demonstrated that our scheme provides new ways to comprehensively analyze any elements of the small ribosomal subunit, with the goal of improving our understanding of ribosomal biogenesis, function, and engineering. Shimojo et al. demonstrate the use of individually purified ribosomal proteins added into iSAT (integrated ribosomal synthesis, assembly, and translation) system to enable assembly of functional 30S subunits. They further show that while some 30S r-proteins must be full synthesized before transcription, others may be co-transcriptionally produced, to enable the assembly of 30S particles.
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Affiliation(s)
- Masaru Shimojo
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, 565-0874, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan
| | - Kazuaki Amikura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06520, USA
| | - Keiko Masuda
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, 565-0874, Japan
| | | | - Takuya Ueda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8562, Japan.,Department of Integrative Bioscience and Biomedical Engineering, Graduate School of Science and Engineering, Waseda University, Shinjuku, Tokyo, 162-8480, Japan
| | - Yoshihiro Shimizu
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research (BDR), Suita, Osaka, 565-0874, Japan.
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17
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Hammerling MJ, Krüger A, Jewett MC. Strategies for in vitro engineering of the translation machinery. Nucleic Acids Res 2020; 48:1068-1083. [PMID: 31777928 PMCID: PMC7026604 DOI: 10.1093/nar/gkz1011] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/07/2019] [Accepted: 10/17/2019] [Indexed: 01/06/2023] Open
Abstract
Engineering the process of molecular translation, or protein biosynthesis, has emerged as a major opportunity in synthetic and chemical biology to generate novel biological insights and enable new applications (e.g. designer protein therapeutics). Here, we review methods for engineering the process of translation in vitro. We discuss the advantages and drawbacks of the two major strategies-purified and extract-based systems-and how they may be used to manipulate and study translation. Techniques to engineer each component of the translation machinery are covered in turn, including transfer RNAs, translation factors, and the ribosome. Finally, future directions and enabling technological advances for the field are discussed.
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Affiliation(s)
- Michael J Hammerling
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Antje Krüger
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Center for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
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18
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Ueda K, Mizuuchi R, Matsuda F, Ichihashi N. A Fusion Method to Develop an Expanded Artificial Genomic RNA Replicable by Qβ Replicase. Chembiochem 2019; 20:2331-2335. [PMID: 31037814 DOI: 10.1002/cbic.201900120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 04/28/2019] [Indexed: 11/10/2022]
Abstract
RNA-based genomes are used to synthesize artificial cells that harbor genome replication systems. Previously, continuous replication of an artificial genomic RNA that encoded an RNA replicase was demonstrated. The next important challenge is to expand such genomes by increasing the number of encoded genes. However, technical difficulties are encountered during such expansions because the introduction of new genes disrupts the secondary structure of RNA and makes RNA nonreplicable through replicase. Herein, a fusion method that enables the construction of a longer RNA from two replicable RNAs, while retaining replication capability, is proposed. Two replicable RNAs that encode different genes at various positions are fused, and a new parameter, the unreplicable index, which negatively correlates with the replication ability of the fused RNAs better than that of the previous parameter, is determined. The unreplicable index represents the expected value of the number of G or C nucleotides that are unpaired in both the template and complementary strands. It is also observed that some of the constructed fused RNAs replicate efficiently by using the internally translated replicase. The method proposed herein could contribute to the development of an expanded RNA genome that can be used for the purpose of artificial cell synthesis.
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Affiliation(s)
- Kensuke Ueda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Ryo Mizuuchi
- Department of Chemistry, Portland State University, Portland, OR, 97207, USA
| | - Fumio Matsuda
- 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
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19
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Marinko J, Huang H, Penn WD, Capra JA, Schlebach JP, Sanders CR. Folding and Misfolding of Human Membrane Proteins in Health and Disease: From Single Molecules to Cellular Proteostasis. Chem Rev 2019; 119:5537-5606. [PMID: 30608666 PMCID: PMC6506414 DOI: 10.1021/acs.chemrev.8b00532] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Indexed: 12/13/2022]
Abstract
Advances over the past 25 years have revealed much about how the structural properties of membranes and associated proteins are linked to the thermodynamics and kinetics of membrane protein (MP) folding. At the same time biochemical progress has outlined how cellular proteostasis networks mediate MP folding and manage misfolding in the cell. When combined with results from genomic sequencing, these studies have established paradigms for how MP folding and misfolding are linked to the molecular etiologies of a variety of diseases. This emerging framework has paved the way for the development of a new class of small molecule "pharmacological chaperones" that bind to and stabilize misfolded MP variants, some of which are now in clinical use. In this review, we comprehensively outline current perspectives on the folding and misfolding of integral MPs as well as the mechanisms of cellular MP quality control. Based on these perspectives, we highlight new opportunities for innovations that bridge our molecular understanding of the energetics of MP folding with the nuanced complexity of biological systems. Given the many linkages between MP misfolding and human disease, we also examine some of the exciting opportunities to leverage these advances to address emerging challenges in the development of therapeutics and precision medicine.
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Affiliation(s)
- Justin
T. Marinko
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Hui Huang
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
| | - Wesley D. Penn
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - John A. Capra
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240, United States
- Department
of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37245, United States
| | - Jonathan P. Schlebach
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Charles R. Sanders
- Department
of Biochemistry, Vanderbilt University, Nashville, Tennessee 37240, United States
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20
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Caschera F, Karim AS, Gazzola G, d’Aquino AE, Packard NH, Jewett MC. High-Throughput Optimization Cycle of a Cell-Free Ribosome Assembly and Protein Synthesis System. ACS Synth Biol 2018; 7:2841-2853. [PMID: 30354075 DOI: 10.1021/acssynbio.8b00276] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Building variant ribosomes offers opportunities to reveal fundamental principles underlying ribosome biogenesis and to make ribosomes with altered properties. However, cell viability limits mutations that can be made to the ribosome. To address this limitation, the in vitro integrated synthesis, assembly and translation (iSAT) method for ribosome construction from the bottom up was recently developed. Unfortunately, iSAT is complex, costly, and laborious to researchers, partially due to the high cost of reaction buffer containing over 20 components. In this study, we develop iSAT in Escherichia coli BL21Rosetta2 cell lysates, a commonly used bacterial strain, with a cost-effective poly sugar and nucleotide monophosphate-based metabolic scheme. We achieved a 10-fold increase in protein yield over our base case with an evolutionary design of experiments approach, screening 490 reaction conditions to optimize the reaction buffer. The computationally guided, cell-free, high-throughput technology presented here augments the way we approach multicomponent synthetic biology projects and efforts to repurpose ribosomes.
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Affiliation(s)
| | | | - Gianluca Gazzola
- Rutgers Center for Operations Research, Rutgers Business School, 100 Rockafeller Road, Piscataway, New Jersey 08854, United States
| | | | - Norman H. Packard
- ProtoLife, Inc., 57 Post Street Suite 908, San Francisco, California 94104, United States
| | - Michael C. Jewett
- Rutgers Center for Operations Research, Rutgers Business School, 100 Rockafeller Road, Piscataway, New Jersey 08854, United States
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21
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Self-replication of circular DNA by a self-encoded DNA polymerase through rolling-circle replication and recombination. Sci Rep 2018; 8:13089. [PMID: 30166584 PMCID: PMC6117322 DOI: 10.1038/s41598-018-31585-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 08/22/2018] [Indexed: 11/09/2022] Open
Abstract
A major challenge in constructing artificial cells is the establishment of a recursive genome replication system coupled with gene expression from the genome itself. One of the simplest schemes of recursive DNA replication is the rolling-circle replication of a circular DNA coupled with recombination. In this study, we attempted to develop a replication system based on this scheme using self-encoded phi29 DNA polymerase and externally supplied Cre recombinase. We first identified that DNA polymerization is significantly inhibited by Cre recombinase. To overcome this problem, we performed in vitro evolution and obtained an evolved circular DNA that can replicate efficiently in the presence of the recombinase. We also showed evidence that during replication of the evolved DNA, the circular DNA was reproduced through recombination by Cre recombinase. These results demonstrate that the evolved circular DNA can reproduce itself through gene expression of a self-encoded polymerase. This study provides a step forward in developing a simple recursive DNA replication system for use in an artificial cell.
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22
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Yoshiyama T, Ichii T, Yomo T, Ichihashi N. Automated in vitro evolution of a translation-coupled RNA replication system in a droplet flow reactor. Sci Rep 2018; 8:11867. [PMID: 30089835 PMCID: PMC6082869 DOI: 10.1038/s41598-018-30374-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 07/27/2018] [Indexed: 01/23/2023] Open
Abstract
Automation is a useful strategy to make laborious evolutionary experiments faster and easier. To date, several types of continuous flow reactors have been developed for the automated evolutionary experiments of viruses and bacteria. However, the development of a flow reactor applicable to compartmentalized in vitro self-replication systems is still a challenge. In this study, we demonstrate automated in vitro evolution of a translation-coupled RNA system in a droplet flow reactor for the first time. This reactor contains approximately 1010 micro-scale droplets (average diameter is approximately 0.8 μm), which continuously fuse and divide among each other at a controllable rate. In the droplets, an RNA (artificial genomic RNA) replicate through the translation of self-encoded RNA replicase with spontaneously appearing parasitic RNA. We performed two automated replication experiments for more than 400 hours with different mixing intensities. We found that several mutations displayed increased frequencies in the genomic RNA populations and the dominant RNA mutants acquired the ability to replicate faster or acquired resistance to the parasitic RNA, demonstrating that Darwinian evolution occurred during the long-term replication. The droplet flow reactor we developed can be a useful tool to perform in vitro evolutionary experiments of translation-coupled systems.
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Affiliation(s)
- Tomoaki Yoshiyama
- Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Tetsuo Ichii
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Tokyo, Japan
| | - Tetsuya Yomo
- Institute of Biology and Information Science, East China Normal University, 3663 Zhongshan North Rd., Shanghai, 200062, P.R. China
| | - Norikazu Ichihashi
- Graduate School of Information Science and Technology, Osaka University, Osaka, Japan.
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
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23
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Damiati S, Mhanna R, Kodzius R, Ehmoser EK. Cell-Free Approaches in Synthetic Biology Utilizing Microfluidics. Genes (Basel) 2018; 9:E144. [PMID: 29509709 PMCID: PMC5867865 DOI: 10.3390/genes9030144] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 02/26/2018] [Accepted: 02/28/2018] [Indexed: 11/16/2022] Open
Abstract
Synthetic biology is a rapidly growing multidisciplinary branch of science which aims to mimic complex biological systems by creating similar forms. Constructing an artificial system requires optimization at the gene and protein levels to allow the formation of entire biological pathways. Advances in cell-free synthetic biology have helped in discovering new genes, proteins, and pathways bypassing the complexity of the complex pathway interactions in living cells. Furthermore, this method is cost- and time-effective with access to the cellular protein factory without the membrane boundaries. The freedom of design, full automation, and mimicking of in vivo systems reveal advantages of synthetic biology that can improve the molecular understanding of processes, relevant for life science applications. In parallel, in vitro approaches have enhanced our understanding of the living system. This review highlights the recent evolution of cell-free gene design, proteins, and cells integrated with microfluidic platforms as a promising technology, which has allowed for the transformation of the concept of bioprocesses. Although several challenges remain, the manipulation of biological synthetic machinery in microfluidic devices as suitable 'homes' for in vitro protein synthesis has been proposed as a pioneering approach for the development of new platforms, relevant in biomedical and diagnostic contexts towards even the sensing and monitoring of environmental issues.
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Affiliation(s)
- Samar Damiati
- Department of Biochemistry, Faculty of Science, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia.
| | - Rami Mhanna
- Biomedical Engineering Program, The American University of Beirut (AUB), Beirut 1107-2020, Lebanon.
| | - Rimantas Kodzius
- Mathematics and Natural Sciences Department, The American University of Iraq, Sulaimani, Sulaymaniyah 46001, Iraq.
- Faculty of Medicine, Ludwig Maximilian University of Munich (LMU), 80539 Munich, Germany.
- Faculty of Medicine, Technical University of Munich (TUM), 81675 Munich, Germany.
| | - Eva-Kathrin Ehmoser
- Department of Nanobiotechnology, Institute for Synthetic Bioarchitecture, University of Natural Resources and Life Sciences, 1190 Vienna, Austria.
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24
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Synthetic microbial consortia enable rapid assembly of pure translation machinery. Nat Chem Biol 2017; 14:29-35. [DOI: 10.1038/nchembio.2514] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 10/04/2017] [Indexed: 12/23/2022]
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25
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Progress in programming spatiotemporal patterns and machine-assembly in cell-free protein expression systems. Curr Opin Chem Biol 2017. [DOI: 10.1016/j.cbpa.2017.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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26
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Karig DK. Cell-free synthetic biology for environmental sensing and remediation. Curr Opin Biotechnol 2017; 45:69-75. [DOI: 10.1016/j.copbio.2017.01.010] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 01/24/2017] [Indexed: 01/15/2023]
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27
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de Jong H, Geiselmann J, Ropers D. Resource Reallocation in Bacteria by Reengineering the Gene Expression Machinery. Trends Microbiol 2017; 25:480-493. [DOI: 10.1016/j.tim.2016.12.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 12/03/2016] [Accepted: 12/15/2016] [Indexed: 11/27/2022]
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28
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Perez JG, Stark JC, Jewett MC. Cell-Free Synthetic Biology: Engineering Beyond the Cell. Cold Spring Harb Perspect Biol 2016; 8:cshperspect.a023853. [PMID: 27742731 DOI: 10.1101/cshperspect.a023853] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cell-free protein synthesis (CFPS) technologies have enabled inexpensive and rapid recombinant protein expression. Numerous highly active CFPS platforms are now available and have recently been used for synthetic biology applications. In this review, we focus on the ability of CFPS to expand our understanding of biological systems and its applications in the synthetic biology field. First, we outline a variety of CFPS platforms that provide alternative and complementary methods for expressing proteins from different organisms, compared with in vivo approaches. Next, we review the types of proteins, protein complexes, and protein modifications that have been achieved using CFPS systems. Finally, we introduce recent work on genetic networks in cell-free systems and the use of cell-free systems for rapid prototyping of in vivo networks. Given the flexibility of cell-free systems, CFPS holds promise to be a powerful tool for synthetic biology as well as a protein production technology in years to come.
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Affiliation(s)
- Jessica G Perez
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208-3120
| | - Jessica C Stark
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208-3120
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois 60208-3120.,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208-3120.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois 60611-3068.,Simpson Querrey Institute for BioNanotechnology, Northwestern University, Chicago, Illinois 60611-2875
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29
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Ojima-Kato T, Fukui K, Yamamoto H, Hashimura D, Miyake S, Hirakawa Y, Yamasaki T, Kojima T, Nakano H. 'Zipbody' leucine zipper-fused Fab in E. coli in vitro and in vivo expression systems. Protein Eng Des Sel 2016; 29:149-57. [PMID: 26902097 DOI: 10.1093/protein/gzw001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Accepted: 01/12/2016] [Indexed: 02/06/2023] Open
Abstract
A small antibody fragment, fragment of antigen binding (Fab), is favorable for various immunological assays. However, production efficiency of active Fab in microorganisms depends considerably on the clones. In this study, leucine zipper-peptide pairs that dimerize in parallel (ACID-p1 (LZA)/BASE-p1 (LZB) or c-Jun/c-Fos) were fused to the C-terminus of heavy chain (Hc, VH-CH1) and light chain (Lc, VL-CL), respectively, to accelerate the association of Hc and Lc to form Fab in Escherichia coli in vivo and in vitro expression systems. The leucine zipper-fused Fab named 'Zipbody' was constructed using anti-E. coli O157 monoclonal antibody obtained from mouse hybridoma and produced in both in vitro and in vivo expression systems in an active form, whereas Fab without the leucine zipper fusion was not. Similarly, Zipbody of rabbit monoclonal antibody produced in in vitro expression showed significant activity. The purified, mouse Zipbody produced in the E. coli strain Shuffle T7 Express had specificity toward the antigen; in bio-layer interferometry analysis, the KD value was measured to be 1.5-2.0 × 10(-8) M. These results indicate that leucine zipper fusion to Fab C-termini markedly enhances active Fab formation in E. coli.
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Affiliation(s)
- Teruyo Ojima-Kato
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan Knowledge Hub Aichi, Aichi Science and Technology Foundation, Yakusa-cho, Toyota 470-0356, Japan
| | - Kansuke Fukui
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Hiroaki Yamamoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Dai Hashimura
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Shiro Miyake
- Advanced Scientific Technology and Management Research Institute of Kyoto, Chudoji Minamimachi, Shimogyo-ku, Kyoto 600-8813, Japan
| | - Yuki Hirakawa
- Advanced Scientific Technology and Management Research Institute of Kyoto, Chudoji Minamimachi, Shimogyo-ku, Kyoto 600-8813, Japan
| | - Tomomi Yamasaki
- Advanced Scientific Technology and Management Research Institute of Kyoto, Chudoji Minamimachi, Shimogyo-ku, Kyoto 600-8813, Japan
| | - Takaaki Kojima
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Hideo Nakano
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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Awai T, Ichihashi N, Yomo T. Activities of 20 aminoacyl-tRNA synthetases expressed in a reconstituted translation system in Escherichia coli. Biochem Biophys Rep 2015; 3:140-143. [PMID: 29124177 PMCID: PMC5668874 DOI: 10.1016/j.bbrep.2015.08.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 08/06/2015] [Accepted: 08/06/2015] [Indexed: 01/18/2023] Open
Abstract
A significant challenge in the field of in vitro synthetic biology is the construction of a self-reproducing cell-free translation system, which reproduces its components, such as translation proteins, through translation and transcription by itself. As a first step for such construction, in this study we expressed and evaluated the activity of 20 aminoacyl-tRNA synthetases (aaRSs), a major component of a translation system, in a reconstituted translation system (PURE system). We found that 19 aaRS with the exception of phenylalanyl-tRNA synthetase (PheRS) are expressed as soluble proteins and their activities are comparable to those expressed in Escherichia coli . This study provides basic information on the properties of aaRSs expressed in the PURE system, which will be helpful for the future reconstitution of a self-reproducing translation system. We expressed 20 aminoacyl-tRNA synthetases in a reconstituted translation system. All aminoacyl-tRNA synthetases (aaRSs) are expressed as soluble proteins. All aaRSs with the exception of phenylalanyl-tRNA synthetase are active. Their activities are comparable to those expressed in E. coli.
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Affiliation(s)
- Takako Awai
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.,Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University, Japan
| | - Norikazu Ichihashi
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.,Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tetsuya Yomo
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.,Department of Bioinformatics Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.,Graduate School of Frontier Biosciences, Osaka University University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
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Mavelli F, Marangoni R, Stano P. A Simple Protein Synthesis Model for the PURE System Operation. Bull Math Biol 2015; 77:1185-212. [PMID: 25911591 DOI: 10.1007/s11538-015-0082-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 04/07/2015] [Indexed: 11/24/2022]
Abstract
The encapsulation of transcription-translation (TX-TL) cell-free machinery inside lipid vesicles (liposomes) is a key element in synthetic cell technology. The PURE system is a TX-TL kit composed of well-characterized parts, whose concentrations are fine tunable, which works according to a modular architecture. For these reasons, the PURE system perfectly fulfils the requirements of synthetic biology and is widely used for constructing synthetic cells. In this work, we present a simplified mathematical model to simulate the PURE system operations. Based on Michaelis-Menten kinetics and differential equations, the model describes protein synthesis dynamics by using 9 chemical species, 6 reactions and 16 kinetic parameters. The model correctly predicts the time course for messenger RNA and protein production and allows quantitative predictions. By means of this model, it is possible to foresee how the PURE system species affect the mechanism of proteins synthesis and therefore help in understanding scenarios where the concentration of the PURE system components has been modified purposely or as a result of stochastic fluctuations (for example after random encapsulation inside vesicles). The model also makes the determination of response coefficients for all species involved in the TX-TL mechanism possible and allows for scrutiny on how chemical energy is consumed by the three PURE system modules (transcription, translation and aminoacylation).
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Affiliation(s)
- Fabio Mavelli
- Chemistry Department, University of Bari, Via Orabona 4, Bari, Italy,
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