1
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Nishizawa C, Aburaya S, Kosaka Y, Sugase K, Aoki W. Optimizing in vitro expression balance of central dogma-related genes using parallel reaction monitoring. J Biosci Bioeng 2024; 138:97-104. [PMID: 38762340 DOI: 10.1016/j.jbiosc.2024.04.006] [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: 02/20/2024] [Revised: 04/05/2024] [Accepted: 04/25/2024] [Indexed: 05/20/2024]
Abstract
The creation of a self-replicating synthetic cell is an essential to understand life self-replication. One method to create self-replicating artificial cells is to reconstitute the self-replication system of living organisms in vitro. In a living cell, self-replication is achieved via a system called the autonomous central dogma, a system in which central dogma-related factors are autonomously synthesized and genome replication, transcription, and translation are driven by nascent factors. Various studies to reconstitute some processes of the autonomous central dogma in vitro have been conducted. However, in vitro reconstitution of the entire autonomous central dogma system is difficult as it requires balanced expression of several related genes. Therefore, we developed a method to simultaneously quantify and optimize the in vitro expression balance of multiple genes. First, we developed a quantitative mass spectrometry method targeting genome replication-related proteins as a model of central dogma-related factors and acquired in vitro expression profiles of these genes. Additionally, we demonstrated that the in vitro expression balance of these genes can be easily optimized by adjusting the input gene ratio based on the data obtained by the developed method. This study facilitated the easy optimization of the in vitro expression balance of multiple genes. Therefore, extending the scope of this method to other central dogma-related factors will accelerate attempts of self-replicating synthetic cells creation.
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Affiliation(s)
- Chisato Nishizawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.
| | - Shunsuke Aburaya
- Division of Metabolomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan.
| | - Yuishin Kosaka
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan; Japan Society for the Promotion of Science 606-8502, Kyoto, Japan.
| | - Kenji Sugase
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.
| | - Wataru Aoki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka 565-0871, Japan; Kyoto Integrated Science & Technology Bio-Analysis Center, Kyoto 600-8815, Japan.
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2
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Fu X, Shen Y. Synthetic Genomics: Repurposing Biological Systems for Applications in Engineering Biology. ACS Synth Biol 2024; 13:1394-1399. [PMID: 38757697 PMCID: PMC11106769 DOI: 10.1021/acssynbio.4c00006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Indexed: 05/18/2024]
Abstract
Substantial improvements in DNA sequencing and synthesis technologies and increased understanding of genome biology have empowered the development of synthetic genomics. The ability to design and construct engineered living cells boosted up by synthetic chromosomes provides opportunities to tackle enormous current and future challenges faced by humanity and the planet. Here we review the progresses, considerations, challenges, and future direction of the "design-build-test-learn" cycle used in synthetic genomics. We also discuss future applications enabled by synthetic genomics as this emerging field shapes and revolutionizes biomanufacturing and biomedicine.
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Affiliation(s)
- Xian Fu
- BGI
Research, Changzhou 213299, China
- BGI
Research, Shenzhen 518083, China
- Guangdong
Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen 518083, China
| | - Yue Shen
- BGI
Research, Changzhou 213299, China
- BGI
Research, Shenzhen 518083, China
- Guangdong
Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen 518083, China
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3
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Sato G, Kinoshita S, Yamada TG, Arai S, Kitaguchi T, Funahashi A, Doi N, Fujiwara K. Metabolic Tug-of-War between Glycolysis and Translation Revealed by Biochemical Reconstitution. ACS Synth Biol 2024; 13:1572-1581. [PMID: 38717981 DOI: 10.1021/acssynbio.4c00209] [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] [Indexed: 05/18/2024]
Abstract
Inside cells, various biological systems work cooperatively for homeostasis and self-replication. These systems do not work independently as they compete for shared elements like ATP and NADH. However, it has been believed that such competition is not a problem in codependent biological systems such as the energy-supplying glycolysis and the energy-consuming translation system. In this study, we biochemically reconstituted the coupling system of glycolysis and translation using purified elements and found that the competition for ATP between glycolysis and protein synthesis interferes with their coupling. Both experiments and simulations revealed that this interference is derived from a metabolic tug-of-war between glycolysis and translation based on their reaction rates, which changes the threshold of the initial substrate concentration for the success coupling. By the metabolic tug-of-war, translation energized by strong glycolysis is facilitated by an exogenous ATPase, which normally inhibits translation. These findings provide chemical insights into the mechanism of competition among biological systems in living cells and provide a framework for the construction of synthetic metabolism in vitro.
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Affiliation(s)
- Gaku Sato
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Saki Kinoshita
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Takahiro G Yamada
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
- Department of Molecular Biology, University of California San Diego, La Jolla, California 92093, United States
| | - Satoshi Arai
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Tetsuya Kitaguchi
- Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta-cho, Yokohama, Kanagawa 226-8503, Japan
| | - Akira Funahashi
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Nobuhide Doi
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Kei Fujiwara
- Department of Biosciences & Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
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4
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Rothschild LJ, Averesch NJH, Strychalski EA, Moser F, Glass JI, Cruz Perez R, Yekinni IO, Rothschild-Mancinelli B, Roberts Kingman GA, Wu F, Waeterschoot J, Ioannou IA, Jewett MC, Liu AP, Noireaux V, Sorenson C, Adamala KP. Building Synthetic Cells─From the Technology Infrastructure to Cellular Entities. ACS Synth Biol 2024; 13:974-997. [PMID: 38530077 PMCID: PMC11037263 DOI: 10.1021/acssynbio.3c00724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 03/27/2024]
Abstract
The de novo construction of a living organism is a compelling vision. Despite the astonishing technologies developed to modify living cells, building a functioning cell "from scratch" has yet to be accomplished. The pursuit of this goal alone has─and will─yield scientific insights affecting fields as diverse as cell biology, biotechnology, medicine, and astrobiology. Multiple approaches have aimed to create biochemical systems manifesting common characteristics of life, such as compartmentalization, metabolism, and replication and the derived features, evolution, responsiveness to stimuli, and directed movement. Significant achievements in synthesizing each of these criteria have been made, individually and in limited combinations. Here, we review these efforts, distinguish different approaches, and highlight bottlenecks in the current research. We look ahead at what work remains to be accomplished and propose a "roadmap" with key milestones to achieve the vision of building cells from molecular parts.
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Affiliation(s)
- Lynn J. Rothschild
- Space Science
& Astrobiology Division, NASA Ames Research
Center, Moffett
Field, California 94035-1000, United States
- Department
of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Nils J. H. Averesch
- Department
of Civil and Environmental Engineering, Stanford University, Stanford, California 94305, United States
| | | | - Felix Moser
- Synlife, One Kendall Square, Cambridge, Massachusetts 02139-1661, United States
| | - John I. Glass
- J.
Craig
Venter Institute, La Jolla, California 92037, United States
| | - Rolando Cruz Perez
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
- Blue
Marble
Space Institute of Science at NASA Ames Research Center, Moffett Field, California 94035-1000, United
States
| | - Ibrahim O. Yekinni
- Department
of Biomedical Engineering, University of
Minnesota, Minneapolis, Minnesota 55455, United States
| | - Brooke Rothschild-Mancinelli
- School
of Chemistry and Biochemistry, Georgia Institute
of Technology, Atlanta, Georgia 30332-0150, United States
| | | | - Feilun Wu
- J. Craig
Venter Institute, Rockville, Maryland 20850, United States
| | - Jorik Waeterschoot
- Mechatronics,
Biostatistics and Sensors (MeBioS), KU Leuven, 3000 Leuven Belgium
| | - Ion A. Ioannou
- Department
of Chemistry, MSRH, Imperial College London, London W12 0BZ, U.K.
| | - Michael C. Jewett
- Department
of Bioengineering, Stanford University, Stanford, California 94305, United States
| | - Allen P. Liu
- Mechanical
Engineering & Biomedical Engineering, Cellular and Molecular Biology,
Biophysics, Applied Physics, University
of Michigan, Ann Arbor, Michigan 48109, United States
| | - Vincent Noireaux
- Physics
and Nanotechnology, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Carlise Sorenson
- Department
of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Katarzyna P. Adamala
- Department
of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, United States
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5
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Marano JM, Cereghino C, Finkielstein CV, Weger-Lucarelli J. An in vitro workflow to create and modify infectious clones using replication cycle reaction. Virology 2023; 585:109-116. [PMID: 37331111 PMCID: PMC10528026 DOI: 10.1016/j.virol.2023.05.013] [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: 04/19/2023] [Revised: 05/25/2023] [Accepted: 05/28/2023] [Indexed: 06/20/2023]
Abstract
Reverse genetics systems are critical tools in combating emerging viruses which enable a better understanding of the genetic mechanisms by which viruses cause disease. Traditional cloning approaches using bacteria are fraught with difficulties due to the bacterial toxicity of many viral sequences, resulting in unwanted mutations within the viral genome. Here, we describe a novel in vitro workflow that leverages gene synthesis and replication cycle reaction to produce a supercoiled infectious clone plasmid that is easy to distribute and manipulate. We developed two infectious clones as proof of concept: a low passage dengue virus serotype 2 isolate (PUO-218) and the USA-WA1/2020 strain of SARS-CoV-2, which replicated similarly to their respective parental viruses. Furthermore, we generated a medically relevant mutant of SARS-CoV-2, Spike D614G. Results indicate that our workflow is a viable method to generate and manipulate infectious clones for viruses that are notoriously difficult for traditional bacterial-based cloning methods.
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Affiliation(s)
- Jeffrey M Marano
- Translational Biology, Medicine, and Health Graduate Program, Virginia Tech, Roanoke, VA, USA; Department of Biomedical Sciences and Pathobiology, Virginia Tech, VA-MD Regional College of Veterinary Medicine, Blacksburg, VA, United States; Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA, United States.
| | - Chelsea Cereghino
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, VA-MD Regional College of Veterinary Medicine, Blacksburg, VA, United States; Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA, United States.
| | - Carla V Finkielstein
- Molecular Diagnostics Laboratory, Fralin Biomedical Research Institute, Virginia Tech, Roanoke, VA, USA; Integrated Cellular Responses Laboratory, Fralin Biomedical Research Institute at VTC, Roanoke, VA, USA; Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - James Weger-Lucarelli
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, VA-MD Regional College of Veterinary Medicine, Blacksburg, VA, United States; Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Tech, Blacksburg, VA, United States.
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6
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Ito Y, Sasaki R, Asari S, Yasuda T, Ueda H, Kitaguchi T. Efficient Microfluidic Screening Method Using a Fluorescent Immunosensor for Recombinant Protein Secretions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2207943. [PMID: 37093208 DOI: 10.1002/smll.202207943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/20/2023] [Indexed: 05/03/2023]
Abstract
Microbial secretory protein expression is widely used for biopharmaceutical protein production. However, establishing genetically modified industrial strains that secrete large amounts of a protein of interest is time-consuming. In this study, a simple and versatile high-throughput screening method for protein-secreting bacterial strains is developed. Different genotype variants induced by mutagens are encapsulated in microemulsions and cultured to secrete proteins inside the emulsions. The secreted protein of interest is detected as a fluorescence signal by the fluorescent immunosensor quenchbody (Q-body), and a cell sorter is used to select emulsions containing improved protein-secreting strains based on the fluorescence intensity. The concept of the screening method is demonstrated by culturing Corynebacterium glutamicum in emulsions and detecting the secreted proteins. Finally, productive strains of fibroblast growth factor 9 (FGF9) are screened, and the FGF9 secretion increased threefold compared to that of parent strain. This screening method can be applied to a wide range of proteins by fusing a small detection tag. This is a highly simple process that requires only the addition of a Q-body to the medium and does not require the addition of any substrates or chemical treatments. Furthermore, this method shortens the development period of industrial strains for biopharmaceutical protein production.
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Affiliation(s)
- Yoshihiro Ito
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, 226-8503, Japan
- Research Institute for Bioscience Products and Fine Chemicals, Ajinomoto Co., Inc, Kawasaki, Kanagawa, 210-8681, Japan
| | - Ryuichi Sasaki
- Research Institute for Bioscience Products and Fine Chemicals, Ajinomoto Co., Inc, Kawasaki, Kanagawa, 210-8681, Japan
| | - Sayaka Asari
- Research Institute for Bioscience Products and Fine Chemicals, Ajinomoto Co., Inc, Kawasaki, Kanagawa, 210-8681, Japan
| | - Takanobu Yasuda
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa, 226-8503, Japan
| | - Hiroshi Ueda
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa, 226-8503, Japan
| | - Tetsuya Kitaguchi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa, 226-8503, Japan
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7
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Huynh LT, Isoda N, Hew LY, Ogino S, Mimura Y, Kobayashi M, Kim T, Nishi T, Fukai K, Hiono T, Sakoda Y. Generation and Efficacy of Two Chimeric Viruses Derived from GPE - Vaccine Strain as Classical Swine Fever Vaccine Candidates. Viruses 2023; 15:1587. [PMID: 37515273 PMCID: PMC10384557 DOI: 10.3390/v15071587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
A previous study proved that vGPE- mainly maintains the properties of classical swine fever (CSF) virus, which is comparable to the GPE- vaccine seed and is a potentially valuable backbone for developing a CSF marker vaccine. Chimeric viruses were constructed based on an infectious cDNA clone derived from the live attenuated GPE- vaccine strain as novel CSF vaccine candidates that potentially meet the concept of differentiating infected from vaccinated animals (DIVA) by substituting the glycoprotein Erns of the GPE- vaccine strain with the corresponding region of non-CSF pestiviruses, either pronghorn antelope pestivirus (PAPeV) or Phocoena pestivirus (PhoPeV). High viral growth and genetic stability after serial passages of the chimeric viruses, namely vGPE-/PAPeV Erns and vGPE-/PhoPeV Erns, were confirmed in vitro. In vivo investigation revealed that two chimeric viruses had comparable immunogenicity and safety profiles to the vGPE- vaccine strain. Vaccination at a dose of 104.0 TCID50 with either vGPE-/PAPeV Erns or vGPE-/PhoPeV Erns conferred complete protection for pigs against the CSF virus challenge in the early stage of immunization. In conclusion, the characteristics of vGPE-/PAPeV Erns and vGPE-/PhoPeV Erns affirmed their properties, as the vGPE- vaccine strain, positioning them as ideal candidates for future development of a CSF marker vaccine.
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Affiliation(s)
- Loc Tan Huynh
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Hokkaido, Japan
- Faculty of Veterinary Medicine, College of Agriculture, Can Tho University, Can Tho 900000, Vietnam
| | - Norikazu Isoda
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Hokkaido, Japan
- One Health Research Center, Hokkaido University, Sapporo 060-0818, Hokkaido, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Hokkaido, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo 001-0021, Hokkaido, Japan
| | - Lim Yik Hew
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Hokkaido, Japan
| | - Saho Ogino
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Hokkaido, Japan
| | - Yume Mimura
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Hokkaido, Japan
| | - Maya Kobayashi
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Hokkaido, Japan
| | - Taksoo Kim
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Hokkaido, Japan
| | - Tatsuya Nishi
- Kodaira Research Station, National Institute of Animal Health, National Agriculture and Food Research Organization, Kodaira 187-0022, Tokyo, Japan
| | - Katsuhiko Fukai
- Kodaira Research Station, National Institute of Animal Health, National Agriculture and Food Research Organization, Kodaira 187-0022, Tokyo, Japan
| | - Takahiro Hiono
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Hokkaido, Japan
- One Health Research Center, Hokkaido University, Sapporo 060-0818, Hokkaido, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo 001-0021, Hokkaido, Japan
| | - Yoshihiro Sakoda
- Laboratory of Microbiology, Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Hokkaido, Japan
- One Health Research Center, Hokkaido University, Sapporo 060-0818, Hokkaido, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Hokkaido, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo 001-0021, Hokkaido, Japan
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8
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Hagino K, Ichihashi N. In Vitro Transcription/Translation-Coupled DNA Replication through Partial Regeneration of 20 Aminoacyl-tRNA Synthetases. ACS Synth Biol 2023; 12:1252-1263. [PMID: 37053032 DOI: 10.1021/acssynbio.3c00014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
The in vitro reconstruction of life-like self-reproducing systems is a major challenge in in vitro synthetic biology. Self-reproduction requires regeneration of all molecules involved in DNA replication, transcription, and translation. This study demonstrated the continuous DNA replication and partial regeneration of major translation factors, 20 aminoacyl-tRNA synthetases (aaRS), in a reconstituted transcription/translation system (PURE system) for the first time. First, we replicated each DNA that encodes one of the 20 aaRSs through aaRS expression from the DNA by serial transfer experiments. Thereafter, we successively increased the number of aaRS genes and achieved simultaneous, continuous replication of DNA that encodes all 20 aaRSs, which comprised approximately half the number of protein factors in the PURE system, except for ribosomes, by employing dialyzed reaction and sequence optimization. This study provides a step-by-step methodology for continuous DNA replication with an increasing number of self-regenerative genes toward self-reproducing artificial systems.
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Affiliation(s)
- Katsumi Hagino
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
| | - Norikazu Ichihashi
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
- Universal Biology Institute, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
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9
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Seo K, Hagino K, Ichihashi N. Progresses in Cell-Free In Vitro Evolution. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 186:121-140. [PMID: 37306699 DOI: 10.1007/10_2023_219] [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
Biopolymers, such as proteins and RNA, are integral components of living organisms and have evolved through a process of repeated mutation and selection. The technique of "cell-free in vitro evolution" is a powerful experimental approach for developing biopolymers with desired functions and structural properties. Since Spiegelman's pioneering work over 50 years ago, biopolymers with a wide range of functions have been developed using in vitro evolution in cell-free systems. The use of cell-free systems offers several advantages, including the ability to synthesize a wider range of proteins without the limitations imposed by cytotoxicity, and the capacity for higher throughput and larger library sizes than cell-based evolutionary experiments. In this chapter, we provide a comprehensive overview of the progress made in the field of cell-free in vitro evolution by categorizing evolution into directed and undirected. The biopolymers produced by these methods are valuable assets in medicine and industry, and as a means of exploring the potential of biopolymers.
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Affiliation(s)
- Kaito Seo
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, Tokyo, Japan
| | - Katsumi Hagino
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, Tokyo, Japan
| | - Norikazu Ichihashi
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, Tokyo, Japan.
- Komaba Institute for Science, The University of Tokyo, Tokyo, Japan.
- Universal Biology Institute, The University of Tokyo, Tokyo, Japan.
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10
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Bae C, Katoh H, Wakata A, Sakata M, Kato F, Takeda M. Demonstration of bacterium-free very rapid reverse genetics system using mumps virus. Microbiol Immunol 2023; 67:44-47. [PMID: 36259144 PMCID: PMC10092663 DOI: 10.1111/1348-0421.13032] [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: 07/15/2022] [Revised: 09/20/2022] [Accepted: 09/30/2022] [Indexed: 01/10/2023]
Abstract
The reverse genetics system is a very powerful tool for analyzing the molecular mechanisms of viral propagation and pathogenesis. However, full-length genome plasmid construction is highly time-consuming and laborious, and undesired mutations may be introduced by Escherichia coli. This study shows a very rapid E. coli-free method of full-genome construction using the mumps virus as an example. This method was able to reduce dramatically the time for full-genome construction, which was used very efficiently for virus rescue, from several days or more to ~2 days, with a similar accuracy and yield to the conventional method using E. coli/plasmid.
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Affiliation(s)
- Chaewon Bae
- Department of Virology III, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hiroshi Katoh
- Department of Virology III, National Institute of Infectious Diseases, Tokyo, Japan
| | - Aika Wakata
- Department of Virology III, National Institute of Infectious Diseases, Tokyo, Japan
| | - Masafumi Sakata
- Department of Virology III, National Institute of Infectious Diseases, Tokyo, Japan
| | - Fumihiro Kato
- Department of Virology III, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Takeda
- Department of Virology III, National Institute of Infectious Diseases, Tokyo, Japan
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11
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Han F, Xu B, Lu N, Caliari A, Lu H, Xia Y, Su'etsugu M, Xu J, Yomo T. Optimization and compartmentalization of a cell-free mixture of DNA amplification and protein translation. Appl Microbiol Biotechnol 2022; 106:8139-8149. [PMID: 36355086 DOI: 10.1007/s00253-022-12278-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/30/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022]
Abstract
Recent studies have shown that the reconstituted cell-free DNA replisome and in vitro transcription and translation systems from Escherichia coli are highly important in applied and synthetic biology. To date, no attempt has been made to combine those two systems. Here, we study the performance of the mixed two separately exploited systems commercially available as RCR and PURE systems. Regarding the genetic information flow from DNA to proteins, mixtures with various ratios of RCR/PURE gave low protein expression, possibly due to the well-known conflict between replication and transcription or inappropriate buffer conditions. To further increase the compatibility of the two systems, rationally designed reaction buffers with a lower concentration of nucleoside triphosphates in 50 mM HEPES (pH7.6) were evaluated, showing increased performance from RCR/PURE (85%/15%) in a time-dependent manner. The compatibility was also validated in compartmentalized cell-sized droplets encapsulating the same RCR/PURE soup. Our findings can help to better fine-tune the reaction conditions of RCR-PURE systems and provide new avenues for rewiring the central dogma of molecular biology as self-sustaining systems in synthetic cell models. KEY POINTS: • Commercial reconstituted DNA amplification (RCR) and transcription and translation (PURE) systems hamper each other upon mixing. • A newly optimized buffer with a low bias for PURE was formulated in the RCR-PURE mixture. • The performance and dynamics of RCR-PURE were investigated in either bulk or compartmentalized droplets.
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Affiliation(s)
- Fuhai Han
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai, 200062, People's Republic of China
| | - Boying Xu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai, 200062, People's Republic of China.,Tongji University Cancer Center, Shanghai Tenth People's Hospital, School of Medicine, Tongji University, Shanghai, 200072, China
| | - Nan Lu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai, 200062, People's Republic of China
| | - Adriano Caliari
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai, 200062, People's Republic of China
| | - Hui Lu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai, 200062, People's Republic of China
| | - Yang Xia
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai, 200062, People's Republic of China
| | - Masayuki Su'etsugu
- Department of Life Science, College of Science, Rikkyo University, Tokyo, 171-8501, Japan
| | - Jian Xu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai, 200062, People's Republic of China.
| | - Tetsuya Yomo
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai, 200062, People's Republic of China.
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12
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Phospholipid synthesis inside phospholipid membrane vesicles. Commun Biol 2022; 5:1016. [PMID: 36167778 PMCID: PMC9515091 DOI: 10.1038/s42003-022-03999-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/14/2022] [Indexed: 12/24/2022] Open
Abstract
Construction of living artificial cells from genes and molecules can expand our understanding of life system and establish a new aspect of bioengineering. However, growth and division of cell membrane that are basis of cell proliferation are still difficult to reconstruct because a high-yielding phospholipid synthesis system has not been established. Here, we developed a cell-free phospholipid synthesis system that combines fatty acid synthesis and cell-free gene expression system synthesizing acyltransferases. The synthesized fatty acids were sequentially converted into phosphatidic acids by the cell-free synthesized acyltransferases. Because the system can avoid the accumulation of intermediates inhibiting lipid synthesis, sub-millimolar phospholipids could be synthesized within a single reaction mixture. We also performed phospholipid synthesis inside phospholipid membrane vesicles, which encapsulated all the components, and showed the phospholipids localized onto the mother membrane. Our approach would be a platform for the construction of self-reproducing artificial cells since the membrane can grow sustainably.
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13
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Fujita H, Osaku A, Sakane Y, Yoshida K, Yamada K, Nara S, Mukai T, Su’etsugu M. Enzymatic Supercoiling of Bacterial Chromosomes Facilitates Genome Manipulation. ACS Synth Biol 2022; 11:3088-3099. [PMID: 35998348 PMCID: PMC9486964 DOI: 10.1021/acssynbio.2c00353] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The physical stability of bacterial chromosomes is important for their in vitro manipulation, while genetic stability is important in vivo. However, extracted naked chromosomes in the open circular form are fragile due to nicks and gaps. Using a nick/gap repair and negative supercoiling reaction (named SCR), we first achieved the negative supercoiling of the whole genomes extracted from Escherichia coli and Vibrio natriegens cells. Supercoiled chromosomes of 0.2-4.6 megabase (Mb) were separated by size using a conventional agarose gel electrophoresis and served as DNA size markers. We also achieved the enzymatic replication of 1-2 Mb chromosomes using the reconstituted E. coli replication-cycle reaction (RCR). Electroporation-ready 1 Mb chromosomes were prepared by a modified SCR performed at a low salt concentration (L-SCR) and directly introduced into commercial electrocompetent E. coli cells. Since successful electroporation relies on the genetic stability of a chromosome in cells, genetically stable 1 Mb chromosomes were developed according to a portable chromosome format (PCF). Using physically and genetically stabilized chromosomes, the democratization of genome synthetic biology will be greatly accelerated.
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14
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Noji H, Minagawa Y, Ueno H. Enzyme-based digital bioassay technology - key strategies and future perspectives. LAB ON A CHIP 2022; 22:3092-3109. [PMID: 35861036 DOI: 10.1039/d2lc00223j] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Digital bioassays based on single-molecule enzyme reactions represent a new class of bioanalytical methods that enable the highly sensitive detection of biomolecules in a quantitative manner. Since the first reports of these methods in the 2000s, there has been significant growth in this new bioanalytical strategy. The principal strategy of this method is to compartmentalize target molecules in micron-sized reactors at the single-molecule level and count the number of microreactors showing positive signals originating from the target molecule. A representative application of digital bioassay is the digital enzyme-linked immunosorbent assay (ELISA). Owing to their versatility, various types of digital ELISAs have been actively developed. In addition, some disease markers and viruses possess catalytic activity, and digital bioassays for such enzymes and viruses have, thus, been developed. Currently, with the emergence of new microreactor technologies, the targets of this methodology are expanding from simple enzymes to more complex systems, such as membrane transporters and cell-free gene expression. In addition, multiplex or multiparametric digital bioassays have been developed to assess precisely the heterogeneities in sample molecules/systems that are obscured by ensemble measurements. In this review, we first introduce the basic concepts of digital bioassays and introduce a range of digital bioassays. Finally, we discuss the perspectives of new classes of digital bioassays and emerging fields based on digital bioassay technology.
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Affiliation(s)
- Hiroyuki Noji
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan.
| | - Yoshihiro Minagawa
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan.
| | - Hiroshi Ueno
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan.
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15
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Miyachi R, Shimizu Y, Ichihashi N. Transfer RNA Synthesis-Coupled Translation and DNA Replication in a Reconstituted Transcription/Translation System. ACS Synth Biol 2022; 11:2791-2799. [PMID: 35848947 DOI: 10.1021/acssynbio.2c00163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Transfer RNAs (tRNAs) are key molecules involved in translation. In vitro synthesis of tRNAs and their coupled translation are important challenges in the construction of a self-regenerative molecular system. Here, we first purified EF-Tu and ribosome components in a reconstituted translation system of Escherichia coli to remove residual tRNAs. Next, we expressed 15 types of tRNAs in the repurified translation system and performed translation of the reporter luciferase gene depending on the expression. Furthermore, we demonstrated DNA replication through expression of a tRNA encoded by DNA, mimicking information processing within the cell. Our findings highlight the feasibility of an in vitro self-reproductive system, in which tRNAs can be synthesized from replicating DNA.
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Affiliation(s)
- Ryota Miyachi
- 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 Shimizu
- Laboratory for Cell-Free Protein Synthesis, RIKEN Center for Biosystems Dynamics Research (BDR), Suita 565-0874, Osaka, 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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16
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Jiang S, Tang Y, Xiang L, Zhu X, Cai Z, Li L, Chen Y, Chen P, Feng Y, Lin X, Li G, Sharif J, Dai J. Efficient de novo assembly and modification of large DNA fragments. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1445-1455. [PMID: 34939159 DOI: 10.1007/s11427-021-2029-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 11/11/2021] [Indexed: 06/14/2023]
Abstract
Synthetic genomics has provided new bottom-up platforms for the functional study of viral and microbial genomes. The construction of the large, gigabase (Gb)-sized genomes of higher organisms will deepen our understanding of genetic blueprints significantly. But for the synthesis and assembly of such large-scale genomes, the development of new or expanded methods is required. In this study, we develop an efficient pipeline for the construction of large DNA fragments sized 100 kilobases (kb) or above from scratches and describe an efficient method for "scar-free" engineering of the assembled sequences. Our method, therefore, should provide a standard framework for producing long DNA molecules, which are critical materials for synthetic genomics and metabolic engineering.
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Affiliation(s)
- Shuangying Jiang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yuanwei Tang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Liang Xiang
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Xinlu Zhu
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Zelin Cai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ling Li
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yingxi Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Peishuang Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Yuge Feng
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Lin
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Guoqiang Li
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Jafar Sharif
- Developmental Genetics Laboratory, RIKEN Center for Integrative Medical Sciences (IMS), Yokohama, 230-0045, Japan
| | - Junbiao Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Guangdong Provincial Key Laboratory of Synthetic Genomics and Shenzhen Key Laboratory of Synthetic Genomics, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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17
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Koster CC, Postma ED, Knibbe E, Cleij C, Daran-Lapujade P. Synthetic Genomics From a Yeast Perspective. Front Bioeng Biotechnol 2022; 10:869486. [PMID: 35387293 PMCID: PMC8979029 DOI: 10.3389/fbioe.2022.869486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 02/28/2022] [Indexed: 11/21/2022] Open
Abstract
Synthetic Genomics focuses on the construction of rationally designed chromosomes and genomes and offers novel approaches to study biology and to construct synthetic cell factories. Currently, progress in Synthetic Genomics is hindered by the inability to synthesize DNA molecules longer than a few hundred base pairs, while the size of the smallest genome of a self-replicating cell is several hundred thousand base pairs. Methods to assemble small fragments of DNA into large molecules are therefore required. Remarkably powerful at assembling DNA molecules, the unicellular eukaryote Saccharomyces cerevisiae has been pivotal in the establishment of Synthetic Genomics. Instrumental in the assembly of entire genomes of various organisms in the past decade, the S. cerevisiae genome foundry has a key role to play in future Synthetic Genomics developments.
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Affiliation(s)
- Charlotte C Koster
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Eline D Postma
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Ewout Knibbe
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Céline Cleij
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands.,Department of Bionanoscience, Delft University of Technology, Delft, Netherlands
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18
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Okauchi H, Ichihashi N. Continuous Cell-Free Replication and Evolution of Artificial Genomic DNA in a Compartmentalized Gene Expression System. ACS Synth Biol 2021; 10:3507-3517. [PMID: 34781676 DOI: 10.1021/acssynbio.1c00430] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
In all living organisms, genomic DNA continuously replicates by the proteins encoded in itself and undergoes evolution through many generations of replication. This continuous replication coupled with gene expression and the resultant evolution are fundamental functions of living things, but they have not previously been reconstituted in cell-free systems. In this study, we combined an artificial DNA replication scheme with a reconstituted gene expression system and microcompartmentalization to realize these functions. Circular DNA replicated through rolling-circle replication followed by homologous recombination catalyzed by the proteins, phi29 DNA polymerase, and Cre recombinase expressed from the DNA. We encapsulated the system in microscale water-in-oil droplets and performed serial dilution cycles. Isolated circular DNAs at Round 30 accumulated several common mutations, and the isolated DNA clones exhibited higher replication abilities than the original DNA due to its improved ability as a replication template, increased polymerase activity, and a reduced inhibitory effect of polymerization by the recombinase. The artificial genomic DNA, which continuously replicates using self-encoded proteins and autonomously improves its sequence, provides a useful starting point for the development of more complex artificial cells.
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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
| | - 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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19
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Uyeda A, Reyes SG, Kanamori T, Matsuura T. Identification of conditions for efficient cell-sized liposome preparation using commercially available reconstituted in vitro transcription-translation system. J Biosci Bioeng 2021; 133:181-186. [PMID: 34789414 DOI: 10.1016/j.jbiosc.2021.10.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/14/2021] [Accepted: 10/24/2021] [Indexed: 12/29/2022]
Abstract
Attempts to create complex molecular systems that mimic parts of cellular systems using a bottom-up approach have become important in the field of biology. Among various molecular systems, in vitro protein synthesis inside lipid vesicles (liposomes), which we refer to as the artificial cell, has become an attractive system because it possesses two fundamental features of living cells: central dogma, and compartmentalization. Here, we investigated the effect of altering the amount or concentration of four constituents of the artificial cell consisting of a commercially available reconstituted in vitro transcription-translation (IVTT) system. As this IVTT system is available worldwide, the results will be useful to the scientific community when shared, unlike those from a lab-made IVTT system. We succeeded in revealing the effect and trend of altering each parameter and identified a suitable condition for preparing liposomes that are unilamellar and can synthesize proteins equally as well as the original IVTT system. Because the commercially available reconstituted IVTT system is an important standardization tool and the constituents can be adjusted as desired, our results will be useful for the bottom-up creation of more complex molecular systems.
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Affiliation(s)
- Atsuko Uyeda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Sabrina Galiñanes Reyes
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-i7E Ookayama, Meguro-Ku, Tokyo 152-8550, Japan.
| | - Takashi Kanamori
- GeneFrontier Corporation, SHARP Kashiwa Building, 4F, 273-1 Kashiwa, Kashiwa-shi, Chiba 277-0005, Japan.
| | - Tomoaki Matsuura
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-i7E Ookayama, Meguro-Ku, Tokyo 152-8550, Japan.
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20
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Ueno H, Sawada H, Soga N, Sano M, Nara S, Tabata KV, Su’etsugu M, Noji H. Amplification of over 100 kbp DNA from Single Template Molecules in Femtoliter Droplets. ACS Synth Biol 2021; 10:2179-2186. [PMID: 34406762 DOI: 10.1021/acssynbio.0c00584] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Reconstitution of the DNA amplification system in microcompartments is the primary step toward artificial cell construction through a bottom-up approach. However, amplification of >100 kbp DNA in micrometer-sized reactors has not yet been achieved. Here, implementing a fully reconstituted replisome of Escherichia coli in micrometer-sized water-in-oil droplets, we developed the in-droplet replication cycle reaction (RCR) system. For a 16 kbp template DNA, the in-droplet RCR system yielded positive RCR signals with a high success rate (82%) for the amplification from single molecule template DNA. The success rate for a 208 kbp template DNA was evidently lower (23%). This study establishes a platform for genome-sized DNA amplification from a single copy of template DNA with the potential to build more complex artificial cell systems comprising a large number of genes.
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Affiliation(s)
- Hiroshi Ueno
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Hiroki Sawada
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Naoki Soga
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Mio Sano
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Seia Nara
- Department of Life Science, College of Science, Rikkyo University, Tokyo 171-8501, Japan
| | - Kazuhito V. Tabata
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
| | - Masayuki Su’etsugu
- Department of Life Science, College of Science, Rikkyo University, Tokyo 171-8501, Japan
| | - Hiroyuki Noji
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan
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21
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In vitro amplification of whole large plasmids via transposon-mediated oriC insertion. Biotechniques 2021; 71:528-533. [PMID: 34463121 DOI: 10.2144/btn-2021-0068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
DNA amplification is a fundamental technique in molecular biology. The replication cycle reaction is a new method for amplification of large circular DNA having oriC sequences, which is a replication initiation site of the Escherichia coli chromosome. We here developed a replication cycle reaction-based method useful for amplification of various circular DNAs lacking oriC, even in the absence of any sequence information, via transposon-mediated oriC insertion to the circular DNA template. A 15-kb non-oriC plasmid was amplified from a very small amount of starting DNA (50 fg, 1 fM). The method was also applicable to GC-rich plasmid (69%) or large F-plasmid (230 kb). This method thus provides a powerful tool to amplify various environmental circular DNAs.
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22
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Olivi L, Berger M, Creyghton RNP, De Franceschi N, Dekker C, Mulder BM, Claassens NJ, Ten Wolde PR, van der Oost J. Towards a synthetic cell cycle. Nat Commun 2021; 12:4531. [PMID: 34312383 PMCID: PMC8313558 DOI: 10.1038/s41467-021-24772-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 06/29/2021] [Indexed: 02/08/2023] Open
Abstract
Recent developments in synthetic biology may bring the bottom-up generation of a synthetic cell within reach. A key feature of a living synthetic cell is a functional cell cycle, in which DNA replication and segregation as well as cell growth and division are well integrated. Here, we describe different approaches to recreate these processes in a synthetic cell, based on natural systems and/or synthetic alternatives. Although some individual machineries have recently been established, their integration and control in a synthetic cell cycle remain to be addressed. In this Perspective, we discuss potential paths towards an integrated synthetic cell cycle.
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Affiliation(s)
- Lorenzo Olivi
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | | | | | - Nicola De Franceschi
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | | | - Nico J Claassens
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | | | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
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23
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Xu Y, Wu Y, Lv X, Sun G, Zhang H, Chen T, Du G, Li J, Liu L. Design and construction of novel biocatalyst for bioprocessing: Recent advances and future outlook. BIORESOURCE TECHNOLOGY 2021; 332:125071. [PMID: 33826982 DOI: 10.1016/j.biortech.2021.125071] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Bioprocess, a biocatalysis-based technology, is becoming popular in many research fields and widely applied in industrial manufacturing. However, low bioconversion, low productivity, and high costs during industrial processes are usually the limitation in bioprocess. Therefore, many biocatalyst strategies have been developed to meet these challenges in recent years. In this review, we firstly discuss protein engineering strategies, which are emerged for improving the biocatalysis activity of biocatalysts. Then, we summarize metabolic engineering strategies that are promoting the development of microbial cell factories. Next, we illustrate the necessity of using the combining strategy of protein engineering and metabolic engineering for efficient biocatalysts. Lastly, future perspectives about the development and application of novel biocatalyst strategies are discussed. This review provides theoretical guidance for the development of efficient, sustainable, and economical bioprocesses mediated by novel biocatalysts.
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Affiliation(s)
- Yameng Xu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Yaokang Wu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Guoyun Sun
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Hongzhi Zhang
- Shandong Runde Biotechnology Co., Ltd., Tai'an 271000, PR China
| | - Taichi Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, PR China; Science Center for Future Foods, Jiangnan University, Wuxi 214122, PR China.
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24
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Yoneji T, Fujita H, Mukai T, Su'etsugu M. Grand scale genome manipulation via chromosome swapping in Escherichia coli programmed by three one megabase chromosomes. Nucleic Acids Res 2021; 49:8407-8418. [PMID: 33907814 PMCID: PMC8421210 DOI: 10.1093/nar/gkab298] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/06/2021] [Accepted: 04/10/2021] [Indexed: 11/30/2022] Open
Abstract
In bacterial synthetic biology, whole genome transplantation has been achieved only in mycoplasmas that contain a small genome and are competent for foreign genome uptake. In this study, we developed Escherichia coli strains programmed by three 1-megabase (Mb) chromosomes by splitting the 3-Mb chromosome of a genome-reduced strain. The first split-chromosome retains the original replication origin (oriC) and partitioning (par) system. The second one has an oriC and the par locus from the F plasmid, while the third one has the ori and par locus of the Vibrio tubiashii secondary chromosome. The tripartite-genome cells maintained the rod-shaped form and grew only twice as slowly as their parent, allowing their further genetic engineering. A proportion of these 1-Mb chromosomes were purified as covalently closed supercoiled molecules with a conventional alkaline lysis method and anion exchange columns. Furthermore, the second and third chromosomes could be individually electroporated into competent cells. In contrast, the first split-chromosome was not able to coexist with another chromosome carrying the same origin region. However, it was exchangeable via conjugation between tripartite-genome strains by using different selection markers. We believe that this E. coli-based technology has the potential to greatly accelerate synthetic biology and synthetic genomics.
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Affiliation(s)
- Tatsuya Yoneji
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Hironobu Fujita
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Takahito Mukai
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Masayuki Su'etsugu
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
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25
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Lavickova B, Laohakunakorn N, Maerkl SJ. A partially self-regenerating synthetic cell. Nat Commun 2020; 11:6340. [PMID: 33311509 PMCID: PMC7733450 DOI: 10.1038/s41467-020-20180-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/16/2020] [Indexed: 01/16/2023] Open
Abstract
Self-regeneration is a fundamental function of all living systems. Here we demonstrate partial molecular self-regeneration in a synthetic cell. By implementing a minimal transcription-translation system within microfluidic reactors, the system is able to regenerate essential protein components from DNA templates and sustain synthesis activity for over a day. By quantitating genotype-phenotype relationships combined with computational modeling we find that minimizing resource competition and optimizing resource allocation are both critically important for achieving robust system function. With this understanding, we achieve simultaneous regeneration of multiple proteins by determining the required DNA ratios necessary for sustained self-regeneration. This work introduces a conceptual and experimental framework for the development of a self-replicating synthetic cell.
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Affiliation(s)
- Barbora Lavickova
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Nadanai Laohakunakorn
- Institute of Quantitative Biology, Biochemistry, and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Sebastian J Maerkl
- Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
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26
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Coradini ALV, Hull CB, Ehrenreich IM. Building genomes to understand biology. Nat Commun 2020; 11:6177. [PMID: 33268788 PMCID: PMC7710724 DOI: 10.1038/s41467-020-19753-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/29/2020] [Indexed: 02/06/2023] Open
Abstract
Genetic manipulation is one of the central strategies that biologists use to investigate the molecular underpinnings of life and its diversity. Thus, advances in genetic manipulation usually lead to a deeper understanding of biological systems. During the last decade, the construction of chromosomes, known as synthetic genomics, has emerged as a novel approach to genetic manipulation. By facilitating complex modifications to chromosome content and structure, synthetic genomics opens new opportunities for studying biology through genetic manipulation. Here, we discuss different classes of genetic manipulation that are enabled by synthetic genomics, as well as biological problems they each can help solve.
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Affiliation(s)
- Alessandro L V Coradini
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-2910, USA
| | - Cara B Hull
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-2910, USA
| | - Ian M Ehrenreich
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-2910, USA.
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27
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Mukai T, Yoneji T, Yamada K, Fujita H, Nara S, Su'etsugu M. Overcoming the Challenges of Megabase-Sized Plasmid Construction in Escherichia coli. ACS Synth Biol 2020; 9:1315-1327. [PMID: 32459960 DOI: 10.1021/acssynbio.0c00008] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Although Escherichia coli has been a popular tool for plasmid construction, this bacterium was believed to be "unsuitable" for constructing a large plasmid whose size exceeds 500 kilobases. We assumed that traditional plasmid vectors may lack some regulatory DNA elements required for the stable replication and segregation of such a large plasmid. In addition, the use of a few site-specific recombination systems may facilitate cloning of large DNA segments. Here we show two strategies for constructing 1-megabase (1-Mb) secondary chromosomes by using new bacterial artificial chromosome (BAC) vectors. First, the 3-Mb genome of a genome-reduced E. coli strain was split into two chromosomes (2-Mb and 1-Mb), of which the smaller one has the origin of replication and the partitioning locus of the Vibrio tubiashii secondary chromosome. This chromosome fission method (Flp-POP cloning) works via flippase-mediated excision, which coincides with the reassembly of a split chloramphenicol resistance gene, allowing chloramphenicol selection. Next, we developed a new cloning method (oriT-POP cloning) and a fully equipped BAC vector (pMegaBAC1H) for developing a 1-Mb plasmid. Two 0.5-Mb genomic regions were sequentially transferred from two donor strains to a recipient strain via conjugation and captured by pMegaBAC1H in the recipient strain to produce a 1-Mb plasmid. This 1-Mb plasmid was transmissible to another E. coli strain via conjugation. Furthermore, these 1-Mb secondary chromosomes were amplifiable in vitro by using the reconstituted E. coli chromosome replication cycle reaction (RCR). These strategies and technologies would make popular E. coli cells a productive factory for designer chromosome engineering.
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Affiliation(s)
- Takahito Mukai
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Tatsuya Yoneji
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Kayoko Yamada
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Hironobu Fujita
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Seia Nara
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
| | - Masayuki Su'etsugu
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan
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28
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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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29
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Yeh Martín N, Valer L, Mansy SS. Toward long-lasting artificial cells that better mimic natural living cells. Emerg Top Life Sci 2019; 3:597-607. [PMID: 33523164 PMCID: PMC7288992 DOI: 10.1042/etls20190026] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 08/09/2019] [Accepted: 08/13/2019] [Indexed: 01/01/2023]
Abstract
Chemical communication is ubiquitous in biology, and so efforts in building convincing cellular mimics must consider how cells behave on a population level. Simple model systems have been built in the laboratory that show communication between different artificial cells and artificial cells with natural, living cells. Examples include artificial cells that depend on purely abiological components and artificial cells built from biological components and are driven by biological mechanisms. However, an artificial cell solely built to communicate chemically without carrying the machinery needed for self-preservation cannot remain active for long periods of time. What is needed is to begin integrating the pathways required for chemical communication with metabolic-like chemistry so that robust artificial systems can be built that better inform biology and aid in the generation of new technologies.
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Affiliation(s)
- Noël Yeh Martín
- Systems Biophysics, Physics Department, Ludwig-Maximilians-Universität München, Amalienstraße 54, 80799 München, Germany
| | - Luca Valer
- Department CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
| | - Sheref S Mansy
- Department CIBIO, University of Trento, via Sommarive 9, 38123 Povo, Italy
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Drive, Edmonton, AB, Canada T6G 2G2
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30
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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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31
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Islam MM, Odahara M, Yoshizumi T, Oikawa K, Kimura M, Su’etsugu M, Numata K. Cell-Penetrating Peptide-Mediated Transformation of Large Plasmid DNA into Escherichia coli. ACS Synth Biol 2019; 8:1215-1218. [PMID: 31008591 DOI: 10.1021/acssynbio.9b00055] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The highly efficient genetic transformation of cells is essential for synthetic biology procedures, especially for the transformation of large gene clusters. In this technical note, we present a novel cell-penetrating peptide (CPP)-mediated large-sized plasmid DNA transformation system for Escherichia coli. A large plasmid (pMSR227, 205 kb) was complexed with cationic peptides containing a CPP motif and was successfully transformed into E. coli cells. The transformants containing the plasmid DNA exhibited expression of a reporter gene encoding a red fluorescent protein. The transformation efficiency was significantly higher than that obtained using the heat-shock method and was similar to that of electroporation. This technique can be used as a platform for the simple and highly efficient transformation of large DNA molecules under mild conditions without causing significant damage to DNA, accelerating synthetic biology investigations for the design of genetically engineered microorganisms for industrial purposes.
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Affiliation(s)
- Md Monirul Islam
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Masaki Odahara
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Takeshi Yoshizumi
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Kazusato Oikawa
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Mitsuhiro Kimura
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Masayuki Su’etsugu
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo, 171-8501, Japan
| | - Keiji Numata
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
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32
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Ichihashi N. What can we learn from the construction of in vitro replication systems? Ann N Y Acad Sci 2019; 1447:144-156. [PMID: 30957237 DOI: 10.1111/nyas.14042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/25/2019] [Accepted: 02/04/2019] [Indexed: 01/08/2023]
Abstract
Replication is a central function of living organisms. Several types of replication systems have been constructed in vitro from various molecules, including peptides, DNA, RNA, and proteins. In this review, I summarize the progress in the construction of replication systems over the past few decades and discuss what we can learn from their construction. I introduce various types of replication systems, supporting the feasibility of the spontaneous appearance of replication early in Earth's history. In the latter part of the review, I focus on parasitic replicators, one of the largest obstacles for sustainable replication. Compartmentalization is discussed as a possible solution.
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Affiliation(s)
- Norikazu Ichihashi
- Graduate School of Arts and Sciences and Komaba Institute for Science, The University of Tokyo, Tokyo, Japan
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33
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Hasebe T, Narita K, Hidaka S, Su'etsugu M. Efficient Arrangement of the Replication Fork Trap for In Vitro Propagation of Monomeric Circular DNA in the Chromosome-Replication Cycle Reaction. Life (Basel) 2018; 8:life8040043. [PMID: 30257439 PMCID: PMC6315707 DOI: 10.3390/life8040043] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 09/22/2018] [Accepted: 09/23/2018] [Indexed: 11/16/2022] Open
Abstract
Propagation of genetic information is a fundamental prerequisite for living cells. We recently developed the replication cycle reaction (RCR), an in vitro reaction for circular DNA propagation, by reconstitution of the replication cycle of the Escherichia coli chromosome. In RCR, two replication forks proceed bidirectionally from the replication origin, oriC, and meet at a region opposite oriC, yielding two copies of circular DNA. Although RCR essentially propagates supercoiled monomers, concatemer byproducts are also produced due to inefficient termination of the replication fork progression. Here, we examined the effect of the Tus-ter replication fork trap in RCR. Unexpectedly, when the fork traps were placed opposite oriC, mimicking their arrangement on the chromosome, the propagation of circular DNA was inhibited. On the other hand, fork traps flanking oriC allowed efficient propagation of circular DNA and repressed concatemer production. These findings suggest that collision of the two convergence forks through the fork trap is detrimental to repetition of the replication cycle. We further demonstrate that this detrimental effect was rescued by the UvrD helicase. These results provide insights into the way in which circular DNA monomers replicate repetitively without generating concatemers.
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Affiliation(s)
- Tomonori Hasebe
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan.
| | - Kouhei Narita
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan.
| | - Shiomi Hidaka
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan.
| | - Masayuki Su'etsugu
- Department of Life Science, College of Science, Rikkyo University, 3-34-1 Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan.
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34
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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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35
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Hybrid cell reactor system from Escherichia coli protoplast cells and arrayed lipid bilayer chamber device. Sci Rep 2018; 8:11757. [PMID: 30082826 PMCID: PMC6078950 DOI: 10.1038/s41598-018-30231-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/25/2018] [Indexed: 11/09/2022] Open
Abstract
We developed a novel hybrid cell reactor system via functional fusion of single Escherichia coli protoplast cells, that are deficient in cell wall and expose plasma membrane, with arrayed lipid bilayer chambers on a device in order to incorporate the full set of cytosolic and membrane constituents into the artificial chambers. We investigated gene expression activity to represent the viability of the hybrid cell reactors: over 20% of hybrid cells showed gene expression activity from plasmid or mRNA. This suggests that the hybrid cell reactors retained fundamental activity of genetic information transduction. To expand the applicability of the hybrid cell reactors, we also developed the E. coli-in-E. coli cytoplasm system as an artificial parasitism system. Over 30% of encapsulated E. coli cells exhibited normal cell division, showing that hybrid cells can accommodate and cultivate living cells. This novel artificial cell reactor technology would enable unique approaches for synthetic cell researches such as reconstruction of living cell, artificial parasitism/symbiosis system, or physical simulation to test functionality of synthetic genome.
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36
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van Nies P, Westerlaken I, Blanken D, Salas M, Mencía M, Danelon C. Self-replication of DNA by its encoded proteins in liposome-based synthetic cells. Nat Commun 2018; 9:1583. [PMID: 29679002 PMCID: PMC5910420 DOI: 10.1038/s41467-018-03926-1] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/22/2018] [Indexed: 12/31/2022] Open
Abstract
Replication of DNA-encoded information and its conversion into functional proteins are universal properties of life. In an effort toward the construction of a synthetic minimal cell, we implement here the DNA replication machinery of the Φ29 virus in a cell-free gene expression system. Amplification of a linear DNA template by self-encoded, de novo synthesized Φ29 proteins is demonstrated. Complete information transfer is confirmed as the copied DNA can serve as a functional template for gene expression, which can be seen as an autocatalytic DNA replication cycle. These results show how the central dogma of molecular biology can be reconstituted and form a cycle in vitro. Finally, coupled DNA replication and gene expression is compartmentalized inside phospholipid vesicles providing the chassis for evolving functions in a prospective synthetic cell relying on the extant biology.
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Affiliation(s)
- Pauline van Nies
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, Delft, 2629 HZ, The Netherlands
| | - Ilja Westerlaken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, Delft, 2629 HZ, The Netherlands
| | - Duco Blanken
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, Delft, 2629 HZ, The Netherlands
| | - Margarita Salas
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma, Canto Blanco, Madrid, 28049, Spain
| | - Mario Mencía
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma, Canto Blanco, Madrid, 28049, Spain
| | - Christophe Danelon
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, van der Maasweg 9, Delft, 2629 HZ, The Netherlands.
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