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Grasemann L, Thiel Pizarro P, Maerkl SJ. C2CAplus: A One-Pot Isothermal Circle-to-Circle DNA Amplification System. ACS Synth Biol 2023; 12:3137-3142. [PMID: 37729629 PMCID: PMC10594867 DOI: 10.1021/acssynbio.3c00390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Indexed: 09/22/2023]
Abstract
Rolling circle amplification (RCA) is a widely used DNA amplification method that uses circular template DNA as input and produces multimeric, linear single- or double-stranded DNA. Circle-to-circle amplification (C2CA) has further expanded this method by implementing product recircularization using restriction and ligation, leading to a higher amplification yield and enabling the generation of circular products. However, C2CA is a multistep, nonisothermal method, requiring multiple fluid manipulations and thereby compromises several advantages of RCA. Here, we improved C2CA to implement a one-pot, single step, isothermal reaction at temperatures ranging from 25 to 37 °C. Our C2CAplus method is simple, robust, and produces large quantities of product DNA that can be seen with the naked eye.
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Affiliation(s)
- Laura Grasemann
- Institute of Bioengineering,
School of Engineering, École Polytechnique
Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Paula Thiel Pizarro
- Institute of Bioengineering,
School of Engineering, École Polytechnique
Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Sebastian J. Maerkl
- Institute of Bioengineering,
School of Engineering, École Polytechnique
Fédérale de Lausanne, 1015 Lausanne, Switzerland
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2
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Maerkl SJ. On biochemical constructors and synthetic cells. Interface Focus 2023; 13:20230014. [PMID: 37577005 PMCID: PMC10415740 DOI: 10.1098/rsfs.2023.0014] [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: 03/08/2023] [Accepted: 05/30/2023] [Indexed: 08/15/2023] Open
Abstract
Is it possible to build life? More specifically, is it possible to create a living synthetic cell from inanimate building blocks? This question precipitated into one of the most significant grand challenges in biochemistry and synthetic biology, with several large research consortia forming around this endeavour in Europe (European Synthetic Cell Initiative), the USA (Build-a-Cell Initiative) and Japan (Japanese Society for Cell Synthesis Research). The mature field of biochemistry, the advent of synthetic biology in the early 2000s, and the burgeoning field of cell-free synthetic biology made it feasible to tackle this grand challenge.
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Affiliation(s)
- Sebastian J. Maerkl
- Institute of Bioengineering, School of Engineering, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Vaud, Switzerland
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3
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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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4
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De Capitani J, Mutschler H. The Long Road to a Synthetic Self-Replicating Central Dogma. Biochemistry 2023; 62:1221-1232. [PMID: 36944355 PMCID: PMC10077596 DOI: 10.1021/acs.biochem.3c00023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
The construction of a biochemical system capable of self-replication is a key objective in bottom-up synthetic biology. Throughout the past two decades, a rapid progression in the design of in vitro cell-free systems has provided valuable insight into the requirements for the development of a minimal system capable of self-replication. The main limitations of current systems can be attributed to their macromolecular composition and how the individual macromolecules use the small molecules necessary to drive RNA and protein synthesis. In this Perspective, we discuss the recent steps that have been taken to generate a minimal cell-free system capable of regenerating its own macromolecular components and maintaining the homeostatic balance between macromolecular biogenesis and consumption of primary building blocks. By following the flow of biological information through the central dogma, we compare the current versions of these systems to date and propose potential alterations aimed at designing a model system for self-replicative synthetic cells.
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Affiliation(s)
- Jacopo De Capitani
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
| | - Hannes Mutschler
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
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Sieskind R, Cortajarena AL, Manteca A. Cell-Free Production Systems in Droplet Microfluidics. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 185:91-127. [PMID: 37306704 DOI: 10.1007/10_2023_224] [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
The use of cell-free production systems in droplet microfluidic devices has gained significant interest during the last decade. Encapsulating DNA replication, RNA transcription, and protein expression systems in water-in-oil drops allows for the interrogation of unique molecules and high-throughput screening of libraries of industrial and biomedical interest. Furthermore, the use of such systems in closed compartments enables the evaluation of various properties of novel synthetic or minimal cells. In this chapter, we review the latest advances in the usage of the cell-free macromolecule production toolbox in droplets, with a special emphasis on new on-chip technologies for the amplification, transcription, expression, screening, and directed evolution of biomolecules.
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Affiliation(s)
- Rémi Sieskind
- Institut Pasteur, Université de Paris, Unité d'Architecture et de Dynamique des Macromolécules Biologiques, Paris, France
| | - Aitziber L Cortajarena
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Aitor Manteca
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Donostia-San Sebastián, Spain.
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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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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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8
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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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