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Wagner A, Mutschler H. Design of Novel Synthetic RNA Replicons Based on Emesvirus zinderi. ACS Synth Biol 2024; 13:1773-1780. [PMID: 38806167 PMCID: PMC11197098 DOI: 10.1021/acssynbio.4c00097] [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: 02/13/2024] [Revised: 04/04/2024] [Accepted: 05/02/2024] [Indexed: 05/30/2024]
Abstract
Self-replicating RNAs (srRNAs) are synthetic molecules designed to mimic the self-replicating ability of viral RNAs. srRNAs hold significant promise for a range of applications, including enhancing protein expression, reprogramming cells into pluripotent stem cells, and creating cell-free systems for experimental evolution. However, the development of srRNAs for use in bacterial systems remains limited. Here, we demonstrate how a srRNA scaffold from Emesvirus zinderi can be engineered into a self-encoding srRNA by incorporating the coding region of the catalytically active replicase subunit. With the help of in vitro replication assays, including an in vitro translation-coupled replication approach, we show that the resulting system enables complete replication cycles of RNA both in cis and trans, including long cargo RNAs such as tethered 5S, 16S, and 23S rRNAs. In summary, our findings suggest that these srRNAs have significant potential for fundamental research, synthetic biology, and general in vitro evolution.
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Affiliation(s)
- Alexander Wagner
- Biomimetic Chemistry, Department of
Chemistry and Chemical Biology, TU Dortmund
University, Dortmund 44227, Germany
| | - Hannes Mutschler
- Biomimetic Chemistry, Department of
Chemistry and Chemical Biology, TU Dortmund
University, Dortmund 44227, Germany
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2
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Kamiura R, Mizuuchi R, Ichihashi N. Plausible pathway for a host-parasite molecular replication network to increase its complexity through Darwinian evolution. PLoS Comput Biol 2022; 18:e1010709. [PMID: 36454734 PMCID: PMC9714742 DOI: 10.1371/journal.pcbi.1010709] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 11/04/2022] [Indexed: 12/05/2022] Open
Abstract
How the complexity of primitive self-replication molecules develops through Darwinian evolution remains a mystery with regards to the origin of life. Theoretical studies have proposed that coevolution with parasitic replicators increases network complexity by inducing inter-dependent replication. Particularly, Takeuchi and Hogeweg proposed a complexification process of replicator networks by successive appearance of a parasitic replicator followed by the addition of a new host replicator that is resistant to the parasitic replicator. However, the feasibility of such complexification with biologically relevant molecules is still unknown owing to the lack of an experimental model. Here, we investigated the plausible complexification pathway of host-parasite replicators using both an experimental host-parasite RNA replication system and a theoretical model based on the experimental system. We first analyzed the parameter space that allows for sustainable replication in various replication networks ranging from a single molecule to three-member networks using computer simulation. The analysis shows that the most plausible complexification pathway from a single host replicator is the addition of a parasitic replicator, followed by the addition of a new host replicator that is resistant to the parasite, consistent with the previous study by Takeuchi and Hogeweg. We also provide evidence that the pathway actually occurred in our previous evolutionary experiment. These results provide experimental evidence that a population of a single replicator spontaneously evolves into multi-replicator networks through coevolution with parasitic replicators.
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Affiliation(s)
- Rikuto Kamiura
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, Tokyo, Japan
| | - Ryo Mizuuchi
- JST, PRESTO, Kawaguchi, Saitama, Japan
- Komaba Institute for 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
- Research Center for Complex Systems Biology, Universal Biology Institute, The University of Tokyo, Tokyo, Japan
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3
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Furubayashi T, Ichihashi N. How evolution builds up complexity?: In vitro evolution approaches to witness complexification in artificial molecular replication systems. Biophys Physicobiol 2022; 19:1-10. [PMID: 35435608 PMCID: PMC8938154 DOI: 10.2142/biophysico.bppb-v19.0005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 02/10/2022] [Indexed: 12/01/2022] Open
Affiliation(s)
- Taro Furubayashi
- Department of Applied Chemistry, School of Engineering, The University of Tokyo
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Mizuuchi R, Ichihashi N. Primitive Compartmentalization for the Sustainable Replication of Genetic Molecules. Life (Basel) 2021; 11:life11030191. [PMID: 33670881 PMCID: PMC7997230 DOI: 10.3390/life11030191] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 02/21/2021] [Accepted: 02/25/2021] [Indexed: 01/03/2023] Open
Abstract
Sustainable replication and evolution of genetic molecules such as RNA are likely requisites for the emergence of life; however, these processes are easily affected by the appearance of parasitic molecules that replicate by relying on the function of other molecules, while not contributing to their replication. A possible mechanism to repress parasite amplification is compartmentalization that segregates parasitic molecules and limits their access to functional genetic molecules. Although extent cells encapsulate genomes within lipid-based membranes, more primitive materials or simple geological processes could have provided compartmentalization on early Earth. In this review, we summarize the current understanding of the types and roles of primitive compartmentalization regarding sustainable replication of genetic molecules, especially from the perspective of the prevention of parasite replication. In addition, we also describe the ability of several environments to selectively accumulate longer genetic molecules, which could also have helped select functional genetic molecules rather than fast-replicating short parasitic molecules.
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Affiliation(s)
- Ryo Mizuuchi
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
- JST, PRESTO, Kawaguchi, Saitama 332-0012, Japan
- Correspondence: (R.M.); (N.I.)
| | - Norikazu Ichihashi
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
- Department of Life Science, Graduate School of Arts and Science, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
- Universal Biology Institute, The University of Tokyo, Meguro, Tokyo 153-8902, Japan
- Correspondence: (R.M.); (N.I.)
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Furubayashi T, Ueda K, Bansho Y, Motooka D, Nakamura S, Mizuuchi R, Ichihashi N. Emergence and diversification of a host-parasite RNA ecosystem through Darwinian evolution. eLife 2020; 9:e56038. [PMID: 32690137 PMCID: PMC7378860 DOI: 10.7554/elife.56038] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 07/01/2020] [Indexed: 12/11/2022] Open
Abstract
In prebiotic evolution, molecular self-replicators are considered to develop into diverse, complex living organisms. The appearance of parasitic replicators is believed inevitable in this process. However, the role of parasitic replicators in prebiotic evolution remains elusive. Here, we demonstrated experimental coevolution of RNA self-replicators (host RNAs) and emerging parasitic replicators (parasitic RNAs) using an RNA-protein replication system we developed. During a long-term replication experiment, a clonal population of the host RNA turned into an evolving host-parasite ecosystem through the continuous emergence of new types of host and parasitic RNAs produced by replication errors. The host and parasitic RNAs diversified into at least two and three different lineages, respectively, and they exhibited evolutionary arms-race dynamics. The parasitic RNA accumulated unique mutations, thus adding a new genetic variation to the whole replicator ensemble. These results provide the first experimental evidence that the coevolutionary interplay between host-parasite molecules plays a key role in generating diversity and complexity in prebiotic molecular evolution.
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Affiliation(s)
- Taro Furubayashi
- Laboratoire Gulliver, CNRS, ESPCI Paris,
PSL Research UniversityParisFrance
| | - Kensuke Ueda
- Department of Life Science, Graduate
School of Arts and Science, The University of
TokyoTokyoJapan
| | - Yohsuke Bansho
- Graduate School of Frontier Biosciences,
Osaka UniversityOsakaJapan
| | - Daisuke Motooka
- Research Institute for Microbial
Diseases, Osaka UniversityOsakaJapan
| | - Shota Nakamura
- Research Institute for Microbial
Diseases, Osaka UniversityOsakaJapan
| | - Ryo Mizuuchi
- Komaba Institute for Science, The
University of TokyoTokyoJapan
- JST,
PRESTOKawaguchiJapan
| | - Norikazu Ichihashi
- Department of Life Science, Graduate
School of Arts and Science, The University of
TokyoTokyoJapan
- Graduate School of Frontier Biosciences,
Osaka UniversityOsakaJapan
- Komaba Institute for Science, The
University of TokyoTokyoJapan
- Universal Biology Institute, The
University of TokyoTokyoJapan
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Laurent G, Peliti L, Lacoste D. Survival of Self-Replicating Molecules under Transient Compartmentalization with Natural Selection. Life (Basel) 2019; 9:E78. [PMID: 31623412 PMCID: PMC6958486 DOI: 10.3390/life9040078] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/23/2019] [Accepted: 09/27/2019] [Indexed: 12/29/2022] Open
Abstract
The problem of the emergence and survival of self-replicating molecules in origin-of-life scenarios is plagued by the error catastrophe, which is usually escaped by considering effects of compartmentalization, as in the stochastic corrector model. By addressing the problem in a simple system composed of a self-replicating molecule (a replicase) and a parasite molecule that needs the replicase for copying itself, we show that transient (rather than permanent) compartmentalization is sufficient to the task. We also exhibit a regime in which the concentrations of the two kinds of molecules undergo sustained oscillations. Our model should be relevant not only for origin-of-life scenarios but also for describing directed evolution experiments, which increasingly rely on transient compartmentalization with pooling and natural selection.
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Affiliation(s)
- Gabin Laurent
- UMR CNRS Gulliver 7083, ESPCI, 10 rue Vauquelin, CEDEX 05, 75231 Paris, France.
| | - Luca Peliti
- Santa Marinella Research Institute, 00052 Santa Marinella, Italy.
| | - David Lacoste
- UMR CNRS Gulliver 7083, ESPCI, 10 rue Vauquelin, CEDEX 05, 75231 Paris, France.
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Yoshiyama T, Ichii T, Yomo T, Ichihashi N. Automated in vitro evolution of a translation-coupled RNA replication system in a droplet flow reactor. Sci Rep 2018; 8:11867. [PMID: 30089835 PMCID: PMC6082869 DOI: 10.1038/s41598-018-30374-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 07/27/2018] [Indexed: 01/23/2023] Open
Abstract
Automation is a useful strategy to make laborious evolutionary experiments faster and easier. To date, several types of continuous flow reactors have been developed for the automated evolutionary experiments of viruses and bacteria. However, the development of a flow reactor applicable to compartmentalized in vitro self-replication systems is still a challenge. In this study, we demonstrate automated in vitro evolution of a translation-coupled RNA system in a droplet flow reactor for the first time. This reactor contains approximately 1010 micro-scale droplets (average diameter is approximately 0.8 μm), which continuously fuse and divide among each other at a controllable rate. In the droplets, an RNA (artificial genomic RNA) replicate through the translation of self-encoded RNA replicase with spontaneously appearing parasitic RNA. We performed two automated replication experiments for more than 400 hours with different mixing intensities. We found that several mutations displayed increased frequencies in the genomic RNA populations and the dominant RNA mutants acquired the ability to replicate faster or acquired resistance to the parasitic RNA, demonstrating that Darwinian evolution occurred during the long-term replication. The droplet flow reactor we developed can be a useful tool to perform in vitro evolutionary experiments of translation-coupled systems.
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Affiliation(s)
- Tomoaki Yoshiyama
- Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Tetsuo Ichii
- Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Tokyo, Japan
| | - Tetsuya Yomo
- Institute of Biology and Information Science, East China Normal University, 3663 Zhongshan North Rd., Shanghai, 200062, P.R. China
| | - Norikazu Ichihashi
- Graduate School of Information Science and Technology, Osaka University, Osaka, Japan.
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan.
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