2024/12/24 更新

経歴

  • 2023年04月
    -
    継続中

    JST 創発研究者

  • 2023年04月
    -
    継続中

    早稲田大学   理工学術院 電気・情報生命工学科   専任講師

  • 2019年10月
    -
    2023年03月

    JST さきがけ研究者

  • 2019年04月
    -
    2023年03月

    東京大学大学院 総合文化研究科 先進科学研究機構   特任助教

  • 2018年04月
    -
    2019年03月

    日本学術振興会 海外特別研究員(ポートランド州立大学 化学科)

  • 2015年04月
    -
    2018年03月

    日本学術振興会 特別研究員DC1(大阪大学大学院 情報科学研究科)

  • 2015年08月
    -
    2016年02月

    NASA エイムズ研究センター   Research Scholar

▼全件表示

学歴

  • 2013年04月
    -
    2018年03月

    大阪大学大学院   情報科学研究科   バイオ情報工学専攻  

  • 2009年04月
    -
    2013年03月

    大阪大学   工学部 応用自然科学科   応用生物工学コース  

研究分野

  • 進化生物学 / 生物物理学

研究キーワード

  • 生命の起源

  • RNA

  • 実験進化

  • 人工細胞

  • 合成生物学

  • 生物物理学

▼全件表示

受賞

  • 早稲田大学リサーチアワード(国際研究発信力)

    2023年12月  

    受賞者: 水内良

  • 日本生物物理学会 若手奨励賞

    2023年11月  

    受賞者: 水内良

  • Reviewer of the Month

    2023年10月   Communications Chemistry, Nature Portfolio  

    受賞者: 水内 良

  • 文部科学大臣表彰 若手科学者賞

    2023年04月  

    受賞者: 水内 良

  • 研究奨励賞

    2022年06月   日本進化学会  

    受賞者: 水内 良

  • 最優秀ポスター発表賞

    2020年09月   日本進化学会第22回大会  

    受賞者: 水内 良

  • Life Travel Award 2018

    2018年03月   Life, MDPI  

    受賞者: 水内 良

  • 優秀ポスター発表賞

    2017年08月   日本進化学会第19回大会  

    受賞者: 水内 良

  • The NASA Astrobiology Program award

    2015年06月   Astrobiology Science Conference 2015  

    受賞者: 水内 良

  • 情報科学研究科賞

    2015年03月   大阪大学  

    受賞者: 水内 良

  • PhD students honorable

    2014年10月   CEITEC Annual Conference  

    受賞者: 水内 良

  • 工学賞

    2013年03月   大阪大学  

    受賞者: 水内 良

▼全件表示

 

論文

  • How biophysics shapes the origins of life: a 21st IUPAB/62nd BSJ joint congress symposium overview

    Tony Z. Jia, Ryo Mizuuchi

    Biophysical Reviews   in press  2024年07月  [査読有り]  [招待有り]

    担当区分:最終著者, 責任著者

    DOI

    Scopus

    1
    被引用数
    (Scopus)
  • Constraint on an RNA world on montmorillonite clay.

    Ryo Mizuuchi

    Biophysical journal   123 ( 4 ) 421 - 423  2024年02月  [査読有り]  [招待有り]  [国際誌]

    担当区分:筆頭著者, 最終著者, 責任著者

    DOI PubMed

    Scopus

  • Cell-free expression of RuBisCO for ATP production in the synthetic cells.

    Shugo Sugii, Katsumi Hagino, Ryo Mizuuchi, Norikazu Ichihashi

    Synthetic biology   8 ( 1 ) ysad016  2023年12月  [査読有り]  [国際誌]

     概要を見る

    Recent advances in bottom-up synthetic biology have made it possible to reconstitute cellular systems from non-living components, yielding artificial cells with potential applications in industry, medicine and basic research. Although a variety of cellular functions and components have been reconstituted in previous studies, sustained biological energy production remains a challenge. ATP synthesis via ribulose-1,5-diphosphate carboxylase/oxygenase (RuBisCO), a central enzyme in biological CO2 fixation, holds potential as an energy production system, but its feasibility in a cell-free expression system has not yet been tested. In this study, we test RuBisCO expression and its activity-mediated ATP synthesis in a reconstituted Escherichia coli-based cell-free translation system. We then construct a system in which ATP is synthesized by RuBisCO activity in giant vesicles and used as energy for translation reactions. These results represent an advance toward independent energy production in artificial cells. Graphical Abstract.

    DOI PubMed

    Scopus

    1
    被引用数
    (Scopus)
  • Emergence of linkage between cooperative RNA replicators encoding replication and metabolic enzymes through experimental evolution.

    Kensuke Ueda, Ryo Mizuuchi, Norikazu Ichihashi

    PLoS genetics   19 ( 8 ) e1010471  2023年08月  [査読有り]  [国際誌]

    担当区分:責任著者

     概要を見る

    The integration of individually replicating genes into a primitive chromosome is a key evolutionary transition in the development of life, allowing the simultaneous inheritance of genes. However, how this transition occurred is unclear because the extended size of primitive chromosomes replicate slower than unlinked genes. Theoretical studies have suggested that a primitive chromosome can evolve in the presence of cell-like compartments, as the physical linkage prevents the stochastic loss of essential genes upon division, but experimental support for this is lacking. Here, we demonstrate the evolution of a chromosome-like RNA from two cooperative RNA replicators encoding replication and metabolic enzymes. Through their long-term replication in cell-like compartments, linked RNAs emerged with the two cooperative RNAs connected end-to-end. The linked RNAs had different mutation patterns than the two unlinked RNAs, suggesting that they were maintained as partially distinct lineages in the population. Our results provide experimental evidence supporting the plausibility of the evolution of a primitive chromosome from unlinked gene fragments, an important step in the emergence of complex biological systems.

    DOI PubMed

    Scopus

    2
    被引用数
    (Scopus)
  • Minimal RNA self-reproduction discovered from a random pool of oligomers

    Ryo Mizuuchi, Norikazu Ichihashi

    Chemical Science   14 ( 28 ) 7656 - 7664  2023年06月  [査読有り]  [国際誌]

    担当区分:筆頭著者, 責任著者

     概要を見る

    The emergence of RNA self-reproduction from prebiotic components would have been crucial in developing a genetic system during the origins of life. However, all known self-reproducing RNA molecules are complex ribozymes, and how they could have arisen from abiotic materials remains unclear. Therefore, it has been proposed that the first self-reproducing RNA may have been short oligomers that assemble their components as templates. Here, we sought such minimal RNA self-reproduction in prebiotically accessible short random RNA pools that undergo spontaneous ligation and recombination. By examining enriched RNA families with common motifs, we identified a 20-nucleotide (nt) RNA variant that self-reproduces via template-directed ligation of two 10 nt oligonucleotides. The RNA oligomer contains a 2'-5' phosphodiester bond, which typically forms during prebiotically plausible RNA synthesis. This non-canonical linkage helps prevent the formation of inactive complexes between self-complementary oligomers while decreasing the ligation efficiency. The system appears to possess an autocatalytic property consistent with exponential self-reproduction despite the limitation of forming a ternary complex of the template and two substrates, similar to the behavior of a much larger ligase ribozyme. Such a minimal, ribozyme-independent RNA self-reproduction may represent the first step in the emergence of an RNA-based genetic system from primordial components. Simultaneously, our examination of random RNA pools highlights the likelihood that complex species interactions were necessary to initiate RNA reproduction.

    DOI PubMed

  • How prebiotic complexity increases through Darwinian evolution

    Kohtoh Yukawa, Ryo Mizuuchi, Norikazu Ichihashi

    Current Opinion in Systems Biology   34   100456  2023年04月  [査読有り]

    DOI

    Scopus

    1
    被引用数
    (Scopus)
  • Plausible pathway for a host-parasite molecular replication network to increase its complexity through Darwinian evolution.

    Rikuto Kamiura, Ryo Mizuuchi, Norikazu Ichihashi

    PLoS computational biology   18 ( 12 ) e1010709  2022年12月  [査読有り]  [国際誌]

     概要を見る

    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.

    DOI PubMed

    Scopus

    3
    被引用数
    (Scopus)
  • Experimental evidence for the correlation between RNA structural fluctuations and the frequency of beneficial mutations

    Yutaro Maeda, Ryo Mizuuchi, Shuji Shigenobu, Atsushi Shibai, Hazuki Kotani, Chikara Furusawa, Norikazu Ichihashi

    RNA   28 ( 12 ) 1659 - 1667  2022年10月  [査読有り]

     概要を見る

    RNA has been used as a model molecule to understand the adaptive evolution process owing to the simple relationship between the structure (i.e., phenotype) and sequence (i.e., genotype). RNA usually forms multiple substructures with similar thermodynamic stabilities, called structural fluctuations. Ancel and Fontana theoretically proposed that structural fluctuation is directly related to the ease of change in structures by mutations and thus works as a source of adaptive evolution; however, experimental verification is limited. Here, we analyzed 76 RNA genotypes that appeared in our previous in vitro evolution to examine whether 1) RNA fluctuation decreases as adaptive evolution proceeds and 2) RNAs that have larger fluctuations tend to have higher frequencies of beneficial mutations. We first computationally estimated the structural fluctuations of all RNAs and observed that they tended to decrease as their fitness increased. We next measured the frequency of beneficial mutations for 10 RNA genotypes and observed that the total number of beneficial mutations was correlated with the size of the structural fluctuations. These results consistently support the idea that the structural fluctuation of RNA, at least those evaluated in our study, works as a source of adaptive evolution.

    DOI

    Scopus

    2
    被引用数
    (Scopus)
  • Evolutionary transition from a single RNA replicator to a multiple replicator network.

    Ryo Mizuuchi, Taro Furubayashi, Norikazu Ichihashi

    Nature communications   13 ( 1 ) 1460 - 1460  2022年03月  [査読有り]  [国際誌]

    担当区分:筆頭著者, 責任著者

     概要を見る

    In prebiotic evolution, self-replicating molecules are believed to have evolved into complex living systems by expanding their information and functions open-endedly. Theoretically, such evolutionary complexification could occur through successive appearance of novel replicators that interact with one another to form replication networks. Here we perform long-term evolution experiments of RNA that replicates using a self-encoded RNA replicase. The RNA diversifies into multiple coexisting host and parasite lineages, whose frequencies in the population initially fluctuate and gradually stabilize. The final population, comprising five RNA lineages, forms a replicator network with diverse interactions, including cooperation to help the replication of all other members. These results support the capability of molecular replicators to spontaneously develop complexity through Darwinian evolution, a critical step for the emergence of life.

    DOI PubMed

    Scopus

    34
    被引用数
    (Scopus)
  • Relaxed Substrate Specificity in Qβ Replicase through Long-Term In Vitro Evolution

    Kohtoh Yukawa, Ryo Mizuuchi, Norikazu Ichihashi

    Life   12 ( 1 ) 32  2022年01月  [査読有り]  [国際誌]

     概要を見る

    A change from RNA- to DNA-based genetic systems is hypothesized as a major transition in the evolution of early life forms. One of the possible requirements for this transition is a change in the substrate specificity of the replication enzyme. It is largely unknown how such changes would have occurred during early evolutionary history. In this study, we present evidence that an RNA replication enzyme that has evolved in the absence of deoxyribonucleotide triphosphates (dNTPs) relaxes its substrate specificity and incorporates labeled dNTPs. This result implies that ancient replication enzymes, which probably evolved in the absence of dNTPs, could have incorporated dNTPs to synthesize DNA soon after dNTPs became available. The transition from RNA to DNA, therefore, might have been easier than previously thought.

    DOI PubMed

    Scopus

    3
    被引用数
    (Scopus)
  • 原始生命を模した分子複製システムの進化と改良

    Ryo Mizuuchi

    Viva Origino   49 ( 3 ) 10  2021年12月  [査読有り]  [招待有り]

    担当区分:筆頭著者, 最終著者, 責任著者

  • Primitive Compartmentalization for the Sustainable Replication of Genetic Molecules.

    Ryo Mizuuchi, Norikazu Ichihashi

    Life (Basel, Switzerland)   11 ( 3 )  2021年02月  [査読有り]  [国際誌]

    担当区分:筆頭著者, 責任著者

     概要を見る

    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.

    DOI PubMed

    Scopus

    20
    被引用数
    (Scopus)
  • PURE mRNA display and cDNA display provide rapid detection of core epitope motif via high-throughput sequencing.

    Sabrina Galiñanes Reyes, Yutetsu Kuruma, Mai Fujimi, Masako Yamazaki, Sumie Eto, Shota Nishikawa, Satoshi Tamaki, Asaki Kobayashi, Ryo Mizuuchi, Lynn Rothschild, Mark Ditzler, Kosuke Fujishima

    Biotechnology and bioengineering   118 ( 4 ) 1736 - 1749  2021年01月  [査読有り]  [国際誌]

     概要を見る

    The reconstructed in vitro translation system known as the PURE system has been used in a variety of cell-free experiments such as the expression of native and de novo proteins as well as various display methods to select for functional polypeptides. We developed a refined PURE-based display method for the preparation of stable messenger RNA (mRNA) and complementary DNA (cDNA)-peptide conjugates and validated its utility for in vitro selection. Our conjugate formation efficiency exceeded 40%, followed by gel purification to allow minimum carry-over of components from the translation system to the downstream assay enabling clean and efficient random peptide sequence screening. We chose the commercially available anti-FLAG M2 antibody as a target molecule for validation. Starting from approximately 1.7 × 1012 random sequences, a round-by-round high-throughput sequencing showed clear enrichment of the FLAG epitope DYKDDD as well as revealing consensus FLAG epitope motif DYK(D/L/N)(L/Y/D/N/F)D. Enrichment of core FLAG motifs lacking one of the four key residues (DYKxxD) indicates that Tyr (Y) and Lys (K) appear as the two key residues essential for binding. Furthermore, the comparison between mRNA display and cDNA display method resulted in overall similar performance with slightly higher enrichment for mRNA display. We also show that gel purification steps in the refined PURE-based display method improve conjugate formation efficiency and enhance the enrichment rate of FLAG epitope motifs in later rounds of selection especially for mRNA display. Overall, the generalized procedure and consistent performance of two different display methods achieved by the commercially available PURE system will be useful for future studies to explore the sequence and functional space of diverse polypeptides.

    DOI PubMed

    Scopus

    9
    被引用数
    (Scopus)
  • Translation-coupled RNA replication and parasitic replicators in membrane-free compartments.

    Ryo Mizuuchi, Norikazu Ichihashi

    Chemical communications (Cambridge, England)   56 ( 87 ) 13453 - 13456  2020年10月  [査読有り]  [国際誌]

    担当区分:筆頭著者, 責任著者

     概要を見る

    We report RNA self-replication through the translation of its encoded protein within membrane-free compartments generated by liquid-liquid phase separation. The aqueous droplets support RNA self-replication by concentrating a genomic RNA and translation proteins, facilitating the uptake of small substrates, and preventing the replication of parasitic RNAs through compartmentalization.

    DOI PubMed

    Scopus

    15
    被引用数
    (Scopus)
  • Emergence and diversification of a host-parasite RNA ecosystem through Darwinian evolution.

    Taro Furubayashi, Kensuke Ueda, Yohsuke Bansho, Daisuke Motooka, Shota Nakamura, Ryo Mizuuchi, Norikazu Ichihashi

    eLife   9   e56038  2020年07月  [査読有り]  [国際誌]

     概要を見る

    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.

    DOI PubMed

    Scopus

    26
    被引用数
    (Scopus)
  • In vitro evolution of phi29 DNA polymerases through compartmentalized gene expression and rolling-circle replication.

    Yoshihiro Sakatani, Ryo Mizuuchi, Norikazu Ichihashi

    Protein engineering, design & selection   32 ( 11 ) 481 - 487  2020年06月  [査読有り]  [国際誌]

     概要を見る

    Phi29 DNA polymerase is widely used for DNA amplification through rolling-circle replication or multiple displacement amplification. Here, we performed completely in vitro artificial evolution of phi29 DNA polymerase by combining the in vitro compartmentalization and the gene expression-coupled rolling-circle replication of a circular DNA encoding the polymerase. We conducted the experiments in six different conditions composed of three different levels of inhibitor concentrations with two different DNA labeling methods. One of the experiments was performed in our previous study and the other five experiments were newly conducted in this study. Under all conditions, we found several mutations that enhance the rolling-circle amplification by the polymerase when it was expressed in the reconstituted gene expression system. Especially, a combinatorial mutant polymerase (K555T/D570N) exhibits significantly higher rolling-circle activity than the wild type. These highly active mutant polymerases would be useful for various applications.

    DOI PubMed

    Scopus

    7
    被引用数
    (Scopus)
  • Structural transition of replicable RNAs during in vitro evolution with Qβ replicase.

    Mizuuchi R, Usui K, Ichihashi N

    RNA   26 ( 1 ) 83 - 90  2020年01月  [査読有り]  [国際誌]

    担当区分:筆頭著者

    DOI PubMed

    Scopus

    4
    被引用数
    (Scopus)
  • A fusion method to develop an expanded artificial genomic RNA replicable by Qβ replicase

    Ueda K, Mizuuchi R, Matsuda F, Ichihashi N

    ChemBioChem   20 ( 18 ) 2331 - 2335  2019年09月  [査読有り]  [国際誌]

    DOI PubMed

    Scopus

    3
    被引用数
    (Scopus)
  • Spontaneous advent of genetic diversity in RNA populations through multiple recombination mechanisms.

    Smail BA, Clifton BE, Mizuuchi R, Lehman N

    RNA   25 ( 4 ) 453 - 464  2019年03月  [査読有り]

    担当区分:責任著者

    DOI PubMed

    Scopus

    18
    被引用数
    (Scopus)
  • Limited Sequence Diversity Within a Population Supports Prebiotic RNA Reproduction

    Mizuuchi R, Lehman N

    Life   9 ( 1 ) 20  2019年02月  [査読有り]

    担当区分:筆頭著者, 責任著者

    DOI PubMed

    Scopus

    11
    被引用数
    (Scopus)
  • Mineral surfaces select for longer RNA molecules

    Mizuuchi R, Blokhuis A, Vincent L, Nghe P, Lehman N, Baum D

    Chemical Communications   55 ( 14 ) 2090 - 2093  2019年01月  [査読有り]

    担当区分:筆頭著者, 責任著者

    DOI PubMed

    Scopus

    24
    被引用数
    (Scopus)
  • Sustainable replication and coevolution of cooperative RNAs in an artificial cell-like system.

    Mizuuchi R, Ichihashi N

    Nature Ecology & Evolution   2 ( 10 ) 1654 - 1660  2018年08月  [査読有り]

    担当区分:筆頭著者

    DOI PubMed

    Scopus

    39
    被引用数
    (Scopus)
  • Simple rules for construction of a geometric nest structure by pufferfish.

    Mizuuchi R, Kawase H, Shin H, Iwai D, Kondo S

    Scientific reports   8 ( 1 ) 12366 - 12366  2018年08月  [査読有り]  [国際誌]

    担当区分:筆頭著者

    DOI PubMed

    Scopus

    8
    被引用数
    (Scopus)
  • Discovery of an Earliest-Stage “Mystery Circle” and Development of the Structure Constructed by Pufferfish, Torquigener albomaculosus (Pisces: Tetraodontidae)

    Kawase H, Mizuuchi R, Shin H, Kitajima Y, Hosoda K, Shimizu M, Iwai D, Kondo S

    Fishes   2 ( 3 ) 14  2017年08月  [査読有り]

    DOI

    Scopus

    9
    被引用数
    (Scopus)
  • Adaptation and Diversification of an RNA Replication System under Initiation- or Termination-Impaired Translational Conditions

    Ryo Mizuuchi, Norikazu Ichihashi, Tetsuya Yomo

    ChemBioChem   17 ( 13 ) 1229 - 1232  2016年07月  [査読有り]

    担当区分:筆頭著者

     概要を見る

    Adaptation to various environments is a remarkable characteristic of life. Is this limited to extant complex living organisms, or is it also possible for a simpler self-replication system to adapt? In this study, we addressed this question by using a translation-coupled RNA replication system that comprised a reconstituted translation system and an RNA genome that encoded a replicase gene. We performed RNA replication reactions under four conditions, under which different components of translation were partly inhibited. We found that replication efficiency increased with the number of rounds of replication under all the tested conditions. The types of dominant mutations differed depending on the condition, thus indicating that this simple system adapted to different environments in different ways. This suggests that even a primitive self-replication system composed of a small number of genes on the early earth could have had the ability to adapt to various environments.

    DOI PubMed

    Scopus

    7
    被引用数
    (Scopus)
  • Adaptive Evolution of an Artificial RNA Genome to a Reduced Ribosome Environment

    Ryo Mizuuchi, Norikazu Ichihashi, Kimihito Usui, Yasuaki Kazuta, Tetsuya Yomo

    ACS Synthetic Biology   4 ( 3 ) 292 - 298  2015年03月  [査読有り]

    担当区分:筆頭著者

     概要を見る

    The reconstitution of an artificial system that has the same evolutionary ability as a living thing is a major challenge in the in vitro synthetic biology. In this study, we tested the adaptive evolutionary ability of an artificial RNA genome replication system, termed the translation coupled RNA replication (TcRR) system. In a previous work, we performed a study of the long-term evolution of the genome with an excess amount of ribosome. In this study, we continued the evolution experiment in a reduced ribosome environment and observed that the mutant genorne compensated for the reduced ribosome concentration. This result demonstrated the ability of the TcRR system to adapt and may be a step toward generating living things with evolutionary ability.

    DOI PubMed

    Scopus

    15
    被引用数
    (Scopus)

▼全件表示

書籍等出版物

  • RNAの科学 ―時代を拓く生体分子―

    市橋伯一, 水内良( 担当: 共著,  担当範囲: 18章 RNA ワールド仮説と生命の起源)

    朝倉書店  2024年07月

  • 進化を予測するのは想像以上に難しい

    水内良

    羊土社 実験医学  2024年03月

  • 生命の起源の謎を解く 自己複製する最小のRNAとは?

    水内良

    化学同人 月刊化学  2023年12月

講演・口頭発表等

  • 自己複製分子の世界: 寄生・協力・進化の末に生命性が生まれるか?

    水内良  [招待有り]

    ウイルス学若手研究集会2024  

    発表年月: 2024年11月

  • Exploring life’s origins via experimental evolution of artificial RNA replication systems

    Ryo Mizuuchi  [招待有り]

    Joint Symposium between the University of Bonn and Waseda University  

    発表年月: 2024年10月

  • 液-液相分離を利用した人工細胞工学

    水内良  [招待有り]

    第76回 日本生物工学会大会  

    発表年月: 2024年09月

  • 分子から生命への進化を再現できるか?

    水内良  [招待有り]

    生命の起原および進化学会 夏の学校2024  

    発表年月: 2024年09月

  • 生命の起源に迫る分子システムデザイン

    水内良  [招待有り]

    日本生物工学会 東日本支部 生物工学フォーラム「タンパク質・生命デザインの最前線」  

    発表年月: 2024年08月

  • 生命の起源を理解するために何を創るか?

    水内良  [招待有り]

    第76回 日本細胞生物学会大会  

    発表年月: 2024年07月

  • Translation-coupled RNA replication in all-aqueous droplets

    Ryo Mizuuchi

    Mini-symposium “Toward the Understanding and Engineering of Complex Systems: Materials to Life”  

    発表年月: 2024年06月

  • Exploring minimal autocatalytic RNA reproduction

    Ryo Mizuuchi  [招待有り]

    Autocatalysis in Reaction Networks Seminar  

    発表年月: 2024年05月

  • 原始的なRNA 集団と自己複製体の探究

    水内良、柿崎二郎、佐藤颯、市橋伯一

    第48回 生命の起原および進化学会学術講演会  

    発表年月: 2024年03月

  • 生命の起源と初期進化の追体験

    水内良  [招待有り]

    第10回東京女子医科大学・早稲田大学研究交流セミナー  

    発表年月: 2024年02月

  • 生命の起源を追体験する

    水内良  [招待有り]

    定量生物学の会 第十一回年会  

    発表年月: 2024年01月

  • Experimental evolution of artificial RNA replication systems: for understanding the origins of life

    Ryo Mizuuchi  [招待有り]

    International Workshop for Bridging Synthetic, Computational & Evolutionary Biology  

    発表年月: 2023年12月

  • 生命の起源

    水内良  [招待有り]

    EWE三月会  

    発表年月: 2023年11月

  • Minimal RNA self-reproduction discovered from a random pool of oligomers

    Ryo Mizuuchi  [招待有り]

    第61回日本生物物理学会年会  

    発表年月: 2023年11月

  • 原始⽣命モデルの実験進化で観測不能な⽣命の起源に迫る

    水内良  [招待有り]

    日本進化学会第25回大会  

    発表年月: 2023年09月

  • Emergence and evolution of host-parasite ecosystems in a molecular replication system

    Ryo Mizuuchi  [招待有り]

    Confect Symposium 2023 “Marine Microbial Virus Ecology and Evolution  

    発表年月: 2023年08月

  • Evolution of complexity in an artificial RNA replication system

    Ryo Mizuuchi  [招待有り]

    STATPHYS28 Satellite Meeting, Statistical Physics and Information-Processing in Living Systems  

    発表年月: 2023年08月

  • RNA replication systems and evolution: for understanding the origins of life

    Ryo Mizuuchi  [招待有り]

    SPEED × Bottom-up Biotech × ELSI joint workshop  

    発表年月: 2023年07月

  • 分子から生命が生まれる道筋を解き明かすために

    Ryo Mizuuchi  [招待有り]

    生命の分子システムの理解に向けて何を創れば良いか?  

    発表年月: 2023年05月

  • 再構成実験で探る生命の起源:原始生命モデルと実験室内進化

    水内良  [招待有り]

    CHEMINAS 47  

    発表年月: 2023年05月

  • Compartmentalization for RNA replication and evolution

    Ryo Mizuuchi  [招待有り]

    第60回日本生物物理学会年会  

    発表年月: 2022年09月

  • Emergence and Darwinian evolution of RNA replicators

    Ryo Mizuuchi

    Interdisciplinary Origin of Life Meeting for Early Career Researchers (IOoL2022)  

    発表年月: 2022年08月

  • Mineral surfaces select for longer RNA molecules: implication for prebiotic evolution

    Ryo Mizuuchi  [招待有り]

    発表年月: 2022年05月

  • 人工RNA複製体のダーウィン進化による複雑化

    水内良、古林太郎、市橋伯一

    第46回 生命の起原および進化学会学術講演会  

    発表年月: 2022年03月

  • 人工RNA複製システムと生命の起源

    水内良  [招待有り]

    学術変革領域(A)分子サイバネティクス 第10回領域セミナー  

    発表年月: 2022年01月

  • From emergence to Darwinian evolution of RNA replicators

    Ryo Mizuuchi  [招待有り]

    NASA Center for the Origin of Life meeting  

    発表年月: 2022年01月

  • 人工RNA複製体の進化と人工細胞と生命の起源

    水内良

    人工細胞モデル&分子ロボティクス 第2回研究会  

    発表年月: 2021年11月

  • Evolutionary complexification of an artificial RNA replication system

    Ryo Mizuuchi, Taro Furubayashi, Norikazu Ichihashi

    第59回日本生物物理学会年会  

    発表年月: 2021年11月

  • 人工RNA自己複製体と寄生体の長期共進化

    水内良  [招待有り]

    日本微生物生態学会 (環境ウイルス研究部会集会)  

    発表年月: 2021年11月

  • Evolutionary complexification of a replicase-encoding RNA replicator

    Ryo Mizuuchi  [招待有り]

    The XIXth International Conference on the Origin of Life  

    発表年月: 2021年10月

  • Network development in gene-encoding RNA replicators through Darwinian evolution

    Ryo Mizuuchi

    発表年月: 2021年09月

  • 分子複製システムを進化させて原始生命進化を理解する

    水内良  [招待有り]

    生物工学若手会夏のオンラインセミナー2021  

    発表年月: 2021年07月

  • How chemistry gives rise to biology

    Ryo Mizuuchi  [招待有り]

    2nd OoLEN (Origin of Life Early-career Network) virtual meeting  

    発表年月: 2021年05月

  • 原始生命を模した分子複製システムの構築と進化

    水内良  [招待有り]

    第1回分子サイバネティクス定例研究会  

    発表年月: 2021年03月

  • 無細胞翻訳系を用いた液滴内でのRNAの自己複製

    水内良、市橋伯一

    第15回無細胞生命科学研究会  

    発表年月: 2021年03月

  • 原始生命を模した分子複製システムの進化と改良

    水内良  [招待有り]

    生命の起原および進化学会 2021年シンポジウム  

    発表年月: 2021年03月

  • 任意の遺伝情報を持つ人工 RNA 複製系の構築に向けて

    水内良、臼井公人、市橋伯一

    第45回生命の起原のよび進化学会学術講演会  

    発表年月: 2020年03月

  • Compartmentalization for the evolution of cooperation in RNA replicators

    Ryo Mizuuchi  [招待有り]

    Primitive Compartmentalization Symposium (ELSI)  

    発表年月: 2019年11月

  • Autocatalytic sets, Mineral surfaces, and the evolution of RNA

    Ryo Mizuuchi  [招待有り]

    Ribonucleoprotein reconstruction/evolution mini-workshop (ELSI)  

    発表年月: 2019年11月

  • 協力して複製するRNAのダーウィン進化—協力性の維持と強化

    水内良、市橋伯一  [招待有り]

    日本遺伝学会第91回大会  

    発表年月: 2019年09月

  • 分子複製体間に協力性がどうやって生まれるか?

    水内良  [招待有り]

    UBI meeting  

    発表年月: 2019年05月

  • Evolution of an artificial RNA replication system—adaptation, diversification, and cooperation

    Ryo Mizuuchi  [招待有り]

    Evolution Seminar Series, University of Wisconsin-Madison  

    発表年月: 2019年02月

  • Sustainable cooperation and coevolution of encapsulated gene-encoding RNA replicators

    Ryo Mizuuchi, Norikazu Ichihashi

    Second Joint Congress on Evolutionary Biology  

    発表年月: 2018年08月

  • プロト細胞モデルでの協力的な RNA 複製体の安定化と共進化

    水内良、市橋伯一

    第43回 生命の起源および進化学会  

    発表年月: 2018年03月

  • Darwinian evolution of mutualistic RNA replicators with different genes

    Ryo Mizuuchi, Norikazu Ichihashi

    The XVIIIth International Conference on the Origin of Life  

    発表年月: 2017年07月

  • Darwinian evolution of two distinct cooperative RNA replicators

    Ryo Mizuuchi, Norikazu Ichihashi

    Astrobiology Science Conference 2017  

    発表年月: 2017年04月

  • フグが「ミステリーサークル」を建設するロジックを解明する―ミステリーサークル形成のシミュレーション

    水内良

    第64回 日本生態学会大会  

    発表年月: 2017年03月

  • 生命の初期進化を実験で追体験する

    水内良  [招待有り]

    Keio Astrobiology Camp 2017  

    発表年月: 2017年03月

  • Adaptation, diversification, and evolution of complexity of a simple artificial RNA self-replication system

    Ryo Mizuuchi

    3rd NoR HGT & LUCA conference  

    発表年月: 2016年11月

  • シンセティック・アストロバイオロジー -単純生命のモデルや部品を実験的に創る-

    水内良  [招待有り]

    Keio Spring Science Camp 2016  

    発表年月: 2016年03月

  • 人工RNA自己複製システムの環境への適応進化

    水内良、市橋伯一、臼井公人、数田恭章、四方哲也

    日本進化学会 第16回大阪大会  

    発表年月: 2014年08月

  • Adaptive Evolution of an Artificial RNA through in vitro Translation-Coupled Replication System to a Severer Translational, Less Ribosome Environment

    Ryo Mizuuchi, Norikazu Ichihashi, Kimihito Usui, Yasuaki Kazuta, Tetsuya Yomo

    Origins2014: 2nd ISSOL‐The International Astrobiology Society and Bioastronomy Joint International Conference  

    発表年月: 2014年07月

  • Evolution and adaptation of a life-like complex system to severe environments

    Ryo Mizuuchi, Norikazu Ichihashi, Kimihito Usui, Yasuaki Kazuta, Tetsuya Yomo

    OWECS2013: OIST Winter Course “Evolution of Complex Systems”  

    発表年月: 2013年12月

▼全件表示

共同研究・競争的資金等の研究課題

  • 原始RNA集団における自己複製体の創発と進化

    JST  創発的研究支援事業

    研究期間:

    2023年04月
    -
    2026年03月
     

    水内 良

  • 人工多細胞におけるゲノム複製の時空間制御

    日本学術振興会  学術変革領域研究 (A) (公募研究)

    研究期間:

    2023年04月
    -
    2025年03月
     

    水内良

  • 最小自己複製RNAの構築

    日本学術振興会  若手研究

    研究期間:

    2023年04月
    -
    2025年03月
     

    水内 良

  • 長鎖DNA合成と自律型人工細胞創出のための人工細胞リアクタシステム

    JST  CREST

    研究期間:

    2023年04月
    -
    2025年03月
     

    野地 博行

  • 人工多細胞型ゲノム複製システムの構築

    日本学術振興会  学術変革領域研究 (A) (公募研究)

    研究期間:

    2021年10月
    -
    2023年03月
     

    水内 良

  • 原始生命の進化に学ぶゲノム拡張基盤の構築

    JST  さきがけ研究

    研究期間:

    2019年10月
    -
    2023年03月
     

    水内 良

  • 原始複製体モデルを用いた複雑化仮説の実験的検証

    日本学術振興会  研究活動スタート支援

    研究期間:

    2019年10月
    -
    2021年03月
     

    水内 良

  • 短いランダム配列RNAから自己複製体が創発する可能性の探求

    日本学術振興会  海外特別研究員

    研究期間:

    2018年04月
    -
    2019年03月
     

    水内 良

  • シッポウフグの巣の形成原理の解明

    ヒューマンウェアイノベーションプログラム  融合研究費

    研究期間:

    2017年07月
    -
    2018年03月
     

    近藤 滋

  • 実験進化モデルを用いた共働する遺伝子の適応進化

    日本学術振興会  特別研究員 DC1

    研究期間:

    2015年04月
    -
    2018年03月
     

    水内 良

  • Direct observation of co-evolution at the RNA-protein interface

    NASA  NASA Science Innovation Fund

    研究期間:

    2015年10月
    -
    2016年09月
     

    Mark A Ditzler

▼全件表示

Misc

  • アマミホシゾラフグがつくる「ミステリーサークル」の謎を解く

    川瀬裕司, 水内良, 進寛史, 北嶋友喜, 細田耕, 清水正宏, 岩井大輔, 近藤滋

    計測自動制御学会システム・情報部門学術講演会講演論文集 ROMBUNNO.GS03‐5    2017年  [査読有り]

  • Evolution and Adaptation of the RNA Coupled with an Artificial Life-Like Self-Replication System to a Severe Translational Environment

    Ryo Mizuuchi, Norikazu Ichihashi, Kimihito Usui, Tetsuya Yomo

    Proceeding of International Astrobiology Workshop 2013     1006  2013年  [査読有り]

 

現在担当している科目

▼全件表示

 

他学部・他研究科等兼任情報

  • 理工学術院   大学院先進理工学研究科

学内研究所・附属機関兼任歴

  • 2023年
    -
    2024年

    理工学術院総合研究所   兼任研究員

特定課題制度(学内資金)

  • 液滴が自己複製分子システムの進化に与える影響の調査

    2023年  

     概要を見る

    生命が誕生する前にはRNAなどの自己複製する分子システムが存在し、ダーウィン進化によって複雑化したと考えられている。進化には細胞等の区画構造が必要であり、原始区画の候補として液-液相分離した液滴が提唱されている。一方、先行研究において自己複製分子の進化は油中水滴でしか実証されていない。本研究では液滴でRNA自己複製システムが進化可能であるかを検証するために、まずRNAの液滴内での複製ダイナミクスを継代実験により調査した。その結果、持続的な複製には液滴同士の融合や変異体の出現を抑えるような継代手法が必要であることを示唆する結果が得られた。現在、持続的な複製の達成に向けて継代手法を改良中である。