Details of the Researcher

PHOTO

Hideaki Matsubayashi
Section
Frontier Research Institute for Interdisciplinary Sciences
Job title
Assistant Professor
Degree

  • 博士（医科学）（東京大学）

  • 修士（生命科学）（東京大学）

e-Rad No.
00853061

Research History 5

  • 2022/04 - Present
    Tohoku University　Frontier Research Institute for Interdisciplinary Sciences Creative Interdisciplinary Research Division

  • 2021/04 - 2025/03
    Japan Science and Technology Agency

  • 2016/04 - 2022/03
    Johns Hopkins University　Cell Biology Department, School of Medicine　Post-doctral fellow

  • 2016/04 - 2018/03
    Japan Society for the Promotion of Science

  • 2013/04 - 2016/03
    Japan Society for the Promotion of Science

Education 5

  • The University of Tokyo　Graduate School of Frontier Sciences

    2013/04 - 2016/03

  • The University of Tokyo　Graduate School of Frontier Sciences　Department of Medical Genome Sciences

    2011/04 - 2013/03

  • The University of Tokyo　The Faculty of Engineering　Department of Chemistry and Biotechnology

    2009/04 - 2011/03

  • The University of Tokyo　College of Arts and Sciences

    2007/04 - 2009/03

  • 東京都立日比谷高等学校

    2004/04 - 2007/03

Research Interests 7

  • actin

  • Light inducible dimerization

  • cytoskeleton

  • liposome

  • cell-free translation system

  • artificial cell

  • synthetic biology

Research Areas 3

  • Life sciences / Cell biology /

  • Life sciences / Biophysics /

  • Life sciences / Functional biochemistry /

Awards 8

  1. the Young Scientist Award for Presentation

    2025/07　Light-guided Actin Dynamics Drive Directed Motility in Synthetic Cells

  2. 日本蛋白質科学会 若手奨励賞

    2024/06　日本蛋白質科学会　PI3-kinase iSH2 ドメインによる細胞運動のアクセルとブレーキ

  3. Postdoctoral Researcher Award

    2021/04　Experimental Biology 2021

  4. Best poster prize

    2018/07　he FASEB 2018 SRC, Phospholipids: Dynamic Lipid Signaling in Health and Disease

  5. ポスター賞特別賞

    2014/08　第54回生命科学夏の学校　無細胞翻訳系による SecYEG トランスロコンの合成

  6. 口頭発表賞

    2014　第11回21世紀大腸菌研究会

  7. 英語論文発表会「優秀賞」

    2013　東京大学新領域創成科学研究科メディカルゲノム専攻

  8. ポスター賞優秀賞

    2011/07　第51回生命科学夏の学校　無細胞タンパク質合成系を用いた SecYEG translocon の構築

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Papers 23

  1. A bacterial actin with high ATPase activity regulates the polymerization of a partner MreB isoform essential for Spiroplasma swimming motility. International-journal

    Daichi Takahashi, Hana Kiyama, Hideaki T Matsubayashi, Ikuko Fujiwara, Makoto Miyata

    The Journal of biological chemistry　110462-110462　2025/07/07

    DOI： 10.1016/j.jbc.2025.110462 　

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    Spiroplasma is a wall-less helical bacterium that is characterized by a unique swimming motility involving five isoforms of the bacterial actin MreBs (SMreB1-5). The functions of SMreBs are unique in the MreB family proteins, as their counterparts in walled-bacteria localize the cell-wall synthesis complex by forming filaments that slowly turn over to maintain the cell shape. In vitro analyses of individual SMreBs provide clues to understand the detailed molecular mechanism of Spiroplasma swimming. However, the purification difficulties have hampered in vitro analyses of one of the SMreBs, SMreB1, which drives the swimming. Here, we isolated soluble SMreB1 of Spiroplasma eriocheiris (SpeMreB1) and evaluated its activity. SpeMreB1 was expressed as a fusion with a solubilization-tag, ProteinS (PrS), which allowed us to purify it in the soluble fraction. SpeMreB1 exhibited the highest phosphate (Pi) release rate and the fold changes of critical concentrations for polymerization across the nucleotide states among the MreB family proteins. SpeMreB1 interacted with polymerized SpeMreB5, another SMreB essential for Spiroplasma swimming. In the AMPPNP- or ADP-bound state, SpeMreB1 decreased the amount of SpeMreB5 filaments, possibly reflecting their disassembly. Regardless of the nucleotide state, SpeMreB1 bound to negatively charged lipids. These results suggest that SpeMreB1 utilizes its highest activity to manage SpeMreB5 filaments underneath the cell membrane to drive Spiroplasma swimming. IMPORTANCE: In most bacterial species, MreB forms stable filaments that are involved in cell-shape maintenance by localizing the bacterial cell-wall synthesis complex. In contrast, five isoforms of MreBs in the pathogenic wall-less helical bacterium Spiroplasma are involved in its unique motility system driven by a kink propagation along the helical cell. Our integrated biochemical assays show that one isoform of MreBs involved in the swimming of a crustacean pathogen S. eriocheiris (SpeMreB1) is exceptionally active in the MreB family proteins and manages the polymerization of another MreB essential for the swimming (SpeMreB5). This study sheds light on an evolutionary mystery how Spiroplasma has adapted static MreB proteins to a dynamic phenomenon like its swimming motility.

  2. A unified purification method for actin-binding proteins using a TEV-cleavable His-Strep-tag International-journal International-coauthorship Peer-reviewed

    Daichi Nakajima, Nozomi Takahashi, Takanari Inoue, Shin-ichiro M. Nomura, Hideaki T. Matsubayashi

    MethodsX　2024/12

    DOI： 10.1016/j.mex.2024.102884 　

  3. Light-guided actin polymerization drives directed motility in protocells International-coauthorship

    Hideaki T. Matsubayashi, Shiva Razavi, T. Willow Rock, Daichi Nakajima, Hideki Nakamura, Daniel A. Kramer, Tomoaki Matsuura, Baoyu Chen, Satoshi Murata, Shinichiro M. Nomura, Takanari Inoue

    BioRxiv　2024/10/15

    DOI： 10.1101/2024.10.14.617543 　

  4. A highly active bacterial actin actuates the polymerization of another isoform essential for swimming motility ofSpiroplasma

    Daichi Takahashi, Hana Kiyama, Hideaki Matsubayashi, Ikuko Fujiwara, Makoto Miyata

    BioRxiv　2024/09/08

    Publisher: Cold Spring Harbor Laboratory

    DOI： 10.1101/2024.09.04.611326 　

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    Spiroplasmais a wall−less helical bacterium possessing five isoforms of bacterial actin MreBs (SMreB1−5) for its swimming, speculated to be the sole motility system driven by endogenous bacterial actin proteins. Its detailed molecular mechanism remains elusive due to the lack of soluble constructs of SMreB1 essential forSpiroplasmaswimming. Here, we isolated soluble SMreB1 ofSpiroplasma eriocheiris(SpeMreB1) and evaluated its activity. The phosphate release rate and fold changes of polymerization−critical concentrations over the nucleotide states of SpeMreB1 are the highest among the MreB family proteins. SpeMreB1 interacts with polymerized SpeMreB5, another SMreB essential forSpiroplasmaswimming, and decreases SpeMreB5 filament amount depending on the nucleotide state. A decrease in SpeMreB5 filament amount is independent of SpeMreB1 polymerization, although it is essential for swimming motility. SpeMreB1 binds to negatively charged lipids, regardless of their nucleotide state. These results suggest that SpeMreB1 manages SpeMreB5 filaments to driveSpiroplasmaswimming.

  5. Transmembrane DNA Sequence Signaling via Hybridization

    Kai Yoshida, Keita Abe, Yusuke Sato, Ibuki Kawamata, Richard James Archer, Hideaki T. Matsubayashi, Shogo Hamada, Satoshi Murata, Shin-ichiro NOMURA

    ChemRxiv　2024/07/16

    DOI： 10.26434/chemrxiv-2024-571kp 　

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    <jats:p>This study explored a novel transmembrane signaling mechanism using DNA hybridization to facilitate molecular communication across lipid membranes. We designed a system where single-stranded DNA (ssDNA) with cholesterol groups, termed “Driver,” anchors to giant unilamellar vesicles (GUVs). The Driver hybridizes with a complementary ssDNA, “Packet,” carrying signaling sequences. This hybridization enables the transport of DNA sequences across the lipid membrane, triggering internal fluorescence signaling. We demonstrated that this system, named “Chabashira,” effectively facilitates DNA sequence transfer and information processing within GUVs. Our findings suggest potential applications in artificial molecular systems and DNA-based information processing, highlighting the capability for complex and compartmentalized molecular communication.</jats:p>

  6. Micrometer-sized Reverse Vesicle with DNA Membrane in Oil Peer-reviewed

    Hinata Kariya, Hideaki Matsubayashi, Shin-ichiro M. Nomura

    MARSS2024　2024/07

  7. Synthetic control of actin polymerization and symmetry breaking in active protocells. International-journal Peer-reviewed

    Shiva Razavi, Felix Wong, Bedri Abubaker-Sharif, Hideaki T Matsubayashi, Hideki Nakamura, Nhung Thi Hong Nguyen, Douglas N Robinson, Baoyu Chen, Pablo A Iglesias, Takanari Inoue

    Science advances　10　(24)　eadk9731　2024/06/14

    DOI： 10.1126/sciadv.adk9731 　

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    <jats:title>Abstract</jats:title><jats:p>Non-linear biomolecular interactions on the membranes drive membrane remodeling that underlies fundamental biological processes including chemotaxis, cytokinesis, and endocytosis. The multitude of biomolecules, the redundancy in their interactions, and the importance of spatiotemporal context in membrane organization hampers understanding the physical principles governing membrane mechanics. A minimal, in vitro system that models the functional interactions between molecular signaling and membrane remodeling, while remaining faithful to cellular physiology and geometry is powerful yet remains unachieved. Here, inspired by the biophysical processes underpinning chemotaxis, we reconstituted externally-controlled actin polymerization inside giant unilamellar vesicles, guiding self-organization on the membrane. We show that applying undirected external chemical inputs to this system results in directed actin polymerization and membrane deformation that are uncorrelated with upstream biochemical cues, indicating symmetry breaking. A biophysical model of the dynamics and mechanics of both actin polymerization and membrane shape suggests that inhomogeneous distributions of actin generate membrane shape deformations in a non-linear fashion, a prediction consistent with experimental measurements and subsequent local perturbations. The active protocellular system demonstrates the interplay between actin dynamics and membrane shape in a symmetry breaking context that is relevant to chemotaxis and a suite of other biological processes.</jats:p>

  8. Non-catalytic role of phosphoinositide 3-kinase in mesenchymal cell migration through non-canonical induction of p85β/AP2-mediated endocytosis. International-journal Peer-reviewed

    Hideaki T Matsubayashi, Jack Mountain, Nozomi Takahashi, Abhijit Deb Roy, Tony Yao, Amy F Peterson, Cristian Saez Gonzalez, Ibuki Kawamata, Takanari Inoue

    Nature communications　15　(1)　2612-2612　2024/03/23

    DOI： 10.1038/s41467-024-46855-y 　

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    Class IA phosphoinositide 3-kinase (PI3K) galvanizes fundamental cellular processes such as migration, proliferation, and differentiation. To enable these multifaceted roles, the catalytic subunit p110 utilizes the multi-domain, regulatory subunit p85 through its inter SH2 domain (iSH2). In cell migration, its product PI(3,4,5)P3 generates locomotive activity. While non-catalytic roles are also implicated, underlying mechanisms and their relationship to PI(3,4,5)P3 signaling remain elusive. Here, we report that a disordered region of iSH2 contains AP2 binding motifs which can trigger clathrin and dynamin-mediated endocytosis independent of PI3K catalytic activity. The AP2 binding motif mutants of p85 aberrantly accumulate at focal adhesions and increase both velocity and persistency in fibroblast migration. We thus propose the dual functionality of PI3K in the control of cell motility, catalytic and non-catalytic, arising distinctly from juxtaposed regions within iSH2.

  9. ActuAtor, a Listeria-inspired molecular tool for physical manipulation of intracellular organizations through de novo actin polymerization Peer-reviewed

    Hideki Nakamura, Elmer Rho, Christopher T. Lee, Kie Itoh, Daqi Deng, Satoshi Watanabe, Shiva Razavi, Hideaki T. Matsubayashi, Cuncheng Zhu, Eleanor Jung, Padmini Rangamani, Shigeki Watanabe, Takanari Inoue

    Cell Reports　2023/10

    DOI： 10.1016/j.celrep.2023.113089 　

    ISSN： 2211-1247

  10. Synthetic control of actin polymerization and symmetry breaking in active protocells. International-journal

    Shiva Razavi, Felix Wong, Bedri Abubaker-Sharif, Hideaki T Matsubayashi, Hideki Nakamura, Eduardo Sandoval, Douglas N Robinson, Baoyu Chen, Jian Liu, Pablo A Iglesias, Takanari Inoue

    bioRxiv : the preprint server for biology　2023/09/23

    DOI： 10.1101/2023.09.22.559060 　

    More details Close

    Non-linear biomolecular interactions on the membranes drive membrane remodeling that underlies fundamental biological processes including chemotaxis, cytokinesis, and endocytosis. The multitude of biomolecules, the redundancy in their interactions, and the importance of spatiotemporal context in membrane organization hampers understanding the physical principles governing membrane mechanics. A minimal, in vitro system that models the functional interactions between molecular signaling and membrane remodeling, while remaining faithful to cellular physiology and geometry is powerful yet remains unachieved. Here, inspired by the biophysical processes underpinning chemotaxis, we reconstituted externally-controlled actin polymerization inside giant unilamellar vesicles, guiding self-organization on the membrane. We show that applying undirected external chemical inputs to this system results in directed actin polymerization and membrane deformation that are uncorrelated with upstream biochemical cues, indicating symmetry breaking. A biophysical model of the dynamics and mechanics of both actin polymerization and membrane shape suggests that inhomogeneous distributions of actin generate membrane shape deformations in a non-linear fashion, a prediction consistent with experimental measurements and subsequent local perturbations. The active protocellular system demonstrates the interplay between actin dynamics and membrane shape in a symmetry breaking context that is relevant to chemotaxis and a suite of other biological processes.

  11. Non-catalytic role of phosphoinositide 3-kinase in mesenchymal cell migration through non-canonical induction of p85β/AP-2-mediated endocytosis. International-journal

    Hideaki T Matsubayashi, Jack Mountain, Tony Yao, Amy F Peterson, Abhijit Deb Roy, Takanari Inoue

    bioRxiv : the preprint server for biology　2023/01/02

    DOI： 10.1101/2022.12.31.522383 　

    More details Close

    Class IA phosphoinositide 3-kinase (PI3K) galvanizes fundamental cellular processes such as migration, proliferation, and differentiation. To enable multifaceted roles, the catalytic subunit p110 utilizes a multidomain, regulatory subunit p85 through its inter SH2 domain (iSH2). In cell migration, their product PI(3,4,5)P3 generates locomotive activity. While non-catalytic roles are also implicated, underlying mechanisms and its relationship to PI(3,4,5)P3 signaling remain elusive. Here, we report that a disordered region of iSH2 contains previously uncharacterized AP-2 binding motifs which can trigger clathrin and dynamin-mediated endocytosis independent of PI3K catalytic activity. The AP-2 binding motif mutants of p85 aberrantly accumulate at focal adhesions and upregulate both velocity and persistency in fibroblast migration. We thus propose the dual functionality of PI3K in the control of cell motility, catalytic and non-catalytic, arising distinctly from juxtaposed regions within iSH2.

  12. Dynamin is primed at endocytic sites for ultrafast endocytosis. International-journal Peer-reviewed

    Yuuta Imoto, Sumana Raychaudhuri, Ye Ma, Pascal Fenske, Eduardo Sandoval, Kie Itoh, Eva-Maria Blumrich, Hideaki T Matsubayashi, Lauren Mamer, Fereshteh Zarebidaki, Berit Söhl-Kielczynski, Thorsten Trimbuch, Shraddha Nayak, Janet H Iwasa, Jian Liu, Bin Wu, Taekjip Ha, Takanari Inoue, Erik M Jorgensen, Michael A Cousin, Christian Rosenmund, Shigeki Watanabe

    Neuron　110　(17)　2815-2835　2022/09/07

    DOI： 10.1016/j.neuron.2022.06.010 　

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    Dynamin mediates fission of vesicles from the plasma membrane during endocytosis. Typically, dynamin is recruited from the cytosol to endocytic sites, requiring seconds to tens of seconds. However, ultrafast endocytosis in neurons internalizes vesicles as quickly as 50 ms during synaptic vesicle recycling. Here, we demonstrate that Dynamin 1 is pre-recruited to endocytic sites for ultrafast endocytosis. Specifically, Dynamin 1xA, a splice variant of Dynamin 1, interacts with Syndapin 1 to form molecular condensates on the plasma membrane. Single-particle tracking of Dynamin 1xA molecules confirms the liquid-like property of condensates in vivo. When Dynamin 1xA is mutated to disrupt its interaction with Syndapin 1, the condensates do not form, and consequently, ultrafast endocytosis slows down by 100-fold. Mechanistically, Syndapin 1 acts as an adaptor by binding the plasma membrane and stores Dynamin 1xA at endocytic sites. This cache bypasses the recruitment step and accelerates endocytosis at synapses.

  13. A molecular trap inside microtubules probes luminal access by soluble proteins. International-journal Peer-reviewed

    Yuta Nihongaki, Hideaki T Matsubayashi, Takanari Inoue

    Nature chemical biology　17　(8)　888-895　2021/08/03

    Publisher: Springer Science and Business Media {LLC}

    DOI： 10.1038/s41589-021-00791-w 　

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    The uniquely hollow structure of microtubules (MTs) confers characteristic mechanical and biological properties. Although most regulatory processes take place at the outer surface, molecular events inside MTs, such as α-tubulin acetylation, also play a critical role. However, how regulatory proteins reach the site of action remains obscure. To assess luminal accessibility, we first identified luminally positioned residues of β-tubulin that can be fused to a protein of interest. We then developed a chemically inducible technique with which cytosolic proteins can be rapidly trapped at the lumen of intact MTs in cells. A luminal trapping assay revealed that soluble proteins of moderate size can enter the lumen via diffusion through openings at the MT ends and sides. Additionally, proteins forming a complex with tubulins can be incorporated to the lumen through the plus ends. Our approach may not only illuminate this understudied territory, but may also help understand its roles in MT-mediated functions.

  14. Disordered Region in PI3K Regulatory Subunit p85 Drives Clathrin‐dependent Endocytosis and Regulates Cell Motility

    Hideaki Matsubayashi, Jack Mountain, Amy Peterson, Takanari Inoue

    The FASEB Journal　35　(S1)　2021/05/14

    Publisher: Wiley

    DOI： 10.1096/fasebj.2021.35.s1.01941 　

    ISSN： 0892-6638

    eISSN： 1530-6860

  15. Hetero-oligomerization of Rho and Ras GTPases Connects GPCR Activation to mTORC2-AKT Signaling. International-journal Peer-reviewed

    Hiroshi Senoo, May Wai, Hideaki T Matsubayashi, Hiromi Sesaki, Miho Iijima

    Cell reports　33　(8)　108427-108427　2020/11/24

    Publisher: Elsevier {BV}

    DOI： 10.1016/j.celrep.2020.108427 　

    ISSN： 2211-1247

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    The activation of G-protein-coupled receptors (GPCRs) leads to the activation of mTORC2 in cell migration and metabolism. However, the mechanism that links GPCRs to mTORC2 remains unknown. Here, using Dictyostelium cells, we show that GPCR-mediated chemotactic stimulation induces hetero-oligomerization of phosphorylated GDP-bound Rho GTPase and GTP-bound Ras GTPase in directed cell migration. The Rho-Ras hetero-oligomers directly and specifically stimulate mTORC2 activity toward AKT in cells and after biochemical reconstitution using purified proteins in vitro. The Rho-Ras hetero-oligomers do not activate ERK/MAPK, another kinase that functions downstream of GPCRs and Ras. Human KRas4B functionally replace Dictyostelium Ras in mTORC2 activation. In contrast to GDP-Rho, GTP-Rho antagonizes mTORC2-AKT signaling by inhibiting the oligomerization of GDP-Rho with GTP-Ras. These data reveal that GPCR-stimulated hetero-oligomerization of Rho and Ras provides a critical regulatory step that controls mTORC2-AKT signaling.

  16. The bacterial protein YidC accelerates MPIase-dependent integration of membrane proteins. International-journal Peer-reviewed

    Masaru Sasaki, Hanako Nishikawa, Sonomi Suzuki, Michael Moser, Maria Huber, Katsuhiro Sawasato, Hideaki T Matsubayashi, Kaoru Kumazaki, Tomoya Tsukazaki, Yutetsu Kuruma, Osamu Nureki, Takuya Ueda, Ken-Ichi Nishiyama

    The Journal of biological chemistry　294　(49)　18898-18908　2019/12/06

    DOI： 10.1074/jbc.RA119.011248 　

    ISSN： 0021-9258

    eISSN： 1083-351X

  17. Discovery of the Hedgehog Pathway Inhibitor Pipinib that Targets PI4KIIIß. International-journal Peer-reviewed

    Lea Kremer, Elisabeth Hennes, Alexandra Brause, Andrei Ursu, Lucas Robke, Hideaki T Matsubayashi, Yuta Nihongaki, Jana Flegel, Ivana Mejdrová, Jan Eickhoff, Matthias Baumann, Radim Nencka, Petra Janning, Susanne Kordes, Hans R Schöler, Jared Sterneckert, Takanari Inoue, Slava Ziegler, Herbert Waldmann

    Angewandte Chemie (International ed. in English)　58　(46)　16617-16628　2019/11/11

    DOI： 10.1002/anie.201907632 　

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    The Hedgehog (Hh) signaling pathway is crucial for vertebrate embryonic development, tissue homeostasis and regeneration. Hh signaling is upregulated in basal cell carcinoma and medulloblastoma and Hh pathway inhibitors targeting the Smoothened (SMO) protein are in clinical use. However, the signaling cascade is incompletely understood and novel druggable proteins in the pathway are in high demand. We describe the discovery of the Hh-pathway modulator Pipinib by means of cell-based screening. Target identification and validation revealed that Pipinib selectively inhibits phosphatidylinositol 4-kinase IIIβ (PI4KB) and suppresses GLI-mediated transcription and Hh target gene expression by impairing SMO translocation to the cilium. Therefore, inhibition of PI4KB and, consequently, reduction in phosphatidyl-4-phosphate levels may be considered an alternative approach to inhibit SMO function and thus, Hedgehog signaling.

  18. De Novo Synthesis of Basal Bacterial Cell Division Proteins FtsZ, FtsA, and ZipA Inside Giant Vesicles. International-journal Peer-reviewed

    Takumi Furusato, Fumihiro Horie, Hideaki T Matsubayashi, Kazuaki Amikura, Yutetsu Kuruma, Takuya Ueda

    ACS synthetic biology　7　(4)　953-961　2018/04/20

    DOI： 10.1021/acssynbio.7b00350 　

    eISSN： 2161-5063

  19. Cell-free synthesis of SecYEG translocon as the fundamental protein transport machinery. International-journal Peer-reviewed

    Hideaki Matsubayashi, Yutetsu Kuruma, Takuya Ueda

    Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life　44　(4)　331-4　2014/12/01

    DOI： 10.1007/s11084-014-9389-y 　

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    The cell membrane has many indispensable functions for sustaining cell alive besides a role as merely outer envelope. The most of such functions are implemented by membrane embedded proteins that are emerged through the membrane integration machinery, SecYEG translocon. Here, we synthesized SecYEG by expressing the corresponding gene in vitro to study the process of functionalization of the cell membrane.

  20. Purified cell-free systems as standard parts for synthetic biology. Invited Peer-reviewed

    Hideaki T. Matsubayashi

    Current opinion in chemical biology　22　158-162　2014/10/15

    Publisher: Elsevier BV

    DOI： 10.1016/j.cbpa.2014.09.031 　

    ISSN： 1367-5931

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    A cell free protein synthesis approach is extensively used for biochemical and synthetic biology researches. Unlike lysate based cell free systems, the PURE system is reconstituted with individually purified factors essential for transcriptional and translational processes. Hence, the components in the PURE system can be definitely manipulated as per the desired situation. Because of this high controllability, the PURE system has been applied to a wide range of research scene, such as biochemical analysis in reconstructed system, in vitro protein engineering, reconstitution of an artificial cell. We believe that this purified cell-free protein synthesis system become a basal technology to advance synthetic biology.

  21. In vitro synthesis of the E. coli Sec translocon from DNA. International-journal Peer-reviewed

    Hideaki Matsubayashi, Yutetsu Kuruma, Takuya Ueda

    Angewandte Chemie (International ed. in English)　53　(29)　7535-8　2014/07/14

    DOI： 10.1002/anie.201403929 　

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    Difficulties in constructing complex lipid/protein membranes have severely limited the development of functional artificial cells endowed with vital membrane-related functions. The Sec translocon membrane channel, which mediates the insertion of membrane proteins into the plasma membrane, was constructed in the membrane of lipid vesicles through in vitro expression of its component proteins. The components of the Sec translocon were synthesized from their respective genes in the presence of liposomes, thereby bringing about a functional complex. The synthesized E. coli Sec translocon mediated the membrane translocation of single- and multi-span membrane proteins. The successful translocation of a functional peptidase into the liposome lumen further confirmed the proper insertion of the translocon complex. Our results demonstrate the feasible construction of artificial cells, the membranes of which can be functionalized by directly decoding genetic information into membrane functions.

  22. In vitro reconstruction of functional membrane

    Yutetsu Kuruma, Hideaki Matsubayashi, Takuya Ueda

    Artificial Life 14 - Proceedings of the 14th International Conference on the Synthesis and Simulation of Living Systems, ALIFE 2014　963-964　2014

    Publisher: MIT Press Journals

  23. Autonomous construction of synthetic cell membrane

    Yutetsu Kuruma, Hideaki Matsubayashi

    Advances in Artificial Life, ECAL 2013　9-10　2013/09/02

    Publisher: MIT Press

    DOI： 10.1162/978-0-262-31709-2-ch002 　

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Misc. 4

  1. Toward simulating the origin of eukaryotes in an artificial cell Invited Peer-reviewed

    Hideaki T. Matsubayashi

    Viva Origino　2021/11

    DOI： 10.50968/vivaorigino.49_13 　

    ISSN： 0910-4003 1346-6933

  2. Letters from abroad Invited

    Seibutsu Butsuri　61　(1)　057-058　2021/01

    Publisher: Biophysical Society of Japan

    DOI： 10.2142/biophys.61.057 　

    ISSN： 0582-4052

    eISSN： 1347-4219

  3. 無細胞タンパク質合成系 Invited

    松林英明, 上田卓也

    高分子学会誌「高分子」　63　(6)　379-381　2014/06

  4. Cell-free protein synthesis system

    Hideaki Matsubayashi, Takuya Ueda

    Kobunshi　63　(6)　379-381　2014

    Publisher: Society of Polymer Science

    ISSN： 0454-1138

Presentations 23

  1. Building up cell motility in synthetic cells International-presentation International-coauthorship Invited

    Hideaki Matsubayashi

    Global insights in life sciences: bridging European and Japanese research　2025/02/28

  2. Reconstructing Spatiotemporal Dynamics of the Actin Cytoskeleton in Giant Vesicles: Towards Synthetic Cell Motility International-presentation Invited

    FRESK seminar, ENS Qbio　2025/02/24

  3. Artificial Cells to Explore Functional Transitions in Life Invited

    2025/01/30

  4. Synthesizing motility in artificial cells by asymmetrically reconstituted actin polymerization International-presentation Invited

    Hideaki Matsubayashi

    USCD Friend of Cell Seminar　2024/12/18

  5. 細胞骨格タンパク質の光操作で駆動する 人工細胞の変形と運動 Invited

    松林英明

    細胞を創る研究会17.0　2024/11/11

  6. Reconstituting actin-driven symmetry breaking and cell motility in synthetic cells International-presentation Invited

    Hideaki Matsubayashi, Hideki Nakamura, Shiva Razavi, Daichi Nakajima, Nozomi, Takahashi, Daniel A. Kramer, Tomoaki Matsuura, Baoyu Chen, Satoshi Murata, Shin-ichiro, M. Nomura, Takanari Inoue

    Next-Gen Cytoskeleton Research Seminar　2024/11/07

  7. アクチンによる力発生と細胞運動の再構成 Invited

    松林英明

    CBI学会2024年大会　2024/10/30

  8. アクチン細胞骨格の光操作による細胞運動の再構成

    松林英明

    第12回分子ロボティクス定例研究会　2024/08/22

  9. PI3キナーゼが制御する細胞遊走の「促進」と「抑制」：p85β/AP2を介したエンドサイトーシスとPI3Kの細胞内局在制御機構の解明

    松林英明

    第76回日本細胞生物学会大会　2024/07/17

  10. Non-catalytic role of phosphoinositide 3-kinase in cell migration through non-canonical induction of p85beta/AP2-mediated endocytosis Invited

    2024/06/12

  11. Reconstituting Actin-Driven Symmetry Breaking and Cell Motility in Synthetic Cells International-presentation Invited

    UW-TU:AOS Workshop　2024/06/07

  12. Functionalizing artificial cell membrane with cell-free synthesis and light-inducible proteins Invited

    2023/11/16

  13. 細胞運動を駆動する PI3Kの新規制御機構の解明 とアクチン系の再構成 Invited

    松林英明

    SPEED Journal Club　2023/11/10

  14. 人工細胞内でのアクチン重合光操作と細胞運動の再構成 Invited

    松林英明

    生物物理学会サブグループ「人工細胞モデル＆分子ロボティクス」第４回研究会　2023/01/25

  15. Synthesizing motility in artificial cells by asymmetrically reconstituted actin polymerization International-presentation Invited

    Hideaki Matsubayashi, Shiva Razavi, Willow Rock, Hideki Nakamura, Daniel A. Kramer, Tomoaki Matsuura, Shin-ichiro M. Nomura, Baoyu Chen, Takanari Inoue

    Gordon Research Conference, Directed Cell Migration　2023/01/09

  16. 人工細胞内でのアクチン重合光操作が可能にする細胞運動の再構成

    松林英明, Shiva Razavi, 中村秀樹, Daniel A. Krame, 松浦友亮, 野村M, 慎一郎, Baoyu Chen, 井上尊生

    第6回分子ロボティクス年次大会　2022/11/13

  17. Synthesizing motility in artificial cells by asymmetrically reconstituted actin polymerization Invited

    Hideaki Matsubayashi

    CCD Talk (Johns Hopkins University)　2022/05/27

  18. Disordered region in PI3K regulatory subunit p85 drives clathrin-dependent endocytosis and regulates cell motility

    Hideaki Matsubayashi, Jack Mountain, Amy Peterson, Takanari Inoue

    Experimental Biology 2021　2021/04

  19. 人工細胞内でのタンパク質操作が明らかにする細胞骨格機能の最小要素 Invited

    松林英明

    生命の起源と進化学会 2021 年シンポジウム　2021/03

  20. In Vitro Synthesis and Functional Analysis of SecYEG Translocon Invited

    2016/03

  21. 無細胞翻訳系による SecYEG トランスロコンの合成

    第 37 回 日本分子生物学会年会　2014/11

  22. PURE system による膜タンパク質合成システムの構築

    第9回 無細胞生命科学研究会　2014/10

  23. 無細胞翻訳系による SecYEG トランスロコンの合成

    第11回21世紀大腸菌研究会　2014/06

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Research Projects 9

  1. 細胞運動の再構成によるアクチン細胞骨格の協奏的力発生機構の解明

    松林 英明

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 基盤研究(B)

    Institution: 東北大学

    2025/04/01 - 2029/03/31

  2. 光操作で紡ぐアクチン細胞骨格因子の協奏と高次構造の理解

    松林 英明

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 学術変革領域研究(A)

    Institution: 東北大学

    2025/04/01 - 2027/03/31

  3. 新規⼈⼯細胞⾻格タンパク質の合理設計と細胞操作への応⽤

    Offer Organization: 東北大学学際科学フロンティア研究所

    System: 学際研究共創プログラム

    2024/04 - 2026/03

  4. アクチン重合光操作を基盤とした人工細胞ネットワーク自在配線技術の開発

    松林 英明

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 学術変革領域研究(A)

    Institution: 東北大学

    2023/04/01 - 2025/03/31

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    本研究では、リポソーム型人工細胞のネットワーク構築の方法の開発を目指している。本年度は、多数のリポソームを再現性良く、かつ、サイズを揃えて作成する方法の構築を進め、リポソームを収率よく作成できる条件が見出されたため成果が得られた。また、人工細胞のネットワーク構築にあたり、脂質膜の変形を操作する方法論の開発を目指し、関連するタンパク質の精製を進めた。当初予定していたタンパク質について、十分な量と精製度でタンパク質を取得し、進展があった。特に、膜変形活性があるタンパク質については、リポソームの変形および脂質膜チューブの形成が観察された。次年度、この膜変形の活性について、光制御する方法と条件の検討を進める予定である。アクチン関連タンパク質については、精製タグを改良し、複数種類のアクチン関連タンパク質を統一した方法で精製できるよう実験系を構築した。これについては、現在論文を投稿中である。このような精製法を確立したことで、当初予定にはなかったタンパク質についても並行して取得できたため、次年度、解析を進める予定である。タンパク質光操作についても、これまで用いてきた光応答性タンパク質のペアとは別の光応答性タンパク質について、リポソーム内での活性と光制御が確認できたため、進展した。次年度は、膜変形タンパク質、アクチンとアクチン関連タンパク質、そして、光応答性タンパク質、そしてリポソームを整列させる方法などの検討し、これらを組み合わせることで、リポソームの変形制御やリポソーム間の連結などへと進展させたい。

  5. 人工細胞内アクチン重合光操作が可能にする細胞運動原理の構成的解明

    松林 英明

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 若手研究

    Institution: 東北大学

    2023/04/01 - 2025/03/31

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    本研究では、細胞運動を構成的に理解することを目指している。本年度は、まず、細胞が運動する際に見せる非対称なアクチンの重合をリポソーム型人工細胞の内部で再構築することについて進展が得られた。アクチン重合の操作を可能にするために、アクチン重合核形成促進因子と化合物依存型タンパク質二量体化系や、光依存型タンパク質二量体化系とを組み合わせた手法について、細胞内で応用について共著論文として発表した。さらに、化合物依存型タンパク質二量体化系をリポソーム型人工細胞内で応用し、非対称なアクチン重合や膜変形が観察された。この結果について、BioRxivで報告した。光依存型タンパク質二量体化系をリポソーム型人工細胞内に応用した方法についても研究を進め、大きく進展した。特に、アクチンの局在を光で制御する方法とその条件が見出され、さらに、特定の条件において光刺激方向に脂質膜が突出する結果が得られた。今後、非対称なアクチンの操作による膜の突出について、最小因子の同定などさらに解析を進める予定である。また、細胞の運動原理の理解についても、細胞骨格機能の上流の制御に関わるPI3Kの解析から新たな知見が得られ、その成果を報告した。

  6. 合成細菌JCVI syn3.0B とゲノム操作を用いた細胞進化モデルの構築

    宮田 真人

    Offer Organization: 科学技術振興機構

    System: 戦略的な研究開発の推進 戦略的創造研究推進事業 CREST

    Institution: 大阪市立大学

    2024/04 - 2025/03

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    JCVI-syn3.0は,2016年にマイコプラズマを基に作られた合成細菌で,そのゲノムは増殖に必須な遺伝子のみで構成されています.本研究では,様々な遺伝子をこの合成細菌に移植・発現させて,運動,細胞壁形成,DNA分配,膜リモデリング,などの能力の獲得という原始の細胞から真核生物にいたるイベントを実験で再現します.さらに,細胞を自由にデザインすることにより,新たな細胞の構築を行います.

  7. Decoding Ancestral Cytoskeltal Function in the Genome of Latent Species

    2021/04 - 2025/03

  8. 細胞極性化機能を備えた脂質膜小胞 (Smart GUV) の創成

    Offer Organization: 日本学術振興会

    System: 海外特別研究員

    Institution: ジョンズホプキンス大学

    2016/04 - 2018/03

  9. 無細胞翻訳系を用いたＳｅｃＹＥＧトランスロコンの機能発現メカニズムの解析

    松林 英明

    Offer Organization: 日本学術振興会

    System: 科学研究費助成事業

    Category: 特別研究員奨励費

    Institution: 東京大学

    2013/04/01 - 2016/03/31

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    昨年度までに、無細胞翻訳系によるSecYEGの再構築と、それに基づいて合成する膜タンパク質のliposome膜上でのトポロジー制御について成果をまとめ、論文発表と複数の学会での発表をすることができた。本年度は、さらに研究を発展させるべく、SecYEGの無細胞合成に必要な脂質組成の解析と、合成したSecYEGの１分子観察を行った。 脂質組成の解析について、昨年度までは脂質抽出物を用いた場合でしかSecYEGの活性がみられていなかったが、脂質の脂肪酸の条件検討により合成脂質で再構成することに成功した。脂質抽出物はGiant Unilamellar Vesicle (GUV)の作成などに適さなかったため、今回得られた結果により、人工細胞システムや膜タンパク質の試験管内進化への幅広い応用が期待できる。また、昨年度に見出された糖脂質様の分子について、微量な分子なために解析が難しかったが、岩手大学西山研究室との共同研究先で引き続き解析を行って頂いている。 SecYEGの膜透過活性について、基質の分泌タンパク質であるpOmpAのアミノ酸長を短くした場合に、再構成系においても膜透過のターンオーバーが検出された。詳細な速度論の解析を行うため東京大学野地研究室との共同研究で１分子観察に取り組んだ。まず、無細胞系によるSecY、SecEの蛍光標識と人工脂質平面膜上への再構成の条件を確立し、全反射顕微鏡によって観察したところ、SecYやSecEのサブユニットが単独で存在する場合も、純粋な脂質膜上では安定的に拡散することが初めて明らかになった。また、膜透過反応を観察するためpOmpAを蛍光標識して１分子観察を行ったが、脂質膜への非特異的な結合が見られた。条件検討を行ったものの、顕微鏡上に再構成する平面膜の不安定性もあり膜透過反応を解析するには至らなかったが、精製と再構成の煩雑さから１分子観察系の例が少ない膜タンパク質について、無細胞翻訳系の有用性を示す結果を得た。

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Teaching Experience 3

  1. Biology A (DNA replication)　Tohoku University

  2. Foundation of Molecular Robotics　Tohoku University

  3. Biology B (Cytoskeleton)　Tohoku University

Social Activities 2

  1. Podcast "分子デザインはじめました"

    2024/03/31 - Present

  2. 研究者になるってどんな感じ？ －世界を変える仕事への旅人－

    企画展示「学際研究で蘇る東北の豪族達」 併設展示「知の交差点：異分野との出会いから続く未来への道」

    2024/05/26 -

Academic Activities 6

  1. 日本生物物理学会サブグループ 人工細胞モデル＆分子ロボティクス 第６回研究会

    2023/12/20 -

    Activity type: Academic society, research group, etc.

  2. 植物細胞のロジックとケミカルAI

    2023/11/14 -

    Activity type: Competition, symposium, etc.

  3. Korea-Japan joint workshop of Bottom-up Synthetic Biology

    2023/09/06 -

    Activity type: Competition, symposium, etc.

  4. De novo タンパク質デザイン入門セミナー

    2023/08/08 -

    Activity type: Academic society, research group, etc.

  5. 日本生物物理学会サブグループ 人工細胞モデル＆分子ロボティクス 第５回研究会

    2023/07/05 -

    Activity type: Academic society, research group, etc.

  6. ケミナス４７特別ポスター企画「Bottom-up Biology 分子から組織まで」

    2023/05/14 -

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