Fujiwara, Kei

写真a

Affiliation

Faculty of Science and Technology, Department of Biosciences and Informatics (Yagami)

Position

Associate Professor

Related Websites

External Links
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Profile 【 Display / hide 】

  • Disrupted cells won't go back into its living states. We are trying to clarify why this process is irreversible and developing a method to reconstruct living cells from biomolecules mixtures using artificial cells engineering.

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Career 【 Display / hide 】

  • 2009.04
    -
    2010.03

    The university of Tokyo, Graduate School of Frontier Sciences, Department of Medical Genome Sciences, JSPS research associate

  • 2010.04
    -
    2011.03

    Kyoto university, Institute for Integrated Cell-Material Sciences, Research Associate

  • 2011.04
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    2014.03

    Tohoku University, Department of Bioengineering and Robotics, JSPS research associate

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Academic Background 【 Display / hide 】

  • 2004.04
    -
    2006.03

    The University of Tokyo, Graduate School of Agricultural and Life Sciences, Department of Applied Biological Chemistry

    Graduate School, Completed, Master's course

  • 2006.04
    -
    2009.03

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

    Graduate School, Completed, Doctoral course

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Academic Degrees 【 Display / hide 】

  • 博士(生命科学), The University of Tokyo, Coursework, 2009.03

    シャペロニンGroEL/ESの細胞内における役割の解明

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Research Areas 【 Display / hide 】

  • Life Science / Molecular biology

  • Life Science / Biophysics

  • Life Science / System genome science

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Research Keywords 【 Display / hide 】

  • Artificial-Cell engineering

  • Synthetic Biology

  • Bacteriology

  • Cell-free Life Sciences

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Books 【 Display / hide 】

  • Synthetic Biology: A Very Short Introduction

    藤原 慶,徳永 美恵, ニュートンプレス, 2021.04

    Original author： Jamie A. Davies,

  • ペプチド医薬品のスクリーニング・安定化・製剤化技術

    SUDO Kei, FUJIWARA Kei, DOI Nobuhide, 技術情報協会, 2017.12

    Scope: 1-4. mRNAディスプレイ法によるペプチドのスクリーニング

  • 人工細胞の創製とその応用

    FUJIWARA Kei, CMC出版, 2017.01

    Scope: 「3-4. 無細胞システムによる生命システムの理解」の執筆

  • DNA分子デザインのすべて ～BIOMOD虎の巻

    FUJIWARA Kei, CBT学会eBOOK, 2016.04

    Scope: p. 15-20， p. 33-34の執筆を担当

    　View Summary

    分子ロボティクス研究会編

  • 「自然世界の高分子」

    TANAKA Motohiko, TOKITA masayuki, YANAGISAWA Miho, SAKAUE Takahiro, FUJIWARA Kei, 吉岡書店, 2016.03

    Scope: 9章から11章の翻訳を担当

    　View Summary

    「Giant molecules」Alexander Y. Grosberg and Alexei R. Khokhlovの邦訳版(翻訳)

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Papers 【 Display / hide 】

  • Metabolic Tug-of-War between Glycolysis and Translation Revealed by Biochemical Reconstitution

    Sato G., Kinoshita S., Yamada T.G., Arai S., Kitaguchi T., Funahashi A., Doi N., Fujiwara K.

    ACS Synthetic Biology (ACS Synthetic Biology)  13 ( 5 ) 1572 - 1581 2024.05

    　View Summary

    Inside cells, various biological systems work cooperatively for homeostasis and self-replication. These systems do not work independently as they compete for shared elements like ATP and NADH. However, it has been believed that such competition is not a problem in codependent biological systems such as the energy-supplying glycolysis and the energy-consuming translation system. In this study, we biochemically reconstituted the coupling system of glycolysis and translation using purified elements and found that the competition for ATP between glycolysis and protein synthesis interferes with their coupling. Both experiments and simulations revealed that this interference is derived from a metabolic tug-of-war between glycolysis and translation based on their reaction rates, which changes the threshold of the initial substrate concentration for the success coupling. By the metabolic tug-of-war, translation energized by strong glycolysis is facilitated by an exogenous ATPase, which normally inhibits translation. These findings provide chemical insights into the mechanism of competition among biological systems in living cells and provide a framework for the construction of synthetic metabolism in vitro.

  • Multimolecular Competition Effect as a Modulator of Protein Localization and Biochemical Networks in Cell-Size Space

    Nishikawa S., Sato G., Takada S., Kohyama S., Honda G., Yanagisawa M., Hori Y., Doi N., Yoshinaga N., Fujiwara K.

    Advanced Science (Advanced Science)  11 ( 6 )  2024.02

    　View Summary

    Cells are small, closed spaces filled with various types of macromolecules. Although it is shown that the characteristics of biochemical reactions in vitro are quite different from those in living cells, the role of the co-existence of various macromolecules in cell-size space remains still elusive. Here, using a constructive approach, it is demonstrated that the co-existence of various macromolecules themselves has the ability to tune protein localization for spatiotemporal regulation and a biochemical reaction system in a cell-size space. Both experimental and theoretical analyses reveal that enhancement of interfacial effects by a large surface-area-to-volume ratio facilitates membrane localization of molecules in the cell-size space, and the interfacial effects are alleviated by competitive binding to lipid membranes among multiple proteins even if their membrane affinities are weak. These results indicate that competition for membrane binding among various macromolecules in the cell-size space plays a role in regulating the spatiotemporal molecular organization and biochemical reaction networks. These findings shed light on the importance of surrounding molecules for biochemical reactions using purified elements in small spaces.

  • Phase-Separated Giant Liposomes for Stable Elevation of α-Hemolysin Concentration in Lipid Membranes

    Kobayashi M., Noguchi H., Sato G., Watanabe C., Fujiwara K., Yanagisawa M.

    Langmuir (Langmuir)  39 ( 32 ) 11481 - 11489 2023.08

    ISSN  07437463

    　View Summary

    Staphylococcus aureus α-hemolysin (αHL) is one of the most popular proteins in nanopore experiments within lipid membranes. Higher concentrations of αHL within the lipid membrane are desirable to enhance the mass transport capacity through nanopores. However, the reconstitution of αHL at high concentrations is associated with the problem of membrane lytic disruption. In this study, we present a method that effectively increases αHL concentration while maintaining membrane stability. This method is achieved by using phase-separated giant liposomes, where coexisting liquid-disordered (Ld) and liquid-ordered phases (Lo) are enriched in unsaturated lipids and saturated lipids with cholesterol (Chol), respectively. Fluorescence observation of αHL in liposomes revealed that the presence of Chol facilitates αHL insertion into the membrane. Despite the preferential localization of αHL in the Ld phase rather than the Lo phase, the coexistence of both Lo and Ld phases prevents membrane disruption in the presence of concentrated αHL. We have explained this stabilization mechanism considering the lower membrane tension exhibited by phase-separated liposomes compared to homogeneous liposomes. Under hypertonic conditions, we have successfully increased the local concentration of αHL by invagination of the lipid-only region in the Ld phase, leaving αHL behind. This method exhibits potential for the reconstitution of various nanochannels and membrane proteins that prefer the Ld phase over the Lo phase, thus enabling the production of giant liposomes at high concentrations and the replication of the membrane-crowding condition observed in cells.

  • Cytoplasmic delivery of siRNA using human-derived membrane penetration-enhancing peptide

    Nakamura M., Fujiwara K., Doi N.

    Journal of Nanobiotechnology (Journal of Nanobiotechnology)  20 ( 1 )  2022.12

    　View Summary

    Background: Although protein-based methods using cell-penetrating peptides such as TAT have been expected to provide an alternative approach to siRNA delivery, the low efficiency of endosomal escape of siRNA/protein complexes taken up into cells by endocytosis remains a problem. Here, to overcome this problem, we adopted the membrane penetration-enhancing peptide S19 from human syncytin 1 previously identified in our laboratory. Results: We prepared fusion proteins in which the S19 and TAT peptides were fused to the viral RNA-binding domains (RBDs) as carrier proteins, added the RBD-S19-TAT/siRNA complex to human cultured cells, and investigated the cytoplasmic delivery of the complex and the knockdown efficiency of target genes. We found that the intracellular uptake of the RBD-S19-TAT/siRNA complex was increased compared to that of the RBD-TAT/siRNA complex, and the expression level of the target mRNA was decreased. Because siRNA must dissociate from RBD and bind to Argonaute 2 (Ago2) to form the RNA-induced silencing complex (RISC) after the protein/siRNA complex is delivered into the cytoplasm, a dilemma arises: stronger binding between RBD and siRNA increases intracellular uptake but makes RISC formation more difficult. Thus, we next prepared fusion proteins in which the S19 and TAT peptides were fused with Ago2 instead of RBD and found that the efficiencies of siRNA delivery and knockdown obtained using TAT-S19-Ago2 were higher than those using TAT-Ago2. In addition, we found that the smallest RISC delivery induced faster knockdown than traditional siRNA lipofection, probably due to the decreased time required for RISC formation in the cytoplasm. Conclusion: These results indicated that S19 and TAT-fused siRNA-binding proteins, especially Ago2, should be useful for the rapid and efficient delivery of siRNA without the addition of any endosome-disrupting agent.

  • Controlling the Periodicity of a Reaction-Diffusion Wave in Artificial Cells by a Two-Way Energy Supplier

    Takada S., Yoshinaga N., Doi N., Fujiwara K.

    ACS Nano (ACS Nano)  16 ( 10 ) 16853 - 16861 2022.10

    ISSN  19360851

    　View Summary

    Reaction-diffusion (RD) waves, which are dynamic self-organization structures generated by nanosize molecules, are a fundamental mechanism from patterning in nano- and micromaterials to spatiotemporal regulations in living cells, such as cell division and motility. Although the periods of RD waves are the critical element for these functions, the development of a system to control their period is challenging because RD waves result from nonlinear physical dynamics under far-from-equilibrium conditions. Here, we developed an artificial cell system with tunable period of an RD-driven wave (Min protein wave), which determines a cell division site plane in living bacterial cells. The developed system is based on our finding that Min waves are generated by energy consumption of either ATP or dATP, and the period of the wave is different between these two energy suppliers. We showed that the Min-wave period was modulated linearly by the mixing ratio of ATP and dATP and that it was also possible to estimate the mixing ratio of ATP and dATP from the period. Our findings illuminated a previously unidentified principle to control the dissipative dynamics of biomolecules and, simultaneously, built an important framework to construct molecular robots with spatiotemporal units.

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Papers, etc., Registered in KOARA 【 Display / hide 】

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Reviews, Commentaries, etc. 【 Display / hide 】

  • 酵素をひたすら混ぜる研究

    藤原慶

    生物工学会誌 (日本生物工学会)  101 ( 12 ) 639 - 639 2023.12

    Single Work, Lead author, Last author, Corresponding author

  • 生命の折り合い：単純と複雑の調和

    藤原慶、柳澤実穂

    現代化学 (東京化学同人)   2023.12

    Article, review, commentary, editorial, etc. (trade magazine, newspaper, online media), Joint Work, Lead author, Corresponding author

  • Min波の人工細胞内再構成とそこから見えた細胞サイズ空間効果

    光山 隼史, 義永 那津人, 藤原 慶

    生物物理学会誌 (生物物理学会)   62 ( 1 ) 19 - 23 2022.03

    Article, review, commentary, editorial, etc. (scientific journal), Last author, Corresponding author

  • 酵素を内包した人工細胞が拓く新しい醸造業や医薬品の開発

    藤原慶

    MDB 技術予測レポート    項目36 2019

  • Artificial cell fermentation as a next platform for biosynthesis

    FUJIWARA Kei

    バイオサイエンスとインダストリー ((一財)バイオインダストリー協会)  76 ( 4 ) 302 - 303 2018.07

    Article, review, commentary, editorial, etc. (trade magazine, newspaper, online media), Single Work

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Presentations 【 Display / hide 】

  • 細胞内反応拡散波の人工細胞再構成系で探る細胞空間の時空間パターン形成原理

    藤原慶

    定量生物学の会第十回年会, 

    2022.12

  • 人工細胞内再構成系で探る生化学システムの細胞サイズ効果

    藤原慶

    広島大学健康長寿研究拠点（HiHA）WS「サイズ生物学の探究」, 

    2022.10

  • 細胞を創る研究 (ボトムアップ合成生物学) への誘い

    藤原慶

    TARA Seminar理論合成インシリコ生物学セミナー, 

    2022.07

  • 細胞を創る研究から考える微生物の生

    藤原慶

    第44回日本分子生物学会, 

    2021.12

  • 人工細胞創成から見えたきた新しい生化学とその将来像

    藤原慶

    隅基礎科学創成財団 微生物CS グループ1 第5回定例会, 

    2021.05

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Research Projects of Competitive Funds, etc. 【 Display / hide 】

  • 創るトランスクリプトームにより迫る生命の設計原理

    2023.04
    -
    2027.03

    創発的研究支援事業, Principal investigator

  • 細胞内にチューリングパターンは形成可能か？

    2022.06
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    2024.03

    MEXT,JSPS, Grant-in-Aid for Scientific Research, 挑戦的研究（萌芽）, Principal investigator

  • Establishment of artificial cell fermentation technology as a practical material for industrial usage

    2022.06
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    2024.03

    MEXT,JSPS, Grant-in-Aid for Scientific Research, 学術変革領域研究(A), Principal investigator

  • Conversion between mechanical power and information of intracellular reaction-diffusion wave

    2022.04
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    2024.03

    MEXT,JSPS, Grant-in-Aid for Scientific Research, 新学術領域研究（研究領域提案型）, Principal investigator

  • Elucidation of physics underlying spatiotemporal pattern formation in cell size spaces

    2020.04
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    2023.03

    MEXT,JSPS, Grant-in-Aid for Scientific Research, Grant-in-Aid for Scientific Research (B), Principal investigator

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Courses Taught 【 Display / hide 】

  • TOPICS IN BIOSCIENCES AND INFORMATICS 2

    2024

  • SEMINAR IN BIOSCIENCES AND INFORMATICS

    2024

  • OFF-CAMPUS STUDY PROGRAM 3

    2024

  • OFF-CAMPUS STUDY PROGRAM 2

    2024

  • OFF-CAMPUS STUDY PROGRAM 1

    2024

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Courses Previously Taught 【 Display / hide 】

  • 微生物学

    慶應義塾大学

    2018.04
    -
    2019.03

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