Research activity information

• Mar. 2023 化学工学会, 研究奨励賞（實吉雅郎記念賞）, 酵素基質特異性の合理的改変による有用化合物生産に関する研究

  森 裕太郎


• Mar. 2022 特定国立研究開発法人 理化学研究所, 2021年度理研産業連携奨励賞（桜舞賞）


• Apr. 2021 酵素工学研究会, 酵素工学奨励賞, 有用物質生産に資する酵素変異体の合理的設計に関する研究

  森 裕太郎


• Dec. 2013 日本生物工学会 九州支部学生賞 (博士課程の部), 新規ビオチン化試薬を用いた酵素集合体の形態制御と機能化


• Sep. 2013 IGER International Symposium on Cell Surface Structures and Function, Poster Awards, Fabrication of Higher-Order Protein Supramolecular Complexes


• Nov. 2010 化学工学会 九州支部学生賞 (修士課程の部), Avidin-biotin相互作用と部位特異的酵素修飾を利用した高感度バイオセンサーの開発

• Modular pathway engineering for enhanced production of para -aminobenzoic acid and 4-amino-phenylalanine in Escherichia coli via glucose/xylose co-utilization

  Daisuke Nonaka, Mayumi Kishida, Yuuki Hirata, Ayana Mori, Akihiko Kondo, Yutaro Mori, Shuhei Noda, Tsutomu Tanaka

  ABSTRACT The modularization of biosynthetic pathways is a promising approach for enhancing microbial chemical production. We have developed a co-utilization method with glucose and xylose substrates to divide metabolic pathways into distinct production and energy modules to enhance the biosynthesis of para -aminobenzoic acid (pABA) in Escherichia coli . Optimizing initial glucose/xylose concentrations and eliminating carbon leakage resulted in a pABA titer of 8.22 g/L (yield: 0.23 g/g glucose). This strategy was then applied to the biosynthesis of 4APhe, a compound synthesized from chorismate without pyruvate (PYR) release. Utilizing glucose and xylose as co-substrates resulted in the production of 4.90 g/L 4APhe. Although 4APhe production did not benefit from PYR-driven energy generation as pABA production did, high titer was still achieved. This study highlights the effectiveness of modular metabolic pathway division for enhancing the production of key aromatic compounds and provides valuable insight into microbial production of chemicals that require specific biosynthetic donors such as amino groups. IMPORTANCE Microbial biosynthesis of chemicals from renewable resources offers a sustainable alternative to fossil fuel-based production. However, inefficiencies due to substrate diversion into by-products and biomass hinder optimal yields. In this study, we employed a modular metabolic engineering approach, decoupling pathways for chemical production from cell growth. Using glucose and xylose as co-substrates, we achieved the enhancement of p -aminobenzoic acid production in Escherichia coli . Additionally, we demonstrated the versatility of this approach by applying it to the biosynthesis of 4-amino-phenylalanine production. This study highlights the potential of modular metabolic pathway division for increased production of target compounds and provides valuable insight into microbial production of chemicals that require specific biosynthetic donors such as amino groups.

  American Society for Microbiology, Apr. 2025, Applied and Environmental Microbiology

  Scientific journal


• NHC-Mediated Radical Acylation Catalyzed by Thiamine- and Flavin-Dependent Enzymes.

  Shunsuke Kato, Shuto Fujisawa, Yuto Adachi, Mitsuhiro Bandai, Yutaro Mori, Seiji Mori, Tomokazu Shirai, Takashi Hayashi

  Cross-coupling reactions between short-lifetime radicals are challenging reactions in organic chemistry. Here, we report the development of an N-heterocyclic carbene (NHC)-mediated radical coupling reaction based on the catalytic machinery of thiamine- and flavin-dependent enzymes. Through a series of enzyme screenings, we found that acetolactate synthase from Thermobispora bispora (TbALS) and its engineered variants exhibit promising catalytic activity toward abiotic radical acylation reactions of α-bromo carbonyl compounds. Notably, the TbALS variant has higher catalytic activity for small nonaromatic substrates despite forming less stable radical intermediates. Furthermore, the catalytic system of TbALS can be applied to photocatalytic reactions utilizing the photoredox properties of FAD. Nonbenzylic alkyl radicals generated from N-acyloxyphthalimides are efficiently converted into the corresponding dialkyl ketones under irradiation of a blue LED. These findings highlight the utility of thiamine- and flavin-dependent enzymes for achieving selective cross-coupling reactions of short-lifetime radicals.

  Apr. 2025, Journal of the American Chemical Society, English, International magazine

  Scientific journal


• Catalase-Knockout Complements the Radio-Sensitization Effect of Titanium Peroxide Nanoparticles on Pancreatic Cancer Cells

  Winda Tasia, Amane Washio, Koki Yamate, Kenta Morita, Yutaro Mori, Prihardi Kahar, Ryohei Sasaki, Chiaki Ogino

  Jan. 2025, Molecules

  Scientific journal

  Link to Kobe Univ. Repository (Kernel)


• Parallel metabolic pathway engineering for aerobic 1,2-propanediol production in Escherichia coli.

  Daisuke Nonaka, Yuuki Hirata, Mayumi Kishida, Ayana Mori, Ryosuke Fujiwara, Akihiko Kondo, Yutaro Mori, Shuhei Noda, Tsutomu Tanaka

  The demand for the essential commodity chemical 1,2-propanediol (1,2-PDO) is on the rise, as its microbial production has emerged as a promising method for a sustainable chemical supply. However, the reliance of 1,2-PDO production in Escherichia coli on anaerobic conditions, as enhancing cell growth to augment precursor availability remains a substantial challenge. This study presents glucose-based aerobic production of 1,2-PDO, with xylose utilization facilitating cell growth. An engineered strain was constructed capable of exclusively producing 1,2-PDO from glucose while utilizing xylose to support cell growth. This was accomplished by deleting the gloA, eno, eda, sdaA, sdaB, and tdcG genes for 1,2-PDO production from glucose and introducing the Weimberg pathway for cell growth using xylose. Enhanced 1,2-PDO production was achieved via yagF overexpression and disruption of the ghrA gene involved in the 1,2-PDO-competing pathway. The resultant strain, PD72, produced 2.48 ± 0.15 g L-1 1,2-PDO with a 0.27 ± 0.02 g g-1-glucose yield after 72 h cultivation. Overall, this study demonstrates aerobic 1,2-PDO synthesis through the isolation of the 1,2-PDO synthetic pathway from the tricarboxylic acid cycle.

  Aug. 2024, Biotechnology journal, 19(8) (8), e2400210, English, International magazine

  Scientific journal


• Complete sequence randomness of lactate-based copolymers (LAHBs) with varied lactate monomer fractions employing a series of propionyl-CoA transferases.

  Sangho Koh, Ryota Endo, Prihardi Kahar, Yutaro Mori, Chiaki Ogino, Shinji Tanaka, Shinji Tanaka, Yusuke Imai, Seiichi Taguchi

  Previously, we biosynthesized an evolved version of a bio-based polylactide (PLA) on microbial platforms using our engineered lactate-polymerizing enzyme (LPE). This lactate (LA)-based copolyester, LAHB, has advantages over PLA, including improved flexibility and biodegradability, and its properties can be regulated through the LA fraction. To expand the LA-incorporation capacity and improve polymer properties, in the state of in vivo LAHB production, propionyl-CoA transferases (PCTs) that exhibited enhanced production of LA-CoA than the conventional PCTs were selected. Here, the present study has demonstrated that the LA fraction of LAHB could be altered using various PCTs. Enhanced PCT performance was achieved by balancing polymer production and cell growth. Both events are governed by the use of acetyl-CoA, a commonly shared key metabolite. This could be attributed to the different reactivities of individual PCTs towards acetyl-CoA, which serves both as a CoA donor and a leading compound in the TCA cycle. Interestingly, we found complete sequence randomness in the LAHB copolymers, independent of the LA fraction. The mechanism of LA fraction-independent sequence randomness is discussed. This new PCT-based strategy synergistically combines with the evolution of LPE to advance the LAHB project, and enables us to perform advanced applications other than LAHB production utilizing CoA-linked substrates.

  Aug. 2024, International journal of biological macromolecules, 274(Pt 2) (Pt 2), 133055 - 133055, English, International magazine

  Scientific journal

  Link to Kobe Univ. Repository (Kernel)


• Metabolic and enzymatic engineering approach for the production of 2-phenylethanol in engineered Escherichia coli

  Shuhei Noda, Yutaro Mori, Yuki Ogawa, Ryosuke Fujiwara, Mayumi Dainin, Tomokazu Shirai, Akihiko Kondo

  Elsevier BV, Jun. 2024, Bioresource Technology, 130927 - 130927

  Scientific journal

  Link to Kobe Univ. Repository (Kernel)


• Styrene Production in Genetically Engineered Escherichia coli in a Two-Phase Culture

  Shuhei Noda, Ryosuke Fujiwara, Yutaro Mori, Mayumi Dainin, Tomokazu Shirai, Akihiko Kondo

  Styrene is an important industrial chemical. Although several studies have reported microbial styrene production, the amount of styrene produced in batch cultures can be increased. In this study, styrene was produced using genetically engineered Escherichia coli. First, we evaluated five types of phenylalanine ammonia lyases (PALs) from Arabidopsis thaliana (AtPAL) and Brachypodium distachyon (BdPAL) for their ability to produce trans-cinnamic acid (Cin), a styrene precursor. AtPAL2-expressing E. coli produced approximately 700 mg/L of Cin and we found that BdPALs could convert Cin into styrene. To assess styrene production, we constructed an E. coli strain that co-expressed AtPAL2 and ferulic acid decarboxylase from Saccharomyces cerevisiae. After a biphasic culture with oleyl alcohol, styrene production and yield from glucose were 3.1 g/L and 26.7% (mol/mol), respectively, which, to the best of our knowledge, are the highest values obtained in batch cultivation. Thus, this strain can be applied to the large-scale industrial production of styrene.

  Jan. 2024, BioTech, 13(1) (1), English, International magazine

  Scientific journal

  Link to Kobe Univ. Repository (Kernel)


• p-Nitrobenzoate production from glucose by utilizing p-aminobenzoate N-oxygenase: AurF.

  Ayana Mori, Yuuki Hirata, Mayumi Kishida, Yutaro Mori, Akihiko Kondo, Shuhei Noda, Tsutomu Tanaka

  Nitroaromatic compounds are widely used in industry, but their production is associated with issues such as the hazardousness of the process and low regioselectivity. Here, we successfully demonstrated the production of p-nitrobenzoate (PNBA) from glucose by constructing p-aminobenzoate N-oxygenase AurF-expressing E. coli. We generated this strain, which we named PN-1 by disrupting four genes involved in PNBA degradation: nfsA, nfsB, nemA, and azoR. We then expressed AurF from Streptomyces thioluteus in this strain, which resulted in the production of 945 mg/L PNBA in the presence of 1 g/L p-aminobenzoate. Direct production of PNBA from glucose was achieved by co-expressing the pabA, pabB, and pabC, as well as aurF, resulting in the production of 393 mg/L PNBA from 20 g/L glucose. To improve the PNBA titer, we disrupted genes involved in competing pathways: pheA, tyrA, trpE, pykA, and pykF. The resultant strain PN-4Ap produced 975 mg/L PNBA after 72 h of cultivation. These results highlight the potential of using microorganisms to produce other nitroaromatic compounds.

  Dec. 2023, Enzyme and microbial technology, 171, 110321 - 110321, English, International magazine

  Scientific journal


• Hydroxybenzoic Acid Production Using Metabolically Engineered Corynebacterium glutamicum

  Misa Doke, Mayumi Kishida, Yuuki Hirata, Mariko Nakano, Mayo Horita, Daisuke Nonaka, Yutaro Mori, Ryosuke Fujiwara, Akihiko Kondo, Shuhei Noda, Tsutomu Tanaka

  Sciscan Publishing Limited, 2023, Synthetic Biology and Engineering, 1(1) (1), 1 - 9

  Scientific journal

  Link to Kobe Univ. Repository (Kernel)


• Direct 1,3-butadiene biosynthesis in Escherichia coli via a tailored ferulic acid decarboxylase mutant

  Yutaro Mori, Shuhei Noda, Tomokazu Shirai, Akihiko Kondo

  The C4 unsaturated compound 1,3-butadiene is an important monomer in synthetic rubber and engineering plastic production. However, microorganisms cannot directly produce 1,3-butadiene when glucose is used as a renewable carbon source via biological processes. In this study, we construct an artificial metabolic pathway for 1,3-butadiene production from glucose in Escherichia coli by combining the cis,cis-muconic acid (ccMA)-producing pathway together with tailored ferulic acid decarboxylase mutations. The rational design of the substrate-binding site of the enzyme by computational simulations improves ccMA decarboxylation and thus 1,3-butadiene production. We find that changing dissolved oxygen (DO) levels and controlling the pH are important factors for 1,3-butadiene production. Using DO–stat fed-batch fermentation, we produce 2.13 ± 0.17 g L⁻¹ 1,3-butadiene. The results indicate that we can produce unnatural/nonbiological compounds from glucose as a renewable carbon source via a rational enzyme design strategy.

  Lead, Springer Science and Business Media LLC, Dec. 2021, Nature Communications, 12(1) (1), 2195 - 2195, English, International magazine

  Scientific journal

  Link to Kobe Univ. Repository (Kernel)


• Reprogramming Escherichia coli pyruvate-forming reaction towards chorismate derivatives production

  Shuhei Noda, Yutaro Mori, Ryosuke Fujiwara, Tomokazu Shirai, Tsutomu Tanaka, Akihiko Kondo

  Microbial metabolic pathway engineering is a potent strategy used worldwide to produce aromatic compounds. We drastically rewired the primary metabolic pathway of Escherichia coli to produce aromatics and their derivatives. The metabolic pathway of E. coli was compartmentalized into the production and energy modules. We focused on the pyruvate-forming reaction in the biosynthesis pathway of some compounds as the reaction connecting those modules. E. coli strains were engineered to show no growth unless pyruvate was synthesized along with the compounds of interest production. Production of salicylate and maleate was demonstrated to confirm our strategy's versatility. In maleate production, the production, yield against the theoretical yield, and production rate reached 12.0 g L-1, 67%, and up to fourfold compared to that in previous reports, respectively; these are the highest values of maleate production in microbes to our knowledge. The results reveal that our strategy strongly promotes the production of aromatics and their derivatives.

  Elsevier BV, Sep. 2021, Metabolic Engineering, 67, 1 - 10, English, International magazine

  Scientific journal


• Reconstruction of metabolic pathway for isobutanol production in Escherichia coli

  Shuhei Noda, Yutaro Mori, Sachiko Oyama, Akihiko Kondo, Michihiro Araki, Tomokazu Shirai

  BACKGROUND: The microbial production of useful fuels and chemicals has been widely studied. In several cases, glucose is used as the raw material, and almost all microbes adopt the Embden-Meyerhof (EM) pathway to degrade glucose into compounds of interest. Recently, the Entner-Doudoroff (ED) pathway has been gaining attention as an alternative strategy for microbial production. RESULTS: In the present study, we attempted to apply the ED pathway for isobutanol production in Escherichia coli because of the complete redox balance involved. First, we generated ED pathway-dependent isobutanol-producing E. coli. Thereafter, the inactivation of the genes concerning organic acids as the byproducts was performed to improve the carbon flux to isobutanol from glucose. Finally, the expression of the genes concerning the ED pathway was modified. CONCLUSIONS: The optimized isobutanol-producing E. coli produced 15.0 g/L of isobutanol as the final titer, and the yield from glucose was 0.37 g/g (g-glucose/g-isobutanol).

  Springer Science and Business Media LLC, Dec. 2019, Microbial Cell Factories, 18(1) (1), 124 - 124, English, International magazine

  Scientific journal

  Link to Kobe Univ. Repository (Kernel)


• Designing artificial metabolic pathways, construction of target enzymes, and analysis of their function

  Yutaro Mori, Tomokazu Shirai

  Artificial design of metabolic pathways is essential for the production of useful compounds using microbes. Based on this design, heterogeneous genes are introduced into the host, and then various analysis and evaluation methods are conducted to ensure that the target enzyme reactions are functionalized within the cell. In this chapter, we list successful examples of useful compounds produced by designing artificial metabolic pathways, and describe the methods involved in analyzing, evaluating, and optimizing the target enzyme reaction.

  Lead, Elsevier BV, Dec. 2018, Current Opinion in Biotechnology, 54, 41 - 44, English, International magazine

  Scientific journal


• Casein-based scaffold for artificial cellulosome design

  Geisa A.L.G. Budinova, Yutaro Mori, Tsutomu Tanaka, Noriho Kamiya

  Cellulosomal systems are known as highly efficient biocatalysts in the degradation of lignocellulosic biomass in nature, but they remain unsuitable for industrial applications. In seeking alternatives to natural cellulosomes, casein was chosen as a scaffold for cellulase clustering. Casein is recognized as an excellent substrate for microbial transglutaminase (MTG) because it contains naturally reactive glutamine and lysine residues. A substrate peptide containing an MTG-reactive lysine residue was inserted into the C-terminus of the endoglucanase Cel5A and Cel6A from Thermobifida fusca using genetic engineering. The engineered cellulases, EG(Cel5A) and EG(Cel6A), were conjugated onto casein in different ratios by an MTG-mediated site-specific protein crosslinking reaction. Overall, a more than two-fold increase was observed when EG(Cel5A) was conjugated onto N,N-dimethylcasein, but a small or no change was observed for EG(Cel6A).

  Elsevier Ltd, Mar. 2018, Process Biochemistry, 66, 140 - 145, English

  [Refereed]

  Scientific journal


• Engineering a synthetic pathway for maleate in Escherichia coli

  Shuhei Noda, Tomokazu Shirai, Yutaro Mori, Sachiko Oyama, Akihiko Kondo

  Maleate is one of the most important dicarboxylic acids and is used to produce various polymer compounds and pharmaceuticals. Herein, microbial production of maleate is successfully achieved, to our knowledge for the first time, using genetically modified Escherichia coli. A synthetic pathway of maleate is constructed in E. coli by combining the polyketide biosynthesis pathway and benzene ring cleavage pathway. The metabolic engineering approach used to fine-tune the synthetic pathway drastically improves maleate production and demonstrates that one of the rate limiting steps exists in the conversion of chorismate to gentisate. In a batch culture of the optimised transformant, grown in a 1-L jar fermentor, the amount of produced maleate reaches 7.1 g L-1, and the yield is 0.221 mol mol(-1). Our results suggest that the construction of synthetic pathways by combining a secondary metabolite pathway and the benzene ring cleavage pathway is a powerful tool for producing various valuable chemicals.

  Springer Science and Business Media LLC, Dec. 2017, Nature Communications, 8(1) (1), 1153 - 1153, English

  Scientific journal

  Link to Kobe Univ. Repository (Kernel)


• Salt-Switchable Artificial Cellulase Regulated by a DNA Aptamer

  Mari Takahara, Geisa Aparecida Lopes Gonçalves Budinova, Hikaru Nakazawa, Yutaro Mori, Mitsuo Umetsu, Noriho Kamiya

  © 2016 American Chemical Society. A novel artificial cellulase was developed by conjugating a DNA aptamer to an endoglucanase catalytic domain, thereby substituting the natural carbohydrate-binding module. Circular dichroism spectroscopy and adsorption isotherm showed the binding motif of cellulose-binding DNA aptamer (CelApt) was G-quadruplex and stem-loop structures stabilized in the presence of salts, and CelApt binding preferred the amorphous region of the solid cellulose. By introducing the revealed salt-switchable cellulose-binding nature of CelApt into a catalytic domain of a cellulase, we created CelApt-catalytic domain conjugate possessing both controllable adsorption on the solid substrates and equal enzymatic activity to the wild-type cellulase. Thus potential use of a responsive DNA aptamer for biocatalysis at a solid surface was demonstrated.

  American Chemical Society (ACS), Oct. 2016, Biomacromolecules, 17(10) (10), 3356 - 3362

  Scientific journal


• One-dimensional assembly of functional proteins: Toward the design of an artificial cellulosome

  Y. Mori, H. Nakazawa, G. A.L. Gonçalves, T. Tanaka, M. Umetsu, N. Kamiya

  This journal is © The Royal Society of Chemistry. In biological systems, proteins can form well-organized, higher-order structures with unique functions that would be difficult to achieve with a single protein. These proteinaceous supramolecular structures form by self-assembly, and the spatial arrangement of the protein building blocks in them is very important. In the present study, an artificial system was developed using recombinant proteins as building blocks, which were assembled in a one-dimensional manner. The assembly of these building blocks was based on the avidin-biotin interaction. A tetrameric biotin ligand unit was designed so that the 1:4 stoichiometry of the avidin-biotin interaction was altered to a 1:2 directional interaction between the streptavidin and tetrabiotinylated protein units. In a proof-of-concept study, site-specifically tetrabiotin-labeled endoglucanase and cellulose-binding module units were prepared, and then these components were self-assembled by mixing with streptavidin to mimic a natural cellulosome. The formation of one-dimensional assemblies of the protein units depended on the stoichiometry of the avidin-biotin interaction sites in the system. Interestingly, the saccharification efficiency improved when the component ratio of protein units in the assemblies was changed. The presence of the optimal ratio of the building blocks implies the modularity of the present protein assembly system.

  Lead, 2016, Molecular Systems Design and Engineering, 1(1) (1), 66 - 73

  Scientific journal


• Effect of pretreatment methods on the synergism of cellulase and xylanase during the hydrolysis of bagasse

  Lili Jia, Geisa A.L. Gonçalves, Yusaku Takasugi, Yutaro Mori, Shuhei Noda, Tsutomu Tanaka, Hirofumi Ichinose, Noriho Kamiya

  Elsevier BV, Jun. 2015, Bioresource Technology, 185, 158 - 164

  Scientific journal


• Synergistic effect and application of xylanases as accessory enzymes to enhance the hydrolysis of pretreated bagasse

  Geisa A. L. Goncalves, Yusaku Takasugi, Lili Jia, Yutaro Mori, Shuhei Noda, Tsutomu Tanaka, Hirofumi Ichinose, Noriho Kamiya

  Recently, the new trend in the second-generation ethanol industry is to use mild pretreatments, in order to reduce costs and to keep higher content of hemicellulose in the biomass. Nevertheless, a high enzyme dosage is still required in the conversion of (hemi)cellulose. The interaction between cellulases and xylanases seems to be an effective alternative to reduce enzyme loading in the saccharification process. At first, to evaluate the synergism of xylanases on bagasse degradation, we have produced two xylanases from glycoside hydrolase family 10 (GH10) and three xylanases from glycoside hydrolase family11 (GH11),from two thermophilic organisms, Thermobifida fusca and Clostridium thermocellum, and one mesophilic organism, Streptomyces lividans. Peracetic acid (PAA) pretreated bagasse was used as substrate. The combination of XynZ-C (GH10, from C. thermocellum), and XlnB (GH11, from S. lividans) presented the highest degree of synergy after 6 h (3,62). However, the combination of XynZ-C and Xyn11A (GH11, from T. fusca) resulted in the highest total yield of reducing sugars. To evaluate the synergism between xylanases and cellulases, commercial cellulase preparation from Trichoderma reesei was combined with the selected xylanases, XynZ-C and Xyn11A. About 2-fold increase was observed in the concentration of reducing sugars, when both xylanases, XynZ-C and Xyn11A, were added together with T. reesei cellulases in the reaction mixture. (C) 2015 Elsevier Inc. All rights reserved.

  ELSEVIER SCIENCE INC, May 2015, ENZYME AND MICROBIAL TECHNOLOGY, 72, 16 - 24, English

  Scientific journal


• Biomolecular assembly strategies to develop potential artificial cellulosomes

  Geisa AL Gonçalves, Yutaro Mori, Noriho Kamiya

  Springer Science and Business Media LLC, Dec. 2014, Sustainable Chemical Processes, 2(1) (1)

  Scientific journal


• Protein supramolecular complex formation by site-specific avidin–biotin interactions

  Yutaro Mori, Rie Wakabayashi, Masahiro Goto, Noriho Kamiya

  Lead, Royal Society of Chemistry (RSC), 2013, Org. Biomol. Chem., 11(6) (6), 914 - 922

  Scientific journal


• Aligning an endoglucanase Cel5A from Thermobifida fusca on a DNA scaffold: potent design of an artificial cellulosome

  Yutaro Mori, Shiori Ozasa, Momoko Kitaoka, Shuhei Noda, Tsutomu Tanaka, Hirofumi Ichinose, Noriho Kamiya

  A novel multi-cellulase conjugate assembled on a double-stranded DNA scaffold, a DNA-(endoglucanase)(n) conjugate, exhibited unique hydrolytic activity toward crystalline cellulose (Avicel) depending on the cellulase/DNA ratio on the DNA-based artificial cellulosome.

  Lead, ROYAL SOC CHEMISTRY, 2013, CHEMICAL COMMUNICATIONS, 49(62) (62), 6971 - 6973, English

  Scientific journal


• Transglutaminase-mediated internal protein labeling with a designed peptide loop

  Yutaro Mori, Masahiro Goto, Noriho Kamiya

  Lead, Elsevier BV, Jul. 2011, Biochemical and Biophysical Research Communications, 410(4) (4), 829 - 833

  Scientific journal


• Protein assemblies by site-specific avidin-biotin interactions

  Yutaro Mori, Kosuke Minamihata, Hiroki Abe, Masahiro Goto, Noriho Kamiya

  Exploiting self-assembly systems with biological building blocks is of significant interest in the fabrication of advanced biomaterials. We assessed the potential use of site-specific ligand labeling of protein building blocks in designing functional protein self-assemblies by combining site-specifically biotinylated bacterial alkaline phosphatase (as a bidentate or tetradentate ligand unit) and streptavidin (as a tetrameric receptor).

  Lead, ROYAL SOC CHEMISTRY, 2011, ORGANIC & BIOMOLECULAR CHEMISTRY, 9(16) (16), 5641 - 5644, English

  Scientific journal

• To make tire rubber, add bacteria and sugar

  Yutaro Mori

  Dec. 2021, RIKEN Research


• Bacteria-made chemical offers a renewable source of synthetic rubber

  Yutaro Mori

  Aug. 2021, RIKEN Research


• Ferulic acid decarboxylase の合理的設計による人工代謝経路の構築

  森裕太郎, 白井智量

  Apr. 2021, 酵素工学ニュース, (85) (85), 20 - 24


• 代謝デザインに資する酵素創製と探索

  森 裕太郎, 折下 涼子, 白井 智量

  Lead, Feb. 2018, 生物工学会誌 / 日本生物工学会 編, 96(10) (10), 578


• Design of Artificial Supramolecular Protein Assemblies by Enzymatic Bioconjugation for Biocatalytic Reactions

  Geisa A.L.G. Budinova, Yutaro Mori, Noriho Kamiya

  Wiley-VCH Verlag GmbH & Co. KGaA, 05 Jan. 2018, Emerging Areas in Bioengineering, 93 - 103


• 2P-051 Development of an artificial cellulase utilizing cellulose-binding DNA aptamer

  Takahara Mari, Mori Yutaro, Budinova Geisa A.L.G., Nakazawa Hikaru, Umetsu Mitsuo, Kamiya Noriho

  日本生物工学会, 2015, 日本生物工学会大会講演要旨集, 67, 187 - 187, Japanese


• Substrate Engineering of Microbial Transglutaminase for Site-Specific Protein Modification and Bioconjugation

  Noriho Kamiya, Yutaro Mori

  Springer Japan, 2015, Transglutaminases, 373 - 383


• 「適材適所」―相手に応じたセルロソームの自己最適化―

  森 裕太郎

  日本生物工学会, Nov. 2014, 生物工学会誌, 92(11) (11), 624 - 624, Japanese


• 1P-085 Design and enzymatic preparation of a cellulase-synthetic polymer hydrid molecule

  Saeki Takafumi, Wakabayashi Rie, Yahiro Kensuke, Mori Yutaro, Ichinose Hirofumi, Tanaka Tsutomu, Kamiya Noriho

  日本生物工学会, 2014, 日本生物工学会大会講演要旨集, 66, 38 - 38, Japanese

• 計算科学を用いた酵素設計による機能の改良と改変

  森裕太郎

  第5回 超越分子システム 計算科学を使う勉強会, Jan. 2024

  [Invited]


• 有用化合物生産に向けたin silico酵素設計

  森裕太郎

  MOEフォーラム2022, Oct. 2022

  [Invited]

• 日本生物工学会


• 化学工学会


• 酵素工学研究会

• Fabrication of the rational design strategy for enzyme mutants to enable faster catalytic cycles

  森 裕太郎

  Japan Society for the Promotion of Science, Grants-in-Aid for Scientific Research, Grant-in-Aid for Early-Career Scientists, Institute of Physical and Chemical Research, 01 Apr. 2021 - 31 Mar. 2023

  本研究では、持続可能な環境調和型社会の実現に向けて、目的化合物の生産量を向上させることを目的として、高活性な酵素変異体を合理的に開発するための設計戦略の確立を目指す。具体的には、フェニルアラニン脱アンモニア酵素 (PAL) を鋳型酵素として活性測定を行い、分子動力学シミュレーションとの比較から酵素反応速度に関わる要素の抽出とそれに基づいた高活性な変異体設計のためのルール構築を行う。特に現在、酵素と基質の間の親和力を基準として酵素反応速度パラメーターKmを向上させるような研究例は多く行われているものの、反応速度Vmaxについて基準とできる計算値・指標が存在していない。そこで本研究ではVmaxを向上させうる酵素変異体の設計指針を確立させる。 本年度は鋳型酵素PALの酵素変異体モデルを構築し、基質入り口から活性中心に至るまでの時間を算出するためのメソッドの確立を試みた。しかしながら、基質入り口から活性中心に至るまでの途中の地点で最安定となりそれ以上動かなくなってしまう、そもそも計算に時間がかかる等の課題が明らかとなった。計算法に関してはもっと改善する必要性がある。 またそれと並行して、PALの酵素活性中心を除いた部分に変異を導入した酵素変異体群を作成し、活性評価を行った。その結果、野生型と比較して0倍から最大で1.4倍程度の活性を持つPAL変異体のバリエーション獲得に成功した。今度、順次上記計算値と比較する。


• Fabrication of a rational design method for enzyme mutants based on an understanding of substrate specificity

  MORI YUTARO

  Japan Society for the Promotion of Science, Grants-in-Aid for Scientific Research, Grant-in-Aid for Early-Career Scientists, Institute of Physical and Chemical Research, 01 Apr. 2019 - 31 Mar. 2021

  In this study, we aimed to modifiy and extend the substrate specificity of enzymes by deepening our intrinsic understanding. In addition, this study's objective is to establish rational rules for designing enzyme mutants to catalyze enzymatic reactions with high activity. Several types of Information were accumulated by comparing the results of enzyme screening with the constructed enzyme-substrate binding model. The results suggest that the affinity between the enzyme and the substrate is an important factor for the enzyme to be able to recognize the substrate. In fact, it is suggested that the HOT SPOT, which is likely to contribute to increased activity, can be predicted by in silico calculation. Finally, a 2.8-fold increase in activity was achieved with the enzyme mutant compared to the wild type.


• The Development of Novel Protein Intracellular Affinity Pairs for Fabrication of Designer Metabolons.

  Mori Yutaro

  Japan Society for the Promotion of Science, Grants-in-Aid for Scientific Research Grant-in-Aid for Research Activity Start-up, Grant-in-Aid for Research Activity Start-up, Institute of Physical and Chemical Research, 28 Aug. 2015 - 31 Mar. 2017

  By assembling metabolic enzymes that continuously perform reactions inside E. coli, this study aims to construct a system that improves efficiency of production of valuable chemicals being targeted. As a preliminary step toward that, the applicant developed and designed new protein affinity pairs that exhibit binding affinity within E. coli cells. In this study we achieved the protein expression of affinity pairs in E. coli, and we confirmed that the protein pairs shows the binding affinity in vitro assay.

• サッカロミケス由来フェルラ酸デカルボキシラーゼ変異体、及びそれを用いた不飽和炭化水素化合物の製造

  森 裕太郎, 白井 智量, 和田 理恵子

  特願2019-172227, 2019

  Patent right


• デカルボキシラーゼ、及びそれを用いた不飽和炭化水素化合物の製造方法

  森 裕太郎, 白井 智量, 和田 理恵子

  特願2017-142930, 2017

  Patent right


• ビオチン化合物、ビオチン標識化剤及びタンパク質集合体

  神谷 典穂, 森 裕太郎

  特願2014-118174, 2014, 特開2015-229672, 特許6419460

  Patent right


• ビオチン化合物、ビオチン標識化剤、タンパク質集合体

  神谷 典穂, 森 裕太郎

  特願JP2012065407, 15 Jun. 2012, 特許6226750

  Patent right


• フェニルアラニンアンモニアリアーゼを用いた鎖状の不飽和カルボン酸化合物の製造方法

  白井 智量, 森 裕太郎, 谷地 義秀, 日座操, 赤堀 弥生

  特願 2020-219017

  Patent right