Honda Yuki
| Faculty Division of Natural Sciences Research Group of Chemistry | Associate Professor |
Last Updated :2025/04/27
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Profile Information
Name (Japanese)
HondaName (Kana)
Yuki
Research Areas
Research History
- Apr. 2022 - Present, Nara Women's University, 研究院自然科学系化学領域, Associate Professor, Japan
- Apr. 2017 - Mar. 2022, Nara Women's University, Faculty of Science, Assistant Professor
- Apr. 2014 - Mar. 2017, Kyushu University, International Institute for Carbon-Neutral Energy Research, Postdoctoral Fellow
- Apr. 2013 - Mar. 2014, Kyushu University, Faculty of Agriculture, Postdoctoral Fellow
- Apr. 2010 - Mar. 2013, Waseda University, Faculty of Science and Engineering, Research Associate
Education
- Apr. 2009 - Mar. 2012, Waseda University, Graduate School of Advanced Science and Engineering, 応用化学専攻 博士後期課程, Japan
- Apr. 2007 - Mar. 2009, Waseda University, Graduate School of Advanced Science and Engineering, 応用化学専攻 修士課程, Japan
- Apr. 2002 - Mar. 2007, Waseda University, School of Science and Engineering, 応用化学科, Japan
- Apr. 1999 - Mar. 2002, 私立早稲田大学高等学院, Japan
Professional Memberships
■Ⅱ．研究活動実績
Published Papers
- Refereed, Catalysts and Catalysis, Visible Light-Driven Hydrogen Production Using Recombinant Escherichia coli Forming Metal Sulfide Semiconductor Photocatalyst, Yuki Honda, Oct. 2023, 65, 5, 287, 293
- Refereed, ChemSusChem, Wiley, Photo‐Electro‐Biochemical H2 Production Using the Carbon Material‐Based Cathode Combined with Genetically Engineered Escherichia coli Whole‐Cell Biocatalysis, Yuki Honda; Risa Yuki; Reina Hamakawa; Hiroshi Fujii, Abio/bio hybrids, which incorporate biocatalysts that promote efficient and selective material conversions under mild conditions into existing catalytic reactions, have attracted considerable attention for developing new catalytic systems. This study constructed a H2‐forming biocathode based on a carbon material combined with whole‐cell biocatalysis of genetically‐engineered‒hydrogenase‐overproducing Escherichia coli for the photoelectrochemical water splitting for clean H2 production. Low‐cost and abundant carbon materials are generally not suitable for H2‐forming cathode due to their high overpotential for proton reduction; however, the combination of the reduction of an organic electron mediator on the carbon electrode and the H2 formation with the reduced mediator by the redox enzyme hydrogenase provides a H2‐forming cathodic reaction comparable to that of the noble metal electrode. The present study demonstrates that the recombinant E. coli whole cell can be employed as a part of the H2‐forming biocathode system, and the biocathode system wired with TiO2 photoanode can be a photoelectrochemical water‐splitting system without external voltage assistance under natural pH. The findings of this study expand the feasibility of applications of whole‐cell biocatalysis and contribute to obtaining solar‐to‐chemical conversions by abio/bio hybrid systems, especially for low‐cost, noble‐metal‐free, and clean H2 production., 14 Sep. 2023, 17, 1, e202300958, Scientific journal, 10.1002/cssc.202300958
- Refereed, ACS Omega, American Chemical Society (ACS), Sustainable Approach for Peroxygenase-Catalyzed Oxidation Reactions Using Hydrogen Peroxide Generated from Spent Coffee Grounds and Tea Leaf Residues, Hideaki Kawana; Toru Miwa; Yuki Honda; Toshiki Furuya, 01 Jun. 2022, 7, 23, 20259, 20266, Scientific journal, 10.1021/acsomega.2c02186
- Apr. 2021, 4, 22, 27
- Refereed, ChemBioChem, Wiley, Photo‐Biohydrogen Production by Photosensitization with Biologically Precipitated Cadmium Sulfide in Hydrogen‐Forming Recombinant Escherichia coli, Yuki Honda; Yuka Shinohara; Motonori Watanabe; Tatsumi Ishihara; Hiroshi Fujii, An inorganic-biological hybrid system that integrates features of both stable and efficient semiconductors and selective and efficient enzymes is attractive for facilitating the conversion of solar energy to hydrogen. In this study, we aimed to develop a new photocatalytic hydrogen-production system based onEscherichia coliwhole-cell genetically engineered as a biocatalysis for highly active hydrogen formation. The photocatalysis part was obtained by bacterial precipitation of cadmium sulfide (CdS), which is a visible-light-responsive semiconductor. The recombinantE. colicells were sequentially subjected to CdS precipitation and heterologous [FeFe]-hydrogenase synthesis to yield a CdS@E. colihybrid capable of light energy conversion and hydrogen formation in a single cell. The CdS@E. colihybrid achieved photocatalytic hydrogen production with a sacrificial electron donor, thus demonstrating the feasibility of our system and expanding the current knowledge of photosensitization using a whole-cell biocatalyst with a bacterially precipitated semiconductor., 22 Jul. 2020, 21, 23, 3389, 3397, Scientific journal, 10.1002/cbic.202000383
- Refereed, Catalysis Science & Technology, Royal Society of Chemistry ({RSC}), Visible light-driven, external mediator-free H2 production by a combination of a photosensitizer and a whole-cell biocatalyst: Escherichia coli expressing [FeFe]-hydrogenase and maturase genes, Yuki Honda; Yuka Shinohara; Hiroshi Fujii,
A new visible light-driven, external mediator-free, and highly efficient H2 production system is developed based on the combination of a photosensitizer and a living whole-cell biocatalyst: genetically engineered
, 16 Jul. 2020, 10, 17, 6006, 6012, Scientific journal, 10.1039/D0CY01099EEscherichia coli . - Refereed, Catalysis Science & Technology, Royal Society of Chemistry ({RSC}), Photobiocatalytic H2 evolution of GaN:ZnO and [FeFe]-hydrogenase recombinant Escherichia coli, Nuttavut Kosem; Yuki Honda; Motonori Watanabe; Atsushi Takagaki; Zahra Pourmand Tehrani; Fatima Haydous; Thomas Lippert; Tatsumi Ishihara, The need for sustainable, renewable and low-cost approaches is a driving force behind the development of solar-to-H(2)conversion technologies. This study aims to develop a new strategy using a visible-light photocatalyst coupled to a biocatalyst for H(2)production. Photocatalytic methyl viologen (MV2+) reduction activity was investigated to discover active oxynitrides. In comparative studies with LaTiO2N, BaTaO2N and Ta3N5, it was revealed that the suitable surface area, band gap and band edge potentials are some physical factors that are responsible for the photocatalytic behaviors of GaN:ZnO in MV(2+)reduction. The activity is enhanced at higher concentrations and the alkaline pH of triethanolamine (TEOA). The expression of an active [FeFe]-hydrogenase fromEscherichia coli(Hyd(+)E. coli) as a recombinant biocatalyst was confirmed by its MV center dot+-dependent H(2)production activity. In the photobiocatalytic system of GaN:ZnO and Hyd(+)E. coli, the rate of H(2)production reached the maximum level in the presence of MV(2+)as an electron mediator at neutral pH as a biocompatible condition. The present work reveals a novel hybrid system for H(2)production using visible-light active GaN:ZnO coupled to Hyd(+)E. coli, which shows the feasibility of being developed for photobiocatalytic H(2)evolution under solar light., May 2020, 10, 12, 4042, 4052, Scientific journal, 10.1039/D0CY00128G
- Refereed, 無機-生体ハイブリッド型光触媒反応:無機半導体とヒドロゲナーゼを組み合わせた光駆動型の水素生産, Yuki Honda, Apr. 2020, 83, 19, 24, Scientific journal
- Refereed, Journal of the American Chemical Society, American Chemical Society ({ACS}), Spectroscopic Evidence for Acid-Catalyzed Disproportionation Reaction of Oxoiron(IV) Porphyrin to Oxoiron(IV) Porphyrin π-Cation Radical and Iron(III) Porphyrin, Kana Nishikawa; Yuki Honda; Hiroshi Fujii, 18 Mar. 2020, 142, 11, 4980, 4984, Scientific journal, 10.1021/jacs.9b13503
- Refereed, 光エネルギーによって駆動する生体触媒反応, Yuki Honda, 25 Feb. 2020, 98, 2, 81, Scientific journal
- Refereed, ChemBioChem, Wiley, Coexpression of 5‐Aminolevulinic Acid Synthase Gene Facilitates Heterologous Production of Thermostable Cytochrome P450, CYP119, in Holo Form in Escherichia coli, Yuki Honda; Kii Nanasawa; Hiroshi Fujii, 18 Oct. 2018, 19, 2156, 2159, Scientific journal, 10.1002/cbic.201800331
- Refereed, Applied and environmental microbiology, Improvement of ST0452 GlcNAc-1-phosphate uridyltransferase activity by the cooperative effect of two single mutations identified through structure-based protein engineering., Yuki Honda; Shogo Nakano; Sohei Ito; Mohammad Dadashipour; Zilian Zhang; Yutaka Kawarabayasi, We showed previously that the Y97N mutant of the ST0452 protein, isolated from Sulfolobus tokodaii, exhibited over 4 times higher N-acetylglucosamine-1-phosphate (GlcNAc-1-P) uridyltransferase (UTase) activity, compared with that of the wild-type ST0452 protein. We determined the three-dimensional structure of the Y97N protein to explore the detailed mechanism underlying this increased activity. The overall structure was almost identical to that of the wild-type ST0452 protein (PDB ID 2GGO), with residue 97 (Asn) interacting with the O-5 atom of N-acetylglucosamine (GlcNAc) in the complex without metal ions. The same interaction was observed for Escherichia coli GlmU in the absence of metal ions. These observations indicated that the three-dimensional structure of the Y97N protein was not changed by this substitution but the interactions with the substrate were slightly modified, which might cause the activity to increase. The crystal structure of the Y97N protein also showed that positions 146 (Glu) and 80 (Thr) formed interactions with GlcNAc, and an engineering strategy was applied to these residues to increase activity. All proteins substituted at position 146 had drastically decreased activities, whereas several proteins substituted at position 80 showed higher GlcNAc-1-P UTase activity, compared to that of the wild-type protein. The substituted amino acids at positions 80 and 97 might result in optimized interactions with the substrate; therefore, we predicted that the combination of these two substitutions might cooperatively increase GlcNAc-1-P UTase activity. Of the four double mutant ST0452 proteins generated, T80S/Y97N showed 6.5-times-higher activity, compared to that of the wild-type ST0452 protein, revealing that these two substituted residues functioned cooperatively to increase GlcNAc-1-P UTase activity.IMPORTANCE We demonstrated that the enzymatic activity of a thermostable protein was over 4 times higher than that of the wild-type protein following substitution of a single amino acid, without affecting its thermostability. The three-dimensional structure of the improved mutant protein complexed with substrate was determined. The same overall structure and interaction between the substituted residue and the GlcNAc substrate as observed in the well-characterized bacterial enzyme suggested that the substitution of Tyr at position 97 by Asn might slightly change the interaction. This subtle change in the interaction might potentially increase the GlcNAc-1-P UTase activity of the mutant protein. These observations indicated that a drastic change in the structure of a natural thermostable enzyme is not necessary to increase its activity; a subtle change in the interaction with the substrate might be sufficient. Cooperative effects were observed in the appropriate double mutant protein. This work provides useful information for the future engineering of natural enzymes., Oct. 2018, 84, 24, e02213-18, Scientific journal, True, 10.1128/aem.02213-18
- Refereed, JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS, ELSEVIER SCIENCE BV, [FeFe]-Hydrogenase and its organic molecule mimics-Artificial and bioengineering application for hydrogenproduction, Motonori Watanabe; Yuki Honda; Hidehisa Hagiwara; Tatsumi Ishihara, This study focuses on [FeFe]-hydrogenase and its metallorganic mimics in terms of electronic and photophysical properties, which can be applied to the electrochemical and/or photochemical production of molecular hydrogen. Natural [FeFeJ-hydrogenase, synthetic mimics of its active site and recent progresses in hybrid-type hydrogen production, for example, inorganic-combination photoelectrochemical and photochemical hydrogen production, are reviewed. (C) 2017 Elsevier B.V. All rights reserved., Dec. 2017, 33, 1, 26, 10.1016/j.jphotochemrev.2017.09.001
- Refereed, APPLIED CATALYSIS B-ENVIRONMENTAL, ELSEVIER SCIENCE BV, Inorganic/whole-cell biohybrid photocatalyst for highly efficient hydrogen production from water, Yuki Honda; Motonori Watanabe; Hidehisa Hagiwara; Shintaro Ida; Tatsumi Ishihara, To obtain a clean hydrogen production system, we have developed an inorganic-bio hybrid photocatalyst system based on the combination of anatase TiO2, methylviologen (MV) as an electron mediator, and a whole-cell biocatalyst consisting of [FeFe]-hydrogenase and maturase gene-harboring recombinant Escherichia coli; however, the apparent quantum yield at 300 nm (AQY(300)) for hydrogen production was low (0.3%). The system consists of a two-step reaction: (1) photocatalytic MV reduction by Ti02, and (2) hydrogen production with reduced MV using a biocatalyst. The enhancement of step 1 under biocatalyst-friendly conditions was investigated in an attempt to further improve the reaction efficiency. Among the condition tested, the use of 100mM Tris-HCl (pH 7), 150mM NaCl, and 5% (v/v) glycerol with P-25 TiO2 especially enhanced the step 1 reaction by a 300-fold increase in the MV reduction rate compared with previously tested reaction condition (100 mM Tris-HCl( pH 7), 150 mM NaCl, 5% (v/v) glycerol, and 100 mM ascorbate with anatase Ti02). Under the enhanced step 1 reaction, AQY(300) and AQY350 for photocatalytic MV reduction reached 60.8% and 52.2%, respectively. The enhanced step 1 reaction thus significantly improved the overall photocatalytic hydrogen productivity of the hybrid system and AQY(300) and AQY(350) reached 26.4% and 31.2%, respectively. The inorganic-whole-cell biohybrid system can therefore provide noble metal-free, efficient, and clean hydrogen production. (C) 2017 Elsevier B.V. All rights reserved., Aug. 2017, 210, 400, 406, Scientific journal, 10.1016/j.apcatb.2017.04.015
- Refereed, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, AMER SOC MICROBIOLOGY, Increasing the Thermostable Sugar-1-Phosphate Nucleotidylyltransferase Activities of the Archaeal ST0452 Protein through Site Saturation Mutagenesis of the 97th Amino Acid Position, Yuki Honda; Qian Zang; Yasuhiro Shimizu; Mohammad Dadashipour; Zilian Zhang; Yutaka Kawarabayasi, The ST0452 protein is a bifunctional protein exhibiting sugar-1-phosphate nucleotidylyltransferase (sugar-1-P NTase) and amino-sugar-1-phosphate acetyltransferase activities and was isolated from the thermophilic archaeon Sulfolobus tokodaii. Based on the previous observation that five single mutations increased ST0452 sugar-1-P NTase activity, nine double-mutant ST0452 proteins were generated with the intent of obtaining enzymes exhibiting a further increase in catalysis, but all showed less than 15% of the wild-type N-acetyl-D-glucosamine-1-phosphate uridyltransferase (GlcNAc-1-P UTase) activity. The Y97A mutant exhibited the highest activity of the single-mutant proteins, and thus site saturation mutagenesis of the 97th position (Tyr) was conducted. Six mutants showed both increased GlcNAc-1-P UTase and glucose-1-phosphate uridyltransferase activities, eight mutants showed only enhanced GlcNAc-1-P UTase activity, and six exhibited higher GlcNAc-1-P UTase activity than that of the Y97A mutant. Kinetic analyses of three typical mutants indicated that the increase in sugar-1-P NTase activity was mainly due to an increase in the apparent k(cat) value. We hypothesized that changing the 97th position (Tyr) to a smaller amino acid with similar electronic properties would increase activity, and thus the Tyr at the corresponding 103rd position of the Escherichia coli GlmU (EcGlmU) enzyme was replaced with the same residues. The Y103N mutant EcGlmU showed increased GlcNAc-1-P UTase activity, revealing that the Tyr at the 97th position of the ST0452 protein (103rd position in EcGlmU) plays an important role in catalysis. The present results provide useful information regarding how to improve the activity of natural enzymes and how to generate powerful enzymes for the industrial production of sugar nucleotides.
IMPORTANCE It is typically difficult to increase enzymatic activity by introducing substitutions into a natural enzyme. However, it was previously found that the ST0452 protein, a thermostable enzyme from the thermophilic archaeon Sulfolobus tokodaii, exhibited increased activity following single amino acid substitutions of Ala. In this study, ST0452 proteins exhibiting a further increase in activity were created using a site saturation mutagenesis strategy at the 97th position. Kinetic analyses showed that the increased activities of the mutant proteins were principally due to increased apparent kcat values. These mutant proteins might suggest clues regarding the mechanism underlying the reaction process and provide very important information for the design of synthetic improved enzymes, and they can be used as powerful biocatalysts for the production of sugar nucleotide molecules. Moreover, this work generated useful proteins for three-dimensional structural analysis clarifying the processes underlying the regulation and mechanism of enzymatic activity., Feb. 2017, 83, 3, e02291-16, Scientific journal, 10.1128/AEM.02291-16 - Refereed, ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, WILEY-V C H VERLAG GMBH, Application to Photocatalytic H-2 Production of a Whole-Cell Reaction by Recombinant Escherichia coli Cells Expressing [FeFe]-Hydrogenase and Maturases Genes, Yuki Honda; Hidehisa Hagiwara; Shintaro Ida; Tatsumi Ishihara, A photocatalytic H-2 production system using an inorganic-bio hybrid photocatalyst could contribute to the efficient utilization of solar energy, but would require the development of a new approach for preparing a H-2-forming biocatalyst. In the present study, we constructed a recombinant strain of Escherichia coli expressing the genes encoding the [FeFe]-hydrogenase and relevant maturases from Clostridium acetobutylicum NBRC 13948 for use as a biocatalyst. We investigated the direct application of a whole-cell of the recombinant E. coli. The combination of TiO2, methylviologen, and the recombinant E. coli formed H-2 under light irradiation, demonstrating that whole cells of the recombinant E. coli could be employed for photocatalytic H-2 production without any time-consuming and costly manipulations (for example, enzyme purification). This is the first report of the direct application of a whole-cell reaction of recombinant E. coli to photocatalytic H-2 production., Jul. 2016, 55, 28, 8045, 8048, Scientific journal, 10.1002/anie.201600177
- Refereed, JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY, SPRINGER HEIDELBERG, Oxalic acid production by citric acid-producing Aspergillus niger overexpressing the oxaloacetate hydrolase gene oahA, Keiichi Kobayashi; Takasumi Hattori; Yuki Honda; Kohtaro Kirimura, The filamentous fungus Aspergillus niger is used worldwide in the industrial production of citric acid. However, under specific cultivation conditions, citric acid-producing strains of A. niger accumulate oxalic acid as a by-product. Oxalic acid is used as a chelator, detergent, or tanning agent. Here, we sought to develop oxalic acid hyperproducers using A. niger as a host. To generate oxalic acid hyperproducers by metabolic engineering, transformants overexpressing the oahA gene, encoding oxaloacetate hydrolase (OAH; EC 3.7.1.1), were constructed in citric acid-producing A. niger WU-2223L as a host. The oxalic acid production capacity of this strain was examined by cultivation of EOAH-1 under conditions appropriate for oxalic acid production with 30 g/l glucose as a carbon source. Under all the cultivation conditions tested, the amount of oxalic acid produced by EOAH-1, a representative oahA-overexpressing transformant, exceeded that produced by A. niger WU-2223L. A. niger WU-2223L and EOAH-1 produced 15.6 and 28.9 g/l oxalic acid, respectively, during the 12-day cultivation period. The yield of oxalic acid for EOAH-1 was 64.2 % of the maximum theoretical yield. Our method for oxalic acid production gave the highest yield of any study reported to date. Therefore, we succeeded in generating oxalic acid hyperproducers by overexpressing a single gene, i.e., oahA, in citric acid-producing A. niger as a host., May 2014, 41, 5, 749, 756, Scientific journal, 10.1007/s10295-014-1419-2
- Refereed, BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY, TAYLOR & FRANCIS LTD, Gene Identification and Functional Analysis of Methylcitrate Synthase in Citric Acid-Producing Aspergillus niger WU-2223L, Keiichi Kobayashi; Takasumi Hattori; Yuki Honda; Kohtaro Kirimura, Methylcitrate synthase (EC 2.3.3.5; MCS) is a key enzyme of the methylcitric acid cycle localized in the mitochondria of eukaryotic cells and related to propionic acid metabolism. In this study, cloning of the gene mcsA encoding MCS and heterologous expression of it in Escherichia coli were performed for functional analysis of the MCS of citric acid-producing Aspergillus;tiger WU-2223L. Only one copy of mcsA (1,495 bp) exists in the A. niger WU-2223L chromosome. It encodes a 51-kDa polypeptide consisting of 465 amino acids containing mitochondrial targeting signal peptides. Purified recombinant MCS showed not only MCS activity (27.6 U/mg) but also citrate synthase (EC 2.3.3.1; CS) activity (26.8 U/mg). For functional analysis of MCS, mcsA disruptant strain DMCS-1, derived from A. niger WU-2223L, was constructed. Although A. niger WU-2223L showed growth on propionate as sole carbon source, DMCS-1 showed no growth. These results suggest that MCS is an essential enzyme in propionic acid metabolism, and that the methylcitric acid cycle operates functionally in A. niger WU-2223L. To determine whether MCS makes a contribution to citric acid production, citric acid production tests on DMCS-1 were performed. The amount of citric acid produced from glucose consumed by DMCS-1 in citric acid production medium over 12 d of cultivation was on the same level to that by WU-2223L. Thus it was found that MCS made no contribution to citric acid production from glucose in A. niger WU-2223L, although MCS showed CS activity., Jul. 2013, 77, 7, 1492, 1498, Scientific journal, 10.1271/bbb.130139
- Refereed, CHEMISTRY LETTERS, CHEMICAL SOC JAPAN, l-Menthyl alpha-Maltoside as a Novel Low-molecular-weight Gelator, Kohei Ide; Toshiyuki Sato; Jun Aoi; Hiroyuki Do; Keiichi Kobayashi; Yuki Honda; Kohtaro Kirimura, l-Menthyl alpha-D-glucopyranosyl-(1 -> 4)-alpha-D-glucopyranoside (l-alpha-MenG(2)), an alpha-maltoside of l-menthol, was synthesized through a three-step enzymatic reaction. We found that 1-alpha-MenG(2) possesses the properties of a low-molecular-weight gelator. Aqueous solutions containing l-alpha-MenG(2) at concentrations above 30 g L-1 show a thermally reversible sol gel transition. The sol gel transition temperature of the aqueous l-alpha-MenG(2) solution increases with l-alpha-MenG(2) concentration: 12 degrees C at 30 g L-1 and 24 degrees C at 250 g L-1. d-Menthyl and d-isomenthyl alpha-maltosides were also synthesized enzymatically, but their aqueous solutions showed no sol-gel transition., Jun. 2013, 42, 6, 657, 659, Scientific journal, 10.1246/cl.130122
- Refereed, PLOS ONE, PUBLIC LIBRARY SCIENCE, Generation of Circularly Permuted Fluorescent-Protein-Based Indicators for In Vitro and In Vivo Detection of Citrate, Yuki Honda; Kohtaro Kirimura, Indicators for citrate, particularly those applicable to its in vivo detection and quantitation, have attracted much interest in both biochemical studies and industrial applications since citrate is a key metabolic intermediate playing important roles in living cells. We generated novel fluorescence indicators for citrate by fusing the circularly permuted fluorescent protein (cpFP) and the periplasmic domain of the bacterial histidine kinase CitA, which can bind to citrate with high specificity. The ratiometric fluorescent signal change was observed with one of these cpFP-based indicators, named CF98: upon addition of citrate, the excitation peak at 504 nm increased proportionally to the decrease in the peak at 413 nm, suitable for build-in quantitative estimation of the binding compound. We confirmed that CF98 can be used for detecting citrate in vitro at millimolar levels in the range of 0.1 to 50 mM with high selectivity; even in the presence of other organic acids such as isocitrate and malate, the fluorescence intensity of CF98 remains unaffected. We finally demonstrated the in vivo applicability of CF98 to estimation of the intracellular citrate concentration in Escherichia coli co-expressing the genes encoding CF98 and the citrate carrier CitT. The novel indicator CF98 can be a specific and simple detection tool for citrate in vitro and a non-invasive tool for real-time estimation of intracellular concentrations of the compound in vivo., May 2013, 8, 5, Scientific journal, 10.1371/journal.pone.0064597
- Refereed, BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN, CHEMICAL SOC JAPAN, p-Aminosalicylic Acid Production by Enzymatic Kolbe-Schmitt Reaction Using Salicylic Acid Decarboxylases Improved through Site-Directed Mutagenesis, Saori Ienaga; Sachiyo Kosaka; Yuki Honda; Yoshitaka Ishii; Kohtaro Kirimura, A reversible salicylic acid decarboxylase (Sdc) catalyzes the carboxylation of m-aminophenol (m-AP) to p-aminosalicylic acid (PAS) as an antituberculous agent, through an enzymatic Kolbe-Schmitt reaction. To develop a high-yield PAS production system through such an enzymatic reaction, we generated Sdc mutants by site-directed mutagenesis and succeeded in generating several mutants showing increased carboxylation specific activities. Among them, a Y64T-F195Y-Sdc mutant showed a 12-fold higher carboxylation specific activity toward m-AP than wild-type Sdc. By the whole-cell reaction of recombinant Escherichia coli BL21(DE3) expressing the gene encoding Y64T-F195Y-Sdc, 70mM PAS was produced from 100mM m-AP within 2 h. This reaction time was shortened to one-twelfth that of the PAS production using E. coli BL21(DE3) expressing the gene encoding wild-type Sdc (24h). Moreover, 140mM PAS was produced from 200mM m-AP within 9h by the whole-cell reaction of recombinant E. coli BL21(DE3) expressing the gene encoding Y64T-F195Y-Sdc., May 2013, 86, 5, 628, 634, Scientific journal, 10.1246/bcsj.20130006
- Refereed, JOURNAL OF MOLECULAR CATALYSIS B-ENZYMATIC, ELSEVIER SCIENCE BV, Purification, characterization, and gene identification of an alpha-glucosyl transfer enzyme, a novel type alpha-glucosidase from Xanthomonas campestris WU-9701, Toshiyuki Sato; Nobukazu Hasegawa; Jun Saito; Satoru Umezawa; Yuki Honda; Kuniki Kino; Kohtaro Kirimura, The alpha-glucosyl transfer enzyme (XgtA), a novel type alpha-glucosidase produced by Xanthomonas campestris WU-9701, was purified from the cell-free extract and characterized. The molecular weight of XgtA is estimated to be 57 kDa by SOS-PAGE and 60 kDa by gel filtration, indicating that XgtA is a monomeric enzyme. Kinetic properties of XgtA were determined for alpha-glucosyl transfer and maltose-hydrolyzing activities using maltose as the alpha-glucosyl donor, and if necessary, hydroquinone as the acceptor. The V-max value for alpha-glucosyl transfer activity was 1.3 x 10(-2) (mM/s); this value was 3.9-fold as much as that for maltose-hydrolyzing activity. XgtA neither produced maltooligosaccharides nor hydrolyzed sucrose. The gene encoding XgtA that contained a 1614-bp open reading frame was cloned, identified, and highly expressed in Escherichia coli JM109 as the host. Site-directed mutagenesis identified Asp201,Glu270, and Asp331 as the catalytic sites of XgtA, indicating that XgtA belongs to the glycoside hydrolase family 13. (C) 2012 Elsevier B.V. All rights reserved., Aug. 2012, 80, 20, 27, Scientific journal, 10.1016/j.molcatb.2012.04.014
- Refereed, JOURNAL OF BIOSCIENCE AND BIOENGINEERING, SOC BIOSCIENCE BIOENGINEERING JAPAN, Visual expression analysis of the responses of the alternative oxidase gene (aox1) to heat shock, oxidative, and osmotic stresses in conidia of citric acid-producing Aspergillus niger, Yuki Honda; Takasumi Hattori; Kohtaro Kirimura, The citric acid-producing filamentous fungus Aspergillus niger WU-2223L shows cyanide-insensitive respiration catalyzed by alternative oxidase in addition to the cytochrome pathway. Sequence analysis of the 5' flanking region of the alternative oxidase gene (aox1) revealed a potential heat shock element (HSE) and a stress response element (STRE). We have previously confirmed aox1 expression in conidia. In this study, to confirm whether the upstream region of aox1 responds to various stresses, we used a visual expression analysis system for single-cell conidia of the A. niger strain AOXEGFP-1. This strain harbored a fusion gene comprising aox1 and egfp, which encodes the enhanced green fluorescent protein (EGFP). The fluorescence intensity of EGFP increased in conidia of A. niger AOXEGFP-1 that were subjected to heat shock at 35-45 degrees C, oxidative stress by exposure to 5 mM paraquat or 1 mM r-butylhydroperoxide, or osmotic stresses by exposure to 0.5 M KCl or 1.0 M mannitol. These results indicate that the putative HSE and STRE in the upstream region of aox1 directly or indirectly respond to heat shock, oxidative, and osmotic stresses. (C) 2011, The Society for Biotechnology, Japan. All rights reserved., Mar. 2012, 113, 3, 338, 342, Scientific journal, 10.1016/j.jbiosc.2011.10.026
- Refereed, Comprehensive Biotechnology, Second Edition, Elsevier Inc., Gluconic and Itaconic Acids, K. Kirimura; Y. Honda; T. Hattori, d-Gluconic acid is a naturally occurring polyhydroxycarboxylic acid commonly found in human beings and other organisms. d-Gluconic acid, containing the forms of its δ-lactone and gluconates, is one of the bulk chemicals and is used in many fields such as the food, pharmaceutical, and construction industries. Today, industrial production of d-gluconic acid is mainly performed by Aspergillus niger with glucose as a major carbon source, and the yield is higher than 95%. The annual worldwide production level was approximately 90. 000 tons in 2009. On the other hand, itaconic acid is an unsaturated dicarbonic organic acid and mainly used in the plastic and paint industries. Today, industrial production of itaconic acid is mainly performed by Aspergillus terreus using glucose or pretreated molasses as a major carbon source. The annual worldwide production level was approximately 15. 000 tons in 2009. In this article, we provide a current review of application of gluconic and itaconic acids in the industrial fields and their general production processes., 09 Sep. 2011, 3, 143, 147, In book, 10.1016/B978-0-08-088504-9.00175-6
- Refereed, Comprehensive Biotechnology, Second Edition, Elsevier Inc., Citric Acid, K. Kirimura; Y. Honda; T. Hattori, Citric acid is one of the most widely used organic acids, and its annual worldwide production reached 1.6 million ton during 2009. It is used as an acidulant and preservative in the food industry, and also as a complexing agent in the pharmaceutical and cosmetic industries. Citric acid is also used as a complexing and chelating agent in metal treatment, as a water softener for detergents, and as a buffering agent in toiletry and pharmaceutical industries. Citric acid is exclusively produced by fermentation with the filamentous fungus Aspergillus niger. The industrial production is performed using carbohydrates or agro-industrial residues as substrates by three different types of processes: submerged, surface, and solid fermentations. This article provides a current review of advances in citric acid production by A. niger and application of citric acid in various fields., 09 Sep. 2011, 3, 135, 142, In book, 10.1016/B978-0-08-088504-9.00169-0
- Refereed, BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY, TAYLOR & FRANCIS LTD, Increases in Gene-Targeting Frequencies Due to Disruption of kueA as a ku80 Homo log in Citric Acid-Producing Aspergillus niger, Yuki Honda; Keiichi Kobayashi; Kohtaro Kirimura, Low efficiencies of gene targeting hamper functional genomics in industrially important strains of Aspergillus niger. To generate strains showing high gene-targeting frequencies in A. niger WU-2223L producing citric acid, disruption of kueA encoding Ku80 homolog was performed. Disruption of kueA increased gene-targeting frequencies to 70%, and had no effect on citric acid production., Aug. 2011, 75, 8, 1594, 1596, Scientific journal, 10.1271/bbb.110015
- Refereed, JOURNAL OF BIOSCIENCE AND BIOENGINEERING, SOC BIOSCIENCE BIOENGINEERING JAPAN, Expression of alternative oxidase gene (aox1) at the stage of single-cell conidium in citric acid-producing Aspergillus niger, Takasumi Hattori; Yuki Honda; Kuniki Kino; Kohtaro Kirimura, Mycelia of citric acid-producing Aspergillus niger WU-2223L show cyanide-insensitive respiration catalyzed by alternative oxidase. In this study, the constitutive expression of alternative oxidase gene (aox1) even at the stage of single-cell conidium in A. niger WU-2223L was found using the visual expression analysis system of aox1 with green fluorescent protein under microscopy observation., Jan. 2008, 105, 1, 55, 57, Scientific journal, 10.1263/jbb.105.55
Books etc
Presentations
- Poster presentation, 28 Mar. 2025, 26 Mar. 2025 - 29 Mar. 2025
- Poster presentation, 28 Mar. 2025, 26 Mar. 2025 - 29 Mar. 2025
- Yuki HONDA; Kiho MARUYAMA; Asumi SUZUKI; Hiroshi FUJII, Redox tuning of electron mediators to improve the performance of light-driven hydrogen production in photosensitizer- and recombinant Escherichia coli-based biohybrid, Poster presentation, 08 Mar. 2025, 04 Mar. 2025 - 08 Mar. 2025
- Kotone TAKEUCHI; Sawako HAYAKAWA; Yuki HONDA; Daisuke KOMA; Hiroshi FUJII, Investigation of nif cluster and its promoter for conferring nitrogenase activity in Escherichia coli, Poster presentation, 08 Mar. 2025, 04 Mar. 2025 - 08 Mar. 2025
- Poster presentation, 19 Sep. 2024, 18 Sep. 2024 - 20 Sep. 2024
- Poster presentation, 19 Sep. 2024, 18 Sep. 2024 - 20 Sep. 2024
- Invited oral presentation, 18 Sep. 2024, 18 Sep. 2024 - 20 Sep. 2024
- Invited oral presentation, 12 Sep. 2024
- Oral presentation, 27 Mar. 2024
- Oral presentation, 26 Mar. 2024
- Oral presentation, 20 Mar. 2024
- Poster presentation, 11 Nov. 2023
- Poster presentation, 11 Nov. 2023
- Poster presentation, 26 Sep. 2023
- Poster presentation, 26 Sep. 2023
- Poster presentation, 26 Sep. 2023
- Oral presentation, 04 Sep. 2023, 03 Sep. 2023 - 05 Sep. 2023
- Invited oral presentation, 09 Aug. 2023, 09 Aug. 2023 - 10 Aug. 2023
- Poster presentation, 05 Nov. 2022
- Oral presentation, 20 Oct. 2022
- Oral presentation, 19 Oct. 2022
- Oral presentation, 18 Oct. 2022
- 27 Sep. 2022
- 27 Sep. 2022
- Keynote oral presentation, 23 Jul. 2022
- Sawako Hayakawa; Yuki Honda; Hiroshi Fujii, Towards the heterologous expression of nitrogenase genes in Escherichia coli, Oral presentation, 16 Mar. 2022, 15 Mar. 2022 - 18 Mar. 2022
- Yuki HONDA; Yuka SHINOHARA; Motonori WATANABE; Tatsumi ISHIHARA; Hiroshi FUJII, Visible light-driven hydrogen production using Escherichia coli expressing hydrogenase genes with cadmium sulfide precipitate, Oral presentation, 18 Mar. 2022
- Hideaki Kawana; Yuki Hond; Toshiki Furuya, Cytochrome P450-catalyzed oxidation reactions using hydrogen peroxide generated from tea leaf residues, Oral presentation, 17 Mar. 2022
- Invited oral presentation, 12 Nov. 2021
- Oral presentation, 31 Oct. 2021
- Oral presentation, 28 Oct. 2021
- Oral presentation, 28 Mar. 2020
- Oral presentation, 28 Mar. 2020, Japan, False
- Poster presentation, 23 Mar. 2020
- 23 Mar. 2020
- 22 Sep. 2019
- 22 Sep. 2019
- 22 Sep. 2019
- 22 Sep. 2019
- 18 Sep. 2019
- 05 Sep. 2019
- 16 Mar. 2019
- Invited oral presentation, 04 Feb. 2019
- 01 Nov. 2018
- 01 Nov. 2018
- 01 Nov. 2018
- 01 Nov. 2018
- 09 Sep. 2018
- 09 Sep. 2018
- Jul. 2018
- Jul. 2018
- 27 Apr. 2018
- 22 Mar. 2018
- Mar. 2018
- Mar. 2018
- Sep. 2017
- 22 Mar. 2017
- 19 Mar. 2017
- 29 Sep. 2016
- 21 Sep. 2016
- 25 May 2016
- 29 Mar. 2016
- 25 Mar. 2016
- 04 Feb. 2016
- 16 Dec. 2015
- 27 Mar. 2015
- 19 Sep. 2014
- 01 Aug. 2014
- 13 Mar. 2014
- 27 Mar. 2013
- 26 Mar. 2013
- 25 Mar. 2013
- 24 Mar. 2013
- 24 Mar. 2013
- 23 Mar. 2013
- 26 Oct. 2012
- 25 Oct. 2012
- 25 Oct. 2012
- 06 Sep. 2012
- 06 Sep. 2012
- 06 Sep. 2012
- 27 Mar. 2012
- 27 Mar. 2012
- 24 Mar. 2012
- 24 Mar. 2012
- 19 Nov. 2011
- 19 Nov. 2011
- 16 Nov. 2011
- 16 Nov. 2011
- 27 Sep. 2011
- 26 Sep. 2011
- 26 Sep. 2011
- 14 Sep. 2011
- Jun. 2011
- Jun. 2011
- 29 Mar. 2011
- 28 Mar. 2011
- 27 Mar. 2011
- 26 Mar. 2011
- Dec. 2010
- 29 Oct. 2010
- 29 Oct. 2010
- 28 Oct. 2010
- 28 Oct. 2010
- 29 Mar. 2010
- 29 Mar. 2010
- 29 Mar. 2010
- 18 Nov. 2009
- 15 Nov. 2009
- 24 Sep. 2009
- 23 Sep. 2009
- 13 Sep. 2009
- 13 Sep. 2009
- Sep. 2009
- Sep. 2009
- Jun. 2009
- Jun. 2009
- 28 Mar. 2009
- 28 Aug. 2008
- 27 Mar. 2008
- 25 Sep. 2007
- 05 Sep. 2007
- Invited oral presentation, 09 Aug. 2023 - 10 Aug. 2023
- Invited oral presentation
Industrial Property Rights
Research Projects
- 基盤研究(B), Apr. 2024 - Mar. 2027, 24K01272, Principal investigator, 光と水からの物質生産：バイオハイブリッドによる人工光合成の確立に向けた基盤研究, 本田 裕樹, 日本学術振興会, 科学研究費助成事業, 奈良女子大学, 18590000, 14300000, 4290000, Competitive research funding, kaken
- Apr. 2024 - Mar. 2026, Principal investigator, 光増感剤－微生物ハイブリッド触媒系による光水素生産：電子伝達機構の解明と制御による高効率化, 本田裕樹, 公益財団法人発酵研究所, 2024年度 一般研究助成, 奈良女子大学, 3000000, 3000000, 0, Competitive research funding
- Apr. 2024 - Mar. 2025, Principal investigator, 太陽光エネルギーの利用に向けた無機－バイオ複合系による水素生産, 本田裕樹, 公益財団法人池谷科学技術振興財団, 単年度研究助成（2024年度）, 奈良女子大学, 2000000, 2000000, 0, Competitive research funding
- Apr. 2023 - Mar. 2024, Principal investigator, 金属硫化物半導体を形成した微生物を用いる光－化学エネルギー変換： バイオハイブリッドによる光水素生産, 本田裕樹, 公益財団法人野田産業科学研究所, 2023年度「研究助成（持続可能分野）」, 2000000, 2000000, Competitive research funding
- Oct. 2022 - Sep. 2023, Principal investigator, 色素―酵素ハイブリッド型人工光合成系による光駆動型水素生産, 本田裕樹, 公益財団法人戸部眞紀財団, 2022年度研究助成, 1000000, 1000000, 0, Competitive research funding
- Grant-in-Aid for Scientific Research (C), Apr. 2020 - Mar. 2023, 20K05230, Principal investigator, Inorganic-bio hybrid photocatalytic hydrogen production using a combination of microbial metal sulfide precipitation and hydrogenase reaction, Yuki Honda, Japan Society for the Promotion of Science, Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research (C), Nara Women's University, 4290000, 3300000, 990000, 水素は次世代のエネルギーキャリアとして注目される。一方、工業的な水素生産の大部分は化石燃料の消費に依存しており、再生可能エネルギー（特に太陽光）を用いる水素生産系への転換に期待が寄せられる。本研究は、光エネルギーによって駆動するクリーンな水素生産系の実現に資する新規な反応系の構築を目的として、無機半導体光触媒と生体触媒を組み合わせた無機-生体ハイブリッド型光触媒系による光バイオ水素生産を目指している。
方法として、微生物が有する金属硫化物半導体ナノ粒子の形成能と、高活性な水素生成酵素である[FeFe]-ヒドロゲナーゼを活用する。形成された硫化物半導体による光エネルギー変換と、そこで得られた還元力を用いる酵素での水素生産によって光駆動型水素生産が達成される。2020年度の成果として、大腸菌によって形成された金属硫化物半導体（硫化カドミウム、CdS）による光エネルギー変換能と、遺伝子工学的に付与した水素生成能の共役によって光駆動型水素生産系の構築に成功しており、2021年度は特に大腸菌によるCdS形成能の強化に焦点をあて、光エネルギー変換効率の向上を目指した。
2021年度は、これまで大腸菌に元々備わっている能力に頼っていたCdS形成を、遺伝子工学により積極的に強化した。具体的にはシステインからスルフィドを遊離する酵素の遺伝子を導入し、硫化物形成の基質であるスルフィドの濃度を高めることでCdSの量や質の変化を狙った。実際に、当該遺伝子導入によって、これまでよりも高濃度のCdイオン存在下でCdSを形成し量の向上が見込まれた。さらに、生成したCdSの単位重量当たりの光エネルギー変換能の向上も見出された。現在、CdSの量や質の変化を詳細に解析している。, kaken - Apr. 2021 - Mar. 2022, Principal investigator, 光触媒・生体触媒ハイブリッド系による光電気化学的水素生産, 本田裕樹, 公益財団法人岩谷直治記念財団, 第47回岩谷科学技術研究助成, 2000000
- Apr. 2021 - Mar. 2022, Principal investigator, 非生物的な光増感反応と酵素反応を組み合わせた光エネルギー駆動型の水素生産系, 本田裕樹, 公益財団法人稲盛財団, 2021年度稲盛研究助成, 1000000
- Apr. 2021 - Mar. 2022, Principal investigator, 微生物による金属硫化物・酸化物半導体ナノ粒子形成と光駆動型物質生産への応用, 本田裕樹, Kansai Research Foundation for Technology Promotion, 2020年度試験研究助成, 奈良女子大学
- Mar. 2020 - Mar. 2021, Principal investigator, Development of photobiohydrogen production system using acombination of inorganic photocatalyst and biocatalyst, 本田裕樹, 公益財団法人日立財団, The Kurata Grants 2019, 1000000
- Apr. 2019 - Mar. 2021, Principal investigator, 自己生成させたポルフィリン色素を光増感剤として利用する光駆動型の微生物触媒反応によるバイオ水素生産, 本田 裕樹, 公益財団法人発酵研究所, 平成31年度（2019年度）一般研究助成, 3000000, 3000000, 0, Competitive research funding
- Apr. 2019 - Mar. 2020, Principal investigator, 光エネルギー駆動型の生体触媒反応系の構築, 本田 裕樹, 公益財団法人国際科学技術財団, 研究助成, 1000000, 1000000, 0, Competitive research funding
- Grant-in-Aid for Early-Career Scientists, Apr. 2018 - Mar. 2020, 18K14376, Principal investigator, Creation of Bio-photocatalyst Using Microorganism with Artificial Light-driven Coenzyme Regeneration System, Honda Yuki, Japan Society for the Promotion of Science, Grants-in-Aid for Scientific Research Grant-in-Aid for Early-Career Scientists, Nara Women's University, 4160000, 3200000, 960000, Biocatalysts, including enzymes or microorganisms, are capable of catalyzing highly selective and efficient reactions under environmentally friendly condition. This feature of biocatalysis would contribute to developing an energy-saving process in industry. In an industrial application of biocatalysis, supplying energy to proceed a certain reaction has been a problem in the enzymatic reaction which requires a coenzyme, such as NADH. This study addressed this problem by developing a light-driven biocatalysis system which consists of the combination of photosensitizer and enzyme. In such system, photosensitizer serves energy to enzyme from light energy, instead of costly coenzyme supplementation. This study achieved a large-scale synthesis of porphyrin dye by genetically engineered bacteria, the photoreduction of an artificial coenzyme (MV) by the dye, and one of the light-driven biocatalysis by coupling the photoreduction of MV and the hydrogen-forming enzyme., url
- Dec. 2018 - Nov. 2019, Principal investigator, 微生物の細胞表層への金属硫化物半導体自己形成能を利用する無機―生体ハイブリッド光触媒反応, 本田 裕樹, 公益財団法人カシオ科学振興財団, 第36回（平成30年度）研究助成, 5000000, 5000000, 0, Competitive research funding
- Apr. 2018 - Mar. 2019, Principal investigator, 微生物による物質生産と共役させる光駆動型の NAD(P)H 再生系, 本田 裕樹, 公益財団法人野田産業科学研究所, 2018年度奨励研究助成, 1000000, 1000000, 0, Competitive research funding
- Apr. 2018 - Mar. 2019, Principal investigator, 色素合成能力と物質生産能力を同時に強化した微生物を用いる生体光触媒系の創成, 本田 裕樹, 一般財団法人増屋記念基礎研究振興財団, 平成30年度助成金, 300000, 300000, 0, Competitive research funding
- Nov. 2017 - Nov. 2018, Principal investigator, 光エネルギー変換能と水素生産能を付与した微生物細胞を用いる光駆動型の水素生産, 本田 裕樹, 公益財団法人住友財団, 2017年度基礎科学研究助成, 1200000, 1200000, 0, Competitive research funding
- Grant-in-Aid for Young Scientists (B), Apr. 2014 - Mar. 2016, 26870429, Mechanism Analysis and Improvement of Fluorescence Changes of the Green Fluorescent Protein-based Citrate Sensors, Honda Yuki, Japan Society for the Promotion of Science, Grants-in-Aid for Scientific Research Grant-in-Aid for Young Scientists (B), Kyushu University, 3900000, 3000000, 900000, The aim of this study is to elucidate the citrate-sensing mechanism and to improve sensitivity of the newly developed fluorescent protein-based sensor for citrate. Elucidation of mechanism for citrate sensing have not completed. On the other hand, applicability of the sensor to real samples was investigated for the improvement of sensitivity and the practical use., url
- Apr. 2011 - Mar. 2013, Principal investigator, 蛍光クエン酸センサータンパク質の創製と発酵現象解析への応用, 本田 裕樹, みずほ学術振興財団, 平成23年度（第54回）研究助成, 2000000, 2000000, 0, Competitive research funding
- Apr. 2011 - Mar. 2012, Principal investigator, クロコウジカビによる糖質からのクエン酸生産を目的としたクエン酸輸送系の機能解析, 本田 裕樹, 公益信託日新製糖奨学育英基金, 平成23年度研究資金, 500000, 500000, 0, Competitive research funding
- Apr. 2011 - Mar. 2012, Principal investigator, 糖質からのクエン酸生産を目的としたクエン酸輸送系の機能解析, 本田 裕樹, 公益信託日新製糖奨学育英基金, 平成22年度研究資金, 500000, 500000, 0, Competitive research funding
- Apr. 2011 - Mar. 2012, Principal investigator, グリーンサステイナブル技術を指向した生体触媒を利用した位置選択的水酸化反応によるパラヒドロキシ安息香酸生産バイオプロセスの構築, 本田 裕樹, ゼネラル石油研究奨励財団, 第30回（平成22年度）研究奨励助成, 1000000, 1000000, 0, Competitive research funding
■Ⅲ．社会連携活動実績
