Researchers Database

Honda Yuki

FacultyFaculty Division of Natural Sciences Research Group of Chemistry
PositionAssociate Professor
Last Updated :2022/10/06


Profile and Settings

  • Name (Japanese)

  • Name (Kana)



  • Doctor of Engineering, Waseda University, Mar. 2012

Research Areas

  • Life sciences, Applied microbiology
  • Life sciences, Applied biochemistry

Research Experience

  • 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
  • Apr. 2022, 9999, Nara Women's University, 研究院自然科学系化学領域, Associate Professor, Japan


  • 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

Association Memberships

  • Japanese Society of Enzyme Engineering
  • The Society for Biotechnology, Japan


Published Papers

  • 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, 22 Jul. 2020, 21, 23, 3389, 3397, Scientific journal
  • 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 Escherichia coli.

    , 16 Jul. 2020, 10, 17, 6006, 6012, Scientific journal
  • 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
  • Refereed, 酵素工学ニュース, 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, Scientific journal
  • Refereed, 生物工学会誌, 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, 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
  • 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, Sep. 2018, 19, 2156, 2159, Scientific journal
  • 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
  • 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
  • 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
  • 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
  • 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, 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
  • 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; 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; 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • ACS Omega, 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, Scientific journal


  • 日本生物工学会大会講演要旨集, 日本生物工学会, 1Fp19 Citric Acid Production from Glycerol by Semi-Solid Culture of Aspergillus niger, HONDA Yuki; HATTORI Takasumi; KIRIMURA Kohtaro, 2009, 21, 72, 72
  • 日本生物工学会大会講演要旨集, 日本生物工学会, 1Dp06 Functional Analysis of a Type III Polyketide Synthase Homolog from Aspergillus niger NRRL 328, HAMACHI Tatsuya; MIYAI Nozomi; KOBAYASHI Keiichi; HONDA Yuki; KIRIMURA Kohtaro, 2011, 63, 36, 36
  • 日本生物工学会大会講演要旨集, 日本生物工学会, 1Dp08 Disruption of the Gene Encoding Methylcitrate Synthase in Citric Acid-producing Aspergillus niger, KOBAYASHI Keiichi; HONDA Yuki; KIRIMURA Kohtaro, 2011, 63, 36, 36
  • 日本生物工学会大会講演要旨集, 日本生物工学会, 2P-1056 Novel Metabolic Path-way for Salicylate Biodegradation via Phenol in a Yeast Trichosporon moniliiforme, HONDA Yuki; HATTORI Takasumi; IWASAKI Yuichiro; ISHII Yoshitaka; KIRIMURA Kohtaro, 2010, 22, 22, 22
  • 日本生物工学会大会講演要旨集, 日本生物工学会, 2P-1057 Improvement of Salicylic Acid Synthesis Activity by Site-directed Mutagenesis in Reversible Salicylic Acid Decarboxylase, KOSAKA Sachiyo; HONDA Yuki; HATTORI Takasumi; KIRIMURA Kohtaro, 2010, 22, 23, 23
  • 日本生物工学会大会講演要旨集, 日本生物工学会, 3P-1017 Disruption of ku80 in Citric Acid-Producing Aspergillus niger for Improvement of Homologous Recombination Frequencies, KOBAYASHI Keiichi; HONDA Yuki; KIRIMURA Kohtaro, 2010, 22, 62, 62
  • 日本生物工学会大会講演要旨集, 日本生物工学会, 2Da11 High Level Expression and Functional Analysis of a Gene Encoding beta-Agarase Selectively Producing Neoagarobiose Derived from Cellvibrio sp. E-1, FUKUDA Koichi; HONDA Yuki; SATO Toshiyuki; HATTORI Takasumi; KIRIMURA Kohtaro, 2009, 21, 46, 46
  • 日本生物工学会大会講演要旨集, 日本生物工学会, 2Da01 Gene Silencing of Alternative Oxidase Gene (aox1) by Introduction of Hairpin RNA Expression Cassette in Citric Acid-Producing Aspergillus niger, HATTORI Takasumi; HONDA Yuki; KIRIMURA Kohtaro, 2008, 20, 118, 118
  • 日本生物工学会大会講演要旨集, 日本生物工学会, 1E10-4 Visual Expression Analysis of the Heat Shock Response of the Alternative Oxidase Gene (aoxl) in the Conidia of Citric Acid-Producing Aspergillus niger, HATTORI Takasumi; HONDA Yuki; KINO Kuniki; KIRIMURA Kohtaro, 2007, 19, 114, 114


  • Sawako Hayakawa; Yuki Honda; Hiroshi Fujii, 日本農芸化学会2022年度大会, 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, 日本農芸化学会2022年度大会, 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, 日本農芸化学会2022年度大会, Cytochrome P450-catalyzed oxidation reactions using hydrogen peroxide generated from tea leaf residues, Oral presentation, 17 Mar. 2022
  • 加藤木優里; 本田裕樹; 藤井 浩, 第 54 回酸化反応討論会, マンガン 5 価モノオキソポルフィリン錯体の合成とその反応性に関する研究, Oral presentation, 31 Oct. 2021
  • 川名 秀明; 本田 裕樹; 古屋 俊樹, 第73回日本生物工学会大会, コーヒー滓を電子供与体としたシトクロム P450 による酸化反応プロセスの確立, Oral presentation, 28 Oct. 2021
  • 本田裕樹; 篠原優佳; 藤井浩, 日本農芸化学会2020年度大会(福岡), 光増感剤/組換え大腸菌細胞系を用いた光触媒的水素生産, Oral presentation, 28 Mar. 2020
  • 篠原優佳; 本田裕樹; 渡邊源規; 石原達己; 藤井浩, 日本農芸化学会2020年度大会(福岡), 微生物の金属硫化物生成能と遺伝子工学的な水素生成能付与を組み合わせた光駆動型水素生成, Oral presentation, 28 Mar. 2020, Japan, False
  • Yuki Honda; Yuka Shinohara; Hiroshi Fujii, 日本化学会第100回春季年会, Light-driven and mediator-free hydrogen evolution using a combination of a photosensitizer and a recombinant Escherichia coli whole-cell biocatalyst, Poster presentation, 23 Mar. 2020
  • 加藤木優里; 本田裕樹; 藤井浩, 日本化学会第100回春季年会, マンガン5価モノオキソポルフィリン錯体の合成と反応性に関する研究, 23 Mar. 2020
  • Kana Nishikawa; Yuki Honda; Hiroshi Fujii, 錯体化学会第69回討論会(名古屋), Studies on the disproportionation reaction of iron (IV) oxoporphyrin complexes, 22 Sep. 2019
  • 柳井佳苗; 本田裕樹; 藤井浩, 錯体化学会第69回討論会(名古屋), 水溶性ヘム錯体による末端酸化剤の結合開裂過程の解明と触媒反応の応用, 22 Sep. 2019
  • 竹田彩乃; 本田裕樹; 藤井浩, 錯体化学会第69回討論会(名古屋), シトクロムP450活性部位のモデル錯体の合成の研究, 22 Sep. 2019
  • 上野夏奈子; 石水友梨; 本田裕樹; 藤井浩, 錯体化学会第69回討論会(名古屋), Compound-Iモデル錯体の反応性に対する溶媒効果の研究, 22 Sep. 2019
  • 三浦帆波; 西川佳那; 本田裕樹; 藤井浩; 佐伯和彦, 第92回日本生化学会大会(横浜), ミヤコグサ根粒菌カタラーゼKatEはプロトヘムとヘムdをもつ, 18 Sep. 2019
  • 西川佳那; 本田裕樹; 藤井浩, 第13回バイオ関連化学シンポジウム (東北大学), 鉄 4 価オキソポルフィリン錯体の不均化反応の研究, 05 Sep. 2019
  • 奥泉園子; 本田裕樹; 藤井浩, 日本化学会第99春季年会, シトクロムP450 compound Iによる芳香族水酸化の反応選択性についての研究, 16 Mar. 2019
  • 武藤晴香; 本田裕樹; 藤井浩, 第51回酸化反応討論会(福岡), sMMOを模倣したN架橋二核鉄ポルフィリン錯体の合成と反応性, 01 Nov. 2018
  • 石水友梨; 本田裕樹; 藤井浩, 第51回酸化反応討論会(福岡), 鉄4価オキソポルフィリンπ-カチオンラジカルが触媒するオレフィンのエポキシ化反応の反応機構について, 01 Nov. 2018
  • 岡田沙樹; 本田裕樹; 藤井浩, 第51回酸化反応討論会(福岡), シトクロムP450によるアルカン水酸化反応の反応機構, 01 Nov. 2018
  • 奥泉園子; 本田裕樹; 藤井浩, 第51回酸化反応討論会(福岡), シトクロムP450の反応活性種による芳香族化合物酸化反応の解析, 01 Nov. 2018
  • 岡田沙樹; 本田裕樹; 藤井浩, 第12回バイオ関連化学シンポジウム(大阪), 鉄4価オキソポルフィリンπカチオンラジカル錯体による酸化反応の反応機構, 09 Sep. 2018
  • 奥泉園子; 本田裕樹; 藤井浩, 第12回バイオ関連化学シンポジウム(大阪), シトクロムP450の反応活性種が触媒する芳香族水酸化反応に関する研究, 09 Sep. 2018
  • 西川佳那; 本田裕樹; 藤井浩, 錯体化学会第68回討論会(仙台), 金属4 価オキソポルフィリン錯体における不均化反応とオキソ配位子のpKa の研究, Jul. 2018
  • Kana Nishikawa; Yuki Honda; Hiroshi Fujii, 43rd International Conference on Coordination Chemistry, 2018, Sendai, Japan, Disproportionation of Metal(IV) Oxo Complexes, Jul. 2018
  • Yuki Honda, IUPAC Workshop Advances in Analytical Chemistry II, Nara Women’s University, Japan, Bio/inorganic Photocatalyst for Hydrogen Production, 27 Apr. 2018
  • 西川佳那; 本田裕樹; 藤井浩, 日本化学会第98春季年会 (2018) (千葉), 金属4価オキソポルフィリン錯体による不均化反応の研究, 22 Mar. 2018
  • 本田裕樹; 藤井浩, 日本農芸化学会2018年度大会(名古屋), 組換え大腸菌で生合成された色素を用いる光触媒的補酵素再生, Mar. 2018
  • 岡田沙樹; 本田裕樹; 藤井浩, 日本化学会第98春季年会 (2018) (千葉), シトクロムP450の反応活性種のモデル錯体を用いたベンジル位水酸化反応の速度論的研究, Mar. 2018
  • 本田裕樹; 河原林裕, 第69回日本生物工学会大会(東京), 好熱性アーキアSulfolobus tokodaii strain 7由来耐熱性酵素が有するUDP-GlcNAc合成活性の人為的向上, Sep. 2017
  • Mano Norimichi; Honda Yuki; Kobayashi Keiichi; Kirimura Kohtaro, 日本生物工学会大会講演要旨集, 2P-069 Detection of Citrate in the Escherichia coli Cells Expressing the Gene Encoding Fluorescent Protein-Based Indicators for Citrate, 2013, 2013, 2013, 日本生物工学会, url;url
  • Ienaga Saori; Ito Yuto; Honda Yuki; Ishii Yoshitaka; Kirimura Kohtaro, 日本生物工学会大会講演要旨集, 3Cp19 Production of p-Aminosalicylic Acid by Reversible Salicylic Acid Decarboxylase Obtained through Site-directed Mutagenesis, 2012, 2012, 2012, 日本生物工学会, url
  • Kobayashi Keiichi; Honda Yuki; Kirimura Kohtaro, 日本生物工学会大会講演要旨集, 2Ca13 Detection and Functional Analysis of Methylcitrate Synthase in Citric Acid-Producing Aspergillus niger, 2012, 2012, 2012, 日本生物工学会, url
  • Yuhara Kahori; Yonehara Hiromi; Kobayashi Keiichi; Honda Yuki; Hattori Takasumi; Kirimura Kohtaro, 日本生物工学会大会講演要旨集, 2Ca14 Heterologus Expression in Escherichia coli of Gene Encoding Aconitate Isomerase from Pseudomonas sp. WU-0701, 2012, 2012, 2012, 日本生物工学会, url

Industrial Property Rights

  • Patent right, クエン酸特異的蛍光センサータンパク質及びこれを用いるクエン酸の測定方法, 桐村光太郎, 本田裕樹, 特願2012-254500, 20 Nov. 2012, 特開2014-100100, 05 Jun. 2014

Research Projects

  • 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
  • Mar. 2020, Mar. 2021, Principal investigator, Development of photobiohydrogen production system using acombination of inorganic photocatalyst and biocatalyst, 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
  • 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, Kansai Research Foundation for Technology Promotion, 2020年度試験研究助成, 奈良女子大学
  • 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, 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, 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
  • Apr. 2018, Mar. 2020, 18K14376, Principal investigator
  • Apr. 2014, Mar. 2016, 26870429
  • Apr. 2020, Mar. 2023, 20K05230, Principal investigator
  • 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

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