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YAMADA Naotaka Last modified date:2024.06.03

Assistant Professor / Molecular Bioscience
Department of Bioscience and Biotechnology
Faculty of Agriculture


Graduate School
Undergraduate School


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Homepage
https://kyushu-u.elsevierpure.com/en/persons/naotaka-yamada
 Reseacher Profiling Tool Kyushu University Pure
http://www.agr.kyushu-u.ac.jp/agpm/nouyaku/
Phone
092-802-4720
Academic Degree
Doctor of Agliculture
Country of degree conferring institution (Overseas)
No
Field of Specialization
bioorganic chemistry, pesticide chemistry
Total Priod of education and research career in the foreign country
01years00months
Outline Activities
It is conducting research on the molecular design of nobel plant growth regulators and the elucidation of the mechanism of action of some plant growth regulators. In particular, it is currently involved in elucidating the mechanisms of stomatal opening/closing and opening of plant hormones and other substances, as well as the mechanism of action of phenylalanine ammonia-lyase inhibitors in plants.
In education, it is in charge of lectures on bioorganic chemistry and student experiments on organic chemistry and physical chemistry.
Research
Research Interests
  • Functional elucidation of silkworm pesticide metabolic enzymes (gutathione transferase/sulfotransferasesbase) on protein structure information
    keyword : silkworm, protein structure、gutathione transferase, sulfotransferasesbase,
    2012.04~2023.03.
  • Elucidation of the relationship between stomatal closing activity of various plant hormones and plant growth regulators and K+/H EXCHANGE ANTIPORTER 3 (KEA3) in guard cell chloroplast
    keyword : guard cell, phytohormones, plant growth regulators, K+/H+ antiporter
    2020.04.
  • Search for stomatal open/close inducers of gaseous signaling molecules (nitric oxide and hydrogen sulfide) in guard cells and clarify of their mechanisms of action., and research on its applied use in agriculture.
    keyword : guard cell, phytohormones, active oxygen, nitric oxide, hydrogen sulfide
    2018.04.
Current and Past Project
  • Nitrogen, along with phosphorus and potassium, is an important and indispensable fertilizer component in plant production, and in order to use nitrogen as fertilizer, it is necessary to synthesize ammonia by immobilizing nitrogen (N2) in the atmosphere. The Haber-Bosch process, developed 100 years ago, is still the only industrial synthesis method for producing ammonia, using large amounts of oil and natural gas. In this research project, we will focus on biological nitrogen fixation methods using nitrogen-fixing bacteria, especially rhizobium bacteria that symbiotically fix nitrogen with leguminous plants, and will develop a new nitrogen-fixing method that uses rhizobium bacteria to fix nitrogen, and attempt to develop biological nitrogen fixation. Representative Sakai et al. have already found a population (consortium) composed of several microbial species capable of fixing nitrogen using cellulose isolated from cut grass sediments as a carbon (energy) source. In this study, we will clarify the ecology of each of these hetero-microbial symbiotic nitrogen-fixing bacteria, and metabolome analysis of metabolites required for symbiosis, and we will make it clear the structure, function, and ecology of nitrogen-fixing bacteria with a previously unknown ecotype, and to develop a stabilized biological nitrogen fixation method. The results of this research will provide new knowledge on nitrogen supply systems in soil ecosystems and contribute to nitrogen supply technology for soil utilizing unutilized plant biomass (cellulose) and endogenous plant nitrogen-fixing bacteria.
Academic Activities
Papers
1. 山田 直隆, 遠城 道雄, 園池公毅, 島崎 研一郎, 岩井 純夫, Chloroplast K+/H+ EXCHANGE ANTIPORTER 3 modulates abscisic acid-induced reactive oxygen species generation in guard cells, Physiologia Plantarum , 10.1111/ppl.14136, 3, 5, 2024;176:e14136., 2024.01, [URL], Reactive oxygen species (ROS) are important signaling molecules in stomatal closure. In a previous report, we demonstrated that ROS generated through photosynthetic electron transport (PET) act as signaling molecules in abscisic acid (ABA)-induced stomatal closure. However, the mechanism by which ABA induces ROS generation through PET remains unclear. Here, we assessed the possibility that chloroplast K+/H+ EXCHANGE ANTIPORTER 3 (KEA3) functions in ABA-induced ROS generation in guard cells, resulting in stomatal closure. KEA3 localizes to a thylakoid membrane and allows proton efflux from the thylakoid lumen by K+/H+ antiport, regulating photosynthesis by proton motive force. KEA3 loss-of-function mutants (kea3-1 and kea3-2) were impaired in ABA-induced ROS generation of guard cells and stomatal closure. The small molecule electroneutral K+/H+ antiporter nigericin induced ROS
generation in guard cells and stomatal closures in the kea3 mutants. This study demonstrates that KEA3 is an important factor for ABA-induced ROS generation in guard cells and stomatal closure.
2. Wazifa Afrin, Naotaka Yamada, Shigeki Furuya, Kohji Yamamoto, Characterization of glutathione-specific gamma glutamyl cyclotransferase (ChaC) in Bombyx mori, Arch Insect Biochem Physiol, 10.1002/arch.22027, 2023;114:e22027, 2023.04, Glutathione (GSH) contributes to redox maintenance and detoxification of various xenobiotic and endogenous substances. γ-glutamyl cyclotransferase (ChaC) is involved in GSH degradation. However, the molecular mechanism underlying GSH degradation in silkworms (Bombyx mori) remains unknown. Silkworms are lepidopteran insects that are considered to be an agricultural pest model. We aimed to examine the metabolic mechanism underlying GSH degradation mediated by B. mori ChaC and successfully identified a novel ChaC gene in silkworms (herein, bmChaC). The amino acid sequence and phylogenetic tree revealed that bmChaC was closely related to mammalian ChaC2. We overexpressed recombinant bmChaC in Escherichia coli, and the purified bmChaC showed specific activity toward GSH. Additionally, we examined the degradation of GSH to 5-oxoproline and cysteinyl glycine via liquid chromatography–tandem mass spectrometry. Quantitative real-time polymerase chain reaction revealed that bmChaC mRNA expression was observed in various tissues. Our results suggest that bmChaC participates in tissue protection via GSH homeostasis. This study provides new insights into the activities of ChaC and the underlying molecular mechanisms that can aid the development of insecticides to control agricultural pests..
3. Kohji Yamamoto, Misuzu Yamaguchi and Naotaka Yamada, Investigation of the active site of an unclassified glutathione transferase in Bombyx mori by alanine scanning, Journal of Pesticide Science, https://doi.org/10.1584/jpestics.D20-036, 45, 4, 238-240, e00137, 2020.10, [URL], Glutathione transferase (GST) is an important class of detoxification enzymes that are vital for defense against various xenobiotics and cellular oxidative stress. Previously, we had reported an unclassified glutathione transferase 2 in Bombyx mori (bmGSTu2) to be responsible for detoxifying diazinon. In this study, we aimed to identify the amino acid residues that constitute a hydrogen-bonding network important for GST activity. Site-directed mutagenesis of bmGSTu2 suggested that residues Asn102, Pro162, and Ser166 contribute to its catalytic activity.
4. Fumiko Saruta, Naotaka Yamada, Kohji Yamamoto, An omega‐class glutathione S‐transferase in the brown planthopper Nilaparvata lugens exhibits glutathione transferase and dehydroascorbate reductase activities, Arch Insect Biochem. Physiol., 10.1002/arch.21599, 2019;102:e21599., 2019.07, A complementary DNA that encodes an omega‐class glutathione S‐transferase (GST) of the brown planthopper, Nilaparvata lugens (nlGSTO), was isolated by reverse transcriptase polymerase chain reaction. A recombinant protein (nlGSTO) was obtained via overexpression in the Escherichia
coli cells and purified. nlGSTO catalyzes the biotransformation of glutathione with 1‐chloro‐2,4‐dinitrobenzene, a general substrate for GST, as well as with dehydroascorbate to synthesize ascorbate. Mutation experiments revealed that putative substrate‐binding sites, including Phe28, Cys29, Phe30, Arg176, and Lue225, were important for glutathione transferase and dehydroascorbate reductase activities. As ascorbate is a reducing agent, nlGSTO may participate in antioxidant resistance.
5. 岩井 純夫, 緒方 翔, 山田 直隆, 遠城 道雄, 園池公毅, 島崎 研一郎, Guard cell photosynthesis is crucial in abscisic acid-induced stomatal closure, Plant Direct, 10.1002/pld3.137, 3, 5, e00137, 2019.05, [URL], Reactive oxygen species (ROS) are ubiquitous signaling molecules involved in diverse physiological processes, including stomatal closure. Photosynthetic electron transport (PET) is the main source of ROS generation in plants, but whether it functions in guard cell signaling remains unclear. Here, we assessed whether PET functions in abscisic acid (ABA) signaling in guard cells. ABA-elicited ROS were localized to guard cell chloroplasts in Arabidopsis thaliana, Commelina benghalensis, and Vicia faba in the light and abolished by the PET inhibitors 3-(3, 4-dichlorophenyl)-1, 1-dimethylurea and 2, 5-dibromo-3-methyl-6-isopropyl-p-benzoquinone. These inhibitors reduced ABA-induced stomatal closure in all three species, as well as in the NADPH oxidase-lacking mutant atrboh D/F. However, an NADPH oxidase inhibitor did not fully eliminate ABA-induced ROS in the chloroplasts, and ABA-induced ROS were still observed in the guard cell chloroplasts of atrboh D/F. This study demonstrates that ROS generated through PET act as signaling molecules in ABA-induced stomatal closure and that this occurs in concert with ROS derived through NADPH oxidase..
6. Kohji Yamamoto, Akifumi Higashiura, Aiko Hirowatari1, Naotaka Yamada,Takuya Tsubota, Hideki Sezutsu, Atsushi Nakagawa, Characterisation of a diazinonmetabolising glutathione Stransferase in the silkworm Bombyx mori by X-ray crystallography and genome editing analysis, Scientific REPORTS, 10.1038/s41598-018-35207-8, 8, 16835, 2018.11.
7. Aiko Hirowatari, Sumiharu Nagaoka, Naotaka YAMADA, KOHJI YAMAMOTO, Structural characterization of the catalytic site of a Nilaparvata lugens
delta-class glutathione transferase, Journal of Insect Biotechnology and Sericology, 86, 1-7, 2017.03.
8. KOHJI YAMAMOTO, Aiko Hirowatari, Takahiro Shiotsuki, Naotaka YAMADA, Biochemical characterization of an unclassified glutathione S-transferase of Plutella xylostella, Journal of Pesticide Science, 41, 4, 145-151, 2016.11.
9. Kohji Yamamoto, Naotaka Yamada. , Identification of a diazinon-metabolizing glutathione S-transferase in the silkworm, Bombyx mori. , SCIENTIFIC REPORTS, 10.1038/srep30073. , 2016 Jul 21:6:30073, 2016.07, he glutathione S-transferase superfamily play key roles in the metabolism of numerous xenobiotics. We report herein the identification and characterization of a novel glutathione S-transferase in the silkworm, Bombyx mori. The enzyme (bmGSTu2) conjugates glutathione to 1-chloro-2,4-dinitrobenzene, as well as metabolizing diazinon, one of the organophosphate insecticides. Quantitative reverse transcription-polymerase chain reaction analysis of transcripts demonstrated that bmGSTu2 expression was induced 1.7-fold in a resistant strain of B. mori. Mutagenesis of putative amino acid residues in the glutathione-binding site revealed that Ile54, Glu66, Ser67, and Asn68 are crucial for enzymatic function. These results provide insights into the catalysis of glutathione conjugation in silkworm by bmGSTu2 and into the detoxification of organophosphate insecticides. .
10. Kenj Honda, Naotaka YAMADA, Riichiro Yoshida, Hideshi Ihara, Tomohiro Sawa, Takaaki Akaike, Sumio Iwai, 8-Mercapto-Cyclic GMP Mediates Hydrogen Sulfide-Induced Stomatal Closure in Arabidopsis, PLANT AND CELL PHYSIOLOGY, 10.1093/pcp/pcv069, 56, 8, 1481-1489, 2015.08.
11. KOHJI YAMAMOTO, Akifumi Higashiura, MD. Tofazzal Hossain, Naotaka YAMADA, Takahiro Shiotsuki, Atsushi Nakagawa, Structural characterization of the catalytic site of a Nilaparvata lugens
delta-class glutathione transferase, Archives of Biochemistry and Biophysics, 566, 36-42, 2015.01.
12. KOHJI YAMAMOTO, Yoichi Aso, Naotaka YAMADA, Catalytic function of an Epsilon-class glutathione S-transferase of the silkworm, Insect Molecular Biology , 10.1111, 22, 5, 523-531, 2013.06.
13. Takahiro Joudoi, Yudai Shichiri, Nobuto Kamizono, Takaaki Akaike, Tomohiro Sawa, Jun Yoshitake, 山田 直隆, Sumio Iwaia, Nitrated Cyclic GMP Modulates Guard Cell Signaling in ArabidopsisW, The Plant Cell, 10.1105, 25, 558-571, 2013.02.
14. Kenjiro Furuta, Norihiro Fujita, Tsubasa Ibushi, Takahiro Shiotsuki, Naotaka Yamada and Eiichi Kuwano, Synthesis and anti-juvenile hormone activity of ethyl 4-[(6-substituted 2,2-dimethyl-2H-chromen-7-yl)methoxy]benzoates
, Journal of Pesticide Science , 35, 4, 405-411 , 2010.05.
15. N. Yamada, E. Kuwano,, Synthesis and bleaching activity of 1-ethyl- and 1-propyl-5-substituted imidazoles(II), J. Fac. Agr.,Kyushu Univ., 46 (1), 219-228, 2001.10.
16. Yoshida, S., Furuta, K., Shirahashi, H., Ashibe, K., Fujita, N., Yamada. N , Kuwano. E, Synthesis and Structure-Activity Relationship of a New Series of Anti-Juvenile Hormone Agents: Alkyl 4-(2-Benzylhexyloxy)benzoates and Ethyl 4-Substituted Benzoates. , J.Fac.Agr.,Kyushu Univ.,, 54(1),179-184, 2009.01.
17. S. Hong, N. Yamada,A.Harada, S. Kawai and E. Kuwano, Inhibition of trans-Cinnamate 4-Hydroxylase by 4-amino-5aryl-2,3-dihydro-3H-1,2,4-triazole, J. Pestic. Science, 10.1584/jpestics.30.406, 30, 4, 406-408, 30(4), pp406-408, 2005.12.
18. Watanabe, Y., Yamada. N ., Machida, T., Honjoh, K., Kuwano,E. , Influence of Cold Hardening on Chlorophyll and Carotenoid in Chlorella vulgaris
, J.Fac.Agr.,Kyushu Univ.,, 54(1),195-200(2009), 2009.01.
19. Yoshida, S., Furuta, K., Ashibe, K., Fujita, N., Nishikawa, S., Yamada. N, Kuwano. E , Ethyl 4-[2-(Substituted Benzyl)hexyloxy]benzoates: Anti-Juvenile Hormone Agents with Juvenile Hormone Activity., J.Fac.Agr.,Kyushu Univ.,, 54(1),185-190(2009)
, 2009.01.
20. Naotaka Yamada, Shinya Kawai, Eiichi Kuwano 他3名, 5-Aryl-1,3,4-oxadiazole-2-thiols as a New Series of trans-Cinnamate, Journal of Pesticide Science, 10.1584/jpestics.29.205, 29, 3, 205-208, 29,3, pp205-208, 2004.03.
21. Naotaka Yamada, Daisuke Kusano,Eiich. Kuwano, Bleaching Activity of 4-Phenl-3-(substituted benzylthio)-4H-1,2,4-triazoles.Biosci.Biotech. and Biochem., 66(8) 1671-1676(2002), Bioscience Biotechnology and Biochemistry., (2002), 66, 8, 1671-1676, 66、8、pp1671-1676, 2002.08.
Presentations
1. Role of hydrogen sulfide as a signaling material in induction of stomata closure of salicylic acid.
Naotaka Yamada, Daiki Shinboku, Sumio Iwai.
The 2021 Meeting of the Japan Society for Bioscience, Biotechnology and Agrochemistry..
2. Search for anti-ABA compounds by using ABA agonist, Quinabactin as a lead compound
Kohei Taksugi, Yushiro Fukusaki, Naotaka Yamada (Faculty of agriculture, Kyushu Univ.),
45th Annual Meeting of the Pesticide Science Society of Japan.
3. Biochemical analysis and crystal structure analysis using specific inhibitor Z302 of basidiomytesal yeast and plant-derived phenylalanine ammonia lyase.
Takashi Nakashima, Takahiro Yoshimura, Daiki Tomitaka, Naotaka Yamada, Yoshizumi Ishino.
The 2019 Joint Meeting of The West and Chushikoku Branch of the Japan Society for Bioscience, Biotechnology and Agrochemistry. .
4. Changes in H2S, NO and H2O2 levels in guard cells during the guard closure induction by salicylic acid,
Naotaka Yamada, Daiki Shinboku, Sumio Iwai.
The 2019 Joint Meeting of The West and Chushikoku Branch of the Japan Society for Bioscience, Biotechnology and Agrochemistry..
Educational
Educational Activities
In the undergraduate School of Agriculture, it is in charge of Pesticide Chemistry I , Pesticide Chemistry II, Bioanalysis/Instrumental Analysis Methods II, Physical Chemistry Experiment, Agricultural Chemistry Experiment(Part of Organic Analysis and Organic Synthesis )in the Course of Agricultural Chemistry.
In the graduate School of Agriculture, it is in charge of Molecular Biosciences, Molecular Biosciences Project Exercises in the Course of Molecular Biosciences.