SHIMIZU Takayuki

researchmap

Profile and Settings

• Name (Japanese)

  Shimizu

• Name (Kana)

  Takayuki

Research Interests

• シグナル伝達
• 硫化水素/ポリファルファー
• システイン修飾
• レドックス制御
• 環境応答
• 紅色細菌/光合成細菌
• 植物
• 藻類

Research Areas

• Life sciences, Molecular biology
• Life sciences, Functional biochemistry
• Life sciences, Cell biology
• Life sciences, Plants: molecular biology and physiology
• Life sciences, Applied microbiology

Research Experience

• 2023, 9999, Nara Women's University, 研究院自然科学系 生物科学領域, 准教授
• 2017, 2023, The University of Tokyo, Graduate School of Arts and Sciences Department of Multi-Disciplinary Sciences,General Systems Sciences, 助教

Education

• 2013, 2017, Tokyo Institute of Technology, Graduate School of Bioscience and Biotechnology, 生体システム専攻 博士後期課程
• 2011, 2013, Tokyo Metropolitan University, 大学院理工学研究科, 生命科学専攻 博士前期課程
• 2007, 2011, Tokyo Metropolitan University, Faculty of Urban Liberal Arts, Faculty of Urban Liberal Arts

Teaching Experience

• Oct. 2017, Sep. 2023
• Oct. 2017, Sep. 2023
• Oct. 2017, Sep. 2023
• Oct. 2023, 9999
• Oct. 2023, 9999
• Oct. 2023, 9999
• Oct. 2023, 9999
• Oct. 2023, 9999
• Oct. 2023, 9999
• Oct. 2023, 9999
• Oct. 2023, 9999
• Apr. 2024, 9999
• Apr. 2024, 9999
• Apr. 2024, 9999
• Apr. 2024, 9999
• Apr. 2024, 9999
• Apr. 2024, 9999
• Apr. 2024, 9999
• Apr. 2024, 9999
• Apr. 2024, 9999
• Apr. 2024, 9999
• Apr. 2024, 9999
• Apr. 2024, 9999
• Apr. 2024, 9999

Association Memberships

• THE BOTANICAL SOCIETY OF JAPAN
• THE JAPANESE SOCIETY OF PLANT PHYSIOLOGISTS
• THE JAPANESE SOCIETY OF PHOTOSYNTHESIS RESEARCH
• 日本生化学会

Academic Contribution

• 15th International Conference on Tetrapyrrole Photoreceptors in Photosynthetic Organisms 大会実行委員, 19 Sep. 2023, 22 Sep. 2023

Ⅱ．研究活動実績

Published Papers

• Refereed, Applied Microbiology, Translation Enhancement by a Short Nucleotide Insertion at 5′UTR: Application to an In Vitro Cell-Free System and a Photosynthetic Bacterium, Tomo Kondo; Takayuki Shimizu, 02 Jul. 2023, Scientific journal, 10.3390/applmicrobiol3030047

  DOI URL
• Refereed, Antioxidants, Thioredoxin-2 Regulates SqrR-Mediated Polysulfide-Responsive Transcription via Reduction of a Polysulfide Link in SqrR, Takayuki Shimizu; Masaru Hashimoto; Tatsuru Masuda, 11 Mar. 2023, Scientific journal, 10.3390/antiox12030699

  DOI URL
• Refereed, PNAS Nexus, Polysulfide metabolizing enzymes influence SqrR-mediated sulfide-induced transcription by impacting intracellular polysulfide dynamics, Takayuki Shimizu; Tomoaki Ida; Giuliano T Antelo; Yuta Ihara; Joseph N Fakhoury; Shinji Masuda; David P Giedroc; Takaaki Akaike; Daiana A Capdevila; Tatsuru Masuda, Sulfide plays essential roles in controlling various physiological activities in almost all organisms. Although recent evidence has demonstrated that sulfide is endogenously generated and metabolized into polysulfides inside the cells, the relationship between polysulfide metabolism and polysulfide-sensing mechanisms is not well understood. To better define this interplay between polysulfide metabolism and sensing in cells, we investigated the role of polysulfide-metabolizing enzymes such as sulfide:quinone oxidoreductase (SQR) on the temporal dynamics of cellular polysulfide speciation and on the transcriptional regulation by the persulfide-responsive transcription factor SqrR in Rhodobacter capsulatus. We show that disruption of the sqr gene resulted in the loss of SqrR repression by exogenous sulfide at longer culture times, which impacts the speciation of intracellular polysulfides of Δsqr vs. wild-type strains. Both the attenuated response of SqrR and the change in polysulfide dynamics of the Δsqr strain is fully reversed by the addition to cells of cystine-derived polysulfides, but not by glutathione disulfide (GSSG)-derived polysulfides. Furthermore, cysteine persulfide (CysSSH) yields a higher rate of oxidation of SqrR relative to glutathione persulfide (GSSH), which leads to DNA dissociation in vitro. The oxidation of SqrR was confirmed by a mass spectrometry-based kinetic profiling strategy that showed distinct polysulfide-crosslinked products obtained with CysSSH vs. GSSH. Taken together, these results establish a novel association between the metabolism of polysulfides and the mechanisms for polysulfide sensing inside the cells., 10 Feb. 2023, 2, 3, pgad048, Scientific journal, True, 10.1093/pnasnexus/pgad048

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• Refereed, Antioxidants, The Sulfide-Responsive SqrR/BigR Homologous Regulator YgaV of Escherichia coli Controls Expression of Anaerobic Respiratory Genes and Antibiotic Tolerance, Rajalakshmi Balasubramanian; Koichi Hori; Takayuki Shimizu; Shingo Kasamatsu; Kae Okamura; Kan Tanaka; Hideshi Ihara; Shinji Masuda, Compositions and activities of bacterial flora in the gastrointestinal tract significantly influence the metabolism, health, and disease of host humans and animals. These enteric bacteria can switch between aerobic and anaerobic growth if oxygen tension becomes limited. Interestingly, the switching mechanism is important for preventing reactive oxygen species (ROS) production and antibiotic tolerance. Studies have also shown that intracellular and extracellular sulfide molecules are involved in this switching control, although the mechanism is not fully clarified. Here, we found that YgaV, a sulfide-responsive transcription factor SqrR/BigR homolog, responded to sulfide compounds in vivo and in vitro to control anaerobic respiratory gene expression. YgaV also responded to H2O2 scavenging in the enteric bacterium Escherichia coli. Although the wild-type (WT) showed increased antibiotic tolerance under H2S-atmospheric conditions, the ygaV mutant did not show such a phenotype. Additionally, antibiotic sensitivity was higher in the mutant than in the WT of both types in the presence and absence of exogenous H2S. These results, therefore, indicated that YgaV-dependent transcriptional regulation was responsible for maintaining redox homeostasis, ROS scavenging, and antibiotic tolerance., 28 Nov. 2022, 11, 12, Scientific journal, True, 10.3390/antiox11122359

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• Refereed, Microorganisms, {MDPI} {AG}, Persulfide-Responsive Transcription Factor SqrR Regulates Gene Transfer and Biofilm Formation via the Metabolic Modulation of Cyclic di-GMP in Rhodobacter capsulatus, Takayuki Shimizu; Toma Aritoshi; J. Thomas Beatty; Tatsuru Masuda, 26 Apr. 2022, 10, 5, 908, 908, Scientific journal, 10.3390/microorganisms10050908

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• Refereed, Plant & cell physiology, Repressor Activity of SqrR, a Master Regulator of Persulfide-Responsive Genes, Is Regulated by Heme Coordination., Takayuki Shimizu; Yuuki Hayashi; Munehito Arai; Shawn E McGlynn; Tatsuru Masuda; Shinji Masuda, Reactive sulfur species (RSS) are involved in bioactive regulation via persulfidation of proteins. However, how cells regulate RSS-based signaling and RSS metabolism is poorly understood, despite the importance of universal regulation systems in biology. We previously showed that the persulfide-responsive transcriptional factor SqrR acts as a master regulator of sulfide-dependent photosynthesis in proteobacteria. Here, we demonstrated that SqrR also binds heme at a near one-to-one ratio with a binding constant similar to other heme-binding proteins. Heme does not change the DNA-binding pattern of SqrR to the target gene promoter region; however, DNA-binding affinity of SqrR is reduced by the binding of heme, altering its regulatory activity. Circular dichroism spectroscopy clearly showed secondary structural changes in SqrR by the heme binding. Incremental change in the intracellular heme concentration is associated with small, but significant reduction in the transcriptional repression by SqrR. Overall, these results indicate that SqrR has an ability to bind heme to modulate its DNA-binding activity, which may be important for the precise regulation of RSS metabolism in vivo., 25 Mar. 2021, 62, 1, 100, 110, Scientific journal, False, 10.1093/pcp/pcaa144

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• Refereed, Plants (Basel, Switzerland), The Role of Tetrapyrrole- and GUN1-Dependent Signaling on Chloroplast Biogenesis., Takayuki Shimizu; Tatsuru Masuda, Chloroplast biogenesis requires the coordinated expression of the chloroplast and nuclear genomes, which is achieved by communication between the developing chloroplasts and the nucleus. Signals emitted from the plastids, so-called retrograde signals, control nuclear gene expression depending on plastid development and functionality. Genetic analysis of this pathway identified a set of mutants defective in retrograde signaling and designated genomes uncoupled (gun) mutants. Subsequent research has pointed to a significant role of tetrapyrrole biosynthesis in retrograde signaling. Meanwhile, the molecular functions of GUN1, the proposed integrator of multiple retrograde signals, have not been identified yet. However, based on the interactions of GUN1, some working hypotheses have been proposed. Interestingly, GUN1 contributes to important biological processes, including plastid protein homeostasis, through transcription, translation, and protein import. Furthermore, the interactions of GUN1 with tetrapyrroles and their biosynthetic enzymes have been revealed. This review focuses on our current understanding of the function of tetrapyrrole retrograde signaling on chloroplast biogenesis., 21 Jan. 2021, 10, 2, Scientific journal, True, 10.3390/plants10020196

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• Refereed, Philosophical transactions of the Royal Society of London. Series B, Biological sciences, Proteomic analysis of haem-binding protein from Arabidopsis thaliana and Cyanidioschyzon merolae., Takayuki Shimizu; Rintaro Yasuda; Yui Mukai; Ryo Tanoue; Tomohiro Shimada; Sousuke Imamura; Kan Tanaka; Satoru Watanabe; Tatsuru Masuda, Chloroplast biogenesis involves the coordinated expression of the plastid and nuclear genomes, requiring information to be sent from the nucleus to the developing chloroplasts and vice versa. Although it is well known how the nucleus controls chloroplast development, it is still poorly understood how the plastid communicates with the nucleus. Currently, haem is proposed as a plastid-to-nucleus (retrograde) signal that is involved in various physiological regulations, such as photosynthesis-associated nuclear genes expression and cell cycle in plants and algae. However, components that transduce haem-dependent signalling are still unidentified. In this study, by using haem-immobilized high-performance affinity beads, we performed proteomic analysis of haem-binding proteins from Arabidopsis thaliana and Cyanidioschyzon merolae. Most of the identified proteins were non-canonical haemoproteins localized in various organelles. Interestingly, half of the identified proteins were nucleus proteins, some of them have a similar function or localization in either or both organisms. Following biochemical analysis of selective proteins demonstrated haem binding. This study firstly demonstrates that nucleus proteins in plant and algae show haem-binding properties. This article is part of the theme issue 'Retrograde signalling from endosymbiotic organelles'., 22 Jun. 2020, 375, 1801, 20190488, 20190488, Scientific journal, True, 10.1098/rstb.2019.0488

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• Refereed, Journal of biochemistry, Persulphide-responsive transcriptional regulation and metabolism in bacteria., Takayuki Shimizu; Shinji Masuda, Hydrogen sulphide (H2S) impacts on bacterial growth both positively and negatively; it is utilized as an electron donor for photosynthesis and respiration, and it inactivates terminal oxidases and iron-sulphur clusters. Therefore, bacteria have evolved H2S-responsive detoxification mechanisms for survival. Sulphur assimilation in bacteria has been well studied, and sulphide:quinone oxidoreductase, persulphide dioxygenase, rhodanese and sulphite oxidase were reported as major sulphide-oxidizing enzymes of sulphide assimilation and detoxification pathways. However, how bacteria sense sulphide availability to control H2S and sulphide metabolism remains largely unknown. Recent studies have identified several bacterial (per)sulphide-sensitive transcription factors that change DNA-binding affinity through persulphidation of specific cysteine residues in response to highly reactive sulphur-containing chemicals and reactive sulphur species (RSS). This review focuses on current understanding of the persulphide-responsive transcription factors and RSS metabolism regulated by RSS sensory proteins., 01 Feb. 2020, 167, 2, 125, 132, Scientific journal, True, 10.1093/jb/mvz063

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• Refereed, Proceedings of the National Academy of Sciences of the United States of America, The retrograde signaling protein GUN1 regulates tetrapyrrole biosynthesis., Takayuki Shimizu; Sylwia M Kacprzak; Nobuyoshi Mochizuki; Akira Nagatani; Satoru Watanabe; Tomohiro Shimada; Kan Tanaka; Yuuki Hayashi; Munehito Arai; Dario Leister; Haruko Okamoto; Matthew J Terry; Tatsuru Masuda, The biogenesis of the photosynthetic apparatus in developing seedlings requires the assembly of proteins encoded on both nuclear and chloroplast genomes. To coordinate this process there needs to be communication between these organelles, but the retrograde signals by which the chloroplast communicates with the nucleus at this time are still essentially unknown. The Arabidopsis thaliana genomes uncoupled (gun) mutants, that show elevated nuclear gene expression after chloroplast damage, have formed the basis of our understanding of retrograde signaling. Of the 6 reported gun mutations, 5 are in tetrapyrrole biosynthesis proteins and this has led to the development of a model for chloroplast-to-nucleus retrograde signaling in which ferrochelatase 1 (FC1)-dependent heme synthesis generates a positive signal promoting expression of photosynthesis-related genes. However, the molecular consequences of the strongest of the gun mutants, gun1, are poorly understood, preventing the development of a unifying hypothesis for chloroplast-to-nucleus signaling. Here, we show that GUN1 directly binds to heme and other porphyrins, reduces flux through the tetrapyrrole biosynthesis pathway to limit heme and protochlorophyllide synthesis, and can increase the chelatase activity of FC1. These results raise the possibility that the signaling role of GUN1 may be manifested through changes in tetrapyrrole metabolism, supporting a role for tetrapyrroles as mediators of a single biogenic chloroplast-to-nucleus retrograde signaling pathway., 03 Dec. 2019, 116, 49, 24900, 24906, Scientific journal, True, 10.1073/pnas.1911251116

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• Refereed, Bioscience, Biotechnology and Biochemistry, Japan Society for Bioscience Biotechnology and Agrochemistry, Nitrite-reducing ability is related to growth inhibition by nitrite in Rhodobacter sphaeroides f. sp. denitrificans, Takayuki Shimizu; Kouhei Horiguchi; Yui Hatanaka; Shinji Masuda; Keizo Shimada; Katsumi Matsuura; Shin Haruta, Growth inhibition of Rhodobacter sphaeroides f. sp. denitrificans IL106 by nitrite under anaerobiclight conditions became less pronounced when the gene encoding nitrite reductase was deleted. Growth of another deletion mutant of the genes encoding nitric oxide reductase was severely suppressed by nitrite. Our results suggest that nitrite reductase increases the sensitivity to nitrite through the production of nitric oxide., 2018, 82, 1, 148, 151, Scientific journal, 10.1080/09168451.2017.1412247

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• Refereed, Proceedings of the National Academy of Sciences of the United States of America, NATL ACAD SCIENCES, Sulfide-responsive transcriptional repressor SqrR functions as a master regulator of sulfide-dependent photosynthesis, Takayuki Shimizu; Jiangchuan Shen; Mingxu Fang; Yixiang Zhang; Koichi Hori; Jonathan C. Trinidad; Carl E. Bauer; David P. Giedroc; Shinji Masuda, Sulfide was used as an electron donor early in the evolution of photosynthesis, with many extant photosynthetic bacteria still capable of using sulfur compounds such as hydrogen sulfide (H2S) as a photosynthetic electron donor. Although enzymes involved in H2S oxidation have been characterized, mechanisms of regulation of sulfide-dependent photosynthesis have not been elucidated. In this study, we have identified a sulfide-responsive transcriptional repressor, SqrR, that functions as a master regulator of sulfide-dependent gene expression in the purple photosynthetic bacterium Rhodobacter capsulatus. SqrR has three cysteine residues, two of which, C41 and C107, are conserved in SqrR homologs from other bacteria. Analysis with liquid chromatography coupled with an electrospray-interface tandem-mass spectrometer reveals that SqrR forms an intramolecular tetrasulfide bond between C41 and C107 when incubated with the sulfur donor glutathione persulfide. SqrR is oxidized in sulfide-stressed cells, and tetrasulfide-cross-linked SqrR binds more weakly to a target promoter relative to unmodified SqrR. C41S and C107S R. capsulatus SqrRs lack the ability to respond to sulfide, and constitutively repress target gene expression in cells. These results establish that SqrR is a sensor of H2S-derived reactive sulfur species that maintain sulfide homeostasis in this photosynthetic bacterium and reveal the mechanism of sulfide-dependent transcriptional derepression of genes involved in sulfide metabolism., Feb. 2017, 114, 9, 2355, 2360, Scientific journal, 10.1073/pnas.1614133114

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• Refereed, Communicative & Integrative Biology, Characterization of redox-active cysteine residues of persulfide-responsive transcriptional repressor SqrR, Shimizu T; Masuda S, 2017, 10, 4, e1329786

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• Refereed, PLoS ONE, PUBLIC LIBRARY SCIENCE, Evidence that Altered Cis Element Spacing Affects PpsR Mediated Redox Control of Photosynthesis Gene Expression in Rubrivivax gelatinosus, Takayuki Shimizu; Zhuo Cheng; Katsumi Matsuura; Shinji Masuda; Carl E. Bauer, PpsR is a major regulator of photosynthesis gene expression among all characterized purple photosynthetic bacteria. This transcription regulator has been extensively characterized in Rhodobacter (Rba.) capsulatus and Rba. sphaeroides which are members of the a-proteobacteria lineage. In this study, we have investigated the biochemical properties and mutational effects of a ppsR deletion strain in the beta-proteobacterium Rubrivivax (Rvi.) gelatinosus in order to reveal phylogenetically conserved mechanisms and species-specific characteristics. A deletion of the ppsR gene resulted in de-repression of photosystem synthesis showing that PpsR functions as a repressor of photosynthesis genes in this species. We also constructed a Rvi. gelatinosus PpsR mutant in which a conserved cysteine at position 436 was changed to an alanine to examine whether or not this residue is important for sensing redox, as reported in Rhodobacter species. Surprisingly, the Cys436 Ala mutant retained the ability to repress photosynthesis gene expression under aerobic conditions, suggesting that PpsR from Rvi. gelatinosus has different redox-responding characteristics. Furthermore, biochemical analyses demonstrated that Rvi. gelatinosus PpsR only shows redox-dependent binding to promoters with 9-bp spacing, but not 8-bp spacing, between two PpsR-recognition sequences. These results indicate that redox-dependent binding of PpsR requires appropriate cis configuration of PpsR target sequences in Rvi. gelatinosus. These results also indicate that PpsR homologs from different species regulate photosynthesis genes with altered biochemical properties., Jun. 2015, 10, 6, e0128446, Scientific journal, 10.1371/journal.pone.0128446

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• Refereed, Journal of Bacteriology, AMER SOC MICROBIOLOGY, Complete Genome Sequence of Phototrophic Betaproteobacterium Rubrivivax gelatinosus IL144, Sakiko Nagashima; Akiko Kamimura; Takayuki Shimizu; Sanae Nakamura-Isaki; Eiji Aono; Koji Sakamoto; Natsuko Ichikawa; Hidekazu Nakazawa; Mitsuo Sekine; Shuji Yamazaki; Nobuyuki Fujita; Keizo Shimada; Satoshi Hanada; Kenji V. P. Nagashima, Rubrivivax gelatinosus is a facultative photoheterotrophic betaproteobacterium living in freshwater ponds, sewage ditches, activated sludge, and food processing wastewater. There have not been many studies on photosynthetic betaproteobacteria. Here we announce the complete genome sequence of the best-studied phototrophic betaproteobacterium, R. gelatinosus IL-144 (NBRC 100245)., Jul. 2012, 194, 13, 3541, 3542, Scientific journal, 10.1128/JB.00511-12

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• Plant Physiology, Alternative localization of HEME OXYGENASE 1 in plant cells regulates cytosolic heme catabolism, Yingxi Chen; Kohji Nishimura; Mutsutomo Tokizawa; Yoshiharu Y Yamamoto; Yoshito Oka; Tomonao Matsushita; Kousuke Hanada; Kazumasa Shirai; Shoji Mano; Takayuki Shimizu; Tatsuru Masuda, 28 May 2024, Scientific journal, 10.1093/plphys/kiae288

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MISC

• Not Refereed, 月間「アグリバイオ」, 細菌における超硫黄分子センシング機構と金属の関係性, 清水隆之, Mar. 2022, 6, 4, 58, 62
• Not Refereed, 月刊「細胞」, 細菌における活性硫黄種センシング機構と金属の関係性, 清水隆之, Feb. 2022, 54, 3, 26, 28
• Refereed, 生化学, (公社)日本生化学会, 硫化水素・超硫黄分子のセンシング機構, 清水隆之; 増田真二, 生物が,有用性と有害性を併せ持つ超硫黄分子を生命活動に利用するためには,硫化水素・超硫黄分子を特異的に検知し,その細胞内濃度を厳密に調節する必要がある.近年,硫化水素・超硫黄分子のセンサータンパク質が細菌から複数見つかり,それらはシステインのチオール基のポリスルフィド化を介して硫化水素・超硫黄分子を特異的に検知していることがわかった.種々の酸化剤とも反応しうるチオール基が,超硫黄分子特異的に反応する分子プロセスの理解は不十分であったが,最近,硫化水素・超硫黄分子のセンサータンパク質の一つであるSqrRを用いた精密質量分析と結晶構造解析の結果に基づき,チオール基のポリスルフィド化形成の分子機構が提案された.本稿では,SqrRの硫化水素・超硫黄分子のセンシング機構について,最近の知見を解説する.(著者抄録), Oct. 2021, 93, 5, 637, 642
• Refereed, 光合成研究 = News letter, The Japanese Society of Photosynthesis Research, Tetrapyrrole- and GUN1-Dependent Plastid Signaling on Chloroplast Biogenesis, 清水 隆之; 増田 建, Apr. 2021, 31, 1, 50, 62

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• Institute for Fermentation, Osaka. Research Communications, 細菌性ウイルス様粒子GTAによる環境適応機構の分子基盤, 清水隆之, 2021, 35
• Refereed, 硫酸と工業, 硫酸協会, Molecular basis of transcriptional regulation by the novel persulfide-responsive transcriptional factor SqrR identified from a hydrogen sulfide-utilizing photosynthetic bacterium, 清水 隆之; 増田 真二, Jul. 2018, 71, 7, 95, 102
• Refereed, Seibutsu Butsuri, The Biophysical Society of Japan General Incorporated Association, Sensory Mechanism of H₂S and Reactive-sulfur-species through Polysulfidation of Cysteine Residues, MASUDA Shinji; SHIMIZU Takayuki, 2018, 58, 3, 163, 164
• Refereed, 光合成研究 = News letter, The Japanese Society of Photosynthesis Research, The induction of an electron transport chain involved in sulfide oxidation : The identification and sulfide-responsive mechanism of transcriptional factor SqrR, 清水 隆之, Apr. 2017, 27, 1, 16, 21
• Refereed, バイオサイエンスとインダストリー, 硫化水素に応答した遺伝子発現制御, 清水 隆之; 増田 真二, 2017, 75, 516, 517

Books etc

• 基礎生命科学実験 = Introductory course in life science experiments, 東京大学出版会, 東京大学教養学部基礎生命科学実験編集委員会; 東京大学教養学部, Feb. 2021, x, 213p, 図版 [2] p, 9784130622271

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Presentations

• 清水隆之, 日本生化学会, 紅色細菌をモデルとした超硫黄分子によるシグナル伝達機構の分子基盤, Nominated symposium, 10 Nov. 2022
• Takayuki Shimizu, 4th International Conference on Persulfide and Sulfur Metabolism in Biology and Medicine, Reactive sulfur species (RSS) metabolizing enzymes influence RSS sensing by impacting intracellular persulfide dynamics in bacteria, Invited oral presentation, 01 Nov. 2022, 29 Oct. 2022, 01 Nov. 2022
• 清水隆之, 日本生化学会, 紅色細菌における硫化水素・活性イオウ分子種の応答機構, Nominated symposium, 04 Nov. 2021
• 清水 隆之, 日本光合成学会シンポジウム, 葉緑体形成の制御に関わる葉緑体から核へのシグナル伝達, Nominated symposium, Sep. 2020
• 清水 隆之, 静岡大学 公開セミナー, 硫化水素による生理活性調節とそのシグナル伝達機構, Public discourse, Feb. 2020
• 清水 隆之, 第1回 光合成細菌ワークショップ, 紅色光合成細菌を用いた環境応答性センサータンパク質の研究, Nominated symposium, Mar. 2016
• 高柳なつ; 荒江星拓; 高橋洋和; 清水隆之; 堀口吾朗; 相田光宏; 深城英弘; 増田建; 大谷美沙都, 第87回日本植物学会, ヘムシグナルによる側根形態制御にはpre-mRNAスプライシング制御が介在する, Oral presentation, Sep. 2023
• Yingxi Chen; Kohji Nishimura; Yoshiharu Yamamoto; Yoshito Oka; Tomonao Matsushita; Takayuki Shimizu; Tatsuru Masuda, 第87回日本植物学会, Cytoplasmic Heme Decomposition by HO1 Regulated by TSSs is Critical for Chloroplast Biogenesis, Poster presentation, Sep. 2023
• 清水隆之; オスマンズリナ; 増田建, 第87回日本植物学会, シロイヌナズナの葉緑体形成における硫化水素による光合成器官の制御, Poster presentation, Sep. 2023
• Yingxi Chen; Kohji Nishimura; Yoshiharu Yamamoto; Yoshito Oka; Tomonao Matsushita; Takayuki Shimizu; Tatsuru Masuda, 15th International Conference on Tetrapyrrole Photoreceptors in Photosynthetic Organisms, Cytoplasmic Heme Decomposition by Heme Oxygenase 1 produced by Transcription Start Sites Regulation is Critical for Chloroplast Biogenesis, Oral presentation, Sep. 2023
• Natsu Takayanagi; Toshihiro Arae; Takayuki Shimizu; Gorou Horiguchi; Mitsuhiro Aida; Hidehiro Fukaki; Tatsuru Masuda; Michitaka Notaguchi; Takashi Hirayama; Misato Ohtani, The 33rd International Conference on Arabidopsis Research, Role of pre-mRNA splicing in lateral root morphogenesis regulated by plastid signal, Oral presentation, Jun. 2023
• Kentaro Iwata; Chieko Goto; Hinatamaru Fukumura; Takayuki Shimizu; Kaisei Maruyama; Tomoyuki Furuya; Yuki Kondo; Hiroyuki Kasahara; Tatsuru Masuda; Kimitsune Ishizaki; Hidehiro Fukaki, The 33rd International Conference on Arabidopsis Research, Functional Analysis of RLF, a Cytochrome b 5- Like Heme Binding Protein, in Plant Organ Development, Oral presentation, Jun. 2023
• 清水隆之; 井田智章; Giuliano T. Antelo; 井原雄太; 増田真二; David; P. Giedroc; 赤池孝章; Daiana A. Capdevila; 増田建, 第13回日本光合成学会, 紅色光合成細菌の硫化水素応答における超硫黄分子の代謝動態, Poster presentation, May 2023
• 高柳なつ; 荒江星拓; 高橋洋和; 清水隆之; 堀口吾朗; 相田光宏; 深城英弘; 増田建; 大谷美沙都, 第64回日本植物生理学会, 地上部ヘムシグナルはpre-mRNAスプライシング制御を介して側根形態を制御する, Oral presentation, Mar. 2023
• 岩田健太郎; 後藤千恵子; 福村日向丸; 清水隆之; 丸山海成; 古谷朋之; 近藤侑貴; 笠原博幸; 増田建; 石崎公庸; 深城英弘, 第64回日本植物生理学会, 植物の器官発生におけるシトクロムb5様ヘム結合タンパク質RLFの機能解析, Oral presentation, Mar. 2023
• Yingxi Chen; Kohji Nishimura; Yoshiharu Yamamoto; Yoshito Oka; Tomonao Matsushita; Takayuki Shimizu; Tatsuru Masuda, 第64回日本植物生理学会, Light mediates transcription start sites of heme oxygenase 1 for a cytoplasmic heme decomposition bypass in Arabidopsis, Oral presentation, Mar. 2023
• Zurina Osuman; Takayuki Shimizu; Tatsuru Masuda, 第64回日本植物生理学会, Enhancement of accumulation of photosynthetic pigments and proteins during chloroplast biogenesis by sulfide in Arabidopsis thaliana, Poster presentation, Mar. 2023
• 清水隆之; 井田智章; Giuliano T. Antelo; 井原雄太; 増田真二; David; P. Giedroc; 赤池孝章; Daiana A. Capdevila; 増田建, 第64回日本植物生理学会, 硫化水素依存的光合成の転写制御に関わるポリスルフィド代謝の解析, Oral presentation, Mar. 2023
• Kae Okamura; Shingo Kasamatsu; Takayuki Shimizu; Shinji Masuda; Hideshi Ihara, 4th International Conference on Persulfide and Sulfur Metabolism in Biology and Medicine, Development of ionization-coupled cleavage of oxidized polysulfide structure (iCOPS): a novel detection method for oxidized polysulfide modifications on proteins, Poster presentation, Nov. 2022
• 高柳なつ; 荒江星拓; 高橋洋和; 清水隆之; 堀口吾朗; 相田光宏; 深城英弘; 増田建; 大谷美沙都, 第86回日本植物学会, ヘムシグナルによる側根形成制御にはpre-mRNAスプライシング制御が介在する, Oral presentation, Sep. 2022
• Yingxi Chen; Kohji Nishimura; Yoshiharu Yamamoto; Takayuki Shimizu; Tatsuru Masuda, 第86回日本植物学会, Phytochromes mediated transcription start sites of heme oxygenase 1 in Arabidopsis thaliana, Oral presentation, Sep. 2022
• Zurina Osuman; Takayuki Shimizu; Tatsuru Masuda, 第86回日本植物学会, Effect of Sulfide on phytochrome-dependent photomorphogenesis in Arabidopsis thaliana, Poster presentation, Sep. 2022
• 増田建; 宮地孝明; 西村浩二; 清水隆之, 第86回日本植物学会, シロイヌナズナABCトランスポーターABCG23の機能解析, Oral presentation, Sep. 2022
• 清水隆之; 有年統真; J. Thomas Batty; 増田建, 第12回日本光合成学会, 紅色光合成細菌における硫化水素応答性転写因子SqrRによるファージ様粒子GTAを介した遺伝子伝播の制御機構, Poster presentation, May 2022
• Yingxi Chen; Kohji Nishimura; Yoshiharu Yamamoto; Takayuki Shimizu; Tatsuru Masuda, 第63回日本植物生理学会, Light regulated transcription start sites of heme oxygenase 1 in Arabidopsis thaliana, Oral presentation, Mar. 2022
• 有年統真; 清水隆之; 増田建, 第63回日本植物生理学会, 紅色光合成細菌におけるファージ様粒子GTAを介した遺伝子水平伝播の酸化ストレス応答性制御機構, Poster presentation, Mar. 2022
• 高柳なつ; 荒江星拓; 高橋洋和; 清水隆之; 堀口吾朗; 相田光宏; 深城英弘; 増田建; 大谷美沙都, 第85回日本植物学会, プラスチドシグナル依存的な側根形成制御におけるpre-mRNAスプライシングの役割, Oral presentation, Sep. 2021
• 清水隆之; 増田真二; 増田建, 第85回日本植物学会, 硫化水素による生理活性調節シグナル伝達機構の解明, Oral presentation, Sep. 2021
• 有年統真; 清水隆之; 増田建, 第11回日本光合成学会, 硫化水素応答性転写因子SqrRによる酸化ストレスに応答した細菌性ファージ様粒子GTAの制御機構, Poster presentation, May 2021
• Li Zijing; Takayuki Shimizu; Tatsuru Masuda, 第62回日本植物生理学会年会, nteraction of porphyrins with the loop region of Arabidopsis ABC transporter, Oral presentation, Mar. 2021
• Li Zijing; Takayuki Shimizu; Kohji Nishimura; 〇Tatsuru Masuda, 第62回日本植物生理学会, Biochemical characterization of Arabidopsis ABC transporter that can bind to heme, Oral presentation, Mar. 2021
• 清水隆之; 増田真二; 増田建, 第62回日本植物生理学会, 硫化水素依存的な生理活性調節におけるパースルフィド応答機構の分子基盤, Oral presentation, Mar. 2021
• 清水隆之; 増田真二; 増田建, 第61回日本植物生理学会, 硫化水素による生理活性調節におけるパースルフィド検知機構の分子基盤, Oral presentation, Mar. 2020
• 清水隆之; 増田建; 増田真二, 第10回日本光合成学会, 硫化水素依存的な光合成の制御因子SqrRを起点としたパースルフィド代謝経路の解析, Poster presentation, May 2019
• 清水隆之; 増田建; 増田真二, 第60回日本植物生理学会, 生理活性物質としての硫化水素のシグナル伝達機構に関与するパースルフィド代謝系の解析, Poster presentation, Mar. 2019
• Takayuki Shimizu; Jiangchuan Shen; Mingxu Fang; Yixiang Zhang; Koichi Hori; Jonathan; C. Trinidad; Carl E. Bauer; David P. Giedroc; Shinji Masuda, 16th International Symposium on Phototrophic Prokaryotes, Persulfide-responsive transcriptional repressor SqrR regulates sulfide-dependent photosynthesis, Poster presentation, Aug. 2018
• Takayuki Shimizu; Jiangchuan Shen; Mingxu Fang; Yixiang Zhang; Koichi Hori; Jonathan; C. Trinidad; Carl E. Bauer; David P. Giedroc; Shinji Masuda, The 1st Asia-Oceania International Congress on Photosynthesis, Persulfide-responsive transcriptional repressor SqrR regulates sulfide-dependent photosynthesis, Poster presentation, Aug. 2018
• 清水隆之; 増田建; 増田真二, 第9回日本光合成学会, 硫化水素依存的な光合成の制御因子SqrRはヘム応答性転写因子として機能する, Poster presentation, May 2018
• 清水隆之; 増田建; 増田真二, 第59回日本植物生理学会, 硫化水素依存的な光合成の制御因子SqrRはヘム応答性転写因子として機能する, Poster presentation, Mar. 2018
• 清水隆之; 増田真二, 第58回日本植物生理学会, 初期型光合成電子伝達の硫化水素依存的な制御に関与する転写因子SqrRに結合するテトラピロール環の生理的役割, Oral presentation, Mar. 2017
• Takayuki Shimizu; Jiangchuan Shen; David P. Giedroc; Carl E. Bauer; Shinji Masuda, International Congress on Photosynthesis Research 2016, Identification of;he;sulfide-responsive transcriptional factor SqrR regulating ancestral photosynthesis in purple bacteria, Poster presentation, Aug. 2016
• 清水隆之; Jiangchuan Shen; David; P. Giedroc; Carl E. Bauer; 増田真二, 第7回日本光合成学会, 初期型光合成電子伝達の制御に関与する硫化水素応答性転写因子の分子機構, Poster presentation, May 2016
• 清水隆之; 増田真二, 第57回日本植物生理学会, 初期型光合成電子伝達の硫化水素依存的な制御に関与する転写因子の同定, Oral presentation, Mar. 2016
• Takayuki Shimizu; Zhuo Cheng; Katsumi Matsuura; Shinji Masuda; Carl E. Bauer, 15th International Symposium on Phototrophic Prokaryotes, The purple bacterium Rubrivivax gelatinosus utilizes altered cis element spacing to promote redox sensing by the photosynthesis gene-specific transcription factor PpsR, Poster presentation, Aug. 2015
• 清水隆之; 増田真二, 第56回日本植物生理学会, 初期型光合成電子伝達を硫化水素依存的に誘導する因子の探索, Poster presentation, Mar. 2015
• 清水隆之; 増田真二, 第5回日本光合成学会, 紅色光合成細菌における硫化水素シグナル伝達系の順遺伝学的解析, Poster presentation, May 2014
• 清水隆之; Zhuo Cheng; 松浦克美; 増田真二; Carl E. Bauer, 第55回日本植物生理学会, レドックス応答性転写因子PpsRの光合成遺伝子発現制御におけるcis配列の重要性, Oral presentation, Mar. 2014
• 清水隆之; Zhuo Cheng; 松浦克美; 増田真二; Carl E. Bauer, 第4回日本光合成学会, 紅色光合成細菌Rubrivivax gelatinosusにおける光合成遺伝子の制御に関わる転写因子PpsRの性質, Poster presentation, May 2013
• 清水隆之; Zhuo Cheng; 増田真二; 松浦克美; Carl E. Bauer, 第54回日本植物生理学会, 紅色光合成細菌Rubrivivax gelatinosusにおける光合成遺伝子の酸化還元による転写調節, Oral presentation, Mar. 2013
• 高柳なつ; 荒江星拓; 清水隆之; 相田光宏; 深城英弘; 増田建; 大谷美沙都, 第46回分子生物学会, 植物の光合成活性はpre-mRNAスプライシング制御を介して側根形態に反映される, Oral presentation, Dec. 2023
• 清水隆之; オスマンズリナ; 増田建, 第65回日本植物生理学会, 硫化水素がシロイヌナズナの葉緑体形成における光合成器官の制御に与える影響, Poster presentation, 18 Mar. 2024
• Yingxi Chen; Kohji Nishimura; Mutsutomo Tokizawa; Yoshiharu; Y. Yamamoto; Yoshito Oka; Tomonao Matsushita; Kousuke Hanada; Kazumasa Shirai; Shoji Mano; Takayuki Shimizu; Tatsuru Masuda, 第65回日本植物生理学会, Cytosolic heme metabolism by alternative localization of heme oxygenase 1 in plant cells, Poster presentation, 17 Mar. 2024
• 清水隆之, 第3回原核光合成生物シンポジウム, 紅色光合成細菌をモデルとした 超硫黄分子シグナル制御システムの解析, Nominated symposium, 17 Mar. 2024
• 清水隆之, 第41回 植物生理若手の会, D&Iとどう付き合うか, Public discourse, 16 Mar. 2024

Awards

• 2016年度笹川科学研究奨励賞, 日本科学協会, 清水 隆之, Apr. 2017
• 第22回赤池ジャーナル賞, 東京工業大学, 清水 隆之, Mar. 2017
• 第7回日本光合成学会大会 優秀発表賞, 日本光合成学会, 清水 隆之, May 2016

Industrial Property Rights

• Patent right, 活性イオウ分子種に応答して遺伝子発現を制御するタンパク質, 増田 真二, 清水 隆之, 国立大学法人東京工業大学, 特願2017-015348, 31 Jan. 2017, 特開2018-121557, 09 Aug. 2018, j_global;url

  対象リソースIRI

Research Projects

• 国際共同研究加速基金(海外連携研究), 08 Sep. 2023, 31 Mar. 2027, 23KK0127, 環状化硫黄S8による超硫黄分子シグナル伝達の制御機構, 清水 隆之, 日本学術振興会, 科学研究費助成事業, 東京大学, 20800000, 16000000, 4800000, kaken

  対象リソースIRI
• 学術変革領域研究(A), Sep. 2021, Mar. 2026, 21H05271, Coinvestigator, 硫化水素によるシグナル伝達, 増田 真二、清水 隆之, 日本学術振興会, 科学研究費助成事業 学術変革領域研究(A), 東京工業大学, 81120000, 62400000, 18720000, kaken

  対象リソースIRI
• Apr. 2023, Mar. 2025, Principal investigator, 活性硫黄シグナルを考慮した新たなレドックスシグナル伝達概念の構築, 清水隆之, 公益財団法人 発酵研究所, 若手研究助成
• 若手研究, 01 Apr. 2021, 31 Mar. 2023, 21K15038, タンパク質の過イオウ化によるシグナル伝達機構の分子基盤, 清水 隆之, 日本学術振興会, 科学研究費助成事業 若手研究, 東京大学, 4680000, 3600000, 1080000, 本研究では、申請者が光合成細菌から新規に同定した活性イオウ分子種（Reactive sulfur species; RSS）応答性転写因子SqrRのRSS応答機構および本細菌のRSS代謝系の解析を通じ、RSSシグナル伝達の分子機構を理解することを目指している。 本研究は、これまでに申請者が明らかにしたSqrRのRSS応答機構を踏まえて、1）細胞内のSqrRに対するRSSによる安定な修飾の種類の解明、および、2）SqrRの修飾に関わるRSSの代謝経路の決定を行うことで、RSSによるシグナル伝達の分子機構の詳細解明を試みている。SqrRはRSSによって2つの保存されたシステイン残基の間で分子内テトラスルフィド結合が形成され、標的遺伝子のオペレーター領域へのDNA結合親和性が低下することがわかっている。この修飾について、細胞内のメジャーなRSSであるグルタチオンパースルフィド（GSSH）とシステインパースルフィド（CysSSH）に着目して、in vitroおよびin vivoでの解析を行った。 既にCysSSHによって安定的な修飾を受けることが示唆されていたが、SqrRのDNA結合親和性についてもCysSSHによる影響を強く受けることがわかった。また、SqrRの修飾に関わるRSS代謝系に関して、RSS産生酵素SQRが産生するCysSSHが、SqrRの修飾に寄与するRSSの主要合成経路であることが示唆されていたが、SQRがin vitroでもCysSSH合成活性を持つことを示した。, kaken

  対象リソースIRI
• 基盤研究(A), 01 Apr. 2018, 31 Mar. 2023, 18H03941, 光合成生物に広く保存された栄養欠乏時の脂質転換制御とその応用の分子基盤, 太田 啓之; 増田 建; 西村 浩二; 小林 康一; 堀 孝一; 粟井 光一郎; 下嶋 美恵; 清水 隆之, 日本学術振興会, 科学研究費助成事業 基盤研究(A), 東京工業大学, 43810000, 33700000, 10110000, 生物に必須の栄養元素の欠乏時には種々の応答が起こることが広く知られている。栄養元素の欠乏時には、トランスポーターの活性化などによる細胞外からの栄養元素の取り込みの促進や、栄養元素の細胞内でのリサイクルの活性化など、様々な応答機構が機能する。申請者らは植物の３大栄養元素の一つであるリンの欠乏時に起こる膜リン脂質からのリンの供給と糖脂質による代替を「リン欠乏時の膜脂質転換」と名付け、それに関わる脂質代謝遺伝子群やその重要性を明らかにしてきた。植物や藻類のリン欠乏時には、油脂が大量に蓄積することも見出し、光合成生物での油脂高生産系としても着目されている。また、その膜脂質転換に関わる酵素群や制御機構が光合成生物の進化過程で広く保存されていることも明らかにした。申請者は最近、その制御の根幹に関わると考えられる制御因子を初めて同定することに成功した。本研究では、この制御因子の機能と保存性の解明を柱としてリン欠乏時の脂質転換の仕組みの分子基盤を明らかにし、その応用展開の基盤確立を目的として研究を進めている。 平成30年度は特に、クラミドモナスで見出した脂質転換の制御因子についてその因子が直接ターゲットとしている遺伝子の同定、また本因子と共同して機能している他のクラミドモナス因子の同定を行った。, kaken

  対象リソースIRI
• Nov. 2021, Nov. 2022, Principal investigator, 超硫黄分子による生理活性調節のためのシグナル伝達機構の分子基盤, 清水隆之, 公益財団法人 住友財団, 基礎科学研究助成
• Oct. 2021, Sep. 2022, 水圏に生息する細菌における遺伝子拡散システムの分子基盤の解明（継続）, 清水 隆之, 公益財団法人 クリタ水・環境科学振興財団, 国内研究助成
• Apr. 2021, Mar. 2022, Coinvestigator, 自然プロセスを応用した生物・化学的水処理方法の開発を通じた持続可能な水質汚染問題の解決の検討, 甘蔗 寂樹、Aziz Muhammad、成田 大樹、Isabelle Giraudou、清水 隆之, 公益財団法人 国際科学技術財団, 日本国際賞平成記念研究助成
• Oct. 2020, Sep. 2021, 水圏に生息する細菌における遺伝子拡散システムの分子基盤の解明, 清水 隆之, 公益財団法人 クリタ水・環境科学振興財団, 国内研究助成
• Grant-in-Aid for Early-Career Scientists, 01 Apr. 2018, 31 Mar. 2021, 18K14650, Molecular analysis of persulfide dependent signaling involved in bioactive regulation, Shimizu Takayuki, Japan Society for the Promotion of Science, Grants-in-Aid for Scientific Research, The University of Tokyo, 4160000, 3200000, 960000, Hydrogen sulfide modulates important physiological processes and molecular species containing polysulfur that are called reactive sulfur species (RSS) are the actual signaling molecules. However, RSS signaling and metabolism are not fully understood. To elucidate this, I investigated biochemical properties of RSS sensor protein and RSS metabolic pathways. I revealed that the RSS sensor protein predominantly reacts with specific RSS. Moreover, RSS metabolic enzyme which is related to generation of its RSS was also identified. These results are important to understand the underlying mechanisms of RSS signaling., kaken

  対象リソースIRI
• Apr. 2019, Mar. 2021, Principal investigator, 細菌性ウイルス様粒子GTAによる硫化水素に応答した新規環境適応戦略, 清水 隆之, 公益財団法人 発酵研究所, 一般研究助成, 0, 0, 0, Competitive research funding
• Apr. 2018, Mar. 2019, Principal investigator, 新規生理活性物質である活性イオウ分子種（RSS）によるシグナル伝達の分子機構, 清水 隆之, 日本科学協会, 笹川科学研究助成, 0, 0, 0, Competitive research funding
• Apr. 2016, Mar. 2017, Principal investigator, 生体機能を制御する新物質硫化水素の細胞内ｼｸﾞﾅﾙ伝達の分子機構, 清水 隆之, 日本科学協会, 笹川科学研究助成, 0, 0, 0, Competitive research funding
• Oct. 2023, Mar. 2026, JPMJAX232C, Principal investigator, 超硫黄分子で切り拓くレドックスシグナルの新展開, 清水隆之, 国立研究開発法人科学技術振興機構（JST）, ACT-X, 奈良女子大学
• Oct. 2023, Mar. 2024, 超硫黄分子による光形態形成の制御機構, 東京農業大学 生物資源ゲノム解析センター, 「生物資源ゲノム解析拠点」共同研究
• Nov. 2022, Mar. 2023, 「先進ゲノム支援」（先進ゲノム解析研究推進プラットフォーム）支援課題採択, 文部科学省 （科学研究費助成事業 新学術領域研究『学術研究支援基盤形成』）
• Dec. 2023, Nov. 2024, Principal investigator, 超硫黄分子を利用した「おいしい」作物の効率的な栽培技術の開発基盤, 公益財団法人 ホクト生物科学振興財団, 研究奨励金
• Jan. 2024, Jan. 2025, Principal investigator, 超硫黄分子シグナルで開拓する新規レドックス応答機構, 公益財団法人千里ライフサイエンス振興財団, 岸本基金研究助成

Ⅲ．社会連携活動実績

１．公的団体の委員等（審議会、国家試験委員、他大学評価委員，科研費審査委員等）

• Mar. 2018, Mar. 2021, Others