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Position |
Associate Professor |
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Research Field |
Life Science / Applied biochemistry, Manufacturing Technology (Mechanical Engineering, Electrical and Electronic Engineering, Chemical Engineering) / Biofunction and bioprocess engineering, Nanotechnology/Materials / Bio chemistry |
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External Link |
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Graduating School 【 display / non-display 】
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Tokyo Institute of Technology Faculty of Life Science and Engineering Graduated
- 2001.3
Graduate School 【 display / non-display 】
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Tokyo Institute of Technology Graduate School, Division of Life Science and Engineering Doctor's Course Completed
- 2006.3
Campus Career 【 display / non-display 】
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KONAN UNIVERSITY Frontier of Institute for Biomolecular Engineering Research in Science and Technology Department of Nanobiochemistry Associate Professor
2016.4
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KONAN UNIVERSITY Frontier of Institute for Biomolecular Engineering Research in Science and Technology Department of Nanobiochemistry Lecturer
2009.4 - 2016.3
External Career 【 display / non-display 】
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岡山大学大学院自然科学研究科
2006.4 - 2009.3
Country：Japan
Professional Memberships 【 display / non-display 】
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Division of Biofunctional Chemistry, The Chemical Society of Japan
2012.9
Papers 【 display / non-display 】
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Guanidine modification improves functions of natural RNA-targeting alkaloids Reviewed International coauthorship
T. Endoh, S. Satpathi, Y. Chen, S. Matsumoto, T. Ohyama, P. Podbevšek, J. Plavec, K. Onizuka, F. Nagatsugi, N. Sugimoto
New J. Chem. 48 8529 - 8533 2024.5
Authorship：Lead author
DOI： 10.1039/D3NJ05833F
Other Link： https://pubs.rsc.org/en/content/articlelanding/2024/nj/d3nj05833f
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Nearest-neighbor parameters for the prediction of RNA duplex stability in diverse in vitro and cellular-like crowding conditions. Reviewed International journal
Saptarshi Ghosh, Shuntaro Takahashi, Dipanwita Banerjee, Tatsuya Ohyama, Tamaki Endoh, Hisae Tateishi-Karimata, Naoki Sugimoto
Nucleic acids research 51 ( 9 ) 4101 - 4111 2023.5
RNA performs various spatiotemporal functions in living cells. As the solution environments significantly affect the stability of RNA duplexes, a stability prediction of the RNA duplexes in diverse crowded conditions is required to understand and modulate gene expression in heterogeneously crowded intracellular conditions. Herein, we determined the nearest-neighbor (NN) parameters for RNA duplex formation when subjected to crowding conditions with an ionic concentration relevant to that found in cells. Determination of the individual contributions of excluded volume effect and water activity to each of the NN parameters in crowded environments enabled prediction of the thermodynamic parameters and their melting temperatures for plenty of tested RNA duplex formation in vitro and in cell with significant accuracy. The parameters reported herein will help predicting RNA duplex stability in different crowded environments, which will lead to an improved understanding of the stability-function relationship for RNAs in various cellular organelles with different molecular environments.
DOI： 10.1093/nar/gkad020
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Endogenous G-quadruplex-forming RNAs inhibit the activity of SARS-CoV-2 RNA polymerase. Invited Reviewed International journal
Tamaki Endoh, Shuntaro Takahashi, Naoki Sugimoto
Chemical communications (Cambridge, England) 59 ( 7 ) 872 - 875 2023.1
Authorship：Lead author
Replication of RNA viruses is catalysed by virus-specific polymerases, which can be targets of therapeutic strategies. In this study, we used a selection strategy to identify endogenous RNAs from a transcriptome library derived from lung cells that interact with the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2. Some of the selected RNAs weakened the activity of RdRp by forming G-quadruplexes. These results suggest that certain endogenous RNAs, which potentially form G-quadruplexes, can reduce the replication of viral RNAs.
DOI： 10.1039/d2cc05858h
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Cladogenetic Orthogonal Light-Up Aptamers for Simultaneous Detection of Multiple Small Molecules in Cells. Reviewed International coauthorship International journal
Tamaki Endoh, Jia-Heng Tan, Shuo-Bin Chen, Naoki Sugimoto
Analytical chemistry 95 ( 2 ) 976 - 985 2023.1
Authorship：Lead author, Corresponding author
Recent successes in construction of light-up RNA aptamers allowed fluorescence-based live-cell imaging of RNAs. In addition, light-up aptamers have been converted into signaling aptamers that enable fluorometric detection of small chemicals. To date, only a single target chemical has been detected at a time in cells. In this study, we selected cladogenetic orthogonal light-up aptamers that output three different colors from the RNA library having the same ligand binding core. Two of the three functioned in mammalian cells. These two aptamers, which fluoresce blue and green upon binding of cognate fluorogen, were converted into signaling aptamers. Using these signaling aptamers in combination with a previously described light-up aptamer with red fluorescence, we demonstrated simultaneous detection of multiple chemicals in living cells. The cladogenetic orthogonal light-up aptamers developed in this study and the simple strategy for rational designing of the signaling aptamers will provide innovative advances in the field of RNA-based bioimaging.
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High-temperature adaptation of an OsNRT2.3 allele is thermoregulated by small RNAs. Reviewed International coauthorship International journal
Yong Zhang, Hisae Tateishi-Karimata, Tamaki Endoh, Qiongli Jin, Kexin Li, Xiaoru Fan, Yingjun Ma, Limin Gao, Haiyan Lu, Zhiye Wang, Art E Cho, Xuefeng Yao, Chunming Liu, Naoki Sugimoto, Shiwei Guo, Xiangdong Fu, Qirong Shen, Guohua Xu, Luis Rafael Herrera-Estrella, Xiaorong Fan
Science advances 8 ( 47 ) eadc9785 2022.11
Climate change negatively affects crop yield, which hinders efforts to reach agricultural sustainability and food security. Here, we show that a previously unidentified allele of the nitrate transporter gene OsNRT2.3 is required to maintain high yield and high nitrogen use efficiency under high temperatures. We demonstrate that this tolerance to high temperatures in rice accessions harboring the HTNE-2 (high temperature resistant and nitrogen efficient-2) alleles from enhanced translation of the OsNRT2.3b mRNA isoform and the decreased abundance of a unique small RNA (sNRT2.3-1) derived from the 5' untranslated region of OsNRT2.3. sNRT2.3-1 binds to the OsNRT2.3a mRNA in a temperature-dependent manner. Our findings reveal that allelic variation in the 5' untranslated region of OsNRT2.3 leads to an increase in OsNRT2.3b protein levels and higher yield during high-temperature stress. Our results also provide a breeding strategy to produce rice varieties with higher grain yield and lower N fertilizer input suitable for a sustainable agriculture that is resilient against climate change.
Books and Other Publications 【 display / non-display 】
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核酸科学ハンドブック
杉本 直己, 日本核酸化学会, 講談社サイエンティフィク（ Role： Contributor , 第II部 核酸科学の最前線 15. リボスイッチ）
講談社 2020.12 （ ISBN:9784065207864 ）
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生体分子化学 基礎から応用まで
杉本直己、内藤昌信、橋詰蜂雄、高橋俊太郎、田中直毅、建石寿枝、遠藤玉樹、津本浩平、長門石曉、松原輝彦、上田実、朝山章一郎（ Role： Joint author , 第６章 セントラルドグマ）
講談社 2017.1 （ ISBN:978-4-06-156806-8 ）
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生体分子化学 : 基礎から応用まで = biomolecular chemistry
杉本 直己, 内藤 昌信, 橋詰 峰雄, 高橋 俊太郎, 田中 直毅, 建石 寿枝, 遠藤 玉樹, 津本 浩平, 長門石 曉, 松原 輝彦, 上田 実, 朝山 章一郎, 講談社サイエンティフィク
講談社 2017 （ ISBN:9784061568068 ）
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CSJカレントレビュー ここまで進んだバイオセンシング・イメージング 1分子から細胞、脳まで
遠藤玉樹、杉本直己（ Role： Joint author , 細胞内核酸化学 （pp 86-91））
化学同人 2012
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特定配列RNAの検出法 「新しいDNAチップの科学と応用」
遠藤玉樹（ Role： Sole author）
講談社サイエンティフィック 2007
、関根光雄 編集（講談社サイエンティフィック）、194-204 (2007)
Review Papers (Misc) 【 display / non-display 】
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Nucleic Acids Chemistry and Engineering: Special Issue on Nucleic Acid Conjugates for Biotechnological Applications
Tamaki Endoh, Eriks Rozners, Takashi Ohtsuki
APPLIED SCIENCES-BASEL 11 ( 8 ) 2021.4
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高橋俊太郎, 遠藤玉樹, BHOWMIK Sudipta, 杉本直己
高圧討論会講演要旨集 59th 159 2018.11
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分子クラウディング環境下におけるFMNリボスイッチ由来のアプタマードメインの分子挙動
遠藤玉樹, RODE B.Ambadas, RODE B.Ambadas, 杉本直己
日本RNA学会年会要旨集 20th 30 2018.7
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疾患関連分子の認識技術の革新 mRNA構造のダイナミクスを考慮した疾患関連遺伝子の発現制御技術の構築
遠藤 玉樹, 杉本 直己
生命科学系学会合同年次大会 2017年度 [3AW23 - 3] 2017.12
Publishing type：Research paper, summary (national, other academic conference) Publisher：生命科学系学会合同年次大会運営事務局
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Conformational Dynamics of mRNA in Gene Expression as New Pharmaceutical Target
T. Endoh and N. Sugimoto
The Chemical Record 17 817 - 832 2017.9
Authorship：Lead author Publishing type：Article, review, commentary, editorial, etc. (scientific journal) Publisher：Wiley
Presentations 【 display / non-display 】
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Nucleic Acids Chemistry beyond the Watson-Crick Double Helix (81) : Stability prediction of RNA duplexes under various molecular crowding in vitro and in cell
S. Ghosh, S. Takahashi, D. Banerjee, T. Ohyama, T. Endoh, H. Tateishi-Karimata, N. Sugimoto
日本化学会第103回春季年会 (東京理科大学野田キャンパス)
Event date： 2023.3
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脱ワトソン・クリックの核酸化学 (86): シグナリングライトアップアプタマーによる同一細胞内における複数化合物の多色検出
遠藤玉樹, J.-H. Tan, S.-B. Chen, 杉本直己
日本化学会第103回春季年会 (東京理科大学野田キャンパス)
Event date： 2023.3
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Nucleic Acids Chemistry beyond the Watson-Crick Double Helix (82) : Applications of nearest-neighbor parameters for RNA/DNA hybrid duplexes in the advancement of therapeutics
D. Banerjee, H. Tateishi-Karimata, S. Ghosh, S. Takahashi, T. Ohyama, T. Endoh, M. Toplishek, M. Trajkovski, J. Plavec, N. Sugimoto
日本化学会第103回春季年会 (東京理科大学野田キャンパス)
Event date： 2023.3
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天然アルカロイド化合物の化学的拡張によるRNA機能制御分子の開発
遠藤玉樹、S. Satpathi、Y. Chen、松本咲、大山達也、P. Podbevšek、J. Plavec、鬼塚和光、永次史、杉本直己
第22回東北大学多元物質科学研究所研究発表会 (東北大学片平さくらホール（オンライン参加）)
Event date： 2022.12
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環境応答性を示す非二重らせん核酸構造のスクリーニング法の構築
遠藤 玉樹, 奥田 修二郎, 凌 一葦, 建石 寿枝, 杉本 直己
第95回日本生化学会大会 (名古屋国際会議場)
Event date： 2022.11
Industrial property rights 【 display / non-display 】
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核酸の検出方法
小畠 英理、三重 正和、遠藤 玉樹
Announcement no：特開2006-055017
Country of applicant：Domestic
【特許コード】 P06P003883
Academic Awards Received 【 display / non-display 】
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バイオ関連化学シンポジウム 講演賞
2013.9 第7回バイオ関連化学シンポジウム
遠藤玉樹
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ISNAC Outstanding Oral Presentation Award for Young Scientist in 2012
2012.11 核酸化学シンポジウム組織委員会
遠藤玉樹
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The First International Symposium on Biofunctional Chemistry (ISBC2012) Poster Award
2012.11 日本化学会 生体機能関連化学部会
遠藤玉樹
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日本化学会第92春季年会 優秀講演賞（学術）
2012.3 日本化学会
遠藤玉樹
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遺伝子・デリバリー研究会 第8回シンポジウム 奨励賞
2008.5 遺伝子・デリバリー研究会
遠藤玉樹
Grant-in-Aid for Scientific Research 【 display / non-display 】
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いつ、どこで、どのように、核酸の高次構造は形成し機能するのかを予測する
2022.4 - 2027.3
JSPS Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research(S)
Authorship：Coinvestigator(s)
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Elucidation of the mechanism for dimensional response genome
2021.8 - 2024.3
JSPS Grants-in-Aid for Scientific Research Grant-in-Aid (B) (Tentative)
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生物種の分類枠組みを超えた網羅解析による多元応答深化の解明
2021 - 2023.3
JSPS Grants-in-Aid for Scientific Research Grant-in-Aid (B) (Tentative)
Authorship：Principal investigator
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細胞内で機能するRNA構造スイッチの最適化および合理的設計技術の構築
2019.4 - 2022.3
JSPS Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research(C)
本研究では、細胞内で効率良く機能するRNA構造スイッチを合理的に設計する技術基盤を確立する。
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Rational control of gene expressions by chemically regulating topologies of nucleic acid structures
2019.4 - 2022.3
JSPS Grants-in-Aid for Scientific Research Grant-in-Aid for Scientific Research(A)
Sugimoto Naoki
In this research project, gene regulation mechanisms based on nucleic acid structures, whose topological properties dynamically fluctuate depending on the molecular environment in cells, were investigated through quantitative analyses of their structures and stabilities. Physicochemical factors that affect the structures and stabilities of nucleic acids have been elucidated under molecular crowding conditions. Correlations between the nucleic acid structures and their functions to modulate gene expressions were also investigated. Furthermore, the construction of artificial molecules was demonstrated to apply to the regulation of nucleic acid functions based on the modulation of the dynamics and stabilities of their structures. The results of this research project are expected to provide great advances in not only the academic chemistry and biology of nucleic acids but also in a wide range of applied fields such as therapeutic, diagnostic, and medicinal applications.
Other External funds procured 【 display / non-display 】
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翻訳反応を調節し得るmRNA構造の熱安定性と構造特性との相関解析
2014.4 - 2015.3
ひょうご科学技術協会 ひょうご科学技術協会学術研究助成
Preferred joint research theme 【 display / non-display 】
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幹細胞分化制御 大学等の研究機関との共同研究を希望する。