Basic Information

Email Address

• Email Address

  kawaguchi.shinichi.7fkyoto-u.ac.jp

Professional Memberships

• 日本分子生物学会

Academic Degree

• 25 Mar. 1995

  大阪大学修士（理学）
• 25 Mar. 1998

  大阪大学博士（理学）

Academic Resume (Undergraduate School/Majors)

• 大阪大学, 理学部生物学科, 卒業

Research History

• From Apr. 2026, To Present

  Kyoto University, Graduate School of Biostudies, 特定講師
• From Apr. 2025, To Mar. 2026

  The University of Osaka, Graduate School of Frontier Biosciences, 助教
• From Oct. 2014, To Sep. 2024

  Osaka University, Graduate School of Frontier Biosciences, 助教
• From Jul. 2005, To Sep. 2014

  テマセク生命科学研究所（シンガポール）, リサーチフェロー
• From Apr. 2004, To Mar. 2005

  NECソフト株式会社, 主任研究員
• From Apr. 2002, To Mar. 2004

  日本学術振興会, 海外特別研究員
• From Sep. 2000, To Mar. 2004

  カーネギー研究所（米国）, ポスドク研究員
• From Oct. 1998, To Aug. 2000

  理化学研究所（播磨）, 基礎科学特別研究員
• From Apr. 1998, To Sep. 1998

  理化学研究所（和光）, 奨励研究員
• From Apr. 1995, To Mar. 1998

  日本学術振興会, 特別研究員（DC1）

ID,URL

• J-Global ID

  201901012347836480

researchmap URL

• https://researchmap.jp/1234567890abc

Research

Research Areas

• Life sciences, Molecular biology, 生化学
• Life sciences, Structural biochemistry, バイオインフォマティックス
• Life sciences, Developmental biology, 生殖細胞

Papers

• Transcriptional repression of reaper by Stand still ensures female germline development in Drosophila

  Masaya Matsui; Shinichi Kawaguchi; Toshie Kai

  PLOS Genetics, 05 Mar. 2026, Peer-reviewed

  
• Squash ensures Spindle-E-dependent heterotypic ping-pong amplification of piRNAs in the Drosophila ovary

  XIN XU; Iki Taichiro; Kawaguchi Shinichi; Kai Toshie

  bioRxiv, 15 Dec. 2025, Corresponding author

  
• Pathogenesis and potential therapeutic targets of trichorhinophalangeal syndrome; lessons obtained from animal studies.

  Naoya Saeki; Rinna Kanai; Sayuri Tatsuta; Shinichi Kawaguchi; Masatsune Itoh; Shinsuke Ohba; Makoto Abe

  Developmental dynamics : an official publication of the American Association of Anatomists, 25 Sep. 2025, Peer-reviewed

  
• Factories without walls: The molecular architecture and functions of non-membrane organelles in small RNA-guided genome protection

  Shinichi Kawaguchi; Wakana Isshiki; Toshie Kai

  Biochimica et Biophysica Acta (BBA) - General Subjects, Jun. 2025, Peer-reviewed, Lead author

  
• In silico screening by AlphaFold2 program revealed the potential binding partners of nuage-localizing proteins and piRNA-related proteins

  Kawaguchi Shinichi; Xu Xin; Soga Takashi; Yamaguchi Kenta; Kawasaki Ryuuya; Shimouchi Ryota; Date Susumu; Kai Toshie

  eLife, 22 Apr. 2025, Peer-reviewed, Lead author, Corresponding author

  
• HemK2 functions for sufficient protein synthesis and RNA stability through eRF1 methylation during Drosophila oogenesis

  Fengmei Xu; Ritsuko Suyama; Toshifumi Inada; Shinichi Kawaguchi; Toshie Kai

  Development, 15 Jul. 2024, Peer-reviewed, Corresponding author

  
• Tejas functions as a core component in nuage assembly and precursor processing in Drosophila piRNA biogenesis.

  Yuxuan Lin; Ritsuko Suyama; Shinichi Kawaguchi; Taichiro Iki; Toshie Kai

  The Journal of cell biology, 02 Oct. 2023, Peer-reviewed

  
• miRNA/siRNA-directed pathway to produce noncoding piRNAs from endogenous protein-coding regions ensures Drosophila spermatogenesis

  Taichiro Iki; Shinichi Kawaguchi; Toshie Kai

  Science Advances, 21 Jul. 2023, Peer-reviewed

  
• The Tudor Domain-Containing Protein, Kotsubu (CG9925), Localizes to the Nuage and Functions in piRNA Biogenesis in D. melanogaster.

  Lin-Xenia Lim; Wakana Isshiki; Taichiro Iki; Shinichi Kawaguchi; Toshie Kai

  Frontiers in molecular biosciences, 2022, Peer-reviewed

  
• Drosophila MARF1 ensures proper oocyte maturation by regulating nanos expression.

  Shinichi Kawaguchi; Mizuki Ueki; Toshie Kai

  PloS one, 2020, Peer-reviewed, Lead author

  
• Structural comparison between the open and closed forms of citrate synthase from Thermus thermophilus HB8.

  Eiji Kanamori; Shin-Ichi Kawaguchi; Seiki Kuramitsu; Tsutomu Kouyama; Midori Murakami

  Biophysics and physicobiology, 2015, Peer-reviewed

  
• Biosynthetic mode can determine the mechanism of protein quality control.

  Rupali Prasad; Shinichi Kawaguchi; Davis T W Ng

  Biochemical and biophysical research communications, 31 Aug. 2012, Peer-reviewed

  
• Cell biology. Sensing ER stress.

  Shinichi Kawaguchi; Davis T W Ng

  Science (New York, N.Y.), 30 Sep. 2011, Peer-reviewed, Lead author

  
• Interplay of substrate retention and export signals in endoplasmic reticulum quality control.

  Shinichi Kawaguchi; Chia-Ling Hsu; Davis T W Ng

  PloS one, 24 Nov. 2010, Peer-reviewed, Lead author

  
• A nucleus-based quality control mechanism for cytosolic proteins.

  Rupali Prasad; Shinichi Kawaguchi; Davis T W Ng

  Molecular biology of the cell, 01 Jul. 2010, Peer-reviewed

  
• Regulation of microtubule assembly and organization in mitosis by the AAA+ ATPase Pontin.

  Daniel Ducat; Shin-Ichi Kawaguchi; Hongbin Liu; John R Yates 3rd; Yixian Zheng

  Molecular biology of the cell, Jul. 2008, Peer-reviewed

  
• The EDEM and Yos9p families of lectin-like ERAD factors.

  Kazue Kanehara; Shinichi Kawaguchi; Davis T W Ng

  Seminars in cell & developmental biology, Dec. 2007, Peer-reviewed

  
• SnapShot: ER-associated protein degradation pathways.

  Shinichi Kawaguchi; Davis T W Ng

  Cell, 15 Jun. 2007, Peer-reviewed, Lead author

  
• Crystal structure of the conserved protein TTHA0727 from Thermus thermophilus HB8 at 1.9 A resolution: A CMD family member distinct from carboxymuconolactone decarboxylase (CMD) and AhpD.

  Kaori Ito; Ryoichi Arai; Emiko Fusatomi; Tomomi Kamo-Uchikubo; Shin-Ichi Kawaguchi; Ryogo Akasaka; Takaho Terada; Seiki Kuramitsu; Mikako Shirouzu; Shigeyuki Yokoyama

  Protein science : a publication of the Protein Society, May 2006, Peer-reviewed

  
• Expression and purification of recombinant human histones.

  Yoshinori Tanaka; Maki Tawaramoto-Sasanuma; Shinichi Kawaguchi; Tsutomu Ohta; Kinya Yoda; Hitoshi Kurumizaka; Shigeyuki Yokoyama

  Methods (San Diego, Calif.), May 2004, Peer-reviewed

  
• Characterization of a Drosophila centrosome protein CP309 that shares homology with Kendrin and CG-NAP.

  Shin-ichi Kawaguchi; Yixian Zheng

  Molecular biology of the cell, Jan. 2004, Peer-reviewed, Lead author

  
• Crystal structure of the CENP-B protein-DNA complex: the DNA-binding domains of CENP-B induce kinks in the CENP-B box DNA

  Y Tanaka; O Nureki; H Kurumizaka; S Fukai; S Kawaguchi; M Ikuta; J Iwahara; T Okazaki; S Yokoyama

  EMBO JOURNAL, Dec. 2001, Peer-reviewed

  
• Substrate recognition mechanism of thermophilic dual-substrate enzyme.

  H Ura; T Nakai; S I Kawaguchi; I Miyahara; K Hirotsu; S Kuramitsu

  Journal of biochemistry, Jul. 2001, Peer-reviewed

  
• Structure of the EMAPII domain of human aminoacyl-tRNA synthetase complex reveals evolutionary dimer mimicry.

  L Renault; P Kerjan; S Pasqualato; J Ménétrey; J C Robinson; S Kawaguchi; D G Vassylyev; S Yokoyama; M Mirande; J Cherfils

  The EMBO journal, 01 Feb. 2001, Peer-reviewed

  
• The crystal structure of the ttCsaA protein: an export-related chaperone from Thermus thermophilus.

  S Kawaguchi; J Müller; D Linde; S Kuramitsu; T Shibata; Y Inoue; D G Vassylyev; S Yokoyama

  The EMBO journal, 01 Feb. 2001, Peer-reviewed, Lead author

  
• Crystal structure of citrate synthase closed form from Thermus thermophilus HB8

  Murakami M.; Kanamori E.; Kawaguchi S.; Kuramitsu S.; Yokoyama S.; Kouyama T.

  Seibutsu Butsuri, 2001

  
• Free energy requirement for domain movement of an enzyme.

  J Ishijima; T Nakai; S Kawaguchi; K Hirotsu; S Kuramitsu

  The Journal of biological chemistry, 23 Jun. 2000, Peer-reviewed

  
• The molecular structure of hyperthermostable aromatic aminotransferase with novel substrate specificity from Pyrococcus horikoshii.

  I Matsui; E Matsui; Y Sakai; H Kikuchi; Y Kawarabayasi; H Ura; S Kawaguchi; S Kuramitsu; K Harata

  The Journal of biological chemistry, 18 Feb. 2000, Peer-reviewed

  
• Structural genomics projects in Japan.

  S Yokoyama; Y Matsuo; H Hirota; T Kigawa; M Shirouzu; Y Kuroda; H Kurumizaka; S Kawaguchi; Y Ito; T Shibata; M Kainosho; Y Nishimura; Y Inoue; S Kuramitsu

  Progress in biophysics and molecular biology, 2000, Peer-reviewed

  
• Structure of Thermus thermophilus HB8 aspartate aminotransferase and its complex with maleate.

  T Nakai; K Okada; S Akutsu; I Miyahara; S Kawaguchi; R Kato; S Kuramitsu; K Hirotsu

  Biochemistry, 23 Feb. 1999, Peer-reviewed

  
• The novel substrate recognition mechanism utilized by aspartate aminotransferase of the extreme thermophile Thermus thermophilus HB8.

  Y Nobe; S Kawaguchi; H Ura; T Nakai; K Hirotsu; R Kato; S Kuramitsu

  The Journal of biological chemistry, 06 Nov. 1998, Peer-reviewed

  
• Crystallization and preliminary X-ray characterization of aspartate aminotransferase from an extreme thermophile, Thermus thermophilus HB8.

  T Nakai; K Okada; S Kawaguchi; R Kato; S Kuramitsu; K Hirotsu

  Acta crystallographica. Section D, Biological crystallography, 01 Sep. 1998, Peer-reviewed

  
• Thermodynamics and molecular simulation analysis of hydrophobic substrate recognition by aminotransferases.

  S i Kawaguchi; S Kuramitsu

  The Journal of biological chemistry, 17 Jul. 1998, Peer-reviewed, Lead author

  
• Cloning and characterization of the uvrD gene from an extremely thermophilic bacterium, Thermus thermophilus HB8.

  Y Hiramatsu; R Kato; S Kawaguchi; S Kuramitsu

  Gene, 15 Oct. 1997, Peer-reviewed

  
• Enzyme flexibility: a new concept in recognition of hydrophobic substrates.

  S Kawaguchi; Y Nobe; J Yasuoka; T Wakamiya; S Kusumoto; S Kuramitsu

  Journal of biochemistry, Jul. 1997, Peer-reviewed, Lead author

  
• Separation of heat-stable proteins from Thermus thermophilus HB8 by two-dimensional electrophoresis.

  S Kawaguchi; S Kuramitsu

  Electrophoresis, Jun. 1995, Peer-reviewed, Lead author

  
• Homologous ligation: a novel cloning method.

  S Kawaguchi; S Kuramitsu

  Trends in genetics : TIG, Dec. 1994, Peer-reviewed, Lead author

  
• [Mechanism of enzyme reaction].

  S Kawaguchi; S Kuramitsu

  Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme, May 1994, Peer-reviewed, Lead author

  
• Construction of aminotransferase chimeras and analysis of their substrate specificity.

  K Miyazawa; S Kawaguchi; A Okamoto; R Kato; T Ogawa; S Kuramitsu

  Journal of biochemistry, Mar. 1994, Peer-reviewed

  

Misc.

• AlphaFold2を利用して、新規なタンパク質間相互作用ペアを発見する〜機能解析の新展開

  河口真一

  HPSC (High Performance Scientific Computing) News, Mar. 2024, Lead author, Corresponding author

  
• A thermophilic dual-substrate enzyme has a flexible substrate-binding site

  NAKAI Tadashi; MIYAHARA Ikuko; HIROTSU Ken; URA Hideaki; KAWAGUCHI Shin-ichi; KURAMITSU Seiki

  日本分子生物学会年会プログラム・講演要旨集, 01 Dec. 1998

  
• Dynamism of enzyme : Induced-fit by the hydrophobicity of the substrate.

  ISHIJIMA Jun; NAKAI Tadashi; KAWAGUCHI Shin-ichi; HIROTSU Ken; KURAMITSU Seiki

  日本分子生物学会年会プログラム・講演要旨集, 01 Dec. 1998

  
• Conformational change in extremely thermophilic bacterium aspartate aminotransferase.

  Nakai T.; Okada K.; Miyahara I.; Hirotsu K.; Kawaguchi S.; Kuramitsu S.

  Biophysics, 07 Sep. 1998

  
• Structural-biological whole cell project

  KURAMITSU Seiki; KAWAGUCHI Shinichi

  Bioscience & industry, 01 Sep. 1996

  
• 根粒菌由来の常温菌型および好熱菌型アミノ基転移酵素

  河口 真一; 倉光 成紀

  日本分子生物学会年会プログラム・講演要旨集, Aug. 1996

  
• 高度好熱菌Thermus thermophilus由来アスパラギン酸アミノ基転移酵素の疎水性基質認識機構の解析

  延 優子; 河口 真一; 加藤 龍一; 倉光 成紀

  日本分子生物学会年会プログラム・講演要旨集, Aug. 1996

  
• 高度好熱菌のDNAヘリカーゼのクローニング

  平松 佳晃; 加藤 龍一; 河口 真一; 倉光 成紀

  日本分子生物学会年会プログラム・講演要旨集, 01 Aug. 1996

  
• Crystal structure of aspartate aminotransferase from Thermus thermophilus

  岡田健吾; 中井忠志; 延優子; 河口真一; 岡本明弘; 加藤龍一; 倉光成紀; 広津建

  Nihon Kessho Gakkaishi, 1996

  
• ENZYMES THAT RECOGNIZE 2 DIFFERENT KINDS OF SUBSTRATE

  S KURAMITSU; S KAWAGUCHI; A OKAMOTO

  PROTEIN ENGINEERING, Sep. 1994

  

Presentations

• AlphaFoldを用いたタンパク質間相互作用のin silicoスクリーニング

  河口真一

  京都バイオ計測センター研究交流発表会2025, 02 Oct. 2025, Invited

  

External funds: Kakenhi

• Comprehensive mRNA base modification analysis reveals mechanisms of germline stem cell maintenance and differentiation

  Grant-in-Aid for Scientific Research (C)

  Basic Section 43060:System genome science-related

  Osaka University

  Shinichi Kawaguchi

  From 01 Apr. 2019, To 31 Mar. 2022, Project Closed

  エピトランスクリプトーム;塩基修飾;生殖幹細胞;ナノポア;Direct-mRNA-seq;ナノポア;ポリA鎖長

  https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-19K06628/

Academic, Social Contribution

Academic Contribution

• 第４８回日本分子生物学会マッチングイベント「AlphaFold界隈の人、この指とまれ！」

  Planning, management, etc., Panel moderator

  河口真一, From 04 Dec. 2025, To 04 Dec. 2025