Updated on 2024/10/03

Information

 

写真a

 
NUMATA TOMOYUKI
 
Organization
Faculty of Agriculture Department of Bioscience and Biotechnology Associate Professor
Graduate School of Systems Life Sciences Department of Systems Life Sciences(Concurrent)
School of Agriculture Department of Bioresource and Bioenvironment(Concurrent)
Graduate School of Bioresource and Bioenvironmental Sciences Department of Bioscience and Biotechnology(Concurrent)
Title
Associate Professor
Contact information
メールアドレス
Tel
0928024697
Profile
非コードRNAやそれと相互作用するタンパク質は遺伝子の発現調節をはじめ生命活動において重要な役割を担っている。主として非コードRNAの一種であり真正細菌の遺伝子発現を調節するリボスイッチや原核生物の獲得免疫として知られるCRISPR-Cas系の機能構造解析に興味をもって研究を進めている。これらの研究を通して、非コードRNAやリボ核タンパク質複合体が機能するしくみを明らかにするとともに、これら因子が原核生物の環境適応やストレス応答などに対していかにして関わっているのか解明することを目指す。教育においては、学部生に対して生物化学(遺伝子の発現、エネルギー産生)、大学院生に対して生物機能分子化学を担当している。
External link

Degree

  • Ph.D. in Agriculture

Research History

  • 東京工業大学 大学院生命理工学研究科 産業技術総合研究所 生物機能工学研究部門・バイオメディカル研究部門

Research Interests・Research Keywords

  • Research theme:Functional and Structural analysis of toxin-antitoxin system

    Keyword:Toxin, Antitoxin

    Research period: 2022.1

  • Research theme:Elucidation for the mechanism of action of riboswitch and its application for development of new drugs

    Keyword:Riboswitch, gene expression control, non-coding RNA, bacteria, development of new drugs

    Research period: 2016.1

  • Research theme:Functional and structural analysis of CRISPR-Cas effector complex

    Keyword:CRISPR, Cas, crRNA, effector complex, genome editing

    Research period: 2010.4

Awards

  • 平成26年度農芸化学奨励賞

    2014.3   日本農芸化学会  

  • 平成25年度科学技術分野の文部科学大臣表彰若手科学者賞

    2013.4   文部科学省  

  • 平成18年度手島記念研究賞

    2007.3   財団法人手島工業教育資金団  

Papers

  • Mechanistic analysis of Riboswitch Ligand interactions provides insights into pharmacological control over gene expression. International journal

    Shaifaly Parmar, Desta Doro Bume, Colleen M Connelly, Robert E Boer, Peri R Prestwood, Zhen Wang, Henning Labuhn, Krishshanthi Sinnadurai, Adeline Feri, Jimmy Ouellet, Philip Homan, Tomoyuki Numata, John S Schneekloth Jr

    Nature communications   15 ( 1 )   8173 - 8173   2024.9

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    Riboswitches are structured RNA elements that regulate gene expression upon binding to small molecule ligands. Understanding the mechanisms by which small molecules impact riboswitch activity is key to developing potent, selective ligands for these and other RNA targets. We report the structure-informed design of chemically diverse synthetic ligands for PreQ1 riboswitches. Multiple X-ray co-crystal structures of synthetic ligands with the Thermoanaerobacter tengcongensis (Tte)-PreQ1 riboswitch confirm a common binding site with the cognate ligand, despite considerable chemical differences among the ligands. Structure probing assays demonstrate that one ligand causes conformational changes similar to PreQ1 in six structurally and mechanistically diverse PreQ1 riboswitch aptamers. Single-molecule force spectroscopy is used to demonstrate differential modes of riboswitch stabilization by the ligands. Binding of the natural ligand brings about the formation of a persistent, folded pseudoknot structure, whereas a synthetic ligand decreases the rate of unfolding through a kinetic mechanism. Single round transcription termination assays show the biochemical activity of the ligands, while a GFP reporter system reveals compound activity in regulating gene expression in live cells without toxicity. Taken together, this study reveals that diverse small molecules can impact gene expression in live cells by altering conformational changes in RNA structures through distinct mechanisms.

    DOI: 10.1038/s41467-024-52235-3

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  • Characterization of two rice GH18 chitinases belonging to family 8 of plant pathogenesis-related proteins. International journal

    Jun Tanaka, Tomoya Takashima, Naojiro Abe, Tamo Fukamizo, Tomoyuki Numata, Takayuki Ohnuma

    Plant science : an international journal of experimental plant biology   111524 - 111524   2022.10

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    DOI: 10.1016/j.plantsci.2022.111524

  • Structure, mechanism, and phylogeny of LysM-chitinase conjugates specifically found in fern plants. International journal

    Yoshihito Kitaoku, Toki Taira, Tomoyuki Numata, Takayuki Ohnuma, Tamo Fukamizo

    Plant science : an international journal of experimental plant biology   321   111310 - 111310   2022.8

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    DOI: 10.1016/j.plantsci.2022.111310

  • GET pathway mediates transfer of mislocalized tail-anchored proteins from mitochondria to the ER. International journal

    Shunsuke Matsumoto, Suzuka Ono, Saori Shinoda, Chika Kakuta, Satoshi Okada, Takashi Ito, Tomoyuki Numata, Toshiya Endo

    The Journal of cell biology   221 ( 6 )   2022.6

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    DOI: 10.1083/jcb.202104076

  • Family D DNA polymerase interacts with GINS to promote CMG-helicase in the archaeal replisome. International journal

    Keisuke Oki, Mariko Nagata, Takeshi Yamagami, Tomoyuki Numata, Sonoko Ishino, Takuji Oyama, Yoshizumi Ishino

    Nucleic acids research   50 ( 7 )   3601 - 3615   2022.4

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    DOI: 10.1093/nar/gkab799

  • Genetic and biochemical characterizations of aLhr1 helicase in the thermophilic crenarchaeon sulfolobus acidocaldarius

    Shoji Suzuki, Norio Kurosawa, Takeshi Yamagami, Shunsuke Matsumoto, Tomoyuki Numata, Sonoko Ishino, Yoshizumi Ishino

    Catalysts   12 ( 1 )   2022.1

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    Language:Others   Publishing type:Research paper (scientific journal)  

    DOI: 10.3390/catal12010034

  • A conserved loop structure of GH19 chitinases assists the enzyme function from behind the core-functional region. International journal

    Daiki Kawamoto, Tomoya Takashima, Tamo Fukamizo, Tomoyuki Numata, Takayuki Ohnuma

    Glycobiology   2021.11

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1093/glycob/cwab117

  • A chemical probe based on the PreQ1 metabolite enables transcriptome-wide mapping of binding sites. International journal

    Sumirtha Balaratnam, Curran Rhodes, Desta Doro Bume, Colleen Connelly, Christopher C Lai, James A Kelley, Kamyar Yazdani, Philip J Homan, Danny Incarnato, Tomoyuki Numata, John S Schneekloth Jr

    Nature communications   12 ( 1 )   5856 - 5856   2021.10

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1038/s41467-021-25973-x

  • Minimal protein-only RNase P structure reveals insights into tRNA precursor recognition and catalysis. International journal

    Takamasa Teramoto, Takeshi Koyasu, Naruhiko Adachi, Masato Kawasaki, Toshio Moriya, Tomoyuki Numata, Toshiya Senda, Yoshimitsu Kakuta

    The Journal of biological chemistry   297 ( 3 )   101028 - 101028   2021.7

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1016/j.jbc.2021.101028

  • DNA polymerase D temporarily connects primase to the CMG-like helicase before interacting with proliferating cell nuclear antigen

    Keisuke Oki, Takeshi Yamagami, Mariko Nagata, Kouta Mayanagi, Tsuyoshi Shirai, Naruhiko Adachi, Tomoyuki Numata, Sonoko Ishino, Yoshizumi Ishino

    Nucleic Acids Research   49 ( 8 )   4599 - 4612   2021.5

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    DOI: 10.1093/nar/gkab243

  • Crystal structure and biochemical characterization of CJP38, a β-1,3-glucanase and allergen of Cryptomeria japonica pollen. Reviewed

    116   199 - 207   2019.11

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    DOI: 10.1016/j.molimm.2019.10.016

  • Synthetic ligands for PreQ1 riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure. Reviewed

    Nature communications   10 ( 1 )   1501   2019.4

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    Synthetic ligands for PreQ1 riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure.

    DOI: 10.1038/s41467-019-09493-3

  • Crystal Structures of Csm2 and Csm3 in the Type III-A CRISPR-Cas Effector Complex. Reviewed International journal

    Takeshita D, Sato M, Inanaga H, Numata T

    Journal of molecular biology   431 ( 4 )   748 - 763   2019.2

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    Crystal Structures of Csm2 and Csm3 in the Type III-A CRISPR-Cas Effector Complex.
    Clustered regularly interspaced short palindromic repeat (CRISPR) loci and CRISPR-associated (Cas) genes encode CRISPR RNAs (crRNA) and Cas proteins, respectively, which play important roles in the adaptive immunity system (CRISPR-Cas system) in prokaryotes. The crRNA and Cas proteins form ribonucleoprotein effector complexes to capture and degrade invading genetic materials with base complementarity to the crRNA guide sequences. The Csm complex, a type III-A effector complex, comprises five Cas proteins (Csm1-Csm5) and a crRNA, which co-transcriptionally degrades invading DNA and RNA. Here we report the crystal structures of the Staphylococcus epidermidis Csm2 (SeCsm2) and Thermoplasma volcanium Csm3 (TvCsm3) at 2.4- and 2.7-Å resolutions, respectively. SeCsm2 adopts a monomeric globular fold by itself, in striking contrast to the previously reported Thermotoga maritima Csm2, which adopted an extended conformation and formed a dimeric structure. We propose that the globular monomeric form is the bona fide structure of Csm2. TvCsm3 forms a filamentous structure in the crystals. The molecular arrangement of TvCsm3 is similar to that of the stacked Cmr4 proteins in the Cmr complex, suggesting the functionally relevant architecture of the present Csm3 structure. We constructed model structures of the Csm complex, which revealed that Csm3 binds the crRNA and periodically deforms the crRNA-target duplex by a similar mechanism to that of Cmr4 in the Cmr complex. The model and mutational analysis suggest that the conserved lysine residue of Csm2 is important for target RNA binding, and Csm2 stabilizes the active structure of the Csm complex to facilitate the reaction.

    DOI: 10.1016/j.jmb.2019.01.009

  • Structure and Enzymatic Properties of a Two-Domain Family GH19 Chitinase from Japanese Cedar (Cryptomeria japonica) Pollen Reviewed

    Tomoya Takashima, Tomoyuki Numata, Toki Taira, Tamo Fukamizo, Takayuki Ohnuma

    Journal of Agricultural and Food Chemistry   66 ( 22 )   5699 - 5706   2018.6

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    DOI: 10.1021/acs.jafc.8b01140

  • Metabolic and chemical regulation of tRNA modification associated with taurine deficiency and human disease Reviewed

    Kana Asano, Takeo Suzuki, Ayaka Saito, Fan-Yan Wei, Yoshiho Ikeuchi, Tomoyuki Numata, Ryou Tanaka, Yoshihisa Yamane, Takeshi Yamamoto, Takanobu Goto, Yoshihito Kishita, Kei Murayama, Akira Ohtake, Yasushi Okazaki, Kazuhito Tomizawa, Yuriko Sakaguchi, Tsutomu Suzuki

    Nucleic Acids Research   46 ( 4 )   1565 - 1583   2018.1

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    Language:Others   Publishing type:Research paper (scientific journal)  

    DOI: 10.1093/nar/gky068

  • Crystal structure and thermodynamic dissection of chitin oligosaccharide binding to the LysM module of chitinase-A from Pteris ryukyuensis Reviewed

    Takayuki Ohnuma, Toki Taira, Naoyuki Umemoto, Yoshihito Kitaoku, Morten Sorlie, Tomoyuki Numata, Tamo Fukamizo

    BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS   494 ( 3-4 )   736 - 741   2017.12

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1016/j.bbrc.2017.08.143

  • Chitin oligosaccharide binding to the lysin motif of a novel type of chitinase from the multicellular green alga, Volvox carteri Reviewed

    Yoshihito Kitaoku, Tamo Fukamizo, Tomoyuki Numata, Takayuki Ohnuma

    PLANT MOLECULAR BIOLOGY   93 ( 1-2 )   97 - 108   2017.1

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    DOI: 10.1007/s11103-016-0549-5

  • Mechanism of chitosan recognition by CBM32 carbohydrate-binding modules from a Paenibacillus sp IK-5 chitosanase/glucanase Reviewed

    Shoko Shinya, Shigenori Nishimura, Yoshihito Kitaoku, Tomoyuki Numata, Hisashi Kimoto, Hideo Kusaoke, Takayuki Ohnuma, Tamo Fukamizo

    BIOCHEMICAL JOURNAL   473 ( 8 )   1085 - 1095   2016.4

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    DOI: 10.1042/BCJ20160045

  • A class III chitinase without disulfide bonds from the fern, Pteris ryukyuensis: crystal structure and ligand-binding studies Reviewed

    Yoshihito Kitaoku, Naoyuki Umemoto, Takayuki Ohnuma, Tomoyuki Numata, Toki Taira, Shohei Sakuda, Tamo Fukamizo

    PLANTA   242 ( 4 )   895 - 907   2015.10

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    DOI: 10.1007/s00425-015-2330-4

  • Modulation of the transglycosylation activity of plant family GH18 chitinase by removing or introducing a tryptophan side chain Reviewed

    Naoyuki Umemoto, Takayuki Ohnuma, Takuo Osawa, Tomoyuki Numata, Tamo Fukamizo

    FEBS LETTERS   589 ( 18 )   2327 - 2333   2015.8

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    DOI: 10.1016/j.febslet.2015.07.018

  • Crystallization and preliminary X-ray diffraction analysis of the CRISPR-Cas RNA-silencing Cmr complex Reviewed

    Takuo Osawa, Hideko Inanaga, Tomoyuki Numata

    Acta Crystallographica Section F:Structural Biology Communications   71   735 - 740   2015.6

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1107/S2053230X15007104

  • Crystallization and preliminary X-ray diffraction analysis of the CRISPR-Cas RNA-silencing Cmr complex Reviewed

    Takuo Osawa, Hideko Inanaga, Tomoyuki Numata

    ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS   71 ( Pt 6 )   735 - 740   2015.6

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    DOI: 10.1107/S2053230X15007104

  • Crystal Structure of the CRISPR-Cas RNA Silencing Cmr Complex Bound to a Target Analog Reviewed

    Takuo Osawa, Hideko Inanaga, Chikara Sato, Tomoyuki Numata

    MOLECULAR CELL   58 ( 3 )   418 - 430   2015.5

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    DOI: 10.1016/j.molcel.2015.03.018

  • Crystal structures and inhibitor binding properties of plant class V chitinases: the cycad enzyme exhibits unique structural and functional features Reviewed

    Naoyuki Umemoto, Yuka Kanda, Takayuki Ohnuma, Takuo Osawa, Tomoyuki Numata, Shohei Sakuda, Toki Taira, Tamo Fukamizo

    PLANT JOURNAL   82 ( 1 )   54 - 66   2015.4

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    DOI: 10.1111/tpj.12785

  • Mechanisms of the tRNA wobble cytidine modification essential for AUA codon decoding in prokaryotes Reviewed

    Tomoyuki Numata

    BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY   79 ( 3 )   347 - 353   2015.3

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    Language:English  

    DOI: 10.1080/09168451.2014.975185

  • Crystal Structure of the Csm3-Csm4 Subcomplex in the Type III-A CRISPR-Cas Interference Complex Reviewed

    Tomoyuki Numata, Hideko Inanaga, Chikara Sato, Takuo Osawa

    JOURNAL OF MOLECULAR BIOLOGY   427 ( 2 )   259 - 273   2015.1

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1016/j.jmb.2014.09.029

  • Convergent evolution of AUA decoding in bacteria and archaea Reviewed

    Tsutomu Suzuki, Tomoyuki Numata

    RNA BIOLOGY   11 ( 12 )   1586 - 1596   2014.12

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    DOI: 10.4161/15476286.2014.992281

  • Crystal structure of a "loopless" GH19 chitinase in complex with chitin tetrasaccharide spanning the catalytic center Reviewed

    Takayuki Ohnuma, Naoyuki Umemoto, Takuya Nagata, Shoko Shinya, Tomoyuki Numata, Toki Taira, Tamo Fukamizo

    BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS   1844 ( 4 )   793 - 802   2014.4

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    DOI: 10.1016/j.bbapap.2014.02.013

  • Crystallization and preliminary X-ray diffraction analysis of an active-site mutant of 'loopless' family GH19 chitinase from Bryum coronatum in a complex with chitotetraose Reviewed

    Takayuki Ohnuma, Naoyuki Umemoto, Toki Taira, Tamo Fukamizo, Tomoyuki Numata

    ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS   69 ( Pt 12 )   1360 - 1362   2013.12

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1107/S1744309113028935

  • Crystal Structure of the Cmr2-Cmr3 Subcomplex in the CRISPR-Cas RNA Silencing Effector Complex Reviewed

    Takuo Osawa, Hideko Inanaga, Tomoyuki Numata

    JOURNAL OF MOLECULAR BIOLOGY   425 ( 20 )   3811 - 3823   2013.10

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1016/j.jmb.2013.03.042

  • Complete subsite mapping of a "loopful" GH19 chitinase from rye seeds based on its crystal structure Reviewed

    Takayuki Ohnuma, Naoyuki Umemoto, Kaori Kondo, Tomoyuki Numata, Tamo Fukamizo

    FEBS LETTERS   587 ( 16 )   2691 - 2697   2013.8

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    DOI: 10.1016/j.febslet.2013.07.008

  • Crystallization and preliminary X-ray diffraction analysis of the Cmr2-Cmr3 subcomplex in the CRISPR-Cas RNA-silencing effector complex Reviewed

    Takuo Osawa, Hideko Inanaga, Tomoyuki Numata

    ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS   69 ( Pt 5 )   585 - 587   2013.5

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1107/S1744309113011202

  • A novel transition-state analogue for lysozyme, 4-O-β-tri-N-acetylchitotriosyl moranoline, provided evidence supporting the covalent glycosyl-enzyme intermediate. Reviewed

    288 ( 9 )   6072 - 6082   2013.3

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1074/jbc.M112.439281

  • Crystal structure and chitin oligosaccharide-binding mode of a loopful' family GH19 chitinase from rye, Secale cereale, seeds Reviewed

    Takayuki Ohnuma, Tomoyuki Numata, Takuo Osawa, Hideko Inanaga, Yoko Okazaki, Shoko Shinya, Kaori Kondo, Tatsuya Fukuda, Tamo Fukamizo

    FEBS JOURNAL   279 ( 19 )   3639 - 3651   2012.10

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1111/j.1742-4658.2012.08723.x

  • Role of Tryptophan Residues in a Class V Chitinase from Nicotiana tabacum Reviewed

    Naoyuki Umemoto, Takayuki Ohnuma, Henri Urpilainen, Takanori Yamamoto, Tomoyuki Numata, Tamo Fukamizo

    BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY   76 ( 4 )   778 - 784   2012.4

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1271/bbb.110914

  • Structural basis of tRNA agmatinylation essential for AUA codon decoding Reviewed

    Takuo Osawa, Satoshi Kimura, Naohiro Terasaka, Hideko Inanaga, Tsutomu Suzuki, Tomoyuki Numata

    NATURE STRUCTURAL & MOLECULAR BIOLOGY   18 ( 11 )   1275 - U123   2011.11

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1038/nsmb.2144

  • Biogenesis of 2-agmatinylcytidine catalyzed by the dual protein and RNA kinase TiaS Reviewed

    Naohiro Terasaka, Satoshi Kimura, Takuo Osawa, Tomoyuki Numata, Tsutomu Suzuki

    NATURE STRUCTURAL & MOLECULAR BIOLOGY   18 ( 11 )   1268 - U116   2011.11

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1038/nsmb.2121

  • Crystallization and preliminary X-ray diffraction analysis of an archaeal tRNA-modification enzyme, TiaS, complexed with tRNA(Ile2) and ATP Reviewed

    Takuo Osawa, Hideko Inanaga, Satoshi Kimura, Naohiro Terasaka, Tsutomu Suzuki, Tomoyuki Numata

    ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS   67 ( Pt 11 )   1414 - 1416   2011.11

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1107/S1744309111034890

  • A class V chitinase from Arabidopsis thaliana: gene responses, enzymatic properties, and crystallographic analysis Reviewed

    Takayuki Ohnuma, Tomoyuki Numata, Takuo Osawa, Mamiko Mizuhara, Outi Lampela, Andre H. Juffer, Karen Skriver, Tamo Fukamizo

    PLANTA   234 ( 1 )   123 - 137   2011.7

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1007/s00425-011-1390-3

  • Mechanism for the Alteration of the Substrate Specificities of Template-Independent RNA Polymerases Reviewed

    Yukimatsu Toh, Daijiro Takeshita, Takashi Nagaike, Tomoyuki Numata, Kozo Tomita

    STRUCTURE   19 ( 2 )   232 - 243   2011.2

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    DOI: 10.1016/j.str.2010.12.006

  • Crystal structure and mode of action of a class V chitinase from Nicotiana tabacum Reviewed

    Takayuki Ohnuma, Tomoyuki Numata, Takuo Osawa, Mamiko Mizuhara, Kjell M. Varum, Tamo Fukamizo

    PLANT MOLECULAR BIOLOGY   75 ( 3 )   291 - 304   2011.2

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1007/s11103-010-9727-z

  • Crystallization and preliminary X-ray diffraction analysis of a class V chitinase from Nicotiana tabacum Reviewed

    Takayuki Ohnuma, Takuo Osawa, Tamo Fukamizo, Tomoyuki Numata

    ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS   66 ( Pt 12 )   1599 - 1601   2010.12

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1107/S1744309110039060

  • Agmatine-conjugated cytidine in a tRNA anticodon is essential for AUA decoding in archaea Reviewed

    Yoshiho Ikeuchi, Satoshi Kimura, Tomoyuki Numata, Daigo Nakamura, Takashi Yokogawa, Toshihiko Ogata, Takeshi Wada, Takeo Suzuki, Tsutomu Suzuki

    NATURE CHEMICAL BIOLOGY   6 ( 4 )   277 - 282   2010.4

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    DOI: 10.1038/NCHEMBIO.323

  • Mechanism for the definition of elongation and termination by the class II CCA-adding enzyme Reviewed

    Yukimatsu Toh, Daijiro Takeshita, Tomoyuki Numata, Shuya Fukai, Osamu Nureki, Kozo Tomita

    EMBO JOURNAL   28 ( 21 )   3353 - 3365   2009.11

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    DOI: 10.1038/emboj.2009.260

  • Crystallization and preliminary X-ray diffraction analysis of the tRNA-modification enzyme GidA from Aquifex aeolicus Reviewed

    Takuo Osawa, Hideko Inanaga, Tomoyuki Numata

    ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS   65 ( Pt 5 )   508 - 511   2009.5

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1107/S1744309109013591

  • Conserved Cysteine Residues of GidA Are Essential for Biogenesis of 5-Carboxymethylaminomethyluridine at tRNA Anticodon Reviewed

    Takuo Osawa, Koichi Ito, Hideko Inanaga, Osamu Nureki, Kozo Tomita, Tomoyuki Numata

    STRUCTURE   17 ( 5 )   713 - 724   2009.5

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    DOI: 10.1016/j.str.2009.03.013

  • Molecular basis for maintenance of fidelity during the CCA-adding reaction by a CCA-adding enzyme Reviewed

    Yukimatsu Toh, Tomoyuki Numata, Kazunori Watanabe, Daijiro Takeshita, Osamu Nureki, Kozo Tomita

    EMBO JOURNAL   27 ( 14 )   1944 - 1952   2008.7

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    DOI: 10.1038/emboj.2008.124

  • Snapshots of tRNA sulphuration via an adenylated intermediate Reviewed

    Tomoyuki Numata, Yoshiho Ikeuchi, Shuya Fukai, Tsutomu Suzuki, Osamu Nureki

    NATURE   442 ( 7101 )   419 - 424   2006.7

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    DOI: 10.1038/nature04896

  • Structural basis of RNA-dependent recruitment of glutamine to the genetic code Reviewed

    H Oshikane, K Sheppard, S Fukai, Y Nakamura, R Ishitani, T Numata, RL Sherrer, L Feng, E Schmitt, M Panvert, S Blanquet, Y Mechulam, D Soll, O Nureki

    SCIENCE   312 ( 5782 )   1950 - 1954   2006.6

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1126/science.1128470

  • A fifth protein subunit Ph1496p elevates the optimum temperature for the ribonuclease P activity from Pyrococcus horikoshii OT3 Reviewed

    H Fukuhara, M Kifusa, M Watanabe, A Terada, T Honda, T Numata, Y Kakuta, M Kimura

    BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS   343 ( 3 )   956 - 964   2006.5

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1016/j.bbrc.2006.02.192

  • Purification, crystallization and preliminary X-ray diffraction of SecDF, a translocon-associated membrane protein, from Thermus thermophilus Reviewed

    T Tsukazaki, H Mori, S Fukai, T Numata, A Perederina, H Adachi, H Matsumura, K Takano, S Murakami, T Inoue, Y Mori, T Sasaki, DG Vassylyev, O Nureki, K Ito

    ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS   62 ( Pt 4 )   376 - 380   2006.4

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1107/S1744309106007779

  • Crystallization and preliminary X-ray analysis of the tRNA thiolation enzyme MnmA from Escherichia coli complexed with tRNA(Glu) Reviewed

    T Numata, Y Ikeuchi, S Fukai, H Adachi, H Matsumura, K Takano, S Murakami, T Inoue, Y Mori, T Sasaki, T Suzuki, O Nureki

    ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY AND CRYSTALLIZATION COMMUNICATIONS   62 ( Pt 4 )   368 - 371   2006.4

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1107/S174430910600738X

  • Structural basis for sulfur relay to RNA mediated by heterohexameric TusBCD complex Reviewed

    T Numata, S Fukai, Y Ikeuchi, T Suzuki, O Nureki

    STRUCTURE   14 ( 2 )   357 - 366   2006.2

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1016/j.str.2005.11.009

  • Crystal structure of a ribonuclease P protein Ph1601p from Pyrococcus horikoshii OT3: An archaeal homologue of human nuclear ribonuclease P protein Rpp21 Reviewed

    Y Kakuta, Ishimatsu, I, T Numata, K Kimura, M Yao, Tanaka, I, M Kimura

    BIOCHEMISTRY   44 ( 36 )   12086 - 12093   2005.9

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1021/bi050738z

  • Crystal structure of archaeal ribonuclease P protein Ph1771 p from Pyrococcus horikoshii OT3: An archaeal homolog of eukaryotic ribonuclease P protein Rpp29 Reviewed

    T Numata, Ishimatsu, I, Y Kakuta, Tanaka, I, M Kimura

    RNA-A PUBLICATION OF THE RNA SOCIETY   10 ( 9 )   1423 - 1432   2004.9

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1261/rna.7560904

  • Amino acids conserved at the C-terminal half of the ribonuclease T2 family contribute to protein stability of the enzymes Reviewed

    K Kimura, T Numata, Y Kakuta, M Kimura

    BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY   68 ( 8 )   1748 - 1757   2004.8

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1271/bbb.68.1748

  • Crystal structure of the ribonuclease P protein Ph1877p from hyperthermophilic archaeon Pyrococcus horikoshii OT3 Reviewed

    H Takagi, M Watanabe, Y Kakuta, R Kamachi, T Numata, Tanaka, I, M Kimura

    BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS   319 ( 3 )   787 - 794   2004.7

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1016/j.bbrc.2004.05.055

  • Reconstitution of archaeal ribonuclease P from RNA and four protein components Reviewed

    Y Kouzuma, M Mizoguchi, H Takagi, H Fukuhara, M Tsukamoto, T Numata, M Kimura

    BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS   306 ( 3 )   666 - 673   2003.7

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1016/S0006-291X(03)01034-9

  • Crystal structures of the ribonuclease MC1 mutants N71T and N71S in complex with 5 '-GMP: Structural basis for alterations in substrate specificity Reviewed

    T Numata, A Suzuki, Y Kakuta, K Kimura, M Yao, Tanaka, I, Y Yoshida, T Ueda, M Kimura

    BIOCHEMISTRY   42 ( 18 )   5270 - 5278   2003.5

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    Language:English   Publishing type:Research paper (scientific journal)  

    DOI: 10.1021/bi034103g

  • Contribution of Gln9 and Phe80 to substrate binding in ribonuclease MC1 from bitter gourd seeds Reviewed

    T Numata, M Kimura

    JOURNAL OF BIOCHEMISTRY   130 ( 5 )   621 - 626   2001.11

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  • Amino acid residues in ribonuclease MC1 from bitter gourd seeds which are essential for uridine specificity Reviewed

    Tomoyuki Numata, Akio Suzuki, Min Yao, Isao Tanaka, Makoto Kimura

    Biochemistry   40   524 - 530   2001.1

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    Language:English   Publishing type:Research paper (scientific journal)  

    Amino acid residues in ribonuclease MC1 from bitter gourd seeds which are essential for uridine specificity

    DOI: 10.1021/bi002096f

  • Crystal structures of the ribonuclease MC1 from bitter gourd seeds, complexed with 2'-UMP or 3'-UMP, reveal structural basis for uridine specificity Reviewed

    Akio Suzuki, Min Yao, Isao Tanaka, Tomoyuki Numata, Singo Kikukawa, Nobuyuki Yamasaki, Makoto Kimura

    Biochem.Biophys.Res.Commun.   275   572 - 576   2000.8

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    Language:English   Publishing type:Research paper (scientific journal)  

    Crystal structures of the ribonuclease MC1 from bitter gourd seeds, complexed with 2'-UMP or 3'-UMP, reveal structural basis for uridine specificity

    DOI: 10.1006/bbrc.2000.3318

  • Expression and Mutational Analysis of Amino Acid Residues Involved in Catalytic Activity in a Ribonuclease MC1 from the Seeds of Bitter Gourd

    Numata Tomoyuki, Kashiba Tohru, Hino Madoka, FUNATSU Gunki, ISHIGURO Masatune, YAMASAKI Nobuyuki, KIMURA Makoto

    Bioscience, biotechnology, and biochemistry   64 ( 3 )   603 - 605   2000.3

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    Expression and Mutational Analysis of Amino Acid Residues Involved in Catalytic Activity in a Ribonuclease MC1 from the Seeds of Bitter Gourd
    The ribonuclease MC1 (RNase MC1) from seeds of bitter gourd (Momordica charantia) consists of 190 amino acids and belongs to the RNase T2 family, including fungal RNase typified by RNase Rh from Rhizopus niveus. We expressed RNase MC1 in Escherichia coli cells and made use of site-directed mutagenesis to identify essential amino acid residues for catalytic activity. Mutations of His34 and His88 to Ala completely abolished the enzymatic activity, and considerable decreases in the enzymatic activity were observed in cases of mutations of His83,Glu84,and Lys87,when yeast RNA was used as a substrate. Kinetic parameters for the enzymatic activity of the mutants of His83,Glu84,and Lys87 were analyzed using a dinucleoside monophosphate CpU. K_m values for the mutants were approximately like that for wild-type, while k_<cat> values were decreased by about 6 to 25-fold. These results suggest that His34,His83,Glu84,Lys87,and His88 in RNase MC1 may be involved in the catalytic function. These observation suggests that RNase MC1 from a plant catalyzes RNA degradation in a similar manner to that of fungal RNases.

    DOI: 10.1271/bbb.64.603

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Books

  • 入門 構造生物学 -放射光X線と中性子で最新の生命現象を読み解く-

    富田 耕造, 沼田 倫征( Role: Joint author)

    共立出版  2010.4 

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    Responsible for pages:第4章 生命現象の理解に迫る構造生物学研究 4.3 翻訳 pp 111-119   Language:Japanese   Book type:Scholarly book

Presentations

  • 新規小型CRISPR-Cas12の機能構造解析

    田中葵、亀甲理、石野園子、石野良純、松本俊介、沼田倫征

    第96回日本生化学会大会  2023.10 

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    Event date: 2023.10 - 2023.11

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:福岡国際会議場・マリンメッセ福岡B館 福岡市   Country:Japan  

  • オーキシンデグロン法を用いた出芽酵母におけるペルオキシソーム膜タンパク質の局在解析

    小暮佳希、小野鈴花、岡田悟、沼田倫征、遠藤斗志也、松本俊介

    第96回日本生化学会大会  2023.10 

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    Event date: 2023.10 - 2023.11

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:福岡国際会議場・マリンメッセ福岡B館 福岡市   Country:Japan  

  • 超好熱性アーキアArchaeoglobus fulgidus由来III-B型CRISPR-Cas系の機能に関する研究

    大内凌、松本俊介、沼田倫征

    第96回日本生化学会大会  2023.10 

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    Event date: 2023.10 - 2023.11

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:福岡国際会議場・マリンメッセ福岡B館 福岡市   Country:Japan  

  • ミトコンドリア外膜上の品質管理に関わるAAA-ATPアーゼMsp1の機能構造解析

    稲本大輝、沼田倫征、遠藤斗志也、松本俊介

    第96回日本生化学会大会  2023.10 

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    Event date: 2023.10 - 2023.11

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:福岡国際会議場・マリンメッセ福岡B館 福岡市   Country:Japan  

  • メタゲノムから発見した新規な小型Casタンパク質の機能構造解析

    吉村萌由、中野華歩、亀甲理、石原一輝、石野園子、石野良純、松本俊介、沼田倫征

    第96回日本生化学会大会  2023.10 

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    Event date: 2023.10 - 2023.11

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:福岡国際会議場・マリンメッセ福岡B館 福岡市   Country:Japan  

  • Thermococcus kodakarensis由来DNA末端切断タンパク質複合体の機能構造解析

    宇田敬史朗、山上健、石野園子、松本俊介、中島崇、石野良純、沼田倫征

    令和5年度日本結晶学会年会  2023.10 

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    Event date: 2023.10

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:宇部市文化会館・山口大学常盤キャンパス 山口市   Country:Japan  

  • T-boxリボスイッチを基盤とした半人工アミノアシル化リボザイムの構造と機能

    香川尊、安部紘平、石田啓、Wei Lu、菅裕明、寺坂尚紘、Adrian Ferré-D'Amaré、沼田倫征

    令和5年度日本結晶学会年会  2023.10 

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    Event date: 2023.10

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:宇部市文化会館・山口大学常盤キャンパス 山口市   Country:Japan  

  • 超好熱性アーキア由来ミスマッチ修復酵素Endonuclease MSとPCNAとの複合体の機能構造解析

    井戸川倫子、水島淑華、中島崇、石野園子、山上健、松本俊介、石野良純、沼田倫征

    令和5年度日本結晶学会年会  2023.10 

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    Event date: 2023.10

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:宇部市文化会館・山口大学常盤キャンパス 山口市   Country:Japan  

  • トランスポゾンの転移に関わるCRISPR-Casエフェクターの機能・構造解析とゲノム編集技術への応用

    石原一輝、松本俊介、沼田倫征

    第45回蛋白質と酵素の構造と機能に関する九州シンポジウム  2023.9 

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    Event date: 2023.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:ANAホリデイ・インリゾート宮崎 宮崎市   Country:Japan  

  • 超好熱性アーキアThermococcus kodakarensis由来ファミリーD DNAポリメラーゼ-プライマーゼ複合体の構造解析

    廣瀬優海、沖啓輔、山上健、松本俊介、石野園子、石野良純、沼田倫征

    第45回蛋白質と酵素の構造と機能に関する九州シンポジウム  2023.9 

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    Event date: 2023.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:ANAホリデイ・インリゾート宮崎 宮崎市   Country:Japan  

  • アーキアにおけるミスマッチ修復酵素の進化的な考察

    石野園子、山上健、松尾桃子、沼田倫征、石野良純

    第35回⽇本Archaea研究会  2023.6 

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    Event date: 2023.6 - 2023.7

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:八王子市学園都市センター 八王子市   Country:Japan  

  • PolD–primase interaction in the replisome of Thermococcus kodakarensis

    第35回⽇本Archaea研究会  2023.6 

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    Event date: 2023.6 - 2023.7

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:八王子市学園都市センター 八王子市   Country:Japan  

  • AAA-ATPアーゼMsp1による誤配送タンパク質の認識、膜引き抜き機構の解析

    稲本大輝、遠藤斗志也、沼田倫征、松本俊介

    令和5年度日本生化学会九州支部例会  2023.6 

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    Event date: 2023.6

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:長崎大学 長崎市   Country:Japan  

  • 超好熱性アーキアThermococcus kodakarensis由来NurA-HerA複合体の構造解析

    宇田敬史朗、沼田倫征、石野園子、山上健、松本俊介、中島崇、石野良純

    第23回極限環境生物学会年会  2022.11 

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    Event date: 2022.11

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:東洋大学 川越キャンパス   Country:Japan  

  • 温泉由来新規Cas9の機能構造解析

    亀甲理、松本俊介、石野園子、松本裕之、野口真大、沼田倫征、石野良純

    第96回日本生化学会大会  2023.10 

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    Event date: 2022.10 - 2023.11

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:福岡国際会議場・マリンメッセ福岡B館 福岡市   Country:Japan  

  • メタゲノムから発見した新規な小型Casタンパク質の機能構造解析

    吉村萌由,中野華歩,松本俊介,石野園子,石野良純,沼田倫征

    日本農芸化学会2022年度西日本支部大会  2022.9 

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    Event date: 2022.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:長崎大学文教キャンパス 環境科学部・教養教育講義棟   Country:Japan  

  • 超好熱性アーキアThermococcus kodakarensis由来エンドヌクレアーゼⅣの調製法の確立と立体構造解析

    佐藤星賢,石野園子,松本俊介,中島崇,山上健,石野良純,沼田倫征

    日本農芸化学会2022年度西日本支部大会  2022.9 

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    Event date: 2022.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:長崎大学文教キャンパス 環境科学部・教養教育講義棟   Country:Japan  

  • 温泉試料メタゲノムから見出された新規Casタンパク質の機能解析

    亀甲理,松本俊介,石野園子,松本裕之,野口真大,沼田倫征,石野良純

    日本農芸化学会2022年度西日本支部大会  2022.9 

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    Event date: 2022.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:長崎大学文教キャンパス 環境科学部・教養教育講義棟   Country:Japan  

  • III型CRISPR-Casエフェクターの構造と機能

    沼田倫征

    第34回日本Archaea研究会  2022.7 

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    Event date: 2022.7

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:九州大学 西新プラザ 大会議室   Country:Japan  

  • Vibrio parahaemolyticusに由来するトランスポゾンの配列特異的なDNA転移に関する研究

    石原一輝、石野園子、石野良純、沼田倫征

    第59回化学関連支部合同九州大会  2022.7 

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    Event date: 2022.7

    Language:Japanese   Presentation type:Oral presentation (general)  

    Country:Japan  

    The CRISPR-associated transposons are transferred in a sequence-specific manner of the CRISPR RNA (crRNA). However, the transfer mechanism and physiological role of these transposons remain to be elucidated. Here, we reconstituted the in vivo transposition using the factors from Vibrio parahaemolyticus and showed that the transposons were transferred into the genome of Escherichia coli via crRNA-guided targeting.

  • Vibrio parahaemolyticusが持つCASTによるDNA転移の分子機構の解析

    石原一輝、石野園子、石野良純、沼田倫征

    令和4年度日本生化学会 九州支部例会  2022.6 

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    Event date: 2022.6

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:オンライン   Country:Japan  

  • Structural and functional analysis of the interaction between family D-DNA polymerase and CMG-like helicase in the replisome of Thermococcus kodakarensis.

    Keisuke Oki, Mariko Nagata, Takeshi Yamagami, Tomoyuki Numata, Sonoko Ishino, Takuji Oyama, and Yoshizumi Ishino.

    2021.12 

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    Event date: 2021.12

    Language:Japanese   Presentation type:Oral presentation (general)  

    Country:Japan  

  • 超好熱性アーキアPyrococcus furiosus由来のCMG 様複製ヘリカーゼ複合体の構造と機能

    佐々木敏貴、沖 啓輔、松本俊介、真柳浩太、山上 健、石野園子、沼田倫征、石野良純

    第45回日本分子生物学会年会  2021.12 

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    Event date: 2021.12

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:パシフィコ横浜、横浜市(ハイブリッド)   Country:Japan  

  • Thermococcus kodakarensisのミスマッチ特異的ヌクレアーゼEndoMSに結合するタンパク質の発見

    松尾桃子、山上 健、石野園子、沼田倫征、石野良純

    第45回日本分子生物学会年会  2021.12 

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    Event date: 2021.12

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:パシフィコ横浜、横浜市(ハイブリッド)   Country:Japan  

  • Thermococcus kodakarensisのDNA複製複合体レプリソームの機能的構造変換機構

    沖 啓輔、永田麻梨子、山上 健、真柳 浩太、白井 剛、大山拓次、安達成彦、沼田倫征、松本俊介、石野園子、石野良純

    極限環境生物学会2021年度(第22回)年会  2021.11 

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    Event date: 2021.11

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:オンライン   Country:Japan  

  • 超好熱性アーキアThermococcus kodakarensisのSMCタンパク質の機能解析

    梶川涼夏、石野園子、山上 健、沼田倫征、石野良純

    第44回日本分子生物学会年会  2020.12 

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    Event date: 2020.12

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:オンライン   Country:Japan  

  • 超好熱性アーキアThermococcus kodakarensisのDNAトポイソメラーゼVIの調製確立と性質解析

    池西智憲、石野園子、山上 健、沼田倫征、石野良純

    第44回日本分子生物学会年会  2020.12 

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    Event date: 2020.12

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:オンライン   Country:Japan  

  • 超好熱性アーキアThermococcus kodakarensisはoriC依存のDNA複製能を有するか?

    宮元梨紅、石野園子、松見理恵、山上 健、沼田倫征、石野良純

    第44回日本分子生物学会年会  2020.12 

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    Event date: 2020.12

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:オンライン   Country:Japan  

  • 超好熱性アーキアにおける損傷塩基修復経路に関する研究

    原田明佳、永田麻梨子、沖 啓輔、松見理恵、金井 保、跡見晴幸、沼田倫征、石野園子、石野良純

    極限環境生物学会2020年度(第21回)年会  2020.10 

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    Event date: 2020.10 - 2020.11

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:オンライン   Country:Japan  

  • アーキアのミスマッチ修復酵素Endonuclease MSと酸化損傷修復酵素8-oxoguanine glycosylaseによるDNA修復機構の研究

    市川貴大、佐々木琢也、山上 健、沼田倫征、石野園子、石野良純

    極限環境生物学会2020年度(第21回)年会  2019.10 

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    Event date: 2020.10

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:オンライン   Country:Japan  

  • 超好熱性アーキアThermococcus kodakarensisのDNAトポイソメラーゼVIの調製法確立と性質解明

    池西智憲、石野園子、山上健、沼田倫征、石野良純

    令和2年度 日本生化学会九州支部例会  2020.5 

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    Event date: 2020.5

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:福岡   Country:Japan  

  • 超好熱性アーキアThermococcus kodakarensisのSMCタンパク質の機能解析

    梶川涼夏、石野園子、山上健、沼田倫征、石野良純

    令和2年度 日本生化学会九州支部例会  2019.5 

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    Event date: 2020.5

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:福岡   Country:Japan  

  • 超好熱性アーキアThermococcus kodakarensisはoriC依存のDNA複製開始能を有するか?

    宮元梨紅、石野園子、松見理恵、山上健、沼田倫征、石野良純

    令和2年度 日本生化学会九州支部例会  2020.5 

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    Event date: 2020.5

    Language:Japanese  

    Venue:福岡   Country:Japan  

  • 超好熱性アーキアMethanopyrus kandleri由来ファミリー D DNAポリメラーゼの生化学的解析

    吉田直人、沖 啓輔、松見理恵、石野園子、沼田倫征、山上 健、石野良純

    第42回日本分子生物学会年会  2019.12 

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    Event date: 2019.12

    Language:Japanese  

    Venue:福岡   Country:Japan  

  • PolD上での相互作用因子スウィッチングによるアーキア特有のレプリソーム機能変換機構の提唱

    沖 啓輔、山上 健、永田麻梨子、真柳浩太、沼田倫征、石野園子、石野良純

    第42回日本分子生物学会年会  2019.12 

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    Event date: 2019.12

    Language:Japanese  

    Venue:福岡   Country:Japan  

  • 好熱性アーキアにおけるDNA修復に働く新規ヘリカーゼ様タンパク質の機能解析

    鈴木匠爾、黒沢則夫、山上 健、沼田倫征、石野園子、石野良純

    第42回日本分子生物学会年会  2019.12 

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    Event date: 2019.12

    Language:Japanese  

    Venue:福岡   Country:Japan  

  • クレンアーキオタにおいてレプリソームを構成する未知タンパク質の探索

    瀬戸口勇登、山上 健、沖 啓輔、沼田倫征、石野園子、石野良純

    第42回日本分子生物学会年会  2019.12 

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    Event date: 2019.12

    Language:Japanese  

    Venue:福岡   Country:Japan  

  • 損傷塩基特異的Endonuclease MSによる二本鎖切断末端の可能な構造変換機構

    峯 渉、山上 健、沼田倫征、石野園子、石野良純

    第42回日本分子生物学会年会  2019.12 

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    Event date: 2019.12

    Language:Japanese  

    Venue:福岡   Country:Japan  

  • アーキアのミスマッチ修復酵素Endonuclease MSとの相互作用因子として見出され た8-Oxoguanine glycosylaseの機能解析

    市川貴大、佐々木琢也、山上 健、沼田倫征、石野園子、石野良純

    第42回日本分子生物学会年会  2019.12 

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    Event date: 2019.12

    Language:Japanese  

    Venue:福岡   Country:Japan  

  • 超好熱性アーキア由来ファミリー B3 DNAポリメラーゼの性質比較

    田中志門、石野園子、沼田倫征、山上 健、石野良純

    第42回日本分子生物学会年会  2019.12 

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    Event date: 2019.12

    Language:Japanese  

    Venue:福岡   Country:Japan  

  • The nucS homologs in the genomes of hyperthermophilic archaea encode active mismatch-specific endonuclease, EndoMS International conference

    Takahiro Ichikawa, Enzo Petracco, Hanae Kudo, Takeshi Yamagami, Tomoyuki Numata, Yoshizumi Ishino, and Sonoko Ishino

    15th International Congress on Thermophiles 2019  2019.9 

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    Event date: 2019.9

    Language:English  

    Country:Japan  

  • Crystal structure of the type III CRISPR-Cas Cmr complex bound to a target analog International conference

    Tomoyuki Numata

    15th International Congress on Thermophiles 2019  2019.9 

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    Event date: 2019.9

    Language:English   Presentation type:Oral presentation (general)  

    Country:Japan  

  • Interactions of helicase, DNA polymerase, and primase to form functional replisome in the hyperthermophilic archaeon, Thermococcus kodakarensis International conference

    Keisuke Oki, Mariko Nagata, Sonoko Ishino, Takeshi Yamagami, Tomoyui Numata, Kouta Mayanagi, and Yoshizumi Ishino

    15th International Congress on Thermophiles 2019  2019.9 

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    Event date: 2019.9

    Language:English  

    Country:Japan  

  • Study on diversity of mismatch repair system in archaea International conference

    Wataru Mine, Hanae Kudo, Takeshi Yamagami, Tomoyuki Numata, Patrick Forterre, Mart Krupovic, Yoshizumi Ishino, and Sonoko Ishino

    15th International Congress on Thermophiles 2019  2019.9 

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    Event date: 2019.9

    Language:English  

    Country:Japan  

  • Reconstitution of endonuclease Q-mediated and endonuclease V-mediated repair pathways for deaminated base repair in the hyperthermophilic archaeon, Thermococcus kodakarensis International conference

    Meika Harada, Mariko Nagata, Keisuke Oki, Rie Matsumi, Tamotsu Kanai, Haruyuki Atomi, Tomoyuki Numata, Miyako Shiraishi, Sonoko Ishino, and Yoshizumi Ishino

    15th International Congress on Thermophiles 2019  2019.9 

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    Event date: 2019.9

    Language:English  

    Country:Japan  

  • アーキアの損傷塩基修復経路の生化学的、遺伝学的研究

    原田明佳、永田麻梨子、沖啓輔、松見理恵、金井保、跡見晴幸、沼田倫征、石野園子、石野良純

    第42回日本分子生物学会年会  2019.12 

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    Event date: 2018.12

    Language:Japanese  

    Venue:福岡   Country:Japan  

  • Chemical and structural insights into developing synthetic ligands for a PreQ1 riboswitch International conference

    Connelly, C., Numata, T., Boer, R., Moon, M., Sinniah, R., Ferre-D'Amare, A. and Schneekloth, J.

    256th National Meeting and Exposition of the American-Chemical-Society (ACS) - Nanoscience, Nanotechnology and Beyond  2018.8 

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    Event date: 2018.8

    Language:English   Presentation type:Oral presentation (general)  

    Country:United States  

  • Structure-guided discovery of small molecules targeting the PreQ1 riboswitch International conference

    23rd Annual Meeting of the RNA Society  2018.6 

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    Event date: 2018.5 - 2018.6

    Language:English  

    Country:United States  

  • Structure-guided discovery of small molecules targeting the PreQ1 riboswitch International conference

    Sixteenth Annual NHLBI DIR Research Retreat  2018.4 

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    Event date: 2018.4

    Language:English  

    Country:United States  

  • Involvement of sulfur relay system in the biogenesis of cyclic N6-threonylcarbamoyladenosine (ct6A) of tRNA International conference

    Kenjyo Miyauchi, Takuya Sakashita, Tomoyuki Numata and Tsutomu Suzuki

    The 21st Annual Meeting of the RNA Society  2016.6 

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    Event date: 2016.6 - 2016.7

    Language:English  

    Country:Japan  

  • RNAサイレンシングに関わるCRISPR-Cas系Cmr複合体の作動原理の解明 Invited

    沼田倫征

    微生物学の新たな発展、ゲノムから機能・実用に関する九州シンポジウム  2015.12 

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    Event date: 2015.12

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:宮崎   Country:Japan  

  • RNAのサイレンシングを誘導するCRISPR-Cas系複合体の作動原理 Invited

    沼田倫征

    第34回アグリバイオセミナー  2015.12 

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    Event date: 2015.12

    Language:Japanese   Presentation type:Public lecture, seminar, tutorial, course, or other speech  

    Venue:近畿大学農学部   Country:Japan  

  • 標的アナログと結合したCRISPR-Cas系Cmr複合体の結晶構造 Invited

    沼田倫征

    2015.12 

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    Event date: 2015.12

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:神戸   Country:Japan  

  • 標的類似核酸と結合したCRISPR-Cas系Cmr複合体の結晶構造

    沼田倫征

    平成27年度日本結晶学会年会  2015.10 

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    Event date: 2015.10

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:大阪   Country:Japan  

  • RNAのサイレンシングに関わるCRISPR-Cas系Cmr複合体の結晶構造

    沼田倫征

    第39回蛋白質と酵素の構造と機能に関する九州シンポジウム  2015.9 

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    Event date: 2015.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:大分   Country:Japan  

  • CRISPR-Cas系Cmr複合体の再構成・結晶化・X線回折データの測定

    沼田倫征、大澤拓生

    第39回蛋白質と酵素の構造と機能に関する九州シンポジウム  2015.9 

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    Event date: 2015.9

    Language:Japanese  

    Venue:大分   Country:Japan  

  • 標的アナログと結合したCRISPR-Cas Cmr複合体の結晶構造

    沼田倫征

    第17回日本RNA学会年会  2015.7 

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    Event date: 2015.7

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:札幌   Country:Japan  

  • 標的アナログと結合したCRISPR-Cas Cmr複合体の結晶構造

    沼田倫征、大澤拓生

    第15回日本蛋白質科学会年会  2015.6 

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    Event date: 2015.6

    Language:Japanese  

    Venue:徳島   Country:Japan  

  • N6-スレオニルカルバモイルアデノシンの環化反応を触媒するtRNA修飾酵素CsdLの機能構造解析

    沼田倫征、宮内健常、大澤拓生、鈴木勉

    第3回物構研サイエンスフェスタ  2015.3 

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    Event date: 2015.3

    Language:Japanese  

    Venue:つくば   Country:Japan  

  • tRNA転写後修飾メカニズムの分子的基盤解明 Invited

    沼田倫征

    日本農芸化学会2014年度第2回関東支部例会  2014.11 

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    Event date: 2014.11

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:神奈川   Country:Japan  

  • N6-スレオニルカルバモイルアデノシンの環化反応を触媒するtRNA修飾酵素CsdLの機能構造解析

    沼田倫征、宮内健常、大澤拓生、鈴木勉

    第38回蛋白質と酵素の構造と機能に関する九州シンポジウム  2014.9 

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    Event date: 2014.9

    Language:Japanese  

    Venue:福岡   Country:Japan  

  • Cyclic N6-threonylcarbamoyladenosine (ct6A)の生合成における硫黄リレー系の関与

    宮内健常、坂下卓矢、木村聡、沼田倫征、鈴木勉

    第16回日本RNA学会年会  2014.7 

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    Event date: 2014.7

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:名古屋   Country:Japan  

  • N6-スレオニルカルバモイルアデノシンの環化を触媒するtRNA修飾酵素の結晶構造

    沼田倫征、宮内健常、大澤拓生、鈴木勉

    第14回日本蛋白質科学会年会  2014.6 

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    Event date: 2014.6

    Language:Japanese  

    Venue:横浜   Country:Japan  

  • tRNA転写後修飾メカニズムの分子的基盤解明 Invited

    沼田倫征

    日本農芸化学会2014年度大会  2014.3 

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    Event date: 2014.3

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:東京   Country:Japan  

  • tRNAのアンチコドンをアグマチンで化学修飾するしくみ

    沼田倫征

    第37回蛋白質と酵素の構造と機能に関する九州シンポジウム  2013.9 

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    Event date: 2013.9

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:長崎   Country:Japan  

  • Biogenesis and function of cyclic N6-threonylcarbamoyladenosine (ct6A) as a widely distributed tRNA hypermodification International conference

    Tsutomu Suzuki, Kenjyo Miyauchi, Takuya Sakashita, Satoshi Kimura and Tomoyuki Numata

    The 8th Annual Meeting of the RNA Society  2013.6 

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    Event date: 2013.6

    Language:English   Presentation type:Oral presentation (general)  

    Country:Switzerland  

  • CRISPR-Casシステムのエフェクター複合体を構成するCmr2-Cmr3複合体の結晶構造

    沼田倫征、大澤拓生

    第13回日本蛋白質科学会年会  2013.6 

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    Event date: 2013.6

    Language:Japanese  

    Venue:鳥取   Country:Japan  

  • tRNA修飾酵素TiaSによるtRNAIle2の認識機構

    沼田倫征、大澤拓生、稲永英子、寺坂尚紘、木村聡、鈴木勉

    第12回日本蛋白質科学会年会  2012.6 

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    Event date: 2012.6

    Language:Japanese  

    Venue:愛知   Country:Japan  

  • tRNAIle2アグマチニル化反応の構造的基盤

    大澤拓生、木村聡、寺坂尚紘、稲永英子、鈴木勉、沼田倫征

    第12回日本蛋白質科学会年会  2012.6 

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    Event date: 2012.6

    Language:Japanese  

    Venue:愛知   Country:Japan  

  • tRNAアグマチニル化反応の構造的基盤

    大澤拓生、木村聡、寺坂尚紘、稲永英子、鈴木勉、沼田倫征

    日本農芸化学会2012年度大会  2012.3 

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    Event date: 2012.3

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:京都   Country:Japan  

  • tRNAIle2アグマチニル化反応の構造的基盤

    大澤拓生、沼田倫征

    第29回PFシンポジウム  2012.3 

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    Event date: 2012.3

    Language:Japanese  

    Venue:茨城   Country:Japan  

  • tRNA修飾酵素TiaSによるtRNAIle2の特異的認識機構

    沼田倫征、大澤拓生

    第29回PFシンポジウム  2012.3 

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    Event date: 2012.3

    Language:Japanese  

    Venue:茨城   Country:Japan  

  • Biogenesis and function of 2-agmatinylcytidine found at the wobble position of archaeal tRNAIle International conference

    Suzuki, T., Kimura, S., Terasaka, N., Osawa, T. and Numata, T.

    38th International Symposium on Nucleic Acid Chemistry  2011.11 

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    Event date: 2011.11

    Language:English   Presentation type:Oral presentation (general)  

    Country:Japan  

  • 古細菌tRNAIleのアンチコドン領域に存在するRNA修飾塩基の生合成機構解明

    大澤拓生、寺坂尚紘、木村聡、鈴木勉、沼田倫征

    第35回蛋白質と酵素の構造と機能に関する九州シンポジウム  2011.9 

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    Event date: 2011.9

    Language:Japanese  

    Venue:福岡   Country:Japan  

  • アーキアtRNAIleのアンチコドン領域に見られる新規RNA修飾塩基の生合成機構解明

    大澤拓生、寺坂尚紘、木村聡、鈴木勉、沼田倫征

    第34回蛋白質と酵素の構造と機能に関する九州シンポジウム  2010.9 

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    Event date: 2010.9

    Language:Japanese  

    Venue:福岡   Country:Japan  

  • アーキアtRNAIleに見出された新規RNA修飾塩基アグマチジンの機能と生合成機構の解明

    池内与志穂、木村 聡、寺坂尚紘、沼田倫征、大澤拓生、中村大吾、横川隆志、緒方俊彦、和田 猛、鈴木健夫、鈴木 勉

    第12回日本RNA学会年会  2010.7 

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    Event date: 2010.7

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:東京   Country:Japan  

  • tRNA揺らぎ塩基の5-カルボキシメチルアミノメチル化修飾に関わる酵素GidAおよびMnmEの構造機能解析

    大澤拓生、稲永英子、沼田倫征

    第10回日本蛋白質科学会年会  2010.6 

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    Event date: 2010.6

    Language:Japanese  

    Venue:札幌   Country:Japan  

  • Novel wobble modification in tRNAIle responsible for decoding AUA codon in archaeal species; convergent evolution of the decoding system across domains of life International conference

    Kimura, S., Ikeuchi, Y., Numata, T., Nakamura, D., Yokogawa, T., Nishikawa, K., Wada, T., Suzuki, T. and Suzuki, T.

    23rd International tRNA workshop  2010.1 

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    Event date: 2010.1

    Language:English   Presentation type:Oral presentation (general)  

    Country:Portugal  

  • Requirements for in vitro formation of 5-carboxymethylaminometyluridine at the wobble position in Escherichia coli tRNAs International conference

    Suzuki, T., Numata, T., Osawa, T. and Suzuki, T.

    23rd International tRNA workshop  2010.1 

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    Event date: 2010.1

    Language:English   Presentation type:Oral presentation (general)  

    Country:Portugal  

  • Requirements for in vitro formation of 5-carboxymethylaminometyluridine at the wobble position in Escherichia coli tRNAs

    Suzuki, T., Numata, T., Osawa, T. and Suzuki, T.

    2009.12 

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    Event date: 2009.12

    Language:Japanese   Presentation type:Oral presentation (general)  

    Country:Japan  

  • tRNA揺らぎ塩基の5-カルボキシメチルアミノメチル化修飾に関わる酵素MnmEの結晶構造解析

    大澤拓生、伊藤耕一、稲永英子、沼田倫征

    第9回日本蛋白質科学会年会  2009.5 

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    Event date: 2009.5

    Language:Japanese  

    Venue:熊本   Country:Japan  

  • tRNAアンチコドンの修飾に関わる酵素GidAにおいて保存されているシステインは5-カルボキシメチルアミノメチルウリジン生合成に不可欠である

    大澤拓生、伊藤耕一、稲永英子、沼田倫征

    第9回日本蛋白質科学会年会  2009.5 

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    Event date: 2009.5

    Language:Japanese  

    Venue:熊本   Country:Japan  

  • tRNA揺らぎ塩基の修飾に関わる酵素の構造機能解析(2)

    大澤拓生、伊藤耕一、稲永英子、沼田倫征

    日本農芸化学会2009年度大会  2009.3 

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    Event date: 2009.3

    Language:Japanese  

    Venue:福岡   Country:Japan  

  • tRNA揺らぎ塩基の修飾に関わる酵素の構造機能解析(1)

    大澤拓生、伊藤耕一、稲永英子、沼田倫征

    日本農芸化学会2009年度大会  2009.3 

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    Event date: 2009.3

    Language:Japanese  

    Venue:福岡   Country:Japan  

  • 非翻訳RNAの化学修飾の構造基盤

    沼田倫征、中西孝太郎、鈴木陽子、野間あきこ、池内与志穂、鈴木勉、深井周也、石谷隆一郎、濡木理

    第45回日本生物物理学会年会  2007.12 

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    Event date: 2007.12

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:横浜   Country:Japan  

  • Snapshots of tRNA sulphuration via an adenylated intermediate International conference

    Numata, T., Ikeuchi, Y., Fukai, S., Suzuki, T., and Nureki, O.

    Fifth East Asian biophysics symposium & Forty-fourth annual meeting of the biophysical society of Japan  2006.11 

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    Event date: 2006.11

    Language:English  

    Country:Japan  

  • Snapshots of tRNA sulphuration via an adenylated intermediate International conference

    Numata, T., Ikeuchi, Y., Fukai, S., Suzuki, T., and Nureki, O.

    International conference on aminoacyl-tRNA synthetases  2006.10 

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    Event date: 2006.10

    Language:English  

    Country:United States  

  • Structural basis of RNA-dependent recruitment of amino acid to the genetic code International conference

    International conference on aminoacyl-tRNA synthetases  2006.10 

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    Event date: 2006.10

    Language:English   Presentation type:Oral presentation (general)  

    Country:United States  

  • RNA 修飾に関わる硫黄リレーシステムの発見と反応機構の解析

    池内与志穂、沼田倫征、深井周也、鴫直樹、加藤潤一、西村昭子、濡木理、鈴木勉

    第8回日本RNA学会年会  2006.7 

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    Event date: 2006.7

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:淡路   Country:Japan  

  • タンパク3000プロジェクト(転写・翻訳)拠点の成果(20)RNAチオ化修飾酵素MnmAによる硫黄導入の構造的基盤

    沼田倫征、池内与志穂、深井周也、鈴木勉、濡木理

    第6回日本蛋白質科学会年会  2006.4 

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    Event date: 2006.4

    Language:Japanese  

    Venue:京都   Country:Japan  

  • RNAチオ化修飾酵素MnmAとtRNA複合体の結晶構造解析 Invited

    沼田倫征

    大阪大学蛋白質研究所セミナー  2006.3 

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    Event date: 2006.3

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:大阪   Country:Japan  

  • RNAチオ化修飾機構の構造基盤

    沼田倫征、池内与志穂、深井周也、鈴木勉、濡木理

    文部科学省タンパク3000プロジェクト第3回産学連携フォーラム  2006.2 

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    Event date: 2006.2

    Language:Japanese  

    Venue:東京   Country:Japan  

  • RNA修飾酵素MnmAによるtRNAチオ化修飾の構造基盤

    沼田倫征、深井周也、池内与志穂、鈴木勉、濡木理

    第28回日本分子生物学会年会  2005.12 

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    Event date: 2005.12

    Language:Japanese  

    Venue:福岡   Country:Japan  

  • Structural basis for nucleotide and aminoacyl-group modification on tRNAs International conference

    21st International tRNA workshop  2005.12 

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    Event date: 2005.12

    Language:English  

    Country:India  

  • Crystal structure analyses of the enzymes responsible for the s2U modification at tRNA wobble base International conference

    Numata, T., Fukai, S., Ikeuchi, Y., Suzuki, T. and Nureki, O.

    21st International tRNA workshop  2005.12 

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    Event date: 2005.12

    Language:English  

    Country:India  

  • 離合集散するタンパク質・RNA 複合体

    沼田倫征、深井周也、押鐘浩之、中村裕子、鈴木勉、濡木理

    第43回日本生物物理学会年会  2005.11 

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    Event date: 2005.11

    Language:Japanese   Presentation type:Oral presentation (general)  

    Venue:札幌   Country:Japan  

  • tRNAのチオ化修飾に関与するTusBCD複合体の結晶構造解析

    沼田倫征、深井周也、池内与志穂、鈴木勉、濡木理

    第42回日本生物物理学会年会  2004.12 

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    Event date: 2004.12

    Language:Japanese  

    Venue:京都   Country:Japan  

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MISC

  • Role of Cyclic Oligoadenylate Signaling in the CRISRP-Cas System

    NUMATA Tomoyuki, OUCHI Ryo

    Nihon Kessho Gakkaishi   66 ( 2 )   76 - 77   2024.5   ISSN:03694585 eISSN:18845576

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    Language:Japanese   Publisher:The Crystallographic Society of Japan  

    DOI: 10.5940/jcrsj.66.76

    CiNii Research

  • 細菌RNA を標的とした新たな抗生物質候補化合物の創製と評価 Reviewed

    沼田倫征,Colleen M. Connelly,John S. Schneekloth Jr.,Adrian R. Ferré-D’Amaré

    生化学   2021.8

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    Language:Japanese   Publishing type:Article, review, commentary, editorial, etc. (scientific journal)  

  • Crystal Structure of the CRISPR-Cas RNA Silencing Complex Reviewed

    Numata, T. and Osawa, T.

    Photon Factory Highlights 2015   2016.1

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  • 標的類似体と結合したCRISPR-Cas系Cmr複合体の結晶構造 Reviewed

    沼田 倫征, 大澤 拓生

    日本結晶学会誌   2015.12

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    Language:Japanese   Publishing type:Article, review, commentary, editorial, etc. (scientific journal)  

  • 標的アナログと結合したCRISPR-Cas系のCmr複合体の結晶構造 Reviewed

    沼田 倫征, 大澤 拓生

    ライフサイエンス新着論文レビュー   2015.5

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    Language:Japanese   Publishing type:Article, review, commentary, editorial, etc. (scientific journal)  

    DOI: 10.7875/first.author.2015.061

  • AUAコドンの解読に不可欠なtRNAIleアグマチニル化修飾の分子基盤 Reviewed

    沼田 倫征

    生化学   2012.12

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    Language:Japanese   Publishing type:Article, review, commentary, editorial, etc. (scientific journal)  

  • 結晶構造解析から明らかとなったtRNAのアグマチニル化修飾機構 Reviewed

    沼田 倫征, 大澤 拓生

    日本結晶学会誌   2012.8

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    Language:Japanese   Publishing type:Article, review, commentary, editorial, etc. (scientific journal)  

  • 結晶構造から見る古細菌tRNAIle2のアグマチニル化反応:新しいtRNAアンチコドン修飾メカニズムの解明 Reviewed

    大澤 拓生, 沼田 倫征

    化学と生物   2012.7

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    Language:Japanese   Publishing type:Article, review, commentary, editorial, etc. (scientific journal)  

  • tRNAをアグマチンで化学修飾するしくみ Reviewed

    大澤 拓生, 沼田 倫征

    ライフサイエンス新着論文レビュー   2011.11

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    Language:Japanese   Publishing type:Article, review, commentary, editorial, etc. (scientific journal)  

    DOI: 10.7875/first.author.2011.165

    Other Link: http://first.lifesciencedb.jp/archives/3789

  • tRNAチオ化修飾酵素によるアンチコドンウリジン硫化反応における構造的基盤の解明 Reviewed

    沼田 倫征, 濡木 理

    細胞工学   2006.9

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    Language:Japanese   Publishing type:Article, review, commentary, editorial, etc. (scientific journal)  

  • 植物リボヌクレアーゼの基質認識機構 Reviewed

    沼田 倫征, 河野 慎, 角田 佳充, 木村 誠

    化学と生物   2003.11

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    Language:Japanese   Publishing type:Article, review, commentary, editorial, etc. (scientific journal)  

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Professional Memberships

  • 日本農芸化学会

  • 極限環境生物学会

  • 日本蛋白質科学会

  • 日本結晶学会

  • 日本RNA学会

Committee Memberships

  • 日本結晶学会   生物系編集委員   Domestic

    2024.4 - 2026.3   

  • 日本農芸化学会西日本支部   支部参与   Domestic

    2020.3 - 2026.3   

Academic Activities

  • Screening of academic papers

    Role(s): Peer review

    2023

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    Type:Peer review 

    Number of peer-reviewed articles in foreign language journals:1

  • 科学研究費委員会/専門委員

    Role(s): Review, evaluation

    日本学術振興会  2021.11 - 2022.2

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    Type:Scientific advice/Review 

  • 科学研究費委員会/専門委員

    Role(s): Review, evaluation

    日本学術振興会  2020.12 - 2021.3

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    Type:Scientific advice/Review 

  • プログラムの編成

    日本農芸化学会2020年度大会  2020.3

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    Type:Competition, symposium, etc. 

  • Screening of academic papers

    Role(s): Peer review

    2019

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    Type:Peer review 

    Number of peer-reviewed articles in foreign language journals:1

  • Screening of academic papers

    Role(s): Peer review

    2018

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    Type:Peer review 

    Number of peer-reviewed articles in foreign language journals:1

  • Screening of academic papers

    Role(s): Peer review

    2017

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    Type:Peer review 

    Number of peer-reviewed articles in foreign language journals:3

  • Screening of academic papers

    Role(s): Peer review

    2015

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    Type:Peer review 

    Number of peer-reviewed articles in foreign language journals:3

  • Screening of academic papers

    Role(s): Peer review

    2014

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    Type:Peer review 

    Number of peer-reviewed articles in foreign language journals:3

  • Screening of academic papers

    Role(s): Peer review

    2013

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    Type:Peer review 

    Number of peer-reviewed articles in foreign language journals:2

  • Screening of academic papers

    Role(s): Peer review

    2012

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    Type:Peer review 

    Number of peer-reviewed articles in foreign language journals:1

  • Screening of academic papers

    Role(s): Peer review

    2010

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    Type:Peer review 

    Number of peer-reviewed articles in foreign language journals:1

  • Screening of academic papers

    Role(s): Peer review

    2009

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    Type:Peer review 

    Number of peer-reviewed articles in foreign language journals:1

  • Screening of academic papers

    Role(s): Peer review

    2008

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    Type:Peer review 

    Number of peer-reviewed articles in foreign language journals:3

  • Screening of academic papers

    Role(s): Peer review

    2007

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    Type:Peer review 

    Number of peer-reviewed articles in foreign language journals:1

  • Screening of academic papers

    Role(s): Peer review

    2006

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    Type:Peer review 

    Number of peer-reviewed articles in foreign language journals:3

  • Screening of academic papers

    Role(s): Peer review

    2005

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    Type:Peer review 

    Number of peer-reviewed articles in foreign language journals:2

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Other

  • 2024年度科学研究費補助金基盤研究Aに採択された。

    2024.5

  • 原核生物の生体防御機構の解明とその応用に関する研究において優れた業績をあげている。国立癌研究所(アメリカ国立衛生研究所)の研究者であるJohn S. Schneekloth Jr博士と共同研究を進めており、原核生物の非コードRNA分子の新規かつ特異的なラベリング方法を開発するとともに、その仕組みを明らかにした。また、この技術を利用して、ヒト細胞内において目的リガンドと特異的に結合するRNAを特定することに成功した。この研究成果をNature姉妹誌に投稿し、現在、リバイズしている段階である。このように、国際共同研究が順調に進展している。また、関連研究に対して、2019年度以降に3件の研究助成金を獲得(上原記念財団、内藤記念財団、応用酵素協会)するとともに、2020年度には2件の科学研究費補助金(基盤研究(B)および挑戦的研究(萌芽))を獲得した。また、令和2年度大学改革活性化制度(全学改革推進枠)に採択され、研究の促進と若手研究人材の育成にも貢献している。

    2021.3

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    原核生物の生体防御機構の解明とその応用に関する研究において優れた業績をあげている。国立癌研究所(アメリカ国立衛生研究所)の研究者であるJohn S. Schneekloth Jr博士と共同研究を進めており、原核生物の非コードRNA分子の新規かつ特異的なラベリング方法を開発するとともに、その仕組みを明らかにした。また、この技術を利用して、ヒト細胞内において目的リガンドと特異的に結合するRNAを特定することに成功した。この研究成果をNature姉妹誌に投稿し、現在、リバイズしている段階である。このように、国際共同研究が順調に進展している。また、関連研究に対して、2019年度以降に3件の研究助成金を獲得(上原記念財団、内藤記念財団、応用酵素協会)するとともに、2020年度には2件の科学研究費補助金(基盤研究(B)および挑戦的研究(萌芽))を獲得した。また、令和2年度大学改革活性化制度(全学改革推進枠)に採択され、研究の促進と若手研究人材の育成にも貢献している。

Research Projects

  • 独自に発見したCRISPR-Casエフェクターの機能構造解析と新たなゲノム編集技術の開発

    Grant number:24H00505  2024 - 2026

    日本学術振興会  科学研究費助成事業  基盤研究(A)

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    Authorship:Principal investigator  Grant type:Scientific research funding

  • 2024年度 酵素研究助成/独自の海洋メタゲノムから発見した小型CRISPR-Casエフェクターの機能構造解析とゲノム編集への利用

    2024

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    Grant type:Donation

  • FEN-1の改変によるRNA検出用酵素の開発

    2023.10 - 2024.5

    共同研究

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    Authorship:Principal investigator  Grant type:Other funds from industry-academia collaboration

  • 公益財団法人発酵研究所 2023年度 一般研究助成/病原性ビブリオ属細菌が保有するCRISPR-associated transposonの機能構造解析と⽣理的役割の解明

    2023

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    Grant type:Donation

  • トキシンーアンチトキシンシステムの機能と構造

    2022.1

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    Authorship:Principal investigator 

  • ゲノム編集を含む新規遺伝⼦発現調節技術開発を⽬指したRNA⽣物学領域の研究体制強化

    2020 - 2024

    令和2年度大学改革活性化制度『全学改革推進枠』

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    Authorship:Principal investigator  Grant type:On-campus funds, funds, etc.

  • 細菌の非コードRNAの作動原理の解明と創薬への展開

    Grant number:20K21281  2020 - 2022

    日本学術振興会  科学研究費助成事業  挑戦的研究(萌芽)

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    Authorship:Principal investigator  Grant type:Scientific research funding

  • CRISPR-Cas系とトランスポゾンの相互作用によるDNA転移の分子基盤解明

    Grant number:20H02916  2020 - 2022

    日本学術振興会  科学研究費助成事業  基盤研究(B)

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    Authorship:Principal investigator  Grant type:Scientific research funding

  • 第52回(2020年度)内藤記念科学奨励金・研究助成/ CRISPR-Cas系が誘導する新規なDNA転移メカニズムの解明

    2020

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    Grant type:Donation

  • CRISPR-Cas系の生物学

    2019.4

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    Authorship:Principal investigator 

  • 細菌の非コードRNAの生化学的解析と創薬への展開 International coauthorship

    2019.4

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    Authorship:Principal investigator 

  • 上原記念生命科学財団2019年 度 研究助成金/ 細菌の非コードRNAの生化学的解析と創薬への展開

    2019

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    Grant type:Donation

  • 原核生物に特異的な遺伝子発現調節機構の解明

    Grant number:16KK0166  2017 - 2019

    日本学術振興会  科学研究費助成事業  国際共同研究強化

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    Authorship:Principal investigator  Grant type:Scientific research funding

  • CRISPR-Casエフェクター複合体の構造機能解析

    Grant number:16H04759  2016 - 2019

    日本学術振興会  科学研究費助成事業  基盤研究(B)

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    Authorship:Principal investigator  Grant type:Scientific research funding

  • 平成26年度(第47回)倉田奨励金/ RNA依存的に外来核酸の発現を抑制するCRISPR-Casエフェクター複合体の構造機能解析

    2015

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    Grant type:Donation

  • 平成27年度(2015年度)一般研究助成/ 外来遺伝子の発現を抑制するCRISPR-Casエフェクター複合体の機能構造解析

    2015

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    Grant type:Donation

  • 加藤記念研究助成/ CRISPR-Casエフェクター複合体の機能構造解析

    2015

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    Grant type:Donation

  • 平成27年度持田記念研究助成/ CRISPR-Cas エフェクター複合体による転写反応と共役した標的DNA 切断の分子的基盤解明

    2015

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    Grant type:Donation

  • 平成27 年度(第47 回)海外留学補助金/ 遺伝子の発現を制御するRNA分子装置の作動原理解明

    2015

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    Grant type:Donation

  • CRISPRシステムにおけるエフェクター複合体の構造機能解析

    Grant number:25121744  2013 - 2014

    日本学術振興会・文部科学省  科学研究費助成事業  新学術領域研究(研究領域提案型)

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    Authorship:Principal investigator  Grant type:Scientific research funding

  • ミトコンドリアにおけるtRNAプロセシング機構の解明

    Grant number:23687015  2011 - 2014

    科学研究費助成事業  若手研究(A)

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    Authorship:Principal investigator  Grant type:Scientific research funding

  • CRISPRシステムにおけるAGO2様活性を有するRNP複合体の構造機能解析

    Grant number:23121535  2011 - 2012

    日本学術振興会・文部科学省  科学研究費助成事業  新学術領域研究(研究領域提案型)

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    Authorship:Principal investigator  Grant type:Scientific research funding

  • 2011年度野田産研研究助成/ 古細菌に特異的なtRNA修飾ヌクレオシドの生合成機構解明

    2011

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    Grant type:Donation

  • 2011年度ライフサイエンス研究奨励/ 正しい蛋白質合成に不可欠なtRNA修飾塩基の生合成機構解明

    2011

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    Grant type:Donation

  • 平成20年度研究助成:一般課題(B)/ tRNA揺らぎ塩基修飾の構造的基盤解明

    2009

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    Grant type:Donation

  • 日本人若手研究者研究助成/ X線結晶構造解析によるtRNA転写後修飾メカニズムの分子基盤解明

    2009

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    Grant type:Donation

  • 第27回(平成21年度)持田記念研究助成金/ 正しい蛋白質合成に不可欠なtRNA修飾ヌクレオシドの生合成機構解明

    2009

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    Grant type:Donation

  • 第27回(平成21年度)研究助成/ tRNAのアンチコドン修飾メカニズムの分子基盤解明

    2009

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    Grant type:Donation

  • tRNAアンチコドンの転写後修飾における酵素反応機構の分子的基盤解明

    Grant number:20687007  2008 - 2010

    科学研究費助成事業  若手研究(A)

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    Authorship:Principal investigator  Grant type:Scientific research funding

  • 基礎科学研究助成/ tRNA修飾酵素によるアンチコドンウリジンのチオ化修飾機構の分子的基盤

    2007

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    Grant type:Donation

  • 倉田奨励金/ RNAの転写後修飾における生物マシーナリーの構造的基盤解明

    2007

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    Grant type:Donation

  • 加藤記念研究助成/ 忠実なタンパク質合成に不可欠なtRNA修飾塩基の生合成機構の分子的基盤

    2007

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    Grant type:Donation

  • 研究奨励金/ 遺伝子の発現を調節するノンコーディングRNA(リボスイッチ)の構造機能解析

    2007

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    Grant type:Donation

  • RNAによる生命反応制御機構の構造的基盤の解明

    2006 - 2009

    戦略的創造研究推進事業 (文部科学省)

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    Authorship:Principal investigator  Grant type:Contract research

  • tRNAチオ化修飾経路における硫黄転移反応メカニズムの解明

    Grant number:18770082  2006 - 2007

    科学研究費助成事業  若手研究(B)

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    Authorship:Principal investigator  Grant type:Scientific research funding

  • ニガウリ種子ウリジン特異性リボヌクレアーゼMC1の構造と基質特異性に関する研究

    2002 - 2003

    日本学術振興会  特別研究員

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    Authorship:Principal investigator  Grant type:Joint research

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Educational Activities

  • Molecular Biology

Class subject

  • 分子生物学詳論IV

    2024.12 - 2025.2   Winter quarter

  • 遺伝情報発現制御機構特論

    2024.10 - 2024.12   Fall quarter

  • 分子生物学詳論III

    2024.10 - 2024.12   Fall quarter

  • 生命工学Ⅰ

    2024.6 - 2024.8   Summer quarter

  • 分子生物学詳論II

    2024.6 - 2024.8   Summer quarter

  • Basic Life Engineering Ⅰ

    2024.6 - 2024.8   Summer quarter

  • Seminar in a Specified Field Ⅰ

    2024.4 - 2025.3   Full year

  • Master's Thesis Research Ⅰ

    2024.4 - 2025.3   Full year

  • 応用生命化学実験

    2024.4 - 2024.9   First semester

  • 遺伝子組換え生物の利用と制御

    2024.4 - 2024.9   First semester

  • 学際開拓創成セミナーⅡ

    2024.4 - 2024.9   First semester

  • 生物機能分子化学I

    2024.4 - 2024.6   Spring quarter

  • 分子生物学詳論I

    2024.4 - 2024.6   Spring quarter

  • Molecular Biology

    2024.4 - 2024.6   Spring quarter

  • 分子生物学詳論Ⅳ

    2023.12 - 2024.2   Winter quarter

  • 遺伝情報発現制御機構特論

    2023.10 - 2023.12   Fall quarter

  • 分子生物学詳論Ⅲ

    2023.10 - 2023.12   Fall quarter

  • 基幹教育セミナー

    2023.6 - 2023.8   Summer quarter

  • 分子生物学詳論Ⅱ

    2023.6 - 2023.8   Summer quarter

  • 実地見学

    2023.4 - 2023.9   First semester

  • 遺伝子組換え生物の利用と制御

    2023.4 - 2023.9   First semester

  • Molecular Biology

    2023.4 - 2023.9   First semester

  • 応用生命化学実験

    2023.4 - 2023.9   First semester

  • 分子生物学詳論Ⅰ

    2023.4 - 2023.6   Spring quarter

  • 生物機能分子化学II

    2023.4 - 2023.6   Spring quarter

  • 分子生物学詳論IV

    2022.12 - 2023.2   Winter quarter

  • 生物化学Ⅱ

    2022.12 - 2023.2   Winter quarter

  • 分子生物学詳論III

    2022.10 - 2022.12   Fall quarter

  • 応用生命化学発展実験

    2022.4 - 2022.9   First semester

  • 生物機能分子化学I

    2022.4 - 2022.6   Spring quarter

  • 生物化学Ⅱ

    2021.12 - 2022.2   Winter quarter

  • 生物化学各論Ⅱ

    2021.10 - 2022.3   Second semester

  • 生物機能分子化学II

    2021.4 - 2021.9   First semester

  • 応用生命化学発展実験

    2021.4 - 2021.9   First semester

  • 生物化学各論II

    2020.10 - 2021.3   Second semester

  • 生物化学

    2020.10 - 2021.3   Second semester

  • 生物化学各論I

    2020.4 - 2020.9   First semester

  • 応用生命化学発展実験

    2020.4 - 2020.9   First semester

  • 生物化学各論II

    2019.10 - 2020.3   Second semester

  • 生物機能分子化学II

    2019.4 - 2019.9   First semester

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FD Participation

  • 2023.11   Role:Participation   Title:農学研究院FD:遺伝子組換え実験の安全管理について

    Organizer:[Undergraduate school/graduate school/graduate faculty]

  • 2022.3   Role:Other   Title:リベラルサイエンス教育開発FD 「『ゆるレポ』に学ぶはじめての研究~ゆるく始めて、しっかり仕上げる~」

    Organizer:[Undergraduate school/graduate school/graduate faculty]

  • 2021.9   Role:Participation   Title:JST 次世代研究者挑戦的研究プログラム 説明会

    Organizer:University-wide

  • 2021.7   Role:Other   Title:農学研究院FD「科研費を獲りにいこう! 科研費獲得の技術と工夫」

    Organizer:[Undergraduate school/graduate school/graduate faculty]

  • 2020.12   Role:Other   Title:大学の研究評価の現状と農学研究院の「部局独自の評価基準」案における業績分析

    Organizer:[Undergraduate school/graduate school/graduate faculty]

  • 2020.9   Role:Participation   Title:科研費を獲りにいこう! 勝ち抜く気合と技術

    Organizer:[Undergraduate school/graduate school/graduate faculty]

  • 2019.11   Role:Participation   Title:留学生との共生に向けて

    Organizer:[Undergraduate school/graduate school/graduate faculty]

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Social Activities

  • 出前講義

    西南学院高校(2023年10月31日)  2023.10

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    Audience: Infants, Schoolchildren, Junior students, High school students

    Type:Seminar, workshop

Media Coverage

  • 細菌の生体防御を解明 Newspaper, magazine

    化学工業日報  2015.4

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    細菌の生体防御を解明

  • 細菌の生体防御機構解明 Newspaper, magazine

    日刊工業新聞  2015.4

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    細菌の生体防御機構解明

  • The genetic code: An archaeal path to literacy Newspaper, magazine

    Nature Chemical Biology  2010.4

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    The genetic code: An archaeal path to literacy

  • 生体内の硫化反応・触媒結合の謎解明について Newspaper, magazine

    日経産業新聞  2006.7

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    生体内の硫化反応・触媒結合の謎解明について

  • 硫化反応の新酵素触媒機構について Newspaper, magazine

    日刊工業新聞  2006.7

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    硫化反応の新酵素触媒機構について

Activities contributing to policy formation, academic promotion, etc.

  • 2015.8 - 2020.3   PF-UAタンパク質結晶構造解析ユーザーグループ

    ユーザーグループ会議や講習会を開催し、効率的なX線回折データの収集方法や放射光施設の最新情報について協議した。また、PF構造生物学ビームラインの運営などに関して各ユーザーの希望を調査し結果を取り纏めた。

Acceptance of Foreign Researchers, etc.

  • Laboratory of Nucleic Acids, National Heart, Lung, and Blood Institute, National Institutes of Health

    Acceptance period: 2023.8  

    Nationality:United States

  • Laboratory of RNA Biophysics and Cellular Physiology, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, NIH

    Acceptance period: 2019.11   (Period):Less than 2 weeks

    Nationality:United States

    Business entity:Japan Society for the Promotion of Science

Travel Abroad

  • 2016.1 - 2019.1

    Staying countory name 1:United States   Staying institution name 1:Laboratory of RNA Biophysics and Cellular Physiology, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, NIH