Researcher Database

Tomohisa Shimasaki
Institute for the Advancement of Graduate Education Advancement of Educational Program Division
Assistant Professor

Researcher Profile and Settings


  • Institute for the Advancement of Graduate Education Advancement of Educational Program Division

Job Title

  • Assistant Professor


  • Doctor of Agriculture(2021/09 Kyoto University)

Research funding number

  • 50948792

J-Global ID

Research Interests

  • 植物微生物相互作用   タバコ   ニコチン   

Research Areas

  • Life sciences / Applied microbiology
  • Life sciences / Applied biochemistry

Academic & Professional Experience

  • 2023/04 - Today Hokkaido University Faculty of Science
  • 2022/04 - 2023/03 RIKEN
  • 2022/03 - 2022/07 Max Planck Institute for Plant Breeding Research Department of Plant Microbe Interactions
  • 2018/04 - 2021/03 日本学術振興会特別研究員(DC1)


  • 2018/04 - 2021/03  Kyoto University
  • 2016/04 - 2018/03  Tokyo University of Agriculture and Technology  Institute of Agriculture
  • 2012/04 - 2016/03  Tokyo University of Agriculture and Technology  Faculty of Engineering  Department of Biotechnology and Life Science

Research Activities

Published Papers

  • Noritaka Aoki, Tomohisa Shimasaki, Wataru Yazaki, Tomoaki Sato, Masaru Nakayasu, Akinori Ando, Shigenobu Kishino, Jun Ogawa, Sachiko Masuda, Arisa Shibata, Ken Shirasu, Kazufumi Yazaki, Akifumi Sugiyama
    Abstract Isoflavones are major specialized metabolites found in legume plants, where they contribute to environmental adaptation. Isoflavones also play a role human health as promising therapeutic agents. This metabolite group is involved in interactions with soil microorganisms as initiation signals in rhizobial symbiosis and as modulators of the legume root microbiota. We previously reported that isoflavones enrich the Comamonadaceae, a predominant bacterial family in soybean roots, and that microorganisms in legume rhizosphere soil degrade isoflavones. However, the isoflavone catabolism pathway that underly the isoflavone-mediated legume–microbiota interactions have not yet been clarified. Here, we isolatedVariovoraxsp. strain V35, member of the Comamonadaceae that harbors isoflavone-degrading activity, from soybean roots and discovered a gene cluster responsible for isoflavone degradation namedifc. Strain V35 metabolizes isoflavones in a completely distinct oxidative manner from the reductive isoflavone metabolism pathway elucidated in the gut microbiota, in which resulting products enter the tricarboxylic acid cycle. The characterization ofifcmutants and heterologously expressed IFC enzymes revealed that isoflavones are catabolized via A-ring cleaving fission, which starts with hydroxylation at the 8-position of the A-ring. We further demonstrated thatifcgenes are frequently found in bacterial strains isolated from legume plants, including mutualistic rhizobia, and contribute to detoxification of the antibacterial activity of isoflavones. Taken together, our findings reveal an oxidative catabolism pathway of isoflavone in the soybean root microbiota, providing molecular insights into isoflavone-mediated legume–microbiota interactions. Significance Isoflavones play pivotal roles in plant-environment interactions and in the maintenance and improvement of human health. Bacterial metabolism is a fundamental component of isoflavone-mediated interkingdom interactions. In the human gut, intestinal bacteria convert isoflavones into equol, a highly bioactive compound. However, the fate of isoflavones in the legume rhizosphere has not been elucidated, despite them being the key signaling molecules for nodule symbiosis and modulation of the legume root microbiota. Here, we discovered a novel isoflavone catabolism pathway in the soybean root microbiota and demonstrated the strong association between bacterial catabolic abilities and their interactions with host plants. Collectively, our findings provide new insights into bacterial isoflavone metabolism and a molecular understanding of legume-microbiota interactions.
  • 島﨑 智久
    バイオミディア 100 (4) 188  2022/04 [Not refereed]
  • Tomohisa Shimasaki, Sachiko Masuda, Ruben Garrido-Oter, Takashi Kawasaki, Yuichi Aoki, Arisa Shibata, Wataru Suda, Ken Shirasu, Kazufumi Yazaki, Ryohei Thomas Nakano, Akifumi Sugiyama
    mBio 12 (3) 2021/06/29 
    Host secondary metabolites have a crucial effect on the taxonomic composition of its associated microbiota. It is estimated that a single plant species produces hundreds of secondary metabolites; however, whether different classes of metabolites have distinctive or common roles in the microbiota assembly remains unclear.
  • Wataru Yazaki, Tomohisa Shimasaki, Yuichi Aoki, Sachiko Masuda, Arisa Shibata, Wataru Suda, Ken Shirasu, Kazufumi Yazaki, Akifumi Sugiyama
    Microbes and Environments 36 (3) n/a - n/a 1342-6311 2021
  • Tomohisa Shimasaki, Hiromi Yoshida, Shigehiro Kamitori, Koji Sode
    Scientific Reports 7 (1) 2017/06/05 
    Abstract Current enzymatic systems for quantifying glycated hemoglobin are based on the FAD-containing enzyme fructosyl peptide oxidase (FPOX). FPOX has substrate specificity for fructosyl-αN-valyl-histidine derived from proteolytic digestion of the N-terminus of the HbA1c β-chain. This study reports the X-ray structures of the wild-type and Asn56Ala (N56A) mutant of Phaeosphaeria nodorum fructosyl peptide oxidase (PnFPOX) to elucidate the residues responsible for the oxidative half-reaction. N56A showed decreased oxidase activity compared to the wild -type, while its dye-mediated dehydrogenase activity was higher than that of wild type. In wild-type PnFPOX, Asn56 forms a hydrogen bond with Lys274, thereby preventing it from forming a salt bridge with Asp54. By contrast, Lys274 of PnFPOX N56A moves toward Asp54, and they approach each other to form a salt bridge at a distance of 2.92–3.35 Å. Site-directed mutagenesis studies and protein channel analysis suggest that Asp54 assists in accepting oxygen properly at the position of the bound water molecule in the main oxygen channel. These results reveal that Asn56 in PnFPOX is essential for maintaining an effective oxygen accession path, and support the role of Asp54 as a gate keeper that cooperates with Lys274 to enable oxygen to reach the active site properly.

Conference Activities & Talks

  • Arthrobacter属細菌におけるニコチン分解遺伝子群の比較ゲノム解析
    島﨑 智久, 増田 幸子, 柴田 ありさ, 須田 亙, 白須 賢, 矢﨑 一史, 市橋 泰範, 杉山 暁史, 中野 亮平
    日本農芸化学会 2022年度大会  2022/03
  • ダイズ根圏でのイソフラボン分解に関与する遺伝子の同定
    青木 愛賢, 島﨑 智久, 矢崎 渉, 中安 大, 安藤 晃規, 岸野 重信, 小川 順, 増田 幸子, 柴田 ありさ, 須田 亙, 白須 賢, 矢﨑 一史, 杉山 暁史
    日本農芸化学会 2022年度大会  2022/03
  • 特化代謝産物を介したタバコ–Arthrobacter間相互作用の解析
    島﨑 智久, 増田 幸子, Ruben Garrido-Oter, 川崎 崇, 青木 裕一, 柴田 ありさ, 須田 亙, 白須 賢, 矢﨑 一史, 中野 亮平, 杉山 暁史
    植物微生物研究会第30回研究交流会  2021/09
  • サントパインを介したタバコ-Arthrobacter相互作用の解析
    島﨑智久, 川崎崇, 青木裕一, 矢崎一史, 杉山暁史
    第61回日本植物生理学会年会  2020/03
  • 窒素欠乏条件下におけるダイズ細菌叢の変化
    矢崎渉, 島﨑智久, 矢崎一史, 杉山暁史
    植物微生物研究会第29回研究交流会  2019/09
  • Rhizobium rhizogenes由来T-DNAによるサントパイン生産が タバコ根圏微生物叢に与える影響
    島﨑 智久, 川崎 崇, 青木 裕一, 矢崎 一史, 杉山 暁史
    植物微生物研究会第29回研究交流会  2019/09
  • Analysis of the function of santhopine, an amadori-type opine, in tobacco rhizosphere
    Tomohisa SHIMASAKI, Takashi KAWASAKI, Yuichi AOKI, Kazufumi YAZAKI, Akifumi SUGIYAMA
    Rhizosphere5  2019/07
  • Analysis of the effects of sathopine on the soil bacterial communities and isolation of santhopine degrading bacteria
    Tomohisa SHIMASAKI, Takashi KAWASAKI, Yuichi AOKI, Kazufumi YAZAKI, Akifumi SUGIYAMA
    5th Asian Conference on Plant-Microbe Symbiosis and Nitrogen Fixation  2019/05
  • タバコ根圏におけるサントパイン資化菌の探索
    島﨑 智久, 川崎 崇, 青木 裕一, 矢崎 一史, 杉山 暁史
    日本農芸化学会 2019年度大会  2019/03
  • Analysis of santhopine, an Amadori compound, in rhizosphere
    Tomohisa SHIMASAKI, Takashi KAWASAKI, Kazufumi YAZAKI, Akifumi SUGIYAMA
    The 3rd Asia Research Node (ARN) Symposium on Humanosphere Science  2018/09
  • タバコにおけるサントパインの生合成及び分泌の解析
    島﨑 智久, 川崎 崇, 矢崎 一史, 杉山 暁史
    第28回植物微生物研究会  2018/09
  • サントパイン分解能を有する根粒菌の探索とその特性評価
    島﨑智久, 元 坤, 岡崎 伸, 藤井義晴
    日本農芸化学会 2019年度大会  2018/03
  • santhopine 分解能を有する根粒菌の探索とその代謝遺伝子の同定
    島﨑智久, 元 坤, 岡崎 伸, 藤井義晴
    第27回植物微生物研究会  2017/09
  • Phaeosphaeria nodorum由来フルクトシルペプチド酸化酵素のX線結晶構造解析
    島﨑 智久, 吉田 裕美, 小島 勝博, 津川 若子, 早出 広司
    日本化学会第96春季年会2016  2016/03
  • ゲノム情報より見出された真菌由来フルクトシルペプチド酸化酵素の組換え生産
    島﨑 智久, 小島 勝博, 津川 若子, 早出 広司
    酵素工学研究会  2015/10


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