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YOKOTA Kenji Professor |
From Graduate School 【 display / non-display 】
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Tohoku University Graduate School, Division of Agriculture Doctoral program (second term) Completed
1996.04 - 2000.03
Country：Japan
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Tokyo University of Agriculture Graduate School, Division of Agriculture Master Course Completed
1994.04 - 1996.03
Country：Japan
Studying abroad experiences 【 display / non-display 】
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2012.04 - 2013.03 University of California, Berkeley Visiting scholar
Employment Record in Research 【 display / non-display 】
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Tokyo University of Agriculture Faculty of Applied Bio-Science Department of Applied Biology and Chemistry Research Assistant
2001.04 - 2007.03
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Tokyo University of Agriculture Faculty of Applied Bio-Science Department of Applied Biology and Chemistry Assistant Professor
2007.04 - 2012.09
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Tokyo University of Agriculture Faculty of Applied Bio-Science Department of Applied Biology and Chemistry Associate Professor
2012.10 - 2018.03
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Tokyo University of Agriculture Faculty of Applied Bio-Science Department of Agricultural Chemistry Associate Professor
2018.04 - 2019.03
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Tokyo University of Agriculture Faculty of Applied Bio-Science Department of Agricultural Chemistry Professor
2019.04
External Career 【 display / non-display 】
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東北大学大学院 農学研究科農芸化学専攻 日本学術振興会特別研究員
2000.04 - 2001.03
Country：Japan
Research Areas 【 display / non-display 】
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Life Science / Applied microbiology
Papers 【 display / non-display 】
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The response regulator FpsR controls the flagella–pili transition and mucosal colonization in Ligilactobacillus ruminis Reviewed International journal
Aya Misakia, Shunya Suzuki, Shintaro Maeno, Akihito Endo, Yasuko Sasaki, Gen Enomoto, Kenji Yokota, Akinobu Kajikawa
Gut Microbes 17 ( 1 ) 2025.12
Language：English Publishing type：Research paper (scientific journal)
Ligilactobacillus ruminis is a flagellated lactic acid bacterium found in the intestines of various mammals, including humans. Although this species harbors a complete flagellar gene cluster, flagella formation has not been observed in human-derived strains, and the underlying regulatory mechanisms remain unknown. Here, we isolated a motility-acquired mutant of L. ruminis ATCC 25644 that exhibited full flagellation and a measurable chemotactic response under acidic conditions (pH 3.0). Whole-genome sequencing revealed a ~35 kb deletion encompassing multiple regulatory genes. Functional complementation identified a single response regulator, designated FpsR (flagellation–piliation switchover regulator), as a central switch that suppresses flagella formation while promoting pilus expression. The motility-acquired mutant displayed reduced pilus production, diminished adhesion to murine intestinal mucus and fibronectin, and increased susceptibility to acid (pH 3.0) and bile (0.25–0.5%), resulting in a complete loss of intestinal colonization in a murine model. Furthermore, while flagellin from the motile strain activated TLR5 and induced proinflammatory responses comparable to those of pathogenic bacteria, no such inflammation was observed in vivo, likely due to the strain’s colonization failure. These findings reveal FpsR as a previously unrecognized genetic mechanism that coordinates motility and mucosal colonization in a human commensal bacterium and provide insight into how flagella are regulated and silenced in the gut environment to support host–microbe symbiosis.
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Involvement of iturin and surfactin in inhibition of a post-harvest fungal pathogen on green bell pepper Reviewed International coauthorship International journal
Yuliar, Shun Tomita, Hinako Hishinuma, Kenji Yokota
Journal of Plant Protection Research 65 ( 3 ) 2025.09
Authorship：Last author Language：English Publishing type：Research paper (scientific journal)
This study aimed to investigate the potential of plant-associated bacteria as bio-control agents for the green bell pepper rot lesion caused by Colletotrichum scovillei 244830. A total of 378 bacteria strains isolated from stems and leaves of healthy red chili and tomato were tested for their antagonistic potential. Isolate TS001 associated with tomato stems was identified as Bacillus spp. It was found that TS001 showed remarkable inhibition to C. scovillei 244830 in in vitro and in vivo tests. TS001 significantly reduced rot lesions (P<0.05) of fresh green bell pepper fruits by 71.43%. Furthermore, the result of the LC-ESI-MS/MS showed that the culture broth of the strain Bacillus sp. TS001 contained iturin and surfactin homolog in No. 3S medium. TS001 exhibited the strongest antagonistic activity that effectively suppressed C. scovillei 244830 rot lesion.
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Characterization of the antifungal activity of the bacterial isolate Bacillus velezensis TCG15 Reviewed International journal
Kojiro Ito, Shun Tomita, Takahiro Fujimaki, Minenosuke Matsutani, Gen Enomoto, Akinobu Kajikawa, Kei Asai, Kenji Yokota
Archives of Microbiology 207 2025.05
Authorship：Last author, Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：Springer Nature
Bacillus velezensis TCG15 is a bacterial isolate from soil that shows antifungal activity against Aspergillus spp. and Candida spp. This study aimed to characterize its antifungal activity. TCG15 produces cyclic lipopeptides (cLPs), including surfactin A, plipastatin, and bacillomycin L. We obtained the complete sequence of the operon encoding nonribosomal peptide synthetase for bacillomycin L biosynthesis, bmyL operon (bmyLDABC), using genome analysis of TCG15. The bmyLD gene-disrupted mutant did not produce bacillomycin L, plipastatin, or surfactin A. The mutant showed no antifungal activity, indicating an essential role of cLPs. Among the cLPs, bacillomycin L was identified as the key antifungal compound. This activity was enhanced by surfactin A, which showed no antifungal activity alone. These findings suggested that the synergistic interaction between bacillomycin L and surfactin A contributed to the antifungal activity of TCG15.
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Characterization of the NRPS operon homolog for surfactin A and surfactin C synthesis in Bacillus spp. Reviewed International journal
Kojiro Ito, Mana Adachi, Minenosuke Matsutani, Ryota Kataoka, Gen Enomoto, Akinobu Kajikawa, Kenji Yokota
Archives of Microbiology 207 2025.05
Authorship：Last author, Corresponding author Language：English Publishing type：Research paper (scientific journal) Publisher：Springer Nature
Surfactin is a cyclic lipopeptide produced by Bacillus spp., consisting of a β-hydroxy fatty acid and a heptapeptide synthesized by non-ribosomal peptide synthetases. Surfactin congeners (A, B, and C) differ in amino acid substitutions, with Leu7 in surfactin A replaced by Val in B and Ile in C. Our LC–MS analysis revealed that the elution profiles of surfactin-producing strains could be classified into two distinct patterns under identical culture conditions, corresponding to surfactin A and C production. This suggests that endogenous factors influence surfactin production. Therefore, we aimed to identify the genetic factor that regulates surfactin congener production. The srfA operon for surfactin A biosynthesis in B. subtilis, composed of four open reading frames (ORFs), is srfAABCD. Comparative genomic analysis between the B. subtilis JCM 1465 srfA operon and the TUA12 surfactin biosynthesis genes examined in this study revealed that the operon responsible for surfactin A biosynthesis is distinct, exhibiting 68.7%, 69.2%, 84.7%, and 67.4% homology with the four ORFs, respectively. Similarly, the operon for Ptrs2 surfactin C biosynthesis showed 68.7%, 69.2%, 64.4%, and 67.1% homology. These differences indicate that the identified surfactin A and C biosynthetic operons are novel genetic variants. Further analysis identified the adenylation domain responsible for selecting Ile7 in surfactin C via domain substitution in a surfactin A-producing strain. Average nucleotide identity analysis showed that the surfactin A and C operons were found in B. velezensis and B. amyloliquefaciens, respectively. Our findings suggest that surfactin congener production is species-dependent, with the srf operon specifically distributed in Bacillus spp.
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TAMAKI Mizuna, CHIKU Tsutomu, SUZUKI Shunya, MISAKI Aya, FUNAKUBO Asuka, MATSUSHIMA Yoshitaka, YOKOTA Kenji, IGIMI Shizunobu, KAJIKAWA Akinobu
Bioscience of Microbiota, Food and Health 44 ( 1 ) 70 - 79 2024.09
Language：English Publisher：BMFH Press
Although the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas system has been extensively developed since its discovery for eukaryotic and prokaryotic genome editing and other genetic manipulations, there are still areas warranting improvement, especially regarding bacteria. In this study, BRD0539, a small-molecule inhibitor of Streptococcus pyogenes Cas9 (SpCas9), was used to suppress the activity of the nuclease during genetic modification of Lacticaseibacillus paracasei, as well as to regulate CRISPR interference (CRISPRi). First, we developed and validated a CRISPR-SpCas9 system targeting the sirA gene of L. paracasei. Then BRD0539 was used for CRISPR-dependent DNA cleavage in vivo. Our results suggested that the inhibitor worked partially in both Escherichia coli and L. paracasei. Next, we designed a CRISPRi system in a L. paracasei strain by inserting an inactive SpCas9 gene into the chromosome and introducing a plasmid encoding for a single guide RNA (sgRNA) targeting the sirA gene. Expression of sirA was successfully inhibited in the recombinant strains, and CRISPRi was abolished in an inhibitor-dependent manner. Our findings may help expand the CRISPR toolbox for research on lactic acid bacteria and other microbes.
Books and Other Publications 【 display / non-display 】
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太田寛行，森﨑久雄，大塚重人，渡邉健史，鮫島玲子，中川達功，佐伯雄一，礒井俊行，横田健治，豊田剛己，村瀬 潤，浦嶋泰文，藤井一至，原田直樹，西澤智康，浅川 晋，竹腰 恵（ Role： Contributor）
朝倉書店 2018.08 （ ISBN:978-4-254-43571-9 ）
Total pages：208 Responsible for pages：80-87 Language：Japanese Book type：Scholarly book
植物生育促進根圏微生物について解説した。
担当執筆分：8. 有用微生物3―植物生育促進根圏微生物―
A5版 -
里山の自然とくらし 福島県鮫川村
入江 彰昭, 上地 由朗, 内田 均, 竹内 将俊, 舘 博, 安藤 達彦, 穂坂 賢, 高橋 悟, 渡邉 文雄, 川上 昭太郎, 栗田 和弥, 桝田 信彌, 伊藤 健, 入江 満美, 横田 健治（ Role： Joint author , p78-79、2頁）
東京農業大学出版会 2013.03 （ ISBN:978-4-88694 ）
Language：Japanese Book type：Scholarly book
村内の田畑の土壌分析を行い、本地域の土壌の特性について解説した。四六判、P.112
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Sustainable Farming Practices for Environmental Conservation
Edited by Machito Mihara and Akimi Fujimoto（ Role： Joint author , 抽出不可能）
Institute of Environment Rehabilitation and Conservation, Japan 2009.04 （ ISBN:4-916174-08-9 ）
Language：English Book type：Scholarly book
Misc 【 display / non-display 】
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Bacillus cyclic lipopeptide; elicitors to induce disease resistance in biological control of plant diseases Invited Reviewed
Kenji Yokota
Bioscience, Biotechnology, and Biochemistry 2025.12
Authorship：Lead author, Last author, Corresponding author Language：English Publishing type：Article, review, commentary, editorial, etc. (scientific journal)
Bacillus species have been employed as biocontrol agents in the context of plant disease management. However, the precise mechanisms through which they function remain to be fully elucidated. Cyclic lipopeptides (cLPs) have been deduced to play key roles in the biological control of plant diseases using Bacillus strains. In the early stages of research, the hypothesis was put forward that cLPs could suppress diseases through their antimicrobial activity. However, recent research provides robust evidence that cLPs function primarily as elicitors by inducing disease resistance in host plants. This review introduces recent trends regarding the characteristics of Bacillus cLPs in the context of biological control against plant diseases.
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Strategies for Biological Control of Brown Blotch Disease: Microorganisms Protect Edible Mushrooms from Pathogens via a Range of Modes of Action. Invited Reviewed
Shun Tomita, Hirosuke Shinohara, Kenji Yokota
116 - 124 2023.03
Authorship：Last author Language：Japanese Publishing type：Article, review, commentary, editorial, etc. (scientific journal)
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Bacillus属細菌を用いた植物病害生物防除における環状リポペプチドの機能 Invited
横田 健治
日本農薬学会誌 47 ( 2 ) 124 - 125 2022.08
Authorship：Lead author Language：Japanese Publishing type：Article, review, commentary, editorial, etc. (scientific journal)
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きのこを褐変化させる毒素tolaasinを解毒する細菌 Invited Reviewed
横田健治・富田駿・篠原弘亮
バイオサイエンスとインダストリー 79 ( 3 ) 214 - 215 2021.05
Authorship：Lead author Language：Japanese Publishing type：Article, review, commentary, editorial, etc. (scientific journal)
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拮抗性Bacillus属細菌を利用した植物病害の生物防除 機能性物質とその防除メカニズムを中心に
横田 健治
土と微生物 66 ( 1 ) 27 - 31 2012.04
Language：Japanese Publishing type：Article, review, commentary, editorial, etc. (international conference proceedings) Publisher：日本土壌微生物学会
拮抗性Bacillus属細菌を利用した植物病害の生物防除について報告した。
Industrial Property Rights 【 display / non-display 】
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抗菌剤、農薬、微生物による植物病害の防除方法、および新規バチルス - サブティリス
原 富次郎, 高塚 由美子, 杉村 祐哉, 横田 健治
Application no：WO2017150556A1 Date applied：2017.02
Patent/Registration no：WO2017150556A1 Date registered：2017.09 Date issued：2017.09
Country of applicant：Domestic Country of acquisition：Domestic
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分生胞子増殖因子、分生胞子増殖因子を含む培地及び分生胞子増殖因子の製造方法
横田 健治
Applicant：東京農業大学
Application no：特願2008-263233(P2008-263233) Date applied：2008.10
Announcement no：特開2010-88380(P2010-88380A) Date announced：2010.04
Country of applicant：Domestic
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ANTIMICROBIAL AGENT, PESTICIDE, METHOD FOR PREVENTING PLANT DISEASE CAUSED BY MICROORGANISMS, AND NOVEL Bacillus subtilis
Tomijiro Hara, Yumiko Takatsuka, Yuya Sugimura, Kenji Yokota
Application no：15579831
Honours, Awards and Prizes 【 display / non-display 】
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Best Oral Presenter
2022.11 ISSAAS-SEAPPRO Joint International Seminar and Congress 2022
Award type：Award from international society, conference, symposium, etc. Country：Indonesia
Scientific Research Funds Acquisition Results 【 display / non-display 】
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病害土壌診断バイオマーカーの開発に向けたメタゲノム解析
2016.09 - 2019.08
科学研究費補助金 基盤研究(C)
Authorship：Coinvestigator(s)
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地域資源活用型小規模持続的農業システムのためのアグロエコロジー研究
2016.04 - 2019.03
科学研究費補助金 基盤研究(C)
Authorship：Coinvestigator(s)
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バチルス属菌由来の環状リポペプチドによるシロイヌナズナの病害抵抗性制御機構の解明
2016.04 - 2019.03
科学研究費補助金 基盤研究(C)
Authorship：Principal investigator
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黄色ブドウ球菌の血球崩壊毒素の三次元構造解析による膜孔形成機構の解明
2000.04 - 2001.03
科学研究費補助金 特別研究員推奨費
黄色ブドウ球菌が生産する二成分性膜孔形成型毒素タンパク質γヘモリジンの構成分子LukF成分の赤血球細胞認識及び結合領域の解明
Other External Funds 【 display / non-display 】
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Bacillus属が分泌生産する新規抗菌性環状リポペプチドの構造解析と抗菌活性評価
2020.04 - 2021.03
京都大学エネルギー理工学研究所
横田 健治
Authorship：Principal investigator Grant type：Competitive
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Bacillus属が分泌生産する新規抗菌性環状リポペプチドの構造解析と抗菌活性評価
2019.04 - 2020.03
京都大学エネルギー理工学研究所
横田 健治
Authorship：Principal investigator Grant type：Competitive
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インドネシアのマングローブ根圏から分離された各種拮抗性細菌の拮抗作用の解明
2018.11 - 2019.02
民間財団等
横田 健治
Authorship：Principal investigator Grant type：Competitive
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Bacillus属菌の抗菌性リポペプチド生産を誘導する大豆由来の生理活性物質に関する研究
2010.05 - 2011.04
民間財団等 タカノ農芸化学研究助成財団 若手研究者部門
Authorship：Principal investigator Grant type：Competitive
Presentations 【 display / non-display 】
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Microbacterium foliorum NBRC 103072Tによるtolaasin 解毒機構 -Tolaasin 加水分解酵素は菌体の界面 活性剤処理により可溶化する- International conference
富田 駿, 梶川揚申, 五十君靜信, 篠原弘亮, 横田健治
令和2 年度日本植物病理学会大会 2020.03
Event date： 2020.03
Language：English Presentation type：Oral presentation (general)
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Susceptibility to Tolaasins on Tolaasin-Detoxyfying Microbacterium spp. International conference
Shun Tomita, Hirosuke Shinohara, Kenji Yokota
ISSAAS 2019 International Congress & General Meeting 2019 2019.10
Event date： 2019.10
Language：English Presentation type：Oral presentation (general)
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Comparative Study of Surfactin Homologues on Antibacterial Activity International conference
Takafumi Yoshida and Kenji Yokota
ISSAAS 2019 International Congress & General Meeting 2019 2019.10
Event date： 2019.10
Language：English Presentation type：Oral presentation (general)
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Arthrobacter sp. Isolate Enhance Fusarium Soil-Borne Disease International conference
Mana Adachi, Ryota Kataoka, Yusuke Yamamoto, Ryoko Kato, Kenji Yokota
ISSAAS 2019 International Congress & General Meeting 2019 2019.10
Event date： 2019.10
Language：English Presentation type：Oral presentation (general)
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Analysis of the Inhibitory Effect of Bacterial Growth on Cabbage Leaves in Response to Treatment with Lipopeptides International conference
Carla Suzuki Altrão, Yusuke Yanai, Hirosuke Shinohara, Kenji Yokota
ISSAAS 2019 International Congress & General Meeting 2019 2019.10
Event date： 2019.10
Language：English Presentation type：Oral presentation (general)