RTNakano Lab

Publications

* First author(s)
# Corresponding author(s)

Original articles

  • Horizontal acquisition of nicotine catabolism gene cluster enhances Arthrobacter fitness within tobacco root microbiota
    Microbiome (2026)
    Tomohisa Shimasaki*,#, Yui Nose, Sachiko Masuda, Arisa Shibata, Tsubasa Shoji, Shuhei Yabe, Maiko Furubayashi, Yoshitomo Kikuchi, Ken Shirasu, Kazufumi Yazaki, Yasunori Ichihashi, Akifumi Sugiyama, Ryohei Thomas Nakano#
    https://doi.org/10.1186/s40168-026-02466-x
  • Distinct and Intermediate Bacterial Community Structure of the Wasabi Rhizome Based on Compartment-resolved 16S rRNA Gene Profiling
    Microbes and Environments (2026)
    Masayoshi Hashimoto, Kana Ohata, Ryohei Thomas Nakano, Hisae Hirata, Yusuke Katai
    https://doi.org/10.1264/jsme2.ME26005
  • Evolutionary Trade-off Between Stomatal Defense and Gas Exchange in Brassicaceae
    Current Biology (2025)
    Wenshang Kang, Masahito Nakano, Kaori Fukumoto, Rikako Hirata, Pei Zhai, Yulin Du, Kunqi Hong, Jörg Ziegler, Yayoi Tsuda, Dieter Becker, Eiji Nambara, Ryohei Thomas Nakano, Shunsuke Miyashima, Akira Mine, Xiaowei Han, Kenichi Tsuda
    https://doi.org/10.1016/j.cub.2025.10.037
  • Alkaloids as mediators in plant-microbe interactions: Metabolism and role in the rhizosphere
    Plant Biotechnology (2025) Review
    Tomohisa Shimasaki*,#, Ryohei Thomas Nakano
    https://doi.org/10.5511/plantbiotechnology.25.0310a
  • MYB68 regulates suberin patterning and radially distinct endodermal differentiation
    Cell Reports (2025)
    Leonie Kraska, Josep Mercadal Melia, Ryohei Thomas Nakano, David Molina, Pau Formosa-Jordan, Laura Ragni, Tonni Grube Andersen
    https://doi.org/10.1016/j.celrep.2025.115794
  • Apoplastic barriers are essential for nodule formation and nitrogen fixation in Lotus japonicus
    Science (2025)
    Defeng Shen, Nikola Micic, Rafael E. Venado, Nanna Bjarnholt, Christoph Crocoll, Daniel Pergament Persson, Sebastian Samwald, Stanislav Kopriva, Philip Westhoff, Sabine Metzger, Ulla Neumann, Ryohei Thomas Nakano, Macarena Marín Arancibia, Tonni Grube Andersen
    https://doi.org/10.1126/science.ado8680
  • An Isoflavone catabolism gene cluster underlying Interkingdom interactions in the soybean rhizosphere
    ISME Communications 4:1 (2024)
    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
    https://doi.org/10.1093/ismeco/ycae052
  • Long-term consequences of PTI activation and its manipulation by root-associated microbiota
    Plant and Cell Physiol. pcae033 (2024) Review
    Ryohei Thomas Nakano*,# and Tomohisa Shimasaki
    https://doi.org/10.1093/pcp/pcae033
  • Chromosomal barcodes for simultaneous tracking of near-isogenic bacterial strains in plant microbiota
    Nature Microbiol. 9, 1117-1129 (2024)
    Jana Ordon, Julien Thouin, Ryohei Thomas Nakano, Ka-Wai Ma, Pengfan Zhang, Bruno Huettel, Ruben Garrido-Oter, Paul Schulze-Lefert
    https://doi.org/10.1038/s41564-024-01619-8
  • ER body-resident myrosinases and tryptophan specialized metabolism modulate root microbiota assembly
    New Phytologist, 241: 329-342 (2024)
    Arpan Kumar Basak*, Anna Piasecka, Jana Hucklenbroich, Gözde Merve Türksoy, Rui Guan, Pengfan Zhang, Felix Getzke, Ruben Garrido-Oter, Stéphane Hacquard, Kazimierz Strzałka, Paweł Bednarek, Kenji Yamada, Ryohei Thomas Nakano#.
    https://doi.org/10.1111/nph.19289
  • Apoplastic barrier establishment in roots and nodules of Lotus japonicus is essential for root-shoot signaling and N-fixation
    bioRxiv (2023)
    Defeng Shen, Rafael E. Venado, Ulla Neumann, Nadine Dyballa-Rukes, Swati Mahiwal, Sabine Metzger, Ryohei Thomas Nakano, Macarena Marín, Tonni Grube Andersen
    https://doi.org/10.1101/2023.12.06.570432
  • Tryptophan metabolism and bacterial commensals prevent fungal dysbiosis in Arabidopsis roots.
    PNAS 118 (49) e2111521118 (2021)
    Katarzyna W. Wolinska*, Nathan Vannier, Thorsten Thiergart, Brigitte Pickel, Sjoerd Gremmen, Ryohei Thomas Nakano, Youssef Belkhadir, Pawel Bednarek, Stéphane Hacquard#
    https://doi.org/10.1073/pnas.2111521118
  • Rhizobiales commensal bacteria promote Arabidopsis thaliana root growth via host sulfated peptide pathway.
    bioRxiv (2021)
    Jana Hucklenbroich*, Tamara Gigolashvili, Anna Koprivova, Philipp Spohr, Mahnaz Nezamivand Chegini, Gunnar W Klau, Stanislav Kopriva, Ryohei Thomas Nakano#
    https://doi.org/10.1101/2021.05.25.444716
  • Retrograde sulfur flow from glucosinolates to cysteine in Arabidopsis thaliana.
    PNAS 118 (22) e2017890118 (2021)
    Ryosuke Sugiyama*#, Rui Li*, Ayuko Kuwahara, Ryo Nakabayashi, Naoyuki Sotta, Tetsuya Mori, Takehiro Ito, Naoko Ohkama-Ohtsu, Toru Fujiwara, Kazuki Saito, Ryohei Thomas Nakano, Paweł Bednarek, and Masami Yokota Hirai#
    https://doi.org/10.1073/pnas.2017890118
  • Tobacco root endophytic Arthrobacter harbors genomic features enabling the catabolism of host-specific plant specialized metabolites. mBio 12:e00846-21 (2021)
    Tomohisa Shimasaki*, Sachiko Masuda, Ruben Garrido-Oter, Takashi Kawasaki, Yuichi Aoki, Arisa Shibata, Wataru Suda, Ken Shirasu, Kazufumi Yazaki, Ryohei Thomas Nakano#, Akifumi Sugiyama#
    https://doi.org/10.1128/mBio.00846-21
  • Discovery of a Family of Mixed Lineage Kinase Domain-like Proteins in Plants and Their Role in Innate Immune Signaling.
    Cell Host & Microbe 28(6), 813-824.e6 (2020)
    Lisa Mahdi*, Menghang Huang*, Xiaoxiao Zhang*, Ryohei Thomas Nakano, Leïla Brulé Kopp, Isabel M.L. Saur, Florence Jacob, Viera Kovacova, Dmitry Lapin, Jane E. Parker, James M. Murphy,Kay Hofmann, Paul Schulze-Lefert, Jijie Chai#, and Takaki Maekawa#
    https://doi.org/10.1016/j.chom.2020.08.012
  • Characterization of rhizome transcriptome and identification of a rhizomatous ER body in the clonal plant Cardamine leucantha.
    Scientific Reports 10, 13291 (2020)
    Kiwako S. Araki*#, Atsushi J. Nagano, Ryohei Thomas Nakano, Tatsuya Kitazume, Katsushi Yamaguchi, Ikuko Hara-Nishimura, Shuji Shigenobu, and Hiroshi Kudoh#
    https://doi.org/10.1038/s41598-020-69941-9
  • A Golgi-released subpopulation of the trans-Golgi network mediates constitutive and pathogen-inducible protein secretion in Arabidopsis.
    Plant Physiol. 179 (2) 519-532 (2019)
    Tomohiro Uemura*#, Ryohei Thomas Nakano*, Junpei Takagi, Yiming Wang, Katharina Kramer, Iris Finkemeier, Hirofumi Nakagami, Kenichi Tsuda, Takashi Ueda, Paul Schulze-Lefert, and Akihiko Nakano
    https://doi.org/10.1104/pp.18.01228
  • Modular Traits of the Rhizobiales Root Microbiota and Their Evolutionary Relationship with Symbiotic Rhizobia.
    Cell Host & Microbe 24(1), 155–167 (2018)
    Ruben Garrido-Oter*, Ryohei Thomas Nakano*, Nina Dombrowski*, Ka-Wai Ma, The AgBiome Team, Alice C. McHardy, and Paul Schulze-Lefert#
    https://doi.org/10.1016/j.chom.2018.06.006
  • Glutathione transferase U13 functions in pathogen-triggered glucosinolate metabolism in Arabidopsis.
    Plant Physiol. 176(1): 538-55 (2018)
    Mariola Piślewska-Bednarek*, Ryohei Thomas Nakano, Kei Hiruma, Marta Pastorczyk, Andrea Sanchez-Vallet, Suthitar Singkaravanit-Ogawa, Danuta Ciesiołka, Yoshitaka Takano, Antonio Molina, Paul Schulze-Lefert, and Paweł Bednarek#
    https://doi.org/10.1104%2Fpp.17.01455
  • PYK10 Myrosinase Reveals a Functional Coordination between ER Bodies and Glucosinolates in Arabidopsis thaliana.
    Plant J. 89: 204-220 (2017)
    Ryohei Thomas Nakano*, Mariola Piślewska-Bednarek, Kenji Yamada, Patrick P. Edger, Mado Miyahara, Maki Kondo, Christoph Böttcher, Masashi Mori, Mikio Nishimura, Paul Schulze-Lefert#, Ikuko Hara-Nishimura#, and Pawel Bednarek#
    https://doi.org/10.1111/tpj.13377
  • Root Endophyte Colletotrichum tofieldiae Confers Plant Fitness Benefits that Are Phosphate Status Dependent. 
    CELL 165(2): 464-474 (2016)
    Kei Hiruma*, Nina Gerlach, Soledad Sacristán, Ryohei Thomas Nakano, Stéphane Hacquard, Barbara Kracher, Ulla Neumann, Diana Ramírez, Marcel Bucher, Richard J. O’Connell#, and Paul Schulze-Lefert#
    https://doi.org/10.1016/j.cell.2016.02.028
  • ER bodies in plants of the Brassicales order: biogenesis and association with innate immunity.
    Front. Plant Sci. 5:73 (2014) Review
    Ryohei Thomas Nakano*, Kenji Yamada*, Paweł Bednarek, Mikio Nishimura, and Ikuko Hara-Nishimura#
    https://doi.org/10.3389/fpls.2014.00073
  • ERMO3/MVP1/GOLD36 Is Involved in a Cell Type-Specific Mechanism for Maintaining ER Morphology in Arabidopsis thaliana.
    PLoS ONE 7, e49103 (2012)
    Ryohei Thomas Nakano*, Ryo Matsushima, Atsushi J Nagano, Yoichiro Fukao, Masayuki Fujiwara, Maki Kondo, Mikio Nishimura, and Ikuko Hara-Nishimura#
    https://doi.org/10.1371/journal.pone.0049103
  • GNOM-LIKE1/ERMO1 and SEC24a/ERMO2 Are Required for Maintenance of Endoplasmic Reticulum Morphology in Arabidopsis thaliana.
    THE PLANT CELL 21:3672-3685 (2009)
    Ryohei Thomas Nakano*, Ryo Matsushima, Haruko Ueda, Kentaro Tamura, Tomoo Shimada, Lixin Li, Yasuko Hayashi, Maki Kondo, Mikio Nishimura and Ikuko Hara-Nishimura#
    https://doi.org/10.1105/tpc.109.068270
  • Quantitative Analysis of ER Body Morphology in an Arabidopsis Mutant.
    Plant Cell Physiol. 50(12):2015-22 (2009)
    Atsushi J. Nagano*, Akinori Maekawa, Ryohei Thomas Nakano, Mado Miyahara, Takumi Higaki, Natsumaro Kutsuna, Seiichiro Hasezawa and Ikuko Hara-Nishimura#
    https://doi.org/10.1093/pcp/pcp157

Other articles

  • 『研究者、生活を語る　〜「両立」の舞台裏〜』育児編：海外で4人の子育てをしながら研究をするということ
    岩波書店 ISBN 9784000616614 (2024)
    Purchase from amazon.co.jp
  • Taste of microbes: the terroir explained by rhizospheric microbes
    New Phytologist (2024) Commentary
    Ryohei Thomas Nakano
    https://doi.org/10.1111/nph.19796
  • A Friend in Common: A Small GTPase in Independent PTI and ETI Immune Receptor Complexes
    Plant Cell Physiol. (2021) Commentary
    Ryohei Thomas Nakano
    https://doi.org/10.1093/pcp/pcab154
  • Apoplastic Fluid Preparation from Arabidopsis thaliana Leaves Upon Interaction with a Nonadapted Powdery Mildew Pathogen
    Plant Proteomics. Methods and Protocols. (3rd edition), 79-88 (2020) 
    Ryohei Thomas Nakano*#, Nobuaki Ishihama, Yiming Wang, Junpei Takagi, Tomohiro Uemura, Paul Schulze-Lefert, and Hirofumi Nakagami# 
    https://doi.org/10.1007/978-1-0716-0528-8_6
  • 『共生微生物―生物と密接に関わるミクロな生命体』第14章「根圏微生物」
    化学同人 ISBN-13:978-4759817287(2016)
    大野 博司 (編集)
    Purchase from amazon.co.jp

Essays etc…

Mostly in Japanese…