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Aoki N, Shimasaki T, Yazaki W, Sato T, Nakayasu M, Ando A, Kishino S, Ogawa J, Masuda S, Shibata A, Shirasu K, Yazaki K, Sugiyama A. An isoflavone catabolism gene cluster underlying interkingdom interactions in the soybean rhizosphere. ISME COMMUNICATIONS 2024; 4:ycae052. [PMID: 38707841 PMCID: PMC11069340 DOI: 10.1093/ismeco/ycae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 02/19/2024] [Accepted: 04/03/2024] [Indexed: 05/07/2024]
Abstract
Plant roots secrete various metabolites, including plant specialized metabolites, into the rhizosphere, and shape the rhizosphere microbiome, which is crucial for the plant health and growth. Isoflavones are major plant specialized metabolites found in legume plants, and are involved in interactions with soil microorganisms as initiation signals in rhizobial symbiosis and as modulators of the legume root microbiota. However, it remains largely unknown the molecular basis underlying the isoflavone-mediated interkingdom interactions in the legume rhizosphere. Here, we isolated Variovorax sp. strain V35, a member of the Comamonadaceae that harbors isoflavone-degrading activity, from soybean roots and discovered a gene cluster responsible for isoflavone degradation named ifc. The characterization of ifc mutants and heterologously expressed Ifc enzymes revealed that isoflavones undergo oxidative catabolism, which is different from the reductive metabolic pathways observed in gut microbiota. We further demonstrated that the ifc genes are frequently found in bacterial strains isolated from legume plants, including mutualistic rhizobia, and contribute to the detoxification of the antibacterial activity of isoflavones. Taken together, our findings reveal an isoflavone catabolism gene cluster in the soybean root microbiota, providing molecular insights into isoflavone-mediated legume-microbiota interactions.
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Affiliation(s)
- Noritaka Aoki
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Tomohisa Shimasaki
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Wataru Yazaki
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Tomoaki Sato
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Masaru Nakayasu
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Akinori Ando
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Shigenobu Kishino
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Jun Ogawa
- Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Sachiko Masuda
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Arisa Shibata
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Ken Shirasu
- Plant Immunity Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Kazufumi Yazaki
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Akifumi Sugiyama
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
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Matsuda H, Yamazaki Y, Moriyoshi E, Nakayasu M, Yamazaki S, Aoki Y, Takase H, Okazaki S, Nagano AJ, Kaga A, Yazaki K, Sugiyama A. Apoplast-Localized β-Glucosidase Elevates Isoflavone Accumulation in the Soybean Rhizosphere. PLANT & CELL PHYSIOLOGY 2023; 64:486-500. [PMID: 36718526 DOI: 10.1093/pcp/pcad012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/11/2023] [Accepted: 01/30/2023] [Indexed: 05/17/2023]
Abstract
Plant specialized metabolites (PSMs) are often stored as glycosides within cells and released from the roots with some chemical modifications. While isoflavones are known to function as symbiotic signals with rhizobia and to modulate the soybean rhizosphere microbiome, the underlying mechanisms of root-to-soil delivery are poorly understood. In addition to transporter-mediated secretion, the hydrolysis of isoflavone glycosides in the apoplast by an isoflavone conjugate-hydrolyzing β-glucosidase (ICHG) has been proposed but not yet verified. To clarify the role of ICHG in isoflavone supply to the rhizosphere, we have isolated two independent mutants defective in ICHG activity from a soybean high-density mutant library. In the root apoplastic fraction of ichg mutants, the isoflavone glycoside contents were significantly increased, while isoflavone aglycone contents were decreased, indicating that ICHG hydrolyzes isoflavone glycosides into aglycones in the root apoplast. When grown in a field, the lack of ICHG activity considerably reduced isoflavone aglycone contents in roots and the rhizosphere soil, although the transcriptomes showed no distinct differences between the ichg mutants and wild-types (WTs). Despite the change in isoflavone contents and composition of the root and rhizosphere of the mutants, root and rhizosphere bacterial communities were not distinctive from those of the WTs. Root bacterial communities and nodulation capacities of the ichg mutants did not differ from the WTs under nitrogen-deficient conditions either. Taken together, these results indicate that ICHG elevates the accumulation of isoflavones in the soybean rhizosphere but is not essential for isoflavone-mediated plant-microbe interactions.
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Affiliation(s)
- Hinako Matsuda
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, 611-0011 Japan
| | - Yumi Yamazaki
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, 611-0011 Japan
| | - Eiko Moriyoshi
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, 611-0011 Japan
| | - Masaru Nakayasu
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, 611-0011 Japan
| | - Shinichi Yamazaki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Seiryo 2-1, Sendai, 980-8573 Japan
| | - Yuichi Aoki
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Seiryo 2-1, Sendai, 980-8573 Japan
- Department of Applied Information Sciences, Graduate School of Information Sciences, Tohoku University, Aoba 6-3-09, Aramaki-aza Aoba-ku, Sendai, 980-8579 Japan
| | - Hisabumi Takase
- Department of Bioscience and Biotechnology, Faculty of Bioenvironmental Science, Kyoto University of Advanced Science, Sogabecho Nanjo Otani 1-1, Kameoka, 621-8555 Japan
| | - Shin Okazaki
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Saiwaicho 3-5-8, Fuchu, 183-8509 Japan
- Department of International Environmental and Agricultural Science, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Saiwaicho 3-5-8, Fuchu, 183-8509 Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Seta Oe-cho Yokotani 1-5, Otsu, 520-2194 Japan
- Institute for Advanced Biosciences, Keio University, Nipponkoku 403-1, Daihouji, Tsuruoka, 997-0017 Japan
| | - Akito Kaga
- Institute of Crop Science, National Agriculture and Food Research Organization, Kannondai 2-1-2, Tsukuba, 305-8518 Japan
| | - Kazufumi Yazaki
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, 611-0011 Japan
| | - Akifumi Sugiyama
- Research Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, 611-0011 Japan
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