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Liu J, Liang M, Lin T, Zhao Q, Wang H, Yang S, Guo Q, Wang X, Guo H, Cui L, Yan Y, Hieno A, Kageyama K, Suga H, Li M. A LAMP-Based Toolbox Developed for Detecting the Major Pathogens Affecting the Production and Quality of the Chinese Medicinal Crop Aconitum carmichaelii. Plant Dis 2023; 107:658-666. [PMID: 35852903 DOI: 10.1094/pdis-05-22-1092-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Aconitum carmichaelii Debeaux is a traditional Chinese medicinal herb that has been utilized for approximately 2,000 years. However, as cultivation has increased, there have been more reports of A. carmichaelii infections caused by four major pathogenic fungal species, Fusarium oxysporum, F. solani, Mucor circinelloides, and Sclerotium rolfsii, resulting in increased disease incidences and limited production and quality. To detect these infections, we developed a LAMP-based toolbox in this study. The cytochrome c oxidase subunit 1 (cox1) gene, translation elongation factor-1α (EF-1α), internal transcribed spacer (ITS) regions of rDNA, and alcohol dehydrogenase 1 (ADH1) gene, respectively, were used to design species-specific LAMP primer sets for F. oxysporum, F. solani, S. rolfsii, and M. circinelloides. The results showed that the LAMP-based toolbox was effective at detecting pathogens in soil and plant materials. We also used this toolbox to investigate pathogen infection in the main planting regions of A. carmichaelii. Before harvesting, F. oxysporum, M. circinelloides, and S. rolfsii were commonly found in the planting fields and in infected A. carmichaelii plants. Therefore, the toolbox we developed will be useful for tracking these infections, as well as for disease control in A. carmichaelii.
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Affiliation(s)
- Jingzhe Liu
- The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education (Shaanxi Normal University), Xi'an, Shaanxi 710119, P.R. China
| | - Mengyi Liang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Tao Lin
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Qing Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Huiqin Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Shunyuan Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Qian Guo
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Xinyi Wang
- The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education (Shaanxi Normal University), Xi'an, Shaanxi 710119, P.R. China
| | - Hua Guo
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Langjun Cui
- The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education (Shaanxi Normal University), Xi'an, Shaanxi 710119, P.R. China
| | - Yaping Yan
- The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education (Shaanxi Normal University), Xi'an, Shaanxi 710119, P.R. China
| | - Ayaka Hieno
- River Basin Research Center, Gifu University, Gifu 501-1193, Japan
| | - Koji Kageyama
- River Basin Research Center, Gifu University, Gifu 501-1193, Japan
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, Gifu 501-1193, Japan
| | - Mingzhu Li
- The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education (Shaanxi Normal University), Xi'an, Shaanxi 710119, P.R. China
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
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2
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Nakamura T, Matsumoto M, Amano K, Enokido Y, Zolensky ME, Mikouchi T, Genda H, Tanaka S, Zolotov MY, Kurosawa K, Wakita S, Hyodo R, Nagano H, Nakashima D, Takahashi Y, Fujioka Y, Kikuiri M, Kagawa E, Matsuoka M, Brearley AJ, Tsuchiyama A, Uesugi M, Matsuno J, Kimura Y, Sato M, Milliken RE, Tatsumi E, Sugita S, Hiroi T, Kitazato K, Brownlee D, Joswiak DJ, Takahashi M, Ninomiya K, Takahashi T, Osawa T, Terada K, Brenker FE, Tkalcec BJ, Vincze L, Brunetto R, Aléon-Toppani A, Chan QHS, Roskosz M, Viennet JC, Beck P, Alp EE, Michikami T, Nagaashi Y, Tsuji T, Ino Y, Martinez J, Han J, Dolocan A, Bodnar RJ, Tanaka M, Yoshida H, Sugiyama K, King AJ, Fukushi K, Suga H, Yamashita S, Kawai T, Inoue K, Nakato A, Noguchi T, Vilas F, Hendrix AR, Jaramillo-Correa C, Domingue DL, Dominguez G, Gainsforth Z, Engrand C, Duprat J, Russell SS, Bonato E, Ma C, Kawamoto T, Wada T, Watanabe S, Endo R, Enju S, Riu L, Rubino S, Tack P, Takeshita S, Takeichi Y, Takeuchi A, Takigawa A, Takir D, Tanigaki T, Taniguchi A, Tsukamoto K, Yagi T, Yamada S, Yamamoto K, Yamashita Y, Yasutake M, Uesugi K, Umegaki I, Chiu I, Ishizaki T, Okumura S, Palomba E, Pilorget C, Potin SM, Alasli A, Anada S, Araki Y, Sakatani N, Schultz C, Sekizawa O, Sitzman SD, Sugiura K, Sun M, Dartois E, De Pauw E, Dionnet Z, Djouadi Z, Falkenberg G, Fujita R, Fukuma T, Gearba IR, Hagiya K, Hu MY, Kato T, Kawamura T, Kimura M, Kubo MK, Langenhorst F, Lantz C, Lavina B, Lindner M, Zhao J, Vekemans B, Baklouti D, Bazi B, Borondics F, Nagasawa S, Nishiyama G, Nitta K, Mathurin J, Matsumoto T, Mitsukawa I, Miura H, Miyake A, Miyake Y, Yurimoto H, Okazaki R, Yabuta H, Naraoka H, Sakamoto K, Tachibana S, Connolly HC, Lauretta DS, Yoshitake M, Yoshikawa M, Yoshikawa K, Yoshihara K, Yokota Y, Yogata K, Yano H, Yamamoto Y, Yamamoto D, Yamada M, Yamada T, Yada T, Wada K, Usui T, Tsukizaki R, Terui F, Takeuchi H, Takei Y, Iwamae A, Soejima H, Shirai K, Shimaki Y, Senshu H, Sawada H, Saiki T, Ozaki M, Ono G, Okada T, Ogawa N, Ogawa K, Noguchi R, Noda H, Nishimura M, Namiki N, Nakazawa S, Morota T, Miyazaki A, Miura A, Mimasu Y, Matsumoto K, Kumagai K, Kouyama T, Kikuchi S, Kawahara K, Kameda S, Iwata T, Ishihara Y, Ishiguro M, Ikeda H, Hosoda S, Honda R, Honda C, Hitomi Y, Hirata N, Hirata N, Hayashi T, Hayakawa M, Hatakeda K, Furuya S, Fukai R, Fujii A, Cho Y, Arakawa M, Abe M, Watanabe S, Tsuda Y. Formation and evolution of carbonaceous asteroid Ryugu: Direct evidence from returned samples. Science 2023; 379:eabn8671. [PMID: 36137011 DOI: 10.1126/science.abn8671] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Samples of the carbonaceous asteroid Ryugu were brought to Earth by the Hayabusa2 spacecraft. We analyzed 17 Ryugu samples measuring 1 to 8 millimeters. Carbon dioxide-bearing water inclusions are present within a pyrrhotite crystal, indicating that Ryugu's parent asteroid formed in the outer Solar System. The samples contain low abundances of materials that formed at high temperatures, such as chondrules and calcium- and aluminum-rich inclusions. The samples are rich in phyllosilicates and carbonates, which formed through aqueous alteration reactions at low temperature, high pH, and water/rock ratios of <1 (by mass). Less altered fragments contain olivine, pyroxene, amorphous silicates, calcite, and phosphide. Numerical simulations, based on the mineralogical and physical properties of the samples, indicate that Ryugu's parent body formed ~2 million years after the beginning of Solar System formation.
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Affiliation(s)
- T Nakamura
- Department of Earth Sciences, Tohoku University, Sendai 980-8578, Japan
| | - M Matsumoto
- Department of Earth Sciences, Tohoku University, Sendai 980-8578, Japan
| | - K Amano
- Department of Earth Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Y Enokido
- Department of Earth Sciences, Tohoku University, Sendai 980-8578, Japan
| | - M E Zolensky
- NASA Johnson Space Center; Houston, TX 77058, USA
| | - T Mikouchi
- The University Museum, The University of Tokyo, Tokyo 113-0033, Japan
| | - H Genda
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - S Tanaka
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Department of Space and Astronautical Science, The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193, Japan
| | - M Y Zolotov
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ 85287, USA
| | - K Kurosawa
- Planetary Exploration Research Center, Chiba Institute of Technology, Narashino 275-0016, Japan
| | - S Wakita
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - R Hyodo
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - H Nagano
- Department of Mechanical Systems Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - D Nakashima
- Department of Earth Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Y Takahashi
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan.,Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan
| | - Y Fujioka
- Department of Earth Sciences, Tohoku University, Sendai 980-8578, Japan
| | - M Kikuiri
- Department of Earth Sciences, Tohoku University, Sendai 980-8578, Japan
| | - E Kagawa
- Department of Earth Sciences, Tohoku University, Sendai 980-8578, Japan
| | - M Matsuoka
- Laboratoire d'Etudes Spatiales et d'Instrumentation en Astrophysique (LESIA), Observatoire de Paris, Meudon 92195 France.,Geological Survey of Japan, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, 305-8567, Japan
| | - A J Brearley
- Department of Earth and Planetary Sciences, University of New Mexico, Albuquerque, NM 87131, USA
| | - A Tsuchiyama
- Research Organization of Science and Technology, Ritsumeikan University, Kusatsu 525-8577, Japan.,Key Laboratory of Mineralogy and Metallogeny, Guangdong Provincial Key Laboratory of Mineral Physics and Materials, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences (CAS), Guangzhou 510640, China.,Center for Excellence in Deep Earth Science, CAS, Guangzhou 510640, China
| | - M Uesugi
- Scattering and Imaging Division, Japan Synchrotron Radiation Research Institute, Sayo 679-5198, Japan
| | - J Matsuno
- Research Organization of Science and Technology, Ritsumeikan University, Kusatsu 525-8577, Japan
| | - Y Kimura
- Institute of Low Temperature Science, Hokkaido University, Sapporo 060-0819, Japan
| | - M Sato
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - R E Milliken
- Department of Earth, Environmental, and Planetary Sciences, Brown University, Providence, RI 02912, USA
| | - E Tatsumi
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan.,Instituto de Astrofísica de Canarias, University of La Laguna, Tenerife 38205, Spain
| | - S Sugita
- Planetary Exploration Research Center, Chiba Institute of Technology, Narashino 275-0016, Japan.,Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - T Hiroi
- Department of Earth, Environmental, and Planetary Sciences, Brown University, Providence, RI 02912, USA
| | - K Kitazato
- Aizu Research Center for Space Informatics, The University of Aizu, Aizu-Wakamatsu 965-8580, Japan
| | - D Brownlee
- Department of Astronomy, University of Washington, Seattle, WA 98195 USA
| | - D J Joswiak
- Department of Astronomy, University of Washington, Seattle, WA 98195 USA
| | - M Takahashi
- Department of Earth Sciences, Tohoku University, Sendai 980-8578, Japan
| | - K Ninomiya
- Institute for Radiation Sciences, Osaka University, Toyonaka 560-0043, Japan
| | - T Takahashi
- Kavli Institute for the Physics and Mathematics of the Universe, The University of Tokyo, Kashiwa 277-8583, Japan.,Department of Physics, The University of Tokyo, Tokyo 113-0033, Japan
| | - T Osawa
- Materials Sciences Research Center, Japan Atomic Energy Agency, Tokai 319-1195, Japan
| | - K Terada
- Department of Earth and Space Science, Osaka University, Toyonaka 560-0043, Japan
| | - F E Brenker
- Institute of Geoscience, Goethe University, Frankfurt, 60438 Frankfurt am Main, Germany
| | - B J Tkalcec
- Institute of Geoscience, Goethe University, Frankfurt, 60438 Frankfurt am Main, Germany
| | - L Vincze
- Department of Chemistry, Ghent University, Krijgslaan 281 S12, Ghent, Belgium
| | - R Brunetto
- Institut d'Astrophysique Spatiale, Université Paris-Saclay, Orsay 91405, France
| | - A Aléon-Toppani
- Institut d'Astrophysique Spatiale, Université Paris-Saclay, Orsay 91405, France
| | - Q H S Chan
- Department of Earth Sciences, Royal Holloway, University of London, Egham TW20 0EX, UK
| | - M Roskosz
- Institut de Minéralogie, Physique des Matériaux et Cosmochimie, Muséum National d'Histoire Naturelle, Centre national de la recherche scientifique (CNRS), Sorbonne Université, Paris, France
| | - J-C Viennet
- Institut de Minéralogie, Physique des Matériaux et Cosmochimie, Muséum National d'Histoire Naturelle, Centre national de la recherche scientifique (CNRS), Sorbonne Université, Paris, France
| | - P Beck
- Institut de Planétologie et d'Astrophysique de Grenoble, CNRS, Université Grenoble Alpes, 38000 Grenoble, France
| | - E E Alp
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - T Michikami
- Faculty of Engineering, Kindai University, Higashi-Hiroshima 739-2116, Japan
| | - Y Nagaashi
- Department of Earth Sciences, Tohoku University, Sendai 980-8578, Japan.,Department of Planetology, Kobe University, Kobe 657-8501, Japan
| | - T Tsuji
- Department of Earth Resources Engineering, Kyushu University, Fukuoka 819-0395, Japan.,School of Engineering, The University of Tokyo, Tokyo 113-0033, Japan
| | - Y Ino
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Department of Physics, Kwansei Gakuin University, Sanda 669-1330, Japan
| | - J Martinez
- NASA Johnson Space Center; Houston, TX 77058, USA
| | - J Han
- Department of Earth and Atmospheric Sciences, University of Houston, Houston, TX 77204, USA
| | - A Dolocan
- Texas Materials Institute, The University of Texas at Austin, Austin, TX 78712, USA
| | - R J Bodnar
- Department of Geoscience, Virginia Tech, Blacksburg, VA 24061, USA
| | - M Tanaka
- Materials Analysis Station, National Institute for Materials Science, Tsukuba 305-0047, Japan
| | - H Yoshida
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - K Sugiyama
- Institute for Materials Research, Tohoku University, Sendai 980-8577, Japan
| | - A J King
- Department of Earth Science, Natural History Museum, London SW7 5BD, UK
| | - K Fukushi
- Institute of Nature and Environmental Technology, Kanazawa University, Kanazawa 920-1192, Japan
| | - H Suga
- Spectroscopy Division, Japan Synchrotron Radiation Research Institute, Sayo 679-5198, Japan
| | - S Yamashita
- Department of Materials Structure Science, The Graduate University for Advanced Studies (SOKENDAI), Tsukuba, Ibaraki 305-0801, Japan.,Institute of Materials Structure Science, High-Energy Accelerator Research Organization, Tsukuba 305-0801, Japan
| | - T Kawai
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - K Inoue
- Institute of Nature and Environmental Technology, Kanazawa University, Kanazawa 920-1192, Japan
| | - A Nakato
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - T Noguchi
- Division of Earth and Planetary Sciences, Kyoto University, Kyoto 606-8502, Japan.,Faculty of Arts and Science, Kyushu University, Fukuoka 819-0395, Japan
| | - F Vilas
- Planetary Science Institute, Tucson, AZ 85719, USA
| | - A R Hendrix
- Planetary Science Institute, Tucson, AZ 85719, USA
| | | | - D L Domingue
- Planetary Science Institute, Tucson, AZ 85719, USA
| | - G Dominguez
- Department of Physics, California State University, San Marcos, CA 92096, USA
| | - Z Gainsforth
- Space Sciences Laboratory, University of California, Berkeley, CA 94720, USA
| | - C Engrand
- Laboratoire de Physique des 2 Infinis Irène Joliot-Curie, Université Paris-Saclay, CNRS, 91405 Orsay, France
| | - J Duprat
- Institut de Minéralogie, Physique des Matériaux et Cosmochimie, Muséum National d'Histoire Naturelle, Centre national de la recherche scientifique (CNRS), Sorbonne Université, Paris, France
| | - S S Russell
- Department of Earth Science, Natural History Museum, London SW7 5BD, UK
| | - E Bonato
- Institute for Planetary Research, Deutsches Zentrum für Luftund Raumfahrt, Rutherfordstraße 2 12489 Berlin, Germany
| | - C Ma
- Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena CA 91125, USA
| | - T Kawamoto
- Department of Geosciences, Shizuoka University, Shizuoka 422-8529, Japan
| | - T Wada
- Department of Earth Sciences, Tohoku University, Sendai 980-8578, Japan
| | - S Watanabe
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Kavli Institute for the Physics and Mathematics of the Universe, The University of Tokyo, Kashiwa 277-8583, Japan
| | - R Endo
- Department of Materials Science and Engineering, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - S Enju
- Graduate School of Science and Engineering, Ehime University, Matsuyama 790-8577, Japan
| | - L Riu
- European Space Astronomy Centre, 28692 Villanueva de la Cañada, Spain
| | - S Rubino
- Institut d'Astrophysique Spatiale, Université Paris-Saclay, Orsay 91405, France
| | - P Tack
- Department of Chemistry, Ghent University, Krijgslaan 281 S12, Ghent, Belgium
| | - S Takeshita
- High Energy Accelerator Research Organization, Tokai 319-1106, Japan
| | - Y Takeichi
- Department of Materials Structure Science, The Graduate University for Advanced Studies (SOKENDAI), Tsukuba, Ibaraki 305-0801, Japan.,Institute of Materials Structure Science, High-Energy Accelerator Research Organization, Tsukuba 305-0801, Japan.,Department of Applied Physics, Osaka University, Suita 565-0871, Japan
| | - A Takeuchi
- Scattering and Imaging Division, Japan Synchrotron Radiation Research Institute, Sayo 679-5198, Japan
| | - A Takigawa
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - D Takir
- NASA Johnson Space Center; Houston, TX 77058, USA
| | | | - A Taniguchi
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori 590-0494, Japan
| | - K Tsukamoto
- Department of Earth Sciences, Tohoku University, Sendai 980-8578, Japan
| | - T Yagi
- National Metrology Institute of Japan, AIST, Tsukuba 305-8565, Japan
| | - S Yamada
- Department of Physics, Rikkyo University, Tokyo 171-8501, Japan
| | - K Yamamoto
- Japan Fine Ceramics Center, Nagoya 456-8587, Japan
| | - Y Yamashita
- National Metrology Institute of Japan, AIST, Tsukuba 305-8565, Japan
| | - M Yasutake
- Scattering and Imaging Division, Japan Synchrotron Radiation Research Institute, Sayo 679-5198, Japan
| | - K Uesugi
- Scattering and Imaging Division, Japan Synchrotron Radiation Research Institute, Sayo 679-5198, Japan
| | - I Umegaki
- High Energy Accelerator Research Organization, Tokai 319-1106, Japan.,Toyota Central Research and Development Laboratories, Nagakute 480-1192, Japan
| | - I Chiu
- Institute for Radiation Sciences, Osaka University, Toyonaka 560-0043, Japan
| | - T Ishizaki
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - S Okumura
- Division of Earth and Planetary Sciences, Kyoto University, Kyoto 606-8502, Japan
| | - E Palomba
- Istituto di Astrofisica e Planetologia Spaziali, Istituto Nazionale di Astrofisica, Rome 00133, Italy
| | - C Pilorget
- Institut d'Astrophysique Spatiale, Université Paris-Saclay, Orsay 91405, France.,Institut Universitaire de France, Paris, France
| | - S M Potin
- Laboratoire d'Etudes Spatiales et d'Instrumentation en Astrophysique (LESIA), Observatoire de Paris, Meudon 92195 France.,Faculty of Aerospace Engineering, Delft University of Technology, Delft, Netherlands
| | - A Alasli
- Department of Mechanical Systems Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - S Anada
- Japan Fine Ceramics Center, Nagoya 456-8587, Japan
| | - Y Araki
- Department of Physical Sciences, Ritsumeikan University, Shiga 525-0058, Japan
| | - N Sakatani
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Department of Physics, Rikkyo University, Tokyo 171-8501, Japan
| | - C Schultz
- Department of Earth, Environmental, and Planetary Sciences, Brown University, Providence, RI 02912, USA
| | - O Sekizawa
- Spectroscopy Division, Japan Synchrotron Radiation Research Institute, Sayo 679-5198, Japan
| | - S D Sitzman
- Physical Sciences Laboratory, The Aerospace Corporation, CA 90245, USA
| | - K Sugiura
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - M Sun
- Key Laboratory of Mineralogy and Metallogeny, Guangdong Provincial Key Laboratory of Mineral Physics and Materials, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences (CAS), Guangzhou 510640, China.,Center for Excellence in Deep Earth Science, CAS, Guangzhou 510640, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - E Dartois
- Institut des Sciences Moléculaires d'Orsay, Université Paris-Saclay, CNRS, 91405 Orsay, France
| | - E De Pauw
- Department of Chemistry, Ghent University, Krijgslaan 281 S12, Ghent, Belgium
| | - Z Dionnet
- Institut d'Astrophysique Spatiale, Université Paris-Saclay, Orsay 91405, France
| | - Z Djouadi
- Institut d'Astrophysique Spatiale, Université Paris-Saclay, Orsay 91405, France
| | - G Falkenberg
- Deutsches Elektronen-Synchrotron Photon Science, 22603 Hamburg, Germany
| | - R Fujita
- Department of Mechanical Systems Engineering, Nagoya University, Nagoya 464-8603, Japan
| | - T Fukuma
- Nano Life Science Institute, Kanazawa University, Kanazawa 920-1192, Japan
| | - I R Gearba
- Texas Materials Institute, The University of Texas at Austin, Austin, TX 78712, USA
| | - K Hagiya
- Graduate School of Life Science, University of Hyogo, Hyogo 678-1297, Japan
| | - M Y Hu
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - T Kato
- Japan Fine Ceramics Center, Nagoya 456-8587, Japan
| | - T Kawamura
- Institut de Physique du Globe de Paris, Université de Paris, Paris 75205, France
| | - M Kimura
- Department of Materials Structure Science, The Graduate University for Advanced Studies (SOKENDAI), Tsukuba, Ibaraki 305-0801, Japan.,Institute of Materials Structure Science, High-Energy Accelerator Research Organization, Tsukuba 305-0801, Japan
| | - M K Kubo
- Division of Natural Sciences, International Christian University, Mitaka 181-8585, Japan
| | - F Langenhorst
- Institute of Geosciences, Friedrich-Schiller-Universität Jena, 07745 Jena, Germany
| | - C Lantz
- Institut d'Astrophysique Spatiale, Université Paris-Saclay, Orsay 91405, France
| | - B Lavina
- Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60637, USA
| | - M Lindner
- Institute of Geoscience, Goethe University, Frankfurt, 60438 Frankfurt am Main, Germany
| | - J Zhao
- Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - B Vekemans
- Department of Chemistry, Ghent University, Krijgslaan 281 S12, Ghent, Belgium
| | - D Baklouti
- Institut d'Astrophysique Spatiale, Université Paris-Saclay, Orsay 91405, France
| | - B Bazi
- Department of Chemistry, Ghent University, Krijgslaan 281 S12, Ghent, Belgium
| | - F Borondics
- Optimized Light Source of Intermediate Energy to LURE (SOLEIL) L'Orme des Merisiers, Gif sur Yvette F-91192, France
| | - S Nagasawa
- Kavli Institute for the Physics and Mathematics of the Universe, The University of Tokyo, Kashiwa 277-8583, Japan.,Department of Physics, The University of Tokyo, Tokyo 113-0033, Japan
| | - G Nishiyama
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - K Nitta
- Spectroscopy Division, Japan Synchrotron Radiation Research Institute, Sayo 679-5198, Japan
| | - J Mathurin
- Institut Chimie Physique, Université Paris-Saclay, CNRS, 91405 Orsay, France
| | - T Matsumoto
- Division of Earth and Planetary Sciences, Kyoto University, Kyoto 606-8502, Japan
| | - I Mitsukawa
- Division of Earth and Planetary Sciences, Kyoto University, Kyoto 606-8502, Japan
| | - H Miura
- Graduate School of Science, Nagoya City University, Nagoya 467-8501, Japan
| | - A Miyake
- Division of Earth and Planetary Sciences, Kyoto University, Kyoto 606-8502, Japan
| | - Y Miyake
- High Energy Accelerator Research Organization, Tokai 319-1106, Japan
| | - H Yurimoto
- Department of Natural History Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - R Okazaki
- Department of Earth and Planetary Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - H Yabuta
- Graduate School of Advanced Science and Engineering, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - H Naraoka
- Department of Earth and Planetary Sciences, Kyushu University, Fukuoka 819-0395, Japan
| | - K Sakamoto
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - S Tachibana
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - H C Connolly
- Department of Geology, Rowan University, Glassboro, NJ 08028, USA
| | - D S Lauretta
- Lunar and Planetary Laboratory, University of Arizona, Tucson, AZ 85721, USA
| | - M Yoshitake
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - M Yoshikawa
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Department of Space and Astronautical Science, The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193, Japan
| | - K Yoshikawa
- Research and Development Directorate, JAXA, Sagamihara 252-5210, Japan
| | - K Yoshihara
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - Y Yokota
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - K Yogata
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - H Yano
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Department of Space and Astronautical Science, The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193, Japan
| | - Y Yamamoto
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Department of Space and Astronautical Science, The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193, Japan
| | - D Yamamoto
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - M Yamada
- Planetary Exploration Research Center, Chiba Institute of Technology, Narashino 275-0016, Japan
| | - T Yamada
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - T Yada
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - K Wada
- Planetary Exploration Research Center, Chiba Institute of Technology, Narashino 275-0016, Japan
| | - T Usui
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - R Tsukizaki
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - F Terui
- Department of Mechanical Engineering, Kanagawa Institute of Technology, Atsugi 243-0292, Japan
| | - H Takeuchi
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Department of Space and Astronautical Science, The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193, Japan
| | - Y Takei
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - A Iwamae
- Marine Works Japan, Yokosuka 237-0063, Japan
| | - H Soejima
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Marine Works Japan, Yokosuka 237-0063, Japan
| | - K Shirai
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - Y Shimaki
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - H Senshu
- Planetary Exploration Research Center, Chiba Institute of Technology, Narashino 275-0016, Japan
| | - H Sawada
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - T Saiki
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - M Ozaki
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Department of Space and Astronautical Science, The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193, Japan
| | - G Ono
- Research and Development Directorate, JAXA, Sagamihara 252-5210, Japan
| | - T Okada
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Department of Chemistry, The University of Tokyo, Tokyo 113-0033, Japan
| | - N Ogawa
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - K Ogawa
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - R Noguchi
- Faculty of Science, Niigata University, Niigata 950-2181, Japan
| | - H Noda
- National Astronomical Observatory of Japan, Mitaka 181-8588, Japan
| | - M Nishimura
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - N Namiki
- Department of Space and Astronautical Science, The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193, Japan.,National Astronomical Observatory of Japan, Mitaka 181-8588, Japan
| | - S Nakazawa
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - T Morota
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - A Miyazaki
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - A Miura
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - Y Mimasu
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - K Matsumoto
- Department of Space and Astronautical Science, The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193, Japan.,National Astronomical Observatory of Japan, Mitaka 181-8588, Japan
| | - K Kumagai
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Marine Works Japan, Yokosuka 237-0063, Japan
| | - T Kouyama
- Digital Architecture Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo 135-0064, Japan
| | - S Kikuchi
- Planetary Exploration Research Center, Chiba Institute of Technology, Narashino 275-0016, Japan.,National Astronomical Observatory of Japan, Mitaka 181-8588, Japan
| | - K Kawahara
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - S Kameda
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Department of Physics, Rikkyo University, Tokyo 171-8501, Japan
| | - T Iwata
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Department of Space and Astronautical Science, The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193, Japan
| | - Y Ishihara
- JAXA Space Exploration Center, JAXA, Sagamihara 252-5210, Japan
| | - M Ishiguro
- Department of Physics and Astronomy, Seoul National University, Seoul 08826, Korea
| | - H Ikeda
- Research and Development Directorate, JAXA, Sagamihara 252-5210, Japan
| | - S Hosoda
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - R Honda
- Department of Information Science, Kochi University, Kochi 780-8520, Japan.,Center for Data Science, Ehime University, Matsuyama 790-8577, Japan
| | - C Honda
- Aizu Research Center for Space Informatics, The University of Aizu, Aizu-Wakamatsu 965-8580, Japan
| | - Y Hitomi
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Marine Works Japan, Yokosuka 237-0063, Japan
| | - N Hirata
- Department of Planetology, Kobe University, Kobe 657-8501, Japan
| | - N Hirata
- Aizu Research Center for Space Informatics, The University of Aizu, Aizu-Wakamatsu 965-8580, Japan
| | - T Hayashi
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - M Hayakawa
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - K Hatakeda
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Marine Works Japan, Yokosuka 237-0063, Japan
| | - S Furuya
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - R Fukai
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - A Fujii
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
| | - Y Cho
- Department of Earth and Planetary Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - M Arakawa
- Department of Planetology, Kobe University, Kobe 657-8501, Japan
| | - M Abe
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan.,Department of Space and Astronautical Science, The Graduate University for Advanced Studies (SOKENDAI), Hayama 240-0193, Japan
| | - S Watanabe
- Department of Earth and Environmental Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Y Tsuda
- Institute of Space and Astronautical Science, Japan Aerospace Exploration Agency (JAXA), Sagamihara 252-5210, Japan
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3
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Li F, Ebihara A, Sakahara Y, Matsumoto S, Ueno R, Bao W, Kimura M, Fuji SI, Shimizu M, Kageyama K, Suga H. Synergistic effect of amino acid substitutions in CYP51B for prochloraz resistance in Fusarium fujikuroi. Pestic Biochem Physiol 2023; 189:105291. [PMID: 36549812 DOI: 10.1016/j.pestbp.2022.105291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/08/2022] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
Prochloraz has been used to control Fusarium fujikuroi, the causative pathogen of rice bakanae disease. Linkage analysis of FfCYP51 genes in the progenies obtained from crossing prochloraz moderately resistant and sensitive strains suggested that the FfCYP51B gene is involved in prochloraz resistance. Sequence comparison revealed that the prochloraz-resistant strain had an F511S or S312T/F511S substitution in FfCYP51B compared with the sensitive strains. The contribution of the S312T and F511S substitutions in FfCYP51B to prochloraz resistance was investigated by creating S/F-, T/F-, or T/S- types at 312/511 codons from the S/S-type, which is a natural moderately resistant strain, using a gene-editing technique. T/S exhibited the highest prochloraz resistance, followed by S/S-, T/F-, and S/F-types. These results indicated that the S312T and F511S substitutions in FfCYP51B had a synergistic effect on prochloraz resistance in F. fujikuroi.
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Affiliation(s)
- FangJing Li
- The United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Akio Ebihara
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Yuri Sakahara
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Sarara Matsumoto
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Reina Ueno
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - WanXue Bao
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Makoto Kimura
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Shin-Ichi Fuji
- Faculty of Bioresource Sciences, Akita Prefectural University, 241-438 Kaidobata-Nishi Nakano Shimoshinjo, Akita 010-0195, Japan
| | - Masafumi Shimizu
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Koji Kageyama
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Haruhisa Suga
- Institute for Glyco-core Research (iGCORE), Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan..
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4
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Oka K, Miyagawa T, Suga H, Miyagaki T, Mizuno Y, Hisamoto T, Omori I, Boki H, Takahashi-Shishido N, Sato S. 474 Increased Expression of Squamous Cell Carcinoma Antigen 1 and 2 in Mycosis Fungoides and Sézary Syndrome. J Invest Dermatol 2022. [DOI: 10.1016/j.jid.2022.09.488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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5
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van Neer RHP, Dranchak PK, Liu L, Aitha M, Queme B, Kimura H, Katoh T, Battaile KP, Lovell S, Inglese J, Suga H. Serum-Stable and Selective Backbone-N-Methylated Cyclic Peptides That Inhibit Prokaryotic Glycolytic Mutases. ACS Chem Biol 2022; 17:2284-2295. [PMID: 35904259 PMCID: PMC9900472 DOI: 10.1021/acschembio.2c00403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
N-Methylated amino acids (N-MeAAs) are privileged residues of naturally occurring peptides critical to bioactivity. However, de novo discovery from ribosome display is limited by poor incorporation of N-methylated amino acids into the nascent peptide chain attributed to a poor EF-Tu affinity for the N-methyl-aminoacyl-tRNA. By reconfiguring the tRNA's T-stem region to compensate and tune the EF-Tu affinity, we conducted Random nonstandard Peptides Integrated Discovery (RaPID) display of a macrocyclic peptide (MCP) library containing six different N-MeAAs. We have here devised a "pool-and-split" enrichment strategy using the RaPID display and identified N-methylated MCPs against three species of prokaryotic metal-ion-dependent phosphoglycerate mutases. The enriched MCPs reached 57% N-methylation with up to three consecutively incorporated N-MeAAs, rivaling natural products. Potent nanomolar inhibitors ranging in ortholog selectivity, strongly mediated by N-methylation, were identified. Co-crystal structures reveal an architecturally related Ce-2 Ipglycermide active-site metal-ion-coordinating Cys lariat MCP, functionally dependent on two cis N-MeAAs with broadened iPGM species selectivity over the original nematode-selective MCPs. Furthermore, the isolation of a novel metal-ion-independent Staphylococcus aureus iPGM inhibitor utilizing a phosphoglycerate mimetic mechanism illustrates the diversity of possible chemotypes encoded by the N-MeAA MCP library.
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Affiliation(s)
- R H P van Neer
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - P K Dranchak
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - L Liu
- Protein Structure and X-ray Crystallography Laboratory, Structural Biology Center, University of Kansas, Lawrence, Kansas 66045, United States
| | - M Aitha
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - B Queme
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
| | - H Kimura
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - T Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - K P Battaile
- New York Structural Biology Center, NSLS-II, Upton, New York 11973, United States
| | - S Lovell
- Protein Structure and X-ray Crystallography Laboratory, Structural Biology Center, University of Kansas, Lawrence, Kansas 66045, United States
| | - J Inglese
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850, United States
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - H Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
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6
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Pramunadipta S, Widiastuti A, Wibowo A, Suga H, Priyatmojo A. Development of PCR-RFLP Technique for Identify Several Members of Fusarium incarnatum-equiseti Species Complex and Fusarium fujikuroi Species Complex. Plant Pathol J 2022; 38:254-260. [PMID: 35678059 PMCID: PMC9343909 DOI: 10.5423/ppj.nt.12.2021.0184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/04/2022] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
Fusarium incarnatum-equiseti species complex (FIESC) contain over 40 members. The primer pair Smibo1FM/Semi1RM on the RPB2 partial gene has been reported to be able to identify Fusarium semitectum. The F. fujikuroi species complex (FFSC) contains more than 50 members. The F. verticillioides as a member of this complex can be identified by using VER1/VER2 primer pair on the CaM partial gene. In this research, the Smibo1FM/Semi1RM can amplify F. sulawesiense, F. hainanense, F. bubalinum, and F. tanahbumbuense, members of FIESC at 424 bp. The VER1/VER2 can amplify F. verticillioides, F. andiyazi, and F. pseudocircinatum, members of FFSC at 578 bp. Polymerase chain reaction-restriction fragment length polymorphism by using the combination of three restriction enzymes EcoRV, MspI, and HpyAV can differentiate each species of FIESC used. The two restriction enzymes HpaII and NspI can distinguish each species of FFSC used. The proper identification process is required for pathogen control in the field in order to reduce crop yield loss.
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Affiliation(s)
- Syafiqa Pramunadipta
- Graduate Student of Doctoral Program in Agricultural Science, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta 55281,
Indonesia
| | - Ani Widiastuti
- Departement of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta 55281,
Indonesia
| | - Arif Wibowo
- Departement of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta 55281,
Indonesia
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, Gifu 501-1193,
Japan
| | - Achmadi Priyatmojo
- Departement of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta 55281,
Indonesia
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7
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Li FJ, Komura R, Nakashima C, Shimizu M, Kageyama K, Suga H. Molecular Diagnosis of Thiophanate-Methyl-Resistant Strains of Fusarium fujikuroi in Japan. Plant Dis 2022; 106:634-640. [PMID: 34494869 DOI: 10.1094/pdis-07-21-1501-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Fusarium fujikuroi is the pathogen of rice bakanae disease and is subclassified into gibberellin and fumonisin groups (G and F groups). Thiophanate-methyl (TM), a benzimidazole fungicide, has been used extensively to control F. fujikuroi. Previous investigation showed that F-group strains are TM sensitive (TMS), whereas most G-group strains are TM resistant (TMR) in Japan. The minimum inhibitory concentration in TMS strains was 1 to 10 μg ml-1, whereas that in TMR strains was >100 μg ml-1. E198K and F200Y mutations in β2-tubulin were detected in TMR strains. A loop-mediated isothermal amplification-fluorescent loop primer method was developed for diagnosis of these mutations and applied to 37 TMR strains and 56 TMS strains. The results indicated that 100% of TMR strains were identified as having either the E198K mutation (41%) or the F200Y mutation (59%), whereas none of the TMS strains tested showed either mutation. We found one remarkable TMR strain in the F group that had an F200Y mutation. These results suggest that E198K and F200Y mutations in β2-tubulin contribute to TM resistance in F. fujikuroi.
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Affiliation(s)
- Fang Jing Li
- United Graduate School of Agricultural Science, Gifu University, Gifu 501-1193, Japan
| | - Ryoji Komura
- Graduate School of Bioresources, Mie University, Tsu, Mie 514-8507, Japan
| | - Chiharu Nakashima
- Graduate School of Bioresources, Mie University, Tsu, Mie 514-8507, Japan
| | - Masafumi Shimizu
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - Koji Kageyama
- River Basin Research Center, Gifu University, Gifu 501-1193, Japan
| | - Haruhisa Suga
- Institute for Glyco-core Research (iGCORE), Gifu University, Gifu, 501-1193, Japan
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8
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Li M, Hieno A, Motohashi K, Suga H, Kageyama K. Pythium intermedium, a species complex consisting of three phylogenetic species found in cool-temperate forest ecosystems. Fungal Biol 2021; 125:1017-1025. [PMID: 34776229 DOI: 10.1016/j.funbio.2021.07.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/07/2021] [Accepted: 07/15/2021] [Indexed: 10/20/2022]
Abstract
Pythium intermedium plays a vital role in the carbon cycle of cool-temperate forests and is widely distributed in Japan's forest soils. In this study, we performed a phylogenetic analysis of the P. intermedium species complex using DNA sequences from multiple loci. The study included 35 isolates from cool-temperate forest soils, seven known P. intermedium isolates, and six known Pythium attrantheridium isolates. We also performed morphological observations and mating tests. Our results showed that all the isolates formed one large clade but were divided into three subclades. Furthermore, we observed many mating reactions between isolates from different subclades, including between P. attrantheridium and P. intermedium. Therefore, we suggest that P. intermedium, P. attrantheridium, and another phylogenetic species belong to one species complex. This is the first report of a species complex within P. intermedium and will be helpful in understanding the evolution of Pythium species in natural ecosystems.
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Affiliation(s)
- Mingzhu Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China; River Basin Research Center, Gifu University, Gifu, 501-1193, Japan.
| | - Ayaka Hieno
- River Basin Research Center, Gifu University, Gifu, 501-1193, Japan
| | - Keiichi Motohashi
- Faculty of Regional Environment Science, Tokyo University of Agriculture, Tokyo, 156-8502, Japan
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, Gifu, 501-1193, Japan
| | - Koji Kageyama
- River Basin Research Center, Gifu University, Gifu, 501-1193, Japan
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9
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Abstract
To identify Lysinibacillus strains with the potential to function as plant biostimulants, we screened 10 previously isolated Lysinibacillus strains from the rhizosphere and soil for their plant growth-promoting (PGP) effects. In vitro tests showed that all strains produced indole-3-acetic acid. In primary screening, the PGP effects of these strains were assessed on spinach seedlings grown on Jiffy-7 pellets; strains GIC31, GIC41, and GIC51 markedly promoted shoot growth. In secondary screening, the PGP efficacies of these three strains were examined using spinach seedlings grown in pots under controlled conditions. Only GIC41 exerted consistent and significant PGP effects; therefore, it was selected for subsequent experiments. The results of 6-week glasshouse experiments revealed that GIC41 markedly increased shoot dry weight by ca. 12–49% over that of the control. The impact of fertilization levels on the PGP efficacy of GIC41 was investigated using pot experiments. The application of a specific level of fertilizer was required for the induction of sufficient PGP effects by this strain. The phylogenetic analysis based on the 16S rDNA sequence identified GIC41 as L. xylanilyticus. Collectively, these results show the potential of strain GIC41 to function as a plant biostimulant.
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Affiliation(s)
- Nusrat Ahsan
- The United Graduate School of Agricultural Science, Gifu University
| | - Malek Marian
- The United Graduate School of Agricultural Science, Gifu University
| | | | - Masafumi Shimizu
- The United Graduate School of Agricultural Science, Gifu University
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10
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Afandi A, Subandiyah S, Wibowo A, Hieno A, AFANDI A, Loekito S, Suga H, Kageyama K. Population genetics analysis of Phytophthora nicotianae associated with heart rot in pineapple revealed geneflow between population. Biodiversitas 2021. [DOI: 10.13057/biodiv/d220830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Abstract. Afandi A, Subandiyah S, Wibowo A, Hieno A, Afandi, Loekito S, Suga H, Kageyama K. 2021. Population genetics analysis of Phytophthora nicotianae associated with heart rot in pineapple revealed gene flow between populations. Biodiversitas 22: 3342-3348. Phytophthora nicotianae has caused heart rot in pineapple. This study identified the population genetic diversity of P. nicotianae, collecting 90 isolates of P. nicotianae from the pineapple plantation sites in three provinces of Indonesia and, as comparisons, seven isolates from non-pineapple sites. Six polymorphic microsatellite markers amplified the non-coding region was used to characterize the population diversity. The phylogenetic tree constructed by MEGA revealed three major clades; the first and second clades were dominated by the isolates from pineapple plantation sites, and the third clade contained isolates from the non-pineapple sites. The allelic pattern analysis using Genalex software revealed the local alleles specific to Lampung and Blitar populations. The AMOVA of microsatellite genotypes data showed that the isolates had a low diversity among the population (6%) but high diversity within individual. Conclusively, P. nicotianae population associated with heart rot in pineapple showed geneflow between populations.
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Geiser DM, Al-Hatmi AMS, Aoki T, Arie T, Balmas V, Barnes I, Bergstrom GC, Bhattacharyya MK, Blomquist CL, Bowden RL, Brankovics B, Brown DW, Burgess LW, Bushley K, Busman M, Cano-Lira JF, Carrillo JD, Chang HX, Chen CY, Chen W, Chilvers M, Chulze S, Coleman JJ, Cuomo CA, de Beer ZW, de Hoog GS, Del Castillo-Múnera J, Del Ponte EM, Diéguez-Uribeondo J, Di Pietro A, Edel-Hermann V, Elmer WH, Epstein L, Eskalen A, Esposto MC, Everts KL, Fernández-Pavía SP, da Silva GF, Foroud NA, Fourie G, Frandsen RJN, Freeman S, Freitag M, Frenkel O, Fuller KK, Gagkaeva T, Gardiner DM, Glenn AE, Gold SE, Gordon TR, Gregory NF, Gryzenhout M, Guarro J, Gugino BK, Gutierrez S, Hammond-Kosack KE, Harris LJ, Homa M, Hong CF, Hornok L, Huang JW, Ilkit M, Jacobs A, Jacobs K, Jiang C, Jiménez-Gasco MDM, Kang S, Kasson MT, Kazan K, Kennell JC, Kim HS, Kistler HC, Kuldau GA, Kulik T, Kurzai O, Laraba I, Laurence MH, Lee T, Lee YW, Lee YH, Leslie JF, Liew ECY, Lofton LW, Logrieco AF, López-Berges MS, Luque AG, Lysøe E, Ma LJ, Marra RE, Martin FN, May SR, McCormick SP, McGee C, Meis JF, Migheli Q, Mohamed Nor NMI, Monod M, Moretti A, Mostert D, Mulè G, Munaut F, Munkvold GP, Nicholson P, Nucci M, O'Donnell K, Pasquali M, Pfenning LH, Prigitano A, Proctor RH, Ranque S, Rehner SA, Rep M, Rodríguez-Alvarado G, Rose LJ, Roth MG, Ruiz-Roldán C, Saleh AA, Salleh B, Sang H, Scandiani MM, Scauflaire J, Schmale DG, Short DPG, Šišić A, Smith JA, Smyth CW, Son H, Spahr E, Stajich JE, Steenkamp E, Steinberg C, Subramaniam R, Suga H, Summerell BA, Susca A, Swett CL, Toomajian C, Torres-Cruz TJ, Tortorano AM, Urban M, Vaillancourt LJ, Vallad GE, van der Lee TAJ, Vanderpool D, van Diepeningen AD, Vaughan MM, Venter E, Vermeulen M, Verweij PE, Viljoen A, Waalwijk C, Wallace EC, Walther G, Wang J, Ward TJ, Wickes BL, Wiederhold NP, Wingfield MJ, Wood AKM, Xu JR, Yang XB, Yli-Mattila T, Yun SH, Zakaria L, Zhang H, Zhang N, Zhang SX, Zhang X. Phylogenomic Analysis of a 55.1-kb 19-Gene Dataset Resolves a Monophyletic Fusarium that Includes the Fusarium solani Species Complex. Phytopathology 2021; 111:1064-1079. [PMID: 33200960 DOI: 10.1094/phyto-08-20-0330-le] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. In 2013, the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani species complex (FSSC). Subsequently, this concept was challenged in 2015 by one research group who proposed dividing the genus Fusarium into seven genera, including the FSSC described as members of the genus Neocosmospora, with subsequent justification in 2018 based on claims that the 2013 concept of Fusarium is polyphyletic. Here, we test this claim and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly of Fusarium including the FSSC. We reassert the practical and scientific argument in support of a genus Fusarium that includes the FSSC and several other basal lineages, consistent with the longstanding use of this name among plant pathologists, medical mycologists, quarantine officials, regulatory agencies, students, and researchers with a stake in its taxonomy. In recognition of this monophyly, 40 species described as genus Neocosmospora were recombined in genus Fusarium, and nine others were renamed Fusarium. Here the global Fusarium community voices strong support for the inclusion of the FSSC in Fusarium, as it remains the best scientific, nomenclatural, and practical taxonomic option available.
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Affiliation(s)
- David M Geiser
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | | | - Takayuki Aoki
- Genetic Resources Center, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Tsutomu Arie
- Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Virgilio Balmas
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
| | - Irene Barnes
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Gary C Bergstrom
- Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY 14853, U.S.A
| | | | - Cheryl L Blomquist
- Plant Pest Diagnostics Branch, California Department of Food and Agriculture, Sacramento, CA 95832, U.S.A
| | - Robert L Bowden
- Hard Winter Wheat Genetics Research Unit, U.S. Department of Agriculture Agricultural Research Service (USDA-ARS), Manhattan, KS 66506, U.S.A
| | - Balázs Brankovics
- Wageningen Plant Research, Wageningen University and Research, Wageningen, The Netherlands
| | - Daren W Brown
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, Peoria, IL 61604, U.S.A
| | - Lester W Burgess
- Sydney Institute of Agriculture, Faculty of Science, University of Sydney, Sydney, Australia
| | - Kathryn Bushley
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Mark Busman
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, Peoria, IL 61604, U.S.A
| | - José F Cano-Lira
- Mycology Unit and IISPV, Universitat Rovira i Virgili Medical School, Reus, Spain
| | - Joseph D Carrillo
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598, U.S.A
| | - Hao-Xun Chang
- Department of Plant Pathology and Microbiology, National Taiwan University, Taipei, Taiwan
| | - Chi-Yu Chen
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
| | - Wanquan Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, People's Republic of China
| | - Martin Chilvers
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, U.S.A
| | - Sofia Chulze
- Research Institute on Mycology and Mycotoxicology, National Scientific and Technical Research Council, National University of Rio Cuarto, Rio Cuarto, Córdoba, Argentina
| | - Jeffrey J Coleman
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, U.S.A
| | | | - Z Wilhelm de Beer
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - G Sybren de Hoog
- Department of Medical Mycology and Infectious Diseases, Center of Expertise in Mycology, Radboud University Medical Center, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | | | - Emerson M Del Ponte
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, Brazil
| | | | - Antonio Di Pietro
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba, Spain
| | | | - Wade H Elmer
- Department of Plant Pathology and Ecology, Connecticut Agricultural Experiment Station, New Haven, CT 06504, U.S.A
| | - Lynn Epstein
- Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A
| | - Akif Eskalen
- Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A
| | | | - Kathryne L Everts
- Wye Research and Education Center, University of Maryland, Queenstown, MD 21658, U.S.A
| | - Sylvia P Fernández-Pavía
- Laboratorio de Patología Vegetal, Instituto de Investigaciones Agropecuarias y Forestales, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Michoacán 58880, México
| | | | - Nora A Foroud
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, Alberta T1J 4B1, Canada
| | - Gerda Fourie
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Rasmus J N Frandsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Stanley Freeman
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, U.S.A
| | - Omer Frenkel
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Kevin K Fuller
- Department of Microbiology and Immunology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, U.S.A
| | - Tatiana Gagkaeva
- Laboratory of Mycology and Phytopathology, All-Russian Institute of Plant Protection, St. Petersburg-Pushkin, Russia
| | | | - Anthony E Glenn
- Toxicology and Mycotoxin Research Unit, USDA-ARS, Athens, GA 30605, U.S.A
| | - Scott E Gold
- Toxicology and Mycotoxin Research Unit, USDA-ARS, Athens, GA 30605, U.S.A
| | - Thomas R Gordon
- Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A
| | - Nancy F Gregory
- Department of Plant and Soil Sciences, University of Delaware, DE 19716, U.S.A
| | - Marieka Gryzenhout
- Department of Genetics, University of the Free State, Bloemfontein, South Africa
| | - Josep Guarro
- Unitat de Microbiologia, Departament de Ciències Mèdiques Bàsiques, Universitat Rovira i Virgili, Reus, Spain
| | - Beth K Gugino
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | | | - Kim E Hammond-Kosack
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
| | - Linda J Harris
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C6, Canada
| | - Mónika Homa
- MTA-SZTE Fungal Pathogenicity Mechanisms Research Group, Hungarian Academy of Sciences, University of Szeged, Szeged, Hungary
| | - Cheng-Fang Hong
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
| | - László Hornok
- Institute of Plant Protection, Szent István University, Gödöllő, Hungary
| | - Jenn-Wen Huang
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
| | - Macit Ilkit
- Division of Mycology, Faculty of Medicine, University of Çukurova, Sarıçam, Adana, Turkey
| | - Adriaana Jacobs
- Biosystematics Unit, Plant Health and Protection, Agricultural Research Council, Pretoria, South Africa
| | - Karin Jacobs
- Department of Microbiology, Stellenbosch University, Matieland, South Africa
| | - Cong Jiang
- College of Plant Protection, Northwest Agriculture and Forestry University, Xianyang, People's Republic of China
| | - María Del Mar Jiménez-Gasco
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Seogchan Kang
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Matthew T Kasson
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506, U.S.A
| | - Kemal Kazan
- CSIRO Agriculture and Food, St. Lucia, Australia
| | - John C Kennell
- Biology Department, St. Louis University, St. Louis, MO 63101, U.S.A
| | - Hye-Seon Kim
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, Peoria, IL 61604, U.S.A
| | - H Corby Kistler
- USDA-ARS Cereal Disease Laboratory, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - Gretchen A Kuldau
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Oliver Kurzai
- German National Reference Center for Invasive Fungal Infections NRZMyk, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Jena, Germany
| | - Imane Laraba
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, Peoria, IL 61604, U.S.A
| | - Matthew H Laurence
- Australian Institute of Botanical Science, Royal Botanic Garden and Domain Trust, Sydney, Australia
| | - Theresa Lee
- Microbial Safety Team, National Institute of Agricultural Sciences, Rural Development Administration, Wanju, Republic of Korea
| | - Yin-Won Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - John F Leslie
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, U.S.A
| | - Edward C Y Liew
- Australian Institute of Botanical Science, Royal Botanic Garden and Domain Trust, Sydney, Australia
| | - Lily W Lofton
- Toxicology and Mycotoxin Research Unit, USDA-ARS, Athens, GA 30605, U.S.A
| | - Antonio F Logrieco
- Institute of Sciences of Food Production, Research National Council, Bari, Italy
| | - Manuel S López-Berges
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba, Spain
| | - Alicia G Luque
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Centro de Referencia de Micología, Universidad Nacional de Rosario, Rosario, Argentina
| | - Erik Lysøe
- Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, Høgskoleveien, Ås, Norway
| | - Li-Jun Ma
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, U.S.A
| | - Robert E Marra
- Department of Plant Pathology and Ecology, Connecticut Agricultural Experiment Station, New Haven, CT 06504, U.S.A
| | - Frank N Martin
- Crop Improvement and Protection Research Unit, ARS-USDA, Salinas, CA 93905, U.S.A
| | - Sara R May
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Susan P McCormick
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, Peoria, IL 61604, U.S.A
| | - Chyanna McGee
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Jacques F Meis
- Department of Medical Mycology and Infectious Diseases, Center of Expertise in Mycology, Radboud University Medical Center, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Quirico Migheli
- Dipartimento di Agraria and Nucleo Ricerca Desertificazione, Università degli Studi di Sassari, Sassari, Italy
| | - N M I Mohamed Nor
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Michel Monod
- Laboratoire de Mycologie, Service de Dermatologie, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland
| | - Antonio Moretti
- Institute of Sciences of Food Production, Research National Council, Bari, Italy
| | - Diane Mostert
- Department of Plant Pathology, Stellenbosch University, Matieland, South Africa
| | - Giuseppina Mulè
- Institute of Sciences of Food Production, Research National Council, Bari, Italy
| | | | - Gary P Munkvold
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, U.S.A
| | - Paul Nicholson
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Marcio Nucci
- Hospital Universitário, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Kerry O'Donnell
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, Peoria, IL 61604, U.S.A
| | - Matias Pasquali
- Department of Food, Environmental and Nutritional Sciences, University of Milano, Milan, Italy
| | - Ludwig H Pfenning
- Departamento de Fitopatologia, Universidade Federal de Lavras, Lavras, Minas Gerais State, Brazil
| | - Anna Prigitano
- Department of Biomedical Sciences for Health, University of Milano, Milan, Italy
| | - Robert H Proctor
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, Peoria, IL 61604, U.S.A
| | - Stéphane Ranque
- Institut Hospitalier Universitaire Méditerranée Infection, Aix Marseille University, Marseille, France
| | - Stephen A Rehner
- Mycology and Nematology Genetic Diversity and Biology Laboratory, USDA-ARS, Beltsville, MD 20705, U.S.A
| | - Martijn Rep
- Swammerdam Institute for Life Science, University of Amsterdam, Amsterdam, The Netherlands
| | - Gerardo Rodríguez-Alvarado
- Laboratorio de Patología Vegetal, Instituto de Investigaciones Agropecuarias y Forestales, Universidad Michoacana de San Nicolás de Hidalgo, Tarímbaro, Michoacán 58880, México
| | - Lindy Joy Rose
- Department of Plant Pathology, Stellenbosch University, Matieland, South Africa
| | - Mitchell G Roth
- Department of Plant Pathology, University of Wisconsin, Madison, WI 53706, U.S.A
| | - Carmen Ruiz-Roldán
- Departamento de Genética, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, Córdoba, Spain
| | - Amgad A Saleh
- Department of Plant Protection, College of Food and Agriculture Sciences, King Saud University, Riyadh 11451, Saudi Arabia
| | - Baharuddin Salleh
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Hyunkyu Sang
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, Republic of Korea
| | - María Mercedes Scandiani
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Centro de Referencia de Micología, Universidad Nacional de Rosario, Rosario, Argentina
| | - Jonathan Scauflaire
- Centre de Recherche et de Formation Agronomie, Haute Ecole Louvain en Hainaut, Montignies-sur-Sambre, Belgium
| | - David G Schmale
- School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, U.S.A
| | | | - Adnan Šišić
- Department of Ecological Plant Protection, University of Kassel, Witzenhausen, Germany
| | - Jason A Smith
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611, U.S.A
| | - Christopher W Smyth
- Department of Biological Sciences, Binghamton University, State University of New York, Binghamton, NY 13902, U.S.A
| | - Hokyoung Son
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Ellie Spahr
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV 26506, U.S.A
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521, U.S.A
| | - Emma Steenkamp
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Christian Steinberg
- Agroécologie, AgroSup Dijon, INRAE, University of Bourgogne Franche-Comté, Dijon, France
| | - Rajagopal Subramaniam
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario K1A 0C6, Canada
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, Gifu, Japan
| | - Brett A Summerell
- Australian Institute of Botanical Science, Royal Botanic Garden and Domain Trust, Sydney, Australia
| | - Antonella Susca
- Institute of Sciences of Food Production, Research National Council, Bari, Italy
| | - Cassandra L Swett
- Department of Plant Pathology, University of California, Davis, CA 95616, U.S.A
| | | | - Terry J Torres-Cruz
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Anna M Tortorano
- Department of Biomedical Sciences for Health, University of Milano, Milan, Italy
| | - Martin Urban
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
| | - Lisa J Vaillancourt
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, U.S.A
| | - Gary E Vallad
- Gulf Coast Research and Education Center, University of Florida, Wimauma, FL 33598, U.S.A
| | - Theo A J van der Lee
- Wageningen Plant Research, Wageningen University and Research, Wageningen, The Netherlands
| | - Dan Vanderpool
- Department of Biology, Indiana University, Bloomington, IN 47405, U.S.A
| | - Anne D van Diepeningen
- Wageningen Plant Research, Wageningen University and Research, Wageningen, The Netherlands
| | - Martha M Vaughan
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, Peoria, IL 61604, U.S.A
| | - Eduard Venter
- Department of Botany and Plant Biotechnology, University of Johannesburg, Auckland Park, South Africa
| | - Marcele Vermeulen
- Department of Microbial Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | - Paul E Verweij
- Department of Medical Mycology and Infectious Diseases, Center of Expertise in Mycology, Radboud University Medical Center, Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Altus Viljoen
- Department of Plant Pathology, Stellenbosch University, Matieland, South Africa
| | - Cees Waalwijk
- Wageningen Plant Research, Wageningen University and Research, Wageningen, The Netherlands
| | - Emma C Wallace
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Grit Walther
- German National Reference Center for Invasive Fungal Infections NRZMyk, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, Jena, Germany
| | - Jie Wang
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94702
| | - Todd J Ward
- Mycotoxin Prevention and Applied Microbiology Research Unit, USDA-ARS, Peoria, IL 61604, U.S.A
| | - Brian L Wickes
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center, San Antonio, TX 78229, U.S.A
| | - Nathan P Wiederhold
- Department of Pathology, University of Texas Health Science Center, San Antonio, TX 78229, U.S.A
| | - Michael J Wingfield
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Ana K M Wood
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, United Kingdom
| | - Jin-Rong Xu
- Department of Pathology, University of Texas Health Science Center, San Antonio, TX 78229, U.S.A
| | - Xiao-Bing Yang
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | | | - Sung-Hwan Yun
- Department of Medical Biotechnology, Soonchunhyang University, Asan, Republic of Korea
| | - Latiffah Zakaria
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Hao Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agriculture Sciences, Beijing, People's Republic of China
| | - Ning Zhang
- Department of Plant Biology, Rutgers University, New Brunswick, NJ 08901, U.S.A
| | - Sean X Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287, U.S.A
| | - Xue Zhang
- College of Plant Protection, Northwest Agriculture and Forestry University, Xianyang, People's Republic of China
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Fu HZ, Marian M, Enomoto T, Hieno A, Ina H, Suga H, Shimizu M. Biocontrol of Tomato Bacterial Wilt by Foliar Spray Application of a Novel Strain of Endophytic Bacillus sp. Microbes Environ 2021; 35. [PMID: 33012743 PMCID: PMC7734409 DOI: 10.1264/jsme2.me20078] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The aim of the present study was to identify a strain of endophytic Bacillus species that control tomato bacterial wilt by foliar spray application. Fifty heat-tolerant endophytic bacteria were isolated from the surface-sterilized foliar tissues of symptomless tomato plants that had been pre-inoculated with the pathogen Ralstonia pseudosolanacearum. In the primary screening, we assessed the suppressive effects of a shoot-dipping treatment with bacterial strains against bacterial wilt on tomato seedlings grown on peat pellets. Bacillus sp. strains G1S3 and G4L1 significantly suppressed the incidence of tomato bacterial wilt. In subsequent pot experiments, the biocontrol efficacy of foliar spray application was examined under glasshouse conditions. G4L1 displayed consistent and significant disease suppression, and, thus, was selected as a biocontrol candidate. Moreover, the pathogen population in the stem of G4L1-treated plants was markedly smaller than that in control plants. A quantitative real-time PCR analysis revealed that the foliar spraying of tomato plants with G4L1 up-regulated the expression of PR-1a and LoxD in stem and GluB in roots upon the pathogen inoculation, implying that the induction of salicylic acid-, jasmonic acid-, and ethylene-dependent defenses was involved in the protective effects of this strain. In the re-isolation experiment, G4L1 efficiently colonized foliar tissues for at least 4 weeks after spray application. Collectively, the present results indicate that G4L1 is a promising biocontrol agent for tomato bacterial wilt. Furthermore, to the best of our knowledge, this is the first study to report the biocontrol of bacterial wilt by the foliar spraying with an endophytic Bacillus species.
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Affiliation(s)
- Hui-Zhen Fu
- The United Graduate School of Agricultural Science, Gifu University
| | - Malek Marian
- Faculty of Applied Biological Sciences, Gifu University.,College of Agriculture, Ibaraki University
| | - Takuo Enomoto
- Faculty of Applied Biological Sciences, Gifu University
| | - Ayaka Hieno
- Faculty of Applied Biological Sciences, Gifu University
| | - Hidemasa Ina
- Faculty of Applied Biological Sciences, Gifu University
| | | | - Masafumi Shimizu
- The United Graduate School of Agricultural Science, Gifu University
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13
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Sultana S, Bao W, Shimizu M, Kageyama K, Suga H. Frequency of three mutations in the fumonisin biosynthetic gene cluster of Fusarium fujikuroi that are predicted to block fumonisin production. WORLD MYCOTOXIN J 2021. [DOI: 10.3920/wmj2020.2572] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Fusarium fujikuroi is the most prominent pathogen found in rice. In addition to gibberellin, F. fujikuroi produces various secondary metabolites, including the polyketide mycotoxins, fumonisins. Fumonisin production is conferred by the fumonisin biosynthetic gene (FUM) cluster consisting of 15-17 genes. F. fujikuroi is phylogenetically subclassified into one group with fumonisin production (F-group) and another group in which fumonisin production is undetectable (G-group). In a previous study, a G-to-T substitution (FUM21_G2551T) in the FUM cluster transcription factor gene, FUM21, was identified as a cause of fumonisin-non-production in a G-group strain. In the current study, further analysis of G-group strains identified two additional mutations that involved FUM-cluster genes essential for fumonisin production: (1) a 22.4-kbp deletion in the FUM10-FUM19 region; and (2) a 1.4-kbp insertion in FUM6. PCR analysis of 44 G-group strains, indicated that 84% had the FUM21_G2551T mutation, 50% had the 22.4-kbp FUM10-FUM19 deletion, and 32% had the 1.4-kbp insertion in FUM6, and some strains had two or all the mutations. None of the mutations were detected in the 51 F-group strains examined. Each of the three mutations alone could account for the lack of fumonisin production in G-group strains. However, one G-group strain did not have any of the mutations. Therefore, another mutation(s) is likely responsible for the lack of fumonisin production in some G-group strains of F. fujikuroi.
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Affiliation(s)
- S. Sultana
- The United Graduate School of Agricultural Science, Gifu University, Gifu 501-1193, Japan
| | - W.X. Bao
- The United Graduate School of Agricultural Science, Gifu University, Gifu 501-1193, Japan
| | - M. Shimizu
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - K. Kageyama
- River Basin Research Center, Gifu University, Gifu 501-1193, Japan
| | - H. Suga
- Life Science Research Center, Gifu University, Gifu 501-1193, Japan
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Hieno A, Li M, Otsubo K, Suga H, Kageyama K. Multiplex LAMP Detection of the Genus Phytophthora and Four Phytophthora Species P. ramorum, P. lateralis, P. kernoviae, and P. nicotianae, with a Plant Internal Control. Microbes Environ 2021; 36. [PMID: 34108359 PMCID: PMC8209452 DOI: 10.1264/jsme2.me21019] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Phytophthora species cause destructive plant diseases worldwide. All Phytophthora species, except for one, are listed as plant quarantine organisms in Japan. The exception, Phytophthora nicotianae is considered to be a domestic species. The injurious pests Phytophthora ramorum, Phytophthora lateralis, and Phytophthora kernoviae are invasive pathogens that cause tree mortality worldwide, mainly in the United States and the United Kingdom. To effectively control Phytophthora diseases, we established detection methods that utilize the loop-mediated isothermal amplification (LAMP) of the genus Phytophthora and the four species P. ramorum, P. lateralis, P. kernoviae, and P. nicotianae. LAMP primers for P. ramorum, P. lateralis, and P. kernoviae were newly designed in the present study. Our multiplex assay includes the detection of plant DNA as an internal control. When the optimum ratio between plant and pathogen primers was used in multiplex LAMP assays, 1 pg to 100 fg of pathogen DNA was detected with similar sensitivity to that in simplex LAMP assays. The detection of plant DNA in the absence of pathogens enables us to check for and avoid undesirable negative results caused by enzyme inactivation or the contamination of amplification inhibitors from plant tissues. The total time from sample collection to results is approximately 120 min, and, thus, our multiplex LAMP assay may be used as an accurate and time-saving detection method for Phytophthora pathogens.
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Affiliation(s)
- Ayaka Hieno
- River Basin Research Center, Gifu University
| | - Mingzhu Li
- College of Life Sciences, Shaanxi Normal University
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Hieno A, Li M, Afandi A, Otsubo K, Suga H, Kageyama K. Detection of the Genus Phytophthora and the Species Phytophthora nicotianae by LAMP with a QProbe. Plant Dis 2020; 104:2469-2480. [PMID: 32628090 DOI: 10.1094/pdis-12-19-2523-re] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Phytophthora is an oomycete genus with worldwide distribution, and many of its species cause destructive diseases. In Japan, Phytophthora species are listed as quarantine organisms with the exception of Phytophthora nicotianae. For effective quarantine control, we designed a Phytophthora genus-specific loop-mediated isothermal amplification (LAMP) primer set and a P. nicotianae species-specific quenching probe (QProbe) to establish a simultaneous LAMP-based detection method. We confirmed the specificity of the genus-specific primers, and all 161 taxa were detected. No other species in the closely related genera Pythium and Phytopythium gave positive results with the exception of two species, Phytopythium delawarense and Phytopythium fagopyri. These two species gave inconsistent results. We used annealing curve analysis with the QProbe to demonstrate that P. nicotianae could be distinguished from other species. DNA from inoculated and naturally infected plants was extracted using a time-saving extraction kit and subjected to the simultaneous detection method. We confirmed that all Phytophthora DNAs in the plant samples were detected, and P. nicotianae was specifically identified. This simultaneous detection method will make quarantine inspections faster and easier.
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Affiliation(s)
- Ayaka Hieno
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu-city, Gifu, 501-1193, Japan
| | - Mingzhu Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Auliana Afandi
- Biotechnology Research Center, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Kayoko Otsubo
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu-city, Gifu, 501-1193, Japan
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, 1-1 Yanagido, Gifu-city, Gifu, 501-1193, Japan
| | - Koji Kageyama
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu-city, Gifu, 501-1193, Japan
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Elsharkawy MM, Suga H, Shimizu M. Systemic resistance induced by Phoma sp. GS8-3 and nanosilica against Cucumber mosaic virus. Environ Sci Pollut Res Int 2020; 27:19029-19037. [PMID: 30328040 DOI: 10.1007/s11356-018-3321-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 09/24/2018] [Indexed: 06/08/2023]
Abstract
Cucumber mosaic virus (CMV) is a very serious hazard to vegetable production worldwide. This study is focused on evaluation of resistance stimulated by the plant growth-promoting fungus, Phoma sp. GS8-3, or nanosilica against CMV under pot and field conditions. The specific aim was to illustrate the mechanism of resistance stimulated by GS8-3 against CMV using microarray technology. Treatments with GS8-3 as well as nanosilica significantly decreased CMV severity and titer in tobacco and cucumber under pot and field conditions, respectively. Growth characters of tobacco and cucumber were significantly increased due to GS8-3 inoculation followed by nanosilica compared with control and BTH treatments. Microarray results showed highly upregulation of defense-related genes expression specially those related to heat shock proteins. Therefore, GS8-3 as well as nanosilica is suitable to serve as effective inducers against CMV in cucumber plants.
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Affiliation(s)
- Mohsen Mohamed Elsharkawy
- Department of Agricultural Botany, Faculty of Agriculture, Kafrelsheikh University, Kafr Elsheikh, 33516, Egypt.
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, 1-1 Yanagido, Gifu City, 501-1193, Japan
| | - Masafumi Shimizu
- Laboratory of Plant Pathology, The United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
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Pramunadipta S, Widiastuti A, Wibowo A, Suga H, - AP. Short Communication: Sarocladium oryzae associated with sheath rot disease of rice in Indonesia. Biodiversitas 2020. [DOI: 10.13057/biodiv/d210352] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Abstract. Pramunadipta S, Widiastuti A, Wibowo A, Suga H, Priyatmojo A. 2020. Short Communication: Sarocladium oryzae associated with sheath rot disease of rice in Indonesia. Biodiversitas 21: 1243-1249. One of the obstacles in increasing rice production is the presence of sheath rot pathogen infection, which causes changes in color on the rice sheath to brown or reddish-brown, sometimes does not produce rice grain. The major fungal pathogens that cause sheath rot disease are Sarocladium oryzae and Fusarium spp. The loss of rice yields reaches 85%. The disease found in six provinces, some of which are the largest rice-producing centers in Indonesia. A total of twenty-four Sarocladium sp. were isolated from leaf sheath symptom on potato dextrose agar and water agar medium. Sheath rot pathogen identification based on molecular method was performed using internal transcribed spacer (ITS) rDNA gene sequencing. Necrosis occurs after artificial inoculation in Ciherang rice variety was observed and showed that all isolates were pathogenic. Morphological characterization of the isolates identified them as Sarocladium sp. Molecular identification showed that six representatives isolates belonging to S. oryzae. These findings are important information about the fungal pathogen that causes sheath rot disease in Indonesia, and in studies for formulating control measures of the pathogen in the future to prevent the disease epidemic on rice. This is the first report about the existence of sheath rot disease, morphological characterization and molecular identification of S. oryzae in various rice fields in Indonesia.
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Omori I, Kamijo H, Suga H, Miyagaki T, Taoka K, Toyama K, Kurokawa M, Sato S. Extranodal natural killer/T-cell lymphoma, nasal type with CCR3 and CXCR3 expression. Clin Exp Dermatol 2020; 45:608-610. [PMID: 31965608 DOI: 10.1111/ced.14181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2020] [Indexed: 11/26/2022]
Affiliation(s)
- I Omori
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - H Kamijo
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - H Suga
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - T Miyagaki
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan.,Department of Dermatology, St Marianna University School of Medicine, Kanagawa, Japan
| | - K Taoka
- Department of Hematology and Oncology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - K Toyama
- Department of Hematology and Oncology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - M Kurokawa
- Department of Hematology and Oncology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - S Sato
- Department of Dermatology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
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Fu HZ, Marian M, Enomoto T, Suga H, Shimizu M. Potential Use of L-arabinose for the Control of Tomato Bacterial Wilt. Microbes Environ 2020; 35:ME20106. [PMID: 33087626 PMCID: PMC7734405 DOI: 10.1264/jsme2.me20106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/07/2020] [Indexed: 11/17/2022] Open
Abstract
The present study aimed to investigate the potential of simple sugars for use as protection agents in the control of tomato bacterial wilt caused by Ralstonia pseudosolanacearum. Based on the sugar assimilation patterns of the pathogen, four unassimilable sugars (L-arabinose, maltose, D-raffinose, and D-ribose) were selected from 10 representative sugars present in tomato root exudates. These sugars were evaluated for their effects on bacterial wilt using a tomato seedling bioassay. The application of 0.25% L-arabinose significantly reduced disease severity and was, thus, selected as a candidate for further evaluations in a pot experiment under glasshouse conditions. The results obtained showed that the disease suppressive effects of L-arabinose slightly increased at higher concentrations; drench treatments at 0.1, 0.25, and 0.5% reduced disease severity by ca. 48, 70, and 87%, respectively. The drench treatment with 0.5% L-arabinose significantly reduced the pathogen population in the rhizosphere and stem tissues of tomato plants without any antibacterial activity. Real-time reverse-transcription PCR revealed that the expression of salicylic acid-dependent and ethylene-dependent defense genes was significantly enhanced in the stem tissues of L-arabinose-treated tomato plants following the pathogen inoculation. These results suggest that soil drenching with L-arabinose effectively suppresses tomato bacterial wilt by preventing pathogen proliferation in the rhizosphere and stem tissues of tomato plants. This is the first study to report the potential of L-arabinose as a safe, eco-friendly, and cost-effective plant protection agent for the control of tomato bacterial wilt.
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Affiliation(s)
- Hui-Zhen Fu
- The United Graduate School of Agricultural Science, Gifu University, 1–1 Yanagido, Gifu, Gifu 501–1193, Japan
| | - Malek Marian
- Faculty of Applied Biological Sciences, Gifu University, 1–1 Yanagido, Gifu, Gifu 501–1193, Japan
- College of Agriculture, Ibaraki University, 3–21–1 Chuuo, Ami, Inashiki, Ibaraki 300–0393, Japan
| | - Takuo Enomoto
- Faculty of Applied Biological Sciences, Gifu University, 1–1 Yanagido, Gifu, Gifu 501–1193, Japan
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, 1–1 Yanagido, Gifu, Gifu 501–1193, Japan
| | - Masafumi Shimizu
- The United Graduate School of Agricultural Science, Gifu University, 1–1 Yanagido, Gifu, Gifu 501–1193, Japan
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Matsuda KM, Koguchi A, Toyama T, Sakuishi K, Kobayashi M, Miura S, Miyazaki M, Suga H, Asano Y, Toda T, Sato S. Concurrence of polyarteritis nodosa and multiple sclerosis. J Eur Acad Dermatol Venereol 2019; 34:e188-e191. [PMID: 31769115 DOI: 10.1111/jdv.16107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- K M Matsuda
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - A Koguchi
- Department of Neurology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - T Toyama
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - K Sakuishi
- Department of Neurology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - M Kobayashi
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - S Miura
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - M Miyazaki
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - H Suga
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Y Asano
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - T Toda
- Department of Neurology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - S Sato
- Department of Dermatology, The University of Tokyo Graduate School of Medicine, Tokyo, Japan
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Morimura S, Takahashi-Shishido N, Oka T, Takahashi T, Suga H, Shibata S, Miyagaki T, Asano Y, Sato S, Sugaya M. 219 Epidermal fatty acid-binding protein is expressed by epidermis and dermal infiltrating cells in psoriasis, atopic dermatitis, and cutaneous T-cell lymphoma. J Invest Dermatol 2019. [DOI: 10.1016/j.jid.2019.07.220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Boki H, Kimura T, Miyagaki T, Suga H, Sugaya M, Blauvelt A, Okochi H, Sato S. 331 Lymphatic flow blockade amplifies inflammation in imiquimod-induced psoriasis-like skin lesions. J Invest Dermatol 2019. [DOI: 10.1016/j.jid.2019.07.333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Sultana S, Kitajima M, Kobayashi H, Nakagawa H, Shimizu M, Kageyama K, Suga H. A Natural Variation of Fumonisin Gene Cluster Associated with Fumonisin Production Difference in Fusarium fujikuroi. Toxins (Basel) 2019; 11:toxins11040200. [PMID: 30987138 PMCID: PMC6521250 DOI: 10.3390/toxins11040200] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/14/2019] [Accepted: 03/21/2019] [Indexed: 12/03/2022] Open
Abstract
Fusarium fujikuroi, a member of the Fusarium fujikuroi species complex, stands out as a rice bakanae disease pathogen with a high production of gibberellic acid. Not all, but some F. fujikuroi strains are known to produce a carcinogenic mycotoxin fumonisin. Fumonisin biosynthesis is dependent on the FUM cluster composed of 16 FUM genes. The FUM cluster was detected not only from a fumonisin producing strain, but also from a fumonisin nonproducing strain that does not produce a detectable level of fumonisin. Genetic mapping indicated the causative mutation(s) of fumonisin nonproduction is present in the FUM cluster of the fumonisin nonproducing strain. Comparative analyses of FUM genes between the fumonisin producing and the nonproducing strains and gene complementation indicated that causative mutation of fumonisin nonproduction is not a single occurrence and the mutations are distributed in FUM21 and FUM7. Our research revealed a natural variation in the FUM cluster involving fumonisin production difference in F. fujikuroi.
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Affiliation(s)
- Sharmin Sultana
- The United Graduate School of Agricultural Science, Gifu University, Gifu 501-1193, Japan.
| | - Miha Kitajima
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan.
| | - Hironori Kobayashi
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan.
| | - Hiroyuki Nakagawa
- Faculty of National Food Research Institute, NARO, Tsukuba 305-8642, Japan.
| | - Masafumi Shimizu
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan.
| | - Koji Kageyama
- River Basin Research Center, Gifu University, Gifu 501-1193, Japan.
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, Gifu 501-1193, Japan.
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Tateishi H, Miyake T, Suga H. Polymorphism and expression level of CYP51 (cytochrome P450) and sensitivity to ipconazole in Fusarium fujikuroi isolates. J Pestic Sci 2019; 44:25-32. [PMID: 30820170 PMCID: PMC6389822 DOI: 10.1584/jpestics.d18-011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 11/29/2018] [Indexed: 06/09/2023]
Abstract
The relationship between the nucleotide sequences of CYP51, its expression level and its sensitivity to ipconazole of Fusarium fujikuroi isolates were investigated. Single nucleotide polymorphisms (SNPs) were observed in the CYP51 of isolates with different sensitivities to ipconazole, but no amino acid substitution was detected in the putative amino acid sequence of the CYP51 protein. On the other hand, the expression of CYP51 was enhanced by the presence of ipconazole, and it tended to be higher in isolates with lower sensitivities and no gibberellin productivity. In the presumed promoter region, the upstream nucleotide sequence of CYP51, several common SNPs and insertions of nucleotides were detected in the lower sensitivity isolates. These results suggest that F. fujikuroi isolates consist of 2 different groups in sensitivity and gibberellin productivity, and no amino acid substitution in CYP51 protein may contribute to the stably high efficacy of ipconazole against rice Bakanae disease for more than 25 years.
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Affiliation(s)
- Hideaki Tateishi
- Organic Synthesis Research Laboratories, Agrochemicals Department, Kureha Corporation, 16 Ochiai, Nishiki-machi, Iwaki, Fukushima, 974–8686, Japan
| | - Taiji Miyake
- Agrochemicals Department, Kureha Corporation, 3–26–2 Hyakunin-cho, Shinjuku, Tokyo 169–8503, Japan
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, 1–1 Yanagido, Gifu 501-1193, Japan
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Nishioka T, Marian M, Kobayashi I, Kobayashi Y, Yamamoto K, Tamaki H, Suga H, Shimizu M. Microbial basis of Fusarium wilt suppression by Allium cultivation. Sci Rep 2019; 9:1715. [PMID: 30737419 PMCID: PMC6368641 DOI: 10.1038/s41598-018-37559-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 12/10/2018] [Indexed: 11/22/2022] Open
Abstract
Crop rotation and intercropping with Allium plants suppresses Fusarium wilt in various crops. However, the mechanisms underlying this phenomenon have not been fully elucidated. This study was designed to assess the role of microorganisms inhabiting Allium rhizospheres and antifungal compounds produced by Allium roots in Fusarium wilt suppression by Allium cultivation. Suppression of cucumber Fusarium wilt and the pathogen multiplication by Allium (Welsh onion and/or onion)-cultivated soils were eliminated by heat treatment at 60 °C, whereas those by Welsh onion-root extract were lost at 40 °C. The addition of antibacterial antibiotics eliminated the suppressive effect of Welsh onion-cultivated soil on pathogen multiplication, suggesting the contribution of antagonistic gram-negative bacteria to the soil suppressiveness. The Illumina MiSeq sequencing of 16S rRNA gene amplicons revealed that genus Flavobacterium was the predominant group that preferentially accumulated in Allium rhizospheres. Flavobacterium species recovered from the rhizosphere soils of these Allium plants suppressed Fusarium wilt on cucumber seedlings. Furthermore, confocal laser scanning microscopy revealed that Flavobacterium isolates inhibited the multiplication of the pathogen in soil. Taken together, we infer that the accumulation of antagonistic Flavobacterium species plays a key role in Fusarium wilt suppression by Allium cultivation.
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Affiliation(s)
- Tomoki Nishioka
- The United Graduate school of Agricultural Science, Gifu University, Gifu, Japan
| | - Malek Marian
- The United Graduate school of Agricultural Science, Gifu University, Gifu, Japan
| | - Issei Kobayashi
- Center for Molecular Biology and Genetics, Mie University, Tsu, Mie, Japan
| | - Yuhko Kobayashi
- Center for Molecular Biology and Genetics, Mie University, Tsu, Mie, Japan
| | - Kyosuke Yamamoto
- Bioproduction Research Institute, National Institute of Advanced and Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Hideyuki Tamaki
- Bioproduction Research Institute, National Institute of Advanced and Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, Gifu, Japan
| | - Masafumi Shimizu
- The United Graduate school of Agricultural Science, Gifu University, Gifu, Japan.
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Feng W, Hieno A, Kusunoki M, Suga H, Kageyama K. LAMP Detection of Four Plant-Pathogenic Oomycetes and Its Application in Lettuce Fields. Plant Dis 2019; 103:298-307. [PMID: 30608214 DOI: 10.1094/pdis-05-18-0858-re] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
In Kagawa Prefecture, Japan, the pathogens Phytophthora pseudolactucae, Pythium irregulare, Pythium uncinulatum, and Pythium spinosum have caused huge losses in lettuce production. We used loop-mediated isothermal amplification (LAMP) to analyze soil and plants in lettuce fields for the presence of these four pathogens. To develop an effective on-site detection method, we contrasted the Plant-LAMP and Plant Culture-LAMP procedures for plant samples, and five soil DNA extraction methods for soil samples. Plant-LAMP and a Soil DNA Isolation kit were selected to analyze three fields for the pathogen species present, infected sites, and level of soil contamination. We found that the same wilting symptoms could be caused by Phytophthora or Pythium, or a mixture of species from both genera. Ph. pseudolactucae infects the pith of the lettuce in aboveground parts, whereas Pythium spp. mainly infect roots. Ph. pseudolactucae and Py. uncinulatum caused disease more frequently than the other two pathogens. Furthermore, not all of the pathogens existed in the soil near infected lettuce plants. Therefore, the LAMP method can be used to diagnose pathogenic oomycetes in the field, and will be useful in the development of control strategies in lettuce production.
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Affiliation(s)
- Wenzhuo Feng
- The United Graduate School of Agriculture Science, Gifu University, Gifu 501-1193, Japan
| | - Ayaka Hieno
- River Basin Research Center, Gifu University, Gifu 501-1193, Japan
| | - Mikio Kusunoki
- Kagawa Prefectural Agricultural Experiment Station Plant Protection Office, Kagawa 761-2306, Japan
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, Gifu 501-1193, Japan
| | - Koji Kageyama
- River Basin Research Center, Gifu University, Gifu 501-1193, Japan
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Afandi A, Murayama E, Yin-Ling, Hieno A, Suga H, Kageyama K. Population structures of the water-borne plant pathogen Phytopythium helicoides reveal its possible origins and transmission modes in Japan. PLoS One 2018; 13:e0209667. [PMID: 30586460 PMCID: PMC6306214 DOI: 10.1371/journal.pone.0209667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 12/10/2018] [Indexed: 11/19/2022] Open
Abstract
The purpose of this study was to clarify the genetic diversity of Phytopythium helicoides and to understand the transmission mode of the pathogen in Japan. In total, 232 P. helicoides isolates were collected from various host plants and geographic origins, including farms and natural environments. We developed 6 novel microsatellite markers for use in the study and found 90 alleles among the 6 markers in the 232 isolates. The analysis of molecular variance suggested that P. helicoides has high variance within individuals and low fixation indices between populations. A phylogenetic analysis revealed that isolates collected from the same hosts and/or geographic origins were often grouped together. For example, several isolates from natural environments were grouped with isolates from nearby agricultural areas. On the other hand, 2 geographically distant populations collected from the same host plant had similar genotypes. Our results suggested that migration of the pathogen could be facilitated naturally via drainage systems or by human activity in the transport of agricultural materials.
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Affiliation(s)
- Auliana Afandi
- The United Graduate School of Agricultural Science, Gifu University, Gifu, Japan
- Biotechnology Study Program, Graduate School of Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Emi Murayama
- River Basin Research Center, Gifu University, Gifu, Japan
| | - Yin-Ling
- Inner Mongolia University for Nationalities, Tongliao, China
| | - Ayaka Hieno
- River Basin Research Center, Gifu University, Gifu, Japan
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, Gifu, Japan
| | - Koji Kageyama
- River Basin Research Center, Gifu University, Gifu, Japan
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Mizutani Y, Abraham A, Uesaka K, Kondo H, Suga H, Suzuki N, Chiba S. Novel Mitoviruses and a Unique Tymo-Like Virus in Hypovirulent and Virulent Strains of the Fusarium Head Blight Fungus, Fusarium boothii. Viruses 2018; 10:v10110584. [PMID: 30373133 PMCID: PMC6266667 DOI: 10.3390/v10110584] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 10/22/2018] [Accepted: 10/23/2018] [Indexed: 11/16/2022] Open
Abstract
Hypovirulence of phytopathogenic fungi are often conferred by mycovirus(es) infections and for this reason many mycoviruses have been characterized, contributing to a better understanding of virus diversity. In this study, three strains of Fusarium head blight fungus (Fusarium boothii) were isolated from Ethiopian wheats as dsRNA-carrying strains: hypovirulent Ep-BL13 (>10, 3 and 2.5 kbp dsRNAs), and virulent Ep-BL14 and Ep-N28 (3 kbp dsRNA each) strains. The 3 kbp-dsRNAs shared 98% nucleotide identity and have single ORFs encoding a replicase when applied to mitochondrial codon usage. Phylogenetic analysis revealed these were strains of a new species termed Fusarium boothii mitovirus 1 in the genus Mitovirus. The largest and smallest dsRNAs in Ep-BL13 appeared to possess single ORFs and the smaller was originated from the larger by removal of its most middle part. The large dsRNA encoded a replicase sharing the highest amino acid identity (35%) with that of Botrytis virus F, the sole member of the family Gammaflexiviridae. Given that the phylogenetic placement, large genome size, simple genomic and unusual 3′-terminal RNA structures were far different from members in the order Tymovirales, the virus termed Fusarium boothii large flexivirus 1 may form a novel genus and family under the order.
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Affiliation(s)
- Yukiyoshi Mizutani
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.
| | - Adane Abraham
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan.
| | - Kazuma Uesaka
- Center for Gene Research, Nagoya University, Nagoya 464-8601, Japan.
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan.
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, Gifu 501-1193, Japan.
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan.
| | - Sotaro Chiba
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.
- Asian Satellite Campuses Institute, Nagoya University, Nagoya 464-8601, Japan.
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Feng W, Nukaya A, Satou M, Fukuta N, Ishiguro Y, Suga H, Kageyama K. Use of LAMP Detection to Identify Potential Contamination Sources of Plant-Pathogenic Pythium Species in Hydroponic Culture Systems of Tomato and Eustoma. Plant Dis 2018; 102:1357-1364. [PMID: 30673570 DOI: 10.1094/pdis-10-17-1679-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Hydroponic culture systems are subject to high risks of diseases caused by zoosporic plant pathogens. Control is generally difficult because of the rapid spread of zoospores in the nutrient solutions. In Japan, tomato and eustoma, which are cultivated using the D-tray and nutrient film techniques, respectively, are susceptible to diseases caused by Pythium aphanidermatum and P. irregulare. We used loop-mediated isothermal amplification to identify potential contamination sources of these two pathogens by monitoring their presence in the water supply wells, seedling terraces, nutrient solutions, diseased plants, and ground soils of a tomato greenhouse complex and a eustoma greenhouse complex. The results indicated that the pathogens may enter the culture systems from the soils around the greenhouses. Entry most likely occurs when seedlings are moved from the seedling terraces to the greenhouses, and sterilization of the hydroponic systems may not be sufficient. Therefore, monitoring pathogens in the culture systems and ground soils is very important for the management and prevention of these diseases.
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Affiliation(s)
- Wenzhuo Feng
- The United Graduate School of Agriculture Science, Gifu University, Gifu 501-1193, Japan
| | - Akira Nukaya
- Faculty of Agriculture, Shizuoka University, Shizuoka 422-8529, Japan
| | - Mamoru Satou
- NARO Institute of Floricultural Sciences, Fujimoto 2-1. Tsukuba, Ibaraki 305-8519, Japan
| | - Naoko Fukuta
- NARO Institute of Floricultural Sciences, Fujimoto 2-1. Tsukuba, Ibaraki 305-8519, Japan
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McAllister TE, Yeh TL, Abboud MI, Leung IKH, Hookway ES, King ONF, Bhushan B, Williams ST, Hopkinson RJ, Münzel M, Loik ND, Chowdhury R, Oppermann U, Claridge TDW, Goto Y, Suga H, Schofield CJ, Kawamura A. Non-competitive cyclic peptides for targeting enzyme-substrate complexes. Chem Sci 2018; 9:4569-4578. [PMID: 29899950 PMCID: PMC5969509 DOI: 10.1039/c8sc00286j] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/23/2018] [Indexed: 01/19/2023] Open
Abstract
Affinity reagents are of central importance for selectively identifying proteins and investigating their interactions. We report on the development and use of cyclic peptides, identified by mRNA display-based RaPID methodology, that are selective for, and tight binders of, the human hypoxia inducible factor prolyl hydroxylases (PHDs) - enzymes crucial in hypoxia sensing. Biophysical analyses reveal the cyclic peptides to bind in a distinct site, away from the enzyme active site pocket, enabling conservation of substrate binding and catalysis. A biotinylated cyclic peptide captures not only the PHDs, but also their primary substrate hypoxia inducible factor HIF1-α. Our work highlights the potential for tight, non-active site binding cyclic peptides to act as promising affinity reagents for studying protein-protein interactions.
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Affiliation(s)
- T E McAllister
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - T-L Yeh
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - M I Abboud
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - I K H Leung
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
- School of Chemical Sciences , The University of Auckland , Private Bag 92019 , Auckland 1142 , New Zealand
| | - E S Hookway
- Botnar Research Centre , NIHR Oxford Biomedical Research Unit , University of Oxford , Windmill Road , Oxford , OX3 7LD , UK
| | - O N F King
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - B Bhushan
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
- Division of Cardiovascular Medicine , Radcliffe Department of Medicine , University of Oxford , Wellcome Trust Centre for Human Genetics , Roosevelt Drive , Oxford OX3 7BN , UK
| | - S T Williams
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - R J Hopkinson
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - M Münzel
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - N D Loik
- Department of Chemistry , Graduate School of Science , The University of Tokyo , Tokyo 113-0033 , Japan
| | - R Chowdhury
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - U Oppermann
- Botnar Research Centre , NIHR Oxford Biomedical Research Unit , University of Oxford , Windmill Road , Oxford , OX3 7LD , UK
| | - T D W Claridge
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - Y Goto
- Department of Chemistry , Graduate School of Science , The University of Tokyo , Tokyo 113-0033 , Japan
| | - H Suga
- Department of Chemistry , Graduate School of Science , The University of Tokyo , Tokyo 113-0033 , Japan
- JST , CREST , The University of Tokyo , Tokyo 113-0033 , Japan
| | - C J Schofield
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - A Kawamura
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Road , Oxford OX1 3TA , UK .
- Division of Cardiovascular Medicine , Radcliffe Department of Medicine , University of Oxford , Wellcome Trust Centre for Human Genetics , Roosevelt Drive , Oxford OX3 7BN , UK
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Akatsuka T, Miyagaki T, Oka T, Suga H, Sugaya M, Yoshizaki A, Asano Y, Sato S. 042 Decreased keratinocyte GPNMB expression may augment the development of psoriasis lesion. J Invest Dermatol 2018. [DOI: 10.1016/j.jid.2018.03.046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Oka T, Miyagaki T, Takahashi N, Kamijo H, Nakajima R, Suga H, Sugaya M, Sato S. 140 CD244-CD48 interaction is involved in progression of mycosis fungoides. J Invest Dermatol 2018. [DOI: 10.1016/j.jid.2018.03.145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Nakajima R, Miyagaki T, Hirakawa M, Oka T, Takahashi N, Suga H, Yoshizaki A, Fujita H, Asano Y, Sugaya M, Sato S. Interleukin-25 is involved in cutaneous T-cell lymphoma progression by establishing a T helper 2-dominant microenvironment. Br J Dermatol 2018; 178:1373-1382. [PMID: 29238954 DOI: 10.1111/bjd.16237] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2017] [Indexed: 01/09/2023]
Abstract
BACKGROUND Interleukin (IL)-25 is a member of the IL-17 family, which can promote and augment T-helper (Th) type 2 responses. The expression of IL-25 and its cognate receptor, IL-25 receptor (IL-25R), is upregulated and correlated with disease activity in Th2-associated diseases. OBJECTIVES To examine the expression and function of IL-25 in cutaneous T-cell lymphoma (CTCL). METHODS Expression and location of IL-25 in lesional skin was investigated with immunohistochemistry. The effect of various cytokines on IL-25 production from normal human epidermal keratinocytes was assessed by quantitative reverse-transcription real-time polymerase chain reaction. Serum IL-25 levels were measured by enzyme-linked immunosorbent assay. The direct effect of IL-25 on tumour cells was also examined using CTCL cell lines and peripheral blood mononuclear cells in patients with Sézary syndrome. RESULTS IL-25 expression was increased in epidermal keratinocytes in lesional skin of CTCL. Th2 cytokines, IL-4 and IL-13, and periostin induced IL-25 expression by normal human epidermal keratinocytes. Serum IL-25 levels were increased in patients with advanced CTCL and correlated with serum lactate dehydrogenase levels. MyLa cells expressed IL-25R and its expression was augmented by stimulation with IL-25. IL-25 enhanced IL-13 production from MyLa cells via phosphorylation of signal transducer and activator of transcription 6. Peripheral blood mononuclear cells from one patient with Sézary syndrome expressed IL-25R and showed increase of IL-13 production by IL-25. CONCLUSIONS Th2 cytokines highly expressed in CTCL lesional skin induce IL-25 production by epidermal keratinocytes, which may, in turn, lead to formation of a Th2-dominant microenvironment through the direct induction of IL-13 by tumour cells.
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Affiliation(s)
- R Nakajima
- Department of Dermatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - T Miyagaki
- Department of Dermatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - M Hirakawa
- Department of Dermatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - T Oka
- Department of Dermatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - N Takahashi
- Department of Dermatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - H Suga
- Department of Dermatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - A Yoshizaki
- Department of Dermatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - H Fujita
- Department of Dermatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Y Asano
- Department of Dermatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - M Sugaya
- Department of Dermatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - S Sato
- Department of Dermatology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
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Iwasaki T, Sato H, Suga H, Takemoto Y, Inada E, Saitoh I, Kakuno K, Kanomi R, Yamasaki Y. Influence of pharyngeal airway respiration pressure on Class II mandibular retrusion in children: A computational fluid dynamics study of inspiration and expiration. Orthod Craniofac Res 2018; 20:95-101. [PMID: 28414873 DOI: 10.1111/ocr.12145] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2017] [Indexed: 11/28/2022]
Abstract
OBJECTIVES To examine the influence of negative pressure of the pharyngeal airway on mandibular retraction during inspiration in children with nasal obstruction using the computational fluid dynamics (CFD) method. SETTING AND SAMPLE POPULATION Sixty-two children were divided into Classes I, II (mandibular retrusion) and III (mandibular protrusion) malocclusion groups. MATERIAL AND METHODS Cone-beam computed tomography data were used to reconstruct three-dimensional shapes of the nasal and pharyngeal airways. Airflow pressure was simulated using CFD to calculate nasal resistance and pharyngeal airway pressure during inspiration and expiration. RESULTS Nasal resistance of the Class II group was significantly higher than that of the other two groups, and oropharyngeal airway inspiration pressure in the Class II (-247.64 Pa) group was larger than that in the Class I (-43.51 Pa) and Class III (-31.81 Pa) groups (P<.001). The oropharyngeal airway inspiration-expiration pressure difference in the Class II (-27.38 Pa) group was larger than that in the Class I (-5.17 Pa) and Class III (0.68 Pa) groups (P=.006). CONCLUSION Large negative inspiratory pharyngeal airway pressure due to nasal obstruction in children with Class II malocclusion may be related to their retrognathia.
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Affiliation(s)
- T Iwasaki
- Department of Pediatric Dentistry, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima-City, Japan
| | - H Sato
- Department of Pediatric Dentistry, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima-City, Japan
| | - H Suga
- Department of Pediatric Dentistry, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima-City, Japan
| | - Y Takemoto
- Department of Pediatric Dentistry, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima-City, Japan
| | - E Inada
- Department of Pediatric Dentistry, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima-City, Japan
| | - I Saitoh
- Division of Pediatric Dentistry, Graduate School of Medical and Dental Sciences, Niigata University, Niigata-City, Japan
| | - K Kakuno
- Kanomi Orthodontic Office, Himeji-City, Japan
| | - R Kanomi
- Kanomi Orthodontic Office, Himeji-City, Japan
| | - Y Yamasaki
- Department of Pediatric Dentistry, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima-City, Japan
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Kamijo H, Miyagaki T, Oka T, Takahashi N, Suga H, Sugaya M, Sato S. 522 Blocking CD137-CD137L interactions inhibits proliferation and survival of cutaneous T-cell lymphoma cells via hampering several signaling pathways. J Invest Dermatol 2017. [DOI: 10.1016/j.jid.2017.07.719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Sakamoto M, Miyagaki T, Kamijo H, Oka T, Takahashi N, Suga H, Sugaya M, Sato S. 535 CD147-cyclophilin A interactions promote proliferation of cutaneous T-cell lymphoma. J Invest Dermatol 2017. [DOI: 10.1016/j.jid.2017.07.732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Nakajima R, Miyagaki T, Kamijo H, Oka T, Takahashi N, Suga H, Sugaya M, Sato S. 531 Galectin-9 induces apoptosis of tumor cells through caspase pathways in cutaneous T-cell lymphoma. J Invest Dermatol 2017. [DOI: 10.1016/j.jid.2017.07.728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Mallam S, Streilein R, Suga H, Tedder T, Hall R. LB949 In vitro expansion of desmoglein specific peripheral blood B cells of patients with pemphigus. J Invest Dermatol 2017. [DOI: 10.1016/j.jid.2017.07.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Senda N, Miyagaki T, Kamijo H, Oka T, Takahashi N, Suga H, Sugaya M, Sato S. 552 HMGB1 levels are increased in lesional skin and sera in patients with erythrodermic cutaneous T-cell lymphoma. J Invest Dermatol 2017. [DOI: 10.1016/j.jid.2017.07.749] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Fuchigami T, Kimura N, Kibe T, Tezuka M, Amir MS, Suga H, Takemoto Y, Hashiguchi M, Maeda-Iino A, Nakamura N. Effects of pre-surgical nasoalveolar moulding on maxillary arch and nasal form in unilateral cleft lip and palate before lip surgery. Orthod Craniofac Res 2017; 20:209-215. [PMID: 28921849 DOI: 10.1111/ocr.12199] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2017] [Indexed: 11/30/2022]
Abstract
OBJECTIVES To investigate the effects of pre-surgical nasoalveolar moulding (PNAM) on the maxillary arch and nasal form in patients with unilateral cleft lip and palate (UCLP). SETTING AND SAMPLE POPULATION This is a retrospective case series study. The subjects were infants with complete UCLP who were treated with PNAM (n = 18) at Kagoshima University Medical and Dental Hospital (Japan) between 2006 and 2013. MATERIAL AND METHODS Maxillary dental casts and facial photographs were taken at the time of the first visit and immediately prior to lip surgery to evaluate the maxillary arch and nasal form changes. The dental casts were scanned with a laser scanner, and changes in the 3-Dimensional coordinates of anatomical landmarks and alveolar cleft width were analysed. Moreover, we investigated the correlation between the changes in the maxillary alveolar arch and nasal form. RESULTS Regarding the maxillary alveolar arch form, the anterior points of the major segment had moved significantly to the cleft side just prior to the time of lip repair, and the alveolar cleft width was significantly decreased. For nasal form, the inclination and displacement of the columella were significantly improved. The improvement of columella inclination was moderately correlated with the posterior movement of the anterior points of the major segment. CONCLUSIONS These findings indicate that PNAM for infants with UCLP enhanced symmetry in the maxillary alveolar arch and nasolabial form. In addition, the posterior movement of the anterior points of the maxillary alveolar arch was correlated with the improvement of columella deformation.
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Affiliation(s)
- T Fuchigami
- Department of Oral and Maxillofacial Surgery, Field of Oral and Maxillofacial Rehabilitation, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - N Kimura
- Department of Oral and Maxillofacial Surgery, Field of Oral and Maxillofacial Rehabilitation, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - T Kibe
- Department of Oral and Maxillofacial Surgery, Field of Oral and Maxillofacial Rehabilitation, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - M Tezuka
- Department of Oral and Maxillofacial Surgery, Field of Oral and Maxillofacial Rehabilitation, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - M S Amir
- Department of Oral and Maxillofacial Surgery, Field of Oral and Maxillofacial Rehabilitation, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan.,Department of Oral and Maxillofacial Surgery, Faculty of Dentistry, Airlangga University, Surabaya, Indonesia
| | - H Suga
- Department of Pediatric Dentistry, Field of Developmental Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Y Takemoto
- Department of Pediatric Dentistry, Field of Developmental Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - M Hashiguchi
- Department of Pediatric Dentistry, Field of Developmental Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - A Maeda-Iino
- Department of Orthodontics and Dentofacial Orthopedics, Field of Developmental Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - N Nakamura
- Department of Oral and Maxillofacial Surgery, Field of Oral and Maxillofacial Rehabilitation, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
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Villa NO, Kageyama K, Asano T, Suga H. Phylogenetic relationships ofPythiumandPhytophthoraspecies based on ITS rDNA, cytochrome oxidase II and β-tubulin gene sequences. Mycologia 2017. [DOI: 10.1080/15572536.2006.11832676] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Neilyn O. Villa
- Genetics and Molecular Biology Division, Institute of Biological Sciences, University of the Philippines Los Baños, College, Laguna, Philippines 4031
| | | | - Takahiro Asano
- River Basin Research Center, Gifu University, 1-1 Yanagido, Japan 501-1193
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, 1-1 Yanagido, Japan 501-1193
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Jongkees SAK, Umemoto S, Suga H. Linker-free incorporation of carbohydrates into in vitro displayed macrocyclic peptides. Chem Sci 2016; 8:1474-1481. [PMID: 28572907 PMCID: PMC5452274 DOI: 10.1039/c6sc04381j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 10/18/2016] [Indexed: 12/13/2022] Open
Abstract
We report a strategy for efficient post-translational modification of a library of ribosomally-translated peptides by activation and elimination of cysteine to dehydroalanine then conjugate addition of a range of exogenous thiols, with an emphasis on carbohydrates.
We report a strategy for efficient post-translational modification of a library of ribosomally-translated peptides by activation and elimination of cysteine to dehydroalanine then conjugate addition of a range of exogenous thiols, with an emphasis on carbohydrates. These reactions are selective for cysteine, and do not interfere with amplification of the nucleic acid component of an mRNA-displayed peptide. Furthermore, these reactions are shown to be compatible with two different macrocyclisation chemistries, and when applied to a peptide containing an N-terminal cysteine give a ketone that can be functionalised in an orthogonal manner. This new strategy can overcome a limitation of ribosomal translation, providing a means to incorporate untranslatable groups such as carbohydrates in amino acid side chains, and will allow for the ribosomal generation of glycopeptides, requiring only the introduction of a free thiol in the molecule to be incorporated. In combination with in vitro selection techniques, this strategy is envisaged to allow the discovery of biologically-active glycopeptides with a near-natural, but hydrolytically stable, thioglycosidic bond.
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Affiliation(s)
- S A K Jongkees
- Department of Chemistry , Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , 113-0033 Tokyo , Bunkyo-ku , Japan .
| | - S Umemoto
- Department of Chemistry , Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , 113-0033 Tokyo , Bunkyo-ku , Japan .
| | - H Suga
- Department of Chemistry , Graduate School of Science , The University of Tokyo , 7-3-1 Hongo , 113-0033 Tokyo , Bunkyo-ku , Japan . .,JST CREST , The University of Tokyo , 7-3-1 Hongo , 113-0033 Tokyo , Bunkyo-ku , Japan
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Sato Y, Sugaya M, Suga H, Oka T, Ishii T, Nishida H, Ishikawa S, Fukayama M, Sato S. 078 Altered granular layer structure and enhanced percutaneous immune responses in keratinocyte proline-rich protein- deficient mice, a new mouse model for atopic dermatitis. J Invest Dermatol 2016. [DOI: 10.1016/j.jid.2016.06.096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Nishioka T, Elsharkawy MM, Suga H, Kageyama K, Hyakumachi M, Shimizu M. Development of Culture Medium for the Isolation of Flavobacterium and Chryseobacterium from Rhizosphere Soil. Microbes Environ 2016; 31:104-10. [PMID: 27098502 PMCID: PMC4912144 DOI: 10.1264/jsme2.me15144] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
An effective medium designated phosphate separately autoclaved Reasoner’s 2A supplemented with cycloheximide and tobramycin (PSR2A-C/T) has been developed for the isolation of Flavobacterium and Chryseobacterium strains from the plant rhizosphere. It consists of Reasoner’s 2A agar (R2A) prepared by autoclaving phosphate and agar separately and supplementing with 50 mg L−1 cycloheximide and 1 mg L−1 tobramycin. A comparison was made among the following nine media: PSR2A-C/T, PSR2A-C/T supplemented with NaCl, R2A agar, R2A agar supplemented with cycloheximide and tobramycin, 1/4-strength tryptic soy agar (TSA), 1/10-strength TSA, soil-extract agar, Schaedler anaerobe agar (SAA), and SAA supplemented with gramicidin, for the recovery of Flavobacterium and Chryseobacterium strains from the Welsh onion rhizosphere. Flavobacterium strains were only isolated on PSR2A-C/T, and the recovery rate of Chryseobacterium strains was higher from PSR2A-C/T than from the eight other media. In order to confirm the effectiveness of PSR2A-C/T, bacteria were isolated from onion rhizosphere soil with this medium. Flavobacterium and Chryseobacterium strains were successfully isolated from this sample at a similar rate to that from the Welsh onion rhizosphere.
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Affiliation(s)
- Tomoki Nishioka
- Graduate School of Applied Biological Sciences, Gifu University
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Takeichi Y, Inami N, Suga H, Miyamoto C, Ueno T, Mase K, Takahashi Y, Ono K. Design and performance of a compact scanning transmission X-ray microscope at the Photon Factory. Rev Sci Instrum 2016; 87:013704. [PMID: 26827325 DOI: 10.1063/1.4940409] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We present a new compact instrument designed for scanning transmission X-ray microscopy. It has piezo-driven linear stages, making it small and light. Optical components from the virtual source point to the detector are located on a single optical table, resulting in a portable instrument that can be operated at a general-purpose spectroscopy beamline without requiring any major reconstruction. Careful consideration has been given to solving the vibration problem common to high-resolution microscopy, so as not to affect the spatial resolution determined by the Fresnel zone plate. Results on bacteriogenic iron oxides, single particle aerosols, and rare-earth permanent magnets are presented as examples of its performance under diverse applications.
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Affiliation(s)
- Y Takeichi
- Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba 305-0801, Japan
| | - N Inami
- Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba 305-0801, Japan
| | - H Suga
- Department of Earth and Planetary Systems Science, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima 739-8526, Japan
| | - C Miyamoto
- Department of Earth and Planetary Systems Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku 113-0033, Japan
| | - T Ueno
- National Institute for Materials Science, 1-2-1 Sengen, Tsukuba 305-0047, Japan
| | - K Mase
- Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba 305-0801, Japan
| | - Y Takahashi
- Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba 305-0801, Japan
| | - K Ono
- Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba 305-0801, Japan
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Feng W, Ishiguro Y, Hotta K, Watanabe H, Suga H, Kageyama K. Simple detection of Pythium irregulare using loop-mediated isothermal amplification assay. FEMS Microbiol Lett 2015; 362:fnv174. [PMID: 26394643 DOI: 10.1093/femsle/fnv174] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2015] [Indexed: 11/14/2022] Open
Abstract
Pythium irregulare is an important soil-borne pathogen that causes seed, stem and root rot, and seedling damping-off in various crops. Here, we have developed a rapid and reliable approach for detecting the pathogen using loop-mediated isothermal amplification (LAMP) in combination with primers designed from the sequences of the P. irregulare ribosomal DNA internal transcribed spacer region. The specificity of the primers for P. irregulare was tested using 50 isolates of 40 Pythium species, 11 Phytophthora isolates and 8 isolates of 7 other soil-borne pathogens. The assay showed that the limit of sensitivity of the LAMP method was 100 fg of pure DNA, a similar level to that of a polymerase chain reaction. LAMP detected P. irregulare from the supernatant after mixing culture medium (template DNA source) with distilled water. Similarly, positive results were obtained using a 'Plant-LAMP' method applied to a suspension rotted roots in water. A 'Bait-LAMP' method using the supernatant of autoclaved perilla seeds incubated in a soil/water mixture for 1 week at 25°C successfully detected P. irregulare from the soil. The LAMP assay described in this study is therefore a simple and effective way for practical detection of P. irregulare.
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Affiliation(s)
- Wenzhuo Feng
- Graduate School of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Yasushi Ishiguro
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Keisuke Hotta
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Hideki Watanabe
- Gifu Prefectural Agricultural Technology Center, Matamaru, Gifu 501-1152, Japan
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Koji Kageyama
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
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Abstract
The protein synthesis machinery of the cell, the ribosome and associated factors, is able to accurately follow the canonical genetic code, that which maps RNA sequence to protein sequence, to assemble functional proteins from the twenty or so proteinogenic amino acids. A number of innovative methods have arisen to take advantage of this accurate, and efficient, machinery to direct the assembly of non-proteinogenic amino acids. We review and compare these routes to 'reprogram the genetic code' including in vitro translation, engineered aminoacyl tRNA synthetases, and RNA 'flexizymes'. These studies show that the ribosome is highly tolerant of unnatural amino acids, with hundreds of unusual substrates of varying structure and chemistries being incorporated into protein chains. We also discuss how these methods have been coupled to selection techniques, such as phage display and mRNA display, opening up an exciting new avenue for the production of proteins and peptides with properties and functions beyond that which is possible using proteins composed entirely of the proteinogenic amino acids.
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Affiliation(s)
- J M Rogers
- Department of Chemistry, The University of Tokyo, Graduate School of Science, Tokyo, Japan.
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Rahman MZ, Abdelzaher HMA, Mingzhu L, Motohashi K, Suga H, Kageyama K. Pythium rishiriense sp. nov. from water and P. alternatum sp. nov. from soil, two new species from Japan. FEMS Microbiol Lett 2015; 362:fnv086. [PMID: 26062753 DOI: 10.1093/femsle/fnv086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2015] [Indexed: 11/14/2022] Open
Abstract
In an investigation of Pythium species in natural ecosystems of Rishiri Island in Northern Japan, two new species, Pythium rishiriense and P. alternatum, were identified based on morphological and molecular analyses. Pythium rishiriense differed morphologically from other Pythium species by its characteristic oogonial formation which occasionally arranged in chains. Pythium alternatum differed morphologically from other Pythium species by its distinguishing sexual organs where oogonia occasionally arranged alternately with antheridia in chains. Pythium rishiriense is a fast growing, high-temperature loving species, while P. alternatum is a slow growing species. Phylogenetic analyses based on the internal transcribed spacer region and cytochrome c oxidase 1 gene sequences showed that these two species are clearly separate from morphologically similar species.
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Affiliation(s)
| | | | - Li Mingzhu
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Keiichi Motohashi
- Faculty of Regional Environment Science, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Koji Kageyama
- River Basin Research Center, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
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Kobayashi S, Asakura K, Suga H, Sasaki S. Inverse association between dietary habits with high total antioxidant capacity and prevalence of frailty among elderly Japanese women: a multicenter cross-sectional study. J Nutr Health Aging 2015; 18:827-39. [PMID: 25389961 DOI: 10.1007/s12603-014-0478-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
OBJECTIVE To examine the association of dietary habits with high total antioxidant capacity (TAC) with frailty among elderly Japanese women. DESIGN Cross-sectional multicenter study. SETTING Thirty-five of 47 prefectures in Japan. PARTICIPANTS 2121 grandmothers or acquaintances of dietetic students aged 65 and older. MEASUREMENTS Dietary TAC and food intakes were calculated using a validated brief-type self-administered diet history questionnaire. The TAC value of each food was assigned using four different assays, ferric reducing ability of plasma (FRAP), oxygen radical absorbance capacity (ORAC), Trolox equivalent antioxidant capacity (TEAC), and total radical-trapping antioxidant parameter (TRAP). Frailty was defined as the presence three or more of the following four components: slowness and weakness (two points), exhaustion, low physical activity, and unintentional weight loss. RESULTS The number of subjects with frailty was 486 (23%). Multivariate adjusted ORs (95% CI) for frailty in the highest compared to the lowest quintile were 0.35 (0.24, 0.53) for FRAP, 0.35 (0.23, 0.52) for ORAC, 0.40 (0.27, 0.60) for TEAC, and 0.41 (0.28, 0.62) for TRAP. The intakes of green tea, coffee, vegetables, and fruits which contribute to dietary TAC were also associated with lower odds of frailty (the range of multivariate adjusted OR: 0.47 for vegetables to 0.77 for green tea), although the odds ratios were less marked than those of dietary TAC. CONCLUSIONS Dietary habits with high TAC showed a stronger inverse association with frailty in elderly Japanese women than the individual foods examined.
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Affiliation(s)
- S Kobayashi
- S. Sasaki, Department of Social and Preventive Epidemiology, School of Public Health, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; E-mail: ; Tel: +81-3-5841-7872; Fax: +81-3-5841-7873
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