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Kusano S, Yamada Y, Hagihara S. Benzoxaborole Catalyst Embedded with a Lewis Base: A Highly Active and Selective Catalyst for cis-1,2-diol Modification. J Org Chem 2024. [PMID: 38669291 DOI: 10.1021/acs.joc.3c02845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
The regioselective modification of polyols allows rapid access to their derivatives, thereby accelerating the polyol-related biology and drug discovery. We previously reported that benzoxaborole is a potent catalyst for the regioselective modification of polyols containing a cis-1,2-diol structure. In this study, we developed a bifunctional benzoxaborole catalyst embedded with a Lewis base. Benzoxaborole and Lewis base groups were designed to cooperatively activate a substrate (cis-1,2-diol) and reactant (electrophile), respectively, hence lowering the reaction barrier for the cis-1,2-diol moiety. The bifunctional catalyst indeed exhibited a significantly higher catalytic activity and selectivity for cis-1,2-diol modifications rather than a benzoxaborole catalyst without a Lewis base group. Mechanistic analyses, using both experimental and theoretical methods, supported the design of our catalyst. The bifunctional catalyst reported herein would be a new tool for the straightforward synthesis of polyol derivatives.
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Affiliation(s)
- Shuhei Kusano
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yuji Yamada
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Fukuoka 814-0180, Japan
| | - Shinya Hagihara
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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2
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Nishiyama K, Aihara Y, Suzuki T, Takahashi K, Kinoshita T, Dohmae N, Sato A, Hagihara S. Discovery of a Plant 14-3-3 Inhibitor Possessing Isoform Selectivity and In Planta Activity. Angew Chem Int Ed Engl 2024:e202400218. [PMID: 38658314 DOI: 10.1002/anie.202400218] [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: 01/04/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 04/26/2024]
Abstract
Synthetic modulators for plant 14-3-3s are promising chemical tools both for understanding the 14-3-3-related signaling pathways and controlling plant physiology. Here, we describe a novel small-molecule inhibitor for 14-3-3 proteins ofArabidopsis thaliana. The inhibitor was identified from unexpected products in DMSO stock solution of an in-house chemical library. Mass spectroscopy, mutant-based analyses, fluorescence polarization assays, and thermal shift assaysrevealed that the inhibitor covalently binds to an allosteric site of 14-3-3 with isoform selectivity. Moreover, infiltration of the inhibitor to Arabidopsis leaves suppressed the stomatal aperture. The inhibitor should provide a new insight into the design of potent and isoform-selective 14-3-3 modulators.
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Affiliation(s)
- Kotaro Nishiyama
- RIKEN Center for Sustainable Resource Science, Center for Sustainable Resource Science, JAPAN
| | - Yusuke Aihara
- Nagoya University, Institute for Transformative bio-molecule, JAPAN
| | - Takehiro Suzuki
- RIKEN Center for Sustainable Resource Science, enter for Sustainable Resource Science, JAPAN
| | - Koji Takahashi
- Nagoya University, Division of Biological Science, JAPAN
| | | | - Naoshi Dohmae
- RIKEN Center for Sustainable Resource Science, Center for Sustainable Resource Science, JAPAN
| | - Ayato Sato
- Nagoya University, Institute for Transformative bio-Molecules, JAPAN
| | - Shinya Hagihara
- RIKEN Center for Sustainable Resource Science, Center for Sustainable Resource Science, 2-1, Hirosawa, 351-0198, Wako, JAPAN
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3
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Murao M, Kato R, Kusano S, Hisamatsu R, Endo H, Kawabata Y, Kimura S, Sato A, Mori H, Itami K, Torii KU, Hagihara S, Uchida N. A Small Compound, HYGIC, Promotes Hypocotyl Growth Through Ectopic Ethylene Response. Plant Cell Physiol 2023; 64:1167-1177. [PMID: 37498972 DOI: 10.1093/pcp/pcad083] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 07/07/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023]
Abstract
Plant seedlings adjust the growth of the hypocotyl in response to surrounding environmental changes. Genetic studies have revealed key players and pathways in hypocotyl growth, such as phytohormones and light signaling. However, because of genetic redundancy in the genome, it is expected that not-yet-revealed mechanisms can be elucidated through approaches different from genetic ones. Here, we identified a small compound, HYGIC (HG), that simultaneously induces hypocotyl elongation and thickening, accompanied by increased nuclear size and enlargement of cortex cells. HG-induced hypocotyl growth required the ethylene signaling pathway activated by endogenous ethylene, involving CONSTITUTIVE PHOTOMORPHOGENIC 1, ETHYLENE INSENSITIVE 2 (EIN2) and redundant transcription factors for ethylene responses, ETHYLENE INSENSITIVE 3 (EIN3) and EIN3 LIKE 1. By using EBS:GUS, a transcriptional reporter of ethylene responses based on an EIN3-binding-cis-element, we found that HG treatment ectopically activates ethylene responses at the epidermis and cortex of the hypocotyl. RNA-seq and subsequent gene ontology analysis revealed that a significant number of HG-induced genes are related to responses to hypoxia. Indeed, submergence, a representative environment where the hypoxia response is induced in nature, promoted ethylene-signaling-dependent hypocotyl elongation and thickening accompanied by ethylene responses at the epidermis and cortex, which resembled the HG treatment. Collectively, the identification and analysis of HG revealed that ectopic responsiveness to ethylene promotes hypocotyl growth, and this mechanism is activated under submergence.
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Affiliation(s)
- Mizuki Murao
- Center for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
| | - Rika Kato
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
- Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198 Japan
| | - Shuhei Kusano
- Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198 Japan
| | - Rina Hisamatsu
- School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
| | - Hitoshi Endo
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
| | - Yasuki Kawabata
- Center for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
| | - Seisuke Kimura
- Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-ku, Kyoto, 603-8555 Japan
- Center for Plant Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-ku, Kyoto, 603-8555, Japan
| | - Ayato Sato
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
| | - Hitoshi Mori
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
- Institute for Glyco-core Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
| | - Kenichiro Itami
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
| | - Keiko U Torii
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
- Department of Molecular Biosciences, Howard Hughes Medical Institute, The University of Texas at Austin, 2506 Speedway, Austin, TX 78712, USA
| | - Shinya Hagihara
- Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, 351-0198 Japan
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
| | - Naoyuki Uchida
- Center for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602 Japan
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
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Hoshikawa Y, Kanno Y, Tawata H, Sagae T, Ishii T, Imoto S, Hagihara S, Wada T, Nagatsugi F, Aziz A, Nishihara H, Kyotani T, Itoh T. Water-Dispersible Carbon Nano-Test Tubes as a Container for Concentrated DNA Molecules. Chemistry 2023; 29:e202302594. [PMID: 37607317 DOI: 10.1002/chem.202302594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Invited for the cover of this issue are Takashi Kyotani, Tetsuji Itoh and co-workers at Tohoku University, Gunma University and AIST. The image depicts the synthesis of water-dispersible carbon nano-test tubes by using a template technique and the selective adsorption of DNA into the inner space of these test tubes. Read the full text of the article at 10.1002/chem.202301422.
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Affiliation(s)
- Yasuto Hoshikawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Yasuyuki Kanno
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Hanako Tawata
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Takuya Sagae
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Takafumi Ishii
- International Research and Education Center for Element Science, Faculty of Science and Technology, Gunma University, 1-5-1, Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Shuhei Imoto
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Shinya Hagihara
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Takehiko Wada
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Alex Aziz
- Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Hirotomo Nishihara
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
- Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Takashi Kyotani
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Tetsuji Itoh
- National Institute of Advanced Industrial Science Technology (AIST), 4-2-1, Nigatake, Miyagino-ku, Sendai, Miyagi, 983-8551, Japan
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Hoshikawa Y, Kanno Y, Tawata H, Sagae T, Ishii T, Imoto S, Hagihara S, Wada T, Nagatsugi F, Aziz A, Nishihara H, Kyotani T, Itoh T. Water-Dispersible Carbon Nano-Test Tubes as a Container for Concentrated DNA Molecules. Chemistry 2023; 29:e202301422. [PMID: 37392079 DOI: 10.1002/chem.202301422] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/27/2023] [Accepted: 06/30/2023] [Indexed: 07/02/2023]
Abstract
Water-dispersible carbon nano-test tubes (CNTTs) with an inner and outer diameter of about 25 and 35 nm, respectively, were prepared by the template technique and then their inner carbon surface was selectively oxidized to introduce carboxy groups. The adsorption behavior of DNA molecules on the oxidized CNTTs (Ox-CNTTs) was examined in the presence of Ca2+ cations. Many DNA molecules are attracted to the inner space of Ox-CNTTs based on the Ca2+ -mediated electrostatic interaction between DNA phosphate groups and carboxylate anions on the inner carbon surface. Moreover, the total net charge of the DNA adsorbed was found to be equal to the total charge of the carboxylate anions. This selective adsorption into the interior of Ox-CNTTs can be explained from the fact that the electrostatic interaction onto the inner concave surface is much stronger than that on the outer convex surface. On the other hand, the desorption of DNA easily occurs whenever Ca2+ cations are removed by washing with deionized water. Thus, each of Ox-CNTTs works well as a nano-container for a large amount of DNA molecules, thereby resulting in the occurrence of DNA enrichment in the nanospace.
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Affiliation(s)
- Yasuto Hoshikawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Yasuyuki Kanno
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Hanako Tawata
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Takuya Sagae
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Takafumi Ishii
- International Research and Education Center for Element Science, Faculty of Science and Technology, Gunma University, 1-5-1, Tenjin-cho, Kiryu, Gunma, 376-8515, Japan
| | - Shuhei Imoto
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Shinya Hagihara
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Takehiko Wada
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Alex Aziz
- Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Hirotomo Nishihara
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
- Advanced Institute for Materials Research (WPI-AIMR), Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Takashi Kyotani
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan
| | - Tetsuji Itoh
- National Institute of Advanced Industrial Science Technology (AIST), 4-2-1, Nigatake, Miyagino-ku, Sendai, Miyagi, 983-8551, Japan
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Okabe S, Kitaoka K, Suzuki T, Kuruma M, Hagihara S, Yamaguchi S, Fukui K, Seto Y. Desmethyl type germinone, a specific agonist for the HTL/KAI2 receptor, induces the Arabidopsis seed germination in a gibberellin-independent manner. Biochem Biophys Res Commun 2023; 649:110-117. [PMID: 36764113 DOI: 10.1016/j.bbrc.2023.01.086] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 01/27/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023]
Abstract
DWARF14 (D14) and HTL/KAI2 (KAI2) are paralogous receptors in the α/β-hydrolase superfamily. D14 is the receptor for a class of plant hormones, strigolactones (SLs), and KAI2 is the receptor for the smoke-derived seed germination inducer, Karrikin (KAR), in Arabidopsis. Germinone (Ger) was previously reported as a KAI2 agonist with germination-inducing activity for thermo-inhibited Arabidopsis seed. However, Ger was not specific to KAI2, and could also bind to D14. It was reported that SL analogs with a desmethyl-type D-ring structure are specifically recognized by KAI2. On the basis of this observation, we synthesized a desmethyl-type germinone (dMGer). We found that dMGer is highly specific to KAI2. Moreover, dMGer induced Arabidopsis seed germination more effectively than did Ger. In addition, dMGer induced the seed germination of Arabidopsis in a manner independently of GA, a well-known germination inducer in plants.
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Affiliation(s)
- Shoma Okabe
- Laboratory of Plant Chemical Regulation, School of Agriculture, Meiji University, 1-1-1, Higashi-Mita, Tama-ku, Kawasaki, Kanagawa, Japan
| | - Kana Kitaoka
- Department of Biochemistry, Okayama University of Science, Okayama City, Okayama, 700-0005, Japan
| | - Taiki Suzuki
- Laboratory of Plant Chemical Regulation, School of Agriculture, Meiji University, 1-1-1, Higashi-Mita, Tama-ku, Kawasaki, Kanagawa, Japan
| | - Michio Kuruma
- Laboratory of Plant Chemical Regulation, School of Agriculture, Meiji University, 1-1-1, Higashi-Mita, Tama-ku, Kawasaki, Kanagawa, Japan; RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, Japan
| | - Shinya Hagihara
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama, Japan
| | - Shinjiro Yamaguchi
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Kosuke Fukui
- Department of Biochemistry, Okayama University of Science, Okayama City, Okayama, 700-0005, Japan.
| | - Yoshiya Seto
- Laboratory of Plant Chemical Regulation, School of Agriculture, Meiji University, 1-1-1, Higashi-Mita, Tama-ku, Kawasaki, Kanagawa, Japan.
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Nakashima Y, Kobayashi Y, Murao M, Kato R, Endo H, Higo A, Iwasaki R, Kojima M, Takebayashi Y, Sato A, Nomoto M, Sakakibara H, Tada Y, Itami K, Kimura S, Hagihara S, Torii KU, Uchida N. Identification of a pluripotency-inducing small compound, PLU, that induces callus formation via Heat Shock Protein 90-mediated activation of auxin signaling. Front Plant Sci 2023; 14:1099587. [PMID: 36968385 PMCID: PMC10030974 DOI: 10.3389/fpls.2023.1099587] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
Plants retain the ability to generate a pluripotent tissue called callus by dedifferentiating somatic cells. A pluripotent callus can also be artificially induced by culturing explants with hormone mixtures of auxin and cytokinin, and an entire body can then be regenerated from the callus. Here we identified a pluripotency-inducing small compound, PLU, that induces the formation of callus with tissue regeneration potency without the external application of either auxin or cytokinin. The PLU-induced callus expressed several marker genes related to pluripotency acquisition via lateral root initiation processes. PLU-induced callus formation required activation of the auxin signaling pathway though the amount of active auxin was reduced by PLU treatment. RNA-seq analysis and subsequent experiments revealed that Heat Shock Protein 90 (HSP90) mediates a significant part of the PLU-initiated early events. We also showed that HSP90-dependent induction of TRANSPORT INHIBITOR RESPONSE 1, an auxin receptor gene, is required for the callus formation by PLU. Collectively, this study provides a new tool for manipulating and investigating the induction of plant pluripotency from a different angle from the conventional method with the external application of hormone mixtures.
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Affiliation(s)
- Yuki Nakashima
- Center for Gene Research, Nagoya University, Nagoya, Japan
- Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Yuka Kobayashi
- Center for Gene Research, Nagoya University, Nagoya, Japan
- School of Science, Nagoya University, Nagoya, Japan
| | - Mizuki Murao
- Center for Gene Research, Nagoya University, Nagoya, Japan
- Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Rika Kato
- Graduate School of Science, Nagoya University, Nagoya, Japan
- Center for Sustainable Resource Science, RIKEN, Saitama, Japan
| | - Hitoshi Endo
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan
| | - Asuka Higo
- Center for Gene Research, Nagoya University, Nagoya, Japan
- Institute for Advanced Research, Nagoya University, Nagoya, Japan
| | - Rie Iwasaki
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan
| | - Mikiko Kojima
- Center for Sustainable Resource Science, RIKEN, Yokohama, Japan
| | | | - Ayato Sato
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan
| | - Mika Nomoto
- Center for Gene Research, Nagoya University, Nagoya, Japan
- Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Hitoshi Sakakibara
- Center for Sustainable Resource Science, RIKEN, Yokohama, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Yasuomi Tada
- Center for Gene Research, Nagoya University, Nagoya, Japan
- Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Kenichiro Itami
- Graduate School of Science, Nagoya University, Nagoya, Japan
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan
| | - Seisuke Kimura
- Department of Industrial Life Sciences, Faculty of Life Science, Kyoto Sangyo University, Kyoto, Japan
- Center for Plant Sciences, Kyoto Sangyo University, Kyoto, Japan
| | - Shinya Hagihara
- Center for Sustainable Resource Science, RIKEN, Saitama, Japan
| | - Keiko U. Torii
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan
- Howard Hughes Medical Institute and Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, United States
| | - Naoyuki Uchida
- Center for Gene Research, Nagoya University, Nagoya, Japan
- Graduate School of Science, Nagoya University, Nagoya, Japan
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan
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8
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Kusano S, Nakamura S, Izumi M, Hagihara S. Development of 1,8-naphthalimide dyes for rapid imaging of subcellular compartments in plants. Chem Commun (Camb) 2021; 58:1685-1688. [PMID: 34909805 DOI: 10.1039/d1cc05798g] [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: 12/11/2022]
Abstract
Here, we report the installation of 1,8-naphthalimide dyes in live cell imaging of plants. We developed a series of 1,8-naphthalimide-based probes that illuminate different subcellular compartments by altering their spectral characteristics. Simple infiltration of the probes into leaves rapidly visualized the structure of chloroplasts or the vacuole. We further demonstrated that these probes are applicable to monitor the organelle behaviors in an autophagy pathway.
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Affiliation(s)
- Shuhei Kusano
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Sakuya Nakamura
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Masanori Izumi
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Shinya Hagihara
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
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Li N, Nakamura S, Ramundo S, Nishimura Y, Hagihara S, Izumi M. Chloroplast proteotoxic stress-induced autophagy is involved in the degradation of chloroplast proteins in Chlamydomonas reinhardtii. Plant Cell Physiol 2021; 62:e1-e31. [PMID: 33594417 DOI: 10.1093/pcp/pcab029] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/11/2021] [Accepted: 02/15/2021] [Indexed: 06/12/2023]
Abstract
Intraorganellar proteases and cytoplasmic proteolytic systems such as autophagy orchestrate the degradation of organellar proteins to ensure organelle homeostasis in eukaryotic cells. The green alga Chlamydomonas reinhardtii is an ideal unicellular model organism for elucidating the mechanisms maintaining proteostasis in chloroplasts. However, the autophagic pathways targeting the photosynthetic organelles of these algae have not been clearly elucidated. Here, we explored the role of autophagy in chloroplast protein degradation in Chlamydomonas cells. We labeled the chloroplast protein Rubisco small subunit (RBCS) with the yellow fluorescent protein Venus in a Chlamydomonas strain in which expression of the chloroplast gene clpP1, encoding a major catalytic subunit of the chloroplast Clp protease, can be conditionally repressed to selectively perturb chloroplast protein homeostasis. We observed transport of both nucleus-encoded RBCS-Venus fusion protein and chloroplast-encoded Rubisco large subunit (rbcL) from the chloroplast to the vacuoles in response to chloroplast proteotoxic stress induced by clpP1 inhibition. This process was retarded by the addition of autophagy inhibitors. Biochemical detection of lytic cleavage of RBCS-Venus supported the notion that Rubisco is degraded in the vacuoles via autophagy. Electron microscopy revealed vacuolar accumulation of autophagic vesicles and exposed their ultrastructure during repression of clpP1 expression. Treatment with an autophagy activator also induced chloroplast autophagy. These results indicate that autophagy contributes to chloroplast protein degradation in Chlamydomonas cells.
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Affiliation(s)
- Nan Li
- College of Life Science, Liaocheng University, Liaocheng 252000, China
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, 980-8578 Sendai, Japan
| | - Sakuya Nakamura
- Center for Sustainable Resource Science (CSRS), RIKEN, 351-0198 Wako, Japan
| | - Silvia Ramundo
- Department of Biochemistry and Biophysics, University of California, San Francisco,CA 94143, USA
| | - Yoshiki Nishimura
- Department of Botany, Graduate School of Sciences, Kyoto University, Kita-Shirakawa, Oiwake-cho, 606-8502 Kyoto, Japan
| | - Shinya Hagihara
- Center for Sustainable Resource Science (CSRS), RIKEN, 351-0198 Wako, Japan
| | - Masanori Izumi
- Center for Sustainable Resource Science (CSRS), RIKEN, 351-0198 Wako, Japan
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10
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Li N, Nakamura S, Ramundo S, Nishimura Y, Hagihara S, Izumi M. Retraction: Chloroplast proteotoxic stress-induced autophagy is involved in the degradation of chloroplast proteins in Chlamydomonas reinhardtii. Plant Cell Physiol 2021; 62:741. [PMID: 33951175 DOI: 10.1093/pcp/pcab055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
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11
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Nakamura S, Hagihara S, Otomo K, Ishida H, Hidema J, Nemoto T, Izumi M. Autophagy Contributes to the Quality Control of Leaf Mitochondria. Plant Cell Physiol 2021; 62:229-247. [PMID: 33355344 PMCID: PMC8112837 DOI: 10.1093/pcp/pcaa162] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [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: 11/15/2020] [Accepted: 12/05/2020] [Indexed: 05/11/2023]
Abstract
In autophagy, cytoplasmic components of eukaryotic cells are transported to lysosomes or the vacuole for degradation. Autophagy is involved in plant tolerance to the photooxidative stress caused by ultraviolet B (UVB) radiation, but its roles in plant adaptation to UVB damage have not been fully elucidated. Here, we characterized organellar behavior in UVB-damaged Arabidopsis (Arabidopsis thaliana) leaves and observed the occurrence of autophagic elimination of dysfunctional mitochondria, a process termed mitophagy. Notably, Arabidopsis plants blocked in autophagy displayed increased leaf chlorosis after a 1-h UVB exposure compared to wild-type plants. We visualized autophagosomes by labeling with a fluorescent protein-tagged autophagosome marker, AUTOPHAGY8 (ATG8), and found that a 1-h UVB treatment led to increased formation of autophagosomes and the active transport of mitochondria into the central vacuole. In atg mutant plants, the mitochondrial population increased in UVB-damaged leaves due to the cytoplasmic accumulation of fragmented, depolarized mitochondria. Furthermore, we observed that autophagy was involved in the removal of depolarized mitochondria when mitochondrial function was disrupted by mutation of the FRIENDLY gene, which is required for proper mitochondrial distribution. Therefore, autophagy of mitochondria functions in response to mitochondrion-specific dysfunction as well as UVB damage. Together, these results indicate that autophagy is centrally involved in mitochondrial quality control in Arabidopsis leaves.
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Affiliation(s)
- Sakuya Nakamura
- Center for Sustainable Resource Science (CSRS), RIKEN, Wako, 351-0198 Japan
| | - Shinya Hagihara
- Center for Sustainable Resource Science (CSRS), RIKEN, Wako, 351-0198 Japan
| | - Kohei Otomo
- Exploratory Research Center on Life and Living Systems (ExCELLs), National Institute of Natural Sciences, Okazaki, 444-8787 Japan
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, 444-8787 Japan
- Department of Physiological Sciences, The Graduate University for Advanced Study (SOKENDAI), Hayama, 240-0193 Japan
- Research Institute for Electronic Science, Hokkaido University, Sapporo, 001-0020 Japan
| | - Hiroyuki Ishida
- Department of Applied Plant Science, Graduate School of Agricultural Sciences, Tohoku University, Sendai, 980-0845, Japan
| | - Jun Hidema
- Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
| | - Tomomi Nemoto
- Exploratory Research Center on Life and Living Systems (ExCELLs), National Institute of Natural Sciences, Okazaki, 444-8787 Japan
- National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, 444-8787 Japan
- Department of Physiological Sciences, The Graduate University for Advanced Study (SOKENDAI), Hayama, 240-0193 Japan
- Research Institute for Electronic Science, Hokkaido University, Sapporo, 001-0020 Japan
| | - Masanori Izumi
- Center for Sustainable Resource Science (CSRS), RIKEN, Wako, 351-0198 Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, 322-0012 Japan
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12
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Nakamura S, Hagihara S, Izumi M. Mitophagy in plants. Biochim Biophys Acta Gen Subj 2021; 1865:129916. [PMID: 33932484 DOI: 10.1016/j.bbagen.2021.129916] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/06/2021] [Accepted: 04/26/2021] [Indexed: 12/11/2022]
Abstract
Mitochondria play a central role in primary metabolism in plants as well as in heterotrophic eukaryotes. Plants must control the quality and number of mitochondria in response to a changing environment, across cell types and developmental stages. Mitophagy is defined as the degradation of mitochondria by autophagy, an evolutionarily conserved system for the removal and recycling of intracellular components. Recent studies have highlighted the importance of mitophagy in plant stress responses. This review article summarizes our current knowledge of plant mitophagy and discusses the underlying mechanisms. In plants, chloroplasts cooperate with mitochondria for energy production, and autophagy also targets chloroplasts through a process known as chlorophagy. Advances in plant autophagy studies now allow a comparative analysis of the autophagic turnover of mitochondria and chloroplasts, via the selective degradation of their soluble proteins, fragments, or entire organelles.
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Affiliation(s)
- Sakuya Nakamura
- Center for Sustainable Resource Science (CSRS), RIKEN, 351-0198 Wako, Japan
| | - Shinya Hagihara
- Center for Sustainable Resource Science (CSRS), RIKEN, 351-0198 Wako, Japan
| | - Masanori Izumi
- Center for Sustainable Resource Science (CSRS), RIKEN, 351-0198 Wako, Japan.
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13
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Yoshimura M, Kim SF, Takise R, Kusano S, Nakamura S, Izumi M, Yagi A, Itami K, Hagihara S. Development of potent inhibitors for strigolactone receptor DWARF 14. Chem Commun (Camb) 2020; 56:14917-14919. [PMID: 33196066 DOI: 10.1039/d0cc01989e] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Strigolactones (SLs) are plant hormones that suppress shoot branching through perception by their receptor protein DWARF 14 (D14). The artificial regulation of SL signaling has been considered a potent agricultural technique because plant architecture is strongly related to crop yield. In this communication, we describe the development of a small-molecule D14 inhibitor that functions at sub-micromolar levels. This potent inhibitor may be a lead compound for a first-in-class plant growth regulator.
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Affiliation(s)
- Masahiko Yoshimura
- Graduate School of Science Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Sojung F Kim
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA and Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Ryosuke Takise
- Graduate School of Science Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Shuhei Kusano
- Center for Sustainable Resource Science, RIKEN, 2-1 Hirosawa, Wako City, Saitama 351-0198, Japan
| | - Sakuya Nakamura
- Center for Sustainable Resource Science, RIKEN, 2-1 Hirosawa, Wako City, Saitama 351-0198, Japan
| | - Masanori Izumi
- Center for Sustainable Resource Science, RIKEN, 2-1 Hirosawa, Wako City, Saitama 351-0198, Japan
| | - Akiko Yagi
- Graduate School of Science Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Kenichiro Itami
- Graduate School of Science Nagoya University, Chikusa, Nagoya, 464-8602, Japan and Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Shinya Hagihara
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8601, Japan and Center for Sustainable Resource Science, RIKEN, 2-1 Hirosawa, Wako City, Saitama 351-0198, Japan
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14
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Nishimura K, Yamada R, Hagihara S, Iwasaki R, Uchida N, Kamura T, Takahashi K, Torii KU, Fukagawa T. A super-sensitive auxin-inducible degron system with an engineered auxin-TIR1 pair. Nucleic Acids Res 2020; 48:e108. [PMID: 32941625 PMCID: PMC7544234 DOI: 10.1093/nar/gkaa748] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [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: 05/31/2020] [Revised: 08/19/2020] [Accepted: 08/28/2020] [Indexed: 01/27/2023] Open
Abstract
The auxin-inducible degron (AID) system enables rapid depletion of target proteins within the cell by applying the natural auxin IAA. The AID system is useful for investigating the physiological functions of essential proteins; however, this system generally requires high dose of auxin to achieve effective depletion in vertebrate cells. Here, we describe a super-sensitive AID system that incorporates the synthetic auxin derivative 5-Ad-IAA and its high-affinity-binding partner OsTIR1F74A. The super-sensitive AID system enabled more than a 1000-fold reduction of the AID inducer concentrations in chicken DT40 cells. To apply this system to various mammalian cell lines including cancer cells containing multiple sets of chromosomes, we utilized a single-step method where CRISPR/Cas9-based gene knockout is combined with insertion of a pAID plasmid. The single-step method coupled with the super-sensitive AID system enables us to easily and rapidly generate AID-based conditional knockout cells in a wide range of vertebrate cell lines. Our improved method that incorporates the super-sensitive AID system and the single-step method provides a powerful tool for elucidating the roles of essential genes.
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Affiliation(s)
- Kohei Nishimura
- Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan.,Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Ryotaro Yamada
- Institute of Transformative Biomolecules (WPI-ITbM), Nagoya University, Nagoya 464-8601, Japan.,RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Shinya Hagihara
- Institute of Transformative Biomolecules (WPI-ITbM), Nagoya University, Nagoya 464-8601, Japan.,RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Rie Iwasaki
- Institute of Transformative Biomolecules (WPI-ITbM), Nagoya University, Nagoya 464-8601, Japan
| | - Naoyuki Uchida
- Institute of Transformative Biomolecules (WPI-ITbM), Nagoya University, Nagoya 464-8601, Japan.,Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan
| | - Takumi Kamura
- Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Koji Takahashi
- Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan.,Institute of Transformative Biomolecules (WPI-ITbM), Nagoya University, Nagoya 464-8601, Japan
| | - Keiko U Torii
- Institute of Transformative Biomolecules (WPI-ITbM), Nagoya University, Nagoya 464-8601, Japan.,Department of Molecular Biosciences, The University of Texas at Austin, 2506 Speedway, Austin, TX 78712, USA.,Howard Hughes Medical Institute, The University of Texas at Austin, 2506 Speedway, Austin, TX 78712, USA
| | - Tatsuo Fukagawa
- Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
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15
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Kikuchi Y, Nakamura S, Woodson JD, Ishida H, Ling Q, Hidema J, Jarvis RP, Hagihara S, Izumi M. Chloroplast Autophagy and Ubiquitination Combine to Manage Oxidative Damage and Starvation Responses. Plant Physiol 2020; 183:1531-1544. [PMID: 32554506 PMCID: PMC7401110 DOI: 10.1104/pp.20.00237] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 06/04/2020] [Indexed: 05/18/2023]
Abstract
Autophagy and the ubiquitin-proteasome system are the major degradation processes for intracellular components in eukaryotes. Although ubiquitination acts as a signal inducing organelle-targeting autophagy, the interaction between ubiquitination and autophagy in chloroplast turnover has not been addressed. In this study, we found that two chloroplast-associated E3 enzymes, SUPPRESSOR OF PPI1 LOCUS1 and PLANT U-BOX4 (PUB4), are not necessary for the induction of either piecemeal autophagy of chloroplast stroma or chlorophagy of whole damaged chloroplasts in Arabidopsis (Arabidopsis thaliana). Double mutations of an autophagy gene and PUB4 caused synergistic phenotypes relative to single mutations. The double mutants developed accelerated leaf chlorosis linked to the overaccumulation of reactive oxygen species during senescence and had reduced seed production. Biochemical detection of ubiquitinated proteins indicated that both autophagy and PUB4-associated ubiquitination contributed to protein degradation in the senescing leaves. Furthermore, the double mutants had enhanced susceptibility to carbon or nitrogen starvation relative to single mutants. Together, these results indicate that autophagy and chloroplast-associated E3s cooperate for protein turnover, management of reactive oxygen species accumulation, and adaptation to starvation.
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Affiliation(s)
- Yuta Kikuchi
- Graduate School of Life Sciences, Tohoku University, 980-0845 Sendai, Japan
| | - Sakuya Nakamura
- Center for Sustainable Resource Science, RIKEN, 351-0198 Wako, Japan
| | - Jesse D Woodson
- School of Plant Sciences, University of Arizona, Tucson, Arizona 85721-0036
| | - Hiroyuki Ishida
- Graduate School of Agricultural Science, Tohoku University, 980-0845 Sendai, Japan
| | - Qihua Ling
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Jun Hidema
- Graduate School of Life Sciences, Tohoku University, 980-0845 Sendai, Japan
| | - R Paul Jarvis
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Shinya Hagihara
- Center for Sustainable Resource Science, RIKEN, 351-0198 Wako, Japan
| | - Masanori Izumi
- Center for Sustainable Resource Science, RIKEN, 351-0198 Wako, Japan
- PRESTO, Japan Science and Technology Agency, 322-0012 Kawaguchi, Japan
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16
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Miller S, Son YL, Aikawa Y, Makino E, Nagai Y, Srivastava A, Oshima T, Sugiyama A, Hara A, Abe K, Hirata K, Oishi S, Hagihara S, Sato A, Tama F, Itami K, Kay SA, Hatori M, Hirota T. Isoform-selective regulation of mammalian cryptochromes. Nat Chem Biol 2020; 16:676-685. [PMID: 32231341 DOI: 10.1038/s41589-020-0505-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/24/2020] [Indexed: 02/07/2023]
Abstract
CRY1 and CRY2 are essential components of the circadian clock controlling daily physiological rhythms. Accumulating evidences indicate distinct roles of these highly homologous proteins, in addition to redundant functions. Therefore, the development of isoform-selective compounds represents an effective approach towards understanding the similarities and differences of CRY1 and CRY2 by controlling each isoform individually. We conducted phenotypic screenings of circadian clock modulators, and identified KL101 and TH301 that selectively stabilize CRY1 and CRY2, respectively. Crystal structures of CRY-compound complexes revealed conservation of compound-binding sites between CRY1 and CRY2. We further discovered a unique mechanism underlying compound selectivity in which the disordered C-terminal region outside the pocket was required for the differential effects of KL101 and TH301 against CRY isoforms. By using these compounds, we found a new role of CRY1 and CRY2 as enhancers of brown adipocyte differentiation, providing the basis of CRY-mediated regulation of energy expenditure.
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Affiliation(s)
- Simon Miller
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan
| | - You Lee Son
- Laboratory of Chronobiology, Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan
| | - Yoshiki Aikawa
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan
| | - Eri Makino
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Yoshiko Nagai
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan
| | | | - Tsuyoshi Oshima
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Akiko Sugiyama
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan
| | - Aya Hara
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan
| | - Kazuhiro Abe
- Cellular and Structural Physiology Institute, Nagoya University, Nagoya, Japan
| | | | - Shinya Oishi
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Shinya Hagihara
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Ayato Sato
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan
| | - Florence Tama
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan.,Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan.,Computational Structural Biology Unit, RIKEN-Center for Computational Science, Hyogo, Japan
| | - Kenichiro Itami
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Steve A Kay
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Megumi Hatori
- Laboratory of Chronobiology, Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan.
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan.
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17
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Hagihara S, Yamada R, Itami K, Torii KU. Dissecting plant hormone signaling with synthetic molecules: perspective from the chemists. Curr Opin Plant Biol 2019; 47:32-37. [PMID: 30248557 DOI: 10.1016/j.pbi.2018.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 09/05/2018] [Accepted: 09/06/2018] [Indexed: 05/09/2023]
Abstract
Synthetic molecules can be powerful tools to overcome the limitations of the biological approaches. Especially redundancy, lethality, and intractability of the target genes, which often hamper the progress of plant science, could be bypassed by elaborately designed small molecules. In this review, we discuss how synthetic chemistry can contribute to increasing our understanding of plant hormone signaling. Specific focus will be on the visualization and hijacking of hormone signaling with novel synthetic chemicals, with emphasis on perception of ABA, strigolactones, and auxins.
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Affiliation(s)
- Shinya Hagihara
- Center for Sustainable Resource Science (CSRS), RIKEN, Wako, Saitama, Japan; Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8601, Japan; PRESTO, JST, Japan; Department of Chemistry, Graduate School of Science, Nagoya University, Japan.
| | - Ryotaro Yamada
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8601, Japan; Department of Chemistry, Graduate School of Science, Nagoya University, Japan
| | - Kenichiro Itami
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8601, Japan; Department of Chemistry, Graduate School of Science, Nagoya University, Japan
| | - Keiko U Torii
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya 464-8601, Japan; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195-1800, USA; Department of Biology, University of Washington, Seattle, WA 98195-1800, USA.
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18
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Oshima T, Niwa Y, Kuwata K, Srivastava A, Hyoda T, Tsuchiya Y, Kumagai M, Tsuyuguchi M, Tamaru T, Sugiyama A, Ono N, Zolboot N, Aikawa Y, Oishi S, Nonami A, Arai F, Hagihara S, Yamaguchi J, Tama F, Kunisaki Y, Yagita K, Ikeda M, Kinoshita T, Kay SA, Itami K, Hirota T. Cell-based screen identifies a new potent and highly selective CK2 inhibitor for modulation of circadian rhythms and cancer cell growth. Sci Adv 2019; 5:eaau9060. [PMID: 30746467 PMCID: PMC6357737 DOI: 10.1126/sciadv.aau9060] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 12/11/2018] [Indexed: 05/08/2023]
Abstract
Compounds targeting the circadian clock have been identified as potential treatments for clock-related diseases, including cancer. Our cell-based phenotypic screen revealed uncharacterized clock-modulating compounds. Through affinity-based target deconvolution, we identified GO289, which strongly lengthened circadian period, as a potent and selective inhibitor of CK2. Phosphoproteomics identified multiple phosphorylation sites inhibited by GO289 on clock proteins, including PER2 S693. Furthermore, GO289 exhibited cell type-dependent inhibition of cancer cell growth that correlated with cellular clock function. The x-ray crystal structure of the CK2α-GO289 complex revealed critical interactions between GO289 and CK2-specific residues and no direct interaction of GO289 with the hinge region that is highly conserved among kinases. The discovery of GO289 provides a direct link between the circadian clock and cancer regulation and reveals unique design principles underlying kinase selectivity.
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Affiliation(s)
- Tsuyoshi Oshima
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan
| | - Yoshimi Niwa
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Ashutosh Srivastava
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Tomoko Hyoda
- Department of Health Sciences, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yoshiki Tsuchiya
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Megumi Kumagai
- Department of Physiology, Faculty of Medicine, Saitama Medical University, Saitama 350-0495, Japan
| | - Masato Tsuyuguchi
- Graduate School of Science, Osaka Prefecture University, Osaka 599-8531, Japan
| | - Teruya Tamaru
- Department of Physiology and Advanced Research Center for Medical Science, Toho University School of Medicine, Tokyo 143-8540, Japan
| | - Akiko Sugiyama
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Natsuko Ono
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Norjin Zolboot
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Yoshiki Aikawa
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Shunsuke Oishi
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Atsushi Nonami
- Center for Advanced Medical Innovation, Kyushu University, Fukuoka 812-8582, Japan
| | - Fumio Arai
- Department of Stem Cell Biology and Medicine/Cancer Stem Cell Research, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Shinya Hagihara
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan
- PRESTO, JST, Nagoya 464-8601, Japan
| | | | - Florence Tama
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan, and RIKEN Center for Computational Science, Kobe 650-0047, Japan
| | - Yuya Kunisaki
- Department of Stem Cell Biology and Medicine/Cancer Stem Cell Research, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Kazuhiro Yagita
- Department of Physiology and Systems Bioscience, Kyoto Prefectural University of Medicine, Kyoto 602-8566, Japan
| | - Masaaki Ikeda
- Department of Physiology, Faculty of Medicine, Saitama Medical University, Saitama 350-0495, Japan
| | - Takayoshi Kinoshita
- Graduate School of Science, Osaka Prefecture University, Osaka 599-8531, Japan
| | - Steve A. Kay
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Kenichiro Itami
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
- Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan
- ERATO Itami Molecular Nanocarbon Project, JST, Nagoya 464-8601, Japan
- Corresponding author. (T.H.); (K.I.)
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
- PRESTO, JST, Nagoya 464-8601, Japan
- Corresponding author. (T.H.); (K.I.)
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19
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Torii KU, Hagihara S, Uchida N, Takahashi K. Harnessing synthetic chemistry to probe and hijack auxin signaling. New Phytol 2018; 220:417-424. [PMID: 30088268 DOI: 10.1111/nph.15337] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [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: 04/20/2018] [Accepted: 05/24/2018] [Indexed: 06/08/2023]
Abstract
Contents Summary 417 I. Introduction 417 II. Auxin analogs 1: Plant growth regulators 418 III. Auxin analogs 2: Molecular genetics and chemical biology 418 IV. Auxin analogs 3: Structure-guided chemical design 418 V. Auxin analogs 4: Synthetic orthogonal auxin-TIR1 pair 420 VI. Conclusions and future perspectives 422 Acknowledgements 422 References 423 SUMMARY: Plant biologists have been fascinated by auxin - a small chemical hormone so simple in structure yet so powerful - which regulates virtually every aspect of plant growth, development and behavior. Synthetic chemistry has played a major role in unraveling the physiological effects of auxin and the application of synthetic analogs has had a dramatic effect on tissue culture, horticulture and the agriculture of economically relevant plant species. Chemical genetics of the model plant, Arabidopsis thaliana, has helped to elucidate the nuclear auxin signaling pathway mediated by the receptor, TIR1, and opened the door to structure-guided, rational designs of auxin agonists and antagonists. Further improvement and tuning of such analogs has been achieved through derivatization and screening. Finally, by harnessing synthetic chemistry and receptor engineering, an orthogonal auxin-TIR1 pair has been created and developed, enabling spatiotemporal control of auxin perception and response. This synergism of chemistry, biology and engineering sparks new ideas and directions to delineate, uncover and manipulate auxin signaling.
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Affiliation(s)
- Keiko U Torii
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA
- Department of Biology, University of Washington, Seattle, WA, 98195, USA
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8601, Japan
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Shinya Hagihara
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8601, Japan
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
- RIKEN Center for Sustainable Resource Science (CSRS), Wako, Saitama, 351-0198, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, 332-0012, Japan
| | - Naoyuki Uchida
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8601, Japan
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Koji Takahashi
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, 464-8601, Japan
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
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20
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Kitano H, Choi JH, Ueda A, Ito H, Hagihara S, Kan T, Kawagishi H, Itami K. Discovery of Plant Growth Stimulants by C–H Arylation of 2-Azahypoxanthine. Org Lett 2018; 20:5684-5687. [DOI: 10.1021/acs.orglett.8b02407] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hiroyuki Kitano
- Institute of Transformative Bio-Molecules (WPI-ITbM) and Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Jae-Hoon Choi
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Ayaka Ueda
- Institute of Transformative Bio-Molecules (WPI-ITbM) and Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8601, Japan
| | - Hideto Ito
- Institute of Transformative Bio-Molecules (WPI-ITbM) and Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8601, Japan
- JST-ERATO, Itami Molecular Nanocarbon Project, Nagoya University, Chikusa, Nagoya 464-8602, Japan
| | - Shinya Hagihara
- Institute of Transformative Bio-Molecules (WPI-ITbM) and Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8601, Japan
- Center for Sustainable Resource Science, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Toshiyuki Kan
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526 Japan
| | - Hirokazu Kawagishi
- Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
- Graduate School of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Kenichiro Itami
- Institute of Transformative Bio-Molecules (WPI-ITbM) and Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8601, Japan
- JST-ERATO, Itami Molecular Nanocarbon Project, Nagoya University, Chikusa, Nagoya 464-8602, Japan
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Yamada R, Murai K, Uchida N, Takahashi K, Iwasaki R, Tada Y, Kinoshita T, Itami K, Torii KU, Hagihara S. A Super Strong Engineered Auxin-TIR1 Pair. Plant Cell Physiol 2018; 59:1538-1544. [PMID: 29986114 PMCID: PMC6084576 DOI: 10.1093/pcp/pcy127] [Citation(s) in RCA: 18] [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] [Received: 01/30/2018] [Accepted: 07/01/2018] [Indexed: 05/21/2023]
Abstract
Auxin regulates diverse aspects of plant growth and development through induction of the interaction between TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALING F-BOX proteins (TIR1/AFBs) and AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) co-receptor proteins and the subsequent transcriptional regulation. The artificial control of endogenous auxin signaling should enable the precise delineation of auxin-mediated biological events as well as the agricultural application of auxin. To this end, we previously developed a synthetic auxin-receptor pair that consists of 5-(3-methoxyphenyl)-IAA (convexIAA, cvxIAA) and the engineered TIR1 whose phenylalanine at position 79 in the auxin-binding pocket is substituted to glycine (TIR1F79G) (concaveTIR1, ccvTIR1). This synthetic auxin-receptor pair works orthogonally to natural auxin signaling in transgenic plants harboring the engineered TIR1 by exogenous application of 5-(3-methoxyphenyl)-IAA, and has potential to be utilized as novel agricultural/horticultural tools. In the present study, we report an improved version of the synthetic cvxIAA-ccvTIR1 pair such that synthetic IAA can act at lower concentrations. Using a yeast two-hybrid system, we screened various 5-substituted IAAs and identified 5-adamantyl-IAA, named pico_cvxIAA, which mediates interaction of TIR1F79G and IAA3 proteins at a 1,000-fold lower concentration than the original version, 5-(3-methoxyphenyl)-IAA. Furthermore, we found that TIR1F79A interacts with IAA3 protein in the presence of picomolar concentrations of 5-adamantyl-IAA, 10,000-fold lower than our prototype version of the cvxIAA-ccvTIR1 pair. In addition, pull-down assays confirmed that 5-adamantyl-IAA mediates in vitro interaction of TIR1F79A and IAA7-DII peptides at lower concentrations. The improved synthetic IAA-TIR1 pair with high affinity would be beneficial for basic science as well as for practical use in agriculture/horticulture.
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Affiliation(s)
- Ryotaro Yamada
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
| | - Keiichiro Murai
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
| | - Naoyuki Uchida
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, Japan
| | - Koji Takahashi
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, Japan
| | - Rie Iwasaki
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, Japan
| | - Yasuomi Tada
- Center for Gene Research, Nagoya University, Chikusa, Nagoya, Japan
| | - Toshinori Kinoshita
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, Japan
| | - Kenichiro Itami
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, Japan
| | - Keiko U Torii
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, Japan
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
- Department of Biology, University of Washington, Seattle, WA, USA
- Corresponding authors: Keiko U. Torii, E-mail, ; Fax, +1-206-685-1728; Shinya Hagihara, E-mail,
| | - Shinya Hagihara
- Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Chikusa, Nagoya, Japan
- PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
- Corresponding authors: Keiko U. Torii, E-mail, ; Fax, +1-206-685-1728; Shinya Hagihara, E-mail,
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Yamada K, Abe Y, Murase H, Ida Y, Hagihara S, Nagatsugi F. Synthesis and Properties of 2′-OMe-RNAs Modified with Cross-Linkable 7-Deazaguanosine Derivatives. J Org Chem 2018; 83:8851-8862. [DOI: 10.1021/acs.joc.8b01002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ken Yamada
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi 980-8577, Japan
| | - Yusuke Abe
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi 980-8577, Japan
| | - Hirotaka Murase
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi 980-8577, Japan
| | - Yuta Ida
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi 980-8577, Japan
| | - Shinya Hagihara
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi 980-8577, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials (IMRAM), Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi 980-8577, Japan
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Fendrych M, Akhmanova M, Merrin J, Glanc M, Hagihara S, Takahashi K, Uchida N, Torii KU, Friml J. Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nat Plants 2018; 4:453-459. [PMID: 29942048 PMCID: PMC6104345 DOI: 10.1038/s41477-018-0190-1] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 06/01/2018] [Indexed: 05/18/2023]
Abstract
The phytohormone auxin is the information carrier in a plethora of developmental and physiological processes in plants1. It has been firmly established that canonical, nuclear auxin signalling acts through regulation of gene transcription2. Here, we combined microfluidics, live imaging, genetic engineering and computational modelling to reanalyse the classical case of root growth inhibition3 by auxin. We show that Arabidopsis roots react to addition and removal of auxin by extremely rapid adaptation of growth rate. This process requires intracellular auxin perception but not transcriptional reprogramming. The formation of the canonical TIR1/AFB-Aux/IAA co-receptor complex is required for the growth regulation, hinting to a novel, non-transcriptional branch of this signalling pathway. Our results challenge the current understanding of root growth regulation by auxin and suggest another, presumably non-transcriptional, signalling output of the canonical auxin pathway.
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Affiliation(s)
- Matyáš Fendrych
- Institute of Science and Technology (IST) Austria, Klosterneuburg, Austria
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czechia
| | - Maria Akhmanova
- Institute of Science and Technology (IST) Austria, Klosterneuburg, Austria
| | - Jack Merrin
- Institute of Science and Technology (IST) Austria, Klosterneuburg, Austria
| | - Matouš Glanc
- Institute of Science and Technology (IST) Austria, Klosterneuburg, Austria
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czechia
| | - Shinya Hagihara
- Institute of Transformative Biomolecules (WPI-ITbM) and Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
| | - Koji Takahashi
- Institute of Transformative Biomolecules (WPI-ITbM) and Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
| | - Naoyuki Uchida
- Institute of Transformative Biomolecules (WPI-ITbM) and Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
| | - Keiko U Torii
- Institute of Transformative Biomolecules (WPI-ITbM) and Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
- Howard Hughes Medical Institute and Department of Biology, University of Washington, Seattle, WA, USA
| | - Jiří Friml
- Institute of Science and Technology (IST) Austria, Klosterneuburg, Austria.
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24
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Hagihara S, Aoyama J, Limbong D, Tsukamoto K. Interspecific and sexual differences in riverine distribution of tropical eels Anguilla spp. J Fish Biol 2018. [PMID: 29882214 DOI: 10.1111/jfb.13673] [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] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 04/19/2018] [Indexed: 06/08/2023]
Abstract
A total of 261 individuals of the four tropical eel species, Anguilla celebesensis, Anguilla marmorata, Anguilla bicolor pacifica and Anguilla interioris, were collected from 12 locations around Sulawesi Island, Indonesia, to gain knowledge about the riverine distribution of tropical eels. Anguilla marmorata was predominant in the lower reaches of Poso River (94·4% of total eel catch in the sampling area), Poso Lake (93·3%), three small inlet rivers of Tomini Bay (100%) and Laa River (92·3%). Anguilla celebesensis occurred frequently in the inlet rivers of Poso Lake (63·5%). Anguilla bicolor pacifica and Anguilla interioris were rare (1.5% and 0.4%, respectively). Otolith Sr:Ca ratio electron-probe micro analysis (EPMA) for individual migratory histories revealed that 15 A. celebesensis caught in Poso Lake and its inlet rivers were categorized into 14 river eels (Sr:Ca < 2·5) showing upstream migration seemingly at their elver stage and only one sea eel (Sr:Ca ≥ 6·0) that stayed in the marine habitat for the majority of its life after recruiting to Sulawesi Island before its late upstream migration. In A. marmorata, 19 examined eels from Poso Lake and its inlet rivers were all river eels, while 17 eels from the lower reaches of Poso River were two river eels, six sea eels and nine estuarine eels (2·5 ≤ Sr:Ca <6·0) that mostly lived in the brackish water. The sex ratio of A. celebesensis was highly skewed towards a dominance of females (99%). In A. marmorata, females were predominant in Poso Lake (95·2%), its inlet rivers (94·7%) and Laa River (100%), while males were more frequent in the lower reaches of Poso River (76·5%) and small inlet rivers of Tomini Bay (94·1%). These results indicate that the riverine distribution pattern of tropical eels differs among species and between sexes. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- S Hagihara
- Nihon University, College of Bioresource Sciences, Fujisawa, Kanagawa, Japan
| | - J Aoyama
- Atmosphere and Ocean Research Institute, International Coastal Research Center, Iwate, Japan
| | - D Limbong
- Sintuwu Maroso University, Indonesia
| | - K Tsukamoto
- Nihon University, College of Bioresource Sciences, Fujisawa, Kanagawa, Japan
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Hagihara S, Aoyama J, Limbong D, Tsukamoto K. Age and growth of migrating tropical eels, Anguilla celebesensis and Anguilla marmorata. J Fish Biol 2018; 92:1526-1544. [PMID: 29633275 DOI: 10.1111/jfb.13608] [Citation(s) in RCA: 3] [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] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 02/25/2018] [Indexed: 06/08/2023]
Abstract
The age and growth of migrating tropical eels, Anguilla celebesensis and Anguilla marmorata from central Sulawesi, Indonesia, were examined. Migrating eels (63 A. celebesensis and 38 A. marmorata) were obtained from weirs near the Poso Lake outlet and non-migrating eels (35 A. celebesensis and 119 A. marmorata) were captured by baited hooks, eel pots, scoop net and electro-fishing in the Poso River system, Laa River system, Baluga River, Tongku River and Padapu River from February 2009 to October 2010. In both species, the proportion of eels with opaque otolith edges showed a single peak in July, suggesting that one annulus (a pair of translucent and opaque zones) was formed each year in their otoliths. Mean ± s.d. and range of total length (LT ) and age was 785·2 ± 114·9 (585-1083) mm and 7·5 ± 1·6 (5-11) years in migrating female A. celebesensis and 1132·2 ± 173·7 (800-1630) mm and 11·6 ± 3·3 (7-23) years in A. marmorata. The age of migrating female eels was negatively correlated with annual growth rate, 100·7 ± 17·2 (68·1-145·0) mm year-1 in A. celebesensis and 97·9 ± 19·3 (66·6-131·6) mm year-1 in A. marmorata, but there was no significant correlation between the LT and annual growth rate in either species. The annual growth rates of these female tropical eels were typically higher than those of temperate anguillid species, suggesting a latitudinal cline in growth rate in the genus Anguilla reflecting the environmental conditions of their growth habitat.
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Affiliation(s)
- S Hagihara
- College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 255-0880, Japan
| | - J Aoyama
- International Coastal Research Center, Atmosphere and Ocean Research Institute, The University of Tokyo, 2-106-1 Akahama, Otsuchi, Iwate, 028-1102, Japan
| | - D Limbong
- Sintuwu Maroso University, Jl. Pulau Timor No.1, Poso, Central Sulawesi, 94619, Indonesia
| | - K Tsukamoto
- College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 255-0880, Japan
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Tsuchiya Y, Yoshimura M, Hagihara S. The dynamics of strigolactone perception in Striga hermonthica: a working hypothesis. J Exp Bot 2018; 69:2281-2290. [PMID: 29474634 DOI: 10.1093/jxb/ery061] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 02/14/2018] [Indexed: 06/08/2023]
Abstract
Plant-derived strigolactones have diverse functions at ecological scale, including effects upon the growth of plants themselves. The parasitic plants from the family Orobanchaceae interfere with the ecological and hormonal functions of strigolactones to generate unique germination abilities based on the sensing of host-derived strigolactones. Although the recent discovery of strigolactone receptors has enabled us to begin elucidating the mechanism of strigolactone perception, how perception relates to plant parasitism is still a mystery. In this review, we explore emerging questions by introducing recent advances in strigolactone research in parasitic plants. We also attempt to construct a conceptual framework for the unique in planta dynamics of strigolactone perception uncovered through the use of fluorescent probes for strigolactone receptors. Understanding the mechanisms of strigolactone-related processes is essential for controlling the parasitic plant Striga hermonthica, which has caused devastating damage to crop production in Africa.
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Affiliation(s)
- Yuichiro Tsuchiya
- Institute of Transformative Bio-Molecules, Nagoya University, Chikusa, Nagoya, Japan
| | - Masahiko Yoshimura
- Department of Chemistry, Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
| | - Shinya Hagihara
- Department of Chemistry, Graduate School of Science, Nagoya University, Chikusa, Nagoya, Japan
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Yoshimura M, Sato A, Kuwata K, Inukai Y, Kinoshita T, Itami K, Tsuchiya Y, Hagihara S. Discovery of Shoot Branching Regulator Targeting Strigolactone Receptor DWARF14. ACS Cent Sci 2018; 4:230-234. [PMID: 29532023 PMCID: PMC5833010 DOI: 10.1021/acscentsci.7b00554] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Indexed: 05/22/2023]
Abstract
DWARF14 (D14) is a strigolactone receptor that plays a central role in suppression of shoot branching, and hence is a potential target to increase crop productions and biomass. Recently, we reported a fluorescence turn-on probe, Yoshimulactone Green (YLG), which generates a strong fluorescence upon the hydrolysis by D14-type strigolactone receptors. Herein, we applied a YLG-based in vitro assay to a high-throughput chemical screening and identified a novel small molecule DL1 as a potent inhibitor of D14. DL1 competes with endogenous strigolactones, thereby increasing the number of shoot branching in a model plant Arabidopsis as well as in rice. Thus, DL1 is expected to be useful not only as a tool to understand the biological roles of D14 receptors in plant growth and development, but also as a potent agrochemical to improve the crop yield.
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Affiliation(s)
- Masahiko Yoshimura
- Graduate
School of Science Nagoya University,
Chikusa, Nagoya, 464-8602, Japan
| | - Ayato Sato
- Institute of Transformative Bio-Molecules
(WPI-ITbM) and International Cooperation
Center for Agricultural Education, Nagoya
University, Chikusa, Nagoya, 464-8601, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules
(WPI-ITbM) and International Cooperation
Center for Agricultural Education, Nagoya
University, Chikusa, Nagoya, 464-8601, Japan
| | - Yoshiaki Inukai
- Institute of Transformative Bio-Molecules
(WPI-ITbM) and International Cooperation
Center for Agricultural Education, Nagoya
University, Chikusa, Nagoya, 464-8601, Japan
| | - Toshinori Kinoshita
- Graduate
School of Science Nagoya University,
Chikusa, Nagoya, 464-8602, Japan
- Institute of Transformative Bio-Molecules
(WPI-ITbM) and International Cooperation
Center for Agricultural Education, Nagoya
University, Chikusa, Nagoya, 464-8601, Japan
| | - Kenichiro Itami
- Graduate
School of Science Nagoya University,
Chikusa, Nagoya, 464-8602, Japan
- Institute of Transformative Bio-Molecules
(WPI-ITbM) and International Cooperation
Center for Agricultural Education, Nagoya
University, Chikusa, Nagoya, 464-8601, Japan
| | - Yuichiro Tsuchiya
- Institute of Transformative Bio-Molecules
(WPI-ITbM) and International Cooperation
Center for Agricultural Education, Nagoya
University, Chikusa, Nagoya, 464-8601, Japan
- (Y.T.) E-mail:
| | - Shinya Hagihara
- Graduate
School of Science Nagoya University,
Chikusa, Nagoya, 464-8602, Japan
- Institute of Transformative Bio-Molecules
(WPI-ITbM) and International Cooperation
Center for Agricultural Education, Nagoya
University, Chikusa, Nagoya, 464-8601, Japan
- JST-PRESTO, Kawaguchi, Saitama 332-0012, Japan
- (S.H.)
E-mail:
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28
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Ziadi A, Uchida N, Kato H, Hisamatsu R, Sato A, Hagihara S, Itami K, Torii KU. Discovery of synthetic small molecules that enhance the number of stomata: C–H functionalization chemistry for plant biology. Chem Commun (Camb) 2017; 53:9632-9635. [DOI: 10.1039/c7cc04526c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The first-in-class synthetic small molecules enhancing the number of stomata in Arabidopsis thaliana have been discovered.
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Affiliation(s)
- Asraa Ziadi
- Institute of Transformative Bio-Molecules (WPI-ITbM)
- Nagoya University
- Nagoya
- Japan
| | - Naoyuki Uchida
- Institute of Transformative Bio-Molecules (WPI-ITbM)
- Nagoya University
- Nagoya
- Japan
- Graduate School of Science
| | - Hiroe Kato
- Institute of Transformative Bio-Molecules (WPI-ITbM)
- Nagoya University
- Nagoya
- Japan
| | - Rina Hisamatsu
- Institute of Transformative Bio-Molecules (WPI-ITbM)
- Nagoya University
- Nagoya
- Japan
- Graduate School of Science
| | - Ayato Sato
- Institute of Transformative Bio-Molecules (WPI-ITbM)
- Nagoya University
- Nagoya
- Japan
| | - Shinya Hagihara
- Institute of Transformative Bio-Molecules (WPI-ITbM)
- Nagoya University
- Nagoya
- Japan
- Graduate School of Science
| | - Kenichiro Itami
- Institute of Transformative Bio-Molecules (WPI-ITbM)
- Nagoya University
- Nagoya
- Japan
- Graduate School of Science
| | - Keiko U. Torii
- Institute of Transformative Bio-Molecules (WPI-ITbM)
- Nagoya University
- Nagoya
- Japan
- Graduate School of Science
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Uno K, Sasaki T, Sugimoto N, Ito H, Nishihara T, Hagihara S, Higashiyama T, Sasaki N, Sato Y, Itami K. Key Structural Elements of Unsymmetrical Cyanine Dyes for Highly Sensitive Fluorescence Turn-On DNA Probes. Chem Asian J 2016; 12:233-238. [PMID: 27860278 DOI: 10.1002/asia.201601430] [Citation(s) in RCA: 16] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/14/2016] [Indexed: 01/02/2023]
Abstract
Unsymmetrical cyanine dyes, such as thiazole orange, are useful for the detection of nucleic acids with fluorescence because they dramatically enhance the fluorescence upon binding to nucleic acids. Herein, we synthesized a series of unsymmetrical cyanine dyes and evaluated their fluorescence properties. A systematic structure-property relationship study has revealed that the dialkylamino group at the 2-position of quinoline in a series of unsymmetrical cyanine dyes plays a critical role in the fluorescence enhancement. Four newly designed unsymmetrical cyanine dyes showed negligible intrinsic fluorescence in the free state and strong fluorescence upon binding to double-stranded DNA (dsDNA) with a quantum yield of 0.53 to 0.90, which is 2 to 3 times higher than previous unsymmetrical cyanine dyes. A detailed analysis of the fluorescence lifetime revealed that the dialkylamino group at the 2-position of quinoline suppressed nonradiative decay in favor of increased fluorescence quantum yield. Moreover, these newly developed dyes were able to stain the nucleus specifically in fixed HeLa cells examined by using a confocal laser-scanning microscope.
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Affiliation(s)
- Kakishi Uno
- Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
| | - Taeko Sasaki
- Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
| | - Nagisa Sugimoto
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, 464-8601, Japan
| | - Hideto Ito
- Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
| | - Taishi Nishihara
- Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan.,JST-ERATO, Itami Molecular Nanocarbon Project, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Shinya Hagihara
- Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan.,Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, 464-8601, Japan
| | - Tetsuya Higashiyama
- Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan.,Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, 464-8601, Japan.,JST-ERATO, Higashiyama Live-Holonics Project, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
| | - Narie Sasaki
- Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
| | - Yoshikatsu Sato
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, 464-8601, Japan
| | - Kenichiro Itami
- Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan.,Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, 464-8601, Japan.,JST-ERATO, Itami Molecular Nanocarbon Project, Nagoya University, Chikusa, Nagoya, 464-8602, Japan
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Hasegawa Y, Kiyota N, Takahashi S, Yokota T, Yen CJ, Iwae S, Shimizu Y, Hong RL, Goto M, Namba Y, Ferris R, Monga M, Lynch M, Hagihara S, Tahara M. 360O_PR Efficacy and safety of nivolumab for recurrent or metastatic (R/M) squamous cell carcinoma of the head and neck (SCCHN) in Asia: CheckMate 141 subgroup analysis. Ann Oncol 2016. [DOI: 10.1093/annonc/mdw587.002] [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: 11/12/2022] Open
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31
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Hasegawa Y, Kiyota N, Takahashi S, Yokota T, Yen CJ, Iwae S, Shimizu Y, Hong RL, Goto M, Namba Y, Ferris R, Monga M, Lynch M, Hagihara S, Tahara M. 360O_PR Efficacy and safety of nivolumab for recurrent or metastatic (R/M) squamous cell carcinoma of the head and neck (SCCHN) in Asia: CheckMate 141 subgroup analysis. Ann Oncol 2016. [DOI: 10.1016/s0923-7534(21)00518-4] [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: 11/30/2022] Open
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32
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Yamashita S, Bergmann D, Sato A, Nomoto M, Tada Y, Humpf HU, Itami K, Hagihara S. High-throughput Assay for Quantification of Aminoglycoside–Ribosome Interaction. CHEM LETT 2016. [DOI: 10.1246/cl.160508] [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: 11/12/2022]
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33
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Zhang H, Hagihara S, Itami K. Making Dimethylamino a Transformable Directing Group by Nickel-Catalyzed CN Borylation. Chemistry 2015; 21:16796-800. [DOI: 10.1002/chem.201503596] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Indexed: 01/20/2023]
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34
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Tsuchiya Y, Yoshimura M, Sato Y, Kuwata K, Toh S, Holbrook-Smith D, Zhang H, McCourt P, Itami K, Kinoshita T, Hagihara S. PARASITIC PLANTS. Probing strigolactone receptors in Striga hermonthica with fluorescence. Science 2015; 349:864-8. [PMID: 26293962 DOI: 10.1126/science.aab3831] [Citation(s) in RCA: 180] [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: 01/02/2023]
Abstract
Elucidating the signaling mechanism of strigolactones has been the key to controlling the devastating problem caused by the parasitic plant Striga hermonthica. To overcome the genetic intractability that has previously interfered with identification of the strigolactone receptor, we developed a fluorescence turn-on probe, Yoshimulactone Green (YLG), which activates strigolactone signaling and illuminates signal perception by the strigolactone receptors. Here we describe how strigolactones bind to and act via ShHTLs, the diverged family of α/β hydrolase-fold proteins in Striga. Live imaging using YLGs revealed that a dynamic wavelike propagation of strigolactone perception wakes up Striga seeds. We conclude that ShHTLs function as the strigolactone receptors mediating seed germination in Striga. Our findings enable access to strigolactone receptors and observation of the regulatory dynamics for strigolactone signal transduction in Striga.
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Affiliation(s)
- Yuichiro Tsuchiya
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan. Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario M5S 3B2, Canada.
| | - Masahiko Yoshimura
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan. Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Yoshikatsu Sato
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Keiko Kuwata
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Shigeo Toh
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario M5S 3B2, Canada
| | - Duncan Holbrook-Smith
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario M5S 3B2, Canada
| | - Hua Zhang
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Peter McCourt
- Department of Cell and Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, Ontario M5S 3B2, Canada
| | - Kenichiro Itami
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan. Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan. Japan Science and Technology Agency-Exploratory Research for Advanced Technology, Itami Molecular Nanocarbon Project, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Toshinori Kinoshita
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan. Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Shinya Hagihara
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan. Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan.
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35
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Affiliation(s)
- Hua Zhang
- Institute of Transformative Bio-Molecules (WPI-ITbM) and Graduate School of Science, Nagoya University
| | - Shinya Hagihara
- Institute of Transformative Bio-Molecules (WPI-ITbM) and Graduate School of Science, Nagoya University
| | - Kenichiro Itami
- Institute of Transformative Bio-Molecules (WPI-ITbM) and Graduate School of Science, Nagoya University
- JST-ERATO, Itami Molecular Nanocarbon Project, Nagoya University
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Kusano S, Haruyama T, Ishiyama S, Hagihara S, Nagatsugi F. Development of the crosslinking reactions to RNA triggered by oxidation. Chem Commun (Camb) 2014; 50:3951-4. [DOI: 10.1039/c3cc49463b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this paper, we have reported a novel oxidation triggered crosslinking nucleobase ATVP (1) and demonstrated that the oxidized form ASVP (2) showed a very fast and selective crosslinking reaction to cytosine in RNA.
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Affiliation(s)
- Shuhei Kusano
- Institute of Multidisciplinary Research for Advanced Materials
- Tohoku University
- Sendai-shi, Japan
| | - Takuya Haruyama
- Institute of Multidisciplinary Research for Advanced Materials
- Tohoku University
- Sendai-shi, Japan
| | - Shogo Ishiyama
- Institute of Multidisciplinary Research for Advanced Materials
- Tohoku University
- Sendai-shi, Japan
| | - Shinya Hagihara
- Institute of Transformative Bio-Molecules (WPI-ITbM)
- Nagoya University
- Nagoya, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials
- Tohoku University
- Sendai-shi, Japan
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Hagihara S, Lin WC, Kusano S, Chao XG, Hori T, Imoto S, Nagatsugi F. Cover Picture: The Crosslink Formation of 2′-OMe Oligonucleotide Containing 2-Amino-6-vinylpurine Protects mRNA from miRNA-Mediated Silencing (ChemBioChem 12/2013). Chembiochem 2013. [DOI: 10.1002/cbic.201390042] [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: 11/10/2022]
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38
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Hagihara S, Lin WC, Kusano S, Chao XG, Hori T, Imoto S, Nagatsugi F. The Crosslink formation of 2'-OMe oligonucleotide containing 2-amino-6-vinylpurine protects mRNA from miRNA-mediated silencing. Chembiochem 2013; 14:1427-9. [PMID: 23893865 DOI: 10.1002/cbic.201300382] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [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: 06/13/2013] [Indexed: 12/21/2022]
Abstract
Masking the miRNA binding site: Crosslink-forming oligonucleotide (CFO) was used for target gene-specific inhibition of microRNA (miRNA) functions. This method can interfere with specific miRNA-mRNA interactions by recognizing sequences unique to the 3'-UTR that are inherent in each mRNA.
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Affiliation(s)
- Shinya Hagihara
- Institute of Transformative Bio-molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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Nagatsugi F, Takahashi Y, Kobayashi M, Kuwahara S, Kusano S, Chikuni T, Hagihara S, Harada N. Synthesis of peptide-conjugated light-driven molecular motors and evaluation of their DNA-binding properties. Mol BioSyst 2013; 9:969-73. [DOI: 10.1039/c2mb25520k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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40
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Kusano S, Sakuraba T, Hagihara S, Nagatsugi F. Synthesis of 6-amino-2-vinylpurine derivatives for cross-linking and evaluation of the reactivity. Bioorg Med Chem Lett 2012; 22:6957-61. [PMID: 23044366 DOI: 10.1016/j.bmcl.2012.08.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Revised: 07/25/2012] [Accepted: 08/30/2012] [Indexed: 01/01/2023]
Abstract
Oligodeoxynucleotides (ODNs) have been widely used for inhibiting the gene expression in antisense or antigene methods, and the interstrand cross-linking (ICL) forming ODNs have been expected to ensure the inhibition by these methods. Previously, we reported a highly efficient and selective ICL reaction toward cytosine using the 2-amino-6-vinylpurine derivative under acidic conditions. In this Letter, we report the synthesis of ODN containing 6-amino-2-vinylpurine derivatives and evaluation of the cross-linking reactivity.
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Affiliation(s)
- Shuhei Kusano
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai-shi, Miyagi 980-8577, Japan
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Hagihara S, Aoyama J, Limbong D, Tsukamoto K. Morphological and physiological changes of female tropical eels, Anguilla celebesensis and Anguilla marmorata, in relation to downstream migration. J Fish Biol 2012; 81:408-426. [PMID: 22803717 DOI: 10.1111/j.1095-8649.2012.03332.x] [Citation(s) in RCA: 10] [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: 06/01/2023]
Abstract
The morphological and physiological characteristics of migrating and non-migrating female tropical eels, Anguilla celebesensis and Anguilla marmorata were examined in relation to their downstream migration on central Sulawesi Island, Indonesia. Migrating eels (64 A. celebesensis and 37 A. marmorata) were obtained from weirs set near the outlet area of Poso Lake and non-migrating eels (21 A. celebesensis and 21 A. marmorata) were sampled by set-lines and eel pots in Poso Lake, its inlet rivers, and in the La River system during February 2009 to October 2010. In both species, values of eye index, pectoral-fin length index, gonado-somatic index (I(G)), hepato-somatic index, swimbladder-somatic index and cardio-somatic index of migrating eels were significantly higher than those of non-migrating eels and the gut-somatic index values of the migrating eels were significantly lower than that of non-migrating eels. When silvering stages of eels were classified by the silvering index for Anguilla japonica, in A. celebesensis, all non-migrating eels were Y1 stage and the migrating eels consisted of Y2, S1 and S2 stages eels. In A. marmorata, the non-migrating eels consisted of Y1 and Y2 eels, and the migrating eels consisted of Y2 and S1 eels, but there were no S2 eels. Results of principal component analysis (PCA) of morphological and physiological variables suggested that these characteristics changed drastically between the Y1 and Y2 stages in A. celebesensis, while A. marmorata showed a gradual change with silvering, which differs from the temperate species A. japonica. The mean ±S.D. I(G) value of migrating A. celebesensis (6.9 ± 1.8, 3.3-11.4) was very high and that of A. marmorata (3.1 ± 0.8, 1.8-5.7) was comparatively low. The very different rates of maturation that were found between these two species provide support for the hypothesis that the reproductive characteristics of silver eels can reflect their migration scale.
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Affiliation(s)
- S Hagihara
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Chiba, Japan.
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Hagihara S, Kusano S, Lin WC, Chao XG, Hori T, Imoto S, Nagatsugi F. Production of truncated protein by the crosslink formation of mRNA with 2'-OMe oligoribonucleotide containing 2-amino-6-vinylpurine. Bioorg Med Chem Lett 2012; 22:3870-2. [PMID: 22613261 DOI: 10.1016/j.bmcl.2012.04.123] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 04/27/2012] [Accepted: 04/28/2012] [Indexed: 12/29/2022]
Abstract
The development of convenient methods for controlling the protein expression is an important challenge in the postgenomic era. We applied the crosslink forming oligonucleotide (CFO) as a terminator of the ribosomal translation. In this study, we demonstrated that the improved reactivity of our CFO under physiological conditions enabled the sequence-specific introduction of a steric block for a ribosome on mRNAs. In vitro and in cell translation experiments revealed that the crosslinked mRNA can produce the truncated proteins in which the translation terminates at the desired position.
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Affiliation(s)
- Shinya Hagihara
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Miyagi 980-8577, Japan
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Imoto S, Hori T, Hagihara S, Taniguchi Y, Sasaki S, Nagatsugi F. Alteration of cross-linking selectivity with the 2'-OMe analogue of 2-amino-6-vinylpurine and evaluation of antisense effects. Bioorg Med Chem Lett 2010; 20:6121-4. [PMID: 20817451 DOI: 10.1016/j.bmcl.2010.08.027] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Revised: 08/03/2010] [Accepted: 08/05/2010] [Indexed: 11/28/2022]
Abstract
We previously reported that oligodeoxynucleotides containing 2-amino-6-vinylpurine (2-AVP: 1) exhibit efficient selective cross-linking to cytosine. In this study, the 2'-OMe nucleoside analogue (2) of 2-AVP was designed in order to increase its affinity to RNA and enhance metabolic stability. It has been demonstrated that 2'-OMe oligonucleotides bearing 2 achieve highly selective cross-linking to the thymine base in DNA and show higher antisense effect on luciferase production in cell lysate.
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Affiliation(s)
- Shuhei Imoto
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Aoba-ku, Sendai-shi, Miyagi, Japan
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Hennig A, Hagihara S, Matile S. Hydrazinoanthrylboronic acids as exciton-coupled circular dichroism (ECCD) probes for multivalent catechols, particularly epigallocatechin gallate. Chirality 2009; 21:826-35. [DOI: 10.1002/chir.20693] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Kuroki M, Aoyama J, Miller MJ, Yoshinaga T, Shinoda A, Hagihara S, Tsukamoto K. Sympatric spawning of Anguilla marmorata and Anguilla japonica in the western North Pacific Ocean. J Fish Biol 2009; 74:1853-1865. [PMID: 20735676 DOI: 10.1111/j.1095-8649.2009.02299.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Extensive collections were made of the larvae of the temperate Japanese eel Anguilla japonica and the tropical giant mottled eel Anguilla marmorata in an overlapping area of the North Equatorial Current region of the western North Pacific Ocean. Collections of 189 A. marmorata and > 2500 A. japonica larvae during nine surveys from 1991 to 2007 showed that these two anguillid eels have similar spawning areas just west of the southern West Mariana Ridge. In July to August 2006 and August 2007, morphologically and genetically identified A. marmorata preleptocephali were mainly collected between 14.5-15 degrees N and 142-142.5 degrees E, where A. japonica preleptocephali were also caught in some of the same net tows. Fewer A. marmorata preleptocephali, however, were collected (n = 31) compared to those of A. japonica (n = c. 165), and fewer small larvae of A. marmorata were collected per tow than A. japonica (n = 1-10 and 1-294, respectively), suggesting relatively smaller spawning aggregations of A. marmorata. The distribution of preleptocephali and small larvae was wider in longitude in A. marmorata (131- 143 degrees E) than in A. japonica (137-143 degrees E), while the latitudinal range was almost the same (12-17 degrees N). Although spawning by these two species overlaps both spatially and temporally, the tropical eels of the North Pacific population of A. marmorata probably have a much longer spawning season with fewer spawners, at least in summer, and recruit to a much wider latitudinal range of growth habitats.
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Affiliation(s)
- M Kuroki
- Ocean Research Institute, University of Tokyo, Nakano, Tokyo 164-8639, Japan.
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46
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Yamada H, Yoshida Y, Terada N, Hagihara S, Komatsu T, Terasawa A. Fabrication of gravity-driven microfluidic device. Rev Sci Instrum 2008; 79:124301. [PMID: 19123582 DOI: 10.1063/1.3030859] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We have studied the micro total analysis system as a blood test. A microfluidic device with a three-pronged microchannel and artificial capillary vessels was fabricated. The microchannel is to transport blood, focus blood cells, and line them up. The vessels are to observe red blood cell deformation. An excimer laser was used to form grooves and so on. Numbers of thermosetting resin film and fluororesin were piled up on a cover glass. A laser fabricated part of the channel at the each film every lamination, and then a three-dimensional structure microchannel was fabricated. The channel sizes have widths of 50-150 microm and depths of 45 mum. Through holes used as artificial capillary vessels are made in the fluororesin having a minimum diameter of 5 microm and a length of 100 microm. As blood and a physiological saline are injected into the microchannel, the device stands upward facing the channel, and blood cells go into the vessels by the force of gravity and sheath flow of the saline. By gravity various groove patterns were made changing the width and length for measurement of blood focusing. Moreover, the red blood cell deformation was observed in the vessels with a microscope.
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Affiliation(s)
- H Yamada
- Graduate School of Engineering, Toyo University, 2100 Kujirai, Kawagoe, Saitama 350-8585, Japan.
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Miyazaki A, Matsuo I, Hagihara S, Kakegawa A, Suzuki T, Ito Y. Systematic synthesis and inhibitory activity of haloacetamidyl oligosaccharide derivatives toward cytoplasmic peptide:N-glycanase. Glycoconj J 2008; 26:133-40. [PMID: 18695987 DOI: 10.1007/s10719-008-9171-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2007] [Revised: 06/25/2008] [Accepted: 07/08/2008] [Indexed: 11/29/2022]
Abstract
A series of glycosyl haloacetamides were synthesized as potential inhibitors of cytoplasmic peptide:N-glycanase (PNGase), an enzyme that removes N-glycans from misfolded glycoproteins. Chloro-, bromo-, and iodoacetamidyl chitobiose and chitotetraose derivatives exhibited a significant inhibitory activity. No inhibitory activity was observed with of fluoroacetamididyl derivatives. Moreover, N-acetylglucosamine derivatives, beta-chloropropionamidyl chitobiose, and chloroacetamidyl cellooligosaccharide derivatives did not show any activity. These results underscore the importance of the N-acetyl groups of chitobiose for PNGase recognition. In addition, reactivity and position of the leaving group at the reducing end are also important factors.
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Affiliation(s)
- Ayako Miyazaki
- The Institute of Physical and Chemical Research, Wako, Saitama, Japan
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Hagihara S, Tanaka H, Matile S. Boronic Acid Converters for Reactive Hydrazide Amplifiers: Polyphenol Sensing in Green Tea with Synthetic Pores. J Am Chem Soc 2008; 130:5656-7. [DOI: 10.1021/ja801094p] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shinya Hagihara
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Hiroyuki Tanaka
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Stefan Matile
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
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Hagihara S, Gremaud L, Bollot G, Mareda J, Matile S. Screening of π-Basic Naphthalene and Anthracene Amplifiers for π-Acidic Synthetic Pore Sensors. J Am Chem Soc 2008; 130:4347-51. [DOI: 10.1021/ja078256t] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shinya Hagihara
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Ludovic Gremaud
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Guillaume Bollot
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Jiri Mareda
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Stefan Matile
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
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Hagihara S, Tanaka H, Matile S. Signal amplification by conjugate addition for differential sensing with synthetic pores. Org Biomol Chem 2008; 6:2259-62. [DOI: 10.1039/b805863f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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