1
|
Inoue N, Tsuge K, Yanagita T, Oikawa A, Nagao K. Time-Course Metabolomic Analysis: Production of Betaine Structural Analogs by Fungal Fermentation of Seaweed. Metabolites 2024; 14:201. [PMID: 38668329 PMCID: PMC11051755 DOI: 10.3390/metabo14040201] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 03/28/2024] [Accepted: 04/02/2024] [Indexed: 04/28/2024] Open
Abstract
Betaine structural analogs are compounds characterized by the presence of positive and negative charges in a single molecule and have been reported to have physiological properties, such as anti-inflammatory activities. In this study, we performed a metabolomic analysis of metabolite composition changes during the fermentation of Neopyropia yezoensis, an edible red alga, with Aspergillus oryzae for 72 h. The results indicated that three specific betaine structural analogs (betaine, stachydrine, and carnitine) exhibited significant changes in production by the end of the 72 h fermentation period. Time-course analysis suggested that betaine was generated from the precursor choline at 12-24 h during the late stage of fungal growth, while stachydrine was generated from the precursor-related compound glutamic acid at 48-72 h during the sporulation stage. However, the contribution of the precursor lysine to the increased production of carnitine during the 12-72 h period was unclear. This study provides useful information on the efficient production of betaine structural analogs by the fungal fermentation of seaweed as well as various other food materials.
Collapse
Affiliation(s)
- Nao Inoue
- Department of Biological Resource Science, Saga University, 1 Honjo-machi, Saga 840-8502, Japan; (N.I.); (T.Y.)
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan
| | - Keisuke Tsuge
- Saga Regional Industry Support Center, Saga 849-0932, Japan;
| | - Teruyoshi Yanagita
- Department of Biological Resource Science, Saga University, 1 Honjo-machi, Saga 840-8502, Japan; (N.I.); (T.Y.)
| | - Akira Oikawa
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan;
| | - Koji Nagao
- Department of Biological Resource Science, Saga University, 1 Honjo-machi, Saga 840-8502, Japan; (N.I.); (T.Y.)
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan
| |
Collapse
|
2
|
Kawade K, Sugiura D, Oikawa A, Kawaguchi M. Control of root nodule formation ensures sufficient shoot water availability in Lotus japonicus. Plant Physiol 2024:kiae126. [PMID: 38438136 DOI: 10.1093/plphys/kiae126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 02/02/2024] [Accepted: 02/18/2024] [Indexed: 03/06/2024]
Abstract
Leguminous plants provide carbon to symbiotic rhizobia in root nodules to fuel the energy-consuming process of nitrogen fixation. The carbon investment pattern from the acquired sources is crucial for shaping the growth regime of the host plants. The autoregulation of nodulation (AON) signaling pathway tightly regulates the number of nodules that form. AON disruption leads to excessive nodule formation and stunted shoot growth. However, the physiological role of AON in adjusting the carbon investment pattern is unknown. Here, we show that AON plays an important role in sustaining shoot water availability, which is essential for promoting carbon investment in shoot growth in Lotus japonicus. We found that AON-defective mutants exhibit substantial accumulation of non-structural carbohydrates, such as sucrose. Consistent with this metabolic signature, resilience against water-deficit stress was enhanced in the shoots of the AON-defective mutants. Furthermore, the water uptake ability was attenuated in the AON-defective mutants, likely due to the increased ratio of nodulation zone, which is covered with hydrophobic surfaces, on the roots. These results increase our physiological understanding of legume-rhizobia symbiosis by revealing a trade-off between root nodule formation and shoot water availability.
Collapse
Affiliation(s)
- Kensuke Kawade
- Graduate School of Science and Engineering, Saitama University, Shimo-Okubo 255, Sakura-ku, Saitama City, Saitama 338-8570, Japan
- RIKEN Center for Sustainable Resource Science (CSRS), Suehiro 1-7-22, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Daisuke Sugiura
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
| | - Akira Oikawa
- RIKEN Center for Sustainable Resource Science (CSRS), Suehiro 1-7-22, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Graduate School of Agriculture, Kyoto University, Kitashirakawaoiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Masayoshi Kawaguchi
- National Institute for Basic Biology, 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
- School of Life Science, Graduate University for Advanced Studies (SOKENDAI), 38 Nishigonaka, Myodaiji, Okazaki, Aichi 444-8585, Japan
| |
Collapse
|
3
|
Oikawa A, Takeuchi K, Morita K, Horibe Y, Sasaki R, Murayama H. Effects of Climate Conditions before Harvest Date on Edamame Metabolome. Plants (Basel) 2023; 13:87. [PMID: 38202395 PMCID: PMC10780805 DOI: 10.3390/plants13010087] [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: 10/02/2023] [Revised: 12/06/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024]
Abstract
Edamame is a green soybean that is rich in nutrients. Boiled edamame has been traditionally used for food in the East Asia region. It was known among farmers that conditions, such as temperature and climate on the day of harvest, affect the quality of edamame. Large-scale farmers harvest edamame on multiple days in the same year; however, the quality of edamame varies from day to day due to variations in climate conditions. In this study, we harvested edamame over several days between 2013 and 2018, obtained the climate conditions on the harvest date, and performed metabolome analysis using capillary electrophoresis mass spectrometry. To clarify the correlation between climate conditions before the harvest date and edamame components, comparative analyses of the obtained meteorological and metabolomic data were conducted. We found positive and negative correlations between the sunshine duration and average temperature, and the amounts of some edamame components. Furthermore, correlations were observed between the annual fluctuations in climate conditions and edamame components. Our findings suggest that the climate conditions before the date of harvesting are closely related to edamame quality.
Collapse
Affiliation(s)
- Akira Oikawa
- Graduate School of Agriculture, Kyoto University, Kitashirakawaoiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
- Faculty of Agriculture, Yamagata University, Wakaba-machi 1-23, Tsuruoka 997-8555, Japan (H.M.)
- RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama 230-0045, Japan;
| | - Katsutaka Takeuchi
- Faculty of Agriculture, Yamagata University, Wakaba-machi 1-23, Tsuruoka 997-8555, Japan (H.M.)
| | - Kei Morita
- Faculty of Agriculture, Yamagata University, Wakaba-machi 1-23, Tsuruoka 997-8555, Japan (H.M.)
| | - Yamato Horibe
- Faculty of Agriculture, Yamagata University, Wakaba-machi 1-23, Tsuruoka 997-8555, Japan (H.M.)
| | - Ryosuke Sasaki
- RIKEN Center for Sustainable Resource Science, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama 230-0045, Japan;
| | - Hideki Murayama
- Faculty of Agriculture, Yamagata University, Wakaba-machi 1-23, Tsuruoka 997-8555, Japan (H.M.)
| |
Collapse
|
4
|
Tantriani, Cheng W, Oikawa A, Tawaraya K. Phosphorus deficiency alters root length, acid phosphatase activity, organic acids, and metabolites in root exudates of soybean cultivars. Physiol Plant 2023; 175:e14107. [PMID: 38148232 DOI: 10.1111/ppl.14107] [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] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 11/15/2023] [Accepted: 11/21/2023] [Indexed: 12/28/2023]
Abstract
Phosphorus (P) deficiency alters the root morphological and physiological traits of plants. This study investigates how soybean cultivars with varying low-P tolerance values respond to different P levels in hydroponic culture by assessing alterations in root length, acid phosphatase activity, organic acid exudation, and metabolites in root exudates. Three low-P-tolerant cultivars ('Maetsue,' 'Kurotome,' and 'Fukuyutaka') and three low-P-sensitive cultivars ('Ihhon,' 'Chizuka,' and 'Komuta') were grown under 0 (P0) and 258 μM P (P8) for 7 and 14 days after transplantation (DAT). Low-P-tolerant cultivars increased root length by 31% and 119%, which was lower than the 62% and 144% increases in sensitive cultivars under P0 compared to P8 at 7 and 14 DAT, respectively. Acid phosphatase activity in low-P-tolerant cultivars exceeded that in sensitive cultivars by 5.2-fold and 2.0-fold at 7 and 14 DAT. Root exudates from each cultivar revealed 177 metabolites, with higher organic acid exudation in low-P-tolerant than sensitive cultivars under P0. Low-P-tolerant cultivars increased concentrations of specific metabolites (oxalate, GABA, quinate, citrate, AMP, 4-pyridoxate, and CMP), distinguishing them from low-P-sensitive cultivars under P0. The top five metabolomic pathways (purine metabolism, arginine and proline metabolism, TCA cycle, glyoxylate and dicarboxylate metabolism, alanine, aspartate, and glutamate metabolism) were more pronounced in low-P-tolerant cultivars at 14 DAT. These findings indicate that increasing root length was not an adaptation strategy under P deficiency; instead, tolerant cultivars exhibit enhanced root physiological traits, including increased acid phosphatase activity, organic acid exudation, specific metabolite release, and accelerated metabolic pathways under P deficiency.
Collapse
Affiliation(s)
- Tantriani
- The United Graduate School of Agricultural Sciences, Iwate University, Iwate, Japan
- Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, Indonesia
- Faculty of Agriculture, Yamagata University, Yamagata, Japan
| | - Weiguo Cheng
- Faculty of Agriculture, Yamagata University, Yamagata, Japan
| | - Akira Oikawa
- Faculty of Agriculture, Yamagata University, Yamagata, Japan
| | - Keitaro Tawaraya
- The United Graduate School of Agricultural Sciences, Iwate University, Iwate, Japan
- Faculty of Agriculture, Yamagata University, Yamagata, Japan
| |
Collapse
|
5
|
Inazu M, Nemoto T, Omata Y, Suzuki S, Ono S, Kanno Y, Seo M, Oikawa A, Masuda S. Complete loss of RelA and SpoT homologs in Arabidopsis reveals the importance of the plastidial stringent response in the interplay between chloroplast metabolism and plant defense response. Plant Cell Physiol 2023:pcad136. [PMID: 37925598 DOI: 10.1093/pcp/pcad136] [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] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 10/23/2023] [Accepted: 10/30/2023] [Indexed: 11/06/2023]
Abstract
The highly phosphorylated nucleotide, guanosine tetraphosphate (ppGpp), functions as a secondary messenger in bacteria and chloroplasts. The accumulation of ppGpp alters plastidial gene expression and metabolism, which are required for proper photosynthetic regulation and robust plant growth. However, because four plastid-localized ppGpp synthases/hydrolases function redundantly, the impact of the loss of ppGpp-dependent stringent response on plant physiology remains unclear. We used the CRISPR/Cas9 technology to generate an Arabidopsis thaliana mutant lacking all four ppGpp synthases/hydrolases, and characterized its phenotype. The mutant showed over 20-fold less ppGpp levels than the wild type (WT) under normal growth conditions, and exhibited leaf chlorosis and increased expression of defense-related genes as well as salicylic acid and jasmonate levels upon transition to nitrogen-starvation conditions. These results demonstrate that proper levels of ppGpp in plastids are required for controlling not only plastid metabolism but also phytohormone signaling, which is essential for plant defense.
Collapse
Affiliation(s)
- Masataka Inazu
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Takanari Nemoto
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Yuto Omata
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Sae Suzuki
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Sumire Ono
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Yuri Kanno
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Mitsunori Seo
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
- Tropical Biosphere Research Center, University of the Ryukyus, Nishihara 903-0213, Japan
| | - Akira Oikawa
- Graduate School of Agriculture, Kyoto University, Uji 611-0011, Japan
| | - Shinji Masuda
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| |
Collapse
|
6
|
Tsuchiya Y, Seki T, Kobayashi K, Komazawa-Sakon S, Shichino S, Nishina T, Fukuhara K, Ikejima K, Nagai H, Igarashi Y, Ueha S, Oikawa A, Tsurusaki S, Yamazaki S, Nishiyama C, Mikami T, Yagita H, Okumura K, Kido T, Miyajima A, Matsushima K, Imasaka M, Araki K, Imamura T, Ohmuraya M, Tanaka M, Nakano H. Fibroblast growth factor 18 stimulates the proliferation of hepatic stellate cells, thereby inducing liver fibrosis. Nat Commun 2023; 14:6304. [PMID: 37813881 PMCID: PMC10562492 DOI: 10.1038/s41467-023-42058-z] [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: 06/29/2022] [Accepted: 09/28/2023] [Indexed: 10/11/2023] Open
Abstract
Liver fibrosis results from chronic liver injury triggered by factors such as viral infection, excess alcohol intake, and lipid accumulation. However, the mechanisms underlying liver fibrosis are not fully understood. Here, we demonstrate that the expression of fibroblast growth factor 18 (Fgf18) is elevated in mouse livers following the induction of chronic liver fibrosis models. Deletion of Fgf18 in hepatocytes attenuates liver fibrosis; conversely, overexpression of Fgf18 promotes liver fibrosis. Single-cell RNA sequencing reveals that overexpression of Fgf18 in hepatocytes results in an increase in the number of Lrat+ hepatic stellate cells (HSCs), thereby inducing fibrosis. Mechanistically, FGF18 stimulates the proliferation of HSCs by inducing the expression of Ccnd1. Moreover, the expression of FGF18 is correlated with the expression of profibrotic genes, such as COL1A1 and ACTA2, in human liver biopsy samples. Thus, FGF18 promotes liver fibrosis and could serve as a therapeutic target to treat liver fibrosis.
Collapse
Affiliation(s)
- Yuichi Tsuchiya
- Department of Biochemistry, Faculty of Medicine, Toho University, 5-21-16 Omori-Nishi, Ota-ku, Tokyo, 143-8540, Japan
- Department of Biochemistry, Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi-shi, Chiba, 274-8510, Japan
| | - Takao Seki
- Department of Biochemistry, Faculty of Medicine, Toho University, 5-21-16 Omori-Nishi, Ota-ku, Tokyo, 143-8540, Japan
| | - Kenta Kobayashi
- Department of Biochemistry, Faculty of Medicine, Toho University, 5-21-16 Omori-Nishi, Ota-ku, Tokyo, 143-8540, Japan
- Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Sachiko Komazawa-Sakon
- Department of Biochemistry, Faculty of Medicine, Toho University, 5-21-16 Omori-Nishi, Ota-ku, Tokyo, 143-8540, Japan
| | - Shigeyuki Shichino
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute for Biomedical Sciences, Tokyo University of Science, 2669 Yamazaki, Noda-shi, Chiba, 278-0022, Japan
| | - Takashi Nishina
- Department of Biochemistry, Faculty of Medicine, Toho University, 5-21-16 Omori-Nishi, Ota-ku, Tokyo, 143-8540, Japan
| | - Kyoko Fukuhara
- Department of Gastroenterology, Faculty of Medicine and Graduate School of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
| | - Kenichi Ikejima
- Department of Gastroenterology, Faculty of Medicine and Graduate School of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
| | - Hidenari Nagai
- Department of Gastroenterology, Toho University Omori Medical Center, 6-11-1 Omori-Nishi, Ota-ku, Tokyo, 143-8541, Japan
| | - Yoshinori Igarashi
- Department of Gastroenterology, Toho University Omori Medical Center, 6-11-1 Omori-Nishi, Ota-ku, Tokyo, 143-8541, Japan
| | - Satoshi Ueha
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute for Biomedical Sciences, Tokyo University of Science, 2669 Yamazaki, Noda-shi, Chiba, 278-0022, Japan
| | - Akira Oikawa
- Laboratory of Quality Analysis and Assessment, Graduate School of Agriculture, Kyoto University, Gokasyo, Uji-shi, Kyoto, 611-0011, Japan
| | - Shinya Tsurusaki
- Department of Regenerative Medicine, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo, 162-8655, Tokyo, Japan
- Laboratory of Stem Cell Regulation, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Tokyo, Japan
| | - Soh Yamazaki
- Department of Biochemistry, Faculty of Medicine, Toho University, 5-21-16 Omori-Nishi, Ota-ku, Tokyo, 143-8540, Japan
| | - Chiharu Nishiyama
- Department of Biological Science and Technology, Faculty of Advanced Engineering, Tokyo University of Science, 6-3-1 Niijuku, Katsushika-ku, Tokyo, 125-8585, Japan
| | - Tetuo Mikami
- Department of Pathology, Faculty of Medicine, Toho University, 5-21-16 Omori-Nishi, Ota-ku, Tokyo, 143-8540, Japan
| | - Hideo Yagita
- Department of Immunology, Faculty of Medicine and Graduate School of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
| | - Ko Okumura
- Atopy Research Center, Faculty of Medicine and Graduate School of Medicine, Juntendo University, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Taketomo Kido
- Laboratory of Cell Growth and Differentiation, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Atsushi Miyajima
- Laboratory of Cell Growth and Differentiation, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan
| | - Kouji Matsushima
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute for Biomedical Sciences, Tokyo University of Science, 2669 Yamazaki, Noda-shi, Chiba, 278-0022, Japan
| | - Mai Imasaka
- Department of Genetics, Hyogo Medical University, 1-1 Mukogawa-cho, Nishinomiya-shi, Hyogo, 663-8501, Japan
| | - Kimi Araki
- Center for Animal Resources and Development, Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto, 860-0811, Japan
- Center for Metabolic Regulation of Healthy Aging, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto, 860-8556, Japan
| | - Toru Imamura
- Hoshi University School of Pharmacy and Pharmaceutical Sciences, 2-4-41 Ebara, Shinagawa-ku, Tokyo, 142-8501, Japan
- National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba-shi, Ibaraki, 305-8560, Japan
| | - Masaki Ohmuraya
- Department of Genetics, Hyogo Medical University, 1-1 Mukogawa-cho, Nishinomiya-shi, Hyogo, 663-8501, Japan
| | - Minoru Tanaka
- Department of Regenerative Medicine, Research Institute, National Center for Global Health and Medicine, 1-21-1 Toyama, Shinjuku-ku, Tokyo, 162-8655, Tokyo, Japan
- Laboratory of Stem Cell Regulation, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Tokyo, Japan
| | - Hiroyasu Nakano
- Department of Biochemistry, Faculty of Medicine, Toho University, 5-21-16 Omori-Nishi, Ota-ku, Tokyo, 143-8540, Japan.
| |
Collapse
|
7
|
Ishibashi M, Zaitsu K, Yoshikawa I, Otagaki S, Matsumoto S, Oikawa A, Shiratake K. High-throughput analysis of anthocyanins in horticultural crops using probe electrospray ionization tandem mass spectrometry (PESI/MS/MS). Hortic Res 2023; 10:uhad039. [PMID: 37082655 PMCID: PMC10111199 DOI: 10.1093/hr/uhad039] [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] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 02/23/2023] [Indexed: 05/03/2023]
Abstract
Plant secondary metabolites exhibit various horticultural traits. Simple and rapid analysis methods for evaluating these metabolites are in demand in breeding and consumer markets dealing with horticultural crops. We applied probe electrospray ionization (PESI) to evaluate secondary metabolite levels in horticultural crops. PESI does not require pre-treatment and separation of samples, which makes it suitable for high-throughput analysis. In this study, we targeted anthocyanins, one of the primary pigments in horticultural crops. Eighty-one anthocyanins were detected in approximately 3 minutes in the selected reaction-monitoring mode. Tandem mass spectrometry (MS/MS) could adequately distinguish between the fragments of anthocyanins and flavonols. Probe sampling, an intuitive method of sticking a probe directly to the sample, could detect anthocyanins qualitatively on a micro-area scale, such as achenes and receptacles in strawberry fruit. Our results suggest that PESI/MS/MS can be a powerful tool to characterize the profile of anthocyanins and compare their content among cultivars.
Collapse
Affiliation(s)
| | - Kei Zaitsu
- Faculty of Biology-Oriented Science and Technology, Kindai University, Nishimitani, Kinokawa, Wakayama 649-6493, Japan
| | - Ikue Yoshikawa
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Shungo Otagaki
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Aichi 464-8601, Japan
- Faculty of Agriculture, Meijo University, Tenpaku, Nagoya, Aichi 468-8502, Japan
| | - Shogo Matsumoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Akira Oikawa
- Graduate School of Agriculture, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | | |
Collapse
|
8
|
Honda S, Yamazaki Y, Mukada T, Cheng W, Chuba M, Okazaki Y, Saito K, Oikawa A, Maruyama H, Wasaki J, Wagatsuma T, Tawaraya K. Lipidome Profiling of Phosphorus Deficiency-Tolerant Rice Cultivars Reveals Remodeling of Membrane Lipids as a Mechanism of Low P Tolerance. Plants (Basel) 2023; 12:1365. [PMID: 36987053 PMCID: PMC10057753 DOI: 10.3390/plants12061365] [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] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 06/19/2023]
Abstract
Plants have evolved various mechanisms for low P tolerance, one of which is changing their membrane lipid composition by remodeling phospholipids with non-phospholipids. The objective of this study was to investigate the remodeling of membrane lipids among rice cultivars under P deficiency. Rice (Oryza sativa L.) cultivars (Akamai, Kiyonishiki, Akitakomachi, Norin No. 1, Hiyadateine, Koshihikari, and Netaro) were grown in 0 (-P) and 8 (+P) mg P L-1 solution cultures. Shoots and roots were collected 5 and 10 days after transplanting (DAT) in solution culture and subjected to lipidome profiling using liquid chromatography-mass spectrometry. Phosphatidylcholine (PC)34, PC36, phosphatidylethanolamine (PE)34, PE36, phosphatidylglycerol (PG)34, phosphatidylinositol (PI)34 were the major phospholipids and digalactosyldiacylglycerol (DGDG)34, DGDG36, 1,2-diacyl-3-O-alpha-glucuronosylglycerol (GlcADG)34, GlcADG36, monogalactosyldiacylglycerol (MGDG)34, MGDG36, sulfoquinovosyldiacylglycerol (SQDG)34 and SQDG36 were the major non-phospholipids. Phospholipids were lower in the plants that were grown under -P conditions than that in the plants that were grown under +P for all cultivars at 5 and 10 DAT. The levels of non-phospholipids were higher in -P plants than that in +P plants of all cultivars at 5 and 10 DAT. Decomposition of phospholipids in roots at 5 DAT correlated with low P tolerance. These results suggest that rice cultivars remodel membrane lipids under P deficiency, and the ability of remodeling partly contributes to low P tolerance.
Collapse
Affiliation(s)
- Soichiro Honda
- Faculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan
| | - Yumiko Yamazaki
- Faculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan
| | - Takumi Mukada
- Faculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan
| | - Weiguo Cheng
- Faculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan
| | - Masaru Chuba
- Yamagata Integrated Agricultural Research Center, Tsuruoka 997-7601, Japan
| | - Yozo Okazaki
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Akira Oikawa
- Faculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Hayato Maruyama
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Jun Wasaki
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8521, Japan
| | - Tadao Wagatsuma
- Faculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan
| | - Keitaro Tawaraya
- Faculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan
| |
Collapse
|
9
|
Ozawa H, Kambe A, Hibi K, Murakami S, Oikawa A, Handa T, Fujiki K, Nakato R, Shirahige K, Kimura H, Shiraki N, Kume S. Transient Methionine Deprivation Triggers Histone Modification and Potentiates Differentiation of Induced Pluripotent Stem Cells. Stem Cells 2023; 41:271-286. [PMID: 36472570 DOI: 10.1093/stmcls/sxac082] [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: 03/29/2022] [Accepted: 11/03/2022] [Indexed: 12/12/2022]
Abstract
Human induced pluripotent stem cells (iPSCs) require high levels of methionine (Met). Met deprivation results in a rapid decrease in intracellular S-adenosyl-methionine (SAM), poising human iPSCs for differentiation and leading to the apoptosis of undifferentiated cells. Met deprivation triggers rapid metabolic changes, including SAM, followed by reversible epigenetic modifications. Here, we show that short-term Met deprivation impairs the pluripotency network through epigenetic modification in a 3D suspension culture. The trimethylation of lysine 4 on histone H3 (H3K4me3) was drastically affected compared with other histone modifications. Short-term Met deprivation specifically affects the transcription start site (TSS) region of genes, such as those involved in the transforming growth factor β pathway and cholesterol biosynthetic process, besides key pluripotent genes such as NANOG and POU5F1. The expression levels of these genes decreased, correlating with the loss of H3K4me3 marks. Upon differentiation, Met deprivation triggers the upregulation of various lineage-specific genes, including key definitive endoderm genes, such as GATA6. Upon differentiation, loss of H3K27me3 occurs in many endodermal genes, switching from a bivalent to a monovalent (H3K4me3) state. In conclusion, Met metabolism maintains the pluripotent network with histone marks, and their loss potentiates differentiation.
Collapse
Affiliation(s)
- Hiroki Ozawa
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
| | - Azusa Kambe
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
| | - Kodai Hibi
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
| | - Satoshi Murakami
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
| | - Akira Oikawa
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Tetsuya Handa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
| | - Katsunori Fujiki
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Ryuichiro Nakato
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Katsuhiko Shirahige
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Kimura
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
| | - Nobuaki Shiraki
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
| | - Shoen Kume
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
| |
Collapse
|
10
|
Gunji S, Kawade K, Tabeta H, Horiguchi G, Oikawa A, Asaoka M, Hirai MY, Tsukaya H, Ferjani A. Tissue-targeted inorganic pyrophosphate hydrolysis in a fugu5 mutant reveals that excess inorganic pyrophosphate triggers developmental defects in a cell-autonomous manner. Front Plant Sci 2022; 13:945225. [PMID: 35991393 PMCID: PMC9386291 DOI: 10.3389/fpls.2022.945225] [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] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Excess PPi triggers developmental defects in a cell-autonomous manner. The level of inorganic pyrophosphate (PPi) must be tightly regulated in all kingdoms for the proper execution of cellular functions. In plants, the vacuolar proton pyrophosphatase (H+-PPase) has a pivotal role in PPi homeostasis. We previously demonstrated that the excess cytosolic PPi in the H+-PPase loss-of-function fugu5 mutant inhibits gluconeogenesis from seed storage lipids, arrests cell division in cotyledonary palisade tissue, and triggers a compensated cell enlargement (CCE). Moreover, PPi alters pavement cell (PC) shape, stomatal patterning, and functioning, supporting specific yet broad inhibitory effects of PPi on leaf morphogenesis. Whereas these developmental defects were totally rescued by the expression of the yeast soluble pyrophosphatase IPP1, sucrose supply alone canceled CCE in the palisade tissue but not the epidermal developmental defects. Hence, we postulated that the latter are likely triggered by excess PPi rather than a sucrose deficit. To formally test this hypothesis, we adopted a spatiotemporal approach by constructing and analyzing fugu5-1 PDF1 pro ::IPP1, fugu5-1 CLV1 pro ::IPP1, and fugu5-1 ICL pro ::IPP1, whereby PPi was removed specifically from the epidermis, palisade tissue cells, or during the 4 days following seed imbibition, respectively. It is important to note that whereas PC defects in fugu5-1 PDF1 pro ::IPP1 were completely recovered, those in fugu5-1 CLV1 pro ::IPP1 were not. In addition, phenotypic analyses of fugu5-1 ICL pro ::IPP1 lines demonstrated that the immediate removal of PPi after seed imbibition markedly improved overall plant growth, abolished CCE, but only partially restored the epidermal developmental defects. Next, the impact of spatial and temporal removal of PPi was investigated by capillary electrophoresis time-of-flight mass spectrometry (CE-TOF MS). Our analysis revealed that the metabolic profiles are differentially affected among all the above transgenic lines, and consistent with an axial role of central metabolism of gluconeogenesis in CCE. Taken together, this study provides a conceptual framework to unveil metabolic fluctuations within leaf tissues with high spatio-temporal resolution. Finally, our findings suggest that excess PPi exerts its inhibitory effect in planta in the early stages of seedling establishment in a tissue- and cell-autonomous manner.
Collapse
Affiliation(s)
- Shizuka Gunji
- Department of Biology, Tokyo Gakugei University, Koganei, Tokyo, Japan
- United Graduate School of Education, Tokyo Gakugei University, Tokyo, Japan
| | - Kensuke Kawade
- National Institute for Basic Biology, Okazaki, Aichi, Japan
- Department of Basic Biology, School of Life Sciences, Graduate University for Advanced Studies (SOKENDAI), Okazaki, Aichi, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Hiromitsu Tabeta
- Department of Biology, Tokyo Gakugei University, Koganei, Tokyo, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Gorou Horiguchi
- Department of Life Science, College of Science, Rikkyo University, Tokyo, Japan
- Research Center for Life Science, College of Science, Rikkyo University, Tokyo, Japan
| | - Akira Oikawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Faculty of Agriculture, Yamagata University, Tsuruoka, Japan
| | - Mariko Asaoka
- Department of Biology, Tokyo Gakugei University, Koganei, Tokyo, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Department of Applied Biosciences, Graduate School of Bioagricultural Science, Nagoya University, Nagoya, Japan
| | - Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Ali Ferjani
- Department of Biology, Tokyo Gakugei University, Koganei, Tokyo, Japan
| |
Collapse
|
11
|
Utsumi Y, Tanaka M, Utsumi C, Takahashi S, Matsui A, Fukushima A, Kobayashi M, Sasaki R, Oikawa A, Kusano M, Saito K, Kojima M, Sakakibara H, Sojikul P, Narangajavana J, Seki M. Integrative omics approaches revealed a crosstalk among phytohormones during tuberous root development in cassava. Plant Mol Biol 2022; 109:249-269. [PMID: 32757126 DOI: 10.1007/s11103-020-01033-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [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: 01/14/2020] [Accepted: 07/06/2020] [Indexed: 05/23/2023]
Abstract
Integrative omics approaches revealed a crosstalk among phytohormones during tuberous root development in cassava. Tuberous root formation is a complex process consisting of phase changes as well as cell division and elongation for radial growth. We performed an integrated analysis to clarify the relationships among metabolites, phytohormones, and gene transcription during tuberous root formation in cassava (Manihot esculenta Crantz). We also confirmed the effects of the auxin (AUX), cytokinin (CK), abscisic acid (ABA), jasmonic acid (JA), gibberellin (GA), brassinosteroid (BR), salicylic acid, and indole-3-acetic acid conjugated with aspartic acid on tuberous root development. An integrated analysis of metabolites and gene expression indicated the expression levels of several genes encoding enzymes involved in starch biosynthesis and sucrose metabolism are up-regulated during tuberous root development, which is consistent with the accumulation of starch, sugar phosphates, and nucleotides. An integrated analysis of phytohormones and gene transcripts revealed a relationship among AUX signaling, CK signaling, and BR signaling, with AUX, CK, and BR inducing tuberous root development. In contrast, ABA and JA inhibited tuberous root development. These phenomena might represent the differences between stem tubers (e.g., potato) and root tubers (e.g., cassava). On the basis of these results, a phytohormonal regulatory model for tuberous root development was constructed. This model may be useful for future phytohormonal studies involving cassava.
Collapse
Affiliation(s)
- Yoshinori Utsumi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
| | - Maho Tanaka
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Chikako Utsumi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Satoshi Takahashi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Akihiro Matsui
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Atsushi Fukushima
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Makoto Kobayashi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Ryosuke Sasaki
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Akira Oikawa
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Faculty of Agriculture, Yamagata University, Tsuruoka, Japan
| | - Miyako Kusano
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Chiba, 260-8675, Japan
| | - Mikiko Kojima
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Punchapat Sojikul
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Jarunya Narangajavana
- Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Motoaki Seki
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
- RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813, Japan.
| |
Collapse
|
12
|
Nagao K, Inoue N, Tsuge K, Oikawa A, Kayashima T, Yanagita T. Dried and Fermented Powders of Edible Algae ( Neopyropia yezoensis) Attenuate Hepatic Steatosis in Obese Mice. Molecules 2022; 27:molecules27092640. [PMID: 35565990 PMCID: PMC9099931 DOI: 10.3390/molecules27092640] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/16/2022] [Accepted: 04/19/2022] [Indexed: 11/29/2022]
Abstract
Edible algae Neopyropia yezoensis is used as “Nori”, its dried sheet product, in Japanese cuisine. Its lipid components reportedly improve hepatic steatosis in obese db/db mice. In this study, we prepared “Nori powder (NP)” and “fermented Nori powder (FNP)” to utilize the functional lipids contained in “Nori” and examined their nutraceutical effects in vivo. Male db/db mice were fed a basal AIN-76 diet, a 10% NP-supplemented diet, or a 10% FNP-supplemented diet for 4 weeks. We detected eicosapentaenoic acid (EPA) present in both NP and FNP in the serum and liver of db/db mice in a dose-dependent manner. The NP diet reduced hepatic triglyceride accumulation (by 58%) in db/db mice by modulating gene expression, which resulted in the inhibition of lipogenic enzyme activity. Additionally, NP intake significantly suppressed the expression of inflammatory genes in the liver and hepatic injury marker levels in the sera (by 26%) of db/db mice. The FNP diet also led to a marked reduction in hepatic triglyceride accumulation (by 50%) and hepatic injury (by 28%) in db/db mice, and the mechanism of these alleviative actions was similar to that of the NP diet. Although the EPA content of FNP was one-third that of NP, metabolomic analysis revealed that bioactive betaine analogs, such as stachydrine, betaine, and carnitine, were detected only in FNP. In conclusion, we suggest that (1) mechanical processing of “Nori” makes its lipid components readily absorbable by the body to exert their lipid-lowering effects, and (2) fermentation of “Nori” produces anti-inflammatory molecules and lipid-lowering molecules, which together with the lipid components, can exert hepatic steatosis-alleviating effects.
Collapse
Affiliation(s)
- Koji Nagao
- Department of Biological Resource Science, Saga University, 1 Honjo-machi, Saga 840-8502, Japan; (N.I.); (T.Y.)
- The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima 890-0065, Japan
- Correspondence: ; Tel.: +81-952-28-8781
| | - Nao Inoue
- Department of Biological Resource Science, Saga University, 1 Honjo-machi, Saga 840-8502, Japan; (N.I.); (T.Y.)
| | - Keisuke Tsuge
- Saga Regional Industry Support Center, Saga 849-0932, Japan;
| | - Akira Oikawa
- Graduate School of Agriculture, Kyoto University, Uji 611-0011, Japan;
| | - Tomoko Kayashima
- Faculty of Education, Saga University, 1 Honjo-machi, Saga 840-8502, Japan;
| | - Teruyoshi Yanagita
- Department of Biological Resource Science, Saga University, 1 Honjo-machi, Saga 840-8502, Japan; (N.I.); (T.Y.)
| |
Collapse
|
13
|
Goto M, Oikawa A, Masuda S. Metabolic changes contributing to large biomass production in the Arabidopsis ppGpp-accumulating mutant under nitrogen deficiency. Planta 2022; 255:48. [PMID: 35079894 DOI: 10.1007/s00425-022-03835-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Abstract
The Arabidopsis ppGpp-overproducing mutant indicates a larger biomass than wild type by modulated amino-acid metabolism under nitrogen-limiting conditions. The regulatory nucleotide, guanosine 3', 5'-bis(pyrophosphate; ppGpp)-originally identified in Escherichia coli-controls gene expression and enzyme activities in the bacteria and plastids of plant cells. We recently reported that the ppGpp over-producing mutant of Arabidopsis thaliana had a larger shoot weight than wild type (WT), especially under nutrient-deficient conditions. However, the mechanisms behind the influence of ppGpp on plant growth and biomass remain elusive. To understand the impact of the ppGpp accumulation on plant growth, we characterized metabolic changes in the ppGpp-overproducing mutant upon transition from nitrogen-rich to nitrogen-limiting concentrations. We found that the fresh weight of the mutant was significantly larger than WT when the total nitrogen source (KNO3 and NH4NO3) concentration was below 0.9 mM. When the nitrogen content in the medium decreased, aromatic and branched-chain amino acids increased in WT due to accelerated protein degradation and/or attenuated protein synthesis. These amino-acid levels in the ppGpp over-accumulating mutant decreased upon nitrogen deficiency. The results suggest that the ppGpp-overaccumulation affects amino-acid and protein homeostasis and facilitates growth under nitrogen-limiting conditions.
Collapse
Affiliation(s)
- Mina Goto
- Department of Life Science & Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Akira Oikawa
- Faculty of Agriculture, Yamagata University, Tsuruoka, 997-8555, Japan
- Present Address: Graduate School of Agriculture, Kyoto University, Uji, 611-0011, Japan
| | - Shinji Masuda
- Department of Life Science & Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan.
| |
Collapse
|
14
|
Matsushima C, Shenton M, Kitahara A, Wasaki J, Oikawa A, Cheng W, Ikeo K, Tawaraya K. Multiple analysis of root exudates and microbiome in rice (Oryza sativa) under low P conditions. Arch Microbiol 2021; 203:5599-5611. [PMID: 34455446 DOI: 10.1007/s00203-021-02539-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 05/12/2021] [Revised: 08/11/2021] [Accepted: 08/18/2021] [Indexed: 12/29/2022]
Abstract
Plants release various metabolites from roots and root exudates contribute to differences in stress tolerance among plant species. Plant and soil microbes have complex interactions that are affected by biotic and abiotic factors. The purpose of this study was to examine the differences in metabolites in root exudates of rice (Oryza sativa) cultivars and their correlation with bacterial populations in the rhizosphere. Two rice cultivars (O. sativa cv. Akamai and O. sativa cv. Koshihikari) were grown in soils fertilized with 0 g P kg-1 (- P) or 4.8 g P kg-1 (+ P). Root exudates and root-attached soil were collected at 13 and 20 days after transplanting (DAT) and their metabolites and bacterial community structure were determined. The exudation of proline, serine, threonine, valine and 4-coumarate were increased under low P conditions in both cultivars. There was a positive correlation between the concentration of pantothenate in root exudates and the representation of members of the genera Clostridium and Sporosarcina, which were negatively correlated with root dry weight. Gracilibacter, Opitutus, Pelotomaculum, Phenylobacterium and Oxobacter were positively correlated with root dry weight and presence of allantoin, 2-aminobtyrate and GlcNac. This study provides new information about the response of plants and rhizosphere soil bacteria to low P conditions.
Collapse
Affiliation(s)
| | - Matthew Shenton
- Plant Genetics Laboratory, National Institute of Genetics, Mishima, 411-8540, Japan.,Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, 305-8518, Japan
| | - Ayaka Kitahara
- Faculty of Agriculture, Yamagata University, Tsuruoka, 997-8555, Japan
| | - Jun Wasaki
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi, Hiroshima, 739-8521, Japan
| | - Akira Oikawa
- Faculty of Agriculture, Yamagata University, Tsuruoka, 997-8555, Japan
| | - Weiguo Cheng
- Faculty of Agriculture, Yamagata University, Tsuruoka, 997-8555, Japan
| | - Kazuho Ikeo
- DNA Data Analysis Laboratory, National Institute of Genetics, Mishima, 411-8540, Japan
| | - Keitaro Tawaraya
- Faculty of Agriculture, Yamagata University, Tsuruoka, 997-8555, Japan.
| |
Collapse
|
15
|
Ahmad Z, Bashir K, Matsui A, Tanaka M, Sasaki R, Oikawa A, Hirai MY, Zu Y, Kawai-Yamada M, Rashid B, Husnain T, Seki M. Overexpression of nicotinamidase 3 (NIC3) gene and the exogenous application of nicotinic acid (NA) enhance drought tolerance and increase biomass in Arabidopsis. Plant Mol Biol 2021; 107:63-84. [PMID: 34460049 DOI: 10.1007/s11103-021-01179-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/02/2021] [Indexed: 05/27/2023]
Abstract
Overexpressing Nicotinamidase 3 gene, and the exogenous application of its metabolite nicotinic acid (NA), enhance drought stress tolerance and increase biomass in Arabidopsis thaliana. With progressive global climatic changes, plant productivity is threatened severely by drought stress. Deciphering the molecular mechanisms regarding genes responsible for balancing plant growth and stress amelioration could imply multiple possibilities for future sustainable goals. Nicotinamide adenine dinucleotide (NAD) biosynthesis and recycling/ distribution is a crucial feature for plant growth. The current study focuses on the functional characterization of nicotinamidase 3 (NIC3) gene, which is involved in the biochemical conversion of nicotinamide (NAM) to nicotinic acid (NA) in the salvage pathway of NAD biosynthesis. Our data show that overexpression of NIC3 gene enhances drought stress tolerance and increases plant growth. NIC3-OX plants accumulated more NA as compared to WT plants. Moreover, the upregulation of several genes related to plant growth/stress tolerance indicates that regulating the NAD salvage pathway could significantly enhance plant growth and drought stress tolerance. The exogenous application of nicotinic acid (NA) showed a similar phenotype as the effect of overexpressing NIC3 gene. In short, we contemplated the role of NIC3 gene and NA application in drought stress tolerance and plant growth. Our results would be helpful in engineering plants with enhanced drought stress tolerance and increased growth potential.
Collapse
Affiliation(s)
- Zarnab Ahmad
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, 230-0045, Japan
- Plant Genomics Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Khurram Bashir
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, 230-0045, Japan
- Laboratory of Plant Biotechnology, Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences (LUMS), Lahore, Pakistan
| | - Akihiro Matsui
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, 230-0045, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, 230-0045, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Ryosuke Sasaki
- Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, 230-0045, Japan
| | - Akira Oikawa
- Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, 230-0045, Japan
- Faculty of Agriculture, Yamagata University, Tsuruoka, 997-8555, Japan
| | - Masami Yokota Hirai
- Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, 230-0045, Japan
- Metabolic Systems Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, 230-0045, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601, Japan
| | - Yanhui Zu
- Graduate School of Science and Engineering, Saitama University, 225 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Maki Kawai-Yamada
- Graduate School of Science and Engineering, Saitama University, 225 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Bushra Rashid
- Plant Genomics Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Tayyab Husnain
- Plant Genomics Laboratory, Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, 230-0045, Japan.
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan.
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, 244-0813, Japan.
| |
Collapse
|
16
|
Luthfiana N, Inamura N, Sato T, Saito K, Oikawa A, Chen W, Tawaraya K. Metabolite profiling of the hyphal exudates of Rhizophagus clarus and Rhizophagus irregularis under phosphorus deficiency. Mycorrhiza 2021; 31:403-412. [PMID: 33459866 DOI: 10.1007/s00572-020-01016-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
Arbuscular mycorrhizal (AM) fungal extraradical hyphae exude their metabolites into the soil. Root exudate metabolites are affected by plant species and P status. However, the effect of P status on AM hyphal exudate metabolites has been unknown. This study aimed to examine hyphal exudate metabolite composition of two AM fungal species and their response to P deficiency through metabolite profiling. Rhizophagus clarus and R. irregularis were grown in a two-compartment in vitro culture system of Linum usitatissimum roots on solid modified Strullu-Romand medium in combination with two P levels (3 µM (P3) and 30 µM (P30)). Hyphal exudates were collected from the hyphal compartment at 118 days after inoculation (DAI). The metabolite composition of the hyphal exudates was determined by capillary electrophoresis/time-of-flight mass spectrometry, resulting in the identification of a total of 141 metabolites at 118 DAI. In the hyphal exudates of R. clarus, the concentrations of 18 metabolites, including sugars, amino acids, and organic acids, were significantly higher (p < 0.05) under P3 than under P30 conditions. In contrast, the concentrations of 10 metabolites, including sugar and amino acids, in the hyphal exudates of R. irregularis were significantly lower (p < 0.05) under P3 than under P30 conditions. These findings suggest that the extraradical hyphae of AM fungi exude diverse metabolites of which concentrations are affected by P conditions and differ between AM fungal species.
Collapse
Affiliation(s)
- Nuri Luthfiana
- Faculty of Agriculture, Yamagata University, Tsuruoka, 997-8555, Japan
| | - Nozomi Inamura
- Faculty of Agriculture, Yamagata University, Tsuruoka, 997-8555, Japan
| | - Takumi Sato
- Faculty of Agriculture, Yamagata University, Tsuruoka, 997-8555, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Akira Oikawa
- Faculty of Agriculture, Yamagata University, Tsuruoka, 997-8555, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Weiguo Chen
- Faculty of Agriculture, Yamagata University, Tsuruoka, 997-8555, Japan
| | - Keitaro Tawaraya
- Faculty of Agriculture, Yamagata University, Tsuruoka, 997-8555, Japan.
| |
Collapse
|
17
|
Okamura M, Hirai MY, Sawada Y, Okamoto M, Oikawa A, Sasaki R, Arai-Sanoh Y, Mukouyama T, Adachi S, Kondo M. Analysis of carbon flow at the metabolite level reveals that starch synthesis from hexose is a limiting factor in a high-yielding rice cultivar. J Exp Bot 2021; 72:2570-2583. [PMID: 33481019 DOI: 10.1093/jxb/erab016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 01/20/2021] [Indexed: 06/12/2023]
Abstract
Understanding the limiting factors of grain filling is essential for the further improvement of grain yields in rice (Oryza sativa). The relatively slow grain growth of the high-yielding cultivar 'Momiroman' is not improved by increasing carbon supply, and hence low sink activity (i.e. the metabolic activity of assimilate consumption/storage in sink organs) may be a limiting factor for grain filling. However, there is no metabolic evidence to corroborate this hypothesis, partly because there is no consensus on how to define and quantify sink activity. In this study, we investigated the carbon flow at a metabolite level from photosynthesis in leaves to starch synthesis in grains of three high-yielding cultivars using the stable isotope 13C. We found that a large amount of newly fixed carbon assimilates in Momiroman was stored as hexose instead of being converted to starch. In addition, the activity of ADP-glucose pyrophosphorylase and the expression of AGPS2b, which encodes a subunit of the ADP-glucose pyrophosphorylase enzyme, were both lower in Momiroman than in the other two cultivars in grains in superior positions on panicle branches. Hence, slower starch synthesis from hexose, which is partly explained by the low expression level of AGPS2b, may be the primary metabolic reason for the lower sink activity observed in Momiroman.
Collapse
Affiliation(s)
- Masaki Okamura
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, Japan
- Central Region Agricultural Research Center, NARO, 1-2-1, Inada, Joetsu, Niigata, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Yuji Sawada
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Mami Okamoto
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Akira Oikawa
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
- Faculty of Agriculture, Yamagata University, Tsuruoka, Yamagata, Japan
| | - Ryosuke Sasaki
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, Japan
| | - Yumiko Arai-Sanoh
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, Japan
| | - Takehiro Mukouyama
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, Japan
- Yamanashi Prefectural Agritechnology Center 1100, Shimoimai, Kai, Yamanashi, Japan
| | - Shunsuke Adachi
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, Japan
- College of Agriculture, Ibaraki University, 3-21-1, Chuo, Ami, Inashiki, Ibaraki, Japan
| | - Motohiko Kondo
- Institute of Crop Science, NARO, 2-1-2 Kannondai, Tsukuba, Ibaraki, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| |
Collapse
|
18
|
Sangpong L, Khaksar G, Pinsorn P, Oikawa A, Sasaki R, Erban A, Watanabe M, Wangpaiboon K, Tohge T, Kopka J, Hoefgen R, Saito K, Sirikantaramas S. Assessing Dynamic Changes of Taste-Related Primary Metabolism During Ripening of Durian Pulp Using Metabolomic and Transcriptomic Analyses. Front Plant Sci 2021; 12:687799. [PMID: 34220909 PMCID: PMC8250156 DOI: 10.3389/fpls.2021.687799] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/24/2021] [Indexed: 05/07/2023]
Abstract
Durian is an economically important fruit of Southeast Asia. There is, however, a lack of in-depth information on the alteration of its metabolic networks during ripening. Here, we annotated 94 ripening-associated metabolites from the pulp of durian cv. Monthong fruit at unripe and ripe stages, using capillary electrophoresis- and gas chromatography- time-of-flight mass spectrometry, specifically focusing on taste-related metabolites. During ripening, sucrose content increased. Change in raffinose-family oligosaccharides are reported herein for the first time. The malate and succinate contents increased, while those of citrate, an abundant organic acid, were unchanged. Notably, most amino acids increased, including isoleucine, leucine, and valine, whereas aspartate decreased, and glutamate was unchanged. Furthermore, transcriptomic analysis was performed to analyze the dynamic changes in sugar metabolism, glycolysis, TCA cycle, and amino acid pathways to identify key candidate genes. Taken together, our results elucidate the fundamental taste-related metabolism of durian, which can be exploited to develop durian metabolic and genetic markers in the future.
Collapse
Affiliation(s)
- Lalida Sangpong
- Molecular Crop Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Gholamreza Khaksar
- Molecular Crop Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Pinnapat Pinsorn
- Molecular Crop Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Akira Oikawa
- Faculty of Agriculture, Yamagata University, Yamagata, Japan
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Ryosuke Sasaki
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Alexander Erban
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Mutsumi Watanabe
- Plant Secondary Metabolism, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Nara, Japan
| | - Karan Wangpaiboon
- Molecular Crop Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Takayuki Tohge
- Plant Secondary Metabolism, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Nara, Japan
| | - Joachim Kopka
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Kazuki Saito
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Supaart Sirikantaramas
- Molecular Crop Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Molecular Sensory Science Center, Chulalongkorn University, Bangkok, Thailand
- *Correspondence: Supaart Sirikantaramas,
| |
Collapse
|
19
|
Sasaki T, Watanabe Y, Kuboyama A, Oikawa A, Shimizu M, Yamauchi Y, Sato R. Muscle-specific TGR5 overexpression improves glucose clearance in glucose-intolerant mice. J Biol Chem 2021; 296:100131. [PMID: 33262218 PMCID: PMC7949087 DOI: 10.1074/jbc.ra120.016203] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 11/09/2020] [Accepted: 12/01/2020] [Indexed: 01/05/2023] Open
Abstract
TGR5, a G protein-coupled bile acid receptor, is expressed in various tissues and regulates several physiological processes. In the skeletal muscle, TGR5 activation is known to induce muscle hypertrophy; however, the effects on glucose and lipid metabolism are not well understood, despite the fact that the skeletal muscle plays a major role in energy metabolism. Here, we demonstrate that skeletal muscle-specific TGR5 transgenic (Tg) mice exhibit increased glucose utilization, without altering the expression of major genes related to glucose and lipid metabolism. Metabolite profiling analysis by capillary electrophoresis time-of-flight mass spectrometry showed that glycolytic flux was activated in the skeletal muscle of Tg mice, leading to an increase in glucose utilization. Upon long-term, high-fat diet challenge, blood glucose clearance was improved in Tg mice without an accompanying increase in insulin sensitivity in skeletal muscle and a reduction of body weight. Moreover, Tg mice showed improved age-associated glucose intolerance. These results strongly suggest that TGR5 ameliorated glucose metabolism disorder that is caused by diet-induced obesity and aging by enhancing the glucose metabolic capacity of the skeletal muscle. Our study demonstrates that TGR5 activation in the skeletal muscle is effective in improving glucose metabolism and may be beneficial in developing a novel strategy for the prevention or treatment of hyperglycemia.
Collapse
Affiliation(s)
- Takashi Sasaki
- Food Biochemistry Laboratory, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan.
| | - Yuichi Watanabe
- Food Biochemistry Laboratory, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Ayane Kuboyama
- Food Biochemistry Laboratory, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Akira Oikawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan; Faculty of Agriculture, Yamagata University, Tsuruoka, Yamagata, Japan
| | - Makoto Shimizu
- Nutri-Life Science Laboratory, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Yoshio Yamauchi
- Food Biochemistry Laboratory, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
| | - Ryuichiro Sato
- Food Biochemistry Laboratory, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan; Nutri-Life Science Laboratory, Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan; AMED-CREST, Japan Agency for Medical Research and Development, Tokyo, Japan.
| |
Collapse
|
20
|
Ito D, Kawamura H, Oikawa A, Ihara Y, Shibata T, Nakamura N, Asano T, Kawabata SI, Suzuki T, Masuda S. ppGpp functions as an alarmone in metazoa. Commun Biol 2020; 3:671. [PMID: 33188280 PMCID: PMC7666150 DOI: 10.1038/s42003-020-01368-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 10/09/2020] [Indexed: 01/20/2023] Open
Abstract
Guanosine 3′,5′-bis(pyrophosphate) (ppGpp) functions as a second messenger in bacteria to adjust their physiology in response to environmental changes. In recent years, the ppGpp-specific hydrolase, metazoan SpoT homolog-1 (Mesh1), was shown to have important roles for growth under nutrient deficiency in Drosophila melanogaster. Curiously, however, ppGpp has never been detected in animal cells, and therefore the physiological relevance of this molecule, if any, in metazoans has not been established. Here, we report the detection of ppGpp in Drosophila and human cells and demonstrate that ppGpp accumulation induces metabolic changes, cell death, and eventually lethality in Drosophila. Our results provide the evidence of the existence and function of the ppGpp-dependent stringent response in animals. Ito et al. succeed in detecting guanosine tetraphosphate (ppGpp) in measurable levels in metazoan, specifically in Drosophila. They further demonstrate that the ppGpp-specific hydrolase, metazoan SpoT homolog-1 (Mesh1), is necessary, at least in certain conditions, to maintain low ppGpp levels, hence providing insights into the role of Mesh1 as a ppGpp hydrolase in vivo.
Collapse
Affiliation(s)
- Doshun Ito
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Hinata Kawamura
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Akira Oikawa
- Faculty of Agriculture, Yamagata University, Tsuruoka, Japan
| | - Yuta Ihara
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Toshio Shibata
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Nobuhiro Nakamura
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Tsunaki Asano
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | | | - Takashi Suzuki
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Shinji Masuda
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.
| |
Collapse
|
21
|
Furukawa T, Katayama H, Oikawa A, Negishi L, Ichikawa T, Suzuki M, Murase K, Takayama S, Sakuda S. Dioctatin Activates ClpP to Degrade Mitochondrial Components and Inhibits Aflatoxin Production. Cell Chem Biol 2020; 27:1396-1409.e10. [PMID: 32888498 DOI: 10.1016/j.chembiol.2020.08.006] [Citation(s) in RCA: 6] [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: 12/17/2019] [Revised: 07/28/2020] [Accepted: 08/07/2020] [Indexed: 12/25/2022]
Abstract
Aflatoxin contamination of crops is a serious problem worldwide. Utilization of aflatoxin production inhibitors is attractive, as the elucidation of their modes of action contributes to clarifying the mechanism of aflatoxin production. Here, we identified mitochondrial protease ClpP as the target of dioctatin, an inhibitor of aflatoxin production of Aspergillus flavus. Dioctatin conferred uncontrolled caseinolytic capacity on ClpP of A. flavus and Escherichia coli. Dioctatin-bound ClpP selectively degraded mitochondrial energy-related proteins in vitro, including a subunit of respiratory chain complex V, which was also reduced by dioctatin in a ClpP-dependent manner in vivo. Dioctatin enhanced glycolysis and alcohol fermentation while reducing tricarboxylic acid cycle metabolites. These disturbances were accompanied by reduced histone acetylation and reduced expression of aflatoxin biosynthetic genes. Our results suggest that dioctatin inhibits aflatoxin production by inducing ClpP-mediated degradation of mitochondrial energy-related components, and that mitochondrial energy metabolism functions as a key determinant of aflatoxin production.
Collapse
Affiliation(s)
- Tomohiro Furukawa
- Department of Biosciences, Faculty of Science and Engineering, Teikyo University, 1-1 Toyosatodai, Utsunomiya-shi, Tochigi 320-0003, Japan
| | - Hidekazu Katayama
- Department of Applied Biochemistry, School of Engineering, Tokai University, 4-1-1 Kitakaname, Hiratsuka-shi, Kanagawa 259-1292, Japan
| | - Akira Oikawa
- Department of Food, Life, and Environmental Sciences, Faculty of Agriculture, Yamagata University, 1-4-12 Kojirakawa-machi, Yamagata-shi, Yamagata 990-8560, Japan; RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-chou, Tsurumi-ku, Yokohama-shi, Kanagawa 230-0045, Japan
| | - Lumi Negishi
- Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Takuma Ichikawa
- Department of Applied Biochemistry, School of Engineering, Tokai University, 4-1-1 Kitakaname, Hiratsuka-shi, Kanagawa 259-1292, Japan
| | - Michio Suzuki
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kohji Murase
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Seiji Takayama
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Shohei Sakuda
- Department of Biosciences, Faculty of Science and Engineering, Teikyo University, 1-1 Toyosatodai, Utsunomiya-shi, Tochigi 320-0003, Japan.
| |
Collapse
|
22
|
Sakae Y, Oikawa A, Sugiura Y, Mita M, Nakamura S, Nishimura T, Suematsu M, Tanaka M. Starvation causes female-to-male sex reversal through lipid metabolism in the teleost fish, medaka ( Olyzias latipes). Biol Open 2020; 9:9/4/bio050054. [PMID: 32265199 PMCID: PMC7132775 DOI: 10.1242/bio.050054] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The teleost fish, medaka (Oryzias latipes), employs the XX/XY genetic sex determination system. We show here that the phenotypic sex of medaka is affected by changes in lipid metabolism. Medaka larvae subjected to 5 days of starvation underwent female-to-male sex reversal. Metabolomic and RT-qPCR analyses indicated that pantothenate metabolism was suppressed by starvation. Consistently, inhibiting the pantothenate metabolic pathway caused sex reversal. The final metabolite in this pathway is coenzyme A, an essential factor for lipogenesis. Inhibiting fatty acid synthesis, the first step of lipogenesis, also caused sex reversal. The expression of dmrt1, a critical gene for male development, was suppressed by starvation, and a dmrt1 (Δ13) mutant did not show sex reversal under starvation. Collectively, these results indicate that fatty acid synthesis is involved in female-to-male sex reversal through ectopic expression of male gene dmrt1 under starvation. Summary: We investigated the effects of starvation on sex differentiation in medaka. Starvation caused female-to-male sex reversal through pantothenate metabolism, fatty acid synthesis and dmrt1 expression.
Collapse
Affiliation(s)
- Yuta Sakae
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan.,Laboratory of Molecular Genetics for Reproduction, National Institute for Basic Biology, Okazaki 444-8787, Japan.,SOKENDAI (The Graduate University for Advanced Studies), Department of Basic Biology, Faculty of Life Science, Okazaki 444-8787, Japan
| | - Akira Oikawa
- RIKEN Center for Sustainable Resource Science, Metabolomics Research Group, Yokohama 230-0045, Japan.,Faculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan
| | - Yuki Sugiura
- Department of Biochemistry, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Masatoshi Mita
- Department of Biochemistry, Showa University School of Medicine, Tokyo 142-8555, Japan
| | - Shuhei Nakamura
- Institute for Advanced Co-Creation Studies, Osaka University, Osaka 565-0871, Japan.,Department of Intracellular Membrane Dynamics, Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan.,Department of Genetics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan
| | - Toshiya Nishimura
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Makoto Suematsu
- Department of Biochemistry, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Minoru Tanaka
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan .,Laboratory of Molecular Genetics for Reproduction, National Institute for Basic Biology, Okazaki 444-8787, Japan.,SOKENDAI (The Graduate University for Advanced Studies), Department of Basic Biology, Faculty of Life Science, Okazaki 444-8787, Japan
| |
Collapse
|
23
|
Fukushima A, Kuroha T, Nagai K, Hattori Y, Kobayashi M, Nishizawa T, Kojima M, Utsumi Y, Oikawa A, Seki M, Sakakibara H, Saito K, Ashikari M, Kusano M. Metabolite and Phytohormone Profiling Illustrates Metabolic Reprogramming as an Escape Strategy of Deepwater Rice during Partially Submerged Stress. Metabolites 2020; 10:metabo10020068. [PMID: 32075002 PMCID: PMC7074043 DOI: 10.3390/metabo10020068] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 02/03/2020] [Accepted: 02/11/2020] [Indexed: 02/02/2023] Open
Abstract
Rice varieties that can survive under submergence conditions respond to flooding either by enhancing internode elongation or by quiescence of shoot elongation. Despite extensive efforts to identify key metabolites triggered by complete submergence of rice possessing SUBMERGENCE 1 (SUB1) locus, metabolic responses of internode elongation of deepwater rice governed by the SNORKEL 1 and 2 genes remain elusive. This study investigated specific metabolomic responses under partial submergence (PS) to deepwater- (C9285) and non-deepwater rice cultivars (Taichung 65 (T65)). In addition, we examined the response in a near-isogenic line (NIL-12) that has a C9285 genomic fragment on chromosome 12 introgressed into the genetic background of T65. Under short-term submergence (0-24 h), metabolite profiles of C9285, NIL-12, and T65 were compared to extract significantly changed metabolites in deepwater rice under PS conditions. Comprehensive metabolite and phytohormone profiling revealed increases in metabolite levels in the glycolysis pathway in NIL-12 plants. Under long-term submergence (0-288 h), we found decreased amino acid levels. These metabolomic changes were opposite when compared to those in flood-tolerant rice with SUB1 locus. Auxin conjugate levels related to stress response decreased in NIL-12 lines relative to T65. Our analysis helped clarify the complex metabolic reprogramming in deepwater rice as an escape strategy.
Collapse
Affiliation(s)
- Atsushi Fukushima
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
| | - Takeshi Kuroha
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan; (T.K.); (K.N.); (Y.H.); (M.A.)
| | - Keisuke Nagai
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan; (T.K.); (K.N.); (Y.H.); (M.A.)
| | - Yoko Hattori
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan; (T.K.); (K.N.); (Y.H.); (M.A.)
| | - Makoto Kobayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
| | - Tomoko Nishizawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
| | - Mikiko Kojima
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
| | - Yoshinori Utsumi
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
| | - Akira Oikawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
- Faculty of Agriculture, Yamagata University, Tsuruoka, Yamagata 997-8555, Japan
| | - Motoaki Seki
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
| | - Hitoshi Sakakibara
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 263-8522, Japan
| | - Motoyuki Ashikari
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan; (T.K.); (K.N.); (Y.H.); (M.A.)
| | - Miyako Kusano
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan; (A.F.); (M.K.); (T.N.); (M.K.); (Y.U.); (A.O.); (M.S.); (H.S.); (K.S.)
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
- Correspondence:
| |
Collapse
|
24
|
Aoi Y, Oikawa A, Sasaki R, Huang J, Hayashi KI, Kasahara H. Arogenate dehydratases can modulate the levels of phenylacetic acid in Arabidopsis. Biochem Biophys Res Commun 2020; 524:83-88. [PMID: 31980164 DOI: 10.1016/j.bbrc.2020.01.041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 01/06/2020] [Indexed: 02/06/2023]
Abstract
Phenylacetic acid (PAA) is one type of natural auxin and widely exists in plants. Previous biochemical studies demonstrate that PAA in plants is synthesized from phenylalanine (Phe) via phenylpyruvate (PPA), but the PAA biosynthetic genes and its regulation remain unknown. In this article, we show that the AROGENATE DEHYDRATASE (ADT) family, which catalyzes the conversion of arogenate to Phe, can modulate the levels of PAA in Arabidopsis. We found that overexpression of ADT4 or ADT5 remarkably increased the amounts of PAA. Due to an increase in PAA levels, ADT4ox and ADT5ox plants can partially restore the auxin-deficient phenotypes caused by treatments with an inhibitor of the biosynthesis of indole-3-acetic acid (IAA), a main auxin in plants. In contrast, the levels of PAA were significantly reduced in adt multiple knockout mutants. Moreover, the levels of PPA are substantially increased in ADT4 or ADT5 overexpression plants but reduced in adt multiple knockout mutants, suggesting that PPA is a key intermediate of PAA biosynthesis. These results provide an evidence that members of the ADT family of Arabidopsis can modulate PAA level via the PPA-dependent pathway.
Collapse
Affiliation(s)
- Yuki Aoi
- Department of Bioregulation and Biointeraction, Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan
| | - Akira Oikawa
- Faculty of Agriculture, Yamagata University, Tsuruoka, Yamagata, 997-8555, Japan; RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Ryosuke Sasaki
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan
| | - Jirong Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai, 200234, China
| | - Ken-Ichiro Hayashi
- Department of Biochemistry, Okayama University of Science, Okayama, 700-0005, Japan
| | - Hiroyuki Kasahara
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, 230-0045, Japan; Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509, Japan.
| |
Collapse
|
25
|
|
26
|
Kurosawa T, Miyoshi S, Yamazaki S, Nishina T, Mikami T, Oikawa A, Homma S, Nakano H. A murine model of acute lung injury identifies growth factors to promote tissue repair and their biomarkers. Genes Cells 2018; 24:112-125. [PMID: 30474194 DOI: 10.1111/gtc.12659] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 11/17/2018] [Accepted: 11/18/2018] [Indexed: 11/30/2022]
Abstract
Type II alveolar epithelial cells (AEC2s) play a crucial role in the regeneration of type I AECs after acute lung injury. The mechanisms underlying the regeneration of AEC2s are not fully understood. To address this issue, here, we investigated a murine model of acute lung injury using mice expressing human Diphtheria Toxin Receptor (DTR) under the control of Lysozyme M promoter (LysM-DTR). DT injection induced the depletion of AEC2s, alveolar macrophages, and bone marrow (BM)-derived myeloid cells in LysM-DTR mice, and the mice died within 6 days after DT injection. Apoptotic AEC2s and bronchiolar epithelial cells appeared at 24 hr, whereas Ki67-positive proliferating cells appeared in the alveoli and bronchioles in the lung of LysM-DTR mice at 72-96 hr after DT injection. Transfer of wild-type BM cells into LysM-DTR mice accelerated the regeneration of AEC2s along with the up-regulation of several growth factors. Moreover, several metabolites were significantly decreased in the sera of LysM-DTR mice compared with WT mice after DT injection, suggesting that these metabolites might be biomarkers to predict AEC2s injury. Together, LysM-DTR mice might be useful to identify growth factors to promote lung repair and the metabolites to predict the severity of lung injury.
Collapse
Affiliation(s)
- Takeyuki Kurosawa
- Department of Biochemistry, Toho University Graduate School of Medicine, Tokyo, Japan.,Department of Respiratory Medicine, Toho University Graduate School of Medicine, Tokyo, Japan.,Department of Respiratory Medicine, Omori Medical Center, Tokyo, Japan
| | - Shion Miyoshi
- Department of Biochemistry, Toho University Graduate School of Medicine, Tokyo, Japan.,Department of Respiratory Medicine, Toho University Graduate School of Medicine, Tokyo, Japan.,Department of Respiratory Medicine, Omori Medical Center, Tokyo, Japan
| | - Soh Yamazaki
- Department of Biochemistry, Toho University Graduate School of Medicine, Tokyo, Japan
| | - Takashi Nishina
- Department of Biochemistry, Toho University Graduate School of Medicine, Tokyo, Japan
| | - Tetuo Mikami
- Department of Pathology, Toho University Graduate School of Medicine, Tokyo, Japan
| | - Akira Oikawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan.,Faculty of Agriculture, Yamagata University, Tsuruoka, Japan
| | - Sakae Homma
- Department of Respiratory Medicine, Toho University Graduate School of Medicine, Tokyo, Japan.,Department of Respiratory Medicine, Omori Medical Center, Tokyo, Japan
| | - Hiroyasu Nakano
- Department of Biochemistry, Toho University Graduate School of Medicine, Tokyo, Japan.,Host Defense Research Center, Toho University Graduate School of Medicine, Tokyo, Japan
| |
Collapse
|
27
|
Iwase A, Mita K, Favero DS, Mitsuda N, Sasaki R, Kobayshi M, Takebayashi Y, Kojima M, Kusano M, Oikawa A, Sakakibara H, Saito K, Imamura J, Sugimoto K. WIND1 induces dynamic metabolomic reprogramming during regeneration in Brassica napus. Dev Biol 2018; 442:40-52. [DOI: 10.1016/j.ydbio.2018.07.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 06/11/2018] [Accepted: 07/09/2018] [Indexed: 01/01/2023]
|
28
|
Ohnishi M, Anegawa A, Sugiyama Y, Harada K, Oikawa A, Nakayama Y, Matsuda F, Nakamura Y, Sasaki R, Shichijo C, Hatcher PG, Fukaki H, Kanaya S, Aoki K, Yamazaki M, Fukusaki E, Saito K, Mimura T. Molecular Components of Arabidopsis Intact Vacuoles Clarified with Metabolomic and Proteomic Analyses. Plant Cell Physiol 2018; 59:1353-1362. [PMID: 29660082 DOI: 10.1093/pcp/pcy069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 03/22/2018] [Indexed: 05/24/2023]
Abstract
We analyzed the metabolites and proteins contained in pure intact vacuoles isolated from Arabidopsis suspension-cultured cells using capillary electrophoresis-mass spectrometry (CE-MS), Fourier transform-ion cyclotron resonance (FT-ICR)-MS and liquid chromatography (LC)-MS. We identified 21 amino acids and five organic acids as major primary metabolites in the vacuoles with CE-MS. Further, we identified small amounts of 27 substances including well-known vacuolar molecules, but also some unexpected substances (e.g. organic phosphate compounds). Non-target analysis of the vacuolar sample with FT-ICR-MS suggested that there are 1,106 m/z peaks that could predict the 5,090 molecular formulae, and we have annotated 34 compounds in these peaks using the KNapSAck database. By conducting proteomic analysis of vacuolar sap, we found 186 proteins in the same vacuole samples. Since the vacuole is known as a major degradative compartment, many of these were hydrolases, but we also found various oxidoreductases and transferases. The relationships between the proteins and metabolites in the vacuole are discussed.
Collapse
Affiliation(s)
- Miwa Ohnishi
- Department of Biology, Graduate School of Science, Kobe University, Nada, Kobe, Japan
- CREST, JST, Sanbancho Bldg, 5 Sanban-cho, Chiyoda-ku, Tokyo, Japan
| | - Aya Anegawa
- Department of Biology, Graduate School of Science, Kobe University, Nada, Kobe, Japan
- CREST, JST, Sanbancho Bldg, 5 Sanban-cho, Chiyoda-ku, Tokyo, Japan
| | - Yuko Sugiyama
- CREST, JST, Sanbancho Bldg, 5 Sanban-cho, Chiyoda-ku, Tokyo, Japan
- Department of Science, Okayama University of Science, Okayama, Japan
| | - Kazuo Harada
- Graduate School of Pharmaceutical Science, Osaka University, Suita, Japan
| | - Akira Oikawa
- Faculty of Agriculture, Yamagata University, Tsuruoka, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | | | - Fumio Matsuda
- Graduate School of Information Science and Technology, Osaka University, Suita, Japan
| | - Yukiko Nakamura
- Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, Japan
| | - Ryosuke Sasaki
- CREST, JST, Sanbancho Bldg, 5 Sanban-cho, Chiyoda-ku, Tokyo, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Chizuko Shichijo
- Department of Biology, Graduate School of Science, Kobe University, Nada, Kobe, Japan
- CREST, JST, Sanbancho Bldg, 5 Sanban-cho, Chiyoda-ku, Tokyo, Japan
| | - Patrick G Hatcher
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, VA, USA
| | - Hidehiro Fukaki
- Department of Biology, Graduate School of Science, Kobe University, Nada, Kobe, Japan
- CREST, JST, Sanbancho Bldg, 5 Sanban-cho, Chiyoda-ku, Tokyo, Japan
| | - Shigehiko Kanaya
- Graduate School of Information Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara, Japan
| | - Koh Aoki
- CREST, JST, Sanbancho Bldg, 5 Sanban-cho, Chiyoda-ku, Tokyo, Japan
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Naka-ku, Sakai, Japan
| | - Mami Yamazaki
- CREST, JST, Sanbancho Bldg, 5 Sanban-cho, Chiyoda-ku, Tokyo, Japan
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | | | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Tetsuro Mimura
- Department of Biology, Graduate School of Science, Kobe University, Nada, Kobe, Japan
- CREST, JST, Sanbancho Bldg, 5 Sanban-cho, Chiyoda-ku, Tokyo, Japan
| |
Collapse
|
29
|
Pinsorn P, Oikawa A, Watanabe M, Sasaki R, Ngamchuachit P, Hoefgen R, Saito K, Sirikantaramas S. Metabolic variation in the pulps of two durian cultivars: Unraveling the metabolites that contribute to the flavor. Food Chem 2018; 268:118-125. [PMID: 30064738 DOI: 10.1016/j.foodchem.2018.06.066] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [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: 01/20/2018] [Revised: 06/06/2018] [Accepted: 06/13/2018] [Indexed: 11/25/2022]
Abstract
Durian (Durio zibethinus M.) is a major economic fruit crop in Thailand. In this study, two popular cultivars, namely Chanee and Mon Thong, were collected from three orchards located in eastern Thailand. The pulp metabolome, including 157 annotated metabolites, was explored using capillary electrophoresis-time of flight/mass spectrometry (CE-TOF/MS). Cultivars and harvest years had more impact on metabolite profile separation than cultivation areas. We identified cultivar-dependent metabolite markers related to durian fruit quality traits, such as nutritional value (pyridoxamine), odor (cysteine, leucine), and ripening process (aminocyclopropane carboxylic acid). Interestingly, durian fruit were found to contain high amounts of γ-glutamylcysteine (810.3 ± 257.5 mg/100 g dry weight) and glutathione (158.1 ± 80.4 mg/100 g dry weight), which act as antioxidants and taste enhancers. This metabolite information could be related to consumer preferences and exploited for durian fruit quality improvement.
Collapse
Affiliation(s)
- Pinnapat Pinsorn
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok 10330, Thailand
| | - Akira Oikawa
- Faculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan; RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan.
| | - Mutsumi Watanabe
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany.
| | - Ryosuke Sasaki
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan.
| | - Panita Ngamchuachit
- Department of Food Technology, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok 10330, Thailand; Center of Molecular Sensory Science, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok 10330, Thailand.
| | - Rainer Hoefgen
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany.
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan.
| | - Supaart Sirikantaramas
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Phayathai Road, Bangkok 10330, Thailand; Omics Sciences and Bioinformatics Center, Chulalongkorn University, 254 Phayathai Road, Bangkok 10330, Thailand.
| |
Collapse
|
30
|
Netzer F, Herschbach C, Oikawa A, Okazaki Y, Dubbert D, Saito K, Rennenberg H. Seasonal Alterations in Organic Phosphorus Metabolism Drive the Phosphorus Economy of Annual Growth in F. sylvatica Trees on P-Impoverished Soil. Front Plant Sci 2018; 9:723. [PMID: 29928284 PMCID: PMC5998604 DOI: 10.3389/fpls.2018.00723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/14/2018] [Indexed: 05/15/2023]
Abstract
Phosphorus (P) is one of the most important macronutrients limiting plant growth and development, particularly in forest ecosystems such as temperate beech (Fagus sylvatica) forests in Central Europe. Efficient tree internal P cycling during annual growth is an important strategy of beech trees to adapt to low soil-P. Organic P (Porg) is thought to play a decisive role in P cycling, but the significance of individual compounds and processes has not been elucidated. To identify processes and metabolites involved in P cycling of beech trees, polar-metabolome and lipidome profiling was performed during annual growth with twig tissues from a sufficient (Conventwald, Con) and a low-soil-P (Tuttlingen, Tut) forest. Autumnal phospholipid degradation in leaves and P export from senescent leaves, accumulation of phospholipids and glucosamine-6-phosphate (GlcN6P) in the bark, storage of N-acetyl-D-glucosamine-6-phosphate (GlcNAc6P) in the wood, and establishing of a phospholipid "start-up capital" in buds constitute main processes involved in P cycling that were enhanced in beech trees on low-P soil of the Tut forest. In spring, mobilization of P from storage pools in the bark contributed to an effective P cycling. Due to the higher phospholipid "start-up capital" in buds of Tut beeches, the P metabolite profile in developing leaves in spring was similar in beech trees of both forests. During summer, leaves of Tut beeches meet their phosphate (Pi) needs by replacing phospholipids by galacto- and sulfolipids. Thus, several processes contribute to adequate Pi supply on P impoverished soil thereby mediating similar growth of beech at low and sufficient soil-P availability.
Collapse
Affiliation(s)
- Florian Netzer
- Chair of Tree Physiology, Institute of Forest Sciences, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Cornelia Herschbach
- Chair of Tree Physiology, Institute of Forest Sciences, Albert-Ludwigs-University Freiburg, Freiburg, Germany
- Ecosystem Physiology, Institute of Forest Sciences, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Akira Oikawa
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - Yozo Okazaki
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | - David Dubbert
- Ecosystem Physiology, Institute of Forest Sciences, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Kazuki Saito
- Metabolomics Research Group, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
| | - Heinz Rennenberg
- Chair of Tree Physiology, Institute of Forest Sciences, Albert-Ludwigs-University Freiburg, Freiburg, Germany
- College of Science, King Saud University, Riyadh, Saudi Arabia
| |
Collapse
|
31
|
Honoki R, Ono S, Oikawa A, Saito K, Masuda S. Significance of accumulation of the alarmone (p)ppGpp in chloroplasts for controlling photosynthesis and metabolite balance during nitrogen starvation in Arabidopsis. Photosynth Res 2018; 135:299-308. [PMID: 28536785 DOI: 10.1007/s11120-017-0402-y] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 05/16/2017] [Indexed: 06/07/2023]
Abstract
The regulatory nucleotides, guanosine 5'-triphosphate 3'-diphosphate (pppGpp) and guanosine 5'-diphosphate 3'-diphosphate (ppGpp), were originally identified in Escherichia coli, and control a large set of gene expression and enzyme activities. The (p)ppGpp-dependent control of cell activities is referred to as the stringent response. A growing number of (p)ppGpp synthase/hydrolase homologs have been identified in plants, which are localized in plastids in Arabidopsis thaliana. We recently reported that the Arabidopsis mutant overproducing ppGpp in plastids showed dwarf chloroplasts, and transcript levels in the mutant plastids were significantly suppressed. Furthermore, the mutant showed more robust growth than the wild type (WT), especially under nutrient-deficient conditions, although the mechanisms are unclear. To better understand the impact of the ppGpp accumulation on plant responses to nutrient deficiency, photosynthetic activities and metabolic changes in the ppGpp-overproducing mutant were characterized here. Upon transition to the nitrogen-deficient conditions, the mutant showed reduction of ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) contents, and effective and maximum quantum yield of photosystem II compared with WT. The mutant also showed more obvious changes in key metabolite levels including some amino acid contents than WT; similar metabolic change is known to be critical for plants to maintain carbon-nitrogen balance in their cells. These results suggest that artificially overproducing ppGpp modulates the organelle functions that play an important role in controlling photosynthetic performance and metabolite balance during nitrogen starvation.
Collapse
Affiliation(s)
- Rina Honoki
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Sumire Ono
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, 226-8501, Japan
| | - Akira Oikawa
- Faculty of Agriculture, Yamagata University, Tsuruoka, 997-8555, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260-8675, Japan
| | - Shinji Masuda
- Center for Biological Resources & Informatics, Tokyo Institute of Technology, Yokohama, 226-8501, Japan.
- Earth-life Science Institute, Tokyo Institute of Technology, Tokyo, 152-8551, Japan.
| |
Collapse
|
32
|
Tawaraya K, Honda S, Cheng W, Chuba M, Okazaki Y, Saito K, Oikawa A, Maruyama H, Wasaki J, Wagatsuma T. Ancient rice cultivar extensively replaces phospholipids with non-phosphorus glycolipid under phosphorus deficiency. Physiol Plant 2018; 163:297-305. [PMID: 29412473 DOI: 10.1111/ppl.12699] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 01/15/2018] [Accepted: 01/31/2018] [Indexed: 05/27/2023]
Abstract
Recycling of phosphorus (P) from P-containing metabolites is an adaptive strategy of plants to overcome soil P deficiency. This study was aimed at demonstrating differences in lipid remodelling between low-P-tolerant and -sensitive rice cultivars using lipidome profiling. The rice cultivars Akamai (low-P-tolerant) and Koshihikari (low-P-sensitive) were grown in a culture solution with [2 mg l-1 (+P)] or without (-P) phosphate for 21 and 28 days after transplantation. Upper and lower leaves were collected. Lipids were extracted from the leaves and their composition was analysed by liquid chromatography/mass spectrometry (LC-MS). Phospholipids, namely phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylglycerol (PG) and phosphatidylinositol (PI), lysophosphatidylcholine (lysoPC), diacylglycerol (DAG), triacylglycerol (TAG) and glycolipids, namely sulfoquinovosyl diacylglycerol (SQDG), digalactosyldiacylglycerol (DGDG), monogalactosyldiacylglycerol (MGDG) and 1,2-diacyl-3-O-alpha-glucuronosyl glycerol (GlcADG), were detected. GlcADG level was higher in both cultivars grown in -P than in +P and the increase was larger in Akamai than in Koshihikari. DGDG, MGDG and SQDG levels were higher in Akamai grown in -P than in +P and the increase was larger in the upper leaves than in the lower leaves. PC, PE, PG and PI levels were lower in both cultivars grown in -P than in +P and the decrease was larger in the lower leaves than in the upper leaves and in Akamai than in Koshihikari. Akamai catabolised more phospholipids in older leaves and synthesised glycolipids in younger leaves. These results suggested that extensive phospholipid replacement with non-phosphorus glycolipids is a mechanism underlying low-P-tolerance in rice cultivars.
Collapse
Affiliation(s)
- Keitaro Tawaraya
- Faculty of Agriculture, Yamagata University, Tsuruoka, 997-8555, Japan
| | - Soichiro Honda
- Faculty of Agriculture, Yamagata University, Tsuruoka, 997-8555, Japan
| | - Weiguo Cheng
- Faculty of Agriculture, Yamagata University, Tsuruoka, 997-8555, Japan
| | - Masaru Chuba
- Yamagata Integrated Agricultural Research Center, Tsuruoka, 997-7601, Japan
| | - Yozo Okazaki
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Akira Oikawa
- Faculty of Agriculture, Yamagata University, Tsuruoka, 997-8555, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045, Japan
| | - Hayato Maruyama
- Graduate School of Biosphere Science, Hiroshima University, Higashihiroshima, 739-8521, Japan
| | - Jun Wasaki
- Graduate School of Biosphere Science, Hiroshima University, Higashihiroshima, 739-8521, Japan
| | - Tadao Wagatsuma
- Faculty of Agriculture, Yamagata University, Tsuruoka, 997-8555, Japan
| |
Collapse
|
33
|
Piao X, Yamazaki S, Komazawa-Sakon S, Miyake S, Nakabayashi O, Kurosawa T, Mikami T, Tanaka M, Van Rooijen N, Ohmuraya M, Oikawa A, Kojima Y, Kakuta S, Uchiyama Y, Tanaka M, Nakano H. Depletion of myeloid cells exacerbates hepatitis and induces an aberrant increase in histone H3 in mouse serum. Hepatology 2017; 65:237-252. [PMID: 27770461 DOI: 10.1002/hep.28878] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 08/18/2016] [Accepted: 09/14/2016] [Indexed: 12/14/2022]
Abstract
UNLABELLED Tissue-resident macrophages and bone marrow (BM)-derived monocytes play a crucial role in the maintenance of tissue homeostasis; however, their contribution to recovery from acute tissue injury is not fully understood. To address this issue, we generated an acute murine liver injury model using hepatocyte-specific Cflar-deficient (CflarHep-low ) mice. Cellular FLICE-inhibitory protein expression was down-regulated in Cflar-deficient hepatocytes, which thereby increased susceptibility of hepatocytes to death receptor-induced apoptosis. CflarHep-low mice developed acute hepatitis and recovered with clearance of apoptotic hepatocytes at 24 hours after injection of low doses of tumor necrosis factor α (TNFα), which could not induce hepatitis in wild-type (WT) mice. Depletion of Kupffer cells (KCs) by clodronate liposomes did not impair clearance of dying hepatocytes or exacerbate hepatitis in CflarHep-low mice. To elucidate the roles of BM-derived monocytes and neutrophils in clearance of apoptotic hepatocytes, we examined the effect of depletion of these cells on TNFα-induced hepatitis in CflarHep-low mice. We reconstituted CflarHep-low mice with BM cells from transgenic mice in which human diphtheria toxin receptor (DTR) was expressed under control of the lysozyme M (LysM) promoter. TNFα-induced infiltration of myeloid cells, including monocytes and neutrophils, was completely ablated in LysM-DTR BM-reconstituted CflarHep-low mice pretreated with diphtheria toxin, whereas KCs remained present in the livers. Under these experimental conditions, LysM-DTR BM-reconstituted CflarHep-low mice rapidly developed severe hepatitis and succumbed within several hours of TNFα injection. We found that serum interleukin-6 (IL-6), TNFα, and histone H3 were aberrantly increased in LysM-DTR BM-reconstituted, but not in WT BM-reconstituted, CflarHep-low mice following TNFα injection. CONCLUSION These findings indicate an unexpected role of myeloid cells in decreasing serum IL-6, TNFα, and histone H3 levels via the suppression of TNFα-induced hepatocyte apoptosis. (Hepatology 2017;65:237-252).
Collapse
Affiliation(s)
- Xuehua Piao
- Department of Biochemistry, Toho University School of Medicine, Tokyo, Japan
| | - Soh Yamazaki
- Department of Biochemistry, Toho University School of Medicine, Tokyo, Japan
| | | | - Sanae Miyake
- Department of Biochemistry, Toho University School of Medicine, Tokyo, Japan
| | - Osamu Nakabayashi
- Department of Biochemistry, Toho University School of Medicine, Tokyo, Japan
| | - Takeyuki Kurosawa
- Department of Biochemistry, Toho University School of Medicine, Tokyo, Japan
| | - Tetsuo Mikami
- Department of Pathology, Toho University School of Medicine, Tokyo, Japan
| | - Minoru Tanaka
- Department of Regenerative Medicine, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Nico Van Rooijen
- Department of Molecular Cell Biology, Faculty of Medicine, Vrije Universiteit, Amsterdam, Netherlands
| | - Masaki Ohmuraya
- Center for Animal Resources and Development, Kumamoto University, Kumamoto, Japan
| | - Akira Oikawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Japan.,Faculty of Agriculture, Yamagata University, Yamagata, Japan
| | - Yuko Kojima
- Laboratory of Biomedical Imaging Research, Biomedical Research Center, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Soichiro Kakuta
- Department of Cell Biology and Neuroscience, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yasuo Uchiyama
- Department of Cell Biology and Neuroscience, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Masato Tanaka
- Laboratory of Immune regulation, School of Life Science, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
| | - Hiroyasu Nakano
- Department of Biochemistry, Toho University School of Medicine, Tokyo, Japan
| |
Collapse
|
34
|
Nakano M, Kamada N, Oikawa A, Shibata C, Sasahara Y, Hosokawa H, Nakayama T, Nonaka K, Ohara O, Nakamura Y, Matsue H. LB788 Development of a novel three-dimensional human epidermal model from plucked hair follicle-derived keratinocytes. J Invest Dermatol 2016. [DOI: 10.1016/j.jid.2016.05.039] [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: 11/16/2022]
|
35
|
Bunsupa S, Hanada K, Maruyama A, Aoyagi K, Komatsu K, Ueno H, Yamashita M, Sasaki R, Oikawa A, Saito K, Yamazaki M. Molecular Evolution and Functional Characterization of a Bifunctional Decarboxylase Involved in Lycopodium Alkaloid Biosynthesis. Plant Physiol 2016; 171:2432-44. [PMID: 27303024 PMCID: PMC4972286 DOI: 10.1104/pp.16.00639] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 06/09/2016] [Indexed: 05/03/2023]
Abstract
Lycopodium alkaloids (LAs) are derived from lysine (Lys) and are found mainly in Huperziaceae and Lycopodiaceae. LAs are potentially useful against Alzheimer's disease, schizophrenia, and myasthenia gravis. Here, we cloned the bifunctional lysine/ornithine decarboxylase (L/ODC), the first gene involved in LA biosynthesis, from the LA-producing plants Lycopodium clavatum and Huperzia serrata We describe the in vitro and in vivo functional characterization of the L. clavatum L/ODC (LcL/ODC). The recombinant LcL/ODC preferentially catalyzed the decarboxylation of l-Lys over l-ornithine (l-Orn) by about 5 times. Transient expression of LcL/ODC fused with the amino or carboxyl terminus of green fluorescent protein, in onion (Allium cepa) epidermal cells and Nicotiana benthamiana leaves, showed LcL/ODC localization in the cytosol. Transgenic tobacco (Nicotiana tabacum) hairy roots and Arabidopsis (Arabidopsis thaliana) plants expressing LcL/ODC enhanced the production of a Lys-derived alkaloid, anabasine, and cadaverine, respectively, thus, confirming the function of LcL/ODC in plants. In addition, we present an example of the convergent evolution of plant Lys decarboxylase that resulted in the production of Lys-derived alkaloids in Leguminosae (legumes) and Lycopodiaceae (clubmosses). This convergent evolution event probably occurred via the promiscuous functions of the ancestral Orn decarboxylase, which is an enzyme involved in the primary metabolism of polyamine. The positive selection sites were detected by statistical analyses using phylogenetic trees and were confirmed by site-directed mutagenesis, suggesting the importance of those sites in granting the promiscuous function to Lys decarboxylase while retaining the ancestral Orn decarboxylase function. This study contributes to a better understanding of LA biosynthesis and the molecular evolution of plant Lys decarboxylase.
Collapse
Affiliation(s)
- Somnuk Bunsupa
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
| | - Kousuke Hanada
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
| | - Akira Maruyama
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
| | - Kaori Aoyagi
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
| | - Kana Komatsu
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
| | - Hideki Ueno
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
| | - Madoka Yamashita
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
| | - Ryosuke Sasaki
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
| | - Akira Oikawa
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
| | - Kazuki Saito
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
| | - Mami Yamazaki
- Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba 260-8675, Japan (S.B., A.M., K.A., K.K., H.U., Mad.Y., K.S., Mam.Y.);Faculty of Pharmacy, Mahidol University, Ratchathewi, Bangkok 10400, Thailand (S.B.);Kyushu Institute of Technology, Iizuka-shi, Fukuoka 820-8502, Japan (K.H.);RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan (R.S., A.O., K.S.); andFaculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan (A.O.)
| |
Collapse
|
36
|
Hashidume T, Kato A, Tanaka T, Miyoshi S, Itoh N, Nakata R, Inoue H, Oikawa A, Nakai Y, Shimizu M, Inoue J, Sato R. Single ingestion of soy β-conglycinin induces increased postprandial circulating FGF21 levels exerting beneficial health effects. Sci Rep 2016; 6:28183. [PMID: 27312476 PMCID: PMC4911586 DOI: 10.1038/srep28183] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 05/31/2016] [Indexed: 01/20/2023] Open
Abstract
Soy protein β-conglycinin has serum lipid-lowering and anti-obesity effects. We showed that single ingestion of β-conglycinin after fasting alters gene expression in mouse liver. A sharp increase in fibroblast growth factor 21 (FGF21) gene expression, which is depressed by normal feeding, resulted in increased postprandial circulating FGF21 levels along with a significant decrease in adipose tissue weights. Most increases in gene expressions, including FGF21, were targets for the activating transcription factor 4 (ATF4), but not for peroxisome proliferator-activated receptor α. Overexpression of a dominant-negative form of ATF4 significantly reduced β-conglycinin-induced increases in hepatic FGF21 gene expression. In FGF21-deficient mice, β-conglycinin effects were partially abolished. Methionine supplementation to the diet or primary hepatocyte culture medium demonstrated its importance for activating liver or hepatocyte ATF4-FGF21 signaling. Thus, dietary β-conglycinin intake can impact hepatic and systemic metabolism by increasing the postprandial circulating FGF21 levels.
Collapse
Affiliation(s)
- Tsutomu Hashidume
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan.,Institute of Gerontology, The University of Tokyo, Tokyo 113-8656, Japan
| | - Asuka Kato
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Tomohiro Tanaka
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Shoko Miyoshi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Nobuyuki Itoh
- Medical Innovation Center, Kyoto University Graduate School of Medicine, Sakyo, Kyoto 606-8507, Japan
| | - Rieko Nakata
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya-Nishi-Machi, Nara, 630-8506, Japan
| | - Hiroyasu Inoue
- Department of Food Science and Nutrition, Nara Women's University, Kita-Uoya-Nishi-Machi, Nara, 630-8506, Japan
| | - Akira Oikawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan; Faculty of Agriculture, Yamagata University, Tsuruoka-shi, Yamagata 997-8555, Japan
| | - Yuji Nakai
- Institute for Food Science, Hirosaki University, Aomori 038-0012, Japan
| | - Makoto Shimizu
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Jun Inoue
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Ryuichiro Sato
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| |
Collapse
|
37
|
Carrabba M, De Maria C, Oikawa A, Reni C, Rodriguez-Arabaolaza I, Spencer H, Slater S, Avolio E, Dang Z, Spinetti G, Madeddu P, Vozzi G. Design, fabrication and perivascular implantation of bioactive scaffolds engineered with human adventitial progenitor cells for stimulation of arteriogenesis in peripheral ischemia. Biofabrication 2016; 8:015020. [DOI: 10.1088/1758-5090/8/1/015020] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
38
|
Reuscher S, Fukao Y, Morimoto R, Otagaki S, Oikawa A, Isuzugawa K, Shiratake K. Quantitative Proteomics-Based Reconstruction and Identification of Metabolic Pathways and Membrane Transport Proteins Related to Sugar Accumulation in Developing Fruits of Pear (Pyrus communis). Plant Cell Physiol 2016; 57:505-18. [PMID: 26755692 DOI: 10.1093/pcp/pcw004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [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: 10/15/2015] [Accepted: 01/05/2016] [Indexed: 05/09/2023]
Abstract
During their 6 month development, pear (Pyrus communis) fruits undergo drastic changes in their morphology and their chemical composition. To gain a better understanding of the metabolic pathways and transport processes active during fruit development, we performed a time-course analysis using mass spectrometry (MS)-based protein identification and quantification of fruit flesh tissues. After pre-fractionation of the samples, 2,841 proteins were identified. A principal component analysis (PCA) separated the samples from seven developmental stages into three distinct clusters representing the early, mid and late developmental phase. Over-representation analysis of proteins characteristic of each developmental phase revealed both expected and novel biological processes relevant at each phase. A high abundance of aquaporins was detected in samples from fruits in the cell expansion stage. We were able quantitatively to reconstruct basic metabolic pathways such as the tricarboxylic acid (TCA) cycle, which indicates sufficient coverage to reconstruct other metabolic pathways. Most of the enzymes that presumably contribute to sugar accumulation in pear fruits could be identified. Our data indicate that invertases do not play a major role in the sugar conversions in developing pear fruits. Rather, sucrose might be broken down by sucrose synthases. Further focusing on sugar transporters, we identified several putative sugar transporters from diverse families which showed developmental regulation. In conclusion, our data set comprehensively describes the proteome of developing pear fruits and provides novel insights about sugar accumulation as well as candidate genes for key reactions and transport steps.
Collapse
Affiliation(s)
- Stefan Reuscher
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
| | - Yoichiro Fukao
- College of Life Sciences, Ritsumeikan University, Kusatsu, 525-8577 Japan
| | - Reina Morimoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
| | - Shungo Otagaki
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
| | - Akira Oikawa
- Faculty of Agriculture, Yamagata University, Tsuruoka, 997-8555 Japan RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045 Japan
| | - Kanji Isuzugawa
- Yamagata Integrated Agricultural Research Center, Sagae, 999-7601 Japan
| | - Katsuhiro Shiratake
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
| |
Collapse
|
39
|
Maekawa M, Honoki R, Ihara Y, Sato R, Oikawa A, Kanno Y, Ohta H, Seo M, Saito K, Masuda S. Impact of the plastidial stringent response in plant growth and stress responses. Nat Plants 2015; 1:15167. [PMID: 27251712 DOI: 10.1038/nplants.2015.167] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 10/01/2015] [Indexed: 05/06/2023]
Abstract
The regulatory nucleotide guanosine 5'-diphosphate 3'-diphosphate (ppGpp), which was originally identified in Escherichia coli, controls the expression of a large gene set and many enzyme activities. The ppGpp-dependent control of cell activities is referred to as the stringent response. Recently, genes responsible for the synthesis and degradation of ppGpp have been identified not only in bacteria, but also in eukaryotes, including plants and animals, indicating that the stringent response is, unexpectedly, widely conserved. However, the exact function of the eukaryotic stringent response remains elusive. Here, we isolated an Arabidopsis mutant that overproduces ppGpp in chloroplasts. This mutant shows metabolite reduction, dwarf chloroplasts and significantly suppressed plastidial transcription and translation. Under nutrient-deficient conditions, the mutant shows more robust growth than the wild type. These results indicate that the ppGpp-dependent control of the organelle function is crucial for the systematic growth of host organisms.
Collapse
Affiliation(s)
- Mikika Maekawa
- Graduate School of Bioscience &Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Rina Honoki
- Graduate School of Bioscience &Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Yuta Ihara
- Graduate School of Bioscience &Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Ryoichi Sato
- Graduate School of Bioscience &Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Akira Oikawa
- Faculty of Agriculture, Yamagata University, Tsuruoka 997-8555, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Yuri Kanno
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Hiroyuki Ohta
- Graduate School of Bioscience &Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8551, Japan
| | - Mitsunori Seo
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan
| | - Shinji Masuda
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8551, Japan
- Center for Biological Resources &Informatics, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| |
Collapse
|
40
|
Oikawa A, Otsuka T, Nakabayashi R, Jikumaru Y, Isuzugawa K, Murayama H, Saito K, Shiratake K. Metabolic Profiling of Developing Pear Fruits Reveals Dynamic Variation in Primary and Secondary Metabolites, Including Plant Hormones. PLoS One 2015; 10:e0131408. [PMID: 26168247 PMCID: PMC4500446 DOI: 10.1371/journal.pone.0131408] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2015] [Accepted: 06/02/2015] [Indexed: 02/08/2023] Open
Abstract
Metabolites in the fruits of edible plants include sweet sugars, visually appealing pigments, various products with human nutritional value, and biologically active plant hormones. Although quantities of these metabolites vary during fruit development and ripening because of cell division and enlargement, there are few reports describing the actual dynamics of these changes. Therefore, we applied multiple metabolomic techniques to identify the changes in metabolite levels during the development and ripening of pear fruits (Pyrus communis L. ‘La France’). We quantified and classified over 250 metabolites into six groups depending on their specific patterns of variation during development and ripening. Approximately half the total number of metabolites, including histidine and malate, accumulated transiently around the blooming period, during which cells are actively dividing, and then decreased either rapidly or slowly. Furthermore, the amounts of sulfur-containing amino acids also increased in pear fruits around 3–4 months after the blooming period, when fruit cells are enlarging, but virtually disappeared from ripened fruits. Some metabolites, including the plant hormone abscisic acid, accumulated particularly in the receptacle prior to blooming and/or fruit ripening. Our results show several patterns of variation in metabolite levels in developing and ripening pear fruits, and provide fundamental metabolomic data that is useful for understanding pear fruit physiology and enhancing the nutritional traits of new cultivars.
Collapse
Affiliation(s)
- Akira Oikawa
- RIKEN Center for Sustainable Resource Science, Yokohama, 230–0045, Japan
- Faculty of Agriculture, Yamagata University, Tsuruoka, 997–8555, Japan
- * E-mail:
| | - Takao Otsuka
- RIKEN Center for Sustainable Resource Science, Yokohama, 230–0045, Japan
| | - Ryo Nakabayashi
- RIKEN Center for Sustainable Resource Science, Yokohama, 230–0045, Japan
| | - Yusuke Jikumaru
- RIKEN Center for Sustainable Resource Science, Yokohama, 230–0045, Japan
| | - Kanji Isuzugawa
- Yamagata Integrated Agricultural Research Center, Sagae, 999–7601, Japan
| | - Hideki Murayama
- Faculty of Agriculture, Yamagata University, Tsuruoka, 997–8555, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, 230–0045, Japan
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, 260–8675, Japan
| | - Katsuhiro Shiratake
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464–8601, Japan
| |
Collapse
|
41
|
Zargar SM, Kurata R, Inaba S, Oikawa A, Fukui R, Ogata Y, Agrawal GK, Rakwal R, Fukao Y. Quantitative proteomics of Arabidopsis shoot microsomal proteins reveals a cross-talk between excess zinc and iron deficiency. Proteomics 2015; 15:1196-201. [PMID: 25641898 DOI: 10.1002/pmic.201400467] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [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: 10/07/2014] [Revised: 12/08/2014] [Accepted: 01/13/2015] [Indexed: 11/07/2022]
Abstract
Iron (Fe) deficiency significantly effects plant growth and development. Plant symptoms under excess zinc (Zn) resemble symptoms of Fe-deficient plants. To understand cross-talk between excess Zn and Fe deficiency, we investigated physiological parameters of Arabidopsis plants and applied iTRAQ-OFFGEL quantitative proteomic approach to examine protein expression changes in microsomal fraction from Arabidopsis shoots under those physiological conditions. Arabidopsis plants manifested shoot inhibition and chlorosis symptoms when grown on Fe-deficient media compared to basal MGRL solid medium. iTRAQ-OFFGEL approach identified 909 differentially expressed proteins common to all three biological replicates; the majority were transporters or proteins involved in photosynthesis, and ribosomal proteins. Interestingly, protein expression changes between excess Zn and Fe deficiency showed similar pattern. Further, the changes due to excess Zn were dramatically restored by the addition of Fe. To obtain biological insight into Zn and Fe cross-talk, we focused on transporters, where STP4 and STP13 sugar transporters were predominantly expressed and responsive to Fe-deficient conditions. Plants grown on Fe-deficient conditions showed significantly increased level of sugars. These results suggest that Fe deficiency might lead to the disruption of sugar synthesis and utilization.
Collapse
Affiliation(s)
- Sajad Majeed Zargar
- Plant Global Educational Project, Nara Institute of Science and Technology, Ikoma, Nara, Japan; School of Biotechnology, SK University of Agricultural Sciences and Technology, Chatha, Jammu, Jammu and Kashmir, India
| | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Kusuda H, Koga W, Kusano M, Oikawa A, Saito K, Hirai MY, Yoshida KT. Ectopic expression of myo-inositol 3-phosphate synthase induces a wide range of metabolic changes and confers salt tolerance in rice. Plant Sci 2015; 232:49-56. [PMID: 25617323 DOI: 10.1016/j.plantsci.2014.12.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [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: 10/31/2014] [Revised: 12/08/2014] [Accepted: 12/11/2014] [Indexed: 05/06/2023]
Abstract
Salt stress is an important factor that limits crop production worldwide. The salt tolerance of plants is a complex biological process mediated by changes in gene expression and metabolite composition. The enzyme myo-inositol 3-phosphate synthase (MIPS; EC 5.5.1.4) catalyzes the first step of myo-inositol biosynthesis, and overexpression of the MIPS gene enhances salt stress tolerance in several plant species. In this study, we performed metabolite profiling of both MIPS-overexpressing and wild-type rice. The enhanced salt stress tolerance of MIPS-overexpressing plants was clear based on growth and the metabolites under salt stress. We found that constitutive overexpression of the rice MIPS gene resulted in a wide range of metabolic changes. This study demonstrates for the first time that overexpression of the MIPS gene increases various metabolites responsible for protecting plants from abiotic stress. Activation of both basal metabolism, such as glycolysis, the pentose phosphate pathway, and the tricarboxylic acid cycle, and inositol metabolism is induced in MIPS-overexpressing plants. We discuss the relationship between the metabolic changes and the improved salt tolerance observed in transgenic rice.
Collapse
Affiliation(s)
- Hiroki Kusuda
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Wataru Koga
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Miyako Kusano
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Akira Oikawa
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan; Faculty of Agriculture, Yamagata University, Tsuruoka-shi, Yamagata, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan; Graduate School of Pharmaceutical Sciences, Chiba University, Chuo-ku, Chiba, Japan
| | | | - Kaoru T Yoshida
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.
| |
Collapse
|
43
|
|
44
|
Osanai T, Oikawa A, Iijima H, Kuwahara A, Asayama M, Tanaka K, Ikeuchi M, Saito K, Hirai MY. Metabolomic analysis reveals rewiring of Synechocystis sp. PCC 6803 primary metabolism by ntcA overexpression. Environ Microbiol 2014; 16:3304-17. [PMID: 25039649 DOI: 10.1111/1462-2920.12554] [Citation(s) in RCA: 18] [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: 02/23/2014] [Accepted: 06/30/2014] [Indexed: 11/26/2022]
Abstract
NtcA is a cAMP receptor protein-type transcription factor conserved among cyanobacteria and is essential for gene expression in response to nitrogen status. NtcA has been widely studied; however, no metabolomic analysis has been conducted using the ntcA mutant. Here, we generated a strain that overexpresses ntcA in Synechocystis sp. PCC 6803, named NOX10, and performed physiological, transcriptomic and metabolomic analyses. NOX10 grew faster than the wild-type strain under photoautotrophic conditions, but slower under light-activated heterotrophic conditions. Transcriptome analysis revealed that the expression of genes related to primary metabolism was altered by ntcA overexpression particularly under nitrogen-depleted conditions. Metabolomic analysis revealed that metabolite levels in sugar, purine/pyrimidine nucleotide, organic acid and amino acid metabolism were widely altered by ntcA overexpression. The protein levels of nitrogen-regulated transcriptional regulators were altered by ntcA overexpression during nitrogen starvation. These results demonstrate the alteration of primary metabolism by genetic engineering of NtcA, and they contribute to the current understanding of metabolic regulation of unicellular cyanobacteria.
Collapse
Affiliation(s)
- Takashi Osanai
- RIKEN, Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan; Japan Science and Technology Agency (JST), PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Satou M, Enoki H, Oikawa A, Ohta D, Saito K, Hachiya T, Sakakibara H, Kusano M, Fukushima A, Saito K, Kobayashi M, Nagata N, Myouga F, Shinozaki K, Motohashi R. Integrated analysis of transcriptome and metabolome of Arabidopsis albino or pale green mutants with disrupted nuclear-encoded chloroplast proteins. Plant Mol Biol 2014; 85:411-28. [PMID: 24793022 PMCID: PMC4052017 DOI: 10.1007/s11103-014-0194-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [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: 04/16/2013] [Accepted: 04/17/2014] [Indexed: 05/08/2023]
Abstract
We used four mutants having albino or pale green phenotypes with disrupted nuclear-encoded chloroplast proteins to analyze the regulatory system of metabolites in chloroplast. We performed an integrated analyses of transcriptomes and metabolomes of the four mutants. Transcriptome analysis was carried out using the Agilent Arabidopsis 2 Oligo Microarray, and metabolome analysis with two mass spectrometers; a direct-infusion Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR/MS) and a gas chromatograph-time of flight mass spectrometer. Among approximately 200 known metabolites detected by the FT-ICR/MS, 71 metabolites showed significant changes in the mutants when compared with controls (Ds donor plants). Significant accumulation of several amino acids (glutamine, glutamate and asparagine) was observed in the albino and pale green mutants. Transcriptome analysis revealed altered expressions of genes in several metabolic pathways. For example, genes involved in the tricarboxylic acid cycle, the oxidative pentose phosphate pathway, and the de novo purine nucleotide biosynthetic pathway were up-regulated. These results suggest that nitrogen assimilation is constitutively promoted in the albino and pale green mutants. The accumulation of ammonium ions in the albino and pale green mutants was consistently higher than in Ds donor lines. Furthermore, genes related to pyridoxin accumulation and the de novo purine nucleotide biosynthetic pathway were up-regulated, which may have occurred as a result of the accumulation of glutamine in the albino and pale green mutants. The difference in metabolic profiles seems to be correlated with the disruption of chloroplast internal membrane structures in the mutants. In albino mutants, the alteration of metabolites accumulation and genes expression is stronger than pale green mutants.
Collapse
Affiliation(s)
- Masakazu Satou
- Plant Science Center (Center for Sustainable Resource Science), RIKEN, Yokohama, Kanagawa 230-0045 Japan
- Present Address: Dragon Genomics Center, TAKARA BIO INC., Ootsu, Shiga 520-2198 Japan
| | - Harumi Enoki
- Department of Agriculture, Shizuoka University, 836 Ohoya Suruga-ku, Shizuoka, Shizuoka 422-8529 Japan
| | - Akira Oikawa
- Graduate School of Agricultural and Biological Science, Osaka Prefecture University, Sakai, Osaka 599-8531 Japan
| | - Daisaku Ohta
- Graduate School of Agricultural and Biological Science, Osaka Prefecture University, Sakai, Osaka 599-8531 Japan
| | - Kazunori Saito
- K.K., Bruker Daltonics, Yokohama, Kanagawa 221-0022 Japan
| | - Takushi Hachiya
- Plant Science Center (Center for Sustainable Resource Science), RIKEN, Yokohama, Kanagawa 230-0045 Japan
| | - Hitoshi Sakakibara
- Plant Science Center (Center for Sustainable Resource Science), RIKEN, Yokohama, Kanagawa 230-0045 Japan
| | - Miyako Kusano
- Plant Science Center (Center for Sustainable Resource Science), RIKEN, Yokohama, Kanagawa 230-0045 Japan
| | - Atsushi Fukushima
- Plant Science Center (Center for Sustainable Resource Science), RIKEN, Yokohama, Kanagawa 230-0045 Japan
| | - Kazuki Saito
- Plant Science Center (Center for Sustainable Resource Science), RIKEN, Yokohama, Kanagawa 230-0045 Japan
- Department of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Chiba 263-8522 Japan
| | | | - Noriko Nagata
- Faculty of Science, Japan Woman’s University, Bunkyou-ku, Tokyo, 112-8681 Japan
| | - Fumiyoshi Myouga
- Plant Science Center (Center for Sustainable Resource Science), RIKEN, Yokohama, Kanagawa 230-0045 Japan
| | - Kazuo Shinozaki
- Plant Science Center (Center for Sustainable Resource Science), RIKEN, Yokohama, Kanagawa 230-0045 Japan
| | - Reiko Motohashi
- Department of Agriculture, Shizuoka University, 836 Ohoya Suruga-ku, Shizuoka, Shizuoka 422-8529 Japan
| |
Collapse
|
46
|
Osanai T, Oikawa A, Numata K, Kuwahara A, Iijima H, Doi Y, Saito K, Hirai MY. Pathway-level acceleration of glycogen catabolism by a response regulator in the cyanobacterium Synechocystis species PCC 6803. Plant Physiol 2014; 164:1831-41. [PMID: 24521880 PMCID: PMC3982746 DOI: 10.1104/pp.113.232025] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Response regulators of two-component systems play pivotal roles in the transcriptional regulation of responses to environmental signals in bacteria. Rre37, an OmpR-type response regulator, is induced by nitrogen depletion in the unicellular cyanobacterium Synechocystis species PCC 6803. Microarray and quantitative real-time polymerase chain reaction analyses revealed that genes related to sugar catabolism and nitrogen metabolism were up-regulated by rre37 overexpression. Protein levels of GlgP(slr1367), one of the two glycogen phosphorylases, in the rre37-overexpressing strain were higher than those of the parental wild-type strain under both nitrogen-replete and nitrogen-depleted conditions. Glycogen amounts decreased to less than one-tenth by rre37 overexpression under nitrogen-replete conditions. Metabolome analysis revealed that metabolites of the sugar catabolic pathway and amino acids were altered in the rre37-overexpressing strain after nitrogen depletion. These results demonstrate that Rre37 is a pathway-level regulator that activates the metabolic flow from glycogen to polyhydroxybutyrate and the hybrid tricarboxylic acid and ornithine cycle, unraveling the mechanism of the transcriptional regulation of primary metabolism in this unicellular cyanobacterium.
Collapse
|
47
|
Osanai T, Numata K, Oikawa A, Kuwahara A, Iijima H, Doi Y, Tanaka K, Saito K, Hirai MY. Increased bioplastic production with an RNA polymerase sigma factor SigE during nitrogen starvation in Synechocystis sp. PCC 6803. DNA Res 2013; 20:525-35. [PMID: 23861321 PMCID: PMC3859321 DOI: 10.1093/dnares/dst028] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Because cyanobacteria directly harvest CO2 and light energy, their carbon metabolism is important for both basic and applied sciences. Here, we show that overexpression of the sigma factor sigE in Synechocystis sp. PCC 6803 widely changes sugar catabolism and increases production of the biodegradable polyester polyhydroxybutyrate (PHB) during nitrogen starvation. sigE overexpression elevates the levels of proteins implicated in glycogen catabolism, the oxidative pentose phosphate pathway, and polyhydroxyalkanoate biosynthesis. PHB accumulation is enhanced by sigE overexpression under nitrogen-limited conditions, yet the molecular weights of PHBs synthesized by the parental glucose-tolerant and sigE overexpression strain are similar. Although gene expression induced by nitrogen starvation is changed and other metabolites (such as GDP-mannose and citrate) accumulate under sigE overexpression, genetic engineering of this sigma factor altered the metabolic pathway from glycogen to PHB during nitrogen starvation.
Collapse
Affiliation(s)
- Takashi Osanai
- 1RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Osanai T, Oikawa A, Shirai T, Kuwahara A, Iijima H, Tanaka K, Ikeuchi M, Kondo A, Saito K, Hirai MY. Capillary electrophoresis-mass spectrometry reveals the distribution of carbon metabolites during nitrogen starvation in Synechocystis sp. PCC 6803. Environ Microbiol 2013; 16:512-24. [PMID: 23796428 DOI: 10.1111/1462-2920.12170] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2013] [Revised: 05/23/2013] [Accepted: 05/25/2013] [Indexed: 12/01/2022]
Abstract
Nitrogen availability is one of the most important factors for the survival of cyanobacteria. Previous studies on Synechocystis revealed a contradictory situation with regard to metabolism during nitrogen starvation; that is, glycogen accumulated even though the expressions of sugar catabolic genes were widely upregulated. Here, we conducted transcript and metabolomic analyses using capillary electrophoresis-mass spectrometry on Synechocystis sp. PCC 6803 under nitrogen starvation. The levels of some tricarboxylic acid cycle intermediates (succinate, malate and fumarate) were greatly increased by nitrogen deprivation. Purine and pyrimidine nucleotides were markedly downregulated under nitrogen depletion. The levels of 19 amino acids changed under nitrogen deprivation, especially those of amino acids synthesized from pyruvate and phosphoenolpyruvate, which showed marked increases. Liquid chromatography-mass spectrometry analysis demonstrated that the amount of NADPH and the NADPH/NADH ratio decreased under nitrogen depletion. These data demonstrate that there are increases in not only glycogen but also in metabolites downstream of sugar catabolism in Synechocystis sp. PCC 6803 under nitrogen starvation, resolving the contradiction between glycogen accumulation and induction of sugar catabolic gene expression in this unicellular cyanobacterium.
Collapse
Affiliation(s)
- Takashi Osanai
- RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan; PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Nashima K, Takahashi H, Nakazono M, Shimizu T, Nishitani C, Yamamoto T, Itai A, Isuzugawa K, Hanada T, Takashina T, Kato M, Matsumoto S, Oikawa A, Shiratake K. Transcriptome Analysis of Giant Pear Fruit with Fruit-specific DNA Reduplication on a Mutant Branch. ACTA ACUST UNITED AC 2013. [DOI: 10.2503/jjshs1.82.301] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
50
|
Kim J, Choi JN, John KMM, Kusano M, Oikawa A, Saito K, Lee CH. GC-TOF-MS- and CE-TOF-MS-based metabolic profiling of cheonggukjang (fast-fermented bean paste) during fermentation and its correlation with metabolic pathways. J Agric Food Chem 2012; 60:9746-53. [PMID: 22913417 DOI: 10.1021/jf302833y] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [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
Metabolic changes in fast-fermented bean paste (cheonggukjang) as a function of fermentation time were observed in inoculated Bacillus strains using gas chromatography time-of-flight mass spectrometry (GC-TOF-MS)- and capillary electrophoresis TOF-MS (CE-TOF-MS)-based metabolomics techniques. From the combined GC-MS and CE-MS analysis of fermented cheonggukjang samples, 123 metabolites were recovered (55% by GC-MS and 45% by CE-MS). Multivariate statistical analysis of fermented cheonggukjang samples showed that the separation of metabolites was influenced by the fermentation period (range, 0-72 h) and not by strain. When comparing the metabolites of fermented cheonggukjang with the metabolic pathways, uracil and thymine contents showed a rapid 20-fold increase after 24 h fermentation up to the end of fermentation. Xanthine and adenine levels increased slightly from 24 to 48 h fermentation and then decreased slightly at the end of fermentation. Hypoxanthine and guanine levels also increased remarkably during fermentation. Purine metabolism differed according to the microorganism used for cheonggukjang fermentation. Most intermediates in nucleoside biosynthesis were detected by CE-TOF-MS and were related to amino acid metabolism.
Collapse
Affiliation(s)
- Jiyoung Kim
- Department of Bioscience and Biotechnology, Konkuk University , Seoul 143-701, Republic of Korea
| | | | | | | | | | | | | |
Collapse
|