代謝システム研究チーム

研究室一覧へ

実績

2018

原著論文

Hirai, M.Y. and Shiraishi, F.(2018) Using metabolome data for mathematical modeling of plant metabolic systems. Curr Opin Biotechnol. , 54 ; 138-144, DOI: 10.1016/j.copbio.2018.08.005.

Abstract

Watanabe, S., Sato, M., Sawada, Y., Tanaka, M., Matsui, A., Kanno, Y., Hirai, M.Y., Seki, M., Sakamoto, A. and Seo, M.(2018) Arabidopsis molybdenum cofactor sulfurase ABA3 contributes to anthocyanin accumulation and oxidative stress tolerance in ABA-dependent and independent ways. Sci Rep., 8 ; 16592. doi: 10.1038/s41598-018-34862-1.

Abstract

Ferjani, A., Kawade, K., Asaoka, M., Oikawa, A., Okada, T., Mochizuki, A., Maeshima, M., Hirai, M.Y., Saito, K. and Tsukaya, H.(2018) Pyrophosphate inhibits gluconeogenesis by restricting UDP-glucose formation in vivo. Sci Rep., 8 ; 14696, DOI: 10.1038/s41598-018-32894-1.

Abstract

Kawade, K., Li, Y., Koga, H., Sawada, Y., Okamoto, M., Kuwahara, A., Tsukaya, H. and Hirai, M.Y.(2018) The cytochrome P450 CYP77A4 is involved in auxin-mediated patterning of the Arabidopsis thaliana embryo. Development., 145 ; 168369, DOI: 10.1242/dev.168369.

Abstract

Akashi, H., Okamura, E., Nishihama, R.,Kohchi, T. and Hirai, M.Y.(2018) Identification and Biochemical Characterization of the Serine Biosynthetic Enzyme 3-Phosphoglycerate Dehydrogenase in Marchantia polymorpha. Front. Plant Sci., DOI: 10.3389/fpls.2018.00956.

Abstract

Vergara, F., Itouga, M., Becerra, R.G., Hirai, M.Y., Ordaz-Ortiz, J.J. and Winkler, R.(2018) Funaria hygrometrica Hedw. elevated tolerance to D2O: its use for the production of highly deuterated metabolites. Planta., 247 ; 405-412, DOI: 10.1007/s00425-017-2794-5.

Abstract

プレスリリース

植物の双葉を2枚にする酵素を発見 -植物の形づくりと代謝反応の関係のさらなる理解に貢献-
(2018年9月13日)

▲ページトップへ

2017

原著論文

Arae, T., Isai, S., Sakai, A., Mineta, K., Hirai, M.Y., Suzuki, Y., Kanaya, S., Yamaguchi, J., Naito, S. and Chiba, Y. (2017) Co-ordinated Regulations of mRNA Synthesis and Decay during Cold Acclimation in Arabidopsis Cells. Plant and Cell Physiology, 58 : 1090-1102, DOI: 10.1093/pcp/pcx059.

Abstract

Miwa, A., Sawada, Y., Tamaoki, D., Hirai, M.Y., Kimura, M., Sato, K. and Nishiuchi, T. (2017) Nicotinamide mononucleotide and related metabolites induce disease resistance against fungal phytopathogens in Arabidopsis and barley. Scientific Reports, 7 : 6389, DOI: 10.1038/s41598-017-06048-8.

Abstract

Vergara, F., Rymen, B., Kuwahara, A., Sawada, Y., Sato, M. and Hirai, M.Y. (2017) Autopolyploidization, geographic origin, and metabolome evolution in Arabidopsis thaliana. Am. J. Bot., 104 ; 905-914, DOI: 10.3732/ajb.1600419.

Abstract

Okamura, E. and Hirai, M.Y. (2017) Novel regulatory mechanism of serine biosynthesis associated with 3-phosphoglycerate dehydrogenase in Arabidopsis thaliana. Sci. Rep., 7 : 3533, DOI: 10.1038/s41598-017-03807-5.

Abstract

Sawada, Y., Tsukaya, H., Li, Y., Sato, M., Kawade, K. and Hirai, M.Y. (2017) A novel method for single-grain-based metabolic profiling of Arabidopsis seed. Metabolomics, 13 : 75, DOI: 10.1007/s11306-017-1211-1.

Abstract

Osanai, T., Kuwahara, A., Otsuki, H., Saito, K. and Hirai, M.Y. (2017) ACR11 is an activator of plastid-type glutamine synthetase GS2 in Arabidopsis thaliana. Plant Cell Physiol., 58 ; 650-657, DOI: 10.1093/pcp/pcx033.

Abstract

Takeya, M., Hirai, M.Y. and Osanai, T. (2017) Allosteric inhibition of phosphoenolpyruvate carboxylases is determined by a single amino acid residue in cyanobacteria. Sci. Rep., 7 : 41080, DOI: 10.1038/srep41080.

Abstract

プレスリリース

セリン生合成の新しい制御機構を発見 -セリン生合成酵素は複数のアミノ酸による制御を受ける-
(2017年6月14日)

その他の発行物

株式会社 島津製作所 GCMSテクニカルレポート
植物メタボローム解析のためのGC/MS/MSメソッドの最適運用:複数イオン情報の活用
Appropriate use of the GC/MS/MS method for plant metabolome analysis
岡本真美、高信淳子、佐藤心郎、八巻聡、増田潤一、澤田有司、平井優美

株式会社 島津製作所 GCMSテクニカルレポート
Quality Control サンプルを用いた多検体植物メタボロームデータ解析
Analyzing for Multiple Plant Metabolome Data by Normalization using QC samples
岡本真美、高信淳子、佐藤心郎、八巻聡、増田潤一、澤田有司、平井優美

株式会社 島津製作所 GCMSアプリケーションデータシート
GC/MS/MS を利用した多検体植物メタボロームデータの代謝経路への投影
Multiple Plant Metabolome Data on Metabolic Pathway Map
岡本真美、高信淳子、佐藤心郎、山田豊、八巻聡、増田潤一、澤田有司、平井優美

▲ページトップへ

2016

原著論文

Tomita, Y., Yoshioka, K., Iijima, H., Nakashima, A., Iwata, O., Suzuki, K., Hasunuma, T., Kondo, A., Hirai, M.Y. and Osanai, T. (2016) Succinate and lactate production from Euglena gracilis during dark, anaerobic conditions. Front. Microbiol., 7 : 2050, DOI: 10.3389/fmicb.2016.02050.

Abstract

Ueda, S., Kawamura, Y., Iijima, H., Nakajima, M., Shirai, T., Okamoto, M., Kondo, A., Hirai, M.Y. and Osanai, T. (2016) Anionic metabolite biosynthesis enhanced by potassium under dark, anaerobic conditions in cyanobacteria. Sci. Rep., 6 : 32354, DOI: 10.1038/srep32354.

Abstract

Iijima, H., Shirai, T., Okamoto, M., Pinto, F., Tamagnini. P., Hasunuma, T., Kondo, A., Hirai, M.Y. and Osanai, T. (2016) Metabolomics-based analysis revealing the alteration of primary carbon metabolism by the genetic manipulation of a hydrogenase HoxH in Synechocystis sp. PCC 6803. Algal Res., 18 : 305-313., DOI: 10.1016/j.algal.2016.06.026.

Abstract

Yamada, M., Iwanaga, M., Sriyudthsak, K., Hirai, M.Y. and Shiraishi, F. (2016) Investigation of kinetic-order sensitivities in metabolic reaction networks. Journal of Theoretical Biology., 415 : 32-40., DOI: 10.1016/j.jtbi.2016.12.001.

Abstract

Miyawaki, A., Sriyudthsak, K., Hirai, M.Y. and Shiraishi, F. (2016) A new parametric method to smooth time-series data of metabolites in metabolic networks. Mathematical Biosciences., 282 : 21-33., DOI: 10.1016/j.mbs.2016.09.011.

Abstract

Sriyudthsak, K., Mejia, R.F., Arita, M. and Hirai, M.Y. (2016) PASMet: a web-based platform for prediction, modelling and analyses of metabolic systems. Nucleic Acids Res., 44(W1) : W205-W211., DOI: 10.1093/nar/gkw415.(Epub 2016 May 12.)

Abstract PDF

Sriyudthsak, K., Shiraishi, F. and Hirai, M.Y. (2016) Mathematical modeling and dynamic simulation of metabolic reaction systems using metabolome time series data. Frontiers in Molecular Biosciences., 3 : 1-11., DOI: 10.3389/fmolb.2016.00015.

Abstract PDF

Osanai, T., Iijima, H. and Hirai, M.Y. (2016) Understanding sugar catabolism in unicellular cyanobacteria toward the application in biofuel and biomaterial production. Subcellular Biochemistry., 86 : 511-523., DOI: 10.1007/978-3-319-25979-6_20.

Abstract

Kawahigashi, H., Kasuga, S., Sawada, Y., Yonemaru, J.-i., Ando, T., Kanamori, H., Wu, J., Mizuno, H., Momma, M., Fujimoto, Z., Hirai, M.Y. and Matsumoto, T. (2016) The sorghum gene for leaf color changes upon wounding (P) encodes a flavanone 4-reductase in the 3-deoxyanthocyanidin biosynthesis pathway. G3: Genes|Genomes|Genetics., 6 : 1439-1447., DOI: 10.1534/g3.115.026104.

Abstract

Nakabayashi, R., Sawada, Y., Aoyagi, M., Yamada, Y., Hirai, M.Y., Sakurai, T., Kamoi, T., Rowan, D.D. and Saito, K. (2016) Chemical assignment of structural isomers of sulfur-containing metabolites in garlic by liquid chromatography Fourier transform ion cyclotron resonance mass spectrometry. Journal of Nutrition., 146 : 397S-402S., DOI: 10.3945/jn.114.202317.(Epub 2016 Jan 13.)

Abstract

▲ページトップへ

2015

原著論文

Abdelrahman, M., Sawada, Y., Nakabayashi, R., Sato, S., Hirakawa, H., El-Sayed, M., Hirai, M.Y., Saito, K., Yamauchi, N. and Shigyo, M. (2015) Integrating transcriptome and target metabolome variability in doubled haploids of Allium cepa for abiotic stress protection. Molecular Breeding., 35 : 195., DOI: 10.1007/s11032-015-0378-2.

Abstract

Tsukaya, H., Sawada, Y., Oikawa, A., Shiratake, K., Isuzugawa, K., Saito, K. and Hirai, M.Y. (2015) Intraspecific comparative analyses of metabolites between diploid and tetraploid Arabidopsis thaliana and Pyrus communis. New Negatives in Plant Science., 1-2 : 53-61., DOI: 10.1016/j.neps.2015.06.001.

Abstract

Onda, Y., Hashimoto, K., Yoshida, T., Sakurai, T., Sawada, Y., Hirai, M.Y., Toyooka, K., Mochida, K. and Shinozaki, K. (2015) Determination of growth stages and metabolic profiles in Brachypodium distachyon for comparison of developmental context with Triticeae crops. Proceedings of the Royal Society B-Biological Sciences., 282, pii 20150964., DOI: 10.1098/rspb.2015.0964.

Abstract

Kusuda, H., Koga, W., Kusano, M., Oikawa, A., Saito, K., Hirai, M.Y. and Yoshida, K.T. (2015) Ectopic expression of myo-inositol 3-phosphate synthase induces a wide range of metabolic changes and confers salt tolerance in rice. Plant Science., 232 : 49-56., DOI: 10.1016/j.plantsci.2014.12.009. (Epub 2014 Dec 18.)

Abstract

Furuhashi, T., Ogawa, T., Nakai, R., Nakazawa, M., Okazawa, A., Padermschoke, A., Nishio, K., Hirai, M.Y., Arita, M. and Ohta, D. (2015) Wax ester and lipophilic compound profiling of Euglena gracilis by gas chromatography-mass spectrometry: toward understanding of wax ester fermentation under hypoxia. Metabolomics., 11 : 175-183., DOI: 10.1007/s11306-014-0687-1.

Abstract

Kuwahara, A., Arisaka, S., Takeya, M., Iijima, H., Hirai, M.Y. and Osanai, T. (2015) Modification of photosynthetic electron transport and amino acid levels by overexpression of a circadian-related histidine kinase hik8 in Synechocystis sp. PCC 6803., Front. Microbiol., 6 : 1150., DOI: 10.3389/fmicb.2015.01150.

Abstract

Osanai, T., Shirai, T., Iijima, H., Nakaya, Y., Okamoto, M., Kondo, A. and Hirai, M.Y. (2015) Genetic manipulation of a metabolic enzyme and a transcriptional regulator increasing succinate excretion from unicellular cyanobacterium., Front. Microbiol., 6 : 1064., DOI: 10.3389/fmicb.2015.01064.

Abstract

Iijima, H., Shirai, T., Okamoto, M., Kondo, A., Hirai, M.Y. and Osanai, T. (2015) Changes in primary metabolism under light and dark conditions in response to overproduction of a response regulator RpaA in the unicellular cyanobacterium Synechocystis sp. PCC 6803., Front. Microbiol., 6 : 888., DOI: 10.3389/fmicb.2015.00888.

Abstract

Iijima, H., Nakaya, Y., Kuwahara, A., Hirai, M.Y. and Osanai, T. (2015) Seawater cultivation of freshwater cyanobacterium Synechocystis sp. PCC 6803 drastically alters amino acid composition and glycogen metabolism., Front. Microbiol., 6 : 362., DOI: 10.3389/fmicb.2015.00326.

Abstract

Sriyudthsak, K., Uno, H., Gunawan, R. and Shiraishi, F.(2015) Using dynamic sensitivities to characterize metabolic reaction systems. Mathematical Bioscience., 269 : 153-163., DOI: 10.1016/j.mbs.2015.09.002. (Epub 2015 Sep 16.)

Abstract

Nakaya, Y., Iijima, H., Takanobu, J., Watanabe, A., Hirai, M.Y. and Osanai, T.(2015) One day of nitrogen starvation reveals the effect of sigE and rre37 overexpression on the expression of genes related to carbon and nitrogen metabolism in Synechocystis sp. PCC 6803.J Biosci Bioeng., 120 : 128-134., DOI: 10.1016/j.jbiosc.2014.12.020. (Epub 2015 Jan 29.)

Abstract

▲ページトップへ

2014

原著論文

Mizuno, H., Yazawa, T., Kasuga, S., Sawada, Y., Ogata, J., Ando, T., Kanamori, H., Yonemaru, J.-i., Wu, J., Hirai, M.Y., Matsumoto, T. and Kawahigashi, H. (2014) Expression level of a flavonoid 3'-hydroxylase gene determines pathogen-induced color variation in sorghum. BMC Research Notes., 7 : 761., DOI: 10.1186/1756-0500-7-761.

Abstract

Sato, Y., Kawagoe, T., Sawada, Y., Hirai, M.Y. and Kudoh, H. (2014) Frequency-dependent herbivory by a leaf beetle, Phaedon brassicae, on hairy and glabrous plants of Arabidopsis halleri subsp gemmifera. Evolutionary Ecology., 28 : 545-559.

Abstract

Tawaraya, K., Horie, R., Saito, S., Wagatsuma, T., Saito, K. and Oikawa, A. (2014) Metabolite Profiling of Root Exudates of Common Bean under Phosphorus Deficiency. Metabolites., 4 : 599-611., DOI: 10.3390/metabo4030599.

Abstract

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. and Motohashi, R. (2014) Integrated analysis of transcriptome and metabolome of Arabidopsis albino or pale green mutants with disrupted nuclear-encoded chloroplast proteins. Plant Mol Biol., 85 : 411-428., DOI: 10.1007/s11103-014-0194-9. (Epub 2014 May 3.)

Abstract

Furuhashi, T., Kojima, M., Sakakibara, H., Fukushima, A., Hirai, M.Y. and Furuhashi, K. (2014) Morphological and plant hormonal changes during parasitization by Cuscuta japonica on Momordica charantia. Journal of Plant Interactions., 9 : 220-232., DOI: 10.1080/17429145.2013.816790.

Abstract

Osanai, T., Shirai, T., Iijima, H., Suzuki, I., Kondo, A. and Hirai, M.Y. (2014) Alteration of cyanobacterial sugar and amino acid metabolism by overexpression hik8, encoding a KaiC-associated histidine kinase. Environmental Microbiology., 17 : 2430-2440., DOI: 10.1111/1462-2920.12715. (Epub 2015 Jan 27.)

Abstract

Iijima, H., Watanabe, A., Takanobu, J., Hirai, M.Y. and Osanai,T. (2014) rre37 overexpression alters gene expression related to the tricarboxylic acid cycle and pyruvate metabolism in Synechocystis sp. PCC 6803. The Scientific World Journal., Volume 2014, ArticleID 921976., DOI: 10.1155/2014/921976. (Epub 2014 Dec 28.)

Abstract

Sriyudthsak, K., Sawada, Y., Chiba, Y., Yamashita, Y., Kanaya, S., Onouchi, H., Fujiwara, T., Naito, S., Voit, E.O., Shiraishi, F. and Hirai, M.Y.(2014) A U-system approach for predicting metabolic behaviors and responses based on an alleged metabolic reaction network. BMC. Syst. Biol., 8 Suppl5 : S4., DOI: 10.1186/1752-0509-8-S5-S4. (Epub 2014 Dec 12.)

Abstract PDF

Osanai, T., Oikawa, A., Iijima, H., Kuwahara, A., Saito, K. and Hirai, M.Y.(2014) Metabolomic Analysis Reveals Rewiring of Synechocystis sp. PCC 6803 Primary Metabolism by ntcA-overexpression. Environ Microbiol., 16 : 3304-3317., DOI: 10.1111/1462-2920.12554. (Epub 2014 Aug 29.)

Abstract

Sriyudthsak, K., Iwata, M., Hirai, M.Y. and Shiraishi, F. (2014) PENDISC: A Simple Method for Constructing a Mathematical Model from Time-Series Data of Metabolite Concentrations. Bull. Math. Biol., 76 : 1333-1351., DOI: 10.1007/s11538-014-9960-8. (Epub 2014 May 7.)

Abstract PDF

Osanai, T., Oikawa, A., Numata, K., Kuwahara, A., Iijima, H., Doi, Y., Saito, K. and Hirai, M.Y.(2014) Pathway-Level Acceleration of Glycogen Catabolism by Response Regulator Rre37 in the Cyanobacterium Synechocystis sp. PCC 6803. Plant Physiol., 164 : 1831-1841., DOI: 10.1104/pp.113.232025. (Epub 2014 Feb 12.)

Abstract

Iwata, M., Sriyudthsak, K., Hirai, M.Y. and Shiraishi, F.(2014) Estimation of kinetic parameters in an S-system equation model for a metabolic reaction system using the Newton-Raphson method.Math Biosci., 248 : 11-21., DOI: 10.1016/j.mbs.2013.11.002. (Epub 2013 Nov 27.)

Abstract

Joseph, A., Aikawa, S., Sasaki, K., Teramura, H., Hasunuma, T., Matsuda, F., Osanai, T., Hirai, M.Y. and Kondo, A.(2014) Rre37 stimulates accumulation of 2-oxoglutarate and glycogen under nitrogen starvation in Synechocystis sp. PCC 6803. FEBS Lett., 588 : 466-471., DOI: 10.1016/j.febslet.2013.12.008. (Epub 2013 Dec 24.)

Abstract

受賞

川出健介 2013年度 理化学研究所 基礎科学特別研究員 研究成果発表会 ポスター賞(医科学部門) 「アミノ酸代謝システムから理解する器官機能の恒常性」

▲ページトップへ

2013

原著論文

  • Abe, H., Tateishi, K., Seo, S., Kugimiya, S., Hirai, M.Y., Sawada, Y., Murata, Y., Yara, K., Shimoda, T. and Kobayashi, M. (2013) Disarming the jasmonate-dependent plant defense makes non-host Arabidopsis plants accessible to the American serpentine leafminer. Plant Physiol., 163 : 1242-1253., DOI: 10.1104/pp.113.222802. (Epub 2013 Sep 10.)
  • Kawade, K., Horiguchi, G., Ishikawa, N., Hirai, M.Y. and Tsukaya, H. (2013)Promotion of chloroplast proliferation upon enhanced post-mitotic cell expansion in leaves. BMC Plant Biol., 13 : 143., DOI: 10.1186/1471-2229-13-143. [Epub ahead of print]
  • Araki, R., Hasumi, A, Nishizawa, O.I., Sasaki, K., Kuwahara, A., Sawada, Y., Totoki, Y., Toyoda, A, Sakaki, Y., Li, Y., Saito, K., Ogawa, T. and Hirai, M.Y. (2013) Novel bioresources for studies of Brassica oleracea: identification of a kale MYB transcription factor responsible for glucosinolate production. Plant Biotechnol J., 11 : 1017-1027., DOI: 10.1111/pbi.12095. (Epub 2013 Jul 30.)
  • Katsuragi, T., Ono, N., Yasumoto, K., Altaf-Ul-Amin, M., Hirai, M.Y., Sriyudthsak, K., Sawada, Y., Yamashita, Y., Chiba, Y., Onouchi, H., Fujiwara, T., Naito, S., Shiraishi, F. and Kanaya, S. (2013) SS-mPMG and SS-GA: tools for finding pathways and dynamic simulation of metabolic networks. Plant Cell Physiol., 54 : 728-739., DOI: 10.1093/pcp/pct052. (Epub 2013 Apr 9.)

Osanai, T., Kuwahara, A., Iijima, H., Toyooka, K., Sato, M., Tanaka, K., Ikeuchi, M., Saito, K. and Hirai, M.Y.(2013) Pleiotropic effect of sigE overexpression on cell morphology, photosynthesis, and hydrogen production in Synechocystis sp. PCC 6803. The Plant Journal., 76 : 456-465., DOI: 0.1111/tpj.12310. (Epub 2013 Aug 13.)
Abstract

Osanai, T., Numata, K., Oikawa, A., Kuwahara, A., Iijima, H., Doi, Y., Tanaka, K., Saito, K. and Hirai, M.Y.(2013) Increased Bioplastic Production with an RNA Polymerase Sigma Factor SigE during Nitrogen Starvation in Synechocystis sp. PCC 6803. DNA Res., 20 : 525-535., DOI: 10.1093/dnares/dst028. (Epub 2013 Jul 15.)
Abstract

Osanai, T., Oikawa, A., Shirai, T., Kuwahara, A., Iijima, H., Tanaka, K., Ikeuchi, M., Kondo, A., Saito, K. and Hirai, M.Y.(2013) Capillary electrophoresis–mass spectrometry reveals the distribution of carbon metabolites during nitrogen starvation in Synechocystis sp. PCC 6803. Environmental Microbiology., 16 : 512-524., DOI: 10.1111/1462-2920.12170. (Epub 2013 Jun 25.)
Abstract

Li, Y., Sawada, Y., Hirai, A., Sato, M., Kuwahara, K., Yan, X. and Hirai, M.Y (2013) Novel insights into the function of Arabidopsis R2R3-MYB transcription factors regulating aliphatic glucosinolate biosynthesis. Plant Cell Physiol., 54 : 1335-1344., DOI: 10.1093/pcp/pct085.(Epub 2013 Jun 20.)
Abstract

Sawada, Y. and Hirai, M.Y. (2013) Integrated LC-MS/MS system for plant metabolomics. CSBJ., 4 : e201301011., DOI: 10.5936/csbj.201301011.
Abstract

Kawade, K., Horiguchi, G., Usami, T., Hirai, M.Y. and Tsukaya, H. (2013) ANGUSTIFOLIA3 Signaling Coordinates Proliferation between Clonally Distinct Cells in Leaves. Curr Biol., 23 : 788-792., DOI: 10.1016/j.cub.2013.03.044. (Epub 2013 Apr 18.)
Abstract

Chiba, Y., Mineta, K., Hirai, M.Y., Suzuki, Y., Kanaya, S., Takahashi, H., Onouchi, H., Yamaguchi, J. and Naito, S. (2013) Changes in mRNA Stability Associated with Cold Stress in Arabidopsis Cells. Plant Cell Physiol., 54 : 180-194., DOI: 10.1093/pcp/pcs164. (Epub 2012 Dec 4.)
Abstract

Okazaki, Y., Otsuki, H., Narisawa, T., Kobayashi, M., Sawai, S., Kamide, Y., Kusano, M., Aoki, T., Hirai, M.Y. and Saito, K. (2013) A new class of plant lipid is essential for protection against phosphorus depletion. Nature Commun., 4 : 1510., DOI: 10.1038/ncomms2512
Abstract

Okazaki, Y., Kamide, Y., Hirai, M.Y. and Saito, K. (2013) Plant lipidomics based on hydrophilic interaction chromatography coupled to ion trap time-of-flight mass spectrometry. Metabolomics., 9 : 121–131. (Epub 2011 May 31.)
Abstract

Nakabayashi, R., Sawada, Y., Yamada, Y., Suzuki, M., Hirai, M.Y., Sakurai, T. and Saito, K. (2013) Combination of liquid chromatography-fourier transform ion cyclotron resonance-mass spectrometry with (13)c-labeling for chemical assignment of sulfur-containing metabolites in onion bulbs. Analytical Chemistry., 85 : 1310–1315., DOI: 10.1021/ac302733c. (Epub 2013 Jan 17.)
Abstract

Sriyudthsak, K., Shiraishi, F. and Hirai, M.Y. (2013) Identification of a metabolic reaction network from time-series data of metabolite concentrations.PLoS One., 8 : e51212., DOI: 10.1371/journal.pone.0051212. (Epub 2013 Jan 10.)
Abstract

Sakurai, T., Yamada, Y., Sawada, Y., Matsuda, F., Akiyama, K., Shinozaki, K., Hirai, M.Y. and Saito, K. (2013) PRIMe Update: Innovative Content for Plant Metabolomics and Integration of Gene Expression and Metabolite Accumulation. Plant Cell Physiol., 54 : e5., DOI: 10.1093/pcp/pcs184. (Epub 2013 Jan 3.)
Abstract

プレスリリース

ラン藻を利用したバイオプラスチックの生産
(2013年12月20日)

ラン藻の水素生産量を2倍以上増加させることに成功-水素とバイオプラスチックの生産は同じタンパク質「SigE」が制御-
(2013年9月11日)

ラン藻が作るバイオプラスチックの増産に成功 - 代謝経路を制御する新手法
(2013年7月16日)

窒素欠乏時のラン藻の代謝を網羅的に解析し、代謝の矛盾を解消 -窒素欠乏時には炭素とエネルギーを分散させて蓄積することを発見-
(2013年7月8日)

組織間での情報伝達を介した葉の成長メカニズムを解明-農作物の収量増産など応用分野に期待-
(2013年4月19日)

複雑な代謝反応ネットワークを実測データだけから推定する手法を開発-未知の代謝経路を理論的に探索することが可能に-
(2013年1月11日)

▲ページトップへ

2012

原著論文

Sawada, Y., Nakabayashi, R., Yamada, Y., Suzuki, M., Sato, M., Sakata, A., Akiyama, K., Sakurai, T., Matsuda, F., Aoki T., Hirai, M.Y. and Saito K. (2012) RIKEN tandem mass spectral database (ReSpect) for phytochemicals: A plant-specific MS/MS-based data resource and database. Phytochemistry. (Epub 3 Aug.)
Abstract ReSpect 

Wada, M., Takahashi, H., Altaf-Ul-Amin, M., Nakamura, K., Hirai, M.Y., Ohta, D. and Kanaya, S. (2012) Prediction of operon-like gene clusters in the Arabidopsis thaliana genome based on co-expression analysis of neighboring genes. Gene. 503, 56-64
Abstract

Kamiya, T., Yamagami, M., Hirai, M.Y. and Fujiwara, T. (2012) Establishment of an in planta magnesium monitoring system using CAX3 promoter-luciferase in Arabidopsis. J .Exp. Bot., 63: 355-363
Abstract

受賞

川出健介 日本植物学会 若手奨励賞 「多細胞系で進行する葉のサイズ制御」

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2011

原著論文

Osanai. T., Oikawa, A., Azuma, M., Tanaka, K., Saito, K., Hirai, M.Y. and Ikeuchi, M. (2011) Genetic engineering of group 2 sigma factor SigE widely activates expressions of sugar catabolic genes in Synechocystis species PCC 6803. J. Biol. Chem., 286:30962-30971.
Abstract

Izawa, T., Mihara. M., Suzuki, Y., Gupta, M., Itoh, H., Nagano, AJ., Motoyama, R., Sawada, Y., Yano, M., Hirai, M.Y., Makino, A. and Nagamura, Y. (2011) Os-GIGANTEA confers robust diurnal rhythms on the global transcriptome of rice in the field. Plant Cell., 23:1741-1755.
Abstract

Stotz, H.U., Sawada, Y., Shimada, Y., Hirai, M.Y., Sasaki, E., Krischke, M., Brown, P.D., Saito, K. and Kamiya, Y. (2011) Role of camalexin, indole glucosinolates, and side chain modification of glucosinolate-derived isothiocyanates in defense of Arabidopsis against Sclerotinia sclerotiorum. Plant J., 67:81-93.
Abstract

Azuma, M., Osanai, T., Hirai, M.Y. and Tanaka, K. (2011) A response regulator Rre37 and an RNA polymerase sigma factor SigE represent two parallel pathways to activate sugar catabolism in a cyanobacterium Synechocystis sp. PCC 6803. Plant Cell Physiol., 52:404-412.
Abstract

Ide, Y., Kusano, M., Oikawa, A., Fukushima, A., Tomatsu, H., Saito, K., Hirai, M.Y. and Fujiwara, T. (2011) Effects of molybdenum deficiency and defects in molybdate transporter MOT1 on transcript accumulation and nitrogen/sulphur metabolism in Arabidopsis thaliana. J .Exp. Bot., 62:1483-1497.
Abstract

Ohkama-Ohtsu, N., Sasaki-Sekimoto, Y., Oikawa, A., Jikumaru, Y., Shinoda, S., Inoue, E., Kamide, Y., Yokoyama, T., Hirai, M.Y., Shirasu, K., Kamiya, Y., Oliver, D.J. and Saito, K. (2011) 12-oxo-phytodienoic acid-glutathione conjugate is transported into the vacuole in Arabidopsis. Plant Cell Physiol., 52:205-209.
Abstract

Hanada, K., Sawada, Y., Kuromori, T., Klausnitzer, R., Saito, K., Toyoda, T., Shinozaki, K., Li, W. H. and Hirai, M. Y. (2011) Functional compensation of primary and secondary metabolites by duplicate genes in Arabidopsis thaliana, Mol Biol Evol., 28:377-382.
Open Access

総 説

Redestig, H., Szymanski, J., Hirai, M.Y., Selbig, J., Willmitzer, L., Nikoloski, Z. and Saito, K. (2011) Data integration, metabolic networks and systems biology. in Annual Plant Reviews Volume 43: Biology of Plant Metabolomics. ed. Hall, R.D. (Wiley) pp. 261-316.
Summary

Invited Oral Presentation in International Meeting

Sriyudthsak, K., Okamura, E., Sawada, Y. and Hirai, M.Y. An omics approach to elucidating amino acid metabolism in plant. 12th International Congress on Amino Acids, Peptides and Proteins, Beijing, August 4th, 2011

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2010

原著論文

Horai, H., Arita, M., Kanaya, S., Nihei, Y., Ikeda, T., Suwa, K., Ojima, Y., Tanaka, K., Tanaka, S., Aoshima, K., Oda, Y., Kakazu, Y., Kusano, M., Tohge, T., Matsuda, F., Sawada, Y., Hirai, M.Y., Nakanishi, H., Ikeda, K., Akimoto, N., Maoka, T., Takahashi, H., Ara, T., Sakurai, N., Suzuki, H., Shibata, D., Neumann, S., Iida, T., Tanaka, K., Funatsu, K., Matsuura, F., Soga, T., Taguchi, R., Saito, K. and Nishioka, T. (2010) MassBank: a public repository for sharing mass spectral data for life sciences. J. Mass. Spectrom., 45:703-714.
Abstract

Hirai, M.Y., Sawada, Y., Kanaya, S., Kuromori, T., Kobayashi, M., Klausnitzer, R., Hanada, K., Akiyama, K., Sakurai, T., Saito, K. and Shinozaki, K.(2010) Toward genome-wide metabolotyping and elucidation of metabolic system: metabolic profiling of large-scale bioresources, J plant Res., 123:291-298
Open Access

Kusano, M., Fukushima, A., Redestig, H., Kobayashi, M., Otsuki, H., Onouchi, H., Naito, S., Hirai, M.Y. and Saito, K. (2010) Comparative metabolomics charts the impact of genotype-dependent methionine accumulation in Arabidopsis thaliana. Amino Acids., 39:1013-1021
Abstract

Maruyama-Nakashita, A., Hirai, M.Y., Funada, S. and Fueki, S. (2010) Exogenous application of 5-aminolevulinic acid increases the transcript levels of sulfur transport and assimilatory genes, sulfate uptake, and cysteine and glutathione contents in Arabidopsis thaliana. Soil Science & Plant Nutrition., 56:281-288.
Abstract

Kasajima, I., Ide, Y., Hirai, M.Y. and Fujiwara, T. (2010) WRKY6 is involved in the response to boron deficiency in Arabidopsis thaliana. Physiol. Plant., 139: 80-92.
Abstract

Baek, D., Pathange, P., Chung, J-S., Jiang, J., Gao, L., Oikawa, A., Hirai, M.Y., Saito, K., Pare, P.W. and Shi, H. (2010) A Stress-inducible Sulfotransferase Sulfonates Salicylic Acid and Confers Pathogen Resistance in Arabidopsis. Plant, Cell & Environment., 33:1383-1392.
Abstract

Matsuda, F., Hirai, M.Y., Sasaki, E., Akiyama, K., Yonekura-Sakakibara, K., Provart, N.J., Sakurai, T., Shimada, Y. and Saito, K. (2010) AtMetExpress development: A phytochemical atlas of Arabidopsis thaliana development. Plant Physiol., 152:566-578.
Open Access

総 説

Albinsky, D., Sawada, Y., Kuwahara, A., Nagano, M., Hirai, A., Saito, K. and Hirai, M.Y. (2010) Widely targeted metabolomics and coexpression analysis as tools to identify genes involved in the side-chain elongation steps of aliphatic glucosinolate biosynthesis. Amino Acids., 39:1067-1075
Abstract

平井優美 (2010) オミクス統合解析によるフィトケミカル生合成遺伝子の解明. 遺伝子医学MOOK16号「メタボロミクス:その解析技術と臨床・創薬応用研究の最前線」. 田口良 編集 pp. 234-239.

プレスリリース

メタボローム解析を用いて生命維持機能(頑健性)の仕組みを解明 ―生命維持機能は、重複遺伝子と複雑なネットワーク構造による相補が必須―  (2010年8月18日)

Invited Oral Presentation in International Meeting

Hirai, M.Y. An omics approach to understanding plant metabolism. International Symposium on Plant Membrane Transport. Tokyo, March 12 – 13, 2010

Hirai, M.Y. Omics approach to elucidation of plant metabolism. 2010 International Symposium on Agricultural Biotechnology: Application and New Development on Metabolomics, Taipei, October 28, 2010

特許

発明者: 澤田有司 平井優美、 出願者: 独立行政法人理化学研究所
「スケジューリング装置、スケジューリング方法、スケジューリングプログラム、記録媒体、および質量分析システム」
(特願2010-104563)

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2009

原著論文

Matsuda, F., Redestig, H., Sawada, Y., Shinbo, Y., Hirai, M.Y., Kanaya, S. and Saito, K. (2009) Visualization of metabolite identifier information. Plant Biotechology 26: 479-483.
PDF

Takahashi, H., Kawazoe, M., Wada, M., Hirai, A., Nakamura, K., Altaf-Ul-Amin, M., Sawada, Y., Hirai, M.Y. and Kanaya, S. (2009) KNApSAcK gene classification system for Arabidopsis thaliana: Comparative genomic analysis of unicellular to seed plants. Plant Biotechnology 26: 509-516.
PDF

Sawada, Y., Toyooka, K., Kuwahara, A., Sakata, A., Nagano, M., Saito, K. and Hirai, M.Y. (2009) Arabidopsis bile acid: sodium symporter family protein 5 is involved in methionine-derived glucosinolate biosynthesis. Plant and Cell Physiology 50: 1579-1586
Open Access

Sawada, Y., Kuwahara, A., Nagano, M., Narisawa, T., Sakata, A., Saito, K. and Hirai, M.Y. (2009) Omics-based approaches to methionine side-chain elongation in Arabidopsis: characterization of the genes encoding methylthioalkylmalate isomerase and methylthioalkylmalate dehydrogenase. Plant and Cell Physiology 50: 1181-1190
Open Access

Matsuda, F., Shinbo, Y., Oikawa, A., Hirai, M.Y., Fiehn, O., Kanaya, S. and Saito, K. (2009) Assessment of metabolome annotation quality: a method for evaluating the false discovery rate of elemental composition searches. PLoS ONE 4: e7490
Open Access

Okazaki, Y., Shimojima, M., Sawada, Y., Toyooka, K., Narisawa, T., Mochida, K., Tanaka, H., Matsuda, F., Hirai, A., Hirai, M.Y., Ohta, H. and Saito, K. (2009) A chloroplastic UDP-glucose pyrophosphorylase from arabidopsis is the committed enzyme for the first step of sulfolipid biosynthesis. Plant Cell 21: 892-909
Open Access

Sawada, Y., Akiyama, K., Sakata, A., Kuwahara, A., Otsuki, H., Sakurai, T., Saito, K. and Hirai, M.Y. (2009) Widely targeted metabolomics based on large-scale MS/MS data for elucidating metabolite accumulation patterns in plants. Plant Cell Physiol. 50:37-47
Open Access

総 説

Fujiwara, T., Maruyama-Nakashita, A, Ide, Y. and Hirai, M.Y. (2009) Toward comprehensive understanding of regulatory network of sulfur metabolism.,Conference Proceedings of the 7th International Workshop on Plant Sulfur Metabolism

Araki, R., Sawada, Y., Hirai, A., Suzuki, A., Saito, K. and Hirai, M.Y. (2009) Could PMG transcription factors become an indicator for the productivity of methionine-derived glucosinolates in crop cultivation? in Sulfur Metabolism in Plants. eds. Sirko, A., De Kok, L. J., Haneklaus, S., Hawkesford, M. J., Rennenberg, H.., Saito, K., Schnug, E., and Stulen, I. (Backhuys Publishers, Leiden), pp.235-238.

Hirai, M.Y., Sawada, Y., Araki, R. and Saito, K. (2009) Omics-based identification of the genes involved in glucosinolate biosynthesis. in Sulfur Metabolism in Plants. eds. Sirko, A., De Kok, L. J., Haneklaus, S., Hawkesford, M. J., Rennenberg, H., Saito, K., Schnug, E., and Stulen, I. (Backhuys Publishers, Leiden), pp. 239-244.

Hirai, M.Y. (2009) A robust omics-based approach for the identification of glucosinolate biosynthetic genes. Phytochemistry Reviews 8:15-23
PDF

平井優美 (2009) 遺伝子共発現解析による二次代謝の解明. 植物の生長調節 44: 67-76.

平井優美、東泰弘、斉藤和季 (2009) オミクス統合解析による遺伝子機能同定、種子の 科学とバイオテクノロジー、195-198、学会出版センター、原田久也 監修、種子生理生 化学研究会 編

Invited Oral Presentation in International Meeting

Hirai, M.Y. Omics-based understanding of plant metabolism — Met-derived glucosinolate biosynthesis as a case study. 2nd Conference on Glucosinolates - Taking the Field into the Next Decade, Elsinore, Denmark, May 24 – 27, 2009

Hirai, M.Y. Amino acid metabolism as an entry point to secondary metabolism. 11th International Congress on Amino Acids, Peptides and Proteins, Vienna, Austria, August 3, 2009

Hirai, M.Y. Omics approach to elucidation of glucosinolate metabolism. 2009 Annual Autumn Conference of the Korean Society for Horticultural Science, Seoul, Korea, October 24, 2009

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2008

原著論文

Akiyama, K., Chikayama, E., Yuasa, H., Shimada, Y., Tohge, T., Shinozaki, K., Hirai, M.Y., Sakurai, T., Kikuchi, J. and Saito, K. (2008) PRIMe: a Web site that assembles tools for metabolomics and transcriptomics. In Silico Biol 8: 339-345
Abstract

Goda, H., Sasaki, E., Akiyama, K., Maruyama-Nakashita, A., Nakabayashi, K., Li, W., Ogawa, M., Yamauchi, Y., Preston, J., Aoki, K., Kiba, T., Takatsuto, S., Fujioka, S., Asami, T., Nakano, T., Kato, H., Mizuno, T., Sakakibara, H., Yamaguchi, S., Nambara, E., Kamiya, Y., Takahashi, H., Hirai, MY., Sakurai, T., Shinozaki, K., Saito, K., Yoshida, S. and Shimada, Y. (2008) The AtGenExpress hormone- and chemical-treatment data set: Experimental design, data evaluation, model data analysis, and data access. Plant J. 55, 526-542
Abstract

総 説

Hirai, M.Y. and Saito, K. (2008) Analysis of systemic sulphur metabolism in plants by using integrated "-omics" strategies. Molecular BioSystems, 4: 967-973
PDF

Saito, K., Hirai, M.Y., and Yonekura-Sakakibara, K. (2008) Decoding genes with coexpression networks and metabolomics - 'majority report by precogs'. Trends in Plant Science, 13: 36-43.
Abstract

平井優美(2008) オミクス統合解析による植物代謝の解明、メタボロミクスの先端技術と応用、212-221、シーエムシー出版、福崎英一郎 監修

平井優美(2008)オミクス解析による植物の有用物質生産遺伝子の発見、バイオサイエンスとインダストリー、66,15-19

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2007

原著論文

Morioka, R., Kanaya, S., Hirai, M.Y., Yano, M., Ogasawara, N. and Saito, K. (2007) Predicting state transitions in the transcriptome and metabolome using a linear dynamical system model. BMC bioinformatics, 8: 343.
Open Access

Hirai, M.Y., Sugiyama, K., Sawada, Y., Tohge, T., Obayashi, T., Suzuki, A., Araki, R, Sakurai, N., Suzuki, H., Aoki, K., Goda, H., Nishizawa, OI., Shibata, D. and Saito, K. (2007) Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis, Proc. Natl. Acad. USA, 104,6478-6483.
Open Access

総 説

Tohge, T., Nishiyama, Y., Hirai, M.Y., Yano, M., Nakajima, J.-i., Awazuhara, M., Inoue, E., Takahashi, H., Goodenowe, D.B., Kitayama, M., Noji, M., Yamazaki, M. and Saito, K. (2007) Identification of Genes Involved in Anthocyanin Accumulation by Integrated Analysis of Metabolome and Transcriptome in Pap1-Overexpressing Arabidopsis Plants, In "Concepts in Plant Metabolomics" Nikolau, B. J. & Wurtele, E. S. eds: pp. 159-168, Springer Verlag, Heidelberg.

平井優美(2007)オミクス研究による植物遺伝子機能の解明:癌予防成分グルコシノレートの生合成制御因子の同定、細胞工学、26,920-921

平井優美(2007)がん予防成分を多く含む健康機能野菜の開発に向けて、月報野菜情報7月号、13-16

プレスリリース

がん予防成分をアブラナ科野菜に作らせる新規遺伝子を発見 - 健康機能性の高い野菜の開発に新たな道 - (2007年4月10日)

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2006

原著論文

Higashi, Y., Hirai, M.Y., Fujiwara, T., Naito, S., Noji, M. and Saito, K. (2006) Proteomic and transcriptomic analysis of Arabidopsis seeds: molecular evidence for successive processing of seed proteins and its implication in the stress response to sulfur nutrition. Plant J., 48, 557-571.
Abstract

Yano, M., Kanaya, S., Altaf-Ul-Amin, M., Kurokawa, K., Hirai, M.Y. and Saito K. (2006) Integrated Data Mining of Transcriptome and Metabolome Based on BL-SOM. Journal of Computer Aided Chemistry, 7, 125-136.
Abstract

総 説

Hirai, M.Y., Tohge, T. and Saito, K. (2006) Systems-based analysis of plant metabolism by integration of metabolomics with transcriptomics, In "Biotechnology in Agriculture and Forestry 57 Plant Metabolomics" Kazuki Saito, Richard A. Dixon, Lothar Willmitzer eds: pp. 199-210, Springer Verlag, Heidelberg.

▲ページトップへ

2005

原著論文

Hirai, M.Y., Klein, M., Fujikawa, Y., Yano, M., Goodenowe, D.B., Yamazaki, Y., Kanaya, S., Nakamura, Y., Kitayama, M., Suzuki, H., Sakurai, N., Shibata, D., Tokuhisa, J., Reichelt, M., Gershenzon, J., Papenbrock, J. and Saito, K. (2005) Elucidation of gene-to-gene and metabolite-to-gene networks in Arabidopsis by integration of metabolomics and transcriptomics. J Biol Chem. 280, 25590-25595.
Abstract

Sasaki-Sekimoto, Y., Taki, N., Obayashi, T., Aono, M., Matsumoto, F., Sakurai, N., Suzuki, H., Hirai, M.Y., Noji, M., Saito, K., Masuda, T., Takamiya, K., Shibata, D. and Ohta, H. (2005) Coordinated activation of metabolic pathways for antioxidants and defense compounds by jasmonates and their roles in stress tolerance in Arabidopsis. Plant J. 44, 653-668.
Abstract

総 説

Yano, M., Hirai, M.Y., Kusano, M., Kitayama, M., Kanaya, S. and Saito, K. (2005) Studies for elucidation of jasmonate signaling in the response of Arabidopsis to sulfur deficiency, In "Sulfur Transport and Assimilation in Plants in the Post Genomics Eras" Saito, K., De Kok, L.J., Stulen, I. , Hawkesford, M.J., Schnug, E., Sirko, A., Rennenberg, H. eds. Pp. 165-167, Backhuys Publishers, Leiden .

Higashi, Y., Hirai, M.Y., Fujiwara, T., Naito, S., Noji, M. and Saito, K. (2005) Proteomics of Arabidopsis seeds grown under sulfur-deficient condition, In "Sulfur Transport and Assimilation in Plants in the Post Genomics Eras" Saito, K., De Kok, L.J., Stulen, I. , Hawkesford, M.J., Schnug, E., Sirko, A., Rennenberg, H. eds. Pp. 177-178, Backhuys Publishers, Leiden .

Morioka, R., Kanaya, S., Yano, M., Minato, K., Nakamura, Y., Hirai, M.Y. and Saito, K. (2005) Statistical analysis of the adaptation process of Arabidopsis thaliana to the sulfur deficiency, In "Sulfur Transport and Assimilation in Plants in the Post Genomics Eras" Saito, K., De Kok, L.J., Stulen, I. , Hawkesford, M.J., Schnug, E., Sirko, A., Rennenberg, H. eds. Pp. 177-178, Backhuys Publishers, Leiden .

Nakamura, Y., Shinbo, Y., Asahi, H., Altaf-Ul-Amin, M., Kurosawa, K., Oikawa, A., Kimura, A., Ogura, T., Morishita, Y., Sakurai, N., Suzuki, H., Nishi, T., Hirai, M.Y., Yano, M., Saito, K., Ohta, D., Shibata, D., Kitayama, M. and Kanaya, S. (2005) METABOLIX: Metabolite profiling system based on mass spectrometry, In "Sulfur Transport and Assimilation in Plants in the Post Genomics Eras" Saito, K., De Kok, L.J., Stulen, I. , Hawkesford, M.J., Schnug, E., Sirko, A., Rennenberg, H. eds. Pp. 179-182, Backhuys Publishers, Leiden .