Publications
2016
Original Papers
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. 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. 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. 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. 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. 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.) 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.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.
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.
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.)
2015
Original Papers
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.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.
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.
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.)
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.
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.
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.
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.
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.
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.)
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.)
2014
Original Papers
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. 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. 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. 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.) 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.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.)
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.)
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.)
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.)
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.)
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.)
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.)
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.)
Awards
Dr. Kensuke Kawade was awarded at FY2013 Special Postdoctoral & Foreign Postdoctoral Researchers’ Poster Presentation of Research Results. "Homeostasis of organ functions modulated by amino acid metabolism"2013
Original Papers
- 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
2012
Original Papers
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
Awards
Kawade Kensuke : The Botanical Society of Japan, The encouragement award for young researchers, 2012.
2011
Original Papers
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
Review Papers
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. & 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
2010
Original Papers
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
Press Release
How genes hide their function (18/Aug/2010)
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
2009
Original Papers
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
Review Papers
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., & 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., & 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
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
2008
Original Papers
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., 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
Review Papers
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
2007
Original Papers
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
Review Papers
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.
2006
Original Papers
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
Review Papers
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.
2005
Original Papers
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
Review Papers
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,
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,
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,
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,