Publications

2016

Original Papers

Fukushima, A., Nakamura, M., Suzuki, H., Yamazaki, M., Knoch, E., Mori, T., Umemoto, N., Morita, M., Hirai, G., Sodeoka, M. and Saito, K. (2016) Comparative Characterization of the Leaf Tissue of Physalis alkekengi and Physalis peruviana Using RNA-seq and Metabolite Profiling. Front Plant Sci., 20, doi.org/10.3389/fpls.2016.01883

Kamata, Y., Aoyagi, M., Sawada, Y., Nakabayashi, R., Hirai, M.Y., Saito, K. and Imai, S. (2016) Changes in trans-S-1-Propenyl-l-cysteine Sulfoxide and Related Sulfur-Containing Amino Acids during Onion Storage. J Agric Food Chem., 64, 9063-9071

Mochida, K., Sakurai, T., Seki, H., Yoshida, T., Takahagi, K., Sawai, S., Uchiyama, H., Muranaka, T and Saito, K. (2016) Draft genome assembly and annotation of Glycyrrhiza uralensis, a medicinal legume. Plant J.,89, 181-194

Nakabayashi, R., Tsugawa, H., Mori, T. and Saito, K. (2016) Automation of Chemical Assignment for Identifying Molecular Formula of S-containing Metabolites by Combining Metabolomics and Chemoinformatics with 34S Labeling. Metabolomics, DOI: 10.1007/s11306-016-1115-5

Rojas, Rodas, F., Di, S., Murai, Y., Iwashina, T., Sugawara, S., Mori, T., Nakabayashi, R., Yonekura-Sakakibara, K., Saito, K. and Takahashi, R. (2016) Cloning and characterization of soybean gene Fg1 encoding flavonol 3-O-glucoside/galactoside (1→6) glucosyltransferase (2016) Plant Mol Biol., 92, 445-456

Tohge, T., Wendenburg, R., Ishihara, H., Nakabayashi, R., Watanabe, M., Sulpice, R., Hoefgen, R., Takayama, H., Saito, K., Stitt, M. and Fernie, A.R. (2016) Characterization of a recently evolved flavonol-phenylacyltransferase gene provides signatures of natural light selection in Brassicaceae. Nat Commun., doi: 10.1038/ncomms12399

Umemoto, N., Nakayasu, M., Ohyama, K., Yotsu-Yamashita, M., Mizutani, M., Seki, H., Saito, K. and Muranaka, T. (2016) Two Cytochrome P450 Monooxygenases Catalyze Early Hydroxylation Steps in the Potato Steroid Glycoalkaloid Biosynthetic Pathway. Plant Physiol., 171, 2458-2467

Tsugawa, H., Kind, T., Nakabayashi, R., Yukihira, D., Tanaka, W., Cajka, T., Saito, K., Fiehn, O. and Arita, M. (2016) Hydrogen Rearrangement Rules: Computational MS/MS Fragmentation and Structure Elucidation Using MS-FINDER Software. Anal Chem., 88, 7946-7958

Yang, Z., Nakabayashi, R., Mori, T., Takamatsu, S., Kitanaka, S. and Saito, K. (2016) Metabolome Analysis of Oryza sativa (Rice) Using Liquid Chromatography-Mass Spectrometry for Characterizing Organ Specificity of Flavonoids with Anti-inflammatory and Anti-oxidant Activity, Chem. Pharm. Bull. 64, 952–956

Nuoendagula, Kamimura, N., Mori, T., Nakabayashi, R., Tsuji, Y., Hishiyama, S., Saito, K., Masai, E. and Kajita, S.(2016) Expression and functional analyses of a putative phenylcoumaran benzylic ether reductase in Arabidopsis thaliana. Plant Cell Rep., 353, 513-526

Bunsupa, S., Hanada, K., Maruyama, A., Aoyagi, K., Komatsu, K., Ueno, H., Yamashita, M., Sasaki, R., Oikawa, A., Saito, K. and Yamazaki, M. (2016) Molecular Evolution and Functional Characterization of a Bifunctional Decarboxylase Involved in Lycopodium Alkaloid Biosynthesis. Plant Physiol., 171, 2432-2444

Rai, A., Yamazaki, M., Takahashi, H., Nakamura, M., Kojoma, M., Suzuki, H. and Saito, K. (2016) RNA-seq Transcriptome Analysis of Panax japonicus, and Its Comparison with Other Panax Species to Identify Potential Genes Involved in the Saponins Biosynthesis. Front. Plant Sci., doi.org/10.3389/fpls.2016.00481

Rohani, E.R., Chiba, M., Kawaharada, M., Asano, T., Oshima, Y., Mitsuda, N., Ohme-Takagi, M., Fukushima, A., Rai, A., Saito, K. and Yamazaki, M. (2016) An MYB transcription factor regulating specialized metabolisms in Ophiorrhiza pumila. Plant Biotech., 33, 1-9

Thagun, C., Imanishi, S., Kudo, T., Nakabayashi, R., Ohyama, K., Mori, T., Kawamoto, K., Nakamura, Y., Katayama, M., Nonaka, S., Matsukura, C., Yano, K., Ezura, H., Saito, K., Hashimoto, T. and Shoji, T. (2016) Jasmonate-responsive ERF transcription factors regulate steroidal glycoalkaloid biosynthesis in tomato. Plant Cell Physiol., doi: 10.1093/pcp/pcw067

Nakagawa, T., Itoh, M., Ohta, K., Hayashi, Y., Hayakawa, M., Yamada, Y., Akanabe, H., Chikaishi, T., Nakabawa, K., Itoh, Y., Muro, T., Yanagida, D., Nakabayashi, R., Mori, T., Saito, K., Ohzawa, K., Suzuki C., Li, S., Ueda, M., Wang, MX., Nishida, E., Tana, S. I., Kobori, M. and Inuzuka, T. (2016) Improvement of memory recall by quercetin in rodent contextual fear conditioning and uman early-stage Alzheimer's disease patients. NeuroReports, 27, 671-676

Poudel, A.N., Zhang, T., Kwasniewski, M., Nakabayashi, R., Saito, K. and Koo, A.J. (2016) Mutations in jasmonoyl-L-isoleucine-12-hydroxylases suppress multiple JA-dependent wound responses in Arabidopsis thaliana. Biochim Biophys Acta., 1861, 1396-1408

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. J. Nutr., 146, 397S-402S

Matsushima, R., Maekawa, M., Kusano, M., Tomita, K., Kondo, H., Nishimura, H., Crofts, N., Fujita, N. and Sakamoto, W. (2016) Amyloplast Membrane Protein SUBSTANDARD STARCH GRAIN6 Controls Starch Grain Size in Rice Endosperm. Plant Physiol., 170, 1445-1459

Araki, T., Saga, Y., Marugami, M., Otaka, J., Araya, H., Saito, K., Yamazaki, M., Suzuki, H. and Kushiro, T. (2016) Onocerin Biosynthesis Requires Two Highly Dedicated Triterpene Cyclases in a Fern Lycopodium clavatum. Chembiochem., 17, 288-290

Okada, T., Afendi, F.M., Yamazaki, M., Chida, K.N., Suzuki, M., Kawai, R., Kim, M., Namiki, T., Kanaya, S. and Saito, K. (2016) Informatics framework of traditional Sino-Japanese medicine (Kampo) unveiled by factor analysis. J Nat Med., 70, 107–114

Toyosawa, Y., Kawagoe, Y., Matsushima, R., Crofts, N., Ogawa, M., Fukuda, M., Kumamaru, T., Okazaki, Y., Kusano, M., Saito, K., Toyooka, K., Sato, M., Ai, Y., Jane, J.L., Nakamura, Y. and Fujita, N. (2016) Deficiency of Starch Synthase IIIa and IVb Alters Starch Granule Morphology from Polyhedral to Spherical in Rice Endosperm. Plant Physiol., 170, 1255-1270

Ogo, Y., Mori, T., Nakabayashi, R., Saito, K. and Takaiwa, F. (2016) Transgenic rice seed expressing flavonoid biosynthetic genes accumulates variously glycosylated and/or acylated flavonoids in protein bodies. J. Exp. Bot., 67, 95-106

Review Papers

Nakabayashi, R. and Saito, K. (2016) Ultrahigh resolution metabolomics for S-containing metabolites. Curr. Opin. Biotechnol., Curr Opin Biotechnol., 43, 8-16

Okazaki, Y. and Saito, K. (2016) Integrated metabolomics and phytochemical genomics approaches for studies on rice. Gigascience, doi: 10.1186/s13742-016-0116-7

Kusano, M., Kobayashi, M., Iizuka, Y., Fukushima, A. and Saito, K. (2016) Unbiased profiling of volatile organic compounds in the headspace of Allium plants using an in-tube extraction device. BMC Res Notes. 29, 133

Rai A and Saito K. (2016) Omics data input for metabolic modeling. Curr Opin Biotechnol., 37, 127-134

Press Releases

New flavonoids protect plants from damaging UV rays (23/Aug/2016)

Non-poisonous potatoes (26/Jul/2016)

Plant alkaloid productivity from convergent evolution of metabolizing enzymes (24/jun/2016)

Awards

Kazuki Saito : Winners of 2016 JSPP Awards(2016), Plant metabolomics and phytochemical genomics

2015

Original Papers

Sako, K., Kim, J.M., Matsui, A., Nakamura, K., Tanaka, M., Kobayashi, M., Saito, K., Nishino, N., Kusano, M., Taji, T., Yoshida, M. and Seki, M. (2015) Ky-2, a histone deacetylase inhibitor, enhances high-salinity stress tolerance in Arabidopsis thaliana. Plant Cell Physiol., doi: 10.1093/pcp/pcv199

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, DOI 10.1007/s11032-015-0378-2

Nakabayashi, R., Tsugawa, H., Kitajima, M., Takayama, H., and Saito, K. (2015) Boosting Sensitivity in Liquid Chromatography-Fourier Transform Ion Cyclotron Resonance-Tandem Mass Spectrometry for Product Ion Analysis of Monoterpene Indole Alkaloids. Front. Plant Sci., doi: 10.3389/fpls.2015.01127

Nuoen, D., Kamimura, N., Mori, T., Nakabayashi, R., Tsuji, Y., Hishiyama, S., Saito, K. Masai, E. and Kajita, S. (2015) Expression and functional analyses of a putative phenylcoumaran benzylic ether reductase in Arabidopsis thaliana. Plant Cell Rep., DOI 10.1007/s00299-015-1899-1

Maekawa, M., Honoki, R., Ihara, Y., Sato, R., Oikawa, A., Kanno, Y., Ohta, H., Seo, M., Saito, K. and Masuda, S. (2015) Impact of the plastidial stringent response in plant growth and stress responses. Nature Plants, doi:10.1038/nplants.2015.167

Suzuki, M., Nakabayashi, R., Mori, T., Saito, K. and Shiratake, K. (2015) The metabolic profile of grape berry skin and a comparison of metabolomes before veraison and at harvest. Plant Biotech., DOI:10.5511/plantbiotechnology.15.0729b

Oikawa, A., Otsuka, T., Nakabayashi, R., Jikumaru, Y., Isuzugawa, K., Murayama, H., Saito, K. and Shiratake, K. (2015) Metabolic Profiling of Developing Pear Fruits Reveals Dynamic Variation in Primary and Secondary Metabolites, Including Plant Hormones. PLoS One., doi: 10.1371/journal.pone.0131408

Yoshimoto, N., Onuma, M., Mizuno, S., Sugino, Y., Nakabayashi, R., Imai, S., Tsuneyoshi, T., Sumi, S. and Saito, K. (2015) Identification of a flavin-containing S-oxygenating monooxygenase involved in alliin biosynthesis in garlic. Plant J., 83, 941-951

Clevenger, J.P., Van Houten, J., Blackwood, M., Rodríguez, G.R., Jikumaru, Y., Kamiya, Y., Kusano, M., Saito, K., Visa, S. and van der Knaap, E. (2015) Network Analyses Reveal Shifts in Transcript Profiles and Metabolites That Accompany the Expression of SUN and an Elongated Tomato Fruit. Plant Physiol., 168, 1164-1178

Hayakawa, Y., Duan, Z., Yadake, M., Tsukano, J., Yamaoka, Y., Inatsugi, R., Fujiki, Y., Oikawa, A., Saito, K. and Nishida, I. (2015) Epigenetic floral homeotic mutation in pD991-AP3-derived T-DNA-tagged lines for CTP:Phosphorylcholine cytidylyltransferase (CCT) Genes: The homeotic mutation of the cct1-1 allele is enhanced by the cct2 allele and alleviated by CCT1 overexpression. J. Plant Biol., 58, 183-192

Higashi, Y., Okazaki, Y., Myouga, F., Shinozaki, K. and Saito, K. (2015) Landscape of the lipidome and transcriptome under heat stress in Arabidopsis thaliana. Sci Rep., doi:10.1038/srep10533

Takayama, M., Koike, S., Kusano, M., Matsukura, C., Saito, K., Ariizumi, T. and Ezura, H. (2015) Tomato Glutamate Decarboxylase Genes SlGAD2 and SlGAD3 Play Key Roles in Regulating γ-Aminobutyric Acid Levels in Tomato (Solanum lycopersicum). Plant Cell Physiol., 56, 1533-1545

Di, S., Yan, F., Rodas, FR., Rodriguez, TO., Murai, Y., Iwashina, T., Sugawara, S., Mori, T., Nakabayashi, R., Yonekura-Sakakibara, K., Saito, K. and Takahashi, R. (2015) Linkage mapping, molecular cloning and functional analysis of soybean gene Fg3 encoding flavonol 3-O-glucoside/galactoside (1 → 2) glucosyltransferase. BMC Plant Biol., doi: 10.1186/s12870-015-0504-7

Nakabayashi, R., Yang, Z., Nishizawa, T., Mori, T. and Saito, K. (2015) Top-down Targeted Metabolomics Reveals a Sulfur-Containing Metabolite with Inhibitory Activity against Angiotensin-Converting Enzyme in Asparagus officinalis. J. Nat. Prod., 78, 1179-1183

Maruyama-Nakashita, A., Watanabe-Takahashi, A., Inoue, E., Yamaya, T., Saito, K. and Takahashi, H. (2015) Sulfur-Responsive Elements in the 3'-Nontranscribed Intergenic Region Are Essential for the Induction of SULFATE TRANSPORTER 2;1 Gene Expression in Arabidopsis Roots under Sulfur Deficiency. Plant Cell, 27, 1279-1296

Suzuki, M., Nakabayashi, R., Ogata, Y., Sakurai, N., Tokimatsu, T., Goto, S., Suzuki, M., Jasinski, M., Martinoia, E., Otagaki, S., Matsumoto, S., Saito, K. and Shiratake, K. (2015) Multiomics in grape berry skin revealed specific induction of stilbene synthetic pathway by UV-C irradiation. Plant Physiol., 168, 47-59

Okazaki ,Y., Nishizawa, T., Takano, K., Ohnishi, M., Mimura, T and Saito, K. (2015) Induced accumulation of glucuronosyldiacylglycerol in tomato and soybean under phosphorus deprivation. Physiol Plant., 155, 33-42

Yoshimoto, N., Yabe, A., Sugino, Y., Murakami, S., Sai-Ngam, N., Sumi, S., Tsuneyoshi, T. and Saito, K. (2015) Garlic γ-glutamyl transpeptidases that catalyze deglutamylation of biosynthetic intermediate of alliin. Front. Plant Sci., doi:10.3389/fpls.2014.00758

Bohrer, A.S., Yoshimoto, N., Sekiguchi, A., Rykulski, N., Saito, K. and Takahashi, H. (2015) Alternative translational initiation of ATP sulfurylase underlying dual localization of sulfate assimilation pathways in plastids and cytosol in Arabidopsis thaliana. Front. Plant Sci., doi:10.3389/fpls.2014.00750

Matsuda, F., Nakabayashi, R., Yang, Z., Okazaki, Y., Yonemaru, J., Ebana, K., Yano, M. and Saito, K. (2015) Metabolome-genome-wide association study dissects genetic architecture for generating natural variation in rice secondary metabolism. Plant J., 81, 13-23

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

Speiser, A., Haberland, S., Watanabe, M., Wirtz, M., Dietz, K.J., Saito, K. and Hell, R. (2015) The significance of cysteine synthesis for acclimation to high light conditions. Front. Plant Sci., doi: 10.3389/fpls.2014.00776

Ohashi, M., Ishiyama, K., Kusano, M., Fukushima, A., Kojima, S., Hanada, A., Kanno, K., Hayakawa, T., Seto, Y., Kyozuka, J., Yamaguchi, S., and Yamaya, T. (2015) Lack of cytosolic glutamine synthetase1;2 in vascular tissues of axillary buds caused severe reduction in their outgrowth and disorder of metabolic balance in rice seedlings. Plant J., 81, 347-356

Review Papers

Nakabayashi, R. and Saito, K. (2015) Integrated metabolomics for abiotic stress responses in plants. Curr Opin Plant Biol., 24, 10-16

Kusano, M., Yang, Z., Okazaki, Y., Nakabayashi, R., Fukushima, A. and Saito, K. (2015) Using metabolomic approaches to explore chemical diversity in rice. Mol Plant, 8, 58-67

Sumner, L.W., Lei, Z., Nikolau, B.J. and Saito, K. (2015) Modern plant metabolomics: advanced natural product gene discoveries, improved technologies, and future prospects. Nat Prod Rep., 32, 212-229

Awards

Yozo Okazaki : Japanese Society for Plant Cell and Molecular Biology Award for Young Scientists, 2015

Satoru Sawai : RIKEN Research Incentive Awards (2015), Discovery of key biosynthetic genes and metabolic engineering of bioactive plant triterpenoids

2014

Original Papers

Bunsupa, S., Komastsu, K., Nakabayashi, R., Saito, K. and Yamazaki, M. (2014) Revisiting anabasine biosynthesis in tobacco hairy roots expressing plant lysine decarboxylase gene by using ¹⁵N-labeled lysine. Plant Biotech., 31, 511–518

Kind, T., Okazaki, Y., Saito, K. and Fiehn, O. (2014) LipidBlast Templates As Flexible Tools for Creating New in-Silico Tandem Mass Spectral Libraries. Anal Chem., 18, 11024-11027

Kusano, M., Baxter, I., Fukushima, A., Oikawa, A., Okazaki, Y., Nakabayashi, R., Bouvrette, D., Achard, F., Jakubowski, A., Ballam, J., Phillips, J., Culler, A., Saito, K. and Harrigan, G. (2014). Assessing metabolomic and chemical diversity of a soybean lineage representing 35 years of breeding. Metabolomics, DOI: 10.1007/s11306-014-0702-6

Sawai, S., Ohyama, K., Yasumoto, S., Seki, H., Sakuma, T., Yamamoto, T., Takebayashi, Y., Kojima, M., Sakakibara, H., Aoki, T., Muranaka, T., Saito, K. and Umemoto, N. (2014) Sterol Side Chain Reductase 2 Is a Key Enzyme in the Biosynthesis of Cholesterol, the Common Precursor of Toxic Steroidal Glycoalkaloids in Potato. Plant Cell, 26, 3763-3774

Yonekura-Sakakibara, K., Nakabayashi, R., Sugawara, S., Tohge, T., Ito, T., Koyanagi, M., Kitajima, M., Takayama, H. and Saito, K. (2014) A flavonoid 3-O-glucoside:2″-O-glucosyltransferase responsible for terminal modification of pollen-specific flavonols in Arabidopsis thaliana. Plant J., 79, 769-782

Tamura, M., Tsuji, Y., Kusunose, T., Okazawa, A., Kamimura, N., Mori, T., Nakabayashi, R., Hishiyama, S., Fukuhara, Y., Hara, H., Sato-Izawa, K., Muranaka, T., Saito, K., Katayama, Y., Fukuda, M., Masai, E. and Kajita, S. (2014) Successful expression of a novel bacterial gene for pinoresinol reductase and its effect on lignan biosynthesis in transgenic Arabidopsis thaliana. Appl Microbiol Biotechnol., 98, 8165-8177

Osanai, T., Oikawa, A., Iijima, H., Kuwahara, A., Asayama, M., Tanaka, K., Ikeuchi, M., 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

Fukushima, A., Kusano, M., Mejia, R.F., Iwasa, M., Kobayashi, M., Hayashi, N., Watanabe-Takahashi, A., Narisawa, T., Tohge, T., Hur, M., Wurtele, E.S., Nikolau, B.J. and Saito, K. (2014) Metabolomic Characterization of Knock-Out Mutants in Arabidopsis - Development of a Metabolite Profiling Database for Knock-Out Mutants in Arabidopsis (MeKO). Plant Physiol., 165, 948-961

Maruyama, K., Urano, K., Yoshiwara, K., Morishita, Y., Sakurai, N., Suzuki, H., Kojima, M., Sakakibara, H., Shibata, D., Saito, K., Shinozaki, K. and Yamaguchi-Shinozaki, K. (2014) Integrated analysis of the effects of cold and dehydration on rice metabolites, phytohormones, and gene transcripts. Plant Physiol., 164,1759-1771

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

Kurusu, T., Koyano, T., Hanamata, S., Kubo, T., Noguchi, Y., Yagi, C., Nagata, N., Yamamoto, T., Ohnishi, T., Okazaki, Y., Kitahata, N., Ando, D., Ishikawa, M., Wada, S., Miyao, A., Hirochika, H., Shimada, H., Makino, A., Saito, K., Ishida, H., Kinoshita, T., Kurata, N. and Kuchitsu, K. (2014) OsATG7 is required for autophagy-dependent lipid metabolism in rice postmeiotic anther development. Autophagy, 10, 878-888

Zhou, J., Yang, Y., Yu, J., Wang, L., Yu, X., Otani M., Kusano, M., Saito, K., Demura, T. and Zhuge, Q. (2014) Responses of Populus trichocarpa galactinol synthase genes to abiotic stresses. J. Plant Res., 127, 347-358

Matsushima, R., Maekawa, M., Kusano, M., Kondo, H., Fujita, N., Kawagoe, Y and Sakamoto, W. (2014) Amyloplast-localized SSG4 protein influences the size of starch grains in rice endosperm. Plant Physiol., 164, 623-636

Kurepa, J., Nakabayashi, R., Paunesku, T., Suzuki, M., Saito, K., Woloschak, G.E. and Smalle, J.A. (2014) Direct isolation of flavonoids from plants using ultra-small anatase TiO₂nanoparticles. Plant J., 77, 443-453

Shimada, T.L., Takano, Y., Shimada, T., Fujiwara, M., Fukao, Y., Mori, M., Okazaki, Y., Saito, K., Sasaki, R., Aoki, K. and Hara-Nishimura, I. (2014) Leaf oil body functions as a subcellular factory for the production of a phytoalexin in Arabidopsis. Plant Physiol., 164, 105-118

Rojas R.F., Rodriguez, T.O., Murai, Y., Iwashina, T., Sugawara, S., Suzuki, M., Nakabayashi, R., Yonekura-Sakakibara, K., Saito, K., Kitajima, J., Toda, K. and Takahashi, R. (2014) Linkage mapping, molecular cloning and functional analysis of soybean gene Fg2 encoding flavonol 3-O-glucoside (1 → 6) rhamnosyltransferase. Plant Mol Biol., 84, 287-300

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 a Response Regulator in the Cyanobacterium Synechocystis sp. PCC 6803. Plant Physiol., 164, 1831-1841

Osanai, T., Oikawa, A., Shirai, T., Kuwahara, A., Iijima, H., Tanaka, K., Ikeuchi, M., Kondo, A., Saito, K. and Hirai, M.Y. (2014) Capillary Electrophoresis-Mass Spectrometry Reveals the Distribution of Carbon Metabolites during Nitrogen Starvation in Synechocystis sp. PCC 6803. Environ Microbiol., 16, 512-524

Nakabayashi, R., Yonekura-Sakakibara, K., Urano, K., Suzuki, M., Yamada, Y., Nishizawa, T., Matsuda, F., Kojima, M., Sakakibara, H., Shinozaki, K., Michael, A.J., Tohge, T., Yamazaki, M. and Saito, K. (2014) Enhancement of oxidative and drought tolerance in Arabidopsis by overaccumulation of antioxidant flavonoids. Plant J., 77, 367-379

Yang, Z., Nakabayashi, R., Okazaki, Y., Mori, T., Takamatsu, S., Kitanaka, S., Kikuchi, J. and Saito, K. (2014) Toward better annotation in plant metabolomics: Isolation and structure elucidation of 36 specialized metabolites from Oryza sativa (rice) by using MS/MS and NMR analyses. Metabolomics, 10, 543-555

 

Review Papers

Yonekura-Sakakibara, K. and Saito, K. (2014) Function, Structure, and Evolution of Flavonoid Glycosyltransferases in Plants. In:“Recent Advances in Polyphenol Research Volume 4” Annalisa Romani, Vincenzo Lattanzio, Stephane Quideau, eds.: pp. 61-82, Wiley-Blackwell, Oxford

Sirikantaramas, S., Yamazaki, M. and Saito, K (2014) How Plants Avoid the Toxicity of Self-Produced Defense Bioactive Compounds. In:“Natural Products: Discourse, Diversity, and Design” Anne Osbourn, Rebecca J. Goss, Guy T. Carter, eds.: pp. 69 – 82, Wiley-Blackwell, Oxford

Fukushima, A., and Kusano, M. (2014) A network perspective on nitrogen metabolism from model to crop plants using integrated ‘omics’ approaches. J. Exp. Bot. 65, 5619-5630

Okazaki, Y. and Saito, K. (2014) Roles of lipids as signaling molecules and mitigators during stress response in plants. Plant J., 79, 584-596

Yamaya, T. and Kusano, M. (2014) Evidences supporting distinct functions of three cytosolic glutamine synthetases and two NADH-glutamate synthases in rice. J. Exp. Bot., doi: 10.1093/jxb/eru103

Press Releases

Genome-wide association study on all metabolites from 175 Japanese rice cultivars (28/Oct/2014)

Cutting cholesterol to make a safer potato (16/Sep/2014)

Awards

Kazuki Saito : The PSJ Award (2014)

Kazuki Saito : JSPP Plant and Cell Physiology Award for the Paper of Excellence (2014), KNApSAcK family databases: integrated metabolite-plant species databases for multifaceted plant research. Plant Cell Physiol., 2012, 53, e1. doi: 10.1093/pcp/pcr165

Yozo Okazaki : RIKEN Research Incentive Awards (2014), Study on a new class of plant lipid and its biosynthetic mechanism for protection against phosphorus depletion by development of metabolomics

2013

Original Papers

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. Plant J., 76, 456-465

Kimbara, J., Yoshida, M., Ito, H., Kitagawa, M., Takada, W., Hayashi, K., Shibutani, Y., Kusano, M., Okazaki, Y., Nakabayashi, R., Mori, T., Saito, K., Ariizumi, T. and Ezura, H. (2013) Inhibition of CUTIN DEFICIENT 2 causes defects in cuticle function and structure and metabolite changes in tomato fruit. Plant Cell Physiol., 54, 1535-1548

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

Yoshida, K., Ohnishi, M., Fukao, Y., Okazaki, Y., Fujiwara, M., Song, C., Nakanishi, Y., Saito, K., Shimmen, T., Suzaki, T., Hayashi, F., Fukaki, H., Maeshima, M. and Mimura, T. (2013) Studies on vacuolar membrane microdomains isolated from Arabidopsis suspension-cultured cells: Local distribution of vacuolar membrane proteins. Plant Cell Physiol., 54, 1571-1584

Matsuda, F., Tsugawa, H. and Fukusaki, E. (2013) Method for assessing the statistical significance of mass spectral similarities using BLAST statistics. Anal. Chem., 85, 8291-8297

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., doi: 10.1093/dnares/dst028

Ramilowski, J.A., Sawai, S., Seki, H., Mochida, K., Yoshida, T., Sakurai, T., Muranaka, T., Saito, K. and Daub, C.O. (2013) Glycyrrhiza uralensis Transcriptome Landscape and Study of Phytochemicals.Plant Cell Physiol., 54, 697-710

Tawaraya,K., Horie, R., Saito, A., Shinano, T., Wagatsuma, T., Saito, K. and Oikawa, A. (2013) Metabolote profiling of shoot extracts, root extracts, and root exudates of rice plant under phosphorus deficiency. Journal of Plant Nutrition, 36, 1138-1159

Yamazaki, M., Mochida, K., Asano, T., Nakabayashi, R., Chiba, M., Udomson, N., Yamazaki, Y., Goodenowe, D.B., Sankawa, U., Yoshida, T., Toyoda, A., Totoki, Y., Sakaki, Y., Góngora-Castillo, E., Buell, C.R., Sakurai, T. and Saito, K. (2013) Coupling Deep Transcriptome Analysis with Untargeted Metabolic Profiling in Ophiorrhiza pumila to Further the Understanding of the Biosynthesis of the Anti-Cancer Alkaloid Camptothecin and Anthraquinones. Plant Cell Physiol., 54, 686-696

Pang, Y., Cheng, X., Huhman, D.V., Ma, J., Peel, G.J., Yonekura-Sakakibara, K., Saito, K., Shen, G., Sumner, L.W., Tang, Y., Wen, J., Yun, J. and Dixon, R.A. (2013) Medicago glucosyltransferase UGT72L1: potential roles in proanthocyanidin biosynthesis. Planta, 238, 139-154

Kusano, M., Iizuka, Y., Kobayashi, M., Fukushima, A. and Saito, K. (2013) Development of a Direct Headspace Collection Method from Arabidopsis Seedlings Using HS-SPME-GC-TOF-MS Analysis. Metabolites, 3, 223-242

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., 26;4:1510. doi: 10.1038/ncomms2512

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

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 13C-labeling for Chemical Assignment of Sulfur-containing Metabolites in Onion Bulbs. Analytical Chemistry, 85, 1310–1315

Fukushima, E.O., Seki, H., Sawai, S., Suzuki, M., Ohyama, K., Saito, K. and Muranaka, T. (2013) Combinatorial biosynthesis of legume natural and rare triterpenoids in engineered yeast. Plant Cell Physiol., 54, 740-749

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(1-8)

Review Papers

Kusano, M. and Fukushima, A. (2013) Current challenges and future potential of tomato breeding using omics approaches. Breeding Science, 63, 31-41

Matsuda. F. and Saito, K. (2013) Integrative Analysis of Secondary Metabolism and Transcript Regulation in Arabidopsis Thaliana. The Handbook of Plant Metabolomics, DOI: 10.1002/9783527669882.ch9

Bunsupa, S., Saito, K. and Yamazaki, M. (2013) Molecular Biology and Biotechnology of Quinolizidine Alkaloid Biosynthesis in Leguminosae Plants. Biotechnology for Medicinal Plants, 263-273

Nakabayashi, R. and Saito, K. (2013) Metabolomics for unknown plant metabolites. Analytical and Bioanalytical Chemistry, 405, 5005-5011

Saito, K. (2013) Phytochemical genomics — a new trend. Curr Opin Plant Biol., 16, 373-380

Suzuki, H., Takita, E., Ohyama,K., Sawai, S., Seki,H., Sakurai, N., Muranaka, T., Ishimoto, M., Sudo, H., Saito, K. and Shibata, D. (2013) Multi-Gene Transformation for Pathway Engineering of Secondary Metabolites. The Handbook of Plant Metabolomics, DOI: 10.1002/9783527669882.ch12

Yonekura-Sakakibara, K. and Saito, K. (2013) Transcriptome Coexpression Analysis Using ATTED-II for Integrated Transcriptomic/Metabolomic Analysis. Methods Mol Biol., 1011, 317-326

Muranaka, T. and Saito, K. (2013) Phytochemical Genomics on the Way. Plant Cell Physiol., 54, 645-646

Fukushima, A. and Kusano, M. (2013) Recent progress in the development of metabolome databases for plant systems biology. Front. Plant Sci., doi: 10.3389/fpls.2013.00073

Yonekura-Sakakibara, K., Fukushima, A. and Saito, K. (2013) Transcriptome data modeling for targeted plant metabolic engineering. Curr Opin Biotechnol., 24, 285-290

Saito, K., Yonekura-Sakakibara, K., Nakabayashi, R., Higashi, Y., Yamazaki, M., Tohge, T. and Fernie, A.R. (2013) The flavonoid biosynthetic pathway in Arabidopsis: Structural and genetic diversity. Plant Physiol Biochem., 72, 21-34

Higashi, Y. and Saito, K. (2013) Network analysis for gene discovery in plant specialized metabolism. Plant Cell Environ., 36, 1597-1606

Press Releases

Discovery of the Regulator of Bioplastic Production in Cyanobacteria (16/Jul/2013)

2012

Original Papers

Afendi, F.M., Okada, T., Yamazaki, M., Hirai-Morita, A., Nakamura, Y., Nakamura, K., Ikeda, S., Takahashi, H., Altaf-Ul-Amin, M., Darusman, L.K., Saito, K. and Kanaya, S. (2012) KNApSAcK family databases: integrated metabolite-plant species databases for multifaceted plant research. Plant Cell Physiol., 53, e1. doi: 10.1093/pcp/pcr165

Yonekura-Sakakibara, K., Fukushima, A., Nakabayashi, R., Hanada, K., Matsuda, F., Sugawara, S., Inoue, E., Kuromori, T., Ito, T., Shinozaki, K., Wangwattana, B., Yamazaki, M. and Saito, K. (2012) Two glycosyltransferases involved in anthocyanin modification delineated by transcriptome independent component analysis in Arabidopsis thaliana. Plant J., 69, 154-167

Kim, J., Choi, J.N., John, K.M., Kusano, M., Oikawa, A., Saito, K. and Lee, C.H. (2012) 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., 60, 9746-9753

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. Phytochem., 82, 38-45

Kimbara, J., Yoshida, M., Ito, H., Hosoi, K., Kusano,M., Kobayashi, M., Ariizumi, T., Asamizu, E. and Ezura, H. (2012) A novel class of sticky peel and light green mutations causes cuticle deficiency in leaves and fruits of tomato (Solanum lycopersicum). Planta, 236, 1559-1570

Matsuda, F., Okazaki, Y., Oikawa, A., Kusano, M., Nakabayashi, R., Kikuchi, J., Yonemaru, J., Ebana, K., Yano, M. and Saito, K. (2012) Dissection of genotype-phenotype associations in rice grains using metabolome quantitative trait loci analysis. Plant J., 70, 624-636

Fukushima, A., Nishizawa, T., Hayakumo, M., Hikosaka, S., Saito, K., Goto, E. and Kusano, M. (2012) Exploring Tomato Gene Functions Based on Coexpression Modules Using Graph Clustering and Differential Coexpression Approaches. Plant Physiol., 158, 1487-1502

Kusano, M., Fukushima, A., Fujita, N., Okazaki, Y., Kobayashi, M., Fujita Oitome, N., Ebana, K., and Saito, K. (2012) Deciphering starch quality of rice kernels using metabolite profiling and pedigree network analysis. Mol Plant, 5, 442-451

Bunsupa, S., Katayama, K., Ikeura, E., Oikawa, A., Toyooka, K., Saito, K. and Yamazaki, M. (2012) Lysine Decarboxylase Catalyzes the First Step of Quinolizidine Alkaloid Biosynthesis and Coevolved with Alkaloid Production in Leguminosae. Plant Cell, 24, 1202-1216

Endo, A., Tatematsu, K., Hanada, K., Duermeyer, L., Okamoto, M., Yonekura-Sakakibara, K., Saito, K., Toyoda, T., Kawakami, N., Kamiya, Y., Seki, M. and Nambara, E. (2012) Tissue-Specific Transcriptome Analysis Reveals Cell Wall Metabolism, Flavonol Biosynthesis and Defense Responses are Activated in the Endosperm of Germinating Arabidopsis thaliana Seeds. Plant Cell Physiol., 53, 16-27

Review Papers

Kusano, M. and Saito, K. (2012) Role of Metabolomics in Crop Improvement, J. Plant Biochem. Biotechnol. 21, 24-31

Oikawa, A. and Saito, K. (2012) Metabolite analyses of single cells. Plant J., 70, 30-38

Okazaki, Y. and Saito, K. (2012) Recent advances of metabolomics in plant biotechnology. Plant Biotech. Rep., 6, 1-15

Press Releases

New study sheds light on genetics of rice metabolism (8/Feb/2012)

Awards

Miyako Kusano : Japanese Society for Plant Cell and Molecular Biology Award for Young Scientists, 2012

Ery Odette Fukushima : Japanese Society for Plant Cell and Molecular Biology Student Award, 2012

2011

Original Papers

Oikawa, A., Otsuka, T., Jikumaru, Y., Yamaguchi, S., Matsuda, F., Nakabayashi, R., Takashina, T., Isuzugawa, K., Saito, K. and Shiratake, K. (2011) Effects of freeze-drying of samples on metabolite levels in metabolome analyses. J Sep Sci. 34, 3561-3567

Kusano, M., Jonsson, P., Fukushima, A., Gullberg, J., Sjöström, M., Trygg, J. and Moritz, T. (2011) Metabolite Signature during Short-Day Induced Growth Cessation in Populus. frontiers IN PLANT PHYSIOLOGY, doi: 10.3389/fpls.2011.00029

Toyokura, K., Watanabe, K., Oiwaka, A., Kusano, M., Tameshige, T., Tatematsu, K., Matsumoto, N., Tsugeki, R., Saito, K. and Okada K. (2011) Succinic semialdehyde dehydrogenase is involved in the robust patterning of Arabidopsis leaves along the adaxial-abaxial axis. Plant Cell Physiol., 52, 1340-1353

Diaz, C., Kusano, M., Sulpice, R., Araki, M., Redestig, H., Saito, K., Stitt, M. and Shin, R. (2011) Determining novel functions of Arabidopsis 14-3-3 proteins in central metabolic processes. BMC Sys. Biol., 5, 192

Seki, H., Sawai, S., Ohyama, K., Mizutani, M., Ohnishi, T., Sudo, H., Fukushima, E. O., Akashi, T., Aoki, T., Saito, K.andMuranaka, T. (2011) Triterpene functional genomics in licorice for identification of CYP72A154 involved inthebiosynthesis of glycyrrhizin. Plant Cell, 23, 4112-4123

Fukushima, E. O., Seki, H., Ohyama, K., Ono, E., Umemoto, N., Mizutani, M., Saito, K. and Muranaka, T. (2011) CYP716A Subfamily Members are Multifunctional Oxidases in Triterpenoid Biosynthesis. Plant Cell Physiol., 52, 2050-2061

Redestig, H., Kusano, M., Ebana, K., Kobayashi, M., Oikawa, A., Okazaki, Y., Matsuda, F., Arita, M., Fujita, N. and Saito, K. (2011) Exploring molecular backgrounds of quality traits in rice by predictive models based on high-coverage metabolomics. BMC Sys. Biol., 5, 176

Tohge, T., Kusano, M., Fukushima, A., Saito, K. and Fernie, A. R. (2011) Transcriptional and metabolic programs following exposure of plants to UV-B irradiation. Plant Signaling & Behavior, 6, 1987-1992

Redestig, H., Kobayashi, M., Saito, K. and Kusano, M. (2011) Exploring matrix effects and quantification performance in metabolomics experiments using artificial biological gradients. Anal. Chem., 83, 5645–5651

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

Matsuda, F., Nakabayashi, R., Sawada, Y., Suzuki, M., Hirai, M. Y., Kanaya, S. and Saito, K. (2011) Mass spectra-based framework for automated structural elucidation of metabolome data to explore phytochemical diversity. Front. Plant Sci., 2:40. doi: 10.3389/fpls.2011.00040

Oikawa, A., Matsuda, F., Kikuyama, M., Mimura, T. and Saito, K. (2011) Metabolomics of a single vacuole reveals metabolic dynamism in an alga Chara australis. Plant Physiol., 157, 544-551

Akai, M., Onai, K., Kusano, M., Sato, M., Redestig, H., Toyooka, K., Morishita, M., Miyake, H., Hazama, A., Checchetto, V., Szabò, I., Matsuoka, K., Saito, K., Yasui, M., Ishiura, M. and Uozumi, N. (2011) Plasma membrane aquaporin AqpZ is essential for glucose metabolism during photomixotrophic growth of Synechocystis sp. PCC 6803. J. Biol. Chem., 286: 25224-25235

Saika, H., Oikawa, A., Matsuda, F., Onodera, H., Saito, K. and Toki, S. (2011) Application of gene targeting to designed mutation breeding of high-tryptophan rice. Plant Physiol.,156:1269-1277

Kusano, M., Tohge, T., Fukushima, A., Kobayashi, M., Hayashi, N., Otsuki, H., Kondou, Y., Goto, H., Kawashima, M., Matsuda, F., Niida, R., Matsui, M., Saito, K. and Fernie, A. R. (2011) Metabolomics reveals comprehensive reprogramming involving two independent metabolic responses of Arabidopsis to ultraviolet-B light. Plant J., 67:354-369

Skirycz, A., Claeys, H., De Bodt S., Oikawa, A., Shinoda, S., Andriankaja, M., Maleux, K., Eloy N.B., Coppens, F., Yoo, S.D., Saito, K. and Inzé, D. (2011) Pause-and-stop: the effects of osmotic stress on cell proliferation during early leaf development in Arabidopsis and a role for ethylene signaling in cell cycle arrest. Plant Cell, 23:1876-1888

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

Kawashima, C.G., Matthewman, C.A., Huang, S., Lee, B.R., Yoshimoto, N., Koprivova, A., Rubio-Somoza, I., Todesco, M., Rathjen, T., Saito, K., Takahashi, H., Dalmay T. and Kopriva, S. (2011) Interplay of SLIM1 and miR395 in regulation of sulfate assimilation in Arabidopsis. Plant J., 66:863-876

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

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

Sakurai, N., Ara, T., Ogata, Y., Sano, R., Ohno, T., Sugiyama, K., Hiruta, A., Yamazaki, K., Yano, K., Aoki, K., Aharoni, A., Hamada, K., Yokoyama, K., Kawamura, S., Otsuka, H., Tokimatsu, T., Kanehisa, M., Suzuki, H., Saito, K. and Shibata, D. (2011) KaPPA-View4: A metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data. Nucleic Acids Res., 39, D677–D684

Bunsupa, S., Okada, T., Saito, K. and Yamazaki, M. (2011) An acyltransferase-like gene obtained by differential gene expression profiles of quinolizidine alkaloid-producing and nonproducing cultivars of Lupinus angustifolius. Plant Biotech., 28, 89-94

Viraporn, V., Yamazaki, M., Saito, K., Denduangboripant, J., Chayamarit, K., Chuanasa, T. and Sukrong, S. (2011) Correlation of camptothecin-producing ability and phylogenetic relationship in the genus Ophiorrhiza. Planta Medica, 77, 759-764

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

Fukushima, A., Kusano, M., Redestig, H., Arita, M. and Saito, K. (2011) Metabolomic correlation-network modules in Arabidopsis based on a graph-clustering approach. BMC Systems Biology,  doi: 10.1186/1752-0509-5-1

Sakurai, T., Kondou, Y., Akiyama, K., Kurotani, A., Higuchi, M., Ichikawa, T., Kuroda, H., Kusano, M., Mori, M., Saitou, T., Sakakibara, H., Sugano, S., Suzuki, M., Takahashi, H., Takahashi, S., Takatsuji, H., Yokotani, N., Yoshizumi, T., Saito, K., Shinozaki, K., Oda, K., Hirochika, H., and Matsui, M. (2011) RiceFOX: A database of Arabidopsis mutant lines overexpressing rice full-length cDNA that contains a wide range of trait information to facilitate analysis of gene function. Plant Cell Physiol. 52, 265-273

Kusano, M., Tabuchi-Kobayashi, M., Fukushima, A., Funayama, K., Diaz, C., Kobayashi, M., Hayashi, N., Tsuchiya, Y., Takahashi, H., Kamata, A., Yamaya, T. and Saito, K. (2011) Metabolomics data reveal a crucial role of cytosolic glutamine synthetase 1;1 in coordinating metabolic balance in rice. Plant J.,66, 456-466

Kusano, M., Redestig, H., Hirai, T., Oikawa, A., Matsuda, F., Fukushima, A., Arita, M., Watanabe, S., Yano, M., Hiwasa-Tanase, K., Ezura, H. and Saito, K. (2011) Covering chemical diversity of genetically-modified tomatoes using metabolomics for objective substantial equivalence assessment. PLoS ONE, 16;6(2):e16989

Oikawa, A., Fujita, N., Horie, R., Saito, K. and Tawaraya, K. (2011) Solid-phase extraction for metabolomic analysis of high-salinity samples by capillary electrophoresis–mass spectrometry. J. Separation Sci., 34, 1063-1068

Review Papers

Sawai, S. and Saito, K. (2011) Triterpenoid biosynthesis and engineering in plants. Front. Plant Sci., 2:25. doi: 10.3389/fpls.2011.00025

Fernie, A. R., Aharoni, A., Willmitzer, L., Stitt, M., Tohge, T., Kopka, J., Carroll, A. J., Saito, K., Fraser, P. D. and DeLuca, V. (2011) Recommendations for reporting metabolite data. Plant Cell, 23, 2477-2482

Yonekura-Sakakibara, K. and Hanada, K. (2011) An evolutionary view of functional diversity in family 1　glycosyltransferases. Plant J, 66, 182-193

Yamazaki, M. and Saito, K. (2011) Molecular genetic study on the anthocyanins chemotypes of Perilla frutescens var. crispa. Nat. Prod. Commun., 6, 423-427

Okazaki, Y., Oikawa, A., Kusano, M., Matsuda, F. and Saito, K. (2011) Metabolomics in Plant Biotechnology. In: "Plant Metabolism and Biotechnology" Hiroshi Ashihara, Alan Crozier, Atsushi Komamine, eds.: pp. 373-388, Wiley.

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" Robert D. Hall, ed.: pp. 261-316 Wiley-Blackwell, Oxford.

Kusano, M., Fukushima, A., Redestig, H. and Saito, K. (2011) Metabolomic approaches toward understanding nitrogen metabolism in plants. J. Exp. Bot., 62,1439-1453

Takahashi, H., Kopriva, S., Giordano, M., Saito, K. and Hell, R. (2011) Sulfur assimilation in photosynthetic organisms: molecular functions and regulations of transporters and assimilatory enzymes. Annu. Rev. Plant Biol., 62,157-184

Press Releases

Glycosyltransferase Genes Found to Be Involved in Plant Pigment Accumulation (12/Oct/2011)

New technique elucidates dynamics of plant cell metabolites (6/Sep/2011)

Chemical Diversity in Genetically Modified Tomatoes Using Metabolomics for Objective Substantial Equivalence Assessment (17/Feb/2011)

Metabolomics Data Reveal a Crucial Role of Cytosolic Glutamine Synthetase 1;1 in Coordinating Metabolic Balance in Rice (7/Feb/2011)

Awards

Kazuki Saito Group Director won the JSPCMB Award for Distinguished Research 2011 (6/Sep/2011)

2010

Original Papers

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

Yamazaki, M., Asano, T, Yamazaki, Y, Sirikantaramas, S., Sudo, H. and Saito, K. (2010) Biosynthetic system of camptothecin: an anticancer plant product. Pure Appl.Chem., 82, 213-218

Albinsly, D., Kusano, M., Higuchi, M., Hayashi, N., Kobayashi, M., Fukushima, A., Mori, M., Ichikawa, T., Matsui, K., Kuroda, H., Horii, Y., Tsumoto, Y., Sakakibara, H., Hirochika, H., Matsui, M. and Saito, K. (2010) Metabolomic screening applied to rice FOX Arabidopsis lines leads to the identification of a gene changing nitrogen metabolism. Mol. Plant, 3, 125-142

Suzuki, M., Kusano, M., Takahashi, H., Nakamura, Y., Hayashi, N., Kobayashi, M., Ichikawa, T., Matsui, M., Hirochika, H. and Saito, K. (2010) Rice-Arabidopsis FOX line screening with FT-NIR-based fingerprinting for GC-TOF/MS-based metabolite profiling. Metabolomics, 6, 137-145

Chikayama, E., Sekiyama, Y., Okamoto, M., Nakanishi, Y., Tsuboi, Y., Akiyama, K., Saito, K., Shinozaki, K. and Kikuchi, J. (2010) Statistical indices for simultaneous large-scale metabolite detections for a single NMR spectrum. Anal. Chem., 82, 1653-1658

Watanabe, M., Hubberten, H-M., Saito, K. and Hoefgen, R. (2010) General regulatory patterns of plant mineral nutrient depletion as revealed by serat quadruple mutants disturbed in cysteine synthesis. Mol. Plant, 3, 438-466

Kitamura, S., Matsuda, F., Tohge, T., Yonekura-Sakakibara, K., Yamazaki, M., Saito, K. and Narumi, I. (2010) Metabolic profiling and cytological analysis of proanthocyanidins in immature seeds of flavonoid accumulation mutants of Arabidopsis thaliana. Plant J., 62, 549-559

Masumoto, C., Miyazawa, S., Ohkawa, H., Fukuda, T., Taniguchi, Y., Murayama, S., Kusano, M., Saito, K., Fukayama, H. and Miyao, M. (2010) Phosphoenolpyruvate carboxylase intrinsically located in the chloroplast of rice plays a crucial role in ammonium assimilation. Proc. Natl. Acad. Sci. USA, 107, 5226-5231

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

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

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

Baek, D., Pathange, P., Chung, J-S., Jiang, J., Gao, L., Oikawa, A., Hirai, M.Y., Saito, K., Pare, PW. and Shi, H. (2010) A stress-inducible sulphotransferase sulphonates salicylic acid and confers pathogen resistance in Arabidopsis. Plant Cell Environ., 33, 1383-1392

Nishiyama, Y., Choong-Soo Yun, Matsuda, F., Saito, K. and Tozawa, Y. (2010) Expression of bacterial tyrosine ammonia lyase creates a novel p-coumaric acid pathway in the biosynthesis of phenylpropanoids in Arabidopsis. Planta, 232, 209-218

Redestig, H., Kusano, M., Fukushima, A., Matsuda, F., Saito, K. and Arita, M. (2010) Consolidating metabolite identifiers to enable contextual and multi-platform metabolomics data analysis. BMC Bioinformatics, 11: 214, 1471-2105

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

Ishimoto, M., Rahman, SM., Hanafy, MS., Khalafalla, MM., El-Shemy, HA., Nakamoto, Y., Kita, Y., Takanashi, K., Matsuda, F., Murano, Y., Funabashi, T., Miyagawa, H., and Wakasa, K. (2010) Evaluation of amino acid content and nutritional quality of transgenic soybean seeds with high-level tryptophan accumulation. Molecular Breeding, 25: 313-326

Matsuda, F., Ishihara, A., Takanashi, K., Morino, K., Miyazawa, H., Wakasa, K., and Miyagawa, H. (2010) Metabolic profiling analysis of genetically modified rice seedlings that overproduce tryptophan. Plant Biotech., 27, 17-27

Review Papers

Sakurai, T., Akiyama K. and Saito, K. (2010) Analytical platforms and databases ranging from plant transcriptomics to metabolomics. In: "Medicinal Plant Biotechnology" Arora, R., eds.: pp. 222-243, CABI, New York.

Nakabayashi, R., Yamazaki, M. and Saito, K. (2010) A polyhedral approach including natural products chemistry for understanding flavonoid biosynthesis in Arabidopsis. New Biotechnology, 27, 829-836

Muranaka, T. and Saito, K. (2010) Production of Pharmaceuticals by Plant Tissue Cultures. In "Comprehensive Natural Products II Chemistry and Biology" Mander, L., Lui, H.-W., Eds.; volume 3, pp.615-628 Elsevier: Oxford.

Saito, K., and Matsuda, F. (2010) Metabolomics for functional genomics, systems biology, and biotechnology. Annu. Rev. Plant Biol., 61:463-489

Press Releases

Metabolome analysis reveals flavor and aroma components in 'Dadacha-mame' (20/Oct/2010)

A unique mechanism for efficient nitrogen utilization in rice: a finding for an increased crop yield(25/Mar/2010)

AtMetExpress: A Database of Secondary Metabolites of Various Arabidopsis Parts (15/Jan/2010)

Awards

Commendation for Science and Technology by MEST awarded to Prof. Kazuki Saito, Deputy Director (14/Apr/2010)

2009

Original Papers

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, 16:4: e7490

Rubin, G., Tohge, T., Matsuda, F., Saito, K., and Scheible, W. (2009) Members of the LBD family of transcription factors repress anthocyanin synthesis and affect additional nitrogen responses in Arabidopsis. Plant Cell, 21: 3567-3584

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

Cuadros-Inostroza, A., Caldana, C., Redestig, H., Kusano, M., Lisec, J., Pena-Cortes, H., Willmitzer, L., and Hannah, M.A. (2009) TargetSearch--a Bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data. BMC Bioinformatics, 10: 428

Yoshimoto, K., Jikumaru, Y., Kamiya, Y., Kusano, M., Consonni, C., Panstruga, R., Ohsumi, Y. and Shirasu, K. (2009) Autophagy Negatively Regulates Cell Death by Controlling NPR1-Dependent Salicylic Acid Signaling during Senescence and the Innate Immune Response in Arabidopsis. Plant Cell, 21: 2914-2927

Kawashima, C. G., Yoshimoto, N., Maruyama, N. A., Tsuchiya, Y. N., Saito, K., Takahashi, H. and Dalmay, T. (2009) Sulphur starvation induces the expression of microRNA-395 and one of its target genes but in different cell types. Plant J., 57: 313-321

Matsuda, F., Yonekura-Sakakibara, K., Niida, R., Kuromori, T., Shinozaki, K. and Saito, K. (2009) MS/MS spectral tag-based annotation of non-targeted profile of plant secondary metabolites. Plant J., 57: 555-577

Urano, K., Maruyama, K., Ogata, Y., Morishita, Y., Takeda, M., Sakurai, N., Suzuki, H., Saito, K., Shibata, D., Kobayashi, M., Shinozaki, Y. K. and Shinozaki, K. (2009) Characterization of the ABA-regulated global responses to dehydration in Arabidopsis by metabolomics. Plant J., 57: 1065-1078

Ogata, Y., Sakurai, N., Aoki, K., Suzuki, H., Okazaki, K,. Saito, K. and Shibata, D. (2009) KAGIANA: An Excel-based tool for retrieving summary information on Arabidopsis genes. Plant Cell Physiol., 50: 173-177

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

Nakamichi, N., Kusano, M., Fukushima, A., Kita, M., Ito, S., Yamashino, T., Saito, K., Yonekura-Sakakibara, K. and Mizuno, T. (2009) Transcript profiling of an Arabidopsis PSEUDO RESPONSE REGULATOR arrhythmic triple mutant reveals a role for the circadian clock in cold stress response. Plant Cell Physiol., 50: 447-462

Sudo, H., Seki, H., Sakurai, N., Suzuki, H., Shibata, D., Toyoda, A., Totoki, Y., Sakaki, Y., Iida, O., Shibata, T., Kojoma, M., Muranaka, T. and Saito, K. (2009) Expressed sequence tags from rhizomes of Glycyrrhiza uralensis. Plant Biotech., 26: 105-107

Ohyama, K., Suzuki, M., Kikuchi, J., Saito, K. and Muranaka, T. (2009) Dual biosynthetic pathways to phytosterol via cycloartenol and lanosterol in Arabidopsis. Proc Natl Acad Sci USA., 106: 725-730

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

Mugford, S. G., Yoshimoto, N., Reichelt, M., Wirtz, M., Hill, L., Mugford, S. T., Nakazato, Y., Noji, M., Takahashi, H., Kramell, R., Gigolashvili, T., Flugge, U. I., Wasternack, C., Gershenzon, J., Hell, R., Saito, K. and Kopriva, S. (2009) Disruption of adenosine-5'-phosphosulfate kinase in Arabidopsis reduces levels of sulfated secondary metabolites. Plant Cell, 21: 910-927

Suzuki, M., Nakagawa, S., Kamide, Y., Kobayashi, K., Ohyama, K., Hashinokuchi, H., Kiuchi, R., Saito, K., Muranaka, T. and Nagata, N. (2009) Complete blockage of the mevalonate pathway results in male gametophyte lethality. J. Exp. Botany, 60: 2055-2064

Fukushima, A., Kusano, M., Nakamichi, N., Kobayashi M., Hayashi, N., Sakakibara, H., Mizuno, T. and Saito, K. (2009) Impact of clock-associated Arabidopsis pseudo-response regulators in metabolic coordination. Proc. Natl. Acad. Sci. USA, 106: 7251-7256

Nakabayashi, R., Kusano, M., Kobayashi, M., Tohge, T., Yonekura-Sakakibara, K., Kogure, N., Yamazaki, M., Kitajima, M., Saito, K. and Takayama, H. (2009) Metabolomics-oriented isolation and structure elucidation of 37 compounds including two new anthocyanins from Arabidopsis thaliana. Phytochemistry, 70: 1017-1029

Nakamichi, N., Fukushima, A., Kusano, M., Sakakibara, H., Mizuno, T. and Saito, K. (2009) Linkage between circadian clock and tricarboxylic acid cycle in Arabidopsis. Plant Signaling & Behavior, 4: 660-662

Yamazaki, M., Asano, T., Yamazaki, Y., Sirikantaramas, S., Sudo, H. and Saito, K. (2009) Biosynthetic system of camptothecin: an anticancer plant product. Pure Appl.Chem., 82: 213-218

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 Cell Physiol., 50: 1181-1190

Maruyama, K., Takeda, M., Kidokoro, S., Yamada, K., Sakuma, Y., Urano, K., Fujita, M., Yoshiwara, K., Matsukura, S., Morishita, Y., Sasaki, R., Suzuki, H., Saito, K., Shibata, D., Shinozaki, K. and Shinozaki, K. Y. (2009) Metabolic pathways involved in cold acclimation identified by integrated analysis of metabolites and transcripts regulated by DREB1A and DREB2A. Plant Physiol.,150: 1972-1980

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 Cell Phsyiol., 50: 1579-1586

Albinsly, D., Kusano, M., Higuchi, M., Hayashi, N., Kobayashi, M., Fukushima, A., Mori, M., Ichikawa, T., Matsui, K., Kuroda, H., Horii, Y., Tsumoto, Y., Sakakibara, H., Hirochika, H., Matsui, M. and Saito, K. (2009) Metabolomic screening applied to rice FOX Arabidopsis lines leads to the identification of a gene changing nitrogen metabolism. Mol. Plant, 3: 125-142

Redestig, H., Fukushima, A., Stenlund, H., Moritz, T., Arita, M., Saito, K. and Kusano, M. (2009) Compensation for systematic cross-contribution improves normalization of mass-spectrometry based metabolomics data. Anal. Chem., 81: 7974-7980

Reviews and Book Chapters

Yonekura-Sakakibara, K. and Saito, K. (2009) Functional genomics for plant natural product biosynthesis. Natural Product Reports, 26, 1466–1487

Yonekura-Sakakibara, K. (2009) Functional genomics of family 1 glycosyltransferases in Arabidopsis. Plant Biotech., 26, 267-274

Fukushima, A., Kusano, M., Redestig, H., Arita, M., and Saito, K. (2009) Integrated omics approaches in plant systems biology. Curr. Opin. Chem. Biol., 13: 532-538

Saito, K. (2009) Plant functional genomics based on integration of metabolomics and transcriptomics: Toward plant systems biology. In "Systems Biology The Challenge of Complexity", pp. 135-142, Springer, Tokyo.

Asano, T., Sudo, H., Yamazaki, M. and Saito, K. (2009) Camptothecin production by in vitro cultures and plant regeneration in Ophiorrhiza species. In "Methods in Molecular Biology 547. Protocols for In Vitro Cultures and Secondary Metabolite Analysis of Aromatic and Medicinal Plants", pp.337-345, Humana Press - Springer, New York.

Yoshimoto, N., Inoue, E.,Takahashi, A. W., Saito, K. and Takahashi, H. (2009) Post-transcriptional control of high-affinity sulfate transporters for uptake of sulfate in roots of Arabidopsis thaliana. In "Sulfur Metabolism in Plants Regulatory Aspects Significance of Sulfur in the Food Chain, Agriculture and the Environment" , pp 179-184, Backhuys Publishers, Leiden.

Mugford, S. G., Reichelt, M., Yoshimoto, N., Nakazato, Y., Noji, M.,Takahashi, H., Saito, K., Gershenzon, J. and Kopriva, S. (2009) Characterization of the APS kinase gene family in Arabidopsis thaliana. In "Sulfur Metabolism in Plants Regulatory Aspects Significance of Sulfur in the Food Chain, Agriculture and the Environment", pp 185-188, Backhuys Publishers, Leiden.

Watanabe, M., Kusano, M., Oikawa, A., Fukushima, A., Mochida, K., Kato, T., Tabata, S., Yoshimoto, N., Noji, M. and Saito, K. (2009) Cysteine biosynthesis in Arabidopsis: comprehensive reverse genetic study on the functions of BSAS and SERAT gene families. In "Sulfur Metabolism in Plants Regulatory Aspects Significance of Sulfur in the Food Chain, Agriculture and the Environment", pp 201-206, Backhuys Publishers, Leiden.

Araki, R., Sawada, Y., Hirai, A., Suzuki, A., Saito, K. and Hirai, M. Y. (2009) Could PMG transcription factors become an indicator for the production of methionine-derived glucosinolates in crop cultivation? In "Sulfur Metabolism in Plants Regulatory Aspects Significance of Sulfur in the Food Chain, Agriculture and the Environment", pp 235-238, Backhuys Publishers, Leiden.

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 Regulatory Aspects Significance of Sulfur in the Food Chain, Agriculture and the Environment", pp 239-244, Backhuys Publishers, Leiden.

Press Releases

Impact of clock-associated Arabidopsis pseudo-response regulators in metabolic coordination (7/Apr/2009)

A Chloroplastic UDP-Glucose Pyrophosphorylase from Arabidopsis is the Committed Enzyme for the First Step of Sulfolipid Biosynthesis (13/Mar/2009)

Awards

Keiko Yonekura-Sakakibara: JSPP Plant and Cell Physiology Award for the Paper of Excellence,　Engineering of the Rose Flavonoid Biosynthetic Pathway Successfully Generated Blue-Hued Flowers Accumulating Delphinidin. Plant Cell Physiol., 48, 1589-1600, 2007, 2009, Mar

2008

Original Papers

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, M. Y., 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

Wangwattana, B., Koyama, Y., Nishiyama, Y., Kitayama, M., Yamazaki, M. and Saito, K. (2008) Characterization of PAP1-upregulated glutathione S-transferase genes in Arabidopsis thaliana. Plant Biotech., 25: 191-196

Sirikantaramas, S., Yamazaki, M. and Saito, K. (2008) Mutations in topoisomerase I as a self-resistance mechanism coevolved with the production of the anticancer alkaloid camptothecin in plants. Proc. Natl. Acad. Sci. USA, 105: 6782-6786

Yamazaki, M., Shibata, M., Nishiyama, Y., Springob, K., Kitayama, M., Shimada, N., Aoki, T., Ayabe, S. and Saito, K. (2008) Differential gene expression profiles of red and green forms of Perilla frutescens leading to comprehensive identification of anthocyanin biosynthetic genes. FEBS J., 275: 3494-3502

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

Seki, H., Ohyama, K., Sawai, S., Mizutani, M., Ohnishi, T., Sudo, H., Akashi, T., Aoki, T., Saito, K. and Muranaka, T. (2008) Licorice -amyrin 11-oxidase, a cytochrome P450 with a key role in the biosynthesis of the triterpene sweetener glycyrrhizin. Proc. Natl. Acad. Sci. USA, 105: 14204-14209

Yonekura-Sakakibara, K., Tohge, T., Matsuda, F., Nakabayashi, R., Takayama, H., Niida, R., Takahashi, A. W., Inoue, E. and Saito, K. (2008) Comprehensive flavonol profiling and transcriptome coexpression analysis leading to decoding gene-metabolite correlations in Arabidopsis. Plant Cell, 20: 2160-2176

Watanabe, M., Kusano, M., Oikawa, A., Fukushima, A., Noji, M. and Saito, K. (2008) Physiological roles of the -substituted alanine synthase gene family in Arabidopsis. Plant Physiol., 146: 310-320

Watanabe, M., Mochida, K., Kato, T., Tabata, S., Yoshimoto, N., Noji, M. and Saito, K. (2008) Comparative genomics and reverse genetics analysis reveal indispensable functions of the serine acetyltransferase gene family in Arabidopsis. Plant Cell, 20: 2484-2496

Ohtsu, N. O., Oikawa, A., Zhao, P., Xiang, C., Saito, K. and Oliver, J. D. (2008) A gamma-glutamyl transpeptidase-independent pathway of glutathione catabolism to glutamate via 5-oxoproline in Arabidopsis. Plant Physiol., 148: 1603-1613

Book Edition

Yonekura-Sakakibara, K., Nakayama, T., Yamazaki, M. and Saito, K. (2008) Modification and stabilization of anthocyanins. In ", pp.169-190, Springer, New York.

Muranaka, T., Kojoma, M., Sudo, H. and Saito, K.(2008) Medicinal plants. In "Compendium of Transgenic Crop Plants: Transgenic Plantation Crops, Ornamentals and Turf Grasses ", pp. 142-155, Blackwell Publishing Ltd., Oxford, UK.

Reviews and Book Chapters

Saito, K., Yokota-Hirai, M. and Yonekura-Sakakibara, K. (2008) Decoding genes with coexpression networks and metabolomics - 'Majority report by precogs'. Trends Plant Sci., 13: 36-43

Sirikantaramas, S., Yamazaki, M. and Saito, K. (2008) Mechanisms of resistance to self-produced toxic secondary metabolites in plants. Phytochemistry Reviews, 7: 467-477

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

Oikawa, A., Matsuda, F., Kusano, M., Okazaki, Y. and Saito, K., (2008) Rice Metabolomics. Rice, 1: 63-71

Awards

Keiko Yonekura-Sakakibara:　Japanese Society for Plant Cell and Molecular Biology Award for Young Scientists, 2008

Kazuki Saito and Masami Yokota Hirai: Thomson Reuters, Science Watsh, FAST BREAKING PAPERS-2008, 2008, June

Miyako Kusano: 2008 RIKEN PSC Awards, 2008, April

2007

Original Papers

Sirikantaramas, S., Sudo, H., Asano, T., Yamazaki, M., and Saito, K. (2007) Transport of camptothecin in hairy roots of Ophiorrhiza pumila. Phytochemistry, 68: 2881-2886

Morioka, R., Kanaya, S., Yokota-Hirai, M., 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

Shimamura, M., Akashi, T., Sakurai, N., Suzuki, H., Saito, K., Shibata, D., Ayabe, S., and Aoki, T. (2007) 2-Hydroxyisoflavanone dehydratase is a critical determinant of isoflavone productivity in hairy root cultures of Lotus japonicus. Plant Cell Physiol., 48: 1652-1657

Bylesjö, M., Eriksson, D., Kusano, M., Moritz, T. and Trygg, J. (2007) Data integration in plant biology: the O2PLS method for combined modeling of transcript and metabolite data. Plant J., 52: 1181-1191

Kusano, M., Fukushima, A., Arita, M., Jonsson, P., Moritz, T., Kobayashi, M., Hayashi, N., Tohge, T., and Saito, K. (2007) Unbiased characterization of genotype-dependent metabolic regulations by metabolomic approach in Arabidopsis thaliana. BMC Systems Biol., 1: 53

Kusano, M., Fukushima, A., Kobayashi, M., Hayashi, N., Jonsson, P., Moritz, T., Ebana, K. and Saito, K. (2007) Application of a metabolomic method combining one-dimensional and two-dimensional gas chromatography-time-of-flight/mass spectrometry to metabolic phenotyping of natural variants in rice. J. Chromatogr. B., 855: 71-79

Obayashi, T., Kinoshita, K., Nakai, K., Shibaoka, M., Hayashi, S., Saeki, M., Shibata, D., Saito, K. and Ohta, H. (2007) ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucleic Acids Res., 35: D863-D869

Li-Yang, J., Nakajima, J., Kimura, N., Saito, K. and Seo, S. (2007) Oleanane-type triterpene glycosides from Glychyrrhiza ularensis. Nat. Prod. Comm., 2, 243-248

Luo, J., Nishiyama, Y., Fuell, C., Taguchi, G., Elliott, K., Hill, L., Tanaka, Y., Kitayama, M., Yamazaki, M., Bailey, P., Parr, A., Michael, A. J., Saito, K. and Martin, C. (2007) Convergent evolution in the BAHD family of acyl transferases; identification and characterisation of anthocyanin acyl transferases from Arabidopsis thaliana. Plant J., 50:678-695

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

Tohge, T., Yonekura-Sakakibara, K., Niida, R., Watanabe-Takahashi, A. and Saito, K. (2007) Phytochemical genomics in Arabidopsis thaliana: A case study for functional identification of flavonoid biosynthesis genes. Pure and Applied Chemistry, 79, 811-823

Yonekura-Sakakibara, K., Tohge, T., Niida, R. and Saito, K. (2007) Identification of a flavonol 7-O-rhamnosyltransferase gene determining flavonoid pattern in Arabidopsis by transcriptome coexpression and reverse genetics. J Biol. Chem., 282, 14932-14941

Reviews and Book Chapters

Tohge, T., Nishiyama, Y., Hirai, M. Y., M., Yano, M., Nakajima, J., 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", pp. 159-168, Springer, Heidelberg.

Masaaki Noji and Kazuki Saito: Molecular and Biochemical Analysis of Serine Acetyltransferase and Cysteine Synthase. In "Application of Plant Metabolic Engineering", pp. 297-310, Springer, Dordrecht.

Asano, T., Sudo, H., Yamazaki, M. and Saito, K. (2007) Camptothecin production in cell cultures of Ophiorrhiza species.In "Medicinal Plant Biotechnology - From Basic Research to Industrial Applications", pp. 451-468, WILEY-VCH Verlag, Weinheim.

Press Releases

New study released on plant metabolism (10/Dec/2007)

2006

Original Papers

Noji, M., Cintia Goulart Kawashima, Obayashi, T. and Saito, K. (2006) In Silico assessment of gene function involved in cysteine biosynthesis in Arabidopsis: Expression analysis of multiple isoforms of serine acetyltransferase. Amino Acids, 30: 163-171

Nakajima, J., Sato, Y., Hoshino, T., Yamazaki, M. and Saito, K. (2006) Mechanistic study on the oxidation of anthocyanidin synthase by quantum mechanical calculation. J. Biol. Chem., 281: 21387-21398

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

Yano, M., Kanaya, S., Altaf-Ul-Amin, Md., Kurokawa, K., Hirai, M. Y. and Saito, K. (2006) Integrated data mining of transcriptome and metabolome based on BL-SOM. J. Comp. Aid. Chem., 7: 125-136

Maruyama-Nakashita, A., Nakamura, Y., Tohge, T., Saito, K. and Takahashi, H. (2006) Arabidopsis SLIM1 is a Central Transcriptional Regulator of Plant Sulfur Response and Metabolism. Plant Cell, 18: 3235-3251

Oikawa, A., Nakamura, Y., Ogura, T., Kimura, A., Suzuki, H., Sakurai, N., Shinbo, Y., Shibata, D., Kanaya, S. and Ohta, D. (2006). Clarification of Pathway Specific Inhibition by FT-ICR/MS-Based Metabolic Phenotyping Studies. Plant Physiol, 142: 398-413

Morikawa, T., Mizutani, M., Aoki, N., Watanabe, B., Saga, H., Saito, S., Oikawa, A., Suzuki, H., Sakurai, N., Shibata, D., Wadano A., Sakata K. and Ohta D. (2006). Cytochrome P450 CYP710A encodes the sterol C-22 desaturase in Arabidopsis and tomato. Plant Cell, 18: 1008-1022

Jonsson, P., Johansson, E.S., Wuolikainen, A., Lindberg, J., Schuppe-Koistinen, I., Kusano, M., Sjostrom, M., Trygg, J., Moritz, T., and Antti, H. (2006). Predictive metabolite profiling applying hierarchical multivariate curve resolution to GC-MS data-A potential tool for multi-parametric diagnosis. J. Proteome Res., 5: 1407-1414

Book Edition

Saito, K., Dixon , R.A., Willmitzer, L. eds. (2006). Biotechnology in Agriculture and Forestry 57 Plant Metabolomics, Springer Verlag, Heidelberg .

Reviews and Book Chapters

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”, pp. 199-209, Springer Verlag, Heidelberg .

Shinbo, Y., Nakamura, Y., Altaf-Ul-Amin, M., Asahi, H., Kurokawa, K., Arita, M., Saito, K., Ohta, D., Shibata, D. and Kanaya, S. (2006). KNApSAcK: A comprehensive species-metabolite relationship database, In “Biotechnology in Agriculture and Forestry 57 Plant Metabolomics”, pp. 165-181, Springer Verlag, Heidelberg .

Yonekura- Sakakibara, K. and Saito, K. (2006) Review: Genetically modified plants for the promotion of human health. Biotech Lett, 28, 1983-1991

Yamazaki, M. and Saito, K. (2006) Isolation and characterization of anthocyanin 5-O-glucosyltransefrase in Perilla frutescens var. crispa by differential display. Methods in Molecular Biology, vol. 317: Differential Display Methods and Protocols., Humana Press Inc. Totowa, NJ, 255-266

2005

Original Papers

Kitajima, M., Fujii, N., Yoshino, F., Sudo, H., Saito, K., Aimi, N. and Takayama, H. (2005) Camptothecins and two new monoterpene glucosides from Ophiorrhiza liukiuensis, Chem. Pharm. Bull., 53, 1355-1358

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

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

Awazuhara, M., Fujiwara, T., Hayashi, H., Watanabe-Takahashi, A., Takahashi, H. and Saito, K. (2005) The function of SULTR2;1 sulfate transporter during seed development in Arabidopsis thaliana, Physiol.Plant., 125, 95-105

Tokimatsu, T., Sakurai, N., Suzuki, H., Ohta, H., Nishitani, K., Koyama, T., Umezawa, T., Misawa, N., Saito, K. and Shibata, D. (2005) Kappa-View: A web-based analysis tool for integration of transcription and metabolite data on plant metabolic pathway maps, Plant Physiol., 138, 1289-1300

Tohge, T., Nishiyama, Y., Hirai, M.Y., Yano, M., Nakajima, J., Awazuhara, M., Inoue, E., Takahashi, H., Goodenowe, D.B., Kitayama, M., Noji, M., Yamazaki, M., and Saito, K. (2005) Functional genomics by integrated analysis of metabolome and transcriptome of Arabidopsis plants over-expressing an MYB transcription factor, Plant J., 42, 218-235

Tohge, T., Matsui, K., Ohme-Takagi, M., Yamazaki, M. and Saito, K. (2005) Enhanced radical scavenging activity of genetically modified Arabidopsis seeds, Biotech. Lett., 27, 297-303

Okada, T., Hirai, M.Y., Suzuki, H., Yamazaki, M. and Saito, K. (2005) Molecular characterization of a novel quinolizidine alkaloid O-tigloyltransferase: cDNA cloning, catalytic activity of recombinant protein and expression analysis in Lupinus plants, Plant Cell Physiol., 46, 233-244

Kawashima, C.G., Berkowitz, O., Hell, R., Noji, M. and Saito, K. (2005) Characterization and expression analysis of a serine acetyltransferase gene family involved in a key step of the sulfur assimilation pathway in Arabidopsis thaliana, Plant Physiol., 137, 220-230

Book Edition

Saito, K., De Kok, L.J., Stulen, I. , Hawkesford, M.J., Schnug, E., Sirko, A., Rennenberg, H. eds. (2005).“ Sulfur Transport and Assimilation in Plants in the Post Genomics Eras” Backhuys Publishers, Leiden .

Reviews and Book Chapters

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”, pp.195-197, Backhuys Publishers, Leiden .

Shinbo, Y., Nakamura, Y., Altaf-Ul-Amin, M., Asahi, H., Kurokawa, Suzuki, H, Sakurai, N., Oikawa, A., Kitayama, M., Yano, M., Hirai, M.Y., Saito, K., Ohta, D., Shibata, D. and Kanaya, S. (2005) KNApSAcK: Natural product database system for searching relationships between metabolites and species, In “Sulfur Transport and Assimilation in Plants in the Post Genomics Eras”, pp. 191-194, Backhuys Publishers, Leiden.

Sato, S., Naito, Y., Noji, M., Saito, K. and Tomita, M. (2005) Mathematical model of sulfur metabolism in higher plants using the E-Cell system, In “Sulfur Transport and Assimilation in Plants in the Post Genomics Eras”, pp. 187-189, Backhuys Publishers, Leiden .

Hirai, M.Y., Fujikawa, Y., Yano, M., Goodenowe, D.B., Yamazaki, Y., Kanaya, S., Nakamura, Y., Kitayama, M., Suzuki, H., Sakurai, N., Shibata, D. and Saito, K. (2005). Clustering of sulfur-assimilation genefamily members for comprehensive prediction of their functions, In “Sulfur Transport and Assimilation in Plants in the Post Genomics Eras”, pp. 183-186, 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”, pp. 179-182, 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”, pp. 177-178, Backhuys Publishers, Leiden .

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”, pp. 165-167, Backhuys Publishers, Leiden .

Watanabe, M., Noji, M., Kusano, M., Kato, T., Tabata, S. and Saito, K. (2005). Functional analysis of serine acetyltransferase genes (Serat) involved in sulfur assimilation in Arabidopsis thaliana, In “Sulfur Transport and Assimilation in Plants in the Post Genomics Eras”, pp. 99-101, Backhuys Publishers, Leiden .

Noji, M., Higashi, Y., Watanabe M. and Saito, K. (2005). T-DNA insertion mutant of ATP sulfurylase, the first enzyme of sulfur assimilatory metabolism, in Arabidopsis thaliana, In “Sulfur Transport and Assimilation in Plants in the Post Genomics Eras”, pp. 81-82, Backhuys Publishers, Leiden .

Yoshimoto, N., Saito, K. and Takahashi, H. (2005). High-affinity sulfate transporters in Arabidopsis : Physiological roles and regulation of transport activities, In “Sulfur Transport and Assimilation in Plants in the Post Genomics Eras”, pp. 37-38, Backhuys Publishers, Leiden .

Saito, K. (2005). Metabolome analysis of Arabidopsis thaliana, In “Metabolomics The Frontier of Systems Biology”, pp. 141-153, Springer Verlag, Tokyo .

Oksman-Caldentey, K.M., and Saito, K. (2005). Integrating genomics and metabolomics for engineering plant metabolic pathways, Curr. Opin. Biotech., 16, 174-179