Metabolic Systems Research Team

Laboratories

Publications

2017

Original Papers

Vergara, F., Rymen, B., Kuwahara, A., Sawada, Y., Sato, M. and Hirai, M.Y. (2017) Autopolyploidization, geographic origin, and metabolome evolution in Arabidopsis thaliana.Am. J. Bot., 104(5), DOI: 10.3732/ajb.1600419.

Abstract

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

Abstract

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

Abstract

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

Abstract

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

Abstract

▲page top

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.

Abstract

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

Abstract

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

Abstract

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

Abstract

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

Abstract

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

Abstract PDF

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

Abstract PDF

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

Abstract

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

Abstract

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

Abstract

▲page top

2015

Original Papers

Hayakawa, Y., Tachikawa, M. and Mochizuki, A. (2015) Mathematical study for the mechanism of vascular and spot patterns by auxin and PIN dynamics in plant development. J. Theor. Biol., 365 : 12-22., DOI: 10.1016/j.jtbi.2014.09.039. (Epub 2014 Oct 7.)

Abstract

Mochizuki, A. and Fiedler B. (2015) Sensitivity of chemical reaction networks: a structural approach. 1. Examples and the carbon metabolic network. J. Theor. Biol., 367 : 189-202., DOI: 10.1016/j.jtbi.2014.10.025. (Epub 2014 Nov 13.)

Abstract

Kawade, K. and Tanimoto, H. (2015) Mobility of signaling molecules: the key to deciphering plant organogenesis. J. Plant Res., 128 : 17-25., DOI: 10.1007/s10265-014-0692-5. (Epub 2014 Dec 17.)

Abstract

Hisanaga, T., Kawade, K. and Tsukaya, H. (2015) Compensation: a key to clarifying the organ-level regulation of lateral organ size in plants. J. Exp. Bot., 66 : 1055-1063., DOI: 10.1093/jxb/erv028. (Epub 2015 Jan 29.)

Abstract

Zargar SM, Kurata R, Inaba S, Oikawa A, Fukui R, Ogata Y, Agrawal GK, Rakwal R and Fukao Y. (2015) Quantitative proteomics of Arabidopsis shoot microsomal proteins reveals a cross-talk between excess zinc and iron deficiency. Proteomics., 15 : 1196-1201., DOI: 10.1002/pmic.201400467. (Epub 2015 Mar 2.)

Abstract

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

Abstract

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

Abstract

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

Abstract

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

Abstract

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

Abstract

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

Abstract

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

Abstract

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

Abstract

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

Abstract

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

Abstract

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

Abstract

▲page top