11 results on '"Hirai, Masami Y."'
Search Results
2. AtMetExpress Development: A Phytochemical Atlas of Arabidopsis Development.
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Matsuda, Fumio, Hirai, Masami Y., Sasaki, Eriko, Akiyama, Kenji, Yonekura-Sakakibara, Keiko, Provart, Nicholas J., Sakurai, Tetsuya, Shimada, Yukihisa, and Saito, Kazuki
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PLANT development , *ARABIDOPSIS thaliana , *BIOLOGICAL systems , *LIQUID chromatography , *PHYTOCHEMICALS , *PLANT metabolism - Abstract
Plants possess many metabolic genes for the production of a wide variety of phytochemicals in a tissue-specific manner. However, the metabolic systems behind the diversity and tissue-dependent regulation still remain unknown due to incomplete characterization of phytochemicals produced in a single plant species. Thus, having a metabolome dataset in addition to the genome and transcriptome information resources would enrich our knowledge of plant secondary metabolism. Here we analyzed phytochemical accumulation during development of the model plant Arabidopsis (Arabidopsis thaliana) using liquid chromatography-mass spectrometry in samples covering many growth stages and organs. We also obtained tandem mass spectrometry spectral tags of many metabolites as a resource for elucidation of metabolite structure. These are part of the AtMetExpress metabolite accumulation atlas. Based on the dataset, we detected 1,589 metabolite signals from which the structures of 167 metabolites were elucidated. The integrated analyses with transcriptome data demonstrated that Arabidopsis produces various phytochemicals in a highly tissue-specific manner, which often accompanies the expression of key biosynthesis-related genes. We also found that a set of biosynthesis-related genes is coordinately expressed among the tissues. These data suggested that the simple mode of regulation, transcript to metabolite, is an origin of the dynamics and diversity of plant secondary metabolism. [ABSTRACT FROM AUTHOR]
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- 2010
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3. Decoding genes with coexpression networks and metabolomics – ‘majority report by precogs’
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Saito, Kazuki, Hirai, Masami Y., and Yonekura-Sakakibara, Keiko
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MEDICINAL plants , *MOLECULAR genetics , *USEFUL plants , *ARABIDOPSIS , *GENOMICS , *PLANT biotechnology , *TECHNOLOGY transfer - Abstract
Following the sequencing of whole genomes of model plants, high-throughput decoding of gene function is a major challenge in modern plant biology. In view of remarkable technical advances in transcriptomics and metabolomics, integrated analysis of these ‘omics’ by data-mining informatics is an excellent tool for prediction and identification of gene function, particularly for genes involved in complicated metabolic pathways. The availability of Arabidopsis public transcriptome datasets containing data of >1000 microarrays reinforces the potential for prediction of gene function by transcriptome coexpression analysis. Here, we review the strategy of combining transcriptome and metabolome as a powerful technology for studying the functional genomics of model plants and also crop and medicinal plants. [Copyright &y& Elsevier]
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- 2008
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4. Skotomorphogenesis exploits threonine to promote hypocotyl elongation.
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Hiromitsu Tabeta, Yasuhiro Higashi, Yozo Okazaki, Kiminori Toyooka, Mayumi Wakazaki, Mayuko Sato, Kazuki Saito, Hirai, Masami Y., and Ferjani, Ali
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HYPOCOTYLS , *SEED storage , *ARABIDOPSIS , *PLANT metabolism , *METABOLOMICS , *PLANT cell microbodies - Abstract
Mobilisation of seed storage reserves is important for seedling establishment in Arabidopsis. In this process, sucrose is synthesised from triacylglycerol via core metabolic processes. Mutants with defects in triacylglycerol-to-sucrose conversion display short etiolated seedlings. We found that whereas sucrose content in the indole-3-butyric acid response 10 (ibr10) mutant was significantly reduced, hypocotyl elongation in the dark was unaffected, questioning the role of IBR10 in this process. To dissect the metabolic complexity behind cell elongation, a quantitative-based phenotypic analysis combined with a multi-platform metabolomics approach was applied. We revealed that triacylglycerol and diacylglycerol breakdown were disrupted in ibr10, resulting in low sugar content and poor photosynthetic ability. Importantly, batch-learning self-organised map clustering revealed that threonine level was correlated with hypocotyl length. Consistently, exogenous threonine supply stimulated hypocotyl elongation, indicating that sucrose levels are not always correlated with etiolated seedling length, suggesting the contribution of amino acids in this process. [ABSTRACT FROM AUTHOR]
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- 2022
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5. Changes in mRNA Stability Associated with Cold Stress in Arabidopsis Cells.
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Chiba, Yukako, Mineta, Katsuhiko, Hirai, Masami Y., Suzuki, Yuya, Kanaya, Shigehiko, Takahashi, Hiro, Onouchi, Hitoshi, Yamaguchi, Junji, and Naito, Satoshi
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MESSENGER RNA , *PHYSIOLOGICAL effects of cold temperatures , *ARABIDOPSIS , *PLANT cytology , *PLANT RNA , *PLANT genomes , *PENTATRICOPEPTIDE repeat genes - Abstract
Control of mRNA half-life is a powerful strategy to adjust individual mRNA levels to various stress conditions, because the mRNA degradation rate controls not only the steady-state mRNA level but also the transition speed of mRNA levels. Here, we analyzed mRNA half-life changes in response to cold stress in Arabidopsis cells using genome-wide analysis, in which mRNA half-life measurements and transcriptome analysis were combined. Half-lives of average transcripts were determined to be elongated under cold conditions. Taking this general shift into account, we identified more than a thousand transcripts that were classified as relatively stabilized or relatively destabilized. The relatively stabilized class was predominantly observed in functional categories that included various regulators involved in transcriptional, post-transcriptional and post-translational processes. On the other hand, the relatively destabilized class was enriched in categories related to stress and hormonal response proteins, supporting the idea that rapid decay of mRNA is advantageous for swift responses to stress. In addition, pentatricopeptide repeat, cyclin-like F-box and Myb transcription factor protein families were significantly over-represented in the relatively destabilized class. The global analysis presented here demonstrates not only the importance of mRNA turnover control in the cold stress response but also several structural characteristics that might be important in the control of mRNA stability. [ABSTRACT FROM AUTHOR]
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- 2013
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6. Autopolyploidization, geographic origin, and metabolome evolution in Arabidopsis thaliana.
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Vergara, Fredd, Rymen, Bart, Kuwahara, Ayuko, Sawada, Yuji, Sato, Muneo, and Hirai, Masami Y.
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ARABIDOPSIS thaliana genetics , *PLANT evolution , *METABOLOMICS - Abstract
PREMISE OF THE STUDY:: Autopolyploidy, or whole‐genome duplication, is a recurrent phenomenon in plant evolution. Its existence can be inferred from the presence of massive levels of genetic redundancy revealed by comparative plant phylogenomics. Whole‐genome duplication is theoretically associated with evolutionary novelties such as the development of new metabolic reactions and therefore contributes to the evolution of new plant metabolic profiles. However, very little is yet known about the impact of autopolyploidy on the metabolism of recently formed autopolyploids. This study provides a better understanding of the relevance of this evolutionary process. METHODS:: In this study, we compared the metabolic profiles of wild diploids, wild autotetraploids, and artificial autotetraploids of Arabidopsis thaliana using targeted ultra‐high performance liquid chromatography‐triple quadrupole‐ mass spectrometry (UPLC‐QqQ‐MS) metabolomics. KEY RESULTS:: We found that wild and artificial A. thaliana autotetraploids display different metabolic profiles. Furthermore, wild autotetraploids display unique metabolic profiles associated with their geographic origin. CONCLUSIONS:: Autopolyploidy might help plants adapt to challenging environmental conditions by allowing the evolution of novel metabolic profiles not present in the parental diploids. We elaborate on the causes and consequences leading to these distinct profiles. [ABSTRACT FROM AUTHOR]
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- 2017
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7. Investigation of kinetic-order sensitivities in metabolic reaction networks.
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Yamada, Masatsugu, Iwanaga, Masashi, Sriyudthsak, Kansuporn, Hirai, Masami Y., and Shiraishi, Fumihide
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POWER law (Mathematics) , *DIFFERENTIAL equations , *STEADY state conduction , *ANALYTICAL mechanics , *SIMULATION methods & models - Abstract
Kinetic-order sensitivity (the ratio of relative change in a dependent variable to the relative change in a kinetic order in a power-law–type differential equation) has recently become an important indicator in metabolic pathway analysis using mathematical models with parameter values determined from time-series data on cellular metabolite concentrations. Here, we discuss a potential problem in calculating kinetic-order sensitivities. When the steady-state metabolite concentration is less than unity, a slight increase in the kinetic order changes the metabolite concentration in the incorrect direction, yielding a kinetic-order sensitivity value with an incorrect sign. This is caused by a property of the power-law function ( y = X n ): when X is less than unity, y decreases for a larger positive n or for a smaller absolute value of negative n . We propose two solutions. The first is to directly calculate the kinetic-order sensitivities and then reverse the sign of the relevant value if a steady-state metabolite concentration less than unity is involved. The second involves calculation of the kinetic-order sensitivities after setting all metabolite concentrations to values greater than unity (e.g., by changing the units from mM to μM). The latter method changes the absolute values of the kinetic-order sensitivities according to the magnitude of a multiplication factor, because kinetic-order sensitivities do not have unique values. Nevertheless, since the normalized absolute values exhibit an almost identical distribution, it should not be difficult to identify which kinetic order has greater effect, although kinetic order rankings may change slightly under different calculation conditions. [ABSTRACT FROM AUTHOR]
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- 2017
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8. SS-mPMG and SS-GA: Tools for Finding Pathways and Dynamic Simulation of Metabolic Networks.
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Katsuragi, Tetsuo, Ono, Naoaki, Yasumoto, Keiichi, Altaf-Ul-Amin, Md., Hirai, Masami Y., Sriyudthsak, Kansuporn, Sawada, Yuji, Yamashita, Yui, Chiba, Yukako, Onouchi, Hitoshi, Fujiwara, Toru, Naito, Satoshi, Shiraishi, Fumihide, and Kanaya, Shigehiko
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METABOLOMICS , *PLANT cells & tissues , *GENETIC algorithms , *DYNAMIC simulation , *ARABIDOPSIS thaliana , *BIOINFORMATICS , *BIOSYNTHESIS - Abstract
Metabolomics analysis tools can provide quantitative information on the concentration of metabolites in an organism. In this paper, we propose the minimum pathway model generator tool for simulating the dynamics of metabolite concentrations (SS-mPMG) and a tool for parameter estimation by genetic algorithm (SS-GA). SS-mPMG can extract a subsystem of the metabolic network from the genome-scale pathway maps to reduce the complexity of the simulation model and automatically construct a dynamic simulator to evaluate the experimentally observed behavior of metabolites. Using this tool, we show that stochastic simulation can reproduce experimentally observed dynamics of amino acid biosynthesis in Arabidopsis thaliana. In this simulation, SS-mPMG extracts the metabolic network subsystem from published databases. The parameters needed for the simulation are determined using a genetic algorithm to fit the simulation results to the experimental data. We expect that SS-mPMG and SS-GA will help researchers to create relevant metabolic networks and carry out simulations of metabolic reactions derived from metabolomics data. [ABSTRACT FROM AUTHOR]
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- 2013
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9. Prediction of operon-like gene clusters in the Arabidopsis thaliana genome based on co-expression analysis of neighboring genes
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Wada, Masayoshi, Takahashi, Hiroki, Altaf-Ul-Amin, Md., Nakamura, Kensuke, Hirai, Masami Y., Ohta, Daisaku, and Kanaya, Shigehiko
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ARABIDOPSIS thaliana , *OPERONS , *EUKARYOTES , *AVENACINS , *GENE expression in plants , *PLANT genomes - Abstract
Abstract: Operon-like arrangements of genes occur in eukaryotes ranging from yeasts and filamentous fungi to nematodes, plants, and mammals. In plants, several examples of operon-like gene clusters involved in metabolic pathways have recently been characterized, e.g. the cyclic hydroxamic acid pathways in maize, the avenacin biosynthesis gene clusters in oat, the thalianol pathway in Arabidopsis thaliana, and the diterpenoid momilactone cluster in rice. Such operon-like gene clusters are defined by their co-regulation or neighboring positions within immediate vicinity of chromosomal regions. A comprehensive analysis of the expression of neighboring genes therefore accounts a crucial step to reveal the complete set of operon-like gene clusters within a genome. Genome-wide prediction of operon-like gene clusters should contribute to functional annotation efforts and provide novel insight into evolutionary aspects acquiring certain biological functions as well. We predicted co-expressed gene clusters by comparing the Pearson correlation coefficient of neighboring genes and randomly selected gene pairs, based on a statistical method that takes false discovery rate (FDR) into consideration for 1469 microarray gene expression datasets of A. thaliana. We estimated that A. thaliana contains 100 operon-like gene clusters in total. We predicted 34 statistically significant gene clusters consisting of 3 to 22 genes each, based on a stringent FDR threshold of 0.1. Functional relationships among genes in individual clusters were estimated by sequence similarity and functional annotation of genes. Duplicated gene pairs (determined based on BLAST with a cutoff of E <10−5) are included in 27 clusters. Five clusters are associated with metabolism, containing P450 genes restricted to the Brassica family and predicted to be involved in secondary metabolism. Operon-like clusters tend to include genes encoding bio-machinery associated with ribosomes, the ubiquitin/proteasome system, secondary metabolic pathways, lipid and fatty-acid metabolism, and the lipid transfer system. [Copyright &y& Elsevier]
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- 2012
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10. Role of camalexin, indole glucosinolates, and side chain modification of glucosinolate-derived isothiocyanates in defense of Arabidopsis against Sclerotinia sclerotiorum.
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Stotz, Henrik U., Sawada, Yuji, Shimada, Yukihisa, Hirai, Masami Y., Sasaki, Eriko, Krischke, Markus, Brown, Paul D., Saito, Kazuki, and Kamiya, Yuji
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INDOLE , *GLUCOSINOLATES , *ARABIDOPSIS thaliana , *SCLEROTINIA sclerotiorum , *METABOLITES , *ANTI-infective agents , *HOST plants - Abstract
Summary Plant secondary metabolites are known to facilitate interactions with a variety of beneficial and detrimental organisms, yet the contribution of specific metabolites to interactions with fungal pathogens is poorly understood. Here we show that, with respect to aliphatic glucosinolate-derived isothiocyanates, toxicity against the pathogenic ascomycete Sclerotinia sclerotiorum depends on side chain structure. Genes associated with the formation of the secondary metabolites camalexin and glucosinolate were induced in Arabidopsis thaliana leaves challenged with the necrotrophic pathogen S. sclerotiorum. Unlike S. sclerotiorum, the closely related ascomycete Botrytis cinerea was not identified to induce genes associated with aliphatic glucosinolate biosynthesis in pathogen-challenged leaves. Mutant plant lines deficient in camalexin, indole, or aliphatic glucosinolate biosynthesis were hypersusceptible to S. sclerotiorum, among them the myb28 mutant, which has a regulatory defect resulting in decreased production of long-chained aliphatic glucosinolates. The antimicrobial activity of aliphatic glucosinolate-derived isothiocyanates was dependent on side chain elongation and modification, with 8-methylsulfinyloctyl isothiocyanate being most toxic to S. sclerotiorum. This information is important for microbial associations with cruciferous host plants and for metabolic engineering of pathogen defenses in cruciferous plants that produce short-chained aliphatic glucosinolates. [ABSTRACT FROM AUTHOR]
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- 2011
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11. Genetic Variation for Seed Metabolite Levels in Brachypodium distachyon.
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Onda, Yoshihiko, Inoue, Komaki, Sawada, Yuji, Shimizu, Minami, Takahagi, Kotaro, Uehara-Yamaguchi, Yukiko, Hirai, Masami Y., Garvin, David F., and Mochida, Keiichi
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BRACHYPODIUM , *METABOLITES , *METABOLOMICS , *VITAMIN B6 , *VITAMIN metabolism - Abstract
Metabolite composition and concentrations in seed grains are important traits of cereals. To identify the variation in the seed metabolotypes of a model grass, namely Brachypodium distachyon, we applied a widely targeted metabolome analysis to forty inbred lines of B. distachyon and examined the accumulation patterns of 183 compounds in the seeds. By comparing the metabolotypes with the population structure of these lines, we found signature metabolites that represent different accumulation patterns for each of the three B. distachyon subpopulations. Moreover, we found that thirty-seven metabolites exhibited significant differences in their accumulation between the lines Bd21 and Bd3-1. Using a recombinant inbred line (RIL) population from a cross between Bd3-1 and Bd21, we identified the quantitative trait loci (QTLs) linked with this variation in the accumulation of thirteen metabolites. Our metabolite QTL analysis illustrated that different genetic factors may presumably regulate the accumulation of 4-pyridoxate and pyridoxamine in vitamin B6 metabolism. Moreover, we found two QTLs on chromosomes 1 and 4 that affect the accumulation of an anthocyanin, chrysanthemin. These QTLs genetically interacted to regulate the accumulation of this compound. This study demonstrates the potential for metabolite QTL mapping in B. distachyon and provides new insights into the genetic dissection of metabolomic traits in temperate grasses. [ABSTRACT FROM AUTHOR]
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- 2019
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