A5038913847- Plant nutrient uptake and metabolism
- Photosynthetic Processes and Mechanisms
- Nitrogen and Sulfur Effects on Brassica
- Plant Molecular Biology Research
- Genomics, phytochemicals, and oxidative stress
- Metabolomics and Mass Spectrometry Studies
- Microbial Metabolic Engineering and Bioproduction
- Plant Gene Expression Analysis
- Plant Stress Responses and Tolerance
- Lipid metabolism and biosynthesis
- Algal biology and biofuel production
- Physics of Superconductivity and Magnetism
- Plant biochemistry and biosynthesis
- Plant responses to water stress
- Bioinformatics and Genomic Networks
- Legume Nitrogen Fixing Symbiosis
- Microbial Community Ecology and Physiology
- Plant tissue culture and regeneration
- Garlic and Onion Studies
- Genetic Mapping and Diversity in Plants and Animals
- Soybean genetics and cultivation
- Phytase and its Applications
- Plant Parasitism and Resistance
- Genomics and Phylogenetic Studies
- Pharmacy and Medical Practices
RIKEN Center for Sustainable Resource Science
2016-2025
Nagoya University
2018-2025
RIKEN
2024
Mitsubishi Tanabe Pharma Corporation
2017
Odense University Hospital
2016
Japan Science and Technology Agency
2003-2013
University of Tokyo Hospital
2010-2013
Plant (United States)
2009-2013
Chiba University
1984-2009
University of Toronto
2009
Abstract MassBank is the first public repository of mass spectra small chemical compounds for life sciences (<3000 Da). The database contains 605 electron‐ionization spectrometry(EI‐MS), 137 fast atom bombardment MS and 9276 electrospray ionization (ESI)‐MS n data 2337 authentic metabolites, 11 545 EI‐MS 834 other‐MS 10 286 volatile natural synthetic compounds, 3045 ESI‐MS 2 679 drugs contributed by 16 research groups (January 2010). were analyzed under nonstandardized, independent...
Summary The integration of metabolomics and transcriptomics can provide precise information on gene‐to‐metabolite networks for identifying the function unknown genes unless there has been a post‐transcriptional modification. Here, we report comprehensive analysis metabolome transcriptome Arabidopsis thaliana over‐expressing PAP1 gene encoding an MYB transcription factor, identification novel functions involved in flavonoid biosynthesis. For analysis, performed flavonoid‐targeted by...
Plant metabolism is a complex set of processes that produce wide diversity foods, woods, and medicines. With the genome sequences Arabidopsis rice in hands, postgenomics studies integrating all “omics” sciences can depict precise pictures whole-cellular process. Here, we present, to our knowledge, first report investigation for gene-to-metabolite networks regulating sulfur nitrogen nutrition secondary , with integration metabolomics transcriptomics. Transcriptome metabolome analyses were...
Understanding plant metabolism as an integrated system is essential for metabolic engineering aimed at the effective production of compounds useful to human life and global environment. The “omics” approach integrates transcriptome metabolome data into a single set can lead identification unknown genes their regulatory networks involved in pathways interest. One intriguing, although poorly described plants biosynthesis glucosinolates (GSLs), group bioactive secondary products derived from...
Summary We analyzed global gene expression in Arabidopsis response to various hormones and related experiments as part of the AtGenExpress project. The experimental agents included seven basic phytohormones (auxin, cytokinin, gibberellin, brassinosteroid, abscisic acid, jasmonate ethylene) their inhibitors. In addition, was investigated hormone‐related mutants during seed germination sulfate starvation. Hormone‐inducible genes were identified from hormone data. effects each relevance lists...
Since the completion of genome sequences model organisms, functional identification unknown genes has become a principal challenge in biology. Post-genomics sciences such as transcriptomics, proteomics, and metabolomics are expected to discover gene functions. This report outlines elucidation gene-to-gene metabolite-to-gene networks via integration with transcriptomics presents strategy for novel Metabolomics data Arabidopsis grown under sulfur deficiency were combined analyzed by...
The 7S seed storage protein (β-conglycinin) of soybean (Glycine max [L]. Merr.) has three major subunits; α, α′, and β. Accumulation the β-subunit, but not α- α′-subunits, been shown to be repressed by exogenously applied methionine immature cotyledon culture system (LP Holowach, JF Thompson, JT Madison [1984] Plant Physiol 74: 576-583) enhanced under sulfate deficiency in plants (KR Gayler, GE Sykes [1985] 78: 582-585). Transgenic petunia (Petunia hybrida) harboring either α′- or β-subunit...
Summary Jasmonic acid (JA) and methyl jasmonate (MeJA), collectively termed jasmonates, are ubiquitous plant signalling compounds. Several types of stress conditions, such as wounding pathogen infection, cause endogenous JA accumulation the expression jasmonate‐responsive genes. Although jasmonates important components for response in plants, mechanism by which contributes to tolerance has not been clearly defined. A comprehensive analysis jasmonate‐regulated metabolic pathways Arabidopsis...
The fragment pattern analysis of tandem mass spectrometry (MS/MS) has long been used for the structural characterization metabolites. construction a plant-specific MS/MS data resource and database will enable complex phytochemical structures to be narrowed down candidate structures. Therefore, web-based pertaining phytochemicals was developed named ReSpect (RIKEN spectral database). Of 3595 metabolites in ReSpect, 76% were derived from 163 literature reports, whereas rest obtained authentic...
Metabolomics is an 'omics' approach that aims to analyze all metabolites in a biological sample comprehensively. The detailed metabolite profiling of thousands plant samples has great potential for directly elucidating metabolic processes. However, both comprehensive analysis and high throughput are difficult achieve at the same time due wide diversity plants. Here, we have established novel practical metabolomics methodology quantifying hundreds targeted high-throughput manner. Multiple...
Phosphorus supply is a major factor responsible for reduced crop yields. As result, plants utilize various adaptive mechanisms against phosphorus depletion, including lipid remodelling. Here we report the involvement of novel plant lipid, glucuronosyldiacylglycerol, depletion. Lipidomic analysis Arabidopsis cultured in phosphorus-depleted conditions revealed inducible accumulation glucuronosyldiacylglycerol. Investigation using series sulfolipid sulfoquinovosyldiacylglycerol...
Plants incorporate acquired carbon and nitrogen into amino acid metabolism, whereby the building blocks of proteins precursors various metabolites are produced. This fundamental demand requires tight metabolism to sustain physiological homeostasis. There is increasing evidence that undergoes plastic alteration orchestrate specific growth developmental events. Consequently, there has been a gradual exploration interface at which plant morphogenesis mutually affected. research progress offers...
Summary To investigate the changes in profiles of mRNA accumulation response to sulfur deficiency, approximately 13 000 non‐redundant Arabidopsis thaliana ESTs corresponding 9000 genes were analyzed using DNA macroarray. Three‐week‐old plants grown on an agarose‐solidified control medium transferred a sulfate‐free and for 48 h analyses sulfur‐related metabolites global gene expression profiles. Concentrations sulfate, O ‐acetyl‐ l ‐serine (OAS), positive regulator deficiency‐responsive...
Abstract Plants synthesize a sulfur-containing lipid, sulfoquinovosyldiacylglycerol, which is one of three nonphosphorus glycerolipids that provide the bulk structural lipids in photosynthetic membranes. Here, identification novel gene, UDP-glucose pyrophosphorylase3 (UGP3), required for sulfolipid biosynthesis described. Transcriptome coexpression analysis demonstrated highly correlated expression UGP3 with known genes Arabidopsis thaliana. Liquid chromatography–mass spectrometry leaf two...
Abstract The circadian clock controls physiological traits such as flowering time, photosynthesis, and growth in plants under laboratory conditions. Under natural field conditions, however, little is known about the significance of plants. By time-course transcriptome analyses rice (Oryza sativa) leaves, using a newly isolated clock–related mutant carrying null mutation Os-GIGANTEA (Os-GI), we show here that Os-GI controlled 75% (false discovery rate = 0.05) genes among 27,201 tested was...
PRIMe (http://prime.psc.riken.jp/), the Platform for RIKEN Metabolomics, is a Web site that has been designed and implemented to support research analysis workflows ranging from metabolome transcriptome analysis. The provides access growing collection of standardized measurements metabolites obtained by using NMR, GC-MS, LC-MS, CE-MS, metabolomics tools related analyses (SpinAssign identification means KNApSAcK searches within metabolite databases). In addition, transcriptomics provide...
Summary Plant secondary metabolites are known to facilitate interactions with a variety of beneficial and detrimental organisms, yet the contribution specific fungal pathogens is poorly understood. Here we show that, respect aliphatic glucosinolate‐derived isothiocyanates, toxicity against pathogenic ascomycete Sclerotinia sclerotiorum depends on side chain structure. Genes associated formation camalexin glucosinolate were induced in Arabidopsis thaliana leaves challenged necrotrophic...
Plants possess many metabolic genes for the production of a wide variety phytochemicals in tissue-specific manner. However, systems behind diversity and tissue-dependent regulation still remain unknown due to incomplete characterization produced single plant species. Thus, having metabolome dataset addition genome transcriptome information resources would enrich our knowledge secondary metabolism. Here we analyzed phytochemical accumulation during development model Arabidopsis (Arabidopsis...
Upstream open reading frames (uORFs) are often translated ahead of the main ORF a gene and regulate expression, sometimes in condition-dependent manner, but such role for minimum uORF (hereafter referred to as AUG-stop) living organisms is currently unclear. Here, we show that AUG-stop plays an important boron (B)-dependent regulation NIP5;1, encoding boric acid channel required normal growth under low B conditions Arabidopsis thaliana. High enhanced ribosome stalling at AUG-stop, which was...
Because cyanobacteria directly harvest CO2 and light energy, their carbon metabolism is important for both basic applied sciences. Here, we show that overexpression of the sigma factor sigE in Synechocystis sp. PCC 6803 widely changes sugar catabolism increases production biodegradable polyester polyhydroxybutyrate (PHB) during nitrogen starvation. elevates levels proteins implicated glycogen catabolism, oxidative pentose phosphate pathway, polyhydroxyalkanoate biosynthesis. PHB accumulation...
Specialized (secondary) metabolic pathways in plants have long been considered one-way routes of leading primary metabolite precursors to bioactive end products. Conversely, endogenous degradation such “end” products plant tissues has observed following environmental stimuli, including nutrition stress. Therefore, it is general interest whether specialized metabolites can be reintegrated into metabolism recover the invested resources, especially case nitrogen- or sulfur-rich compounds. Here,...
Abstract Plant cell culture has multiple applications in biotechnology and horticulture, from plant propagation to the production of high-value biomolecules. However, interplay between cellular diversity ambient conditions influences metabolism cultured tissues; understanding these factors detail will inform efforts optimize conditions. This study presents multiomics datasets callus cultures tobacco ( Nicotiana tabacum ), rice Oryza sativa two bamboo species Phyllostachys nigra P....