Overview of PRIMe Project

We are responsible for building a research platform aimed at improving plant production capabilities in both quantitative and qualitative terms, based on integrated genome sciences founded on metabolome research. We perform comprehensive analyses of gene expression and exhaustive metabolite analyses, using model plants, such as Arabidopsis, and plants in practical use, such as crops and medicinal plants. Using this information, we investigate metabolism-related functions in plant physiological responses and growth processes, with the objective of identifying new and useful gene function and networks. In addition, we focus on bioinformatics analyses, in order to integrate metabolomes, transcriptomes, and proteomes, with the aim of a systematic analysis of plants.

Metabolomics involves the identification and quantification of all metabolites in a cell and correlating these to genomic functions. Metabolites in the plant kingdom are extremely diverse chemically, with estimates indicating as many as 200,000 different types of chemical substances.

We take an advantage of combination of several different mass spectroscopic methods and advanced multi-dimensional NMR technologies for metabolome analysis. In our study we enforce the development of bio-informatics aiming for integrated analysis of metabolomics and transcriptomics.

Research content and procedures
  • We perform high-throughput metabolite analyses and develop technologies for the comprehensive analysis of metabolites, mainly using high-resolution mass spectrometry. We also collaborate with other research teams within and outside the Center on non-targeted analyses and the identification of unknown gene functions.
  • We obtain metabolome and transcriptome data of wild-type and mutant plants of Arabidopsis grown under various conditions. We collaborate with other research teams to develop the software for metabolome and transcriptome analyses. We elucidate unknown gene function via systems-based analysis of plant metabolism.
  • We intend to initiate an NMR-based metabomics by developing new methods using a hetero-nuclear NMR approach, such as high quantification, non-invasive measurements, localized spectroscopy in vivo, selectivity of nuclear environments, versatility of pre- treatments of the samples, and validity of structure analysis of diverse biomolecules including stereo-isomers. This will be achieved by uniform stable isotope labeling of higher plants allowing application of multi-dimensional NMR experiments used in protein structure determination.
  • We aim at integrating comprehensive genome information and promote the research platform implementation from the aspect of IT such as database construction, and also perform comparative genomics approaches using genome information of various species, and develop data mining for the purpose.
  • We will develop the platform software necessary for metabolomic analyses, network analyses, and simulations. We are also constructing a database that can deal with unidentified metabolites. The software developed will be applied to integrated analysis of metabolomic and transcriptomic data collated by other teams to enable a systematic understanding of plants.
Research plan
  • Metabolomic analysis and technology development by mass spectrometry
  • Metabolomic analysis and technology development by NMR
  • Further development of labeling technology by stable isotopes
  • Metabolomics analysis of mutants and transgenic lines of Arabidopsis and rice
  • Discovery of gene-to-metabolite networks by integrated analysis with transcriptomics
  • Initiation of plant systems biology
  • Development of software for metabolome analysis
  • Development of software for network analysis
  • Construction of metabolome and related database
RIKEN Center for Sustainable Resource Science
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