AtMetExpress Development: A Phytochemical Atlas of Arabidopsis Development
Open Access
- 18 December 2009
- journal article
- Published by Oxford University Press (OUP) in Plant Physiology
- Vol. 152 (2), 566-578
- https://doi.org/10.1104/pp.109.148031
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.Keywords
This publication has 63 references indexed in Scilit:
- Discovery and revision of Arabidopsis genes by proteogenomicsProceedings of the National Academy of Sciences, 2008
- Metabolomics approach for determining growth-specific metabolites based on Fourier transform ion cyclotron resonance mass spectrometryAnalytical and Bioanalytical Chemistry, 2008
- Characterization of Arabidopsis thaliana Pinoresinol Reductase, a New Type of Enzyme Involved in Lignan BiosynthesisJournal of Biological Chemistry, 2008
- Decoding genes with coexpression networks and metabolomics – ‘majority report by precogs’Trends in Plant Science, 2008
- Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesisProceedings of the National Academy of Sciences, 2007
- ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in ArabidopsisNucleic Acids Research, 2006
- [9] TM4 Microarray Software SuiteMethods in Enzymology, 2006
- BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological NetworksBioinformatics, 2005
- A gene expression map of Arabidopsis thaliana developmentNature Genetics, 2005
- NASCArrays: a repository for microarray data generated by NASC's transcriptomics serviceNucleic Acids Research, 2004