Plant Secondary Metabolism

Associate Professor
Takayuki TOHGE
Assistant Professor
Takafumi SHIMIZU
Labs HP

Outline of Research and Education

Plant secondary metabolism (also called “specialized metabolism”) produces compounds having several bioactivities such as resistance factors against various environmental stresses in plants, as well as health benefits for humans. Secondary metabolites are widely diversified in their chemical structures in nature (Fig. 1), since plants have adapted to environmental niches during long evolutionary periods using varied strategies such as gene duplication and convergent evolution of some key genes which contribute to chemical diversity. The Plant Secondary Metabolism Laboratory focuses on, i) the analysis of the natural diversity of secondary metabolites, and ii) the functional genomics approach for metabolic genes using translational analysis of omics studies (genomics, transcriptomics and mass spectrometry-based metabolomics). The specific goal is the identification of key factors of natural chemical diversity and regulatory roles in plant secondary metabolism which enable genome wide metabolic cross-species comparison for metabolic engineering of beneficial compounds.

Major Research Topics

Functional genomics approach by omics-based translational analysis

Currently, after completion of full-genome sequencing of over 100 plant species, the complete biosynthetic framework needs to be applied for integrative approaches with other omics data such as genomics and transcriptomics. However, genome information is not sufficient to compute the size and framework of a species’ metabolism. Therefore, we screen qualitative differences of metabolite levels between tissues, stress treatments and wild accessions for “elucidation of biosynthetic framework” based on gene expression levels predicted from metabolite data (Fig. 2).On the other hand, recent technical developments allowing affordable whole genome sequencing, omics studies and availability of several resources such as knockout mutant library, quantitative trait locus (QTL) lines and wild accessions, have resulted in a dramatic increase in the number of approaches such as metabolic phenotype screening, network/modeling analysis, QTL and genome-wide association studies (GWAS). We employed these approaches supported by metabolomic studies to refine biosynthetic framework of plant secondary metabolism including natural variance, tissue and species specificity, in order to discover key genes involved in the creation of chemical diversity.

Cross species comparison on the neo-functionalized genomic region

Recent technical developments allowing reasonable whole genome sequencing as well as a better inventory of species-by-species chemical diversity have greatly advanced our understanding as to how these pathways vary across species. The range of genetics based strategies for characterization of key genes described above provide several genes and genomic regions involved in neo-functionalization of plant secondary metabolism. We therefore focus on the species specific duplicated genes in these key syntenic regions in order to find neo-functionalized genes having novel functions in plant secondary metabolism.


  1. Tohge et al., Plant J., 42, 218-235, 2005
  2. Yonekura-Sakakibara., Tohge. et al., Plant Cell, 20., 2160-2176., 2008
  3. Tohge & Fernie., Nat Protoc., 5., 1210-1227., 2010
  4. Alejandro et al., Curr. Biol., 22., 1207-1212., 2012
  5. Watanabe et al ., Plant Physiol., 162., 1290-1310, 2013
  6. Tohge et al., Crit Rev Biochem Mol Biol., 48, 123-152, 2013
  7. Alseekh et al., Plant Cell, 27, 485-512, 2015
  8. Tohge et al., Plant J., 83, 686-704, 2015
  9. Tohge et al., Nat Commun., 7, 12399, 2016
Fig.1  Metabolic network of plant polyphenolic biosynthesis and their chemical diversity between plant species
Fig.1  Metabolic network of plant polyphenolic biosynthesis and their chemical diversity between plant species.
Fig.2 Omics-based translational analysis using model plants and crops
Fig.2 Omics-based translational analysis using model plants and crops
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