March 27, 2009

Unearthing the diversity of plant chemicals

Determining the molecular workings of plant cells is now possible using a newly developed method

Figure 1: The model plant Arabidopsis thaliana is being used in research to determine the biological functions of various plant chemicals found in different tissues.

Molecular biologists from RIKEN’s Plant Science Center in Yokohama have published a systematic method for linking the detectable working molecules or metabolites in plant cells to their biological functions.

The technique was developed to assist studies of the diversity of plant chemicals and deliberately avoids targeting particular compounds. “The wide variety of plant chemicals [is] a good source of natural medicines, spices, and toxins,” says first author, Fumio Matsuda.

The method provides enough structural information to allow chains of reactions or pathways to be mapped, compounds to be linked to genes, and the molecular consequences of mutations to be studied. Cells from different tissues can be compared to determine which metabolites are specific to particular species or parts of plants.

The researchers created a library of all the metabolites of a particular cell tissue and labeled them with spectral tags—data on two or more fragments of the same compound that can be used to identify its presence in mass spectrometer information. The compounds were separated by means of liquid chromatography and the tags generated using tandem mass spectrometry. The tags themselves provide data on parts of the molecule which can be used to deduce its structure directly, or can be matched by software with spectral information on standard compounds.

The researchers tested their method using extracts from shoot and flower tissues of the plant genetics model organism Arabidopsis (Fig. 1). They were able to detect more than 1,000 compounds, and about half were tagged. Of these, 95 were identified and annotated with at least some information on their structure and function. The details have been published in a recent paper in The Plant Journal1.

Among the annotated compounds were some which, on the basis of their tags, appeared structurally related. These could be used as the basis of hypotheses about metabolic pathways. The researchers also compared the occurrences of 44 annotated compounds in four different plant tissues. They found several of them to be tissue-dependent, and in some cases were even able to trace unusual metabolites back to the genes coding for them. When the researchers deliberately inserted mutant genes into plants, they found they could track differences in the metabolites the cells produced.

“We showed our technique could be useful for investigating metabolic functions in plants,” Matsuda says. “We are now making a detailed catalogue of phytochemicals in various plant species such as rice, wheat, soybean and tomato.”


  1. Matsuda, F., Yonekura-Sakakibara, K., Niida, R., Kuromori, T., Shinozaki, K. & Saito, K. MS/MS spectral tag-based annotation of non-targeted profile of plant secondary metabolites. The Plant Journal 57, 555–577 (2008). |  | (Link)