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Towards the plant metabolome and beyond

Nature Reviews Molecular Cell Biology volume 8, pages 167–174 (2007)Cite this article

Abstract

Methods for network-wide analysis are increasingly showing that the textbook view of the regulation of plant metabolism is often incomplete and misleading. Recent innovations in small-molecule analysis have created the ability to rapidly identify and quantify numerous compounds, and these data are creating new opportunities for understanding plant metabolism and for plant metabolic engineering.

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Figure 1: Small-molecule analysis by mass spectrometry without chromatographic separation.
Figure 2: Small-molecule analysis by mass spectrometry with chromatographic separation.
Figure 3: Approaches to data reduction.
Figure 4: Use of metabolomics to analyse plants perturbed by genetic or environmental changes.

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Acknowledgements

Research in the Jones, Last and Shachar-Hill laboratories is funded by grants from the National Science Foundation, United States Department of Agriculture Competitive Grants Program, the National Institutes of Health and Michigan State University.

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Authors and Affiliations

  1. Robert L. Last is at the Department of Biochemistry and Molecular Biology and the Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA.,

    Robert L. Last

  2. A. Daniel Jones is at the Department of Biochemistry and Molecular Biology and the Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA.,

    A. Daniel Jones

  3. Yair Shachar-Hill is at the Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA.,

    Yair Shachar-Hill

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Correspondence to Robert L. Last.

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Supplementary information

Supplementary information S1 (box)

Statistical methods used in the analysis of metabolomics data. (PDF 594 kb)

Related links

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FURTHER INFORMATION

Robert L. Last's homepage

A. Daniel Jones's homepage

Yair Shachar-Hill's homepage

AraCyc Arabidopsis metabolic pathway annotations

Genevestigator

Iowa Gene Expression Toolkit

KEGG Pathway Database

L. penellii Introgression Lines

MapMan tool

Metabolic modeling

Metabolic Ontology Working Group

MetAlign tool for GC– or LC–MS data analysis

Pathexplore tool

Plant metabolites database

Solcyc Solanaceae metabolic pathway annotations

The Golm Metabolome Database

WTEC Panel Report on International Research and Development in Systems Biology

Glossary

Allelopathic

The known or postulated ability of a plant-produced chemical to modify the physiology of a nearby plant, which constitutes a form of chemical communication between plants.

Capillary electrophoresis

Separation of compounds by the different times that they take to traverse a narrow column under the influence of an electric field.

Electrospray ionization

(ESI). A gentle method for ionizing compounds that applies high voltage to a solution of compounds that are sprayed through a capillary.

Flavonoid family

A large family of structurally diverse molecules that are produced by plants. They confer common colours to leaves, flowers and fruits, absorb ultraviolet light and have other known and postulated roles in plant growth and development.

Flow-injection analysis

(FIA). Introduction of a sample into a flowing medium that transports the sample components to a detector, such as a mass spectrometer, without chromatographic separation.

Fourier-transform-infrared (FT-IR) spectroscopy

Spectroscopy that enables the identification of classes of compound by analysing their interactions with infrared light. Mass resolution is the ability to distinguish ions of different masses, usually expressed as a ratio of the ion mass to the difference in mass that the mass spectrometer can reliably distinguish.

Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometry

A method for obtaining accurate measurements of the mass-to-charge ratio of ions in a complex mixture, allowing the identification and measurement of the molecules.

Freezing-tolerance response

A measure of the ability of an organism to survive when exposed to below-freezing temperatures.

Gas chromatography

(GC). Method for the separation of volatile compounds in a gas phase through differential binding to a column at elevated temperatures.

High-performance liquid chromatography

(HPLC). Method for separating compounds in solution through their differential interactions with a column.

HPLC with electrochemical or photodiode-array detection

Method for the separation of metabolites by HPLC followed by the detection of the metabolites based on their redox behaviour or spectral absorption properties.

Mass-to-charge ratio

(m/z). The ratio of the mass of an ion (in Daltons, or atomic mass units) to the number of charges on the ion.

Nominal mass

The mass of a molecule, rounded off to the nearest integer value. Two compounds with different elemental formulas can have identical nominal masses, although their exact masses might differ by a small fraction of a Dalton (or atomic mass unit).

Orbitrap mass analyser

A high-resolution mass spectrometer that traps ions in an electric field and measures their abundances and mass-to-charge ratios based on their orbital motions in the ion trap.

Targeted metabolite analysis

Quantitative analysis of a pre-selected list of metabolites.

Thin-layer chromatography

Method for the separation of molecules through their differential interactions with a matrix on a glass or plastic plate.

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Last, R., Jones, A. & Shachar-Hill, Y. Towards the plant metabolome and beyond. Nat Rev Mol Cell Biol 8, 167–174 (2007). https://doi.org/10.1038/nrm2098

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