Metabolomics is the study of chemical phenotype

Studying genes and proteins gives a limited picture of what is going on in a cell. As we have seen, both gene function and protein function are affected by the internal and external environments of the cell. Many proteins are enzymes, and their activities affect the concentrations of their substrates and products. So as the proteome changes, so will the abundances of small molecules called metabolites. The metabolome is the complete set of small molecules present in a cell, tissue, or organism under defined conditions. These include:

Not surprisingly, measuring metabolites involves sophisticated analytical instruments. If you have studied organic or analytical chemistry, you may be familiar with gas chromatography and high-performance liquid chromatography, which separate molecules, and with mass spectrometry and nuclear magnetic resonance spectroscopy, which are used to identify them. These measurements result in “chemical snapshots” of cells or organisms, which can be related to physiological states.

There has been some progress in defining the human metabolome. A database created by David Wishart and colleagues at the University of Alberta contains more than 6,500 metabolite entries. The challenge now is to relate levels of these substances to physiology. For example, you probably know that high levels of glucose in the blood are associated with diabetes. But what about the early stages of heart disease? There may be a pattern of metabolites that is diagnostic of this disease. This could aid in early diagnosis and treatment.

Plant biologists are ahead of medical researchers in the field of metabolomics. Over the years, tens of thousands of secondary metabolites have been identified in plants, many of them made in response to environmental challenges. Some of these will be discussed in Chapter 38. The metabolome of the model organism Arabidopsis thaliana is being described, and will give insight into how a plant copes with stresses such as drought or pathogen attack. This knowledge could be helpful in optimizing plant growth for agriculture.