Purdue research plots new field in plant genomics

August 31, 2003

WEST LAFAYETTE, Ind. - First, there was genomics, or the study of all the genes found in an organism. Then there was proteomics - the study of all the proteins produced by these genes. Now, a Purdue University researcher and his collaborators have developed a new field called "ionomics," or the study of how genes regulate all the ions in a cell.

This research holds the promise of leading to mineral-efficient plants that need little fertilizer, crops with better nutritional value for humans and plants that may remove contamination from the soil.

David Salt, associate professor of plant molecular physiology and primary investigator on the research project, defines the ionome as the collection of all the mineral ions that function in a cell. "Ion" is a general term for any atom or molecule that carries either a positive or negative electrical charge. The ionome, as Salt defines it, includes only those ions composed of a single element, but does not include other charged compounds such as amino acids.

The ionome is the core concept behind the field of ionomics, described for the first time in a paper published on-line today in the journal "Nature Biotechnology."

"All the ions in a cell play critical roles," Salt says. "Ions energize biological membranes, they play a key role in enzyme activity, they regulate the transmission of signals in the cell and the transport of materials throughout the cell. We want to understand how the cell, in turn, regulates those ions."

Plants take up most of their mineral nutrients, such as phosphorus, potassium and zinc, as ions dissolved in water, and the electrical charge of these ions permits them to react with other compounds inside the plant cell. Mineral nutrients are central to many processes inside plant cells, including water transport, photosynthesis and energy production.

Understanding how plants regulate ion transport and uptake could have significant implications for human and plant nutrition, Salt says. For example, by modifying ion uptake and transport, scientists may develop plants that contain elevated levels of nutrients essential to human health. Ionomics may also help scientists produce plants that grow efficiently on nutrient-poor soils, reducing the need for fertilizers.

Ionomics fits into the larger field of functional genomics, or the study of how all the genes in a cell operate. Current research in functional genomics has started to reveal the connections between the genome and the proteome, but none of these approaches has considered how cells regulate minerals and trace elements, or elements found at extremely low concentrations.

The first phase of this project is the proof-of-concept study published today. In this study, Salt and his colleagues generated random mutations in a series of Arabidopsis thaliana plants, then assessed which of those plants exhibited changes in their elemental profile, or the relative proportions of various ions in their cells.

The study focused on a group of 18 ions that play a role in plant nutrition, including the mineral nutrients zinc, copper, iron, manganese and potassium, as well as nonessential trace elements, such as arsenic, cadmium and lead.

The research suggests that 2 percent to 4 percent of the Arabidopsis genome is dedicated to regulating the plant's ionome.

Using the results from the mutated plants, the next phase of the research is to identify which genes in a plant cell play a role in ion regulation. The research team will do this by comparing the elemental profile of the mutant plants to the elemental profile of normal, or "wild-type," plants, and then looking for gene-level changes in the two groups of plants.

"Because we have systems for measuring all the ions in a cell, we can, for example, create a mutant in which gene Y doesn't function," Salt says. "And suddenly, we'll see that calcium goes up. When we knock out gene B, suddenly manganese goes down, but zinc goes up." Ultimately, the researchers will use this information to produce a map of the ionome, which will identify and locate those genes with ion-regulating properties.

As these ion-regulating genes are identified, scientists will try to develop plants that more effectively make use of the ions in their environment. This work could help in the development of foods with higher levels of certain nutrients.

"What people have termed 'hidden hunger' in the world is poor micronutrient content of our food," Salt says. As scientists unravel the molecular and biochemical basis behind plant accumulation of these mineral nutrients, he says, they will be able to develop crop plants with enhanced nutritional value.

Salt is already collaborating with a company called NuCycle Therapies to develop plants enriched in selenium, a potent anti-carcinogenic compound.

Another field that will directly benefit from research in ionomics is phytoremediation, or the use of plants to remove contaminants from the environment. Some plants, Salt explains, can accumulate unusually high levels of metals in their tissues, levels that would kill most plants. "We know these plants have genes that are letting them do this," Salt says. By identifying which genes in those plants regulate the uptake, transport and storage of metal ions, scientists may be able to engineer plants that will clean up polluted soils.

Salt collaborated on this study with researchers at the University of California-San Diego, the University of Missouri, Dartmouth College, the University of Minnesota, and the Scripps Research Institute in California. The National Science Foundation Plant Functional Genomics Program funded this research.

Writer: Jennifer Cutraro, (765) 496-2050, jcutraro@purdue.edu

Source: David Salt, (765) 496-2112, salt@hort.purdue.edu

Related Web sites:

Functional Genomics of Plant Transporters home page: http://plantst.sdsc.edu/

Central Indiana Life Sciences Initiative: http://www.indygov.org/mayor/cilsi/index.htm

Arabidopsis Ionomics database: http://hort.agriculture.purdue.edu/ionomics/database.asp

NuCycle Therapies home page: http://www.nucycletherapy.com/

Nature Biotechnology journal home page: www.nature.com/nbt


David Salt, associate professor of plant molecular physiology, compares growth rates of the plants used in his ionomics research. The plants shown here are Arabidopsis mutants he identified that are growing on media enriched in the mineral nutrients and trace elements arsenic, nickel and zinc. Salt is leading a research team that has developed a new field called "ionomics," or the study of how genes regulate all the ions in a cell.

A publication-quality photograph is available at


Ionomics: the genomic scale profiling of nutrient and trace elements

in Arabidopsis thaliana

B. Lahner, J. Gong, M. Mahmoudian, E.L.Smith, K.B. Abid, E.E. Rogers, M.L. Guerinot, J.F. Harper, J.M. Ward, L. McIntyre, J.I. Schroeder, D. E. Salt

Understanding the functional connections between genes, proteins, metabolites and mineral ions is one of biology's greatest challenges in the post-genomics era. We describe here the use of mineral nutrient and trace element profiling as a new tool to determine the biological significance of connections between a plant's genome and its elemental profile. Using inductively coupled plasma spectroscopy, we quantified 18 elements including essential macro and micronutrients and various nonessential elements in shoots of 6000 mutagenized M2 Arabidopsis thaliana plants. We isolated 51 mutants with altered elemental profiles. One of these mutants contains a deletion in FRD3, a gene known to control Fe deficiency responses in Arabidopsis. Based on the frequency of elemental profile mutations, we estimate 2-4% of the Arabidopsis genome is involved in regulating the plant's "ionome." These results demonstrate the utility of elemental profiling as a new and useful functional genomics tool. Purdue University
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