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A giant leap for plant biology

Giant Leap

The image shows an Arabidopsis plant overlaid on a network map of protein-protein interactions. The clusters of colors represent "communities" of interacting proteins that are enriched in specific plant processes. Image: Joseph R. Ecker, Salk Institute for Biological Studies. Plant photo: Joe Belcovson, Salk Institute for Biological Studies. Network map: Mary Galli, Salk Institute for Biological Studies and Matija Dreze, Center for Cancer Systems Biology at the Dana-Farber Cancer Institute.

An international team of scientists, whose senior investigators included Joseph Ecker, recently reported a giant leap forward in plant biology, describing in the journal Science their mapping and early analyses of thousands of protein-to-protein interactions within the cells of the model plant Arabidopsis thaliana.

"With this one study we managed to double the plant protein interaction data that are available to scientists," says Ecker, noting that these data, along with data from future mapping studies, should enable biologists to make agricultural plants more resistant to drought and diseases, more nutritious and generally more useful to mankind.

The four-year project was headed by Ecker and colleagues at Boston's Dana-Farber Cancer Institute. In its initial stages, members of Ecker's lab converted most of their accumulated library of Arabidopsis protein coding gene clones into a form useful for protein interaction tests. The Dana-Farber scientists systematically ran these through a high-quality protein interaction screening process. Out of more than 40 million possible pair combinations, they found a total of 6,205 Arabidopsis protein-protein interactions, involving 2,774 individual proteins, which represents only about 2 percent of the full protein-protein "interactome" for Arabidopsis. "There will be larger maps after this one," says Ecker.

Even as a preliminary step, though, the new map is clearly useful. The researchers were able to sort the protein interaction pairs they found into functional groups, revealing networks and "communities" of proteins that work together. Further analysis provided new insight into plant evolution. Ecker and colleagues' Arabidopsis genome data, reported a decade ago, had revealed that plants randomly duplicate their genes to a much greater extent than animals do. These gene duplication events apparently give plants some of the genetic versatility they need to stay adapted to shifting environments. In this study, the researchers found 1,900 pairs of the mapped proteins that appeared to be the products of ancient gene duplication events.

Ecker and his colleagues hope that these studies mark the start of a period of rapid advancement in understanding plant biology. "This starts to give us a big, systems-level picture of how Arabidopsis works, and much of that systems-level picture is going to be relevant to—and guide further research on—other plant species, including those used in human agriculture and even pharmaceuticals," Ecker says.