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Proteomics Emerges in Second Half Of 10-Year Arabidopsis 2010 Project


Half-way through the 10-year Arabidopsis 2010 project, which aims to understand the molecular processes and the function of every gene within the weedy model plant, much of the project's genetic work has been completed, and researchers are beginning to focus on proteomic work, according to project officials.

"Proteomic work is the next big area of development," said Philip Benfey, the chairman of the Multinational Arabidopsis Steering Committee that oversees the Arabidopsis 2010 project. "Proteins are the molecules that are really doing the work. Once we can determine the number of proteins [in Arabidopsis thaliana], their concentration and localization within the cell, those will be enormously new and important types of data that will help us understand how cells are interacting and communicating."

Started in 2001 after the completion of the 25,000-gene Arabidopsis genome sequence, the Arabidopsis 2010 project has made great strides with the help of $25 million worth of funding per year from the National Science Foundation. At least one knock-out mutant for almost every gene of the plant has been created, according to Randy Scholl, the director of the Arabidopsis Biological Resource Center at Ohio State University. In addition, about 13,000 cDNA clones have been produced for Arabidopsis thaliana genes, which has led to the creation of Arabidopsis cDNA microarrays.

"Proteomic work is the next big area of development. Once we can determine the number of proteins [in Arabidopsis], their concentration and localization within the cell, that will be enormously new and important type of data that will help us understand how cells are interacting and communicating."

Currently, researchers led by Michael Snyder and Dinesh Kumar at Yale University are working on perfecting an Arabidopsis protein chip. The chip contains approximately 1,000 proteins.

"Proteomics is coming, but slower than genomics," said Kumar. "There are expression clones for most transcription factors — about 1,200 — and approximately 500 protein kinase expression clones [out of the organism's 1,500 protein kinases]."

Other Arabidopsis researchers, including Wilhelm Gruissem of the Federal Institute of Technology in Zurich, Swizerland and Mark Stitt of the Max Planck Institute are using mass spectrometry to characterize cell cycle regulators and transcriptional regulators of metabolic flux.

Understanding how Arabidopsis works at the gene, protein, and metabolite level will probably help improve agricultural and forestry technology more quickly than disease research in mice helps develop therapies for humans, according to Peter McCourt, a professor in the department of botany at the University of Toronto.

"We [humans] have got stem cell controversies, all sorts of ethical things, and we still can't easily transform animals," said McCourt. "With plants, there are some issues about genetically modified organisms, but overall you can really make quite a large impact by understanding the plant genome."

As an example of how understanding a gene in Arabidopsis can translate into improvements in agricultural technology, McCourt pointed to some research on drought tolerance that was done in his laboratory.

McCourt and his research team identified a gene in Arabodopsis that helps improve the water efficiency of the plant. They then took that research out to the corn fields in Alberta, Canada by engineering the downregulation of a homologous gene in Canola.

"In three separate field trials over thousands of acres, they found a 14 to 20 percent efficiency improvement in drought resistance when the gene was downregulated via anti-sense RNA," said McCourt.

While technology is relatively good for manipulating genes, it is just starting to be developed for manipulating proteins, McCourt noted.

"It's actually the proteins we want to manipulate, but proteins are hard to manipulate with the technologies that we have," said McCourt. "Things that we're trying to accomplish through the Arabidopsis 2010 project in terms of proteins are, for example, the crystal structure of every protein in the plant, and the interactome — the interactions between all the proteins within the plant."

In terms of determining the 3D-structures of Arabidopsis proteins, researchers are concentrating first on characterizing proteins that have folds that are unique to plants, Benfey said.

"We [humans] have got stem cell controversies, all sorts of ethical things, and we still can't easily transform animals. With plants, there are some issues about genetically modified organisms, but overall you can really make quite a large impact by understanding the plant genome."

Because flowering plants are very closely related evolutionarily, research on Arabidopsis should be very applicable to crops and trees, McCourt said.

"Although they look very different, the way a tree works and the way Arabidopsis works are not that different," said McCourt. "People have shown that a gene in Arabidopsis that determines the time of flowering — that same gene in a poplar plant or in a wheat plant also determines the time of flowering."

Aside from increasing resistance of plants to environmental factors such as drought, fungi and insects, understanding the fundamental aspects of how Arabidopsis works could also lead to producing corn oil as a viable alternative to fossil fuel, and producing more nutritional crops, McCourt added. The better scientists understand the way plant genes, metabolites, proteins, and pathways work, the better they can engineer solutions to agricultural and environmental problems.

"Why doesn't a rice plant make a lot of vitamin A? That [question] requires basically an understanding of how a metabolite is made," said McCourt. "What are all the genes in the pathway, and how are the proteins in the pathway working?"

In addition to serving as a "blueprint" for plants, Arabidopsis research can also be applied to animals.

"There are some 40 to 50 human disease genes in the Arabidopsis genome," said McCourt. "That just shows us that we're more closely related [to plants] than we thought. If you understand how a protein is degraded in a plant, it's pretty much the same in an animal."

— Tien-Shun Lee ([email protected])

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