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A. Thaliana Wins a Place in the Sun; Researchers to Study Overlooked Weed

SEATTLE, Oct 24 - Arabidopsis thaliana is a plant that’s easy to ignore. It’s not a star in the produce beauty  pageant like its showier relatives, broccoli and cauliflower. It doesn’t rake in big bucks like canola, a more commercially successful family member.

Nope. This mustard plant just grows wild. The sort of weed with a flower so tight it’s hard to see even when it sprouts from sidewalk cracks.

Yet, while it might go unnoticed by the man in the street, this weed recently attracted millions of dollars in funding from the National Science Foundation.

The NSF awarded researchers at Seattle’s Fred Hutchinson Cancer Research Center $2.6 million over two years to learn more about A. thaliana , the best model organism for scientists studying methylation, says Steven Henikoff, a member of the center's basic sciences division.

Methylation, a change to DNA’s C base, can be a causal factor in cancer among humans. But researchers who want to learn more about how methylation works and when the sometimes normal change goes awry are stymied in the lab by organisms such as yeast or fruit flies that do not undergo such changes.

“Working on a weed is not as surprising as it might first sound,” Enrico Coen, a professor in the genetics department at the John Innes Center, in Norwich, UK, wrote about A. thaliana in his book “The Art of Genes: How Organisms Make Themselves.”

“Some of the desirable properties of an organism for genetic studies, such as rapid growth and short time between generations, are also those that make a good weed,” he wrote.

This particular weed has a “very, very small genome,” noted Henikoff, the project leader. In addition to being manageable, the A. thaliana genome is simple and its 25,000 genes are easily accessible.

Using EMS, a tried-and-true chemical that produces a high density of single-base changes, the group can easily introduce mutations into the plant's genome. They'll grow plants from the mutated seeds and will isolate their DNA. Follow-up analysis using PCR can be used to pinpoint the exact genetic mutation.

Researchers from three different groups are working on the project.

Scientists at the Hutch, better known for its bone-marrow transplant research, are developing the technology. At the University of Washington co-investigator Luca Comai, an associate professor of botany, and undergrads are busily making DNA preps and planting and harvesting 10,000 greenhouse plants. And Leroy Hood's Institute for Systems Biology is interested in tapping the nearby institute's robotics and high throughput technology for future plant modification.

The larger aim is to transfer the project's methodology to other plants.

You could take rice, a plant Hood's lab is keenly interested in, and modify or knock out a gene so it would no longer need vitamin-stripping milling. Or you could zap the gene responsible for making caffeine in tea to create a tea plant that doesn't rely on chemicals to become decaffeinated.

“Any plant people can think of, you could modify by knocking out a gene or reducing its activity,” Henikoff said. “I think what we're doing here would be applicable to other plants pretty directly.”

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