By Mari N. Jensen
Dec 11, 2003
For the first time, scientists have figured out which of 22,000 genes are turned off and on in all the different types of cells that make up the growing root of a flowering plant.
The result is the first detailed map of when and where the genes are active in roots of the plant Arabidopsis. The achievement offers biologists a new way to explore how complex tissues and organs develop from a single cell, not only in plants but in other organisms, the researchers said. The new information will also contribute to more sophisticated methods for the genetic improvement of crop plants.
"Each cell is defined by the different genes that are active within the cell," said David Galbraith, a professor of plant sciences at the University of Arizona in Tucson. "We are asking what makes a root a root." The researchers used methods pioneered in his lab, including use of a fluorescence-activated cell sorter, to isolate the different root cells.
About twice the width of a human hair, this Arabidopsis root has one cell layer highlighted by green fluorescent protein. The cell walls have been
counterstained and show up red. Photograph by Changqing Zhang, UA.
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Joanne Tornow, a program director with the National Science Foundation, which funded the research, said, "The creation of the root map is a terrific advance forward."
Galbraith and Georgina Lambert from UA will publish their findings in the December 12 issue of the journal Science. Other authors on the paper include Philip Benfey and Jean Wang of Duke University in Durham, N.C., and Kenneth Birnbaum, Jee W. Jung and Dennis Shasha of New York University.
A fundamental question in biology is how cells multiply and organize themselves to form discrete organs. While scientists knew some of the genes that were turned on in a growing root, no one had yet pinpointed in which root tissues and at what point in time all the genes switched on and off. Grinding up a root to see what genes were activated -- which scientists call "expressed" -- gave an overall picture but didn't provide specifics.
When developmental biologist Philip Benfey heard David Galbraith give a seminar on his fluorescence-activated cell sorter technology, Benfey realized that Galbraith's technology might solve the problem. So the two teamed up.
Galbraith said, "It was a nice balance -- we wouldn't have done it without their presenting the research problem, and they couldn't have done it without this technology."
People from Benfey's lab brought samples of Arabidopsis thaliana, the lab rat of the plant world, to UA so the two groups could work together. To distinguish the various layers of the root, Benfey's team used a telltale green fluorescent protein to highlight each of five different cell types within the roots.
Arabidopsis thaliana, the first plant to have its complete genome sequenced, is a member of the mustard family, which includes cultivated species such as cabbage and radish. Arabidopsis has about 28,000 genes. |
Galbraith's fluorescence-activated cell sorting technology was then used to select individual root cells characteristic of the different cell layers. In addition, the researchers repeated the work using cross-sections of roots that represented various stages of growth, a technique to tell whether the five cell types expressed different genes at different times during development.
Once the researchers had separated a particular cell type of a particular age, they used thumbnail-sized DNA microarrays, or “gene chips,” to measure the activity of about 22,000 genes, about 80 percent of the genes present in an Arabidopsis cell. When genetic material from the cells are added to the gene chips, the chips indicate which genes are activated.
The researchers did not expect to find so many Arabidopsis genes involved in root development.
"To me one of the most surprising things was that almost half of the 10,000 genes expressed in the root showed dramatic levels of tissue-specific expression," said Benfey. "I would have guessed perhaps 10 to 20 percent of Arabidopsis genes would have been so expressed."
Galbraith, whose forte is developing new technologies that other researchers can adopt for their own research, said, "This work is an example of how collaborative research can lead to great progress."
As a member of the UA's Institute for Biomedical Science and Biotechnology, Galbraith anticipates more opportunities for such fruitful partnerships. He said, "IBSB is designed to promote collaboration across disciplines."
- Updated: December 11, 2003
