Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Key root-development pathway mapped using advanced genomic technique

05.05.2006


Biologists have vastly expanded understanding of the biological machinery controlling the intricate process by which plant roots burgeon from single cells into complex tissues. A Duke-led team’s discovery of new components of the root-development pathway in the mustard plant, Arabidopsis thaliana, represents both a scientific and technical achievement, the scientists said.



Scientifically, Arabidopsis is a basic biological model for all flowering plants, so the finding offers insights into a critical function of all such plants, including crop plants, the researchers said. Further, since the root is a useful model for tissue development in general, basic findings regarding the root-development pathway could offer insights into how complex tissues are generated from immature cells, called stem cells.

Technically, the genomic analytical method they used also will offer biologists a highly useful approach to discovering the components of complex biological pathways governing development, the researchers said. Their statistical "meta-analysis" technique involved using computational methods to integrate data from multiple genetic analyses using several DNA microarrays -- popularly known as "gene chips." Each of these chips contained some 24,000 genes representing nearly the entire genome of the Arabidopsis plant.


The team’s findings appeared May 2, 2006, in the online edition of the journal Public Library of Science Biology and will be published in the journal’s May 2006 edition.

Philip Benfey, professor and chair of Duke University’s Department of Biology and a member of the Duke Institute for Genome Sciences & Policy, is senior first author of the report. Joint first authors are Mitchell Levesque and Teva Vernoux, who performed the work in Benfey’s laboratory.

The research was sponsored by the National Institutes of Health and the National Science Foundation.

Before the latest work, Benfey and his colleagues had discovered a gene called SHORT-ROOT (SHR), which produces a protein that appears to be a central regulatory molecule in the root-development pathway. SHR was so named because gene mutations that cause malfunction result in stunted roots with incompletely differentiated tissues. The researchers had also discovered a second gene, SCARECROW, that appeared to be controlled by SHR.

The researchers believed the SHR protein to be a "transcription factor," a master switch that controls activation, or "transcription," of a multitude of target genes. In turn, those target genes might control still other biological regulatory pathways which form a biological network that governs plant root development.

"Before this paper, we had two big questions," Benfey said. "One was whether SHORT-ROOT was actually a transcription factor that activated or repressed genes. The other was the identity of the target genes beyond SCARECROW, which we believed was a target but had no direct evidence for. We basically had no clue what was involved in the root-development process beyond those genes."

To search for genes that were SHR targets, the researchers used the technique of microarray analysis. Basically, such analysis involves isolating the messenger RNA produced by all of the genes in the Arabidopsis genome. Using the microarrays, the researchers could determine the level of messenger RNA produced by each gene, which reflects its activity. Thus, they could pinpoint among thousands of genes only those activated or repressed under different conditions, such as mutation of SHR.

However, in the search for SHR targets, the scientists went a step further in their microarray analysis. They modulated the SHR pathway in several distinct ways by using chemicals or mutation to switch it on or block it under different conditions. By using statistical methods to compare the subtle differences in activity of the multitude of genes under those different conditions, they could identify genes that were likely targets of SHR.

That "meta-analysis" of the results from the microarrays revealed eight genes that appeared likely to be direct targets, as well as numerous genes that appeared to be indirectly affected by SHR activity, the scientists said.

"The next thing we did was to determine whether these target genes were, indeed, expressed in domains that were consistent with SHORT-ROOT expression," Benfey said. "After all, we did not preselect for genes that were expressed in the root."

That analysis, he said, showed that many of the genes were expressed in the same region of the plant as SHR. Also, further studies showed evidence that the SHR protein directly bound some of the target gene promoters. Even though not all of the genes showed such binding, many factors compromise such analyses, he said, such that the lack of evidence does not rule out any of the eight as SHR targets.

Also, the researchers’ analysis of the expression of the SHR targets revealed evidence for a role for SHR where it had not been demonstrated before -- in the central vascular tissue, or "stele," of the plant root.

"So, this meta-analysis enabled us to identify a major new function for a gene that we had been studying for quite a while," Benfey said. "We had seen effects on the stele of mutating SHORT-ROOT in previous studies, but they were so subtle that we couldn’t say for sure whether they were significant."

The researchers also analyzed SHR’s effects on indirect target genes revealing that many of the secondary targets are turned off.

"What we found striking was that over three-quarters of the indirect targets we identified were repressed and only one-quarter upregulated," Benfey said. "That’s not a common finding with transcription factors. So, it leads us to believe that of the direct targets we identified, most are probably working more to repress their target genes than to activate them."

Further studies of the treasure trove of new SHR gene targets will aim at exploring the details of their functions using biochemical and genetic techniques, Benfey said. Also, the new findings will enable the researchers to begin to understand the complex network regulated by SHR.

"We think that SHORT-ROOT is part of a cascade of transcription factors, and that there are many intermediate steps before the end-stage differentiation of cells in tissues," he said. "We’re now actively exploring those intermediate steps."

More broadly, the technique of meta-analysis -- used currently in epidemiological studies -- will find wider use in studying the development of organisms, Benfey said.

"To our knowledge, this is the first time this statistical technique has been used in a developmental context," he said. "It is much more powerful than simply comparing the results from different microarrays. And there is nothing in this technique that is specific to plants, meaning that it can be applied to analyze any organism."

Other co-authors on the paper are Hongchang Cui, Jean Wang, Keji Nakajima and Noritaka Matsumoto, who worked in the Benfey laboratory; Wolfgang Busch and Jan Lohmann of the Max Planck Institute for Developmental Biology; and Hala Hassan and Ben Scheres of Utrecht University.

Monte Basgall | EurekAlert!
Further information:
http://www.duke.edu

More articles from Life Sciences:

nachricht Bare bones: Making bones transparent
27.04.2017 | California Institute of Technology

nachricht Link Discovered between Immune System, Brain Structure and Memory
26.04.2017 | Universität Basel

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Making lightweight construction suitable for series production

More and more automobile companies are focusing on body parts made of carbon fiber reinforced plastics (CFRP). However, manufacturing and repair costs must be further reduced in order to make CFRP more economical in use. Together with the Volkswagen AG and five other partners in the project HolQueSt 3D, the Laser Zentrum Hannover e.V. (LZH) has developed laser processes for the automatic trimming, drilling and repair of three-dimensional components.

Automated manufacturing processes are the basis for ultimately establishing the series production of CFRP components. In the project HolQueSt 3D, the LZH has...

Im Focus: Wonder material? Novel nanotube structure strengthens thin films for flexible electronics

Reflecting the structure of composites found in nature and the ancient world, researchers at the University of Illinois at Urbana-Champaign have synthesized thin carbon nanotube (CNT) textiles that exhibit both high electrical conductivity and a level of toughness that is about fifty times higher than copper films, currently used in electronics.

"The structural robustness of thin metal films has significant importance for the reliable operation of smart skin and flexible electronics including...

Im Focus: Deep inside Galaxy M87

The nearby, giant radio galaxy M87 hosts a supermassive black hole (BH) and is well-known for its bright jet dominating the spectrum over ten orders of magnitude in frequency. Due to its proximity, jet prominence, and the large black hole mass, M87 is the best laboratory for investigating the formation, acceleration, and collimation of relativistic jets. A research team led by Silke Britzen from the Max Planck Institute for Radio Astronomy in Bonn, Germany, has found strong indication for turbulent processes connecting the accretion disk and the jet of that galaxy providing insights into the longstanding problem of the origin of astrophysical jets.

Supermassive black holes form some of the most enigmatic phenomena in astrophysics. Their enormous energy output is supposed to be generated by the...

Im Focus: A Quantum Low Pass for Photons

Physicists in Garching observe novel quantum effect that limits the number of emitted photons.

The probability to find a certain number of photons inside a laser pulse usually corresponds to a classical distribution of independent events, the so-called...

Im Focus: Microprocessors based on a layer of just three atoms

Microprocessors based on atomically thin materials hold the promise of the evolution of traditional processors as well as new applications in the field of flexible electronics. Now, a TU Wien research team led by Thomas Müller has made a breakthrough in this field as part of an ongoing research project.

Two-dimensional materials, or 2D materials for short, are extremely versatile, although – or often more precisely because – they are made up of just one or a...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Expert meeting “Health Business Connect” will connect international medical technology companies

20.04.2017 | Event News

Wenn der Computer das Gehirn austrickst

18.04.2017 | Event News

7th International Conference on Crystalline Silicon Photovoltaics in Freiburg on April 3-5, 2017

03.04.2017 | Event News

 
Latest News

Bare bones: Making bones transparent

27.04.2017 | Life Sciences

Study offers new theoretical approach to describing non-equilibrium phase transitions

27.04.2017 | Physics and Astronomy

From volcano's slope, NASA instrument looks sky high and to the future

27.04.2017 | Earth Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>