"I have been trying, for several decades, to understand how a simple gas—two carbons and four hydrogens—can cause such profound changes in a plant," Ecker says. "Now we can see that by altering the expression of one protein, ethylene produces cascading waves of gene activation that profoundly alters the biology of the plant."
Although the plant they studied is the Arabidopsis thaliana, related to cabbage and mustard, ethylene functions as a key hormone in all plants, he adds.
The researchers looked at what happens in Arabidopsis after ethylene gas causes activation of EIN3, a master transcription factor—a protein that controls gene expression—that Ecker had discovered and cloned in 1997. EIN3 and a related protein, EIL1, are required for the response to ethylene gas; without these proteins, ethylene has no effect on the plant.
"We wanted to know how ethylene is actually doing its job," Ecker says. "Once the plant responds to ethylene by activating EIN3, what happens? What genes are turned on? And what are those genes doing?"
Using a technique known as ChIP-Seq, the researchers exposed Arabidopsis to ethylene and identified all the regions of the plant genome that bound to EIN3, which required using next-generation sequencing. They then used genome-wide mRNA sequencing to identify those targeted genes whose expression actually changes due to interaction with EIN3. "Not all genes targeted by EIN3 have changes in their gene expression," Ecker says.
They found that thousands of genes in the plant responded to EIN3. Then the investigators discovered two interesting things. First, when EIN3 is activated by ethylene, it goes back to control the genes in the pathway that were used to activate the EIN3 transcription factor in the first place. "That tells us that a plant making a critical master regulator like EIN3 wants to keep that production pathway under very tight control," Ecker says. "We had not expected this, and now this gives us a strategy to understand genetic control of other plant hormones."
The second discovery is that EIN3 targets all other hormone signaling pathways in the plant. Ecker offers an analogy to understand the reasons why: "Imagine you are in a recording studio and you have one of those tables in front of you that have all of those switches. If you start pushing up the dials for one sound effect, you probably turn down the dial for other sound.
"If ethylene tells a plant to stop growing, it has to control other hormones that are telling the plant to grow," he says. "We found that about half of the genomic targets of the EIN3 protein are found in other hormone signaling pathways."
Control of those hormones by EIN3 is very complex and is accomplished in a 24-hour period during which four cascading waves of transcriptional regulation takes place, Ecker says.
In addition to gaining insight into how ethylene genetically controls diverse functions within a plant, he adds that findings from the study provides a template by which to decode the workings of other plant hormones—none of which have been as well studied as ethylene.
"Learning how plants coordinate hormone responses is essential to understanding their regulation of growth and development, be it in seed germination, fruit ripening, or responding to drought, insects, or pathogens," says Katherine Chang, the first author of the paper and researcher in Ecker's lab. "In this way, mapping interco
Read more at: http://phys.org/news/2013-06-scientists-thousands-genes-ethylene-gas.html#jCp How ethylene
Although the plant they studied is the Arabidopsis thaliana, related to cabbage and mustard, ethylene functions as a key hormone in all plants, he adds.
The researchers looked at what happens in Arabidopsis after ethylene gas causes activation of EIN3, a master transcription factor—a protein that controls gene expression—that Ecker had discovered and cloned in 1997. EIN3 and a related protein, EIL1, are required for the response to ethylene gas; without these proteins, ethylene has no effect on the plant.
"We wanted to know how ethylene is actually doing its job," Ecker says. "Once the plant responds to ethylene by activating EIN3, what happens? What genes are turned on? And what are those genes doing?"
Using a technique known as ChIP-Seq, the researchers exposed Arabidopsis to ethylene and identified all the regions of the plant genome that bound to EIN3, which required using next-generation sequencing. They then used genome-wide mRNA sequencing to identify those targeted genes whose expression actually changes due to interaction with EIN3. "Not all genes targeted by EIN3 have changes in their gene expression," Ecker says.
They found that thousands of genes in the plant responded to EIN3. Then the investigators discovered two interesting things. First, when EIN3 is activated by ethylene, it goes back to control the genes in the pathway that were used to activate the EIN3 transcription factor in the first place. "That tells us that a plant making a critical master regulator like EIN3 wants to keep that production pathway under very tight control," Ecker says. "We had not expected this, and now this gives us a strategy to understand genetic control of other plant hormones."
The second discovery is that EIN3 targets all other hormone signaling pathways in the plant. Ecker offers an analogy to understand the reasons why: "Imagine you are in a recording studio and you have one of those tables in front of you that have all of those switches. If you start pushing up the dials for one sound effect, you probably turn down the dial for other sound.
"If ethylene tells a plant to stop growing, it has to control other hormones that are telling the plant to grow," he says. "We found that about half of the genomic targets of the EIN3 protein are found in other hormone signaling pathways."
Control of those hormones by EIN3 is very complex and is accomplished in a 24-hour period during which four cascading waves of transcriptional regulation takes place, Ecker says.
In addition to gaining insight into how ethylene genetically controls diverse functions within a plant, he adds that findings from the study provides a template by which to decode the workings of other plant hormones—none of which have been as well studied as ethylene.
"Learning how plants coordinate hormone responses is essential to understanding their regulation of growth and development, be it in seed germination, fruit ripening, or responding to drought, insects, or pathogens," says Katherine Chang, the first author of the paper and researcher in Ecker's lab. "In this way, mapping interco
Read more at: http://phys.org/news/2013-06-scientists-thousands-genes-ethylene-gas.html#jCp How ethylene