Science news from the Bond LSC
New project explores ATP’s role in plant signaling; another expands understanding of the soybean genome
July 18, 2012 | Denise Henderson VaughnBond Life Sciences Center investigator Gary Stacey’s long history of conducting plant genetic research with collaborators has played a major role in his lab being selected for funding of two new projects.
Stacey, an endowed professor in MU’s Division of Plant Science and Biochemistry, has for years worked jointly with the two entities involved: the United Soybean Board, headquartered in St. Louis, and Gyeongsang National University (GSNU), based in Jinju, South Korea.
That cooperation has enabled the continuation of two very different types of plant research. For the United Soybean Board grant, Stacey will be growing soybeans under various conditions and collecting samples of RNA for lab analysis. The tests are expected to show how soybean DNA is translated into plant growth under a range of growing conditions.
In his work with the South Korean university, Stacey will be exploring a certain type of signal emitted by plants that involves the molecule ATP, and trying to learn how and where that signal is perceived by cells within the plant.
Following up on sequencing the soybean genome, Stacey now creating a “gene atlas”
Stacey is among a team of researchers from several universities who have together received $3 million from the United Soybean Board in an effort to push understanding of soybean genetics to a new level.
The soybean genome has already been completely sequenced, and that data is available online. Stacey is one of 45 authors of an article that appeared January 2010 in the journal Nature, which heralded this news, representing the first legume to have its genome sequenced completely. Five of those authors are Bond Life Sciences Center investigators.
Now the United Soybean Board is asking scientists to turn this groundbreaking research into practical applications. Stacey’s role in this new project is to help discover how various soybean genes are translated into plant growth, particularly under different growing conditions.
“My portion of the grant is focused on creating what we call a ‘gene atlas,’” said Stacey. “We’re going to grow soybeans under a variety of different conditions, isolate the RNA and then send that to the Joint Genome Institute (JGI).” That lab, operated in Walnut Creek, Calif., by the Department of Energy, did the work to sequence the soybean genome, and before that, sequenced the human genome.
“The genome is basically the sequence of the DNA, but it doesn’t say anything about how that DNA is being expressed,” said Stacey. Environmental conditions can greatly influence the manner in which DNA, the basic blueprint, is actually translated into a living, growing organism. Different genes can “express,” or be utilized more fully, as a plant grows, and this “expression” process involves ribonucleic acid (RNA). A major task of RNA is to encode proteins; this means an RNA molecule serves as a copy of a segment of DNA, which is used to determine how to build a protein that does the work in a cell. The “gene atlas” will be based on tests on RNA, because “RNA is a reflection of what genes are being expressed under a particular condition,” Stacey said.
Soybean plants in the Stacey Lab
“This gene atlas will tell you which part of the genome is being expressed, where it’s being expressed, and at what level,” Stacey said. For instance, “you’d be able to see that this (a particular) gene is being expressed higher under drought conditions than under well-watered conditions, and therefore the gene may in fact play a role in drought tolerance.”
“By doing this, we’ll be able to see what genes are specifically induced under drought, or what genes are specifically expressed in flowers, or what genes are specifically expressed in the stems or roots,” Stacey said. That information, stored in a database on the web, can save researchers a lot of time, he said. “It will be a very good resource for people who want to know what these genes are doing.”
Stacey initially plans to conduct tests on soybeans grown under some 25 to 40 different conditions, but hopes to test as many as 200 conditions over the three-year period.
Money for projects funded by the United Soybean Board originates from soybean growers in the United States, who have for years paid a percentage of their crop sales to funding research and marketing, on both a state and national level. The United Soybean Board administers this fund nationally.
World-class plant research conducted at GSNU and MU
Stacey’s lab will play a part in a project that involves a competitive, prestigious grant award given by the South Korean government to GSNU; that university, in turn, has contracted with Stacey’s lab to conduct a portion of the research.
The connection between MU and South Korea has decades-long roots. Starting during Harry S. Truman’s presidency, MU has over the years hosted “a steady stream of Koreans who have come to the university to get training or degrees,” Stacey said. Consequently, South Korea is home to a sizeable Mizzou alumni group. “We’ve had a very close relationship (with alumni), and that relationship has continued,” he said.
“The reason that we’re very interested in interacting with GSNU is that they have extremely high quality research going on in the area of plant science. They’re really top-notch, world class,” Stacey said. “Missouri of course is also extremely strong in plant science. So it looked like a very good partnership.”
Dr. Gary Stacey and Dr. J. C. Hong at Jeju Island in South Korea.
About five years ago, a visiting Korean professor, J.C. Hong, and Stacey developed a joint PhD program; students study at both GNSU and MU and receive degrees from both institutions. One of Stacey’s students is the first to complete the program, graduating this spring. Symposia have been held biannually, alternating between Columbia and Korea, during which professors share results and develop collaborative projects.
When GNSU recently received a large grant from the South Korean government to set up a ‘systems and synthetic agro-biotech center,’ Stacey’s lab, along with a lab at Purdue University, were the only two in the U.S. to receive a subcontract to conduct research related to the biotech center’s goals.
Of GSNU’s grant, Stacey said, “Very few of these grants are awarded in Korea. It’s a reflection of the quality of that institution that they were able to compete for this. It is an honor that we were included. Perhaps this not only recognizes our research capabilities, but also reflects the great relationship we have built with Korea over the years.”
Coincidentally, Stacey employs a Korean graduate student who has chosen to work on this project. Another post doc from GNSU will probably be hired, “as a way of furthering the interaction between the two institutions,” Stacey said. Plus, “it’s a way for me to get excellent, well-trained people.”
“Here’s a situation where we’ve developed these close relationships between two institutions. Discussions led to symposia; symposia led to joint projects; joint projects led to funding and the exchange of people,” Stacey said.
The GNSU assignment: find the plant receptor that recognizes the ATP signal
The project for the South Korean university involves investigating the role of ATP (adenosine triphosphate) in plants. ATP is a workhorse inside of cells, carrying out hundreds of functions. “It’s the major energy currency of the cell; it’s like coal or natural gas, in a crude analogy, it’s what our cells burn to carry out the functions of the cell,” Stacey said.
Because of its value inside the cell, “you wouldn’t expect ATP to get outside the cell, that it would be retained inside the cell,” Stacey said. “But in fact it gets out. It’s a very important signal molecule.”
ATP’s role as an extra-cellular signaling molecule has been studied in animals, but not so much in plants. “Only five or six labs in the world are working in this area,” Stacey said. Stacey has taken on the job.
To be effective, a signal must somehow be received, which means that for every signaling molecule there is a corresponding receptor. Thus, Stacey’s specific assignment is to try to identify the plant receptor for extra-cellular ATP. This means answering the question: “what is it inside of plant cells that receives the ATP signal?” Some things are known. “If we look at plants for those kind of receptors that we see in animals and humans, we don’t find them,” he said. “So if they’re in plants, they’re probably going to be quite different than what is found in animals. His lab has already identified some genes that are good candidates for being the receptor, he said.