Grant to create plant genome center
Facts and Figures:
UNL Plant Genome Center
UNL is the lead institution for the Plant Genome Center, established with a grant from the National Science Foundation. The $6 million grant provides support for a multi-disciplinary, multi-institutional center to study proteins that play an important role in how plants respond to environmental stress. UNL provides the expertise in plant genomics research and the advanced facilities for studying protein structures needed to lead the research, which brings together researchers from six universities. The new center grows in part from the research capabilities of UNL's Plant Science Initiative, which uses genomics technologies to gain new understanding of how plants work and how they can be improved for value-added agricultural applications.
Title of UNL Grant: "A Protein Interaction Database for Rice Protein Kinases"
Award: $6.05 million over 4 years
Center partners: University of California at Davis, University of California at San Diego, University of Arizona-Tucson, University of Florida-Gainesville and University of Missouri-Columbia
Research focus: The center's goal is to discover how plants respond to environmental stresses, particularly drought and disease. The research projects will focus on the class of proteins, called protein kinases, that control the plant's response to the environment. Rice is being used as a model crop for this work because sequencing of its genome is nearly complete and, as a cereal crop, rice is highly representative of the other major cereal crops - corn, sorghum and wheat - critical to Nebraska agriculture.
An important part of this project is UNL's Nebraska Center for Mass Spectrometry, which provides advanced capabilities in proteomics. Applying the technology of mass spectrometry to the study of proteomics is relatively new and allows identification of peptides within the protein chains.
Educational Outreach: The grant funds a program that brings students to UNL for research experiences, with an emphasis on students from underrepresented groups. In addition to lab experiences, the students will attend a formal course in research skills and techniques to better prepare them for graduate school and careers as research scientists.
Departments participating: agronomy and horticulture, biochemistry, Center for Biotechnology, and chemistry
Center Director: Michael Fromm, Plant Science Initiative and Department of Agronomy
UNL Faculty Participating: Michael Fromm, Ron Cerny (director of Mass Spectrometry Services and research associate professor of chemistry) and Gautam Sarath (research associate professor of biochemistry and director of Biochemistry's Proteomics/Protein Core Facility)
UNL and Collaborative Student Participation: Grant provides support for eight postdoctoral associates and two graduate students.
By Kim Hachiya, University Communications
The University of Nebraska-Lincoln is the lead recipient of a $6 million, four-year National Science Foundation grant to establish a plant genome research center.
Michael Fromm, director of UNL's Center for Biotechnology and a member of the UNL Plant Science Initiative, is the principal investigator on the team composed of scientists from UNL, the University of California-Davis, the University of Arizona, the University of California-San Diego, the University of Florida and the University of Missouri.
"This grant is a tremendous example of the strength we have built in plant science and a realization of our goals to establish research centers and collaborations with other institutions," said Prem Paul, UNL vice chancellor for research.
The genome center will study protein kinases of plants, focusing mainly on rice. Rice is the first cereal crop for which scientists have sequenced all of the DNA in its genome. This makes rice an important model for other important cereal crops, such as corn, Fromm said.
Protein kinases are enzymes that modulate protein behavior, affecting the way plants perceive and react to their environments. Manipulating kinases could be a way to regulate plant tolerance of disease and environmental stresses, such as drought and cold, Fromm said.
Rice has about 2,600 protein kinases, which can be grouped into about 300 subfamilies. The team will look at those 300 as representative of the whole.
"This would cut a wide swath in terms of new knowledge about protein kinases," Fromm said.
"The main questions we are trying to answer are what are the kinases' role in the rice plant, how they are involved in signaling and how kinases interact with each other and with what they interact," he said. "We hope that through rice protein kinases, we can create a blueprint for other cereals."
The process is complex and will take some time to completely understand, he said. "Cereals are important for a number of reasons, but the research is just so far behind in this area."
Fromm is one of several UNL researchers associated with UNL's Plant Science Initiative. The initiative was established to conduct interdisciplinary research in the basic plant sciences. Faculty research emphases include plant-microbe interactions, plant signaling and organellar biology, abiotic and biotic stress responses, and genomics/proteomics. Among collaborative projects conducted by PSI scientists are those devoted to plant-breeding programs focusing on crop improvement; ecology and evolution studies that look at plant function in the natural environment; and an array of faculty investigating the food safety, environmental impact and economic implications of agricultural biotechnology.
The university's investments in plant sciences through the state-funded Nebraska Research Initiative have encouraged development of large-scale, multi-investigator projects by funding faculty recruitment, equipment acquisition, matching grants and other needs for a research enterprise.
A key factor in winning the grant is UNL's strong track record in using mass spectrometry in the study of proteomics. The word proteome refers to all the proteins expressed by a genome; proteomics involves the identification of proteins in the subject under study and the determination of their role in physiological and pathophysiological functions. While a genome remains unchanged to a large extent during a subject's lifetime, the proteins in any particular cell change dramatically as genes are turned on and off in response to its environment.
Ron Cerny, director of mass spectrometry services at UNL, is one of three UNL scientists involved in the grant. Also associated is Gautam Sarath, research associate professor, Protein Core Facility, Biochemistry.
Mass spectrometry is used to analyze the proteins once they have been isolated. UNL has a high-quality mass spectrometry center, Cerny said; its seven instruments make it one of the best academic mass spectrometry centers in the nation.
Fromm, who joined UNL in July 2001, has been working with the weedy mustard plant known as Arabidopsis. Its genome has been sequenced, and it's commonly used by plant geneticists for a variety of research purposes. Fromm is working to understand how the plant perceives and reacts to drought stress. If that process could be understood, it might be feasible to engineer crop plants to become more drought tolerant.
The NSF grant represents what Fromm calls the second wave of biotechnology. In the first wave, scientists were inserting non-plant genes into plants to give plants new traits. A well-known example is the Bt gene in corn, which gave corn greater insect resistance. The second wave, he said, involves trying to understand and improve the complex properties that control how plants behave and work. This wave is "knowledge intensive," Fromm said, and involves gathering large data sets and analyzing them for patterns and information.
The National Science Foundation is funding larger multi-institutional and multi-investigator projects like this one in part because the amount of information gathered is larger than one individual researcher or laboratory can handle, Fromm said.
Fromm and his partners at the other institutions have been working on similar projects and often confer at meetings and seminars. It was at a recent meeting that the group decided to combine forces to apply for a plant genome center grant, Fromm said.
A unique aspect of this grant is that it contains $200,000, parceled out in $50,000 increments over four years, to encourage minority students to pursue scientific careers. Promising students will take a graduate-level summer course that will teach aspects and techniques of research and will have opportunities to work in laboratories. Fromm said this approach is unusual because the course augments the more typical laboratory-only experience. It's envisioned that the course will better equip students to do more advanced research rather than spending lab time learning to do the projects.
