One plant yields 3 clues to biofuel crops

The analysis of gene activity by researchers at Iowa State University and determination of protein structures by scientists at the Salk Institute for Biological Sciences independently identified three related proteins that appear to be involved in fatty-acid metabolism. The researchers used thale cress (Arabidopsis thaliana) as the model plant. The research groups then joined forces to test this hypothesis, demonstrating a role of these proteins in regulating the amounts and types of fatty acids accumulated in plants. The researchers also showed that the action of the proteins is very sensitive to temperature and that this feature may play an important role in how plants mitigate temperature stress using fatty acids. The discovery is published online in the journal Nature. “This work has major implications for modulating the fatty-acid profiles in plants, which is terribly important, not only to sustainable food production and nutrition but now also to biorenewable chemicals and fuels,” says corresponding author Joseph Noel, a professor and director of the Jack H. Skirball Center for Chemical Biology and Proteomics at the Salk Institute and an investigator with the Howard Hughes Medical Institute. “Because very high-energy molecules such as fatty acids are created in the plant using the energy of the sun, these types of molecules may ultimately provide the most cost-effective and efficient sources for biorenewable products,” adds Iowa State genetic professor Eve Syrkin Wurtele, also a corresponding author of the study. Although the researchers now understand that the three proteins—dubbed fatty-acid-binding proteins one, two, and three, or FAP1, FAP2, and FAP3—are involved in fatty-acid accumulation in plant tissues such as leaves and seeds, Wurtele says researchers still don’t understand the physical mechanism these proteins employ at the molecular level. That knowledge will ultimately allow the two collaborating research groups to predictably engineer better functions in plants. To identify the proteins’ function in plants, Wurtele’s research group used its expertise in molecular biology and bioinformatics, the application of computer technologies to biological studies. One tool the Iowa State researchers used was MetaOmGraph, software they developed to analyze large sets of public data about the patterns of gene activity under different developmental, environmental, and genetic changes. The software revealed that the expression patterns of the FAP genes resemble those of genes encoding enzymes of fatty-acid synthesis. The analyses also showed that the accumulation of two of the proteins is highest in the regions of the plant where the greatest amount of oil is produced. These clues led the researchers to predict that the three FAP proteins are important for fatty-acid accumulation. The Iowa State researchers then tested this theory experimentally by comparing the fatty acids of mutant plants lacking the FAP proteins to those of normal plants. Despite the healthy appearance of the mutant plants, the overall fatty-acid content is greater than in the normal plants, and the types of fatty acids differ. Noel and researchers at the Salk Institute used a variety of techniques—including X-ray crystallography and biochemistry—to characterize the structures of the FAP1, FAP2, and FAP3 proteins, and to determine that the proteins bind fatty acids. “The proteins appear to be crucial missing links in the metabolism of fatty acids in Arabidopsis, and likely serve a similar function in other plant species since we find the same genes spread throughout the plant kingdom,” says Ryan Philippe, a post-doctoral researcher in Noel’s lab. Discovery of the connection between the FAP proteins and plant fatty acids could be very useful to plant scientists. “If the researchers can understand precisely what role the proteins play in seed oil production,” says first author Micheline Ngaki, “they might be able to modify the proteins’ activity in new plant strains that produce more oil or higher quality oil than current crops.” Further, if the three proteins help plants regulate stress, plant scientists might be able to exploit that trait to develop plants that are more resistant to stress, Wurtele says. And that could allow farmers to grow crops for biorenewable fuels and chemicals on marginal land that’s not suited for food crops. All of this, she says, could point to new directions in biological studies. “We are entering the age of predictive biology,” Wurtele says. “That means harnessing computational approaches to deduce gene function, model biological processes and predict the consequences of altering a single gene to the complex biological network of an organism.” First authors of the paper are Ngaki, Gordon Louie of the Salk Institute, and Ling Li of Iowa State. Additional scientists from both the Salk Institute and Iowa State contributed to the project, which was supported in part by the National Science Foundation, including Iowa State’s Engineering Research Center for Biorenewable Chemicals, as well as the National Cancer Institute, the Howard Hughes Medical Institute, and Ngaki’s Fulbright award, and Iowa State’s Plant Sciences Institute.