Plant protein discovery could boost bioeconomy

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," said Ryan Philippe, a post-doctoral researcher in Noel's lab.

First authors of the paper are Micheline Ngaki, a Fulbright Scholar from the Congo and a graduate student in genetics, development and cell biology at Iowa State; Gordon Louie, a research scientist at the Salk Institute; and Philippe. Other collaborators include Ling Li, an Iowa State adjunct assistant professor and associate scientist in genetics, development and cell biology; Gerard Manning, director of Salk's Razavi Newman Center for Bioinformatics; and Marianne Bowman, Florence Pojer and Elise Larsen, Howard Hughes Medical Institute researchers in the Salk's Skirball Center.

The project was supported in part by the National Science Foundation including the Engineering Research Center for Biorenewable Chemicals based at Iowa State, the National Cancer Institute, the Howard Hughes Medical Institute and Ngaki's Fulbright award. Additional support came from Iowa State's Plant Sciences Institute.

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," said 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 said. 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 said, could point to new directions in biological studies.

"We are entering the age of predictive biology," Wurtele said. "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."