Analysis of Superfamily of Plant Genes Yielding Insights to Assist in Optimizing Plants for Biofuel Production

12 April 2009

By studying a superfamily of genes in Populus and Arabidopsis, scientists at the US Department of Energy’s Brookhaven National Laboratory are gaining insights that may assist in engineering plants to be more tractable for biofuel production. The study, published online 3 April in the journal Plant Molecular Biology, also lays a foundation for understanding these genes’ evolutionary and structural properties and for a broader exploration of their roles in plant life.

The team, led by Dr. Chang-Jun Liu, is studying the large specific protein superfamily BAHD, which comprises plant acyl-CoA dependent acyltransferases. Acyl groups attached to cell-wall fibers can act as barriers to hinder the conversion of plant biofibers to sugar. Acyl groups can also form cross-linked networks that make cell walls extra strong.

The Brookhaven researchers searched the genome sequences of Populus (poplar tree) and Arabidopsis (a small flowering plant widely used as a model organism in plant biology), and identified 94 and 61 genes they suspected belonged to this family in those two species, respectively.

They then looked at how the genes were expressed—activated to make their enzyme products—in different parts of the plants. Of particular interest to Liu’s group were a number of genes expressed at high levels in the woody plant tissues.

Our long-term interest is to find the enzymes that control the formation of cell-wall-bound acyl groups, so we can learn how to modify plant cell walls to increase their digestibility. The current study, a thorough investigation of an acyl-modifying enzyme family, provides a starting point for us to pursue this goal.

—Chang-Jun Liu

Some of the genes the scientists found to be expressed at high levels in woody tissues may carry the genetic instructions for making the enzymes the scientists would like to control. The next step will be to use biochemical and biophysical approaches to characterize these individual genes’ functions to find those directly or indirectly related to cell-wall modification. Those genes can then be used to engineer new bioenergy crops for subsequent evaluation as to whether those changes improve the efficiency of converting biomass to biofuel, Liu said.

Liu’s group also discovered a few unique pairs of genes that were inversely overlapped with their neighboring genes on the genome. In this unique organization, the paired genes (sequences of DNA) produce protein-encoding segments (RNAs) that are complementary to one another—meaning the two RNA strands would stick to each other like highly specific Velcro. That would prevent the RNA from building its enzyme, so the expression of one gene in the pair appears to inhibit its partner.

Understanding this natural “anti-sense” regulation for gene expression may assist scientists in their attempts to regulate acyl-modifying enzyme levels.

This work was supported by the DOE-Department of Agriculture joint Plant Feedstock Genomics program and by Brookhaven’s Laboratory Directed Research and Development program. Funding was also provided by DOE’s Office of Science. In addition to Liu, Xiao-Hong Yu, a former postdoctoral research associate, and Jinying Gou, a current postdoc, contributed to this work.

Resources

• Xiao-Hong Yu, Jin-Ying Gou and Chang-Jun Liu (2009) BAHD superfamily of acyl-CoA dependent acyltransferases in Populus and Arabidopsis : bioinformatics and gene expression. Plant Molecular Biology, doi: 10.1007/s11103-009-9482-1