Using the System

Science's hopes of great strides in the pursuit of economical bioenergy depend on the ability to understand how components of a living cell work together.

Learning the function of a single gene or protein is valuable, but science's hopes of great strides in the pursuit of economical bioenergy depend on the ability to understand how components of a living cell or more complex biological systems work together. Such "systems biology" research lies at the heart of the Genomics: Genomes to Life program of the Department of Energy.

A genetically modified poplar is shorter, stockier and richer in leaves (right and left) than the wild-type tree (center).

Accelerating the domestication and increasing the productivity of poplar trees and other energy crops will require new systems biology approaches. So will improving the efficiency and decreasing the costs of microbial enzymes used to convert wood cellulose to sugar and then ethanol in biorefineries.

At the turn of the century, the possibility of performing systems biology emerged with the completion of various genome sequencing projects, the proliferation of genomic and proteomic data and accompanying advances in experimental and computer simulation methodologies.

Brian Davison, ORNL's chief scientist for systems biology and biotechnology, says that ORNL now possesses the suite of "omics" capabilities that make systems biology possible: genomics, transcriptomics, proteomics, interactomics and metabolomics. "Together these are giving ORNL researchers a deeper picture of how a microbe like hydrogen-producing Rhodopseudomonas palustris works, helping identify where improvements can be made by altering protein production coded for by specific genes," Davison says.

In an ORNL project led by Tim Tschaplinski to improve the productivity of drought-stressed poplar trees, researchers used metabolomics to characterize the effects of single gene changes on chemical products of plant metabolism. They analyzed and attempted to identify the genes controlling the production of 58 metabolites made by the normal poplar genome. They also examine the impacts on the plant cell's pool of metabolites of boosting the activity of natural drought tolerance genes to increase water amounts extracted from the soil.

Another ORNL team led by Jonathan Mielenz is applying transcriptomics to understand better the biology of Clostridium thermocellum, a bacterium originally genetically engineered at Dartmouth College to improve its unusual ability to convert pure cellulose to alcohol. By studying the bacterium's gene expression using microarrays they developed, they hope to guide modification of the microbe so it can both digest pretreated, impure cellulose from plant biomass and produce pure ethanol fuel.

Early ORNL research results are reinforcing DOE's confidence that systems biology will help researchers break the biological barriers to economical bioenergy.—Carolyn Krause

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