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Wild Legumes and Microbes as Novel Sources of Genes to Facilitate Systems Level Understanding of Biofuel Production

Enhanced production of bioenergy is a critical national need to reduce dependency on fossil fuel consumption. The two primary approaches for bioenergy production are: (i) to take advantage of the natural ability of plants and microbes to synthesize oil rich products which can be used for biofuel production; (ii) to convert plant biomass to ethanol via microbial fermentation processes. We propose a coordinated effort to utilize the unique features of legumes (Fabaceae/Leguminosae) to improve bioenergy production by both approaches. Using high throughput transcriptomics, metabolomics, and bioinformatics we will unlock the genetic content of domesticated and wild legumes that produce oil rich seeds, and the capability of their rhizobial partners to utilize pentose sugars including xylose, a key lignocellulose constituent, to uncover novel genes and pathways that can be used to improve biofuel production. In the U.S. Sonoran Desert alone 8% of the plants (> 53 species) are legumes (e.g., the Desert Legume Program ) that could provide a source of novel genetic information useful in the manipulation of relevant seed oil production pathways for biofuel production. For example, Jatropha (Pongamia pinnata), a large shrub suited to arid growth conditions and Pongamia (Milletia pinnata), a plant that tolerates drought, frost, and salty soils, both produce unique oil-rich seeds whose biochemical and genetic characteristics are unknown and therefore underexploited. Full scale genomic data are available from soybean and Medicago, and near complete genome sequences have been generated for Lotus, Phaseolus (common bean), and Vigna (cowpea), facilitating gene prospecting in other wild and unexploited legumes. Approximately 1,110 of the 46,000 predicted genes in the soybean genome were suggested to be involved in lipid metabolism. These genes represent potential targets for modification that could bolster output and increase the use of oil for biodiesel production.

Another unique feature of legumes is the symbiotic relationship with nitrogen fixing Rhizobia species. Rhizobia are uniquely adapted to efficiently utilize pentose sugars secreted from host plants. Xylose, one of these sugars, is a major product of lignocellulose breakdown. The most efficient current fermentation processes use genetically engineered S. cerevisiae expressing xylose breakdown enzymes (e.g., 424A(LNH-ST)) from other microbial species to enable utilization of xylose as carbon source for production of ethanol. In addition, the arid land rhizosphere ecosystem harbors diverse, largely unexplored microbial communities including fungi that are extremely efficient in soil organic carbon assimilation, and, therefore, provides an excellent source of novel extracellular enzymes that can function in extreme environments (temperature, salt, pH etc). We will survey the diverse rhizosphere microbial communities associated with wild legumes for novel xylose utilization and lignocellulolytic degradation traits which can further improve microbial mediated fermentation processes.

Integral to this effort will be the development of cyber-infrastructure to manage and integrate multi-dimensional systems biology datasets, conduct data mining for gene and pathway discovery, and coordinate validation to facilitate a systems level understanding of processes leading to enhanced biofuel production.

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