Research article

Genome-scale constraint-based modeling of Geobacter metallireducens

Jun Sun¹ , Bahareh Sayyar² , Jessica E Butler³ , Priti Pharkya¹ , Tom R Fahland¹ , Iman Famili¹ , Christophe H Schilling¹ , Derek R Lovley³ and Radhakrishnan Mahadevan²

¹Genomatica Inc., 10520 Wateridge Circle, San Diego, CA, USA

²Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada

³Department of Microbiology, University of Massachusetts, Amherst, MA, USA

author email corresponding author email

BMC Systems Biology 2009, 3:15doi:10.1186/1752-0509-3-15

Published:	28 January 2009

Abstract

Background

Geobacter metallireducens was the first organism that can be grown in pure culture to completely oxidize organic compounds with Fe(III) oxide serving as electron acceptor. Geobacter species, including G. sulfurreducens and G. metallireducens, are used for bioremediation and electricity generation from waste organic matter and renewable biomass. The constraint-based modeling approach enables the development of genome-scale in silico models that can predict the behavior of complex biological systems and their responses to the environments. Such a modeling approach was applied to provide physiological and ecological insights on the metabolism of G. metallireducens.

Results

The genome-scale metabolic model of G. metallireducens was constructed to include 747 genes and 697 reactions. Compared to the G. sulfurreducens model, the G. metallireducens metabolic model contains 118 unique reactions that reflect many of G. metallireducens' specific metabolic capabilities. Detailed examination of the G. metallireducens model suggests that its central metabolism contains several energy-inefficient reactions that are not present in the G. sulfurreducens model. Experimental biomass yield of G. metallireducens growing on pyruvate was lower than the predicted optimal biomass yield. Microarray data of G. metallireducens growing with benzoate and acetate indicated that genes encoding these energy-inefficient reactions were up-regulated by benzoate. These results suggested that the energy-inefficient reactions were likely turned off during G. metallireducens growth with acetate for optimal biomass yield, but were up-regulated during growth with complex electron donors such as benzoate for rapid energy generation. Furthermore, several computational modeling approaches were applied to accelerate G. metallireducens research. For example, growth of G. metallireducens with different electron donors and electron acceptors were studied using the genome-scale metabolic model, which provided a fast and cost-effective way to understand the metabolism of G. metallireducens.

Conclusion

We have developed a genome-scale metabolic model for G. metallireducens that features both metabolic similarities and differences to the published model for its close relative, G. sulfurreducens. Together these metabolic models provide an important resource for improving strategies on bioremediation and bioenergy generation.