Genome-scale constraint-based modeling of Geobacter metallireducens

Jun Sun, Bahareh Sayyar, Jessica E Butler, Priti Pharkya, Tom R Fahland, Iman Famili, Christophe H Schilling, Derek R Lovley, Radhakrishnan Mahadevan

Research output: Contribution to journalArticle

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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.

Original languageEnglish
Article number15
Number of pages15
JournalBMC Systems Biology
Volume3
DOIs
Publication statusPublished - 28 Jan 2009

Fingerprint

Geobacter
Biomass
Benzoates
Genome
Genes
Electrons
Environmental Biodegradation
Modeling
Acetates
Growth
Electricity
Metabolism
Electron
Pyruvic Acid
Model
Computer Simulation
Oxides
Bioremediation
Energy
Costs and Cost Analysis

Keywords

  • biodegradation, environmental
  • biomass
  • computer simulation
  • ecosystem
  • electron transport
  • energy metabolism
  • genome, bacterial
  • Geobacter
  • iron
  • metabolic networks and pathways
  • models, biological
  • models, genetic
  • mutation
  • phenotype
  • species specificity
  • systems biology

Cite this

Sun, J., Sayyar, B., Butler, J. E., Pharkya, P., Fahland, T. R., Famili, I., ... Mahadevan, R. (2009). Genome-scale constraint-based modeling of Geobacter metallireducens. BMC Systems Biology, 3, [15]. https://doi.org/10.1186/1752-0509-3-15

Genome-scale constraint-based modeling of Geobacter metallireducens. / Sun, Jun; Sayyar, Bahareh; Butler, Jessica E; Pharkya, Priti; Fahland, Tom R; Famili, Iman; Schilling, Christophe H; Lovley, Derek R; Mahadevan, Radhakrishnan.

In: BMC Systems Biology, Vol. 3, 15, 28.01.2009.

Research output: Contribution to journalArticle

Sun, J, Sayyar, B, Butler, JE, Pharkya, P, Fahland, TR, Famili, I, Schilling, CH, Lovley, DR & Mahadevan, R 2009, 'Genome-scale constraint-based modeling of Geobacter metallireducens', BMC Systems Biology, vol. 3, 15. https://doi.org/10.1186/1752-0509-3-15
Sun, Jun ; Sayyar, Bahareh ; Butler, Jessica E ; Pharkya, Priti ; Fahland, Tom R ; Famili, Iman ; Schilling, Christophe H ; Lovley, Derek R ; Mahadevan, Radhakrishnan. / Genome-scale constraint-based modeling of Geobacter metallireducens. In: BMC Systems Biology. 2009 ; Vol. 3.
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N2 - 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.

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KW - biomass

KW - computer simulation

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KW - electron transport

KW - energy metabolism

KW - genome, bacterial

KW - Geobacter

KW - iron

KW - metabolic networks and pathways

KW - models, biological

KW - models, genetic

KW - mutation

KW - phenotype

KW - species specificity

KW - systems biology

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