DOI: 10.1128/aem.72.2.1558-1568.2006. Characterization of Metabolism in the Fe(III)-Reducing Organism <i>Geobacter sulfurreducens</i> by Constraint-Based Modeling

Characterization of Metabolism in the Fe(III)-Reducing Organism Geobacter sulfurreducens by Constraint-Based Modeling

10.1128/aem.72.2.1558-1568.2006

Crossref journal-article

American Society for Microbiology

Applied and Environmental Microbiology (235)

Abstract

ABSTRACT Geobacter sulfurreducens is a well-studied representative of the Geobacteraceae , which play a critical role in organic matter oxidation coupled to Fe(III) reduction, bioremediation of groundwater contaminated with organics or metals, and electricity production from waste organic matter. In order to investigate G. sulfurreducens central metabolism and electron transport, a metabolic model which integrated genome-based predictions with available genetic and physiological data was developed via the constraint-based modeling approach. Evaluation of the rates of proton production and consumption in the extracellular and cytoplasmic compartments revealed that energy conservation with extracellular electron acceptors, such as Fe(III), was limited relative to that associated with intracellular acceptors. This limitation was attributed to lack of cytoplasmic proton consumption during reduction of extracellular electron acceptors. Model-based analysis of the metabolic cost of producing an extracellular electron shuttle to promote electron transfer to insoluble Fe(III) oxides demonstrated why Geobacter species, which do not produce shuttles, have an energetic advantage over shuttle-producing Fe(III) reducers in subsurface environments. In silico analysis also revealed that the metabolic network of G. sulfurreducens could synthesize amino acids more efficiently than that of Escherichia coli due to the presence of a pyruvate-ferredoxin oxidoreductase, which catalyzes synthesis of pyruvate from acetate and carbon dioxide in a single step. In silico phenotypic analysis of deletion mutants demonstrated the capability of the model to explore the flexibility of G. sulfurreducens central metabolism and correctly predict mutant phenotypes. These results demonstrate that iterative modeling coupled with experimentation can accelerate the understanding of the physiology of poorly studied but environmentally relevant organisms and may help optimize their practical applications.

Bibliography

Mahadevan, R., Bond, D. R., Butler, J. E., Esteve-NunÌez, A., Coppi, M. V., Palsson, B. O., Schilling, C. H., & Lovley, D. R. (2006). Characterization of Metabolism in the Fe(III)-Reducing Organism Geobacter sulfurreducens by Constraint-Based Modeling. Applied and Environmental Microbiology, 72(2), 1558â1568.

Authors 8

R. Mahadevan (first)
D. R. Bond (additional)
J. E. Butler (additional)
A. Esteve-Nuñez (additional)
M. V. Coppi (additional)
B. O. Palsson (additional)
C. H. Schilling (additional)
D. R. Lovley (additional)

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Dates

Type	When
Created	19 years, 7 months ago (Feb. 3, 2006, 4:18 p.m.)
Deposited	3 years, 6 months ago (Feb. 23, 2022, 10:37 a.m.)
Indexed	37 minutes ago (Sept. 4, 2025, 2:43 a.m.)
Issued	19 years, 7 months ago (Feb. 1, 2006)
Published	19 years, 7 months ago (Feb. 1, 2006)
Published Print	19 years, 7 months ago (Feb. 1, 2006)

Funders 0

None

BibTeX

@article{Mahadevan_2006, title={Characterization of Metabolism in the Fe(III)-Reducing Organism Geobacter sulfurreducens by Constraint-Based Modeling}, volume={72}, ISSN={1098-5336}, url={http://dx.doi.org/10.1128/aem.72.2.1558-1568.2006}, DOI={10.1128/aem.72.2.1558-1568.2006}, number={2}, journal={Applied and Environmental Microbiology}, publisher={American Society for Microbiology}, author={Mahadevan, R. and Bond, D. R. and Butler, J. E. and Esteve-Nuñez, A. and Coppi, M. V. and Palsson, B. O. and Schilling, C. H. and Lovley, D. R.}, year={2006}, month=feb, pages={1558–1568} }

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