Feist2014 - Geobacter metallireducens GS-15 metabolism

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Model Identifier
MODEL2204190002
Short description
Geobacter species are of great interest for environmental and biotechnology applications as they can carry out direct electron transfer to insoluble metals or other microorganisms and have the ability to assimilate inorganic carbon. Here, we report on the capability and key enabling metabolic machinery of Geobacter metallireducens GS-15 to carry out CO2 fixation and direct electron transfer to iron. An updated metabolic reconstruction was generated, growth screens on targeted conditions of interest were performed, and constraint-based analysis was utilized to characterize and evaluate critical pathways and reactions in G. metallireducens. The novel capability of G. metallireducens to grow autotrophically with formate and Fe(III) was predicted and subsequently validated in vivo. Additionally, the energetic cost of transferring electrons to an external electron acceptor was determined through analysis of growth experiments carried out using three different electron acceptors (Fe(III), nitrate, and fumarate) by systematically isolating and examining different parts of the electron transport chain. The updated reconstruction will serve as a knowledgebase for understanding and engineering Geobacter and similar species.
Format
SBML (L3V1)
Related Publication
  • Constraint-based modeling of carbon fixation and the energetics of electron transfer in Geobacter metallireducens.
  • Feist AM, Nagarajan H, Rotaru AE, Tremblay PL, Zhang T, Nevin KP, Lovley DR, Zengler K
  • PLoS computational biology , 4/ 2014 , Volume 10 , Issue 4 , pages: e1003575 , DOI: 10.1371/journal.pcbi.1003575
  • Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America.
  • Geobacter species are of great interest for environmental and biotechnology applications as they can carry out direct electron transfer to insoluble metals or other microorganisms and have the ability to assimilate inorganic carbon. Here, we report on the capability and key enabling metabolic machinery of Geobacter metallireducens GS-15 to carry out CO2 fixation and direct electron transfer to iron. An updated metabolic reconstruction was generated, growth screens on targeted conditions of interest were performed, and constraint-based analysis was utilized to characterize and evaluate critical pathways and reactions in G. metallireducens. The novel capability of G. metallireducens to grow autotrophically with formate and Fe(III) was predicted and subsequently validated in vivo. Additionally, the energetic cost of transferring electrons to an external electron acceptor was determined through analysis of growth experiments carried out using three different electron acceptors (Fe(III), nitrate, and fumarate) by systematically isolating and examining different parts of the electron transport chain. The updated reconstruction will serve as a knowledgebase for understanding and engineering Geobacter and similar species.
Contributors
Submitter of the first revision: Rodrigo Santibanez
Submitter of this revision: Rodrigo Santibanez
Modellers: Rodrigo Santibanez

Metadata information

hasProperty
Mathematical Modelling Ontology Constraint-based model

Curation status
Non-curated

Modelling approach(es)

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Model files

Gmetallireducens_ac_Fe Updated.xml SBML L2V4 representation of Geobacter metallireducens GS-15 metabolism model. 2.76 MB Preview | Download

Additional files

01_objective.tsv FROG report 85.00 Bytes Preview | Download
02_fva.tsv FROG report 94.14 KB Preview | Download
03_gene_deletion.tsv FROG report 34.00 Bytes Preview | Download
04_reaction_deletion.tsv FROG report 80.40 KB Preview | Download
Gmetallireducens_ac_dcuB Updated.xml SBML L2V4 representation of Geobacter metallireducens GS-15, strain dcuB metabolism model. 2.88 MB Preview | Download
metadata.json FROG report 354.00 Bytes Preview | Download
miniFROG_Geobacter.xlsx miniFROG report 15.67 KB Preview | Download

  • Model originally submitted by : Rodrigo Santibanez
  • Submitted: Apr 19, 2022 2:29:42 AM
  • Last Modified: Apr 19, 2022 2:29:42 AM
Revisions
  • Version: 1 public model Download this version
    • Submitted on: Apr 19, 2022 2:29:42 AM
    • Submitted by: Rodrigo Santibanez
    • With comment: Import of Feist2014 - Geobacter metallireducens GS-15 metabolism