GEM-iPfu, Genome-scale metabolic model of Pyrococcus furiosus

Files in this repository represent the genome-scale model of Pyrococcus furiosus. The model is first reported in the following publication:

• Vailionis, J. Zhao, W., Zhang, K., Rodionov, D., Lipscomb, G. L., Tanwee, T. N. N., O'Quinn, H. C., Kelly R. M., Adams, M. W. W., Zhang, Y. 2023. Optimizing strategies for bio- based ethanol production using genome-scale metabolic model of the hyperthermophilic archaeon, Pyrococcus furiosus. Appl. Environ. Microbiol.

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

List of files

Model files

• model.yaml

  Basic model definition YAML file, configured for the WT model by default

• model_product.yaml

  alternative model definition YAML file, configured to use the EX_YM_adhf.yaml media file and COM1 model by default, which requires additional files to be loaded

Model definitions

• WT_model_def.tsv

  list of reactions that make up the WT (DSM 3638) model

• COM1_model_def.tsv

  list of reactions that make up the COM1 model

• media_def.tsv

  includes additional components that are required to use the EX_YM_adhf.tsv media

Model components

• compounds.yaml

  definition of metabolites

• reactions.yaml

  definition of reactions based on genome annotations of the P. furiosus DSM 3638

• engineered_reactions.yaml

  definition of reactions related to the simulation of engineering designs in P. furiosus

• limits.yaml

  defines bounds on specific reactions that can differ from their enzymatic directionality

• sink.yaml

  definition of compound sink reactions

• transport.yaml

  definition of transport reactions

• EX_byproduct.yaml

  exchange file which allows potential byproducts to be released

• spontaneous.yaml

  definition of spontaneous/non-enzymatic reactions

• biomass.yaml

  definition of biomass reactions

• gapfill.yaml

  gap-filling reactions

• media_compounds.yaml

  additional compounds that are required to use the EX_YM_adhf.tsv media

• media_conversion_rxns.yaml

  additional reactions that are required to use the EX_YM_adhf.tsv media

Media definitions

• EX_Kengen_94.tsv

  Media matching experiments from Kengen and Stams 1994 (Growth and energy conservation in batch cultures of Pyrococcus furiosus. FEMS Microbiol Lett 117:305–309.)

• Adams_media/*

  Media matching various carbon conditions from Adams et al. 2001. (Key Role for Sulfur in Peptide Metabolism and in Regulation of Three Hydrogenases in the Hyperthermophilic Archaeon Pyrococcus furiosus. J Bacteriol 183:716–724.)

  Inlcudes three files:

  • EX_Adams_Peptide-S0.tsv - Peptide medium with sulfur
  • EX_Adams_Malt-Peptide-S0.tsv - Peptide + maltose medium with sulfur
  • EX_Adams_Malt-S0.tsv - Maltose medium with sulfur

• EX_YM_adhf.tsv

  minimal maltose medium, can be configured to use different concentrations of yeast extract