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

Files in this repository represent the genome-scale model of Pyrococcus furiosus. The following are publications associated with the model with simulation code saved in this repository:

• Vailionis, Jason L., Weishu Zhao, Ke Zhang, Dmitry A. Rodionov, Gina L. Lipscomb, Tania N. N. Tanwee, Hailey C. O’Quinn, et al. 2023. “Optimizing Strategies for Bio-Based Ethanol Production Using Genome-Scale Metabolic Modeling of the Hyperthermophilic Archaeon, Pyrococcus Furiosus.” Applied and Environmental Microbiology 89 (6): e0056323.
• O’Quinn, Hailey, Jason Vailionis, Tania Tanwee, Katherine Holandez-Lopez, Ryan Bing, Farris Poole, Ying Zhang, Robert Kelly, and Michael Adams. 2025. “Engineering the Hyperthermophilic Archaeon Pyrococcus Furiosus for 1-Propanol Production.” Applied and Environmental Microbiology.

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

• sbmls/

  snapshots of specific model configurations saved in sbml format

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

• COM1-xyl_model_def.tsv

  list of reactions that make up the COM1 model with engineered xylose consumption pathway from Thermotoga maritima

• propanol_model_def.tsv

  list of reactions that make up the COM1 model with engineered propanol production pathway

• 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

• tmfa_inputs/

  input files required to perform thermodynamic flux balance analysis with PSAMM, including ΔG° predictions for most reactions

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

Manuscript simulations

• manuscripts/Vailionis_2023

  Jupyter notebooks with code to perform all modeling analysis and generate figures in Vailionis et al. 2023

• manuscripts/OQuinn_2025

  Jupyter notebooks with code to perform all modeling analysis and generate figures in O'Quinn et al. 2025