Pereira2018 - Genome-scale metabolic model for Actinobacillus succinogenes 130Z

  public model
Short description

The model, iBP722, was reconstructed based on the functional reannotation of the complete genome sequence of A. succinogenes 130Z and manual inspection of metabolic pathways, covering 1072 enzymatic reactions associated with 722 metabolic genes that involve 713 metabolites. The highly curated model was effective in capturing the growth of A. succinogenes on various carbon sources, as well as the SA production under various growth conditions with fair agreement between experimental and predicted data. Calculated flux distributions under different conditions show that a number of metabolic pathways are affected by the activity of some metabolic enzymes at key nodes in metabolism, including the transport mechanism of carbon sources and the ability to fix carbon dioxide.

Format
SBML (L2V1)
Related Publication
  • Reconstruction of a genome-scale metabolic model for Actinobacillus succinogenes 130Z.
  • Pereira B, Miguel J, Vilaça P, Soares S, Rocha I, Carneiro S, Carneiro S
  • BMC systems biology , 5/ 2018 , Volume 12 , Issue 1 , pages: 61
  • SilicoLife Lda, Rua do Canastreiro 15, 4715-387, Braga, Portugal. CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal. Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal. SilicoLife Lda, Rua do Canastreiro 15, 4715-387, Braga, Portugal. scarneiro@silicolife.com.
  • Actinobacillus succinogenes is a promising bacterial catalyst for the bioproduction of succinic acid from low-cost raw materials. In this work, a genome-scale metabolic model was reconstructed and used to assess the metabolic capabilities of this microorganism under producing conditions.The model, iBP722, was reconstructed based on the functional reannotation of the complete genome sequence of A. succinogenes 130Z and manual inspection of metabolic pathways, covering 1072 enzymatic reactions associated with 722 metabolic genes that involve 713 metabolites. The highly curated model was effective in capturing the growth of A. succinogenes on various carbon sources, as well as the SA production under various growth conditions with fair agreement between experimental and predicted data. Calculated flux distributions under different conditions show that a number of metabolic pathways are affected by the activity of some metabolic enzymes at key nodes in metabolism, including the transport mechanism of carbon sources and the ability to fix carbon dioxide.The established genome-scale metabolic model can be used for model-driven strain design and medium alteration to improve succinic acid yields.
Contributors
Sónia, Rahuman Sheriff

Metadata information


Curation status
Non-curated

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Model files

iBP722.xml SBML L2V1 representation of Genome-scale metabolic model for Actinobacillus succinogenes 130Z 1.35 MB Preview | Download

  • Model originally submitted by : Sónia
  • Submitted: May 16, 2019 5:56:20 PM
  • Last Modified: May 16, 2019 5:56:20 PM
Revisions
  • Version: 6 public model Download this version
    • Submitted on: May 16, 2019 5:56:20 PM
    • Submitted by: Rahuman Sheriff
    • With comment: Edited model metadata online.