diCenzo2020 - Sinorhizobium meliloti 1021 genome-scale metabolic model

  public model
Model Identifier
MODEL2003240001
Short description
An updated representation of S. meliloti metabolism that was manually-curated and encompasses information from 240 literature sources, which includes transposon-sequencing (Tn-seq) data and Phenotype MicroArray data for wild-type and mutant strains.
Format
SBML (L3V1)
Related Publication
  • Genome-scale metabolic reconstruction of the symbiosis between a leguminous plant and a nitrogen-fixing bacterium.
  • George diCenzo, Tesi M, Pfau T, Mengoni A, Fondi M
  • Nature communications , 5/ 2020 , Volume 11 , Issue 1 , pages: 2574 , PubMed ID: 32444627
  • Department of Biology, University of Florence, Sesto Fiorentino, Italy.
  • The mutualistic association between leguminous plants and endosymbiotic rhizobial bacteria is a paradigmatic example of a symbiosis driven by metabolic exchanges. Here, we report the reconstruction and modelling of a genome-scale metabolic network of Medicago truncatula (plant) nodulated by Sinorhizobium meliloti (bacterium). The reconstructed nodule tissue contains five spatially distinct developmental zones and encompasses the metabolism of both the plant and the bacterium. Flux balance analysis (FBA) suggests that the metabolic costs associated with symbiotic nitrogen fixation are primarily related to supporting nitrogenase activity, and increasing N2-fixation efficiency is associated with diminishing returns in terms of plant growth. Our analyses support that differentiating bacteroids have access to sugars as major carbon sources, ammonium is the main nitrogen export product of N2-fixing bacteria, and N2 fixation depends on proton transfer from the plant cytoplasm to the bacteria through acidification of the peribacteroid space. We expect that our model, called 'Virtual Nodule Environment' (ViNE), will contribute to a better understanding of the functioning of legume nodules, and may guide experimental studies and engineering of symbiotic nitrogen fixation.
Contributors
George diCenzo

Metadata information

hasProperty
Mathematical Modelling Ontology Constraint-based model

Curation status
Non-curated

Modelling approach(es)

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Model files

iGD1348.xml SBML L3V1 representation of the Sinorhizobium meliloti iGD1348 genome-scale metabolic model 3.71 MB Preview | Download

  • Model originally submitted by : George diCenzo
  • Submitted: May 30, 2020 2:41:20 PM
  • Last Modified: May 30, 2020 2:41:20 PM
Revisions
  • Version: 4 public model Download this version
    • Submitted on: May 30, 2020 2:41:20 PM
    • Submitted by: George diCenzo
    • With comment: Edited model metadata online.
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