Islam2010_Dehalococcoides_Metabolism

  public model
Model Identifier
MODEL1011080003
Short description

This is metabolic network reconstruction of Dehalococcoides , iAI549, described in the article
Characterizing the metabolism of dehalococcoides with a constraint-based model.
Ahsanul Islam M, Edwards EA, Mahadevan R. PLoS Comput Biol. 2010 Aug 19;6(8). pii: e1000887. PMID: 20811585 , DOI: 10.1371/journal.pcbi.1000887

Abstract:
Dehalococcoides strains respire a wide variety of chloro-organic compounds and are important for the bioremediation of toxic, persistent, carcinogenic, and ubiquitous ground water pollutants. In order to better understand metabolism and optimize their application, we have developed a pan-genome-scale metabolic network and constraint-based metabolic model of Dehalococcoides. The pan-genome was constructed from publicly available complete genome sequences of Dehalococcoides sp. strain CBDB1, strain 195, strain BAV1, and strain VS. We found that Dehalococcoides pan-genome consisted of 1118 core genes (shared by all), 457 dispensable genes (shared by some), and 486 unique genes (found in only one genome). The model included 549 metabolic genes that encoded 356 proteins catalyzing 497 gene-associated model reactions. Of these 497 reactions, 477 were associated with core metabolic genes, 18 with dispensable genes, and 2 with unique genes. This study, in addition to analyzing the metabolism of an environmentally important phylogenetic group on a pan-genome scale, provides valuable insights into Dehalococcoides metabolic limitations, low growth yields, and energy conservation. The model also provides a framework to anchor and compare disparate experimental data, as well as to give insights on the physiological impact of "incomplete" pathways, such as the TCA-cycle, CO(2) fixation, and cobalamin biosynthesis pathways. The model, referred to as iAI549, highlights the specialized and highly conserved nature of Dehalococcoides metabolism, and suggests that evolution of Dehalococcoides species is driven by the electron acceptor availability.

This model was downloaded from the supplementary materials to the article.

This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

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To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Format
SBML (L2V1)
Related Publication
  • Characterizing the metabolism of Dehalococcoides with a constraint-based model.
  • Ahsanul Islam M, Edwards EA, Mahadevan R
  • PLoS computational biology , 0/ 2010 , Volume 6 , pages: 1657-1680 , PubMed ID: 20811585
  • Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada.
  • Dehalococcoides strains respire a wide variety of chloro-organic compounds and are important for the bioremediation of toxic, persistent, carcinogenic, and ubiquitous ground water pollutants. In order to better understand metabolism and optimize their application, we have developed a pan-genome-scale metabolic network and constraint-based metabolic model of Dehalococcoides. The pan-genome was constructed from publicly available complete genome sequences of Dehalococcoides sp. strain CBDB1, strain 195, strain BAV1, and strain VS. We found that Dehalococcoides pan-genome consisted of 1118 core genes (shared by all), 457 dispensable genes (shared by some), and 486 unique genes (found in only one genome). The model included 549 metabolic genes that encoded 356 proteins catalyzing 497 gene-associated model reactions. Of these 497 reactions, 477 were associated with core metabolic genes, 18 with dispensable genes, and 2 with unique genes. This study, in addition to analyzing the metabolism of an environmentally important phylogenetic group on a pan-genome scale, provides valuable insights into Dehalococcoides metabolic limitations, low growth yields, and energy conservation. The model also provides a framework to anchor and compare disparate experimental data, as well as to give insights on the physiological impact of "incomplete" pathways, such as the TCA-cycle, CO(2) fixation, and cobalamin biosynthesis pathways. The model, referred to as iAI549, highlights the specialized and highly conserved nature of Dehalococcoides metabolism, and suggests that evolution of Dehalococcoides species is driven by the electron acceptor availability.
Contributors
Lukas Endler

Metadata information

is
BioModels Database MODEL1011080003
isDescribedBy
PubMed 20811585
isVersionOf
Gene Ontology regulation of growth

Curation status
Non-curated

Original model(s)
http://www.ploscompbiol.org/article/fetchSingleRepresentation.action?uri=info:doi/10.1371/journal.pcbi.1000887.s001

Tags
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Model files

MODEL1011080003_url.xml SBML L2V1 representation of Islam2010_Dehalococcoides_Metabolism 470.68 KB Preview | Download

Additional files

MODEL1011080003-biopax3.owl Auto-generated BioPAX (Level 3) 2.13 MB Preview | Download
MODEL1011080003-biopax2.owl Auto-generated BioPAX (Level 2) 1.10 MB Preview | Download
MODEL1011080003.png Auto-generated Reaction graph (PNG) 5.07 KB Preview | Download
MODEL1011080003.vcml Auto-generated VCML file 637.00 bytes Preview | Download
MODEL1011080003.sci Auto-generated Scilab file 101.27 KB Preview | Download
MODEL1011080003.svg Auto-generated Reaction graph (SVG) 861.00 bytes Preview | Download
MODEL1011080003_urn.xml Auto-generated SBML file with URNs 515.10 KB Preview | Download
MODEL1011080003.m Auto-generated Octave file 743.00 bytes Preview | Download
MODEL1011080003.xpp Auto-generated XPP file 365.00 bytes Preview | Download
MODEL1011080003.pdf Auto-generated PDF file 2.02 MB Preview | Download

  • Model originally submitted by : Lukas Endler
  • Submitted: 08-Nov-2010 14:33:03
  • Last Modified: 08-Nov-2010 14:39:28
Revisions
  • Version: 2 public model Download this version
    • Submitted on: 08-Nov-2010 14:39:28
    • Submitted by: Lukas Endler
    • With comment: Current version of Islam2010_Dehalococcoides_Metabolism
  • Version: 1 public model Download this version
    • Submitted on: 08-Nov-2010 14:33:03
    • Submitted by: Lukas Endler
    • With comment: Original import of Islam2010_Dehalococcoides_Metabolism
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