Kim2011_VvuMBEL943_2022

  public model
Model Identifier
BIOMD0000001064
Short description

This is a model of the genome scale reconstruction of the Vibrio vulnificus metabolic network, VvuMBEL943, described in the article:
Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery
Hyun Uk Kim, Soo Young Kim, Haeyoung Jeong, Tae Yong Kim, Jae Jong Kim, Hyon E Choy, Kyu Yang Yi, Joon Haeng Rhee, and Sang Yup Lee. Molecular Systems Biology 7:460 Jan 2011 doi: 10.1038/msb.2010.115

Abstract:
Although the genomes of many microbial pathogens have been studied to help identify effective drug targets and novel drugs, such efforts have not yet reached full fruition. In this study, we report a systems biological approach that efficiently utilizes genomic information for drug targeting and discovery, and apply this approach to the opportunistic pathogen Vibrio vulnificus CMCP6. First, we partially re-sequenced and fully re-annotated the V. vulnificus CMCP6 genome, and accordingly reconstructed its genome-scale metabolic network, VvuMBEL943. The validated network model was employed to systematically predict drug targets using the concept of metabolite essentiality, along with additional filtering criteria. Target genes encoding enzymes that interact with the five essential metabolites finally selected were experimentally validated. These five essential metabolites are critical to the survival of the cell, and hence were used to guide the cost-effective selection of chemical analogs, which were then screened for antimicrobial activity in a whole-cell assay. This approach is expected to help fill the existing gap between genomics and drug discovery.

This metabolic network model has been thoroughly validated by the authors. VvuMBEL943 is a stoichiometric model that contains the metabolic information of the microbial pathogen, Vibrio vulnificus CMCP6, at genome-scale. The SBML version was generated by Hyun Uk Kim using MetaFluxNet.

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.

In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not..

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 (L3V1)
Related Publication
  • Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery.
  • Kim HU, Kim SY, Jeong H, Kim TY, Kim JJ, Choy HE, Yi KY, Rhee JH, Lee SY
  • Molecular Systems Biology , 1/ 2011 , Volume 7 , pages: 460 , PubMed ID: 21245845
  • Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 program), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.
  • Although the genomes of many microbial pathogens have been studied to help identify effective drug targets and novel drugs, such efforts have not yet reached full fruition. In this study, we report a systems biological approach that efficiently utilizes genomic information for drug targeting and discovery, and apply this approach to the opportunistic pathogen Vibrio vulnificus CMCP6. First, we partially re-sequenced and fully re-annotated the V. vulnificus CMCP6 genome, and accordingly reconstructed its genome-scale metabolic network, VvuMBEL943. The validated network model was employed to systematically predict drug targets using the concept of metabolite essentiality, along with additional filtering criteria. Target genes encoding enzymes that interact with the five essential metabolites finally selected were experimentally validated. These five essential metabolites are critical to the survival of the cell, and hence were used to guide the cost-effective selection of chemical analogs, which were then screened for antimicrobial activity in a whole-cell assay. This approach is expected to help fill the existing gap between genomics and drug discovery.
Contributors
Submitter of the first revision: Hyun Uk Kim
Submitter of this revision: Mikal Daou
Modellers: Hyun Uk Kim, Mikal Daou

Metadata information

isDescribedBy
PubMed 21245845
is
Taxonomy Vibrio vulnificus
BioModels Database MODEL1011300000
Gene Ontology cellular metabolic process
BIOMD0000001064
BioModels Database MODEL1011300000
hasProperty
Mathematical Modelling Ontology Constraint-based model

Curation status
Non-curated

Modelling approach(es)

Tags

Connected external resources

SBGN view in Newt Editor

Name Description Size Actions

Model files

VvuMBEL943_2022.xml SBML L3V1 annotated representation of genome-scale metabolic analysis of Vibrio vulnificus 666.59 KB Preview | Download

Additional files

VvuMBEL943_2022.omex Frog report with annotated model 35.43 KB Preview | Download
VvuMBEL943_FROG.zip FROG report of VvuMBEL943_2022.xml 12.22 KB Preview | Download
VvuMBEL943_MEMOTE.html MEMOTE report of VvuMBEL943_2022.xml 3.67 MB Preview | Download
VvuMBEL943_miniFROG.xlsx miniFROG report of VvuMBEL943_2022.xml 11.23 KB Preview | Download

  • Model originally submitted by : Hyun Uk Kim
  • Submitted: Nov 30, 2010 3:46:29 PM
  • Last Modified: Aug 12, 2022 1:44:36 PM
Revisions
  • Version: 7 public model Download this version
    • Submitted on: Aug 12, 2022 1:44:36 PM
    • Submitted by: Mikal Daou
    • With comment: Automatically added model identifier BIOMD0000001064
  • Version: 6 public model Download this version
    • Submitted on: Aug 12, 2022 1:16:56 PM
    • Submitted by: Mikal Daou
    • With comment: Added annotations to model
  • Version: 5 public model Download this version
    • Submitted on: May 18, 2022 11:30:53 PM
    • Submitted by: Hyun Uk Kim
    • With comment: Following updates were made in the SBML file of 'VvuMBEL943_2022.xml': 1. Objective function was specified. 2. Lower bounds were corrected for the irreversible reactions 3. FROG, miniFROG and MEMOTE reports have been submitted.
  • Version: 2 public model Download this version
    • Submitted on: Jun 23, 2011 2:13:11 PM
    • Submitted by: Hyun Uk Kim
    • With comment: Current version of Kim2010_VvuMBEL943_GSMR
  • Version: 1 public model Download this version
    • Submitted on: Nov 30, 2010 3:46:29 PM
    • Submitted by: Hyun Uk Kim
    • With comment: Original import of HyunUkKim2010_VvuMBEL943_MetabolicModeling

(*) You might be seeing discontinuous revisions as only public revisions are displayed here. Any private revisions unpublished model revision of this model will only be shown to the submitter and their collaborators.

Curator's comment:
(added: 12 Aug 2022, 13:21:34, updated: 12 Aug 2022, 17:03:39)
This model is curated using FROG standards. We used FBA and FROG Matlab toolbox to curate the model. FROG Report , miniFROG Report and MEMOTE report can also be accessed from the model files page.