Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

Title: iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations

Journal Article · · GenomeBiology.com
 [1];  [2];  [3];  [2]
  1. Argonne National Lab. (ANL), Argonne, IL (United States). Mathematics and Computer Science Dept.; DOE/OSTI
  2. Argonne National Lab. (ANL), Argonne, IL (United States). Mathematics and Computer Science Dept.; Univ. of Chicago, IL (United States). Computation Inst.
  3. Argonne National Lab. (ANL), Argonne, IL (United States). Mathematics and Computer Science Dept.
+ Show Author Affiliations

Background: Bacillus subtilis is an organism of interest because of its extensive industrial applications, its similarity to pathogenic organisms, and its role as the model organism for Grampositive, sporulating bacteria. In this work, we introduce a new genome-scale metabolic model of B. subtilis 168 called iBsu1103. This new model is based on the annotated B. subtilis 168 genome generated by the SEED, one of the most up-to-date and accurate annotations of B. subtilis 168 available. Results: The iBsu1103 model includes 1,437 reactions associated with 1,103 genes, making it the most complete model of B. subtilis available. The model also includes Gibbs free energy change (Δr G°) values for 1,403 (97%) of the model reactions estimated by using the group contribution method. These data were used with an improved reaction reversibility prediction method to identify 653 (45%) irreversible reactions in the model. The model was validated against an experimental dataset consisting of 1,500 distinct conditions and was optimized by using an improved model optimization method to increase model accuracy from 89.7% to 93.1%. Conclusions: Basing the iBsu1103 model on the annotations generated by the SEED significantly improved the model completeness and accuracy compared with the most recent previously published model. The enhanced accuracy of the iBsu1103 model also demonstrates the efficacy of the improved reaction directionality prediction method in accurately identifying irreversible reactions in the B. subtilis metabolism. The proposed improved model optimization methodology was also demonstrated to be effective in minimally adjusting model content to improve model accuracy.

Research Organization:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
Grant/Contract Number:
AC02-06CH11357
OSTI ID:
1626733
Journal Information:
GenomeBiology.com, Journal Name: GenomeBiology.com Journal Issue: 6 Vol. 10; ISSN 1465-6906
Publisher:
BioMed CentralCopyright Statement
Country of Publication:
United States
Language:
English

References (60)

Probing the performance limits of theEscherichia coli metabolic network subject to gene additions or deletions journal January 2001
Stoichiometric growth model for riboflavin-producingBacillus subtilis journal January 2001
Group contributions for estimating standard gibbs energies of formation of biochemical compounds in aqueous solution journal December 1990
Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli journal September 2002
Estimation of standard Gibbs energy changes of biotransformations journal August 1991
Putative regulatory sites unraveled by network‐embedded thermodynamic analysis of metabolome data journal January 2006
Enhanced Recombinant Protein Productivity by Genome Reduction in Bacillus subtilis journal January 2008
Reconstruction and Validation of Saccharomyces cerevisiae iND750, a Fully Compartmentalized Genome-Scale Metabolic Model journal June 2004
Physiology and metabolic fluxes of wild-type and riboflavin-producing Bacillus subtilis journal October 1996
The SEED: a peer-to-peer environment for genome annotation journal November 2004
Toward the automated generation of genome-scale metabolic networks in the SEED journal January 2007
Towards the development of Bacillus subtilis as a cell factory for membrane proteins and protein complexes journal April 2008
Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ 661 and proposing alternative drug targets journal June 2007
Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis journal January 2008
A Genome-Scale Metabolic Reconstruction of Mycoplasma genitalium, iPS189 journal February 2009
GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions journal March 2009
Genome-Scale Thermodynamic Analysis of Escherichia coli Metabolism journal February 2006
Thermodynamics-Based Metabolic Flux Analysis journal March 2007
Probing the performance limits of theEscherichia coli metabolic network subject to gene additions or deletions journal January 2001
Stoichiometric growth model for riboflavin-producingBacillus subtilis journal January 2001
Equations and calculations of product yields and preferred pathways for butanediol and mixed-acid fermentations journal January 1985
Group contributions for estimating standard gibbs energies of formation of biochemical compounds in aqueous solution journal December 1990
Metabolic Capabilities of Escherichia coli II. Optimal Growth Patterns journal December 1993
Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli journal September 2002
Estimation of standard Gibbs energy changes of biotransformations journal August 1991
Recursive MILP model for finding all the alternate optima in LP models for metabolic networks journal July 2000
Stoichiometric network constraints on xylose metabolism by recombinant Saccharomyces cerevisiae journal July 2004
Robustness Analysis of the Escherichia coli Metabolic Network journal December 2000
Quantitative Metabolome Analysis Using Capillary Electrophoresis Mass Spectrometry journal October 2003
In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data journal February 2001
A genome‐scale metabolic reconstruction for Escherichia coli K‐12 MG1655 that accounts for 1260 ORFs and thermodynamic information journal January 2007
Large-scale in vivo flux analysis shows rigidity and suboptimal performance of Bacillus subtilis metabolism journal May 2005
A new mutation delivery system for genome-scale approaches in Bacillus subtilis: New mutation delivery systsem in Bacillus subtilis journal October 2002
Essential Bacillus subtilis genes journal April 2003
Genome-scale Reconstruction of Metabolic Network in Bacillus subtilis Based on High-throughput Phenotyping and Gene Essentiality Data journal June 2007
Enhanced Recombinant Protein Productivity by Genome Reduction in Bacillus subtilis journal January 2008
KEGG: Kyoto Encyclopedia of Genes and Genomes journal January 2000
The KEGG databases at GenomeNet journal January 2002
Reconstruction and Validation of Saccharomyces cerevisiae iND750, a Fully Compartmentalized Genome-Scale Metabolic Model journal June 2004
Global phenotypic characterization of bacteria journal January 2009
Cloning, Sequencing, and Disruption of the Bacillus subtilis psd Gene Coding for Phosphatidylserine Decarboxylase journal January 1998
Expanded Metabolic Reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an In Silico Genome-Scale Characterization of Single- and Double-Deletion Mutants journal August 2005
Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. journal January 1994
Physiology and metabolic fluxes of wild-type and riboflavin-producing Bacillus subtilis journal October 1996
The SEED: a peer-to-peer environment for genome annotation journal November 2004
Thermodynamic-based computational profiling of cellular regulatory control in hepatocyte metabolism journal March 2005
Toward the automated generation of genome-scale metabolic networks in the SEED journal January 2007
Optimization based automated curation of metabolic reconstructions journal January 2007
The RAST Server: Rapid Annotations using Subsystems Technology journal January 2008
Modeling Lactococcus lactis using a genome-scale flux model journal June 2005
Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation journal March 2005
Towards the development of Bacillus subtilis as a cell factory for membrane proteins and protein complexes journal April 2008
Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ 661 and proposing alternative drug targets journal June 2007
Reconstruction and analysis of the genetic and metabolic regulatory networks of the central metabolism of Bacillus subtilis journal January 2008
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) journal August 2003
A Genome-Scale Metabolic Reconstruction of Mycoplasma genitalium, iPS189 journal February 2009
GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions journal March 2009
Genome-Scale Thermodynamic Analysis of Escherichia coli Metabolism journal February 2006
Thermodynamics-Based Metabolic Flux Analysis journal March 2007
Group Contribution Method for Thermodynamic Analysis of Complex Metabolic Networks journal August 2008

Cited By (74)

Applications of genome‐scale metabolic reconstructions journal January 2009
Reconstruction and flux‐balance analysis of the Plasmodium falciparum metabolic network journal January 2010
Global probabilistic annotation of metabolic networks enables enzyme discovery journal September 2012
Reconstruction of the metabolic network of Pseudomonas aeruginosa to interrogate virulence factor synthesis journal March 2017
An integrated computational and experimental study to investigate Staphylococcus aureus metabolism journal January 2020
Genome-scale modeling and transcriptome analysis of Leuconostoc mesenteroides unravel the redox governed metabolic states in obligate heterofermentative lactic acid bacteria journal November 2017
Comparative genomics study reveals Red Sea Bacillus with characteristics associated with potential microbial cell factories (MCFs) journal December 2019
Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations journal November 2015
SubtiWiki--a comprehensive community resource for the model organism Bacillus subtilis journal November 2011
Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model journal October 2012
Gene Knockout Identification Using an Extension of Bees Hill Flux Balance Analysis journal January 2015
MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases journal January 2012
Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis journal January 2010
Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data journal December 2010
iRsp1095: A genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network journal January 2011
Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052 journal January 2011
Systematic identification and analysis of frequent gene fusion events in metabolic pathways journal June 2016
Current status and applications of genome-scale metabolic models journal June 2019
Environments that Induce Synthetic Microbial Ecosystems journal November 2010
The Emergence and Early Evolution of Biological Carbon-Fixation journal April 2012
Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM journal July 2013
Using genome-scale metabolic models to compare serovars of the foodborne pathogen Listeria monocytogenes journal June 2018
KBase Narrative - SOMATA - Motivating Example dataset January 2023
KBase Narrative - Genome sequences of four bacterial strains isolated from organofluorine enrichment cultures dataset January 2024
Omics-to-Reactive-Transport (ORT): A workflow linking genome-scale metabolic models with reactive transport codes dataset January 2021
Community Modeling and Flux Balance Analysis of Synthetic Bacterial Community in MOPS Medium dataset January 2021
Community Modeling and Flux Balance Analysis of Synthetic Bacterial Community in R2A Medium dataset January 2021
Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm journal March 2015
Efficient Reconstruction of Predictive Consensus Metabolic Network Models text January 2016
Feedbacks from the metabolic network to the genetic network reveal regulatory modules in E. coli and B. subtilis text January 2018
Metabolic Modelling in the Development of cell Factories by Synthetic Biology journal October 2012
Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology journal December 2009
Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints journal August 2013
Reconstruction of a high-quality metabolic model enables the identification of gene overexpression targets for enhanced antibiotic production in Streptomyces coelicolor A3(2) journal April 2014
The current state of microbial proteomics: Where we are and where we want to go journal January 2012
Developing Bacillus spp. as a cell factory for production of microbial enzymes and industrially important biochemicals in the context of systems and synthetic biology journal June 2013
Biotechnology of riboflavin journal January 2016
Deciphering bacterial xylose metabolism and metabolic engineering of industrial microorganisms for use as efficient microbial cell factories journal September 2018
Applications of genome-scale metabolic network model in metabolic engineering journal December 2014
Applications of genome‐scale metabolic reconstructions journal January 2009
High-throughput generation, optimization and analysis of genome-scale metabolic models journal August 2010
Global probabilistic annotation of metabolic networks enables enzyme discovery journal September 2012
Reconstruction of the metabolic network of Pseudomonas aeruginosa to interrogate virulence factor synthesis journal March 2017
An integrated computational and experimental study to investigate Staphylococcus aureus metabolism journal January 2020
Manually curated genome-scale reconstruction of the metabolic network of Bacillus megaterium DSM319 journal December 2019
Comparative genomics study reveals Red Sea Bacillus with characteristics associated with potential microbial cell factories (MCFs) journal December 2019
SubtiWiki--a comprehensive community resource for the model organism Bacillus subtilis journal November 2011
Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model journal October 2012
An updated metabolic view of the Bacillus subtilis 168 genome journal April 2013
From network models to network responses: integration of thermodynamic and kinetic properties of yeast genome-scale metabolic networks journal December 2011
A refined genome-scale reconstruction of Chlamydomonas metabolism provides a platform for systems-level analyses journal November 2015
Gene Knockout Identification Using an Extension of Bees Hill Flux Balance Analysis journal January 2015
MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases journal January 2012
Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data journal December 2010
Systematic identification and analysis of frequent gene fusion events in metabolic pathways journal June 2016
Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enables in silico design of poly-γ-glutamic acid production strains journal January 2019
Current status and applications of genome-scale metabolic models journal June 2019
Whole-genome metabolic model of Trichoderma reesei built by comparative reconstruction journal November 2016
A design–build–test cycle using modeling and experiments reveals interdependencies between upper glycolysis and xylose uptake in recombinant S. cerevisiae and improves predictive capabilities of large-scale kinetic models journal June 2017
The Emergence and Early Evolution of Biological Carbon-Fixation journal April 2012
Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM journal July 2013
Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models journal October 2014
Efficient Reconstruction of Predictive Consensus Metabolic Network Models journal August 2016
SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models journal October 2012
Differential Bees Flux Balance Analysis with OptKnock for In Silico Microbial Strains Optimization journal July 2014
Using genome-scale metabolic models to compare serovars of the foodborne pathogen Listeria monocytogenes journal June 2018
Feedbacks from the metabolic network to the genetic network reveal regulatory modules in E. coli and B. subtilis journal October 2018
KBase Narrative - SOMATA - Motivating Example dataset January 2023
Omics-to-Reactive-Transport (ORT): A workflow linking genome-scale metabolic models with reactive transport codes dataset January 2021
Community Modeling and Flux Balance Analysis of Synthetic Bacterial Community in MOPS Medium dataset January 2021
Community Modeling and Flux Balance Analysis of Synthetic Bacterial Community in R2A Medium dataset January 2021
Efficient Reconstruction of Predictive Consensus Metabolic Network Models text January 2016
Accomplishments in Genome-Scale In Silico Modeling for Industrial and Medical Biotechnology text January 2009
Feedbacks from the metabolic network to the genetic network reveal regulatory modules in E. coli and B. subtilis text January 2018

Similar Records

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Biotechnology & Applied Microbiology
Genetics & Heredity