Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli

@article{McCloskey2013BasicAA,
  title={Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli},
  author={Douglas McCloskey and Bernhard O. Palsson and Adam M. Feist},
  journal={Molecular Systems Biology},
  year={2013},
  volume={9},
  pages={661 - 661}
}
The genome‐scale model (GEM) of metabolism in the bacterium Escherichia coli K‐12 has been in development for over a decade and is now in wide use. GEM‐enabled studies of E. coli have been primarily focused on six applications: (1) metabolic engineering, (2) model‐driven discovery, (3) prediction of cellular phenotypes, (4) analysis of biological network properties, (5) studies of evolutionary processes, and (6) models of interspecies interactions. In this review, we provide an overview of… 
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326 Citations
Highly Influential Citations
6
Background Citations
90
Methods Citations
39

326 Citations

Reconstructing organisms in silico: genome-scale models and their emerging applications.
TLDR
The overall development of GEMs and their applications are discussed, the evolution of the most complete GEM that has been developed to date is reviewed, and three emerging areas in genome-scale modelling of microbial phenotypes are explored: collections of strain-specific models, metabolic and macromolecular expression models, and simulation of stress responses.
A genome-scale metabolic flux model of Escherichia coli K–12 derived from the EcoCyc database
TLDR
Significant advantages can be derived from the combination of model organism databases and flux balance modeling represented by MetaFlux, and interpretation of the EcoCyc database as a flux balance model results in a highly accurate metabolic model and provides a rigorous consistency check for information stored in the database.
Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments
TLDR
Genome-scale analysis of multiple strains of a species can be used to define the metabolic essence of a microbial species and delineate growth differences that shed light on the adaptation process to a particular microenvironment.
Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction
TLDR
The reconstruction of the yeast metabolic network is indeed gradually improving through the iterative process of model development, and there remains great opportunity for advancing the understanding of biology through continued efforts to reconstruct the full biochemical reaction network that constitutes yeast metabolism.
Current status and applications of genome-scale metabolic models
TLDR
Current reconstructed GEMs are reviewed and discussed, including strain development for chemicals and materials production, drug targeting in pathogens, prediction of enzyme functions, pan-reactome analysis, modeling interactions among multiple cells or organisms, and understanding human diseases.
Computational modelling of genome-scale metabolic networks and its application to CHO cell cultures
Basics of genome-scale metabolic modeling and applications on C1-utilization
TLDR
In this review, genome-scale metabolic models for C1-utilizing bacteria and well-established analysis tools are presented for potential uses for study of C1 metabolism at the genome scale and its application in metabolic engineering.
Escherichia coli as a model organism for systems metabolic engineering
Model-driven discovery of underground metabolic functions in Escherichia coli
TLDR
This study demonstrates how a targeted model-driven approach to discovery can systematically fill knowledge gaps, characterize underground metabolism, and elucidate regulatory mechanisms of adaptation in response to gene KO perturbations.
Software platforms to facilitate reconstructing genome-scale metabolic networks.
TLDR
A number of software platforms have been developed to automate parts of the reconstruction process, thereby alleviating much of the manual effort previously required and are reviewed in the context of established guidelines for network reconstruction.
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