1. Reconstructing organisms in silico: genome-scale models and their emerging applications.
- Author
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Fang X, Lloyd CJ, and Palsson BO
- Subjects
- Actinobacteria classification, Actinobacteria genetics, Actinobacteria growth & development, Actinobacteria metabolism, Computer Simulation, Cyanobacteria classification, Cyanobacteria genetics, Cyanobacteria growth & development, Cyanobacteria metabolism, Escherichia coli growth & development, Escherichia coli metabolism, Firmicutes classification, Firmicutes genetics, Firmicutes growth & development, Firmicutes metabolism, Genomics instrumentation, Phenotype, Proteobacteria classification, Proteobacteria genetics, Proteobacteria growth & development, Proteobacteria metabolism, Stress, Physiological genetics, Thermotoga classification, Thermotoga genetics, Thermotoga growth & development, Thermotoga metabolism, Whole Genome Sequencing, Escherichia coli genetics, Gene Regulatory Networks, Genome, Bacterial, Genomics methods, Metabolic Networks and Pathways genetics, Models, Genetic
- Abstract
Escherichia coli is considered to be the best-known microorganism given the large number of published studies detailing its genes, its genome and the biochemical functions of its molecular components. This vast literature has been systematically assembled into a reconstruction of the biochemical reaction networks that underlie E. coli's functions, a process which is now being applied to an increasing number of microorganisms. Genome-scale reconstructed networks are organized and systematized knowledge bases that have multiple uses, including conversion into computational models that interpret and predict phenotypic states and the consequences of environmental and genetic perturbations. These genome-scale models (GEMs) now enable us to develop pan-genome analyses that provide mechanistic insights, detail the selection pressures on proteome allocation and address stress phenotypes. In this Review, we first discuss the overall development of GEMs and their applications. Next, we review the evolution of the most complete GEM that has been developed to date: the E. coli GEM. Finally, we explore three emerging areas in genome-scale modelling of microbial phenotypes: collections of strain-specific models, metabolic and macromolecular expression models, and simulation of stress responses., (© 2020. Springer Nature Limited.)
- Published
- 2020
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