Genome-scale models of bacterial metabolism: reconstruction and applications

By Maxime Durot, Pierre-Yves Bourguignon, V. Schachter. FEMS Microbiology Reviews, 2008

352 citations recorded by the source corpus.

Genome-scale metabolic models bridge the gap between genome-derived biochemical information and metabolic phenotypes in a principled manner, providing a solid interpretative framework for experimental data related to metabolic states, and enabling simple in silico experiments with whole-cell metabolism. Models have been reconstructed for almost 20 bacterial species, so far mainly through expert curation efforts integrating information from the literature with genome annotation. A wide variety of computational methods exploiting metabolic models have been developed and applied to bacteria, yielding valuable insights into bacterial metabolism and evolution, and providing a sound basis for computer-assisted design in metabolic engineering. Recent advances in computational systems biology and high-throughput experimental technologies pave the way for the systematic reconstruction of metabolic models from genomes of new species, and a corresponding expansion of the scope of their applications. In this review, we provide an introduction to the key ideas of metabolic modeling, survey the methods, and resources that enable model reconstruction and refinement, and chart applications to the investigation of global properties of metabolic systems, the interpretation of experimental results, and the re-engineering of their biochemical capabilities.

Subfields: Biomedical Engineering, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c63e14232e5c4841c442f46e4950a37d81493949

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Citations in the corpus

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 (2007, neutral): “COBRA methods have been used in hundreds of research articles over the past decade, which characterize genome-scale properties of metabolic networks and their phenotypic state”
Applications of genome-scale metabolic reconstructions (2009, methodology): “reconstructions”
Chapter 12: Human Microbiome Analysis (2012, background): “Since we are currently able to infer function for only a fraction of the genes in any given complete genome, let alone metagenome, any of these approaches should be deemed hypothetical at best; nevertheless, like any missing value imputation process, they can provide numerically stable guesses that ”
A protocol for generating a high-quality genome-scale metabolic reconstruction (2010, methodology): “Although the reconstruction process has been reviewed conceptually by numerous groups 8–11 and a good general overview of the necessary data and steps is available, no detailed description of the reconstruction, debugging and iterative validation process has been published.”
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions (2010, background): “The content of other genome-scale metabolic databases cannot be used directly for modeling in the COBRA framework [18].”