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. 2011 Oct 11;7:535.
doi: 10.1038/msb.2011.65.

A Comprehensive Genome-Scale Reconstruction of Escherichia Coli metabolism--2011

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Free PMC article

A Comprehensive Genome-Scale Reconstruction of Escherichia Coli metabolism--2011

Jeffrey D Orth et al. Mol Syst Biol. .
Free PMC article

Abstract

The initial genome-scale reconstruction of the metabolic network of Escherichia coli K-12 MG1655 was assembled in 2000. It has been updated and periodically released since then based on new and curated genomic and biochemical knowledge. An update has now been built, named iJO1366, which accounts for 1366 genes, 2251 metabolic reactions, and 1136 unique metabolites. iJO1366 was (1) updated in part using a new experimental screen of 1075 gene knockout strains, illuminating cases where alternative pathways and isozymes are yet to be discovered, (2) compared with its predecessor and to experimental data sets to confirm that it continues to make accurate phenotypic predictions of growth on different substrates and for gene knockout strains, and (3) mapped to the genomes of all available sequenced E. coli strains, including pathogens, leading to the identification of hundreds of unannotated genes in these organisms. Like its predecessors, the iJO1366 reconstruction is expected to be widely deployed for studying the systems biology of E. coli and for metabolic engineering applications.

Conflict of interest statement

The authors declare that they have no conflict of interest.

Figures

Figure 1
Figure 1
Properties of iJO1366. (A) The number of reactions in each of 11 functional categories. Non-gene-associated (orphan) reactions are indicated by the lighter portion at the far right of each bar. (B) The number of genes with associated reactions in each category. The number of genes unique to each category (i.e. associated only with reactions in one category) is given as a percentage. (C) The number of unique metabolites that participate in at least one reaction in each category, with the number of metabolites unique to each category indicated. (D) Histogram of the years in which the function of each of the 107 new genes was first unambiguously identified. (E) Classification of each of the 107 new genes in iJO1366. ‘New content added' includes genes associated with new (non-gap-filling) pathways and systems in the model. ‘Orphan fill' includes genes associated with orphan reactions from iAF1260. ‘New gene with existing reaction' includes new isozymes for existing gene-associated reactions in iAF1260. ‘Gap fill' includes genes associated with new gap-filling reactions. ‘Others' includes genes that are associated both with new, non-gap-filling reactions, and with a previous orphan reaction or as a new isozyme.
Figure 2
Figure 2
Results of the mapping between the iJO1366 reconstruction and all 38 available E. coli and Shigella strains. (A) The number of strain models capable of producing all components of the iJO1366 core biomass reaction at different PID cutoffs. The PID of 40% used in parts (B, C) of this figure is indicated with a yellow square. At a PID of 40%, only four strains are incapable of complete biomass synthesis. (B) Biomass components that cannot be produced in one or more models with a PID of 40%. The strains are indicated by their KEGG organism code. (C) The fraction of iJO1366 genes present in all 38 strains at a PID of 40%. Strains are listed by their KEGG organism code. Laboratory strains are colored blue, commensal and environmental strains are in green, and pathogens are in red. A dashed line indicates the average fraction of genes present (97%).

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