Core and pan metabolic capabilities of the E. coli species (for 55 unique strains)

Range Figure - link
Organism Bacteria Escherichia coli
Reference Monk JM et al., Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments. Proc Natl Acad Sci U S A. 2013 Dec 10110(50):20338-43. doi: 10.1073/pnas.1307797110. p.20339 figure 1PubMed ID24277855
Method Abstract: "Genome-scale models (GEMs) of metabolism were constructed for 55 fully sequenced Escherichia coli and Shigella strains." P.20343 right column bottom paragraph: "Materials and Methods: The strain-specific model reconstruction procedure, gap filling algorithms, and in silico growth simulation conditions are described in SI Materials and Methods. Heatmap and phylogenetic tree and decision tree construction are described in SI Materials and Methods Carbon source and growth testing protocols are described in SI Materials and Methods. Eleven strains of E. coli and one strain of S. flexneri were tested as part of this study. The 11 E. coli strains are SMS 3–5, CFT073, HS, DH1, UMN 026, K011, Sakai, ATCC 8739, 042, EDL933, and K-12 MG1655. The S. flexneri strain was 2457T. E. coli 042 was a gift from Ian Henderson (Birmingham University, Birmingham, UK). All other strains were purchased from ATCC."
Comments P.20339 left column top paragraph: "Results: Characteristics of E. coli Core and Pan Metabolic Content: A set of 55 E. coli genome-scale reconstructions was built and used to compare gene, reaction, and metabolite content between strains (Datasets S1 and S2). The content shared among all reconstructions thereby defines the core metabolic capabilities among all of the strains. Similarly, the metabolic capabilities of all of the strains were combined to define the full set that encompasses all models and thereby define the “pan” metabolic capabilities among all of the strains. By analogy to mathematical set theory, the core metabolic content is the intersection of the gene, reaction, and metabolite content of all 55 models, whereas the pan metabolic content is the union of these features among the models (Fig. 1A)." P.20339 left column 3rd paragraph: "The pan metabolic capabilities are comprised of the total number of different reactions found in all strains and are thus an indicator of the full metabolic capabilities within a species. The E. coli pan reconstruction content contains 1,460 metabolic genes, 2,501 reactions, and 2,043 metabolites. About 64% of reactions in carbohydrate metabolism were part of the pan reactome, the largest group (Fig. 1B). A majority of these reactions are involved in alternate carbon source metabolism. Cell wall and membrane envelope metabolism accounted for 18% of reactions in the pan reactome. These reactions account for a major phenotypic distinction between E. coli strain’s serogroup, in particular the O antigen (ref 20). Also, 30% of amino acid metabolism reactions are part of the pan reactome." See caption beneath figure
Entered by Uri M
ID 113332