Evaluating E. coli genome-scale metabolic model accuracy with high-throughput mutant fitness data.

ABSTRACT: The Escherichia coli genome-scale metabolic model (GEM) is an exemplar systems biology model for the simulation of cellular metabolism. Experimental validation of model predictions is essential to pinpoint uncertainty and ensure continued development of accurate models. Here, we quantified the accuracy of four subsequent E. coli GEMs using published mutant fitness data across thousands of genes and 25 different carbon sources. This evaluation demonstrated the utility of the area under a precision-recall curve relative to alternative accuracy metrics. An analysis of errors in the latest (iML1515) model identified several vitamins/cofactors that are likely available to mutants despite being absent from the experimental growth medium and highlighted isoenzyme gene-protein-reaction mapping as

SUBMITTER: Bernstein DB 

PROVIDER: S-EPMC10698504 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature