Open AccessMetabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3)
Author(s) -
Hanseol Kim,
Sinyeon Kim,
Sung Ho Yoon
Publication year - 2018
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0204375
Subject(s) - phenome , metabolic flux analysis , metabolic engineering , metabolic network , bioproducts , escherichia coli , metabolomics , computational biology , biology , flux (metallurgy) , systems biology , flux balance analysis , in silico , metabolome , metabolic pathway , biochemistry , bioinformatics , microbiology and biotechnology , chemistry , metabolism , phenotype , gene , biofuel , organic chemistry
Escherichia coli BL21(DE3) is an industrial model microbe for the mass-production of bioproducts such as biofuels, biorefineries, and recombinant proteins. However, despite its important role in scientific research and biotechnological applications, a high-quality metabolic network model for metabolic engineering is yet to be developed. Here, we present the comprehensive metabolic network model of E . coli BL21(DE3), named iHK1487, based on the latest genome reannotation and phenome analysis. The metabolic model consists of 1,164 unique metabolites, 2,701 metabolic reactions, and 1,487 genes. The model was validated and improved by comparing the simulation results with phenome data from phenotype microarray tests. Previous transcriptome profile data was incorporated during model reconstruction, and flux prediction was simulated using the model. iHK1487 was simulated to explore the metabolic features of BL21(DE3) such as broad spectrum amino acid utilization and enhanced flux through the upper glycolytic pathway and TCA cycle. iHK1487 will contribute to systematic understanding of cellular physiology and metabolism of E . coli BL21(DE3) and highlight its biotechnological applications.