Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3)

PLoS One. 2018 Sep 21;13(9):e0204375. doi: 10.1371/journal.pone.0204375. eCollection 2018.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Escherichia coli / genetics
  • Escherichia coli / metabolism*
  • Industry*
  • Metabolic Networks and Pathways*
  • Models, Biological
  • Phenotype*
  • Species Specificity
  • Transcriptome

Grants and funding

This work was supported by the National Research Foundation (NRF) of the Republic of Korea through the Technology Development Program to Solve Climate Changes on Systems Metabolic Engineering for Biorefineries [2012M1A2A2026559] and Bio and Medical Technology Development Program [2018M3A9F3021968]; and by the Ministry of Agriculture, Food, and Rural Affairs through the Strategic Initiative for Microbiomes in Agriculture and Food [918012-4]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.