ArticlePloS one2018
Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3).
Article in PloS one, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
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- Transcriptome-constrained genome-scale metabolic modeling reveals central carbon and amino acid metabolic reprogramming underlying colistin-sulbactam synergy inAntimicrobial agents and chemotherapy · 2026Article
- Coordinating Calvin Cycle and Glycolysis inACS synthetic biology · 2026Article
- Disrupting ribulose-5-phosphate metabolic flux enhances riboflavin production in Escherichia coli BL21(DE3).PloS one · 2025Article
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- Genome-scale metabolic network model and phenome of solvent-tolerant Pseudomonas putida S12.BMC genomics · 2024Article
- High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917.BMC bioinformatics · 2022Article
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- Improved production of the non-native cofactor FScientific reports · 2021Article
- Development of a Genome-Scale Metabolic Model and Phenome Analysis of the ProbioticInternational journal of molecular sciences · 2021Article
- Fluxer: a web application to compute, analyze and visualize genome-scale metabolic flux networks.Nucleic acids research · 2020Article
- A single amino acid substitution in aromatic hydroxylase (HpaB) of Escherichia coli alters substrate specificity of the structural isomers of hydroxyphenylacetate.BMC microbiology · 2020Article
- Crystallographic analysis ofThe Journal of biological chemistry · 2020Article
- Elevated Expression of a Functional Suf Pathway in Escherichia coli BL21(DE3) Enhances Recombinant Production of an Iron-Sulfur Cluster-Containing Protein.Journal of bacteriology · 2020Article
- Multi-Path Optimization for Efficient Production of 2'-Fucosyllactose in an EngineeredFrontiers in bioengineering and biotechnology · 2020Article
- Identification of critical connectors in the directed reaction-centric graphs of microbial metabolic networks.BMC bioinformatics · 2019Article
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Authors and funding
3 authors.
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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.
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