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

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 metabol...

Full description

Bibliographic Details
Main Authors: Hanseol Kim, Sinyeon Kim, Sung Ho Yoon
Format: Article
Language:English
Published: Public Library of Science (PLoS) 2018-01-01
Series:PLoS ONE
Online Access:http://europepmc.org/articles/PMC6150544?pdf=render
id doaj-1a876181439c44ba819e0b99edfddd6a
record_format Article
spelling doaj-1a876181439c44ba819e0b99edfddd6a2020-11-25T01:19:59ZengPublic Library of Science (PLoS)PLoS ONE1932-62032018-01-01139e020437510.1371/journal.pone.0204375Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3).Hanseol KimSinyeon KimSung Ho YoonEscherichia 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.http://europepmc.org/articles/PMC6150544?pdf=render
collection DOAJ
language English
format Article
sources DOAJ
author Hanseol Kim
Sinyeon Kim
Sung Ho Yoon
spellingShingle Hanseol Kim
Sinyeon Kim
Sung Ho Yoon
Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3).
PLoS ONE
author_facet Hanseol Kim
Sinyeon Kim
Sung Ho Yoon
author_sort Hanseol Kim
title Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3).
title_short Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3).
title_full Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3).
title_fullStr Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3).
title_full_unstemmed Metabolic network reconstruction and phenome analysis of the industrial microbe, Escherichia coli BL21(DE3).
title_sort metabolic network reconstruction and phenome analysis of the industrial microbe, escherichia coli bl21(de3).
publisher Public Library of Science (PLoS)
series PLoS ONE
issn 1932-6203
publishDate 2018-01-01
description 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.
url http://europepmc.org/articles/PMC6150544?pdf=render
work_keys_str_mv AT hanseolkim metabolicnetworkreconstructionandphenomeanalysisoftheindustrialmicrobeescherichiacolibl21de3
AT sinyeonkim metabolicnetworkreconstructionandphenomeanalysisoftheindustrialmicrobeescherichiacolibl21de3
AT sunghoyoon metabolicnetworkreconstructionandphenomeanalysisoftheindustrialmicrobeescherichiacolibl21de3
_version_ 1725136142751236096