Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism

Kenji Nakahigashi, Yoshihiro Toya, Nobuyoshi Ishii, Tomoyoshi Soga, Miki Hasegawa, Hisami Watanabe, Yuki Takai, Masayuki Honma, Hirotada Mori, Masaru Tomita

Research output: Contribution to journalArticle

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Abstract

Central carbon metabolism is a basic and exhaustively analyzed pathway. However, the intrinsic robustness of the pathway might still conceal uncharacterized reactions. To test this hypothesis, we constructed systematic multiple-knockout mutants involved in central carbon catabolism in Escherichia coli and tested their growth under 12 different nutrient conditions. Differences between in silico predictions and experimental growth indicated that unreported reactions existed within this extensively analyzed metabolic network. These putative reactions were then confirmed by metabolome analysis and in vitro enzymatic assays. Novel reactions regarding the breakdown of sedoheptulose-7-phosphate to erythrose-4-phosphate and dihydroxyacetone phosphate were observed in transaldolase-deficient mutants, without any noticeable changes in gene expression. These reactions, triggered by an accumulation of sedoheptulose-7-phosphate, were catalyzed by the universally conserved glycolytic enzymes ATP-dependent phosphofructokinase and aldolase. The emergence of an alternative pathway not requiring any changes in gene expression, but rather relying on the accumulation of an intermediate metabolite may be a novel mechanism mediating the robustness of these metabolic networks.

Original languageEnglish
Article number306
JournalMolecular Systems Biology
Volume5
DOIs
Publication statusPublished - 2009 Jan 20

Fingerprint

knockout mutants
Metabolic Networks and Pathways
Metabolism
Gene expression
Mutant
Escherichia coli
Escherichia Coli
Carbon
Phosphates
Transaldolase
Phosphate
Dihydroxyacetone Phosphate
phosphates
Gene Expression
Phosphofructokinases
Fructose-Bisphosphate Aldolase
metabolism
Metabolome
carbon
Enzyme Assays

Keywords

  • Genetic interaction
  • Metabolic flux
  • Metabolomics
  • System biology
  • Transaldolase

ASJC Scopus subject areas

  • Medicine(all)
  • Immunology and Microbiology(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • Computational Theory and Mathematics
  • Information Systems
  • Applied Mathematics

Cite this

Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism. / Nakahigashi, Kenji; Toya, Yoshihiro; Ishii, Nobuyoshi; Soga, Tomoyoshi; Hasegawa, Miki; Watanabe, Hisami; Takai, Yuki; Honma, Masayuki; Mori, Hirotada; Tomita, Masaru.

In: Molecular Systems Biology, Vol. 5, 306, 20.01.2009.

Research output: Contribution to journalArticle

Nakahigashi, Kenji ; Toya, Yoshihiro ; Ishii, Nobuyoshi ; Soga, Tomoyoshi ; Hasegawa, Miki ; Watanabe, Hisami ; Takai, Yuki ; Honma, Masayuki ; Mori, Hirotada ; Tomita, Masaru. / Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism. In: Molecular Systems Biology. 2009 ; Vol. 5.
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