Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism.
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.
Nakahigashi
Kenji
K
Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan. knakahig@sfc.keio.ac.jp
Toya
Yoshihiro
Y
Ishii
Nobuyoshi
N
Soga
Tomoyoshi
T
Hasegawa
Miki
M
Watanabe
Hisami
H
Takai
Yuki
Y
Honma
Masayuki
M
Mori
Hirotada
H
Tomita
Masaru
M
D002244:Carbon / Q000378:metabolism*; D003198:Computer Simulation; D003470:Culture Media / Q000737:chemistry / Q000378:metabolism; D004099:Dihydroxyacetone Phosphate / Q000378:metabolism; D004926:Escherichia coli / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism; D020869:Gene Expression Profiling; D055786:Gene Knockout Techniques / Q000379:methods*; D053858:Metabolic Networks and Pathways / Q000235:genetics; D055442:Metabolome; D008954:Models, Biological; D009154:Mutation; D010641:Phenotype; D013403:Sugar Phosphates / Q000378:metabolism; D049490:Systems Biology / Q000379:methods*; D014153:Transaldolase / Q000378:metabolism
D003470:Culture Media; D029968:Escherichia coli Proteins; D013403:Sugar Phosphates; C020495:sedoheptulose 7-phosphate; D004099:Dihydroxyacetone Phosphate; C026959:erythrose 4-phosphate; D002244:Carbon; D014153:Transaldolase