Single-atom tracing in a model network of carbohydrate metabolism and pathway selection

Research output: Contribution to journalArticle

Abstract

Studies on computation of pathways connecting two metabolites have been reported. However, they did not intend to find pathways containing cycling, although there are biologically important cycles such as citric acid cycle (CAC). Whilst computation of pathways connecting two atoms, single-atom tracing, would contribute to finding pathways which include those containing cycling, it produces too many pathways to examine. The present article proposes a strategy to select pathways from those obtained by single-atom tracing, where coexistence of reactions on each pathway, specifically coexistence of a reaction and its reverse reaction forming a futile cycle together or reactions regulated in a reciprocal manner, is checked to select pathways based on biochemical meaning of the pathway. Using this strategy, 121 pathways were selected from total 7876 pathways from carbon atoms of glucose to CO2 in a model network of carbohydrate metabolism. The selected pathways included pathways using reactions or metabolites of CAC or pentose phosphate pathway multiple times. These results indicate that the proposed strategy can contribute to listing a limited number of pathways which include those containing cycling as possibly biochemically meaningful pathways.

Original languageEnglish
Pages (from-to)1-13
Number of pages13
JournalIPSJ Transactions on Bioinformatics
Volume11
DOIs
Publication statusPublished - Jun 1 2018

Fingerprint

Citric Acid Cycle
Carbohydrate Metabolism
Substrate Cycling
Pentose Phosphate Pathway
Atoms
Metabolites
Carbon
Pentoses
Glucose
Phosphates

Keywords

  • Carbohydrate metabolism
  • Citric acid cycle
  • Connectivity matrix method
  • Gluconeogenesis
  • Glycolysis
  • Metabolic networks
  • Pentose phosphate pathway

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology (miscellaneous)
  • Computer Science Applications

Cite this

Single-atom tracing in a model network of carbohydrate metabolism and pathway selection. / Ohta, Jun.

In: IPSJ Transactions on Bioinformatics, Vol. 11, 01.06.2018, p. 1-13.

Research output: Contribution to journalArticle

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