title: Elementary Flux Mode Analysis Revealed Cyclization Pathway as a Powerful Way for NADPH Regeneration of Central Carbon Metabolism.
abstract: NADPH regeneration capacity is attracting growing research attention due to its important role in resisting oxidative stress. Besides, NADPH availability has been regarded as a limiting factor in production of industrially valuable compounds. The central carbon metabolism carries the carbon skeleton flux supporting the operation of NADPH-regenerating enzyme and offers flexibility in coping with NADPH demand for varied intracellular environment. To acquire an insightful understanding of its NADPH regeneration capacity, the elementary mode method was employed to compute all elementary flux modes (EFMs) of a network representative of central carbon metabolism. Based on the metabolic flux distributions of these modes, a cluster analysis of EFMs with high NADPH regeneration rate was conducted using the self-organizing map clustering algorithm. The clustering results were used to study the relationship between the flux of total NADPH regeneration and the flux in each NADPH producing enzyme. The results identified several reaction combinations supporting high NADPH regeneration, which are proven to be feasible in cells via thermodynamic analysis and coincident with a great deal of previous experimental report. Meanwhile, the reaction combinations showed some common characteristics: there were one or two decarboxylation oxidation reactions in the combinations that produced NADPH and the combination constitution included certain gluconeogenesis pathways. These findings suggested cyclization pathways as a powerful way for NADPH regeneration capacity of bacterial central carbon metabolism.
authors.affiliation: School of Life Science, Anhui Agricultural University, Hefei, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Rui
authors.affiliation: Key Laboratory of Plant Physiology and Development Regulation, Guizhou Province, Guizhou Normal University, Guiyang, China.
authors.forename: Yin
authors.initials: Y
authors.lastname: Yi
authors.affiliation: Key Laboratory of Information and Computing Science, Guizhou Province, Guizhou Normal University, Guiyang, China.
authors.forename: Tie
authors.initials: T
authors.lastname: Shen
authors.affiliation: Guizhou Academy of Testing and Analysis, Guiyang, China.
authors.forename: Meijuan
authors.initials: M
authors.lastname: Zheng
authors.affiliation: Key Laboratory of Information and Computing Science, Guizhou Province, Guizhou Normal University, Guiyang, China.
authors.forename: Wenwei
authors.initials: W
authors.lastname: Zhou
authors.affiliation: Key Laboratory of Information and Computing Science, Guizhou Province, Guizhou Normal University, Guiyang, China.
authors.forename: Honglin
authors.initials: H
authors.lastname: Du
authors.affiliation: School of Life Science, Anhui Agricultural University, Hefei, China.
authors.forename: Yadong
authors.initials: Y
authors.lastname: Fan
authors.affiliation: School of Life Science, Anhui Agricultural University, Hefei, China.
authors.forename: Yongkang
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Key Laboratory of Information and Computing Science, Guizhou Province, Guizhou Normal University, Guiyang, China.
authors.forename: Zhengdong
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: School of Life Science, Anhui Agricultural University, Hefei, China.
authors.forename: Shengsheng
authors.initials: S
authors.lastname: Xu
authors.affiliation: Key Laboratory of Information and Computing Science, Guizhou Province, Guizhou Normal University, Guiyang, China.
authors.forename: Zhijie
authors.initials: Z
authors.lastname: Liu
authors.affiliation: School of Life Science, Anhui Agricultural University, Hefei, China.
authors.forename: Han
authors.initials: H
authors.lastname: Wen
authors.affiliation: Key Laboratory of Information and Computing Science, Guizhou Province, Guizhou Normal University, Guiyang, China.
authors.forename: Xiaoyao
authors.initials: X
authors.lastname: Xie
mesh_terms: D002244:Carbon / Q000378:metabolism*; D003198:Computer Simulation; D003500:Cyclization; D004926:Escherichia coli / Q000201:enzymology / Q000378:metabolism*; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D009249:NADP / Q000378:metabolism*; D010084:Oxidation-Reduction; D013816:Thermodynamics
chemical_list: D009249:NADP; D002244:Carbon