Flux balance analysis of photoautotrophic metabolism: Uncovering new biological details of subsystems involved in cyanobacterial photosynthesis

Xiao Qian, Min Kyung Kim, G. Kenchappa Kumaraswamy, Ananya Agarwal, Desmond S. Lun, G. Charles Dismukes

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

We have constructed and experimentally tested a comprehensive genome-scale model of photoautotrophic growth, denoted iSyp821, for the cyanobacterium Synechococcus sp. PCC 7002. iSyp821 incorporates a variable biomass objective function (vBOF), in which stoichiometries of the major biomass components vary according to light intensity. The vBOF was constrained to fit the measured cellular carbohydrate/protein content under different light intensities. iSyp821 provides rigorous agreement with experimentally measured cell growth rates and inorganic carbon uptake rates as a function of light intensity. iSyp821 predicts two observed metabolic transitions that occur as light intensity increases: 1) from PSI-cyclic to linear electron flow (greater redox energy), and 2) from carbon allocation as proteins (growth) to carbohydrates (energy storage) mode. iSyp821 predicts photoautotrophic carbon flux into 1) a hybrid gluconeogenesis-pentose phosphate (PP) pathway that produces glycogen by an alternative pathway than conventional gluconeogenesis, and 2) the photorespiration pathway to synthesize the essential amino acid, glycine. Quantitative fluxes through both pathways were verified experimentally by following the kinetics of formation of 13C metabolites from 13CO2 fixation. iSyp821 was modified to include changes in gene products (enzymes) from experimentally measured transcriptomic data and applied to estimate changes in concentrations of metabolites arising from nutrient stress. Using this strategy, we found that iSyp821 correctly predicts the observed redistribution pattern of carbon products under nitrogen depletion, including decreased rates of CO2 uptake, amino acid synthesis, and increased rates of glycogen and lipid synthesis.

Original languageEnglish
Pages (from-to)276-287
Number of pages12
JournalBiochimica et Biophysica Acta - Bioenergetics
Volume1858
Issue number4
DOIs
Publication statusPublished - Apr 1 2017

Keywords

  • Carbon partitioning
  • Cyanobacteria
  • Flux balance analysis
  • Gluconeogenesis-pentose phosphate (PP) pathway
  • Metabolism
  • Nitrogen deprivation
  • Photorespiration
  • Synechococcus 7002
  • Transcriptomic

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Cell Biology

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