Table 3 Table of flux constraints used for Flux Balance Analysis (FBA) of the stoichiometric model of Arabidopsis thaliana
Growth conditions | Objective function | Constraints | Interpretation of the constraints |
|---|---|---|---|
‘Light’ | max (T.Biomass.ext) | T.Biomass.ext < = 5000 SK = 0 0.25*RPC_plastide - RPC2_plastide = 0 T.starch.ext = 0 T.CO2.ext = 0 T.CO2.ext_rev > = 0 -----add-on----- FQR = 0 or T.ADP.plastid - T.ATP.plastid = 0 or (0 … 0.5)*FNR - FQR = 0 or RPC2_plastide = 0 GLYK = 0 | Maximization of biomass formation under light assumes that:  • A plant consumes CO2 as the carbon source (T.CO2.ext = 0, T.CO2.ext_rev > = 0) there are two constraints because CO2 transport is reversible  • All formed starch becomes a part of the biomass (T.Starch.ext = 0)  • There is no starch degradation under light and therefore starch kinase is inactive (SK = 0)  • Photorespiration flux was fixed at 20 % of flux through RuBisCo (0.25*RPC_plastide - RPC2_plastide = 0) at all tested conditions Additionally, the impact of different degree of cyclic electron flow through photosynthesis light reactions (particularly through ferredoxin-plastoquinone reductase; FQR) was estimated by means of add-on constraints:  • Either … cyclic electron flow is inactive (FQR = 0)  • Or … flux through ATP/ADP translocator between plastid and cytoplasm is inactive (T.ADP.plastid – T.ATP.plastid = 0), thus plastid’s ATP balance becomes self-sufficient  • Or … flux through FQR varies relative to the non-cyclic electron flow through ferredoxin-NADP+-oxidoreductase (FNR) ((0 … 0.5)*FNR – FQR = 0)  • Or … flux through photorespiration pathway is zero (RPC2_plastide = 0; GLYK = 0), but cyclic electron flow through FQR is subjected to optimization |
Resulted growth stoichiometry for ‘light’ conditions (the stoichiometric coefficients [mol i/mol X] are normalized per biomass): | |||
[PR* = 0.25; FQR = 0]: [PR = 0.25; FQR/FNR = 0.37]: [PR = 0.25; FQR/FNR = 0.5]: [PR = 0; FQR/FNR = 0.1]: | 3.26e7 × CO 2 + 2.12e7 × H 2 O + 1.00e6 × HPO 2 −4 + 1.99e4 × SO 2 −4 + 1.52e6 × H + + 5.04e6 × NO −3 + 5.26e8 × hv = > 3.98e7 × O 2 + Biomass_plant 3.26e7 × CO 2 + 2.12e7 × H 2 O + 1.00e6 × HPO 2 −4 + 1.99e4 × SO 2 −4 + 1.52e6 × H + + 5.04e6 × NO −3 + 5.58e8 × hv = > 3.98e7 × O 2 + Biomass_plant 3.26e7 × CO 2 + 2.12e7 × H 2 O + 1.00e6 × HPO 2 −4 + 1.99e4 × SO 2 −4 + 1.08e6 × H + + 5.04e6 × NO −3 + 5.92e8 × hv = > 3.98e7 × O 2 + Biomass_plant 3.26e7 × CO 2 + 2.12e7 × H 2 O + 1.00e6 × HPO 2 −4 + 1.99e4 × SO 2 −4 + 5.84e6 × H + + 5.04e6 NO −3 × + 3.90e8 × hv = > 3.98e7 × O 2 + Biomass_plant | ||
‘Dark’ | max(T.Biomass.ext) | T.Biomass.ext < = 5000 PGM3_plastid = 0 RPC_plastide = 0 RPC2_plastide = 0 GLYK = 0 GDC = 0 T.starch.ext > = 0 T.hv.ext = 0 | Maximization of the biomass formation in darkness assumes that:  • There is no light (T.hv.ext = 0)  • Therefore RuBisCo is inactive (RPC_plastide = 0)  • Correspondingly photorespiration is also inactive (RPC2_plastide = 0, GLYK = 0, GDC = 0)  • Consequently there is no synthesis of new starch, therefore phosphoglucomutase is inactive (PGM3_plastid = 0)  • Starch is the carbon source for biomass formation (T.Starch.ext > = 0), which previously has been deposited in course of the light phase |
Resulted growth stoichiometry for ‘dark’ conditions (the stoichiometric coefficients [mol i/mol X] are normalized per biomass): 8.48e6 × O 2 + 1.00e6 HPO 2 −4 × + 1.99e4 × SO 2 −4 + 3.84e6 × H ++ 5.04e6 × NO −3 + 1.34e4 × Starch = > 1.55e7 × CO 2 + 1.92e7 × H 2 O + Biomass_plant | |||