Model description

There are several levels of complexity that need to be considered in order to describe the diurnal regulation of carbon metabolism in plants. Firstly, some reactions are lightdependent and happen only or mainly in presence of light (such as carbon fixation and starch synthesis) or in absence of light (such as starch degradation). Secondly, reactions are compartmentalised between chloroplast (carbon fixation, starch synthesis, the initial steps of starch degradation) and cytosol (sucrose synthesis and the later steps of starch degradation). Thirdly, different sets of reactions prevail in source and sink tissues. Additionally we developed the reactions of the diurnal regulation of carbon fluxes, connected with the circadian clock. Therefore the model consists of 6 blocks of reactions, described in the respective sections below: A carbon fixation and starch synthesis; B starch degradation; C sucrose synthesis; D consumption of sucrose by growing sinks; E diurnal/circadian regulation of carbon metabolism and F circadian clock itself as a necessary element of the diurnal regulation of metabolism. The units of concentration are mM in our model. For comparison with experimental data, which are mainly presented in g of fresh weight (g FW) or mg of chlorophyll (mg Chl) units the following volume coefficients were used: the stromal volume is assumed to be =65 μl/g FW=65 μl/mg Chl, the cytosolic volume =23 μl/g FW=23 μl/mg Chl 1, 2 . For estimation of parameters and comparison of the model with data we used Arabidopsis data where they were available or other plant’s data (mainly spinach). The values of the model parameters are presented in Table S1.