Abstract
The coccolithophorid unicellular alga Emiliania huxleyi is known to form large blooms, which have a strong effect on the marine carbon cycle. As a photosynthetic organism, it is subjected to a circadian rhythm due to the changing light conditions throughout the day. For a better understanding of the metabolic processes under these periodically-changing environmental conditions, a genome-scale model based on a genome reconstruction of the E. huxleyi strain CCMP 1516 was created. It comprises 410 reactions and 363 metabolites. Biomass composition is variable based on the differentiation into functional biomass components and storage metabolites. The model is analyzed with a flux balance analysis approach called diurnal flux balance analysis (diuFBA) that was designed for organisms with a circadian rhythm. It allows storage metabolites to accumulate or be consumed over the diurnal cycle, while keeping the structure of a classical FBA problem. A feature of this approach is that the production and consumption of storage metabolites is not defined externally via the biomass composition, but the result of optimal resource management adapted to the diurnally-changing environmental conditions. The model in combination with this approach is able to simulate the variable biomass composition during the diurnal cycle in proximity to literature data.
Highlights
Emiliania huxleyi is a species of unicellular coccolithophorid algae
The approach presented in this work, a diurnal flux balance analysis, is similar to the integrated FBA proposed by Cheung et al, who duplicated the fluxes for a stoichiometric model of Arabidopsis thaliana to simulate day and night metabolism in a single optimization problem [15]
Gap-filling reactions were taken from other genome-scale models, namely the Escherichia coli reconstruction iAF1260 [4], the Arabidopsis thaliana reconstruction AraGEM [7] and the Chlamydomonas reinhardtii reconstruction AlgaGEM [8]
Summary
Emiliania huxleyi is a species of unicellular coccolithophorid algae. As a coccolithophore, it forms highly-structured calcium carbonate plates (coccoliths). An important task while setting up FBA problems is to define an appropriate objective function that results in realistic flux distributions The approach presented in this work, a diurnal flux balance analysis (diuFBA), is similar to the integrated FBA proposed by Cheung et al, who duplicated the fluxes for a stoichiometric model of Arabidopsis thaliana to simulate day and night metabolism in a single optimization problem [15]. This is related to the dFBA DOA, but contains some simplifying assumptions. The diuFBA is applied to the genome-scale reconstruction to simulate a diurnal cycle, with the focus on the biomass composition at the transition from day to night
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