Genome Informatics 11: 458–459 (2000)
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Computer Modeling of Photosynthesis Using the E-CELL System Emily Wang
Yoichi Nakayama
Masaru Tomita
[email protected]
[email protected]
[email protected]
Laboratory for Bioinformatics,Department of Environmental Information, Keio University, 5322 Endo, Fujisawa-shi, Kanagawa 252-8520, Japan
Keywords: computer modeling, photosynthesis, Calvin Benson cycle
1
Introduction
The E-CELL system is a generic software package for whole cell modeling and simulation developed by the Laboratory for Bioinformatics at Keio University [1]. Photosynthesis is generally characterized as the assimilation of CO2 and H2 O to yield O2 and carbohydrates using energy from sunlight, and can be expressed by the following process: 6CO2 + 12H2 O + lightenergy −→ C6 H12 O6 + 6O2 + 6H2 O Photosynthesis occurs in two phases; • Light Reactions converts energy from the sun to ATP and NADPH. Electromagnetic radiation in the form of photons are absorbed by photoreceptor chlorophyll, which are then transported through a series of elctron transport chain yielding O2 , ATP and NADPH • Dark Reactions (Calvin Benson Cycle) assimilates CO2 , and the ATP, NADPH generated in the light reactions into products such as starch and sucrose. The enzyme Ribulose bisphosphate carboxylase, often known as Rubisco, is the key enzyme in catalyzing the CO2 fixation reaction. Using the E-CELL system, we have constructed a prototype model of the Calvin Benson C3 photosynthesis cycle with the pathways for starch production and triose phosphate export.
2
The Calvin Benson photosynthesis model
There are 13 enzymes within the Calvin Benson Cycle. The cycle begins with the phosphorylation Ru5P(ribulose-5 phosphate) to create RuBP (ribulose-1,5-bisphosphate). Following the assimilation of CO2 by Rubisco, two molecules of 3PG are formed, one of which is exported to the cytosol. The other is converted to BPG, then to GAP. GAP is then isomerized to form DHAP. The cycle then follows a series of rections similar to that of the pentose phosphate cycle, regenerating the Ru5P used in the beginning of the cycle. The export enzymes of the triose-phosphates exhibit mechanisms of orthophosphate antiport between the chloroplast stroma and the cell cytosol. The final 4 enzymes are involved in starch production and ATP synthesis. Enzyme reactions and parameters in this model are based on mathematical models presented by Pettersson and Ryde-Pettersson [2] and by Laisk et al. [3]. The pathway of this cycle is shown in Figure 1. Enzymes in the cycle are affected by concentrations of ATP, ADP, and orthophosphate.
Computer Modeling of Photosynthesis
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Figure 1: Calvin Benson cycle pathway.
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Discussion
In this work, a prototype model of the C3 Calvin Benson cycle has been constructed. All initial concentrations used are from models of Pettersson and Ryde-Pettersson [2], and Laisk et al. [3]. Parameter estimations will be made to optimize simulation precision to fit experimental data using modules of E-CELL Manager [4]. In order to simulate whole cell metabolic flux, an extended model is also now being developed to integrate the light reactions and the C4 pathway. C4 plants, most commonly found in tropical regions and other areas with relatively higher temperatures, assimilate CO2 in their photosynthetic cells instead of the Calvin Benson cycle for efficiency. These models will be used to analyze differences in metabolic control of various photosynthetic systems, and their responses to changes in environmental elements.
References [1] Tomita, M., Hashimoto, K., Takahashi, K., Shimizu, T., Matsuzaki, Y., Miyoshi, F., Saito, K., Tanida, S., Yugi, K., Venter, J.C., and Hutchison, C., E-CELL: software environment for whole cell simulation, Bioinformatics, 15(1):72–84, 1999. [2] Pettersson, G. and Ryde-Pettersson, U., A mathematical model of the Calvin photosynthesis cycle, Eur. J. Biochem., 175(3):661–672, 1988. [3] Laisk, A., Eichelmann, H., Oja, V., Eatherall, A., and Walker, D.A., A mathematical model of the carbon metabolism in photosynthesis. Difficulties in explaining oscillations by fructose 2, 6-bisphosphate regulation, Proc. R. Soc. Lond., 237(B):389–415, 1988. [4] Saito, Y., Takahashi, K., Iwata, T., Aikawa, T., and Tomita, M., Parameter estimation mechanism of E-CELL simulation environment, Genome Informatics, 10:358–359, 1999.
