UC San Diego
Kinetic Model Reconstruction of Phytoplankton Light-Dependent Reactions and Implementation Towards Membrane Constraints
- Author(s): Basilio, Andrew
- Advisor(s): Palsson, Bernhard
- et al.
Phytoplankton photosynthesis accounts for much of the oxygen present in the world, which can affect many different global systems. Additionally, understanding phytoplankton photosynthesis and other metabolic processes are important because of their potential to be engineered for human purposes. In this thesis, I constructed a computational kinetic model of the light-dependent photosynthetic reactions of phytoplankton using the MASS Toolbox, an in-house computational tool developed by the UCSD Systems Biology Research Group. This model was based upon the one constructed by Kroon and Thoms and my model simulations were validated against this model. The kinetic model was constructed based on the fact that the photosystem II : cytochrome b6/f : photosystem I ratio was 1:1:1. The objective, therefore, for the second portion of the thesis was to determine thylakoid membrane crowding constraints and solve for the optimized ratio of photosystem II, cytochrome b6/f, and photosystem I. I calculated the crowding constraint equation using the model and incorporating parameters from literature, with hopes that it can be applied to the Phaeodactylum tricornutum genome-scale model in the future.
In the last portion of the thesis, actual physiological ratios of photosystem II, cytochrome b6/f, and photosystem I from the organism T. weissflogii were incorporated into the MASS Toolbox model of phytoplankton. I then simulated the model and observed the differences compared to the original model with the 1:1:1 protein ratio.