Connecting genotype to phenotype: investigation of photoacclimation in the marine diatom Phaeodactylum tricornutum

Increasing atmospheric CO2 levels have led to disastrous consequences that have impacted many people’s lives. In nature, photosynthesis is the primary sink of CO2 in the air and in the ocean. A better understanding of the light harvesting and utilization mechanisms can help us better design photosynthetic organisms or artificial photosynthetic systems to utilize and reduce CO2 levels in the natural environment. Thanks to advancements in computational biology and bioinformatics in the past decade, we are now capable of achieving this task from a new prospective, with data analysis accomplished more quantitatively and comprehensively than ever before. A marine diatom, Phaeodactylum tricornutum, was selected to be the model species in my study because of its wide range of light intensity tolerances and its capability of photoprotection to high light stress. The primary objective of this dissertation is to characterize the light utilization and photoprotection associated energy and metabolic mechanisms in this organism that allow it to have such extraordinary features. In the first chapter, the cross-compartment energy and metabolite rebalancing was investigated by flux simulation developed from physiological experimental data and genome scale metabolic modeling. In the second chapter, a novel instrument for simultaneous measurement of carbon uptake and oxygen evolution was developed to provide additional insight into the light utilization efficiencies during photoacclimation period. In the third chapter, a comprehensive study, using both classic physiology and novel machine learning approaches, was conducted to investigate the function of a high light stress related protein (LHCX1) in photoprotection during acclimation. Taken together, these chapters significantly improve our understanding of photoprotective and energy utilization mechanisms in P. tricornutum that enable their remarkable success in adaptations to varying light conditions