Algae have been considered as sources for renewable bioenergy due their ability to accumulate high cellular percentages of biomass as energy dense molecules, namely starch and triacylglycerols. The accumulation of these compounds is most readily induced through exposing cells to nutrient deprivation, especially from the macronutrient nitrogen. Multiple large scale studies have been carried out to study the metabolism behind starch and oil accumulation in an effort to increase production; however, no sufficient strategy for over accumulation has been determined. Additionally, little is known about the actual motivations for algae to accumulate these compounds in the first place. Current hypothesized roles for these molecules range from aiding recovery from nutrient deprivation to providing sinks for overflowing photosynthetic energy as metabolism slows. The exact relationship between carbon accumulation and photosynthesis remains unresolved.To study the interaction between photosynthesis (energy and carbon input) and carbon accumulation (stored carbon and energy), Chlamydomonas reinhardtii was chosen as a model. Chlamydomonas is the premier algal model system and can accumulate significant amounts of starch and TAG. Second, it can grow auto-, mixo-, and heterotrophically enabling experimentation under a range of light and media conditions. Further, extensive information available on the genome, transcriptome, proteome, and metabolic environment of Chlamydomonas allow for deeper interpretation of systems biology approaches. In this dissertation I explore the relationship between photosynthesis and carbon accumulation during nitrogen deprivation from the perspective of carbon and energy fluxes. Through systems biology methods, physiological measurements, and biomass analysis across multiple stages of nutrient deprivation I show that carbon accumulation is not dependent upon photosynthesis under mixotrophic conditions, pointing to a storage role for starch and TAG, most likely to aid nutrient recovery. Further, through flux modeling efforts using measured constraints, I report on the complexity of starch and TAG accumulations and how they change over the course of nutrient deprivation. This work suggests deeper regulatory interactions between starch and TAG accumulation based upon cellular programming and not simply energy overflows. It is my sincere hope that this work will help guide future engineering efforts concerning biofuel production in algae.
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