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Illuminating circadian algal metabolism: a multiscale multiparadigm modeling approach
Metcalf, Alexander John
Metcalf, Alexander John
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2022
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2023-11-04
Abstract
Algae can synthesize complex and valuable molecules from water, carbon dioxide, and light. This versatility makes them intriguing targets for biological engineering, especially when grown in outdoor ponds with access to inexpensive natural light. However, engineering these organisms requires a metabolic model in order to better guide design - and unfortunately, diurnal growth in ponds induces multiple difficult-to-capture phenomena that complicate modeling efforts; examples of these include self-shading, shifting biomass compositions, and transient metabolic constraints.
This work explores approaches for modeling these organisms in a more accurate fashion. It begins with the construction of an automated pipeline for generating metabolic models from algal genomes. Biomass data is then used to refine an algal model for Chromochloris zofingiensis grown under different culture conditions; thanks to these improvements, this model correctly forecasts the presence of fermentation products when C. zofingiensis is grown on glucose. After that, a pre-existing steady state model of Chlamydomonas reinhardtii is extended into a transient space by utilizing circadian transcriptomic data and a decoupled biomass equation. This approach naturally replicates the accumulation of lipids during steady-state, nitrogen starved conditions without additional constraints; it also successfully predicts qualitative phenotypical outcomes from genotype when grown under diurnal light, an advancement required for in silco design of mutants for outdoor growth. Finally, this transient modeling technique is integrated into a three-dimensional space via agent based modeling and light rendering, thereby capturing self-shading and nutrient diffusion on culture-relevant scales. The results of this simulation suggest that maintenance energies differ significantly between algae grown on constant light and those grown diurnally, reinforcing the need for more investigation into this area. The sum of this work represents a cohesive set of modeling approaches for some of the most complex unicellular species under a variety of different conditions.
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