UC Berkeley

Photosynthesis by plants and algae is the foundation for nearly all of Earth’s food webs. Maintaining photosynthesis is metabolically costly with a high demand for mineral nutrients. Most photosynthetic organisms live in conditions insufficient for optimal rates of photosynthesis. Consequently, diverse biochemical and genetic regulatory mechanisms have evolved to enable acclimation of photosynthesis to non-ideal conditions and thus organismal survival. Sugars are both primary products of photosynthetic fixation and signals to regulate photosynthesis gene expression in plants and algae. The emerging model green alga Chromochloris zofingiensis completely represses photosynthesis in the presence of glucose via a hexokinase 1 (HXK1) dependent pathway. Unlike other green algal models, C. zofingiensis upregulates total fatty acids and accumulates the valuable ketocarotenoid astaxanthin in either glucose-fed or nutrient stress conditions, making it a viable candidate for metabolic bioprospecting. In this dissertation, I reveal that iron deficiency, one the major limits on global photosynthesis, is required for C. zofingiensis’ photosynthetic switch off in addition to HXK1-dependent glucose signaling. Replete iron added at the same time as glucose creates a distinct mixotrophic state which concurrently maintains lipid accumulation with photosynthesis and supports the highest biomass growth rate of any other trophic state.

In Chapter 1, I briefly review sugars as signals in genetic regulation across organisms, which has been involved in some of the most foundational discoveries of molecular biology. Because the emergence of oxygenic photosynthesis drastically changed the carbon repertoire of Earth’s ecosystems, the impacts of carbon sink regulatory feedback and its interplay with mineral nutrient signaling are relevant to all experimental systems understanding sugar feedback. In Chapter 2, I employ physiology and combinatorial proteomics to distinguish the proteins that are distinctly regulated when photosynthesis is switched off from the states where lipid accumulation is activated. Incorporating orthology and cross-species multi-omics experiments reveals novel universal players in photosynthesis and lipid accumulation and reveals how glucose-fed C. zofingiensis has developed evolutionarily novel iron priorities. In Chapter 3, the implications of glucose interactions necessitated an experimental redesign of the medium, where incorporating ionomics with biomass of long-term glucose growth was used to create a medium that could maintain long-term glucose cultures in a replete nutrient state. In Chapter 4, a comprehensive multi-omics time course covering switch off and switch recovery of C. zofingiensis is analyzed to understand the regulatory cascades behind various metabolic transitions. Using time-ordered piece-wise linear models, I reveal temporally distinct molecular events that precede photosynthetic, lipid, iron, and biomass transitions. I incorporate these models to find enriched cis-regulatory elements, in particular, a domain architecture which will aid in engineering green algae to accumulate more biofuel precursors. Finally in Chapter 5, the evolutionary perspective of metabolism is also considered in a literature review with a specific focus on how two distinct algae, C. zofingiensis and Haematococcus pluvialis, accumulate astaxanthin. Phylogenomic and gene expression comparisons show a divergence in carotenoid accumulation and partitioning strategies in both organisms, which will also inform engineering of industrially useful ketocarotenoids.

As described in the chapters of this dissertation, investigating the synergistic impacts of iron and glucose with systems biology approaches provided an unprecedented ability to distinguish novel molecular players and strategies in regulating photosynthesis and lipid biochemistry. Secondly, incorporating bioinformatic predictions of orthologs across several plants and algae helped to reveal several universal players involved in photosynthetic development and divergent strategies of lipid and astaxanthin accumulation. These players will provide a framework for redesigning transcriptional networks for improved photosynthesis and metabolic engineering to enhance the environment and economy.