(CS-25-6) Modeling the impact of micronutrient scarcity on macronutrient flow in a metabolic network - pre-recorded talk

Body of Abstract: The sustainable growth of bioenergy crops is impacted by micronutrient bioavailability; nonetheless, the effect of micronutrient on the flow of carbon and nitrogen in these crops’ larger metabolic network is understudied. As we are now able to transfer knowledge from well-studied model organisms, such as Arabidopsis thaliana, to other bioenergy crop species, and to integrate various omics data; we can better study metals, such as iron and zinc, and their roles as key cofactors within the plants’ primary metabolic network. And in doing so, we generate a deep understanding of these plants’ complex biological systems promoting their sustainable growth.

In this work, we investigate the role of zinc and iron in the primary metabolic reconstruction of Poplar and Sorghum. We focus on the plastidial network given its importance in biosynthesizing many of the primary biomass components such as amino acids, nucleic acids, and fatty acids. We integrate multiple layers of data in our research including annotations of the metabolic networks, gene function predictions, and transcriptomic data generated under various growth conditions. We use PlantSEED (http://modelseed.org) Apps in KBase (http://kbase.us) to generate metabolic annotations and reconstructions of the two species. We then simulate these metabolisms using our enhanced implementation of RIPTiDe, an open-source transcriptome-based parsimonious flux balance analysis (pFBA) simulator. Through these simulations, we could identify metabolic pathways impacted by the varying levels of metal bioavailability and compare results across the two species because the implied homology of the enzymes in turn means the genomes encode the same primary metabolic network. Our findings constitute a major step towards better understanding the impact of micronutrient scarcity and generating new hypotheses on how the bioavailability of iron and zinc affect the growth and yield of the aforementioned species.