Constraint-Based Modeling of Diatoms Metabolism and Quantitative Biology Approaches
Contribution to a Book
The Molecular Life of Diatoms
Diatoms (Bacillarophyceae) are the most abundant and diverse phytoplankton in oceans. They can produce several valuable metabolic products (e.g., lipids) that can be potential feedstocks for many commercial products (e.g., biofuels). Enhancing the yield of such metabolic products requires deep understanding and genetic manipulations of diatoms metabolism. Genome-scale metabolic modeling is a useful tool to explore metabolisms in terms of extra- and intra-cellular fluxes, theoretical yields, and feasibility of knockout and knock-in mutants. This chapter provides a comprehensive overview of current advances in the construction of diatom GEMs and their potential advantages for studying and engineering diatom metabolism. Using some examples, we also highlighted how GEMs could provide insights in understanding the metabolic exchanges between diatoms and surrounding organisms in marine ecosystems.
Moss Landing Marine Laboratories
Manish Kumar, Cristal Zuniga, Juan D. Tibocha-Bonilla, Sarah R. Smith, Joanna Coker, Andrew E. Allen, and Karsten Zengler. "Constraint-Based Modeling of Diatoms Metabolism and Quantitative Biology Approaches" The Molecular Life of Diatoms (2022): 775-808. https://doi.org/10.1007/978-3-030-92499-7_26