Assessing Nitrogen Metabolism Using Genome-Scale Models in Maize

A metabolic model for the leaf of Zea mays L. was created to capture C₄ carbon fixation and investigate nitrogen assimilation. A second-generation genome-scale model simulates the interactions between the bundle sheath and mesophyll cells. Biomass proportions of amino acids, fatty acids, soluble sugars, proteins, chlorophyll, lignocellulose, and nucleic acids were experimentally measured under nitrogen excess, nitrogen limited, and glutamine synthetase mutants yielding condition-specific biomass equations. Proteomic data, transcriptomic data, and literature evidence was used to determine the compartmentalization of reactions within the model. The incorporation of the iRS1563 model with information from the MetaCrop and MaizeCyc databases generated a model spanning 5,824 genes, 8,525 reactions, and 9,153 metabolites. A nitrogen complete, nitrogen limited, and two glutamine synthetase mutant (i.e. gln1-3 and gln1-4) conditions were simulated by introducing regulatory constraints based on transcriptomic and proteomic data. Simulated results achieved 90% accuracy when comparing the wild-type in a nitrogen complete condition with the wild-type in a nitrogen deficient condition. The flux through chlorophyll biosynthesis and directly related pathways decreases in the limited nitrogen wild-type, gln1-3 mutant, and gln1-4 mutant conditions compared to the nitrogen complete wild-type condition confirming the important association between nitrogen metabolism and chlorophyll synthesis.