Assessing the metabolic impact of nitrogen availability using a compartmentalized maize leaf genome-scale model

Margaret Simons, Rajib Saha, Nardjis Amiour, Akhil Kumar, Lenaïg Guillard, Gilles Clément, Martine Miquel, Zhenni Li, Gregory Mouille, Peter J. Lea, Bertrand Hirel, Costas D. Maranas

Research output: Contribution to journalArticle

40 Citations (Scopus)

Abstract

Maize (Zea mays) is an important C4plant due to its widespread use as a cereal and energy crop. A second-generation genomescale metabolic model for the maize leaf was created to capture C4carbon fixation and investigate nitrogen (N) assimilation by modeling the interactions between the bundle sheath and mesophyll cells. The model contains gene-protein-reaction relationships, elemental and charge-balanced reactions, and incorporates experimental evidence pertaining to the biomass composition, compartmentalization, and flux constraints. Condition-specific biomass descriptions were introduced that account for amino acids, fatty acids, soluble sugars, proteins, chlorophyll, lignocellulose, and nucleic acids as experimentally measured biomass constituents. Compartmentalization of the model is based on proteomic/transcriptomic data and literature evidence. With the incorporation of information from the MetaCrop and MaizeCyc databases, this updated model spans 5,824 genes, 8,525 reactions, and 9,153 metabolites, an increase of approximately 4 times the size of the earlier iRS1563 model. Transcriptomic and proteomic data have also been used to introduce regulatory constraints in the model to simulate an N-limited condition and mutants deficient in glutamine synthetase, gln1-3 and gln1-4. Model-predicted results achieved 90% accuracy when comparing the wild type grown under an N-complete condition with the wild type grown under an N-deficient condition.

Original languageEnglish (US)
Pages (from-to)1659-1674
Number of pages16
JournalPlant physiology
Volume166
Issue number3
DOIs
StatePublished - Nov 1 2014

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Biomass
Zea mays
Nitrogen
Genome
Proteomics
genome
corn
nitrogen
Mesophyll Cells
leaves
Nitrogen Fixation
Glutamate-Ammonia Ligase
Chlorophyll
Nucleic Acids
Proteins
Fatty Acids
transcriptomics
Databases
proteomics
Amino Acids

ASJC Scopus subject areas

  • Physiology
  • Genetics
  • Plant Science

Cite this

Assessing the metabolic impact of nitrogen availability using a compartmentalized maize leaf genome-scale model. / Simons, Margaret; Saha, Rajib; Amiour, Nardjis; Kumar, Akhil; Guillard, Lenaïg; Clément, Gilles; Miquel, Martine; Li, Zhenni; Mouille, Gregory; Lea, Peter J.; Hirel, Bertrand; Maranas, Costas D.

In: Plant physiology, Vol. 166, No. 3, 01.11.2014, p. 1659-1674.

Research output: Contribution to journalArticle

Simons, M, Saha, R, Amiour, N, Kumar, A, Guillard, L, Clément, G, Miquel, M, Li, Z, Mouille, G, Lea, PJ, Hirel, B & Maranas, CD 2014, 'Assessing the metabolic impact of nitrogen availability using a compartmentalized maize leaf genome-scale model', Plant physiology, vol. 166, no. 3, pp. 1659-1674. https://doi.org/10.1104/pp.114.245787
Simons, Margaret ; Saha, Rajib ; Amiour, Nardjis ; Kumar, Akhil ; Guillard, Lenaïg ; Clément, Gilles ; Miquel, Martine ; Li, Zhenni ; Mouille, Gregory ; Lea, Peter J. ; Hirel, Bertrand ; Maranas, Costas D. / Assessing the metabolic impact of nitrogen availability using a compartmentalized maize leaf genome-scale model. In: Plant physiology. 2014 ; Vol. 166, No. 3. pp. 1659-1674.
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