Zea mays irs1563

A comprehensive genome-scale metabolic reconstruction of maize metabolism

Rajib Saha, Patrick F. Suthers, Costas D. Maranas

Research output: Contribution to journalArticle

120 Citations (Scopus)

Abstract

The scope and breadth of genome-scale metabolic reconstructions have continued to expand over the last decade. Herein, we introduce a genome-scale model for a plant with direct applications to food and bioenergy production (i.e., maize). Maize annotation is still underway, which introduces significant challenges in the association of metabolic functions to genes. The developed model is designed to meet rigorous standards on gene-protein-reaction (GPR) associations, elementally and charged balanced reactions and a biomass reaction abstracting the relative contribution of all biomass constituents. The metabolic network contains 1,563 genes and 1,825 metabolites involved in 1,985 reactions from primary and secondary maize metabolism. For approximately 42% of the reactions direct literature evidence for the participation of the reaction in maize was found. As many as 445 reactions and 369 metabolites are unique to the maize model compared to the AraGEM model for A. thaliana. 674 metabolites and 893 reactions are present in Zea mays iRS1563 that are not accounted for in maize C4GEM. All reactions are elementally and charged balanced and localized into six different compartments (i.e., cytoplasm, mitochondrion, plastid, peroxisome, vacuole and extracellular). GPR associations are also established based on the functional annotation information and homology prediction accounting for monofunctional, multifunctional and multimeric proteins, isozymes and protein complexes. We describe results from performing flux balance analysis under different physiological conditions, (i.e., photosynthesis, photorespiration and respiration) of a C4 plant and also explore model predictions against experimental observations for two naturally occurring mutants (i.e., bm1 and bm3). The developed model corresponds to the largest and more complete to-date effort at cataloguing metabolism for a plant species.

Original languageEnglish (US)
Article numbere21784
JournalPloS one
Volume6
Issue number7
DOIs
StatePublished - Jul 11 2011

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Metabolism
Zea mays
Genes
Genome
metabolism
genome
corn
Metabolites
Association reactions
metabolites
Proteins
Biomass
genes
proteins
Cataloging
Mitochondria
prediction
Secondary Metabolism
photorespiration
Photosynthesis

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

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Zea mays irs1563 : A comprehensive genome-scale metabolic reconstruction of maize metabolism. / Saha, Rajib; Suthers, Patrick F.; Maranas, Costas D.

In: PloS one, Vol. 6, No. 7, e21784, 11.07.2011.

Research output: Contribution to journalArticle

Saha, Rajib ; Suthers, Patrick F. ; Maranas, Costas D. / Zea mays irs1563 : A comprehensive genome-scale metabolic reconstruction of maize metabolism. In: PloS one. 2011 ; Vol. 6, No. 7.
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