Saha2011- Genome-scale metabolic network of Zea mays (iRS1563)

Saha2011- Genome-scale metabolic network of
Zea mays (iRS1563)

This model is described in the article:

Zea mays iRS1563: a
comprehensive genome-scale metabolic reconstruction of maize
metabolism.

Saha R, Suthers PF, Maranas
CD.
PLoS ONE 2011; 6(7): e21784
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.

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