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Zea mays iRS1563: a comprehensive genome-scale metabolic reconstruction of maize metabolism.
- Source :
-
PloS one [PLoS One] 2011; Vol. 6 (7), pp. e21784. Date of Electronic Publication: 2011 Jul 06. - Publication Year :
- 2011
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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.
- Subjects :
- Acetaldehyde analogs & derivatives
Acetaldehyde pharmacology
Arabidopsis drug effects
Arabidopsis genetics
Arabidopsis radiation effects
Biomass
Carbon Cycle drug effects
Carbon Cycle radiation effects
Cell Compartmentation drug effects
Cell Compartmentation radiation effects
Cell Wall drug effects
Cell Wall metabolism
Cell Wall radiation effects
Galactose metabolism
Genes, Plant genetics
Glucose metabolism
Light
Metabolic Networks and Pathways drug effects
Metabolic Networks and Pathways radiation effects
Models, Genetic
Molecular Sequence Annotation
Mutation genetics
Organelles drug effects
Organelles metabolism
Organelles radiation effects
Species Specificity
Zea mays drug effects
Zea mays radiation effects
Genome, Plant genetics
Metabolic Networks and Pathways genetics
Zea mays genetics
Zea mays metabolism
Subjects
Details
- Language :
- English
- ISSN :
- 1932-6203
- Volume :
- 6
- Issue :
- 7
- Database :
- MEDLINE
- Journal :
- PloS one
- Publication Type :
- Academic Journal
- Accession number :
- 21755001
- Full Text :
- https://doi.org/10.1371/journal.pone.0021784