Metabolic network reconstruction and flux variability analysis of storage synthesis in developing oilseed rape (Brassica napus L.) embryos

Journal Article · Mon Aug 01 00:00:00 EDT 2011 · Plant Journal

DOI:https://doi.org/10.1111/j.1365-313X.2011.04613.x· OSTI ID:1040587

Hay, J; Schwender, J

Computational simulation of large-scale biochemical networks can be used to analyze and predict the metabolic behavior of an organism, such as a developing seed. Based on the biochemical literature, pathways databases and decision rules defining reaction directionality we reconstructed bna572, a stoichiometric metabolic network model representing Brassica napus seed storage metabolism. In the highly compartmentalized network about 25% of the 572 reactions are transport reactions interconnecting nine subcellular compartments and the environment. According to known physiological capabilities of developing B. napus embryos, four nutritional conditions were defined to simulate heterotrophy or photoheterotrophy, each in combination with the availability of inorganic nitrogen (ammonia, nitrate) or amino acids as nitrogen sources. Based on mathematical linear optimization the optimal solution space was comprehensively explored by flux variability analysis, thereby identifying for each reaction the range of flux values allowable under optimality. The range and variability of flux values was then categorized into flux variability types. Across the four nutritional conditions, approximately 13% of the reactions have variable flux values and 10-11% are substitutable (can be inactive), both indicating metabolic redundancy given, for example, by isoenzymes, subcellular compartmentalization or the presence of alternative pathways. About one-third of the reactions are never used and are associated with pathways that are suboptimal for storage synthesis. Fifty-seven reactions change flux variability type among the different nutritional conditions, indicating their function in metabolic adjustments. This predictive modeling framework allows analysis and quantitative exploration of storage metabolism of a developing B. napus oilseed.

• Research Organization: Brookhaven National Lab. (BNL), Upton, NY (United States)
• Sponsoring Organization: USDOE SC OFFICE OF SCIENCE (SC)
• DOE Contract Number: DE-AC02-98CH10886
• OSTI ID: 1040587
• Report Number(s): BNL-95387-2011-JA; R&D Project: BO-133; KC0304000; TRN: US201210%%763
• Journal Information: Plant Journal, Vol. 67, Issue 3; ISSN 0960-7412
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
60 APPLIED LIFE SCIENCES
AMINO ACIDS
AMMONIA
AVAILABILITY
BRASSICA
CARBON
COMPARTMENTS
EMBRYOS
EXPLORATION
ISOENZYMES
METABOLISM
NITROGEN
OPTIMIZATION
REDUNDANCY
SEEDS
SIMULATION
STORAGE
SYNTHESIS
TRANSPORT
flux balance analysis
carbon partitioning
constraint-based model
linear program
stoichiometric model