Integration of a constraint-based metabolic model of Brassica napus developing seeds with (13)C-metabolic flux analysis.

The use of large-scale or genome-scale metabolic reconstructions for modeling and simulation of plant metabolism and integration of those models with large-scale omics and experimental flux data is becoming increasingly important in plant metabolic research. Here we report an updated version of bna572, a bottom-up reconstruction of oilseed rape (Brassica napus L.; Brassicaceae) developing seeds with emphasis on representation of biomass-component biosynthesis.

Transcript abundance on its own cannot be used to infer fluxes in central metabolism.

An attempt has been made to define the extent to which metabolic flux in central plant metabolism is reflected by changes in the transcriptome and metabolome, based on an analysis of in vitro cultured immature embryos of two oilseed rape (Brassica napus) accessions which contrast for seed lipid accumulation. Metabolic flux analysis (MFA) was used to constrain a flux balance metabolic model which included 671 biochemical and transport reactions within the central metabolism. This highly confident flux information was eventually used for comparative analysis of flux vs.

Flux variability analysis: application to developing oilseed rape embryos using toolboxes for constraint-based modeling.

Flux variability analysis enables comprehensive exploration of alternate optimal routes in a metabolic network. This method is especially useful with models such as bna572 for the developing oilseed rape embryo which is highly compartmentalized. Here, we describe a protocol for carrying out flux variability analysis on reactions and network projections of bna572 using well-established software (CellNetAnalyzer and COBRA) for constraint-based analysis of stoichiometric network reconstructions.

Seed architecture shapes embryo metabolism in oilseed rape.

Constrained to develop within the seed, the plant embryo must adapt its shape and size to fit the space available. Here, we demonstrate how this adjustment shapes metabolism of photosynthetic embryo. Noninvasive NMR-based imaging of the developing oilseed rape (Brassica napus) seed illustrates that, following embryo bending, gradients in lipid concentration became established.

Predictive modeling of biomass component tradeoffs in Brassica napus developing oilseeds based on in silico manipulation of storage metabolism.

Seed oil content is a key agronomical trait, while the control of carbon allocation into different seed storage compounds is still poorly understood and hard to manipulate. Using bna572, a large-scale model of cellular metabolism in developing embryos of rapeseed (Brassica napus) oilseeds, we present an in silico approach for the analysis of carbon allocation into seed storage products. Optimal metabolic flux states were obtained by flux variability analysis based on minimization of the uptakes of substrates in the natural environment of the embryo.