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

Hay, Jordan O.; Shi, Hai; Heinzel, Nicolas; Hebbelmann, Inga; Rolletschek, Hardy; Schwender, Jorg

doi:10.3389/fpls.2014.00724

Title: Integration of a constraint-based metabolic model of Brassica napus developing seeds with ¹³C-metabolic flux analysis

Journal Article · Fri Dec 19 00:00:00 EST 2014 · Frontiers in Plant Science

DOI:https://doi.org/10.3389/fpls.2014.00724· OSTI ID:1178233

Hay, Jordan O. ^[1]; Shi, Hai ^[1]; Heinzel, Nicolas ^[2]; Hebbelmann, Inga ^[1]; Rolletschek, Hardy ^[2]; Schwender, Jorg ^[1]

Brookhaven National Lab. (BNL), Upton, NY (United States). Biological, Environmental & Climate Sciences Dept.
Leibniz Inst. for Plant Genetics and Culture Plant Research (IPK), Gatersleben (Germany)

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. New features include additional seed-relevant pathways for isoprenoid, sterol, phenylpropanoid, flavonoid, and choline biosynthesis. Being now based on standardized data formats and procedures for model reconstruction, bna572+ is available as a COBRA-compliant Systems Biology Markup Language (SBML) model and conforms to the Minimum Information Requested in the Annotation of Biochemical Models (MIRIAM) standards for annotation of external data resources. Bna572+ contains 966 genes, 671 reactions, and 666 metabolites distributed among 11 subcellular compartments. It is referenced to the Arabidopsis thaliana genome, with gene-protein-reaction (GPR) associations resolving subcellular localization. Detailed mass and charge balancing and confidence scoring were applied to all reactions. Using B. napus seed specific transcriptome data, expression was verified for 78% of bna572+ genes and 97% of reactions. Alongside bna572+ we also present a revised carbon centric model for ¹³C-Metabolic Flux Analysis (¹³C-MFA) with all its reactions being referenced to bna572+ based on linear projections. By integration of flux ratio constraints obtained from ¹³C-MFA and by elimination of infinite flux bounds around thermodynamically infeasible loops based on COBRA loopless methods, we demonstrate improvements in predictive power of Flux Variability Analysis (FVA). In conclusion, using this combined approach we characterize the difference in metabolic flux of developing seeds of two B. napus genotypes contrasting in starch and oil content.

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Research Organization:: Brookhaven National Laboratory (BNL), Upton, NY (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: SC00112704; AC0298CH10886

OSTI ID:: 1178233

Report Number(s):: BNL-106138-2015-JA; R&D Project: BO-133; KC0304000

Journal Information:: Frontiers in Plant Science, Vol. 5; ISSN 1664-462X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 28 works

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Computational analysis of storage synthesis in developing Brassica napus L. (oilseed rape) embryos: Flux variability analysis in relation to 13C-metabolic flux analysis

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59 BASIC BIOLOGICAL SCIENCES
loopless flux balance analysis
13C-metabolic flux analysis
central metabolism
carbon partitioning
constraint-based reconstruction and analysis

Title: Integration of a constraint-based metabolic model of Brassica napus developing seeds with 13C-metabolic flux analysis

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Title: Integration of a constraint-based metabolic model of Brassica napus developing seeds with ¹³C-metabolic flux analysis