13C-Metabolic Flux Analysis in Developing Flax ( L.) Embryos to Understand Storage Lipid Biosynthesis
Authors: Adrian Troncoso-Ponce
Anthony Degournay
Yannick Rossez
Brigitte Thomasset
Sébastien Acket
Stéphane Mottelet
Pierre Villon
Journal: Metabolites (2019)
Discipline: BIOLOGY & BIOCHEMISTRY
Keywords: embryo; flax; metabolic flux analysis; parallel labeling experiment.
Affiliations: Alliance Sorbonne Université, Université de Technologie de Compiègne, 60205 Compiègne CEDEX, France., Alliance Sorbonne Université, EA 4297 TIMR, Transformations Intégrées de la Matière Renouvelable, Université de Technologie de Compiègne, 60205 Compiègne CEDEX, France., Alliance Sorbonne Université, Laboratoire Roberval, FRE UTC CNRS 2012, Université de Technologie de Compiègne, 60205 Compiègne CEDEX, France.

Abstract:  Flax (Linum usitatissinum L.) oil is an important source of α-linolenic (C18:3 ω-3). This polyunsaturated fatty acid is well known for its nutritional role in human and animal diets. Understanding storage lipid biosynthesis in developing flax embryos can lead to an increase in seed yield via marker-assisted selection. While a tremendous amount of work has been done on different plant species to highlight their metabolism during embryo development, a comprehensive analysis of metabolic flux in flax is still lacking. In this context, we have utilized in vitro cultured developing embryos of flax and determined net fluxes by performing three complementary parallel labeling experiments with 13C-labeled glucose and glutamine. Metabolic fluxes were estimated by computer-aided modeling of the central metabolic network including 11 cofactors of 118 reactions of the central metabolism and 12 pseudo-fluxes. A focus on lipid storage biosynthesis and the associated pathways was done in comparison with rapeseed, arabidopsis, maize and sunflower embryos. In our hands, glucose was determined to be the main source of carbon in flax embryos, leading to the conversion of phosphoenolpyruvate to pyruvate. The oxidative pentose phosphate pathway (OPPP) was identified as the producer of NADPH for fatty acid biosynthesis. Overall, the use of 13C-metabolic flux analysis provided new insights into the flax embryo metabolic processes involved in storage lipid biosynthesis. The elucidation of the metabolic network of this important crop plant reinforces the relevance of the application of this technique to the analysis of complex plant metabolic systems. 

Retracted: No

PubPeer comments:
 I have some questions about this publication: - Figure 4 is based on data provided in supplementary table S5. When making a new plot from the raw data, we can observe differences compared to Fig 4 (R^2_from_fig_4=0.96, R^2_from_table_S5=0.93, and some points are missing in the published figure) - analyzing R^2 is not sufficient to determine whether the model fits or not the data (though this is helpfull to make a rough idea). When ploting simulations vs measurements for individual experiments, I end up with R^2=0.94 for exp B, R^2=0.98 for exp C, and R^2=0.66 for experiment D. Hence, the model cannot fit data from exp D (at least). - authors explicitely indicate the model fits the data based on khi2 statistics (at a 95% confidence interval). Some information is missing to perform a khi2 test. Still, even a degree of freedom of 100 and a precision on isotopic measurements of 0.05 (precision is usually better, as also shown by the authors in their own work - PMID 29452103, PMID 28413815 and PMID 28213171) are not sufficient to pass the test. I have contacted the corresponding author (also first author) to raise these questions and ask him if he could send me the model and flux calculation results file. Unfortunately, he  does not have the data anymore and he is  sorry to not being able to help . This paper was published only 3 months ago... I have firmly insisted, he has finally confirmed that he will look for the data. This was 2 weeks ago, no news yet. I believe it is worth sharing these questions with the community. Of course I will post an update as soon as I get his feedback. ,