A Genome-Scale Metabolic Model of Soybean (Glycine max) Highlights Metabolic Fluxes in Seedlings

Abstract

Until they become photoautotrophic juvenile plants, seedlings depend upon the reserves stored in seed tissues. These reserves must be mobilized and metabolized, and their breakdown products must be distributed to the different organs of the growing seedling. Here, we investigated the mobilization of soybean (Glycine max) seed reserves during seedling growth by initially constructing a genome-scale stoichiometric model for this important crop plant and then adapting the model to reflect metabolism in the cotyledons and hypocotyl/root axis (HRA). A detailed analysis of seedling growth and alterations in biomass composition was performed over 4 d of postgerminative growth and used to constrain the stoichiometric model. Flux balance analysis revealed marked differences in metabolism between the two organs, together with shifts in primary metabolism occurring during different periods postgermination. In particular, from 48 h onward, cotyledons were characterized by the oxidation of fatty acids to supply carbon for the tricarboxylic acid cycle as well as production of sucrose and glutamate for export to the HRA, while the HRA was characterized by the use of a range of imported amino acids in protein synthesis and catabolic processes. Overall, the use of flux balance modeling provided new insight into well-characterized metabolic processes in an important crop plant due to their analysis within the context of a metabolic network and reinforces the relevance of the application of this technique to the analysis of complex plant metabolic systems.

Characterization of raffinose metabolism genes uncovers a wild Arachis galactinol synthase conferring tolerance to abiotic stresses

“…The expression of AdGolS3 transgene in 13 independent Arabidopsis OE lines was confirmed through qRT-PCR analysis as described below (2.10), using specific AdGolS3 primers (Table S1 ). The content of four sugars (glucose, fructose, sucrose and raffinose) was determined in leaves of one-month-old WT and transgenic plants (five individuals per genotype) as described previously 33 . Sugars were extracted using 80% (v/v) ethanol at 80 °C, and the extracts dried and resuspended in water for analysis.…”

The Effects of Domestication on Secondary Metabolite Composition in Legumes

“…Other viable strategies of engineering secondary metabolite pathways include biosynthesis in microorganisms and modulation of gene expressions through manipulating the expressions of transcription factors (Du et al, 2010). Recently, genome-scale models have been used to represent the metabolic capabilities of legumes, including alfalfa and soybean (Pfau et al, 2018;Moreira et al, 2019). This approach allows the integration of different kinds of omics data to get new insights into plantmicrobe interactions (diCenzo et al, 2016;Pfau et al, 2018;Contador et al, 2020).…”

The Impacts of Domestication and Agricultural Practices on Legume Nutrient Acquisition Through Symbiosis With Rhizobia and Arbuscular Mycorrhizal Fungi

“…However, metabolic models have been published for only two legume species, G. max and M. truncatula, despite the significance of legumes to sustainable agriculture. A compartmentalized reconstruction for G. max was used to construct a multi-organ model to represent the reserve mobilization in the cotyledon and hypocotyl/root tissues (Moreira et al, 2019). This reconstruction can also be used to represent other tissues and conditions since the whole set of metabolic reactions in soybean were used to construct the metabolic model.…”