Metabolic and Transcriptional Reprogramming in Developing Soybean (Glycine max) Embryos

Abstract

Soybean (Glycine max) seeds are an important source of seed storage compounds, including protein, oil, and sugar used for food, feed, chemical, and biofuel production. We assessed detailed temporal transcriptional and metabolic changes in developing soybean embryos to gain a systems biology view of developmental and metabolic changes and to identify potential targets for metabolic engineering. Two major developmental and metabolic transitions were captured enabling identification of potential metabolic engineering targets specific to seed filling and to desiccation. The first transition involved a switch between different types of metabolism in dividing and elongating cells. The second transition involved the onset of maturation and desiccation tolerance during seed filling and a switch from photoheterotrophic to heterotrophic metabolism. Clustering analyses of metabolite and transcript data revealed clusters of functionally related metabolites and transcripts active in these different developmental and metabolic programs. The gene clusters provide a resource to generate predictions about the associations and interactions of unknown regulators with their targets based on “guilt-by-association” relationships. The inferred regulators also represent potential targets for future metabolic engineering of relevant pathways and steps in central carbon and nitrogen metabolism in soybean embryos and drought and desiccation tolerance in plants.

Chlorophyll Degradation: The Tocopherol Biosynthesis-Related Phytol Hydrolase in Arabidopsis Seeds Is Still Missing

“…Consistently, the timing of PPH-mediated chlorophyll degradation and tocopherol biosynthesis is more likely overlapped, because unlike the expression of some genes for tocopherol biosynthetic proteins that is high only at the onset of maturation based on publicly available transcriptome datasets of developing seeds of Arabidopsis (Supplemental Fig. S4) and soybean (Glycine max; Collakova et al, 2013), the expression of PPH was relatively high before and during seed maturation (Supplemental Fig. S4).…”

Near-Real-Time Analysis of the Phenotypic Responses of Escherichia coli to 1-Butanol Exposure Using Raman Spectroscopy

“…Fatty acid methyl esters were prepared by transesterification in the presence of methanolic HCl and analyzed on an Agilent 7890A series GC equipped with an FID (Agilent Technologies, Santa Clara, CA). The FAME separation was achieved on an Agilent 30-m DB-23 column (0.25 mm by 0.25 m), and the identities of the individual fatty acids were confirmed by analyzing spectral information of FAME in selected samples on the same GC instrument coupled to an Agilent 5975C series MS apparatus (Agilent Technologies) (48).…”

“…Lipid extractions were performed on 1 mg of lyophilized cells by using biphasic chloroform-methanol-water extractions and 10 g of C 18:2 as an internal standard, according to a standard protocol (48). Fatty acid methyl esters were prepared by transesterification in the presence of methanolic HCl and analyzed on an Agilent 7890A series GC equipped with an FID (Agilent Technologies, Santa Clara, CA).…”

Heat Stress Related Physiological and Metabolic Traits in Peanut Seedlings

“…Trimethylsilyl derivatives of metabolites were analyzed by GC-MS as described (Duran et al, 2003;Collakova et al, 2008;. For lipid-derived fatty acid analysis, 200 ml of the organic phase was dried as for polar metabolites and fatty acid methylesters were prepared and analyzed as described (Lu et al, 2011;Collakova et al, 2013).…”

“…Peak identification and data analysis were performed as described by Collakova et al (2013) and by using the Agilent Enhanced Mass Selective Detector ChemStation software and three different libraries: FiehnLib spectral and retention time library [Kind et al, 2009], our own custom-built spectral and retention time library, and the spectral NIST library (National Institute of Standards and Technology, Gaithersburg, MD). Final relative levels of polar metabolites and absolute levels of fatty acids were standardized for dry weight and internal standard recoveries.…”