A Multi‐Omics Analysis of Glycine max Leaves Reveals Alteration in Flavonoid and Isoflavonoid Metabolism Upon Ethylene and Abscisic Acid Treatment

Abstract

Phytohormones are central to plant growth and development. Despite the advancement in our knowledge of hormone signaling, downstream targets, and their interactions upon hormones action remain largely fragmented, especially at the protein and metabolite levels. With an aim to get new insight into the effects of two hormones, ethylene (ET) and abscisic acid (ABA), this study utilizes an integrated proteomics and metabolomics approach to investigate their individual and combined (ABA+ET) signaling in soybean leaves. Targeting low-abundance proteins, our previously established protamine sulfate precipitation method was applied, followed by label-free quantification of identified proteins. A total of 4129 unique protein groups including 1083 differentially modulated in one (individual) or other (combined) treatments were discerned. Functional annotation of the identified proteins showed an increased abundance of proteins related to the flavonoid and isoflavonoid biosynthesis and MAPK signaling pathway in response to ET treatment. HPLC analysis showed an accumulation of isoflavones (genistin, daidzein, and genistein) upon ET treatment, in agreement with the proteomics results. A metabolome analysis assigned 79 metabolites and further confirmed the accumulation of flavonoids and isoflavonoids in response to ET. A potential cross-talk between ET and MAPK signaling, leading to the accumulation of flavonoids and isoflavonoids in soybean leaves is suggested.

Manipulation of β‐carotene levels in tomato fruits results in increased ABA content and extended shelf life

“…The extent of changes (>10-fold for some flavonoid glycosides) suggests they represent direct effects of the genetic manipulation and thus of the increase in ABA in LCYb-overexpressing fruits, compared to the less pronounced alterations observed in primary metabolites, which are likely to represent secondary effects. This hypothesis finds support in a series of previous studies linking ABA and flavonoid levels in apple (Lu et al, 2017), soybean (Gupta et al, 2018) and tomato (Mou et al, 2015). In agreement with biochemical data, a series of key structural phenylpropanoid genes was up-regulated in LCYb-overexpressing fruits: for instance, PHENYLALANINE AMMONIA-LYASE (PAL) at the MG and B stages, and CHALCONE SYNTHASE (CHS) at the MG and B+10 stages.…”

Global metabolite profiling based on GC–MS and LC–MS/MS analyses in ABF3-overexpressing soybean with enhanced drought tolerance

“…A recent multi-omics study with soybean leaves has revealed that exogenously applied ABA increases the accumulation of glycerolipids, prenol lipids, and phospholipids while the concentrations of secondary metabolites, such as flavonoids and isoflavonoids, remain unchanged [37]. Drought stress is known to have a distinct effect on the metabolism of lipids that play a role in maintaining membrane integrity and preserving cell compartmentation [38,39].…”

A TMT-Based Quantitative Proteome Analysis to Elucidate the TSWV Induced Signaling Cascade in Susceptible and Resistant Cultivars of Solanum lycopersicum

“…In order to examine the reproducibility of the obtained TMT-data among different biological and technical replicates of the same sample, multi-scatter plots were generated using Perseus software. Scatterplots of the same samples showed a typical non-uniform spread, suggesting low accuracy and reproducibility for the peptides which are closer to the background level [12]. Pearson correlation coefficients of different replicates of the same samples were more than 0.980, indicating a high degree of correlation among different replicates of the same samples ( Figure 3A).…”

“…Protein extraction, trypsin digestion and TMT labeling were carried out as described previously [10]. In brief, proteins from the control and TSWV infected leaves of susceptible and resistant cultivars were extracted using Tris-Mg/NP-40 buffer (0.5 M Tris-HCl (pH 8.3), 2% v/v NP-40, 20 mM MgCl 2 ) followed by TCA/Acetone precipitation of the proteins [12]. Trypsin digestion by the FASP method [52], TMT-labeling [9] and MS analysis [53,54] were carried out as described previously.…”