Comparative investigation of seed coats of brown‐ versus yellow‐colored soybean seeds using an integrated proteomics and metabolomics approach

Gupta, Ravi; Min, Chul Woo; Kim, So Wun; Wang, Yiming; Agrawal, Ganesh Kumar; Rakwal, Randeep; Kim, Pil Joo; Lee, Byong Won; Ko, Jong Min; Baek, In Yeol; Bae, Dong Won; Kim, Sun Tae

doi:10.1002/pmic.201400453

Cited by 32 publications

(20 citation statements)

References 33 publications

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“…Total proteins from matured and seed filling stage soybean seeds were isolated using the protamine sulfate (PS) precipitation method with trichloroacetic acid (TCA)/acetone precipitation [5,19]. Briefly, for PS precipitation method, one gram of each seed powder was homogenized with 10 mL of ice-cold Tris-Mg/NP-40 extraction buffer (0.5 M Tris-HCl, pH 8.3, 2% (v/v) NP-40, 20 mM MgCl 2 ) and centrifuged at 15,922× g for 10 min at 4 • C. The sequentially collected clear homogenate was incubated on ice for 30 min with 0.15% (w/v) PS stock solution.…”

Section: Protein Extraction and Digestion By Filter-aided Sample Prepmentioning

confidence: 99%

In-Depth Investigation of Low-Abundance Proteins in Matured and Filling Stages Seeds of Glycine max Employing a Combination of Protamine Sulfate Precipitation and TMT-Based Quantitative Proteomic Analysis

Min

Park

Bae

et al. 2020

Cells

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Despite the significant technical advancements in mass spectrometry-based proteomics and bioinformatics resources, dynamic resolution of soybean seed proteome is still limited because of the high abundance of seed storage proteins (SSPs). These SSPs occupy a large proportion of the total seed protein and hinder the identification of low-abundance proteins. Here, we report a TMT-based quantitative proteome analysis of matured and filling stages seeds of high-protein (Saedanbaek) and low-protein (Daewon) soybean cultivars by application of a two-way pre-fractionation both at the levels of proteins (by PS) and peptides (by basic pH reverse phase chromatography). Interestingly, this approach led to the identification of more than 5900 proteins which is the highest number of proteins reported to date from soybean seeds. Comparative protein profiles of Saedanbaek and Daewon led to the identification of 2200 and 924 differential proteins in mature and filling stages seeds, respectively. Functional annotation of the differential proteins revealed enrichment of proteins related to major metabolism including amino acid, major carbohydrate, and lipid metabolism. In parallel, analysis of free amino acids and fatty acids in the filling stages showed higher contents of all the amino acids in the Saedanbaek while the fatty acids contents were found to be higher in the Daewon. Taken together, these results provide new insights into proteome changes during filling stages in soybean seeds. Moreover, results reported here also provide a framework for systemic and large-scale dissection of seed proteome for the seeds rich in SSPs by two-way pre-fractionation combined with TMT-based quantitative proteome analysis.

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Section: Protein Extraction and Digestion By Filter-aided Sample Prepmentioning

confidence: 99%

In-Depth Investigation of Low-Abundance Proteins in Matured and Filling Stages Seeds of Glycine max Employing a Combination of Protamine Sulfate Precipitation and TMT-Based Quantitative Proteomic Analysis

Min

Park

Bae

et al. 2020

Cells

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“…As of today, very few reports have been published on the proteomic and metabolomic analyses of different tissues of ginseng. Comparative proteomic and metabolomic analyses have been performed on many crop and medicinal plants to examine differentially expressed proteins or metabolites under adverse conditions and in different cultivars ( Purkayastha et al, 2014 ; Gupta et al, 2015b ; Min et al, 2015 ; Ma et al, 2016 ). Metabolome studies have been performed on ginseng to assess the effects of colored light-emitting diode lighting ( Park et al, 2013 ), cultivation ages ( Kim et al, 2011 ) on adventitious roots, and environmental conditions of main roots ( Kim et al, 2010 ).…”

Section: Introductionmentioning

confidence: 99%

An Integrated Biochemical, Proteomics, and Metabolomics Approach for Supporting Medicinal Value of Panax ginseng Fruits

et al. 2016

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Panax ginseng roots are well known for their medicinal properties and have been used in Korean and Chinese traditional medicines for 1000s of years. However, the medicinal value of P. ginseng fruits remain poorly characterized. In this study, we used an integrated biochemical, proteomics, and metabolomics approach to look into the medicinal properties of ginseng fruits. DPPH (1,1-diphenyl-2-picrylhydrazyl) and ABTS [2,2′-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid)] assays showed higher antioxidant activities in ginseng fruits than leaves or roots. Two-dimensional gel electrophoresis (2-DE) profiling of ginseng fruit proteins (cv. Cheongsun) showed more than 400 spots wherein a total of 81 protein spots were identified by mass spectrometry using NCBInr, UniRef, and an in-house developed RNAseq (59,251 protein sequences)-based databases. Gene ontology analysis showed that most of the identified proteins were related to the hydrolase (18%), oxidoreductase (16%), and ATP binding (15%) activities. Further, a comparative proteome analysis of four cultivars of ginseng fruits (cvs. Yunpoong, Gumpoong, Chunpoong, and Cheongsun) led to the identification of 22 differentially modulated protein spots. Using gas chromatography-time of flight mass spectrometry (GC-TOF MS), 66 metabolites including amino acids, sugars, organic acids, phenolic acids, phytosterols, tocopherols, and policosanols were identified and quantified. Some of these are well known medicinal compounds and were not previously identified in ginseng. Interestingly, the concentration of almost all metabolites was higher in the Chunpoong and Gumpoong cultivars. Parallel comparison of the four cultivars also revealed higher amounts of the medicinal metabolites in Chunpoong and Gumpoong cultivars. Taken together, our results demonstrate that ginseng fruits are a rich source of medicinal compounds with potential beneficial health effects.

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“…Proteins were focused on Ettan IPGphor by applying parameters as reported by Gupta et al. . After two equilibration steps, the strip was then placed onto a vertical slab gel (12% SDS–PAGE).…”

Section: Methodsmentioning

confidence: 99%

Proteomic and metabolomic study of wax apple (Syzygium samarangense) fruit during ripening process

et al. 2018

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Wax apple is one of the underutilized fruits that is considered a good source of fibers, vitamins, minerals as well as antioxidants. In this study, a comparative analysis of the developments of wax fruit ripening at the proteomic and metabolomic level was reported. 2D electrophoresis coupled with MALDI-TOF/TOF was used to compare the proteome profile from three developmental stages named immature, young, and mature fruits. In general, the protein expression profile and the identified proteins function were discussed for their potential roles in fruit physiological development and ripening processes. The metabolomic investigation was also performed on the same samples using quadrupole LC-MS (LC-QTOF/MS). Roles of some of the differentially expressed proteins and metabolites are discussed in relation to wax apple ripening during the development. This is the first study investigating the changes in the proteins and metabolites in wax apple at different developmental stages. The information obtained from this research will be helpful in developing biomarkers for breeders and help the plant researchers to avoid wax apple cultivation problems such as fruit cracking.

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Comparative investigation of seed coats of brown‐ versus yellow‐colored soybean seeds using an integrated proteomics and metabolomics approach

Cited by 32 publications

References 33 publications

In-Depth Investigation of Low-Abundance Proteins in Matured and Filling Stages Seeds of Glycine max Employing a Combination of Protamine Sulfate Precipitation and TMT-Based Quantitative Proteomic Analysis

In-Depth Investigation of Low-Abundance Proteins in Matured and Filling Stages Seeds of Glycine max Employing a Combination of Protamine Sulfate Precipitation and TMT-Based Quantitative Proteomic Analysis

An Integrated Biochemical, Proteomics, and Metabolomics Approach for Supporting Medicinal Value of Panax ginseng Fruits

Proteomic and metabolomic study of wax apple (Syzygium samarangense) fruit during ripening process

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