Protein profile of commercial soybean milks analyzed by label-free quantitative proteomics

Battisti, Ilaria; Barnabas, Leonard; Lomolino, Giovanna; Masi, Antonio; Arrigoni, Giorgio

doi:10.1016/j.foodchem.2021.129299

Cited by 21 publications

(16 citation statements)

References 37 publications

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“…TMT‐based high‐throughput proteomics enables highly efficient and accurate detection of proteins. Published studies have reported that proteomic analysis can increase the speed and efficiency of new protein detection and identification (Battisti et al, 2021; Min et al, 2020). Quantitative proteomics of mutants and/or transgenic lines can be used to build regulatory networks related to specific traits with great precision (Komatsu et al, 2021; Xu et al, 2021).…”

Section: Discussionmentioning

confidence: 99%

“…With the development of high‐throughput sequencing, gas chromatography–mass spectrometry (GC–MS), liquid chromatography–MS (LC–MS), and tandem mass tag (TMT)‐based MS, the integration of multiple omics approaches can reveal regulatory networks and provide new insights and more genetic resources for the food industry. Recently, TMT‐based quantitative proteomic analyses have been performed on seed storage–related proteins in soybean seeds and soy milk (Battisti et al, 2021; Min et al, 2020). Furthermore, an integrated transcriptomic and proteomic analysis revealed the molecular mechanisms associated with Coix seed quality, including pathways related to flavonoid biosynthesis, starch and sucrose metabolism, lipid metabolism, and amino acid metabolism (Huang et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

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Integrated transcriptomic and proteomic characterization of a chromosome segment substitution line reveals a new regulatory network controlling the seed storage profile of soybean

Han

Zhao

et al. 2022

Food and Energy Security

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Soybean is a major crop that provides oil and protein worldwide. Soybean products have been consumed for centuries in many different kinds of food. The regulatory network that controls the accumulation of fatty acids (FAs) and storage proteins (SSPs) in seeds is poorly understood. To gain new insights into the molecular mechanisms that contribute to high‐quality seeds, seed FA and SSP contents were analyzed for the effects of chromosome segment substitution in a wild soybean line (CSSL). High‐throughput transcriptomics and tandem mass tag (TMT)‐based quantitative proteomics were performed on the dry seeds of the CSSL and parent lines. In total, 665 differentially expressed genes (DEGs) and 83 differentially accumulated proteins (DAPs) were identified. Of these 27 DEGs and 23 DAPs were found to regulate the seed storage profile. These genes encode proteins involved in photosynthesis, protein processing, protein sorting, and storage protein accumulation. Data are presented showing that FA synthesis was decreased by the regulation of SSP‐accumulation‐related genes and proteins. Taken together, the results provide new insights into the regulation network involved in the accumulation of seed storage compounds involving both source and sink processes that may be used as markers in future soybean breeding programs.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Integrated transcriptomic and proteomic characterization of a chromosome segment substitution line reveals a new regulatory network controlling the seed storage profile of soybean

Han

Zhao

et al. 2022

Food and Energy Security

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“…A total of 50 μg of proteins from CTR and SB3 EVs (three independent preparations) were reduced with dithiothreitol (Fluka, Buchs, Switzerland), alkylated with iodoacetamide (Sigma-Aldrich, St. Louis, MO, USA), and digested with sequencing grade modified trypsin (Promega, Madison, WI, USA) using a filter aided sample preparation protocol (FASP), as previously detailed [ 13 ].…”

Section: Methodsmentioning

confidence: 99%

Engineered EVs for Oxidative Stress Protection

et al. 2021

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Extracellular vesicles (EVs) are increasingly studied as vectors for drug delivery because they can transfer a variety of molecules across biological barriers. SerpinB3 is a serine protease inhibitor that has shown a protective anti-apoptotic function in a variety of stressful conditions. The aim of this study was to evaluate protection from oxidative stress-induced damage, using extracellular vesicles that overexpress SerpinB3 (EVs-SB3) in order to enhance the effect of extracellular vesicles on cellular homeostasis. EVs-SB3s were obtained from HepG2 cells engineered to overexpress SerpinB3 and they revealed significant proteomic changes, mostly characterized by a reduced expression of other proteins compared with EVs from non-engineered cells. These EV preparations showed a significantly higher protection from H2O2 induced oxidative stress in both the hepatoma cell line and in primary cardiomyocytes, compared to cells treated with naïve EVs or SerpinB3 alone, used at the same concentration. In conclusion, the induction of SerpinB3 transgene expression results in the secretion of EVs enriched with the protein product that exhibits enhanced cytoprotective activity, compared with naïve EVs or the nude SerpinB3 protein.

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“…Samples were vacuum-dried and stored at −20 °C. Samples were analyzed using a LTQ Orbitrap XL mass spectrometer (Thermo Fisher Scientific) coupled to a HPLC Ultimate 3000 (Dionex - Thermo Fisher Scientific) through a nanospray source (NSI), as described in Battisti et al 2021 [3]. Samples were resuspended in 30 µl of 3 % ACN/0.1 % FA and each sample was acquired twice.…”

Section: Methodsmentioning

confidence: 99%

“…Beads were then washed three times using 1 ml of RIPA buffer and proteins loaded on pre-cast 4-20 % tris-glycine polyacrylamide gels (Biorad). Gel bands were excised, cut into small pieces and destained with a solution of 60 (Dionex -Thermo Fisher Scientific) through a nanospray source (NSI), as described previously [3].…”

Section: Liquid-chromatography Mass Spectrometry (Lc-ms) Analysismentioning

confidence: 99%

Trafficking of the glutamate transporter is impaired in LRRK2-related Parkinson’s disease

Iovino

Giusti

Pischedda

et al. 2021

Preprint

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The Excitatory Amino Acid Transporter 2 (EAAT2) accounts for 80% of brain glutamate clearance and is mainly expressed in astrocytic perisynaptic processes. EAAT2 function is finely regulated by endocytic events, recycling to the plasma membrane and degradation. Noteworthy, deficits in EAAT2 have been associated with neuronal excitotoxicity and neurodegeneration. In this study, we show that EAAT2 trafficking is impaired by the leucine-rich repeat kinase 2 (LRRK2) pathogenic variant G2019S, a common cause of late-onset familial Parkinson's disease (PD). In LRRK2 G2019S human brains and experimental animal models, EAAT2 protein levels are significantly decreased, which is associated with elevated gliosis. The decreased expression of the transporter correlates with its reduced functionality in mouse LRRK2 G2019S purified astrocytic terminals and in Xenopus laevis oocytes expressing human LRRK2 G2019S. In Lrrk2 G2019S knockin mouse brain, the correct surface localization of the endogenous transporter is impaired, resulting in its interaction with a plethora of endo-vesicular proteins. Mechanistically, we report that pathogenic LRRK2 kinase activity delays the recycling of the transporter to the plasma membrane, causing its intracellular relocalization and degradation. Taken together, our results demonstrate that pathogenic LRRK2 interferes with the physiology of EAAT2, pointing to extracellular glutamate overload as a possible contributor to neurodegeneration in PD.

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Protein profile of commercial soybean milks analyzed by label-free quantitative proteomics

Cited by 21 publications

References 37 publications

Integrated transcriptomic and proteomic characterization of a chromosome segment substitution line reveals a new regulatory network controlling the seed storage profile of soybean

Integrated transcriptomic and proteomic characterization of a chromosome segment substitution line reveals a new regulatory network controlling the seed storage profile of soybean

Engineered EVs for Oxidative Stress Protection

Trafficking of the glutamate transporter is impaired in LRRK2-related Parkinson’s disease

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