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Maheshwari G, Wen G, Gessner DK, Ringseis R, Lochnit G, Eder K, Zorn H, Timm T. Tandem mass tag-based proteomics for studying the effects of a biotechnologically produced oyster mushroom against hepatic steatosis in obese Zucker rats. J Proteomics 2021; 242:104255. [PMID: 33957313 DOI: 10.1016/j.jprot.2021.104255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/22/2021] [Accepted: 04/28/2021] [Indexed: 12/12/2022]
Abstract
Hepatic steatosis is a very common response to liver injury and often attributed to metabolic disorders. Prior studies have demonstrated the efficacy of a biotechnologically produced oyster mushroom (Pleurotus sajor-caju, PSC) in alleviating hepatic steatosis in obese Zucker rats. This study aims to elucidate molecular events underlying the anti-steatotic effects of PSC. Tandem mass tag (TMT) peptide labeling coupled with LC-MS/MS/MS was used to quantify and compare proteins in the livers of lean Zucker rats fed a control diet (LC), obese Zucker rats fed the same control diet (OC) and obese Zucker rats fed the control diet supplemented with 5% PSC (OPSC) for 4 weeks. Using this technique 3128 proteins could be quantified, out of which 108 were differentially abundant between the OPSC and OC group. Functional enrichment analysis of the up-regulated proteins showed that these proteins were mainly involved in metabolic processes, while the down-regulated proteins were involved in inflammatory processes. Results from proteomic analysis were successfully validated for two up-regulated (carbonic anhydrase 3, regucalcin) and two down-regulated (cadherin-17, ceruloplasmin) proteins by means of immunoblotting. SIGNIFICANCE: Valorization of low-grade agricultural waste by edible fungi, such as the mushroom Pleurotus sajor-caju (PSC), represents a promising strategy for the production of protein rich biomass since they boast of a unique enzyme system that has the ability to recover nutrients and energy from biodegradable waste. Herein, we describe the metabolic effects of PSC feeding using a combined quantitative proteomics and bioinformatics approach. In total, 108 proteins were identified to be regulated by PSC feeding in the liver of the obese rats. Complementary usage of a bioinformatics approach allowed us to decipher the mechanisms underlying the recently observed lipid-lowering and anti-inflammatory activity of PSC feeding in obese Zucker rats, namely a reduction of fatty acid synthesis, an improvement of hepatoprotective mechanisms and an enhancement of anti-inflammatory effects.
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Affiliation(s)
- Garima Maheshwari
- Institute of Food Chemistry and Food Biotechnology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany; Institute of Animal Nutrition and Nutrition Physiology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Gaiping Wen
- Institute of Animal Nutrition and Nutrition Physiology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Denise K Gessner
- Institute of Animal Nutrition and Nutrition Physiology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Robert Ringseis
- Institute of Animal Nutrition and Nutrition Physiology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Günter Lochnit
- Protein Analytics, Institute of Biochemistry, Faculty of Medicine, Justus-Liebig-University Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
| | - Klaus Eder
- Institute of Animal Nutrition and Nutrition Physiology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany
| | - Holger Zorn
- Institute of Food Chemistry and Food Biotechnology, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Giessen, Germany.
| | - Thomas Timm
- Protein Analytics, Institute of Biochemistry, Faculty of Medicine, Justus-Liebig-University Giessen, Friedrichstrasse 24, 35392 Giessen, Germany
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Fu Q, Liu Z, Bhawal R, Anderson ET, Sherwood RW, Yang Y, Thannhauser T, Schroyen M, Tang X, Zhang H, Zhang S. Comparison of MS 2, synchronous precursor selection MS 3, and real-time search MS 3 methodologies for lung proteomes of hydrogen sulfide treated swine. Anal Bioanal Chem 2020; 413:419-429. [PMID: 33099676 DOI: 10.1007/s00216-020-03009-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 10/13/2020] [Indexed: 01/02/2023]
Abstract
Tandem mass tags (TMTs) have increasingly become an attractive technique for global proteomics. However, its effectiveness for multiplexed quantitation by traditional tandem mass spectrometry (MS2) suffers from ratio distortion. Synchronous precursor selection (SPS) MS3 has been widely accepted for improved quantitation accuracy, but concurrently decreased proteome coverage. Recently, a Real-Time Search algorithm has been integrated with the SPS MS3 pipeline (RTS MS3) to provide accurate quantitation and improved depth of coverage. In this mechanistic study of the impact of exposure to hydrogen sulfide (H2S) on the respiration of swine, we used TMT-based comparative proteomics of lung tissues from control and H2S-treated subjects as a test case to evaluate traditional MS2, SPS MS3, and RTS MS3 acquisition methods on both the Orbitrap Fusion and Orbitrap Eclipse platforms. Comparison of the results obtained by the MS2 with those of SPS MS3 and RTS MS3 methods suggests that the MS3-driven quantitative strategies provided a more accurate global-scale quantitation; however, only RTS MS3 provided proteomic coverage that rivaled that of traditional MS2 analysis. RTS MS3 not only yields more productive MS3 spectra than SPS MS3 but also appears to focus the analysis more effectively on unique peptides. Furthermore, pathway enrichment analyses of the H2S-altered proteins demonstrated that an additional apoptosis pathway was discovered exclusively by RTS MS3. This finding was verified by RT-qPCR, western blotting, and TUNEL staining experiments. We conclude that RTS MS3 workflow enables simultaneous improvement of quantitative accuracy and proteome coverage over alternative approaches (MS2 and SPS MS3). Graphical abstract.
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Affiliation(s)
- Qin Fu
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, 526 Campus Road, Ithaca, NY, 14853, USA
| | - Zhen Liu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 2 West Yuanmingyuan Road, Beijing, 100193, China.,Precision Livestock and Nutrition Unit, Gembloux Agro-Bio Tech, Teaching and Research Centre, University of Liège, Passage des Déportés 2, 5030, Gembloux, Belgium
| | - Ruchika Bhawal
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, 526 Campus Road, Ithaca, NY, 14853, USA
| | - Elizabeth T Anderson
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, 526 Campus Road, Ithaca, NY, 14853, USA
| | - Robert W Sherwood
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, 526 Campus Road, Ithaca, NY, 14853, USA
| | - Yong Yang
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, 538 Tower Road, Ithaca, NY, 14853, USA
| | - Theodore Thannhauser
- Robert W. Holley Center for Agriculture and Health, USDA-ARS, 538 Tower Road, Ithaca, NY, 14853, USA
| | - Martine Schroyen
- Precision Livestock and Nutrition Unit, Gembloux Agro-Bio Tech, Teaching and Research Centre, University of Liège, Passage des Déportés 2, 5030, Gembloux, Belgium
| | - Xiangfang Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 2 West Yuanmingyuan Road, Beijing, 100193, China.
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 2 West Yuanmingyuan Road, Beijing, 100193, China
| | - Sheng Zhang
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, 526 Campus Road, Ithaca, NY, 14853, USA.
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