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Lu P, Shan M, Ji X, Deng F, Wang Y. EPURISp: Combining Enzymatic Digestion, Ultrafiltration, and Rapid In Situ Sample Purification for High-performance Proteomics. J Proteome Res 2023; 22:3392-3400. [PMID: 37747260 PMCID: PMC10563806 DOI: 10.1021/acs.jproteome.3c00505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Indexed: 09/26/2023]
Abstract
High-performance liquid tandem mass spectrometry (HPLC-MS) is widely employed for protein analysis in biological systems. However, conventional proteomic sample pretreatment methods suffer from multiple steps and poor reproducibility. In this study, we introduce EPURISp (Enzymatic Digestion with Ultrafiltration and Rapid In-situ Sample Purification), a novel proteomic pretreatment technique that combines enzymatic digestion, ultrafiltration, and one-step temperature-controlled vacuum drying for efficient desalting. The EPURISp method exhibits excellent protein recovery rates across a wide range of molecular weights and hydrophilicity, surpassing traditional C18 desalting approaches. Practical proteomic analysis (PXD044209) utilizing EPURISp demonstrates the highest protein identification yield with remarkable reproducibility, which is particularly advantageous in membrane protein identification. Notably, EPURISp exhibits superior performance in minimizing oxidation and deamidation modifications compared with conventional FASP methods. This innovative EPURISp method represents a significant advancement in proteomics analysis, providing reliable and efficient results for mass spectrometry.
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Affiliation(s)
- Ping Lu
- Tianjin
Eye Hospital, Tianjin Eye Institute, Tianjin
Key Laboratory of Ophthalmology and Visual Science, Tianjin 300020, China
| | - Mengyuan Shan
- Tianjin
Eye Hospital, Tianjin Eye Institute, Tianjin
Key Laboratory of Ophthalmology and Visual Science, Tianjin 300020, China
- School
of Medicine, Nankai University, Tianjin 300071, China
- Nankai
University Affiliated Eye Hospital, Nankai
University, Tianjin 300020, China
| | - Xuemeng Ji
- School
of Medicine, Nankai University, Tianjin 300071, China
| | - Fuqi Deng
- Tianjin
Eye Hospital, Tianjin Eye Institute, Tianjin
Key Laboratory of Ophthalmology and Visual Science, Tianjin 300020, China
- Nankai
University Affiliated Eye Hospital, Nankai
University, Tianjin 300020, China
- Clinical
College of Ophthalmology, Tianjin Medical
University, Tianjin 300070, China
| | - Yan Wang
- Tianjin
Eye Hospital, Tianjin Eye Institute, Tianjin
Key Laboratory of Ophthalmology and Visual Science, Tianjin 300020, China
- School
of Medicine, Nankai University, Tianjin 300071, China
- Nankai
University Affiliated Eye Hospital, Nankai
University, Tianjin 300020, China
- Clinical
College of Ophthalmology, Tianjin Medical
University, Tianjin 300070, China
- Nankai
University Eye Institute, Nankai University, Tianjin 300020, China
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2
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Gong Z, Qu Z, Yu Z, Li J, Liu B, Ma X, Cai J. Label-free quantitative detection and comparative analysis of lysine acetylation during the different life stages of Eimeria tenella. J Proteome Res 2023; 22:2785-2802. [PMID: 37562054 DOI: 10.1021/acs.jproteome.2c00726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Proteome-wide lysine acetylation has been documented in apicomplexan parasite Toxoplasma gondii and Plasmodium falciparum. Here, we conducted the first lysine acetylome in unsporulated oocysts (USO), sporulated 7 h oocysts (SO 7h), sporulated oocysts (SO), sporozoites (S), and the second generation merozoites (SMG) of Eimeria tenella through a 4D label-free quantitative technique. Altogether, 8532 lysine acetylation sites on 2325 proteins were identified in E. tenella, among which 5445 sites on 1493 proteins were quantified. In addition, 557, 339, 478, 248, 241, and 424 differentially expressed proteins were identified in the comparisons SO7h vs USO, SO vs SO7h, SO vs USO, S vs SO, SMG vs S, and USO vs SMG, respectively. The bioinformatics analysis of the acetylome showed that the lysine acetylation is widespread on proteins of diverse functions. Moreover, the dynamic changes of lysine acetylome among E. tenella different life stages revealed significant regulation during the whole process of E. tenella growth and stage conversion. This study provides a beginning for the investigation of the regulate role of lysine acetylation in E. tenella and may provide new strategies for anticoccidiosis drug and vaccine development. Raw data are publicly available at iProX with the data set identifier PXD040368.
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Affiliation(s)
| | - Zigang Qu
- State Key Laboratory of Veterinary Etiological Biology; Key Laboratory of Veterinary Parasitology of Gansu Province; Innovation of Research Program of Gastrointestinal Infection and Mucosal Immunity of Poultry and Pig; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, People's Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu Province 225009, People's Republic of China
| | - Zhengqing Yu
- College of Animal Science and Technology, Ningxia University, Yinchuan, Ningxia Province 750021, People's Republic of China
| | - Jidong Li
- College of Animal Science and Technology, Ningxia University, Yinchuan, Ningxia Province 750021, People's Republic of China
| | - Baohong Liu
- State Key Laboratory of Veterinary Etiological Biology; Key Laboratory of Veterinary Parasitology of Gansu Province; Innovation of Research Program of Gastrointestinal Infection and Mucosal Immunity of Poultry and Pig; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, People's Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu Province 225009, People's Republic of China
| | - Xueting Ma
- State Key Laboratory of Veterinary Etiological Biology; Key Laboratory of Veterinary Parasitology of Gansu Province; Innovation of Research Program of Gastrointestinal Infection and Mucosal Immunity of Poultry and Pig; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, People's Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu Province 225009, People's Republic of China
| | - Jianping Cai
- State Key Laboratory of Veterinary Etiological Biology; Key Laboratory of Veterinary Parasitology of Gansu Province; Innovation of Research Program of Gastrointestinal Infection and Mucosal Immunity of Poultry and Pig; Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, People's Republic of China
- Jiangsu Co-Innovation Center for Prevention and Control of Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu Province 225009, People's Republic of China
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3
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Zhang G, Liu D, Wang H. Quantitative proteomics analysis reveals the anthocyanin biosynthetic mechanism in barley. J Cereal Sci 2023. [DOI: 10.1016/j.jcs.2023.103677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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4
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Xu D, Dondup D, Dou T, Wang C, Zhang R, Fan C, Guo A, Lhundrup N, Ga Z, Liu M, Wu B, Gao J, Zhang J, Guo G. HvGST plays a key role in anthocyanin accumulation in colored barley. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:47-59. [PMID: 36377282 DOI: 10.1111/tpj.16033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 10/20/2022] [Accepted: 11/08/2022] [Indexed: 06/16/2023]
Abstract
Blue aleurone of barley is caused by the accumulation of delphinidin-based derivatives. Although these compounds are ideal nutrients for human health, they are undesirable contaminants in malt brewing. Therefore, the ability to add and remove this trait easily would facilitate breeding barley for different purposes. Here we identified a glutathione S-transferase gene (HvGST) that was responsible for the blue aleurone trait in Tibetan qingke barley by performing a genome-wide association study and RNA-sequencing analysis. Gene variation and expression analysis indicated that HvGST also participates in the transport and accumulation of anthocyanin in purple barley. Haplotype and the geographic distribution analyses of HvGST alleles revealed two independent natural variants responsible for the emergence of white aleurone: a 203-bp deletion causing premature termination of translation in qingke barley and two key single nucleotide polymorphisms in the promoter resulting in low transcription in Western barley. This study contributes to a better understanding of mechanisms of colored barley formation, and provides a comprehensive reference for marker-assisted barley breeding.
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Affiliation(s)
- Dongdong Xu
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, 100081, China
| | - Dawa Dondup
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Research Institute of Agriculture, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, Tibet, China
| | - Tingyu Dou
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, 100081, China
| | - Chunchao Wang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, 100081, China
| | - Renxu Zhang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, 100081, China
| | - Chaofeng Fan
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, 100081, China
| | - Aikui Guo
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, 100081, China
| | - Namgyal Lhundrup
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Research Institute of Agriculture, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, 850002, Tibet, China
| | - Zhuo Ga
- Agricultural and Animal Husbandry College of Tibet University, Linzhi, 860000, Tibet, China
| | - Minxuan Liu
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, 100081, China
| | - Bin Wu
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, 100081, China
| | - Jia Gao
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, 100081, China
| | - Jing Zhang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, 100081, China
| | - Ganggang Guo
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, 100081, China
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Wang Z, Ma R, Jia Z, Lin P, Zhao Z, Wang W, Yi S, Li X, Li J. Investigating on the influence mechanism of sausage of sea bass on calcium absorption and transport based on Caco-2 cell monolayer model. Front Nutr 2022; 9:1046945. [PMID: 36330132 PMCID: PMC9623112 DOI: 10.3389/fnut.2022.1046945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 10/03/2022] [Indexed: 11/25/2022] Open
Abstract
A monolayer Caco-2 cell model was established to explore the effects of sea bass sausage digestive juice containing phosphate on calcium ion transport. Differential proteins of Caco-2 cells treated with fish sausage juice were detected and analyzed by gene ontology (GO) functional annotation and kyoto encyclopedia of genes and genomes (KEGG) pathway analyses. Results revealed that after treatment with 0.23 mg/mL digestive juice of perch sausage in vitro, Caco-2 cell viability was the highest at 72 h (99.84%). Additionally, 0.23 mg/mL digestive juice of perch sausage in vitro significantly increased calcium ion transport. The transfer volume was 1.396 μg/well. Fish sausages containing phosphate significantly affected the protein expression levels of Caco-2 cells. Two hundred one differential proteins were detected, including 114 up-regulated and 87 down-regulated proteins. The main differential proteins included P02795, Q9P0W0, Q96PU5, Q9GZT9 and Q5EBL8. The adjustment ratios of the fish sausage group were 0.7485, 1.373, 1.2535, 0.6775, and 0.809, respectively. The pathway analysis showed that phosphate affected calcium ion absorption and transport through the P02795 enrichment pathway. The fish sausage group showed that the immune-related functions of cells were affected. This study expounds the effects of water-retaining agents on the nutritional quality of aquatic products and provides theoretical support for the research and application of surimi products.
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Zhang G, Yan Y, Zeng X, Wang Y, Zhang Y. Quantitative Proteomics Analysis Reveals Proteins Associated with High Melatonin Content in Barley Seeds under NaCl-Induced Salt Stress. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:8492-8510. [PMID: 35759742 DOI: 10.1021/acs.jafc.2c00466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Soil salinization limits hull-less barley cultivation in the Qinghai-Tibet Plateau of China. However, some wild hull-less barley seeds accumulate high melatonin (MEL) during germination with improved salt tolerance; but the mechanism of melatonin-mediated salt tolerance in hull-less barley is not well understood at the protein level. This study investigated proteome changes resulting in high melatonin content in germinating hull-less barley seeds under high saline conditions. The proteome profiles of seed treatment with 240 mM-NaCl (N), water (H), and control (C) taken 7 days after germination were compared using the TMT-based quantitative proteomics. Our results indicate that salt stress-induced global changes in the proteomes of germinating hull-less barley seeds, altering the expression and abundance of proteins related to cell cycle and control, carbohydrate and energy metabolism, and amino acid transport and metabolism including proteins related to melatonin production. Furthermore, proteins associated with cellular redox homeostasis, osmotic stress response, and secondary metabolites derived primarily from amino acid metabolism, purine degradation, and shikimate pathways increased significantly in abundance and may contribute to the high melatonin content in seeds under salt stress. Consequently, triggering the robust response to oxidative stress occasioned by the NaCl-induced salt stress, improved seed germination and strong adaptation to salt stress.
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Affiliation(s)
- Guoqiang Zhang
- College of Biological and Food Engineering, Anhui Polytechnic University, Wuhu, Anhui 241000, China
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Yingying Yan
- Institute of Agricultural Products Processing & Food Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Xingquan Zeng
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Yulin Wang
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Yuhong Zhang
- Institute of Agricultural Products Processing & Food Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
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7
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Pan C, Sun K, Yang X, Wang D, Hu X, Chen S. Insights on Litopenaeus vannamei quality deterioration during partial freezing storage from combining traditional quality studies and label-free based proteomic analysis. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2022.104655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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8
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Zhou J, Wang M, Carrillo C, Hassoun A, Collado MC, Barba FJ. Application of omics in food color. Curr Opin Food Sci 2022. [DOI: 10.1016/j.cofs.2022.100848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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10
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Qin Q, Liu J, Hu S, Dong J, Yu J, Fang L, Huang S, Wang L. Comparative proteomic analysis of different barley cultivars during seed germination. J Cereal Sci 2021. [DOI: 10.1016/j.jcs.2021.103357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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11
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Novel insight into the antioxidant proteins derived from laver (Porphyra haitanensis) by proteomics analysis and protein based bioinformatics. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.101134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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12
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Song W, Zhou F, Shan C, Zhang Q, Ning M, Liu X, Zhao X, Cai W, Yang X, Hao G, Tang F. Identification of Glutathione S-Transferase Genes in Hami Melon ( Cucumis melo var. saccharinus) and Their Expression Analysis Under Cold Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:672017. [PMID: 34168669 PMCID: PMC8217883 DOI: 10.3389/fpls.2021.672017] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/27/2021] [Indexed: 05/12/2023]
Abstract
As a group of multifunctional enzymes, glutathione S-transferases (GSTs) participate in oxidative stress resistance and cellular detoxification. Here, we identified 39 CmGST genes with typical binding sites from the Hami melon genome, and they can be classified into seven subfamilies. Their molecular information, chromosomal locations, phylogenetic relationships, synteny relationships, gene structures, protein-protein interactions, structure of 3-D models, and expression levels under cold stress were analyzed. Expression analysis indicates that cold-tolerant Jia Shi-310 (JS) had higher GST enzyme activities and expression levels of 28 stress-related genes under cold stress. Some CmGSTs belonging to Tau, Phi, and DHAR classes play significant roles under cold stress, and they could be regarded as candidate genes for further studies. The present study systematically investigated the characterization of the Hami melon GST gene family, extending our understanding of Hami melon GST mediated stress-response mechanisms in this worldwide fruit.
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Affiliation(s)
- Wen Song
- Engineering Research Center for Storage and Processing of Xinjiang Characteristic Fruit and Vegetables, Ministry of Education, College of Food, Shihezi University, Shihezi, China
| | - Fake Zhou
- Engineering Research Center for Storage and Processing of Xinjiang Characteristic Fruit and Vegetables, Ministry of Education, College of Food, Shihezi University, Shihezi, China
| | - Chunhui Shan
- Engineering Research Center for Storage and Processing of Xinjiang Characteristic Fruit and Vegetables, Ministry of Education, College of Food, Shihezi University, Shihezi, China
| | - Qin Zhang
- Engineering Research Center for Storage and Processing of Xinjiang Characteristic Fruit and Vegetables, Ministry of Education, College of Food, Shihezi University, Shihezi, China
| | - Ming Ning
- Engineering Research Center for Storage and Processing of Xinjiang Characteristic Fruit and Vegetables, Ministry of Education, College of Food, Shihezi University, Shihezi, China
| | - Xiumin Liu
- Engineering Research Center for Storage and Processing of Xinjiang Characteristic Fruit and Vegetables, Ministry of Education, College of Food, Shihezi University, Shihezi, China
| | - Xinxin Zhao
- Engineering Research Center for Storage and Processing of Xinjiang Characteristic Fruit and Vegetables, Ministry of Education, College of Food, Shihezi University, Shihezi, China
| | - Wenchao Cai
- Engineering Research Center for Storage and Processing of Xinjiang Characteristic Fruit and Vegetables, Ministry of Education, College of Food, Shihezi University, Shihezi, China
| | - Xinquan Yang
- Engineering Research Center for Storage and Processing of Xinjiang Characteristic Fruit and Vegetables, Ministry of Education, College of Food, Shihezi University, Shihezi, China
| | - Guangfei Hao
- College of Life Science and Food Engineering, Hebei University of Engineering, Handan, China
| | - Fengxian Tang
- Engineering Research Center for Storage and Processing of Xinjiang Characteristic Fruit and Vegetables, Ministry of Education, College of Food, Shihezi University, Shihezi, China
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Wang S, Pang J, Liang P. Differential Proteomics Analysis of Penaeus vannamei Muscles with Quality Characteristics by TMT Quantitative Proteomics during Low-Temperature Storage. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:3247-3254. [PMID: 33686858 DOI: 10.1021/acs.jafc.0c08110] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A tandem mass tag technology, based on the quantitative proteomics strategy, was applied to investigate the relationships between proteome changes of Penaeus vannamei (PNVN) muscles and quality characteristics during low-temperature storage. 506 proteins were found as differentially expressed proteins (DEPs) after 10 days of storage under treatments of refrigerated storage (5 °C), ice temperature storage (0 °C), and particle freezing storage (-3 °C) compared with a fresh group (0 day). In addition, Uniprot Knowledgebase (UniprotKB), Gene Ontology enrichment, and Kyoto Encyclopedia of Genes and Genomes were reported. Correlation analysis indicated that nine DEPs were significantly related to quality characteristics-pH, color, and texture. Bioinformatics analysis showed that most of DEPs were involved in binding proteins, metabolic enzyme, and protein turnover. Besides, several DEPs could be good candidate biomarkers of muscle decline. These results could help to further comprehend the proteome changes and mechanisms of the quality decline of PNVN muscles during low-temperature storage.
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Affiliation(s)
- Shengnan Wang
- College of Food Science, Fujian Agriculture and Forestry University, No. 15, Shangxiadian Road, Cangshan District, Fuzhou, Fujian Province 350002, PR China
| | - Jie Pang
- College of Food Science, Fujian Agriculture and Forestry University, No. 15, Shangxiadian Road, Cangshan District, Fuzhou, Fujian Province 350002, PR China
| | - Peng Liang
- College of Food Science, Fujian Agriculture and Forestry University, No. 15, Shangxiadian Road, Cangshan District, Fuzhou, Fujian Province 350002, PR China
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Changes on proteomic and metabolomic profile in serum of mice induced by chronic exposure to tramadol. Sci Rep 2021; 11:1454. [PMID: 33446901 PMCID: PMC7809287 DOI: 10.1038/s41598-021-81109-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 01/04/2021] [Indexed: 01/01/2023] Open
Abstract
Tramadol is an opioid used as an analgesic for treating moderate or severe pain. The long-term use of tramadol can induce several adverse effects. The toxicological mechanism of tramadol abuse is unclear. Limited literature available indicates the change of proteomic profile after chronic exposure to tramadol. In this study, we analyzed the proteomic and metabolomic profile by TMT-labeled quantitative proteomics and untargeted metabolomics between the tramadol and the control group. Proteomic analysis revealed 31 differential expressed serum proteins (9 increased and 22 decreased) in tramadol-treated mice (oral, 50 mg/kg, 5 weeks) as compared with the control ones. Bioinformatics analysis showed that the dysregulated proteins mainly included: enzyme inhibitor-associated proteins (i.e. apolipoprotein C-III (Apoc-III), alpha-1-antitrypsin 1–2 (Serpina 1b), apolipoprotein C-II (Apoc-II), plasma protease C1 inhibitor, inter-alpha-trypsin inhibitor heavy chain H3 (itih3)); mitochondria-related proteins (i.e. 14-3-3 protein zeta/delta (YWHAZ)); cytoskeleton proteins (i.e. tubulin alpha-4A chain (TUBA4A), vinculin (Vcl)). And we found that the differential expressed proteins mainly involved in the pathway of the protein digestion and absorption. Metabolomics analysis revealed that differential expressed metabolites mainly involved in protein ingestion and absorption, fatty acid biosynthesis, steroid hormone biosynthesis and bile secretion. Our overall findings revealed that chronic exposure to tramadol changed the proteomic and metabolomic profile of mice. Moreover, integrated proteomic and metabolomic revealed that the protein digestion and absorption is the common enrichment KEGG pathway. Thus, the combination of proteomics and metabolomics opens new avenues for the research of the molecular mechanisms of tramadol toxicity.
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Zhang G, Zhang G, Zeng X, Xu Q, Wang Y, Yuan H, Zhang Y, Nyima T. Quantitative Proteome Profiling Provides Insight into the Proteins Associated with β-Glucan Accumulation in Hull-less Barley Grains. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:568-583. [PMID: 33371680 DOI: 10.1021/acs.jafc.0c05284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The hull-less barley (Qingke) is widely planted as a staple food crop in the Tibetan area, China, and the grains contains high content of β-glucan (BG). The mechanisms of BG synthesis and accumulation in qingke has not been studied at the protein level. This study characterized the proteins associated with BG synthesis and accumulation during qingke seed development. The proteome profiles of qingke seeds taken at 20, 30, and 40 days after flowering were compared using the TMT-based quantitative proteomics. A total of 4283 proteins were identified, with 759 being differentially expressed (DEPs) throughout seed development. Comparisons of protein expression pattern, functions, and pathway enrichment tests highlight cell wall modification, carbon and energy metabolism, polysaccharide metabolism, post-transcriptional modifications, and vesicular transport as critical biological processes related to qingke BG accumulation. Furthermore, induction of starch synthase, starch branching enzyme, pectin acetyl esterases, beta-glucosidases, beta-amylases, 1,4-beta-xylan, xyloglucan, α-amylase inhibitors, and glycosyltransferases underpinned BG synthesis. The results also indicated that the proteins involved in glycolytic, gluconeogenesis, and glyoxylate bypass pathways provided energy and reducing power for BG storage. Parallel reaction monitoring (PRM) and quantitative real-time PCR (qPCR) analyses confirmed the expression profile of the proteins obtained by TMT-based proteomics. The current results provided an insight into the mechanisms of BG synthesis and accumulation during qingke seed development.
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Affiliation(s)
- Guoqiang Zhang
- College of Biological and Chemical Engineering, Anhui Polytechnic University, Wuhu, Anhui 241000, China
- Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Department of Agronomy, Zhejiang University, Hangzhou 310058, China
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
| | - Guoping Zhang
- Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Department of Agronomy, Zhejiang University, Hangzhou 310058, China
| | - Xingquan Zeng
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
| | - Qijun Xu
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
| | - Yulin Wang
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
| | - Hongjun Yuan
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
| | - Yuhong Zhang
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
| | - Tashi Nyima
- State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, Tibet 850002, China
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Niu H, Zhang H, Wu F, Xiong B, Tong J, Jiang L. Proteomics study on the protective mechanism of soybean isoflavone against inflammation injury of bovine mammary epithelial cells induced by Streptococcus agalactiae. Cell Stress Chaperones 2021; 26:91-101. [PMID: 32865767 PMCID: PMC7736374 DOI: 10.1007/s12192-020-01158-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/21/2020] [Accepted: 08/25/2020] [Indexed: 01/14/2023] Open
Abstract
This study aimed to verify the anti-inflammatory effect of soybean isoflavones (SI) on the inflammatory response induced by Streptococcus agalactiae (S. agalactiae) of bovine mammary epithelial cells (bMECs) and to elucidate its possible mechanism. BMECs were pretreated with SI of different concentrations (20, 40, 60, 80, 100 μg/mL) for 0.5, 3, 6, 9, 12, 15, 18, 24 h. And then, S. agalactiae was used to infect bMECs for 6 h (MOI = 50:1) to establish the inflammation model. Cell viability, growth curves of S. agalactiae, cytotoxicity, and S. agalactiae invasion rate were determined. A proteomics technique was used to further detect differential proteins and enrichment pathways. SI (40 μg/mL) improved the viability of bMECs at 12 h (p < 0.05) and 60 and 80 μg/mL of SI greater (p < 0.01). Moreover, 60 μg/mL of SI protects cells from bacterial damage (p < 0.05). SI could inhibit S. agalactiae growth and internalization into bMECs in a time- and dose-dependent manner. In addition, proteomics results showed that 133 proteins were up-regulated and 89 proteins were down-regulated significantly. The differentially significantly expressed proteins (DSEPs) were mainly related to cell proliferation, differentiation, apoptosis, and migration. GO annotation showed that 222 DSEPs were divided into 23 biological processes (BP) terms, 14 cell components (CC) terms, and 12 molecular functions (MF) terms. DSEPs were significantly enriched in 10 pathways, of which the immune pathway was the main enrichment pathway.
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Affiliation(s)
- Hui Niu
- Department of Animal Science, Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
| | - Hua Zhang
- Department of Animal Science, Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
| | - Fuxin Wu
- Department of Animal Science, Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China
| | - Benhai Xiong
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jinjin Tong
- Department of Animal Science, Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China.
| | - Linshu Jiang
- Department of Animal Science, Animal Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China.
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Gao X, Zhang L, Zhou P, Zhang Y, Wei Y, Wang Y, Liu X. Tandem Mass Tag-Based Quantitative Proteome Analysis of Porcine Deltacoronavirus (PDCoV)-Infected LLC Porcine Kidney Cells. ACS OMEGA 2020; 5:21979-21987. [PMID: 32923756 PMCID: PMC7482077 DOI: 10.1021/acsomega.0c00886] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 08/12/2020] [Indexed: 05/12/2023]
Abstract
Porcine deltacoronavirus (PDCoV) is a newly emerging porcine pathogenic enteric coronavirus that can cause diarrhea, vomiting, dehydration, and a high mortality rate in piglets. At present, the understanding of PDCoV pathogenesis is very limited, which seriously hinders effective prevention and control. In this study, liquid chromatography tandem-mass spectrometry (LC-MS/MS) combined with tandem mass tag (TMT) labeling was performed to compare the differential expression of proteins in PDCoV-infected and mock-infected LLC-PK cells at 18 h post-infection (hpi). In addition, the parallel reaction monitoring (PRM) technique was used to verify the quantitative proteome data. A total of 4624 differentially expressed proteins (DEPs) were quantitated, of which 128 were significantly upregulated, and 147 were significantly downregulated. Bioinformatics analysis revealed that these DEPs were involved mainly in the defense response, apoptosis, and the immune system, and several DEPs may be related to interferon-stimulated genes and the immune system. Based on DEP bioinformatics analysis, we propose that PDCoV infection may utilize the apoptosis pathway of host cells to achieve maximum viral replication. Meanwhile, the host may be able to stimulate the transcription of interferon-stimulated genes (ISGs) through the JAK/STAT signaling pathway to resist the virus. Overall, in this study, we presented the first application of proteomics analysis to determine the protein profile of PDCoV-infected cells, which provides valuable information with respect to better understanding the host response to PDCoV infection and the specific pathogenesis of PDCoV infection.
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Affiliation(s)
- Xiang Gao
- State
Key Laboratory of Veterinary Etiological Biology, Key Laboratory of
Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research
Institute, Chinese Academy of Agricultural
Sciences, Lanzhou 730046, China
- College
of Veterinary Medicine, Gansu Agricultural
University, Lanzhou 730070, China
- Jiangsu
Co-innovation Center for Prevention and Control of Important Animal
Infectious Diseases and Zoonoses, Yangzhou 225009, China
| | - Liping Zhang
- State
Key Laboratory of Veterinary Etiological Biology, Key Laboratory of
Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research
Institute, Chinese Academy of Agricultural
Sciences, Lanzhou 730046, China
- Jiangsu
Co-innovation Center for Prevention and Control of Important Animal
Infectious Diseases and Zoonoses, Yangzhou 225009, China
| | - Peng Zhou
- State
Key Laboratory of Veterinary Etiological Biology, Key Laboratory of
Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research
Institute, Chinese Academy of Agricultural
Sciences, Lanzhou 730046, China
- Jiangsu
Co-innovation Center for Prevention and Control of Important Animal
Infectious Diseases and Zoonoses, Yangzhou 225009, China
| | - Yongguang Zhang
- State
Key Laboratory of Veterinary Etiological Biology, Key Laboratory of
Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research
Institute, Chinese Academy of Agricultural
Sciences, Lanzhou 730046, China
- Jiangsu
Co-innovation Center for Prevention and Control of Important Animal
Infectious Diseases and Zoonoses, Yangzhou 225009, China
| | - Yanming Wei
- College
of Veterinary Medicine, Gansu Agricultural
University, Lanzhou 730070, China
| | - Yonglu Wang
- State
Key Laboratory of Veterinary Etiological Biology, Key Laboratory of
Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research
Institute, Chinese Academy of Agricultural
Sciences, Lanzhou 730046, China
- Jiangsu
Co-innovation Center for Prevention and Control of Important Animal
Infectious Diseases and Zoonoses, Yangzhou 225009, China
| | - Xinsheng Liu
- State
Key Laboratory of Veterinary Etiological Biology, Key Laboratory of
Animal Virology of Ministry of Agriculture, Lanzhou Veterinary Research
Institute, Chinese Academy of Agricultural
Sciences, Lanzhou 730046, China
- Jiangsu
Co-innovation Center for Prevention and Control of Important Animal
Infectious Diseases and Zoonoses, Yangzhou 225009, China
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Molecular Mechanism of Functional Ingredients in Barley to Combat Human Chronic Diseases. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:3836172. [PMID: 32318238 PMCID: PMC7149453 DOI: 10.1155/2020/3836172] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 03/10/2020] [Indexed: 12/18/2022]
Abstract
Barley plays an important role in health and civilization of human migration from Africa to Asia, later to Eurasia. We demonstrated the systematic mechanism of functional ingredients in barley to combat chronic diseases, based on PubMed, CNKI, and ISI Web of Science databases from 2004 to 2020. Barley and its extracts are rich in 30 ingredients to combat more than 20 chronic diseases, which include the 14 similar and 9 different chronic diseases between grains and grass, due to the major molecular mechanism of six functional ingredients of barley grass (GABA, flavonoids, SOD, K-Ca, vitamins, and tryptophan) and grains (β-glucans, polyphenols, arabinoxylan, phytosterols, tocols, and resistant starch). The antioxidant activity of barley grass and grain has the same and different functional components. These results support findings that barley grain and its grass are the best functional food, promoting ancient Babylonian and Egyptian civilizations, and further show the depending functional ingredients for diet from Pliocene hominids in Africa and Neanderthals in Europe to modern humans in the world. This review paper not only reveals the formation and action mechanism of barley diet overcoming human chronic diseases, but also provides scientific basis for the development of health products and drugs for the prevention and treatment of human chronic diseases.
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Distribution of β-Glucan, Phenolic Acids, and Proteins as Functional Phytonutrients of Hull-Less Barley Grain. Foods 2019; 8:foods8120680. [PMID: 31847194 PMCID: PMC6963557 DOI: 10.3390/foods8120680] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 12/06/2019] [Accepted: 12/10/2019] [Indexed: 12/13/2022] Open
Abstract
Two hull-less barley varieties were roller-milled, and breaks (B) and reduction flours (C), shorts, and bran were collected. Shorts, which mainly originate from endosperm cells with a smaller amount of the outer layers, had the largest yield (48.87–51.54%). Ash (0.82–3.10%) and protein (9.95–14.8%) increased from flours toward shorts and bran, while starch decreased (82.31–48.69%). In contrast to clear distribution differences in protein content (bran > shorts > C > B), albumins/globulins content was lowest in bran (0.78–0.90 g/100 gdw), and their distribution between fractions was uneven and genotype dependent. Distribution of hordeins (6.69–10.49 g/100 gdw) was more distinct and generally decreased in order from bran > B > shorts > C. The proportion of nutritionally poor C-hordeins in total hordeins varied from 28.33% to 30.24%, without significant differences between fractions. The β-glucan content varied from 0.80% to 7.49% with decreasing content in the order bran, shorts > C > B. Shorts and bran could be classified as moderate and high β-glucan flour (5.70–7.22%). The total phenolic and antioxidant activities ranged from 0.91 to 2.21 mg GAE/gdw and 28.81–72.06%, respectively. Ferulic and sinapic acids determined by high-performance liquid chromatography (HPLC) were major contributors to the antioxidant activity (45.16–1026.91 ug/gdw and 18.93–206.52 ug/gdw), respectively. The yield and high content of phytonutrients make hull-less barley shorts suitable for the production of health-promoting food and food supplements.
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Analysis of Proteins Associated with Quality Deterioration of Grouper Fillets Based on TMT Quantitative Proteomics during Refrigerated Storage. Molecules 2019; 24:molecules24142641. [PMID: 31330849 PMCID: PMC6680736 DOI: 10.3390/molecules24142641] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 01/02/2023] Open
Abstract
A TMT (Tandem Mass Tag)-based strategy was applied to elucidate proteins that change in proteomes of grouper fillets during refrigerated storage. In addition, quality analyses on pH, centrifugal loss, color (L *, a *, b *) and texture (hardness, chewiness, and gumminess) for grouper fillets were performed. A total of 64 differentially significant expressed proteins (DSEPs) were found in the results in the Day 0 vs. Day 6 group comparison and the Day 0 vs. Day 12 group comparison. It is worth mentioning that more proteome changes were found in the Day 0 vs. Day 12 comparisons. Bioinformatics was utilized to analyze the DSEP. UniProt Knowledgebase (UniProtKB), Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) and protein interaction network analysis were adopted. All DSEPs were classified into seven areas by function: binding proteins, calcium handling, enzymes, heat shock protein, protein turnover, structural proteins and miscellaneous. The numbers of proteins that correlated closely with pH, centrifugal loss, color (L *, a *, b *) and texture (hardness, chewiness, and gumminess) were 4, 3, 6 and 8, respectively.
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