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Chen X, Yu X, Cui Y, Du L, Zhou Q, Xiong W, Li C, Xu C, Wu H. Isoglutaminyl Cyclase Overexpression Enhances KYSE30 Cancer Cell Proliferation and Migration via the MAPK Signaling Pathway. J Proteome Res 2024. [PMID: 38655723 DOI: 10.1021/acs.jproteome.4c00197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
To understand how upregulated isoglutaminyl cyclase (isoQC) is involved in the initiation of diseases such as cancer, we developed a human KYSE30 carcinoma cell model in which isoQC was stably overexpressed. GO and KEGG analysis of the DEGs (228) and DEPs (254) respectively implicated isoQC on the proliferation invasion and metastasis of cells and suggested that isoQC might participate in the regulation of MAPK, RAS, circadian rhythm, and related pathways. At the functional level, isoQC-overexpressing KYSE30 cells showed enhanced proliferation, migration, and invasion capacity. Next, we decided to study the precise effect of isoQC overexpression on JNK, p-JNK, AKT, p-AKT, ERK, p-ERK, and PER2, as RNA levels of these proteins are significantly correlated with signal levels indicated in RNA-Seq analysis, and these candidates are the top correlated DEPs enriched in RT-qPCR analysis. We saw that only p-ERK expression was inhibited, while PER2 was increased. These phenotypes were inhibited upon exposure to PER2 inhibitor KL044, which allowed for the restoration of p-ERK levels. These data support upregulated isoQC being able to promote cancer cell proliferation and migration in vitro, likely by helping to regulate the MAPK and RAS signaling pathways, and the circadian protein PER2 might be a potential mediator.
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Affiliation(s)
- Xiaojie Chen
- School of Pharmacy, Shenzhen University Medical School, Shenzhen 518055, China
| | - Xi Yu
- School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518055, China
| | - Yangqing Cui
- School of Pharmacy, Shenzhen University Medical School, Shenzhen 518055, China
| | - Lang Du
- School of Pharmacy, Shenzhen University Medical School, Shenzhen 518055, China
| | - Qingqing Zhou
- School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518055, China
| | - Wei Xiong
- School of Pharmacy, Shenzhen University Medical School, Shenzhen 518055, China
| | - Chenyang Li
- School of Pharmacy, Shenzhen University Medical School, Shenzhen 518055, China
| | - Chenshu Xu
- School of Pharmacy, Shenzhen University Medical School, Shenzhen 518055, China
| | - Haiqiang Wu
- School of Pharmacy, Shenzhen University Medical School, Shenzhen 518055, China
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Arafat MY, Narula K, Kumar M, Chakraborty N, Chakraborty S. Proteo-metabolomic Dissection of Extracellular Matrix Reveals Alterations in Cell Wall Integrity and Calcium Signaling Governs Wall-Associated Susceptibility during Stem Rot Disease in Jute. J Proteome Res 2024. [PMID: 38572503 DOI: 10.1021/acs.jproteome.3c00781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
The plant surveillance system confers specificity to disease and immune states by activating distinct molecular pathways linked to cellular functionality. The extracellular matrix (ECM), a preformed passive barrier, is dynamically remodeled at sites of interaction with pathogenic microbes. Stem rot, caused by Macrophomina phaseolina, adversely affects fiber production in jute. However, how wall related susceptibility affects the ECM proteome and metabolome remains undetermined in bast fiber crops. Here, stem rot responsive quantitative temporal ECM proteome and metabolome were developed in jute upon M. phaseolina infection. Morpho-histological examination revealed that leaf shredding was accompanied by reactive oxygen species production in patho-stressed jute. Electron microscopy showed disease progression and ECM architecture remodeling due to necrosis in the later phase of fungal attack. Using isobaric tags for relative and absolute quantitative proteomics and liquid chromatography-tandem mass spectrometry, we identified 415 disease-responsive proteins involved in wall integrity, acidification, proteostasis, hydration, and redox homeostasis. The disease-related correlation network identified functional hubs centered on α-galactosidase, pectinesterase, and thaumatin. Gas chromatography-mass spectrometry analysis pointed toward enrichment of disease-responsive metabolites associated with the glutathione pathway, TCA cycle, and cutin, suberin, and wax metabolism. Data demonstrated that wall-degrading enzymes, structural carbohydrates, and calcium signaling govern rot responsive wall-susceptibility. Proteomics data were deposited in Pride (PXD046937; PXD046939).
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Affiliation(s)
- Md Yasir Arafat
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Kanika Narula
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Mohit Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India
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3
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Yao S, Tu R, Jin Y, Zhou R, Wu C, Qin J. Improvement of the viability of Tetragenococcus halophilus under acidic stress by forming the biofilm cell structure based on RNA-Seq and iTRAQ analyses. J Sci Food Agric 2024; 104:3559-3569. [PMID: 38147410 DOI: 10.1002/jsfa.13240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 12/22/2023] [Accepted: 12/23/2023] [Indexed: 12/28/2023]
Abstract
BACKGROUND Tetragenococcus halophilus is a halophilic lactic acid bacterium (LAB) isolated from soya sauce moromi. During the production of these fermented foods, acid stress is an inevitable environmental stress. In our previous study, T. halophilus could form biofilms and the cells in the biofilms exhibited higher cell viability under multiple environmental stresses, including acid stress. RESULTS In this study, the effect of preformed T. halophilus biofilms on cell survival, cellular structure, intracellular environment, and the expression of genes and proteins under acid stress was investigated. The result showed that acid stress with pH 4.30 for 1.5 h reduced the live T. halophilus cell count and caused cellular structure damage. However, T. halophilus biofilm cells exhibited greater cell survival under acid stress than the planktonic cells, and biofilm formation reduced the damage of acid stress to the cell membrane and cell wall. The biofilm cells maintained a higher level of H+ -ATPase activity and intracellular ammonia concentration after acid stress. The RNA-Seq and iTRAQ technologies revealed that the genes and proteins associated with ATP production, the uptake of trehalose and N-acetylmuramic acid, the assembly of H+ -ATPase, amino acid biosynthesis and metabolism, ammonia production, fatty acid biosynthesis, CoA biosynthesis, thiamine production, and acetoin biosynthesis might be responsible for the stronger acid tolerance of T. halophilus biofilm cells together. CONCLUSION These findings further explained the mechanisms that allowed LAB biofilm cells to resist environmental stress. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Shangjie Yao
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
| | - Rongkun Tu
- Luzhou Lao Jiao Co., Ltd., Luzhou, China
| | - Yao Jin
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
| | - Rongqing Zhou
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
| | - Chongde Wu
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
| | - Jiufu Qin
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
- Key Laboratory of Leather Chemistry and Engineering, Ministry of Education, Sichuan University, Chengdu, China
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Shao L, Dong Y, Chen S, Sheng J, Cai L, Xu X, Wang H. Revealing extracellular protein profile and excavating spoilage-related proteases of Aeromonas salmonicida based on multi-omics investigation. Int J Biol Macromol 2024; 265:130916. [PMID: 38492699 DOI: 10.1016/j.ijbiomac.2024.130916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 03/18/2024]
Abstract
Aeromonas is a ubiquitous aquatic bacteria, and it is a significant factor contributing to meat spoilage during processing and consumption. The abilities of Aeromonas salmonicida 29 and 57, which exhibit spoilage heterogeneity, to secrete protease, lipase, hemolysin, gelatinase, amylase, and lecithinase were confirmed by plate method. A total of 3948 proteins were identified by ITRAQ in extracellular secretions of A. salmonicida, and 16 proteases were found to be potentially related to spoilage ability. The complete genome sequence of A. salmonicida 57 consists of one circular chromosome and three plasmids, while A. salmonicida 29 consists of one circular chromosome, without a plasmid. Transcriptomic analysis revealed a significant number of DEGs were up-regulated in A. salmonicida 29, which were mainly enriched in metabolic pathways (e.g., amino acid metabolism, carbohydrate metabolism), indicating that A. salmonicida 29 had better potential to decompose and utilize nutrients in meat. Six protease genes (2 pepB, hap, pepA, ftsI, and pepD) were excavated by combined ITRAQ with transcriptome analysis, which potentially contribute to bacterial spoilage ability and exhibit universality among other dominant spoilage bacteria. This investigation provides new insights and evidence for elucidating metabolic and spoilage phenotypic differences and provides candidate genes and strategies for future prevention and control technology development.
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Affiliation(s)
- Liangting Shao
- State Key Laboratory of Meat Quality Control and Cultured Meat Development, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Yang Dong
- State Key Laboratory of Meat Quality Control and Cultured Meat Development, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Shanshan Chen
- State Key Laboratory of Meat Quality Control and Cultured Meat Development, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Junsheng Sheng
- State Key Laboratory of Meat Quality Control and Cultured Meat Development, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Linlin Cai
- State Key Laboratory of Meat Quality Control and Cultured Meat Development, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xinglian Xu
- State Key Laboratory of Meat Quality Control and Cultured Meat Development, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Huhu Wang
- State Key Laboratory of Meat Quality Control and Cultured Meat Development, College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, PR China.
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Purushothaman K, Crawford AD, Rocha SD, Göksu AB, Lange BM, Mydland LT, Vij S, Qingsong L, Øverland M, Press CM. Cyberlindnera jadinii yeast as a functional protein source: Modulation of immunoregulatory pathways in the intestinal proteome of zebrafish ( Danio rerio). Heliyon 2024; 10:e26547. [PMID: 38468924 PMCID: PMC10925985 DOI: 10.1016/j.heliyon.2024.e26547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/09/2024] [Accepted: 02/15/2024] [Indexed: 03/13/2024] Open
Abstract
Yeasts contain bioactive components that can enhance fish immune robustness and disease resistance. Our study focused on analyzing intestinal immunoregulatory pathways in zebrafish (Danio rerio) using iTRAQ and 2D LC-MS/MS to quantify intestinal proteins. Zebrafish were fed either control diet (C) or diet supplemented with autolyzed Cyberlindnera jadinii (ACJ). KEGG analysis revealed that ACJ yeast diet induced increased abundance of proteins related to arginine and proline metabolism, phagosome, C-lectin receptor signaling, ribosome and PPAR signaling pathways, which can modulate and enhance innate immune responses. ACJ yeast diet also showed decreased abundance of proteins associated with inflammatory pathways, including apoptosis, necroptosis and ferroptosis. These findings indicate boosted innate immune response and control of inflammation-related pathways in zebrafish intestine. Our findings in the well annotated proteome of zebrafish enabled a detailed investigation of intestinal responses and provide insight into health-beneficial effects of yeast species C. jadinii, which is relevant for aquaculture species.
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Affiliation(s)
- Kathiresan Purushothaman
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Alexander D. Crawford
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Sérgio D.C. Rocha
- Department of Animal and Aquaculture Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway
| | - Aleksandar B. Göksu
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Byron Morales Lange
- Department of Animal and Aquaculture Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway
| | - Liv Torunn Mydland
- Department of Animal and Aquaculture Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway
| | - Shubha Vij
- School of Applied Science, Republic Polytechnic, 9 Woodlands Avenue 9, Singapore 738964, Singapore
- Tropical Futures Institute, James Cook University Singapore, 149 Sims Drive, 387380, Singapore
| | - Lin Qingsong
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Margareth Øverland
- Department of Animal and Aquaculture Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, Ås, Norway
| | - Charles McL. Press
- Department of Preclinical Sciences and Pathology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
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Shi F, Zhang X, Wang Z, Wang X, Zou C. Unveiling molecular mechanisms of pepper resistance to Phytophthora capsici through grafting using iTRAQ-based proteomic analysis. Sci Rep 2024; 14:4789. [PMID: 38413819 PMCID: PMC10899238 DOI: 10.1038/s41598-024-55596-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 02/26/2024] [Indexed: 02/29/2024] Open
Abstract
Phytophthora blight severely threatens global pepper production. Grafting bolsters plant disease resistance, but the underlying molecular mechanisms remain unclear. In this study, we used P. capsici-resistant strain 'ZCM334' and susceptible strain 'Early Calwonder' for grafting. Compared to self-rooted 'Early Calwonder' plants, 'ZCM334' grafts exhibited delayed disease onset, elevated resistance, and reduced leaf cell damage, showcasing the potential of grafting in enhancing pepper resistance to P. capsici. Proteomic analysis via the iTRAQ technology unveiled 478 and 349 differentially expressed proteins (DEPs) in the leaves and roots, respectively, between the grafts and self-rooted plants. These DEPs were linked to metabolism and cellular processes, stimulus responses, and catalytic activity and were significantly enriched in the biosynthesis of secondary metabolites, carbon fixation in photosynthetic organizations, and pyruvate metabolism pathways. Twelve DEPs exhibiting consistent expression trends in both leaves and roots, including seven related to P. capsici resistance, were screened. qRT-PCR analysis confirmed a significant correlation between the protein and transcript levels of DEPs after P. capsici inoculation. This study highlights the molecular mechanisms whereby grafting enhances pepper resistance to Phytophthora blight. Identification of key genes provides a foundation for studying the regulatory network governing the resistance of pepper to P. capsici.
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Affiliation(s)
- Fengyan Shi
- Vegetable Research Institute, Liaoning Academy of Agricultural Sciences, 84 Dongling Road, Shenhe District, Shenyang, 110161, China
| | - Xi Zhang
- Vegetable Research Institute, Liaoning Academy of Agricultural Sciences, 84 Dongling Road, Shenhe District, Shenyang, 110161, China
| | - Zhidan Wang
- College of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenhe District, Shenyang, 110866, China
| | - Xiuxue Wang
- Vegetable Research Institute, Liaoning Academy of Agricultural Sciences, 84 Dongling Road, Shenhe District, Shenyang, 110161, China
| | - Chunlei Zou
- Vegetable Research Institute, Liaoning Academy of Agricultural Sciences, 84 Dongling Road, Shenhe District, Shenyang, 110161, China.
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Su H, Zhu L, Su L, Li M, Wang R, Zhu J, Chen Y, Chen T. Impact of miR-29c-3p in the Nucleus Accumbens on Methamphetamine-Induced Behavioral Sensitization and Neuroplasticity-Related Proteins. Int J Mol Sci 2024; 25:942. [PMID: 38256016 PMCID: PMC10815255 DOI: 10.3390/ijms25020942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/26/2023] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
Methamphetamine (METH) abuse inflicts both physical and psychological harm. While our previous research has established the regulatory role of miR-29c-3p in behavior sensitization, the underlying mechanisms and target genes remain incompletely understood. In this study, we employed the isobaric tags for relative and absolute quantitation (iTRAQ) technique in conjunction with Ingenuity pathway analysis (IPA) to probe the putative molecular mechanisms of METH sensitization through miR-29c-3p inhibition. Through a microinjection of AAV-anti-miR-29c-3p into the nucleus accumbens (NAc) of mice, we observed the attenuation of METH-induced locomotor effects. Subsequent iTRAQ analysis identified 70 differentially expressed proteins (DEPs), with 22 up-regulated potential target proteins identified through miR-29c-3p target gene prediction and IPA analysis. Our focus extended to the number of neuronal branches, the excitatory synapse count, and locomotion-related pathways. Notably, GPR37, NPC1, and IREB2 emerged as potential target molecules for miR-29c-3p regulation, suggesting their involvement in the modulation of METH sensitization. Quantitative PCR confirmed the METH-induced aberrant expression of Gpr37, Npc1, and Ireb2 in the NAc of mice. Specifically, the over-expression of miR-29c-3p led to a significant reduction in the mRNA level of Gpr37, while the inhibition of miR-29c-3p resulted in a significant increase in the mRNA level of Gpr37, consistent with the regulatory principle of miRNAs modulating target gene expression. This suggests that miR-29c-3p potentially influences METH sensitization through its regulation of neuroplasticity. Our research indicates that miR-29c-3p plays a crucial role in regulating METH-induced sensitization, and it identified the potential molecular of miR-29c-3p in regulating METH-induced sensitization.
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Affiliation(s)
- Hang Su
- College of Forensic Medicine, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China; (H.S.); (L.Z.); (L.S.); (M.L.); (R.W.); (J.Z.)
- The Key Laboratory of Health Ministry for Forensic Science, Xi’an Jiaotong University, Xi’an 710061, China
- National Biosafety Evidence Foundation, Bio-Evidence Sciences Academy, Western China Science and Technology Innovation Harbor, Xi’an Jiaotong University, Xi’an 710115, China
| | - Li Zhu
- College of Forensic Medicine, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China; (H.S.); (L.Z.); (L.S.); (M.L.); (R.W.); (J.Z.)
- The Key Laboratory of Health Ministry for Forensic Science, Xi’an Jiaotong University, Xi’an 710061, China
- National Biosafety Evidence Foundation, Bio-Evidence Sciences Academy, Western China Science and Technology Innovation Harbor, Xi’an Jiaotong University, Xi’an 710115, China
| | - Linlan Su
- College of Forensic Medicine, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China; (H.S.); (L.Z.); (L.S.); (M.L.); (R.W.); (J.Z.)
- The Key Laboratory of Health Ministry for Forensic Science, Xi’an Jiaotong University, Xi’an 710061, China
- National Biosafety Evidence Foundation, Bio-Evidence Sciences Academy, Western China Science and Technology Innovation Harbor, Xi’an Jiaotong University, Xi’an 710115, China
| | - Min Li
- College of Forensic Medicine, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China; (H.S.); (L.Z.); (L.S.); (M.L.); (R.W.); (J.Z.)
- The Key Laboratory of Health Ministry for Forensic Science, Xi’an Jiaotong University, Xi’an 710061, China
- National Biosafety Evidence Foundation, Bio-Evidence Sciences Academy, Western China Science and Technology Innovation Harbor, Xi’an Jiaotong University, Xi’an 710115, China
| | - Rui Wang
- College of Forensic Medicine, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China; (H.S.); (L.Z.); (L.S.); (M.L.); (R.W.); (J.Z.)
- The Key Laboratory of Health Ministry for Forensic Science, Xi’an Jiaotong University, Xi’an 710061, China
- National Biosafety Evidence Foundation, Bio-Evidence Sciences Academy, Western China Science and Technology Innovation Harbor, Xi’an Jiaotong University, Xi’an 710115, China
| | - Jie Zhu
- College of Forensic Medicine, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China; (H.S.); (L.Z.); (L.S.); (M.L.); (R.W.); (J.Z.)
- The Key Laboratory of Health Ministry for Forensic Science, Xi’an Jiaotong University, Xi’an 710061, China
- National Biosafety Evidence Foundation, Bio-Evidence Sciences Academy, Western China Science and Technology Innovation Harbor, Xi’an Jiaotong University, Xi’an 710115, China
| | - Yanjiong Chen
- Department of Immunology and Pathogenic Biology, College of Basic Medicine, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China;
| | - Teng Chen
- College of Forensic Medicine, Xi’an Jiaotong University Health Science Center, Xi’an 710061, China; (H.S.); (L.Z.); (L.S.); (M.L.); (R.W.); (J.Z.)
- The Key Laboratory of Health Ministry for Forensic Science, Xi’an Jiaotong University, Xi’an 710061, China
- National Biosafety Evidence Foundation, Bio-Evidence Sciences Academy, Western China Science and Technology Innovation Harbor, Xi’an Jiaotong University, Xi’an 710115, China
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Tian L, Zhao X, Hu Z, Liu J, Ma J, Fan Y, Liu D. iTRAQ-based proteomics identifies proteins associated with betaine accumulation in Lycium barbarum L. J Proteomics 2024; 290:105033. [PMID: 37879564 DOI: 10.1016/j.jprot.2023.105033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 10/27/2023]
Abstract
In order to better understand the mechanism of betaine accumulation in Lycium barbarum L. (LBL), we used iTRAQ (Isotope relative and absolute quantitative labeling) proteomics to screen and identify differentially abundant proteins (DAPs) at five stages (S1-young fruit stage, S2-green fruit stage, S3-early yellowing stage, S4-late yellowing stage, S5-ripening stage). A total of 1799 DAPs and 171 betaine-related DAPs were identified, and phosphatidylethanolamine N-methyltransferase (NMT), choline monooxygenase (CMO), and betaine aldehyde dehydrogenase (BADH) were found to be the key enzymes related to betaine metabolism. These proteins are mainly involved in carbohydrates, amino acids and their derivatives, fatty acids, carboxylic acids, photosynthesis and photoprotection, isoquinoline alkaloid biosynthesis, peroxisomes, and glycine, serine, and threonine metabolism. Three of the key enzymes were also up- and down-regulated to different degrees at the mRNA level. The study provide new insights into the of mechanism of betaine accumulation in LBL. SIGNIFICANCE: Betaine, a class of naturally occurring, water-soluble alkaloids, has been found to be widespread in animals, higher plants, and microbes. In addition to being an osmotic agent, betaine has biological functions such as hepatoprotection, neuroprotection, and antioxidant activity. Betaine metabolism (synthesis and catabolism) is complexly regulated by developmental and environmental signals throughout the life cycle of plant fruit maturation. As a betaine-accumulating plant, little has been reported about the regulatory mechanisms of betaine metabolism during the growth and development of Lycium barbarum L. (LBL) fruit. Therefore, this study used iTRAQ quantitative proteomics technology to investigate the abundance changes of betaine-related proteins in LBL fruit, screen and analyze the differential abundance proteins related to betaine metabolism, and provide theoretical references for the in-depth study of the mechanism of betaine metabolism in LBL fruit.
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Affiliation(s)
- Lingli Tian
- School of Food Science & Engineering, Ningxia University, Yinchuan 750021, People's Republic of China
| | - Xiaolu Zhao
- School of Agriculture, Ningxia University, Yinchuan 750021, People's Republic of China
| | - Ziying Hu
- School of Food Science & Engineering, Ningxia University, Yinchuan 750021, People's Republic of China; State Administration of Market Supervision (Key Laboratory of Wolfberry and Wine), Ningxia University, Yinchuan 750021, People's Republic of China
| | - Jun Liu
- Hubei Key Laboratory of Edible Wild Plants Conservation and Utilization, Hubei Normal University, Hubei 435002, People's Republic of China
| | - Jiao Ma
- School of Food Science & Engineering, Ningxia University, Yinchuan 750021, People's Republic of China
| | - Yanli Fan
- School of Food Science & Engineering, Ningxia University, Yinchuan 750021, People's Republic of China
| | - Dunhua Liu
- School of Food Science & Engineering, Ningxia University, Yinchuan 750021, People's Republic of China; School of Agriculture, Ningxia University, Yinchuan 750021, People's Republic of China; State Administration of Market Supervision (Key Laboratory of Wolfberry and Wine), Ningxia University, Yinchuan 750021, People's Republic of China.
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9
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Zhen C, Wang C, Ma Y, Pang Y, Cai F, Meng J, He Y, Xiao P, Liu J, Mei X, Li S, Wu G, Jin G, Zheng B, Liang R, Tan Z. Mechanism of Antidepressant Action of (2R,6R)-6-Hydroxynorketamine (HNK) and Its Compounds: Insights from Proteomic Analysis. Mol Neurobiol 2024; 61:465-475. [PMID: 37632679 DOI: 10.1007/s12035-023-03555-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/02/2023] [Indexed: 08/28/2023]
Abstract
The effects of HNK, I5, and I6 on the expression of protein in hippocampus of depressed mice were studied by isobaric tags for relative and absolute quantitation (iTRAQ) to explore the mechanism of their antidepressant action. HNK, I5, and I6 were administered intragastric administration once a day in the morning for 7 days. The drug was subsequently discontinued for 7 days (without any treatment). On the 15th day, mice in each group were given the drug (1.0, 10.0, 30.0 mg/kg) intragastric stimulation and mouse hippocampal tissues were taken to perform iTRAQ to identify differentially expressed proteins, and bioinformatics was used to analyze the functional enrichment of the differentially expressed proteins. Compared with Ctr group, the number of differentially expressed proteins in HNK, I5, and I6 treatment groups was 158, 88, and 105, respectively. The three groups shared 29 differentially expressed proteins. In addition, compared with HNK group, the number of differentially expressed proteins in I5 and I6 groups was 201 and 203, respectively. A total of 47 and 56 differentially expressed proteins were co-expressed in I5 and I6 groups. Bioinformatics analysis showed that these differentially expressed proteins mainly had the functions of binding, biocatalysis, and transport, and mainly participated in cellular process, biological regulation process, biological metabolism process, and stress reaction process. GO and KEGG pathway analysis found that these differentially expressed proteins were involved long-term potentiation, G13 pathway, platelet activation pathway, and MAPK signaling pathway. HNK, I5, and I6 antidepressants are closely related to sudden stress sensitivity, stress resistance, neurotransmitter, and metabolic pathways. This study provides a scientific basis to further elucidate the mechanism and clinical application of HNK, I5, and I6 antidepressants.
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Affiliation(s)
- Chaohui Zhen
- Department of Surgery, The First Dongguan Affiliated Hospital of Guangdong Medical University, Dongguan City, 523000, Guangdong Province, China
| | - Chong Wang
- Department of Neurosurgery, Shenzhen Children's Hospital, Shenzhen City, 518026, Guangdong Province, China
| | - Yanjun Ma
- Shenzhen Ruijian Biotechnology Co., Ltd, Shenzhen City, 518057, Guangdong Province, China
| | - Yuli Pang
- Health Management Center, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University, Shenzhen City, 518055, Guangdong Province, China
| | - Feiyue Cai
- Health Management Center, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University, Shenzhen City, 518055, Guangdong Province, China
- General Practice Alliance, Shenzhen City, Guangdong Province, China
| | - Jiali Meng
- General Practice Alliance, Shenzhen City, Guangdong Province, China
- Department of General Practice, Shenzhen University General Hospital, Shenzhen University, Shenzhen City, 518055, Guangdong Province, China
| | - Yuefei He
- General Practice Alliance, Shenzhen City, Guangdong Province, China
- Department of General Practice, Shenzhen University General Hospital, Shenzhen University, Shenzhen City, 518055, Guangdong Province, China
| | - Ping Xiao
- Department of Otorhinolaryngology Head and Neck Surgery, Shenzhen Children's Hospital, Shenzhen City, 518026, Guangdong Province, China
| | - Jianxi Liu
- Shenzhen Ruijian Biotechnology Co., Ltd, Shenzhen City, 518057, Guangdong Province, China
| | - Xi Mei
- Zhuhai Pengkun Biomedicine Technology Co. Ltd, Zhuhai City, 519000, Guangdong Province, China
| | - Shupeng Li
- State Key Laboratory of Oncogenomics, School of Chemical Biology and Biotechnology, Peking University, Shenzhen City, 518055, Guangdong Province, China
| | - Guanzheng Wu
- College of Textiles and Clothing, Yancheng Institute of Technology, Yancheng City, 224051, Jiangsu Province, China
| | - Guangzhen Jin
- Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan, 31116, Korea
| | - Biao Zheng
- Department of Surgery, The First Dongguan Affiliated Hospital of Guangdong Medical University, Dongguan City, 523000, Guangdong Province, China.
| | - Rui Liang
- Department of Surgery, The First Dongguan Affiliated Hospital of Guangdong Medical University, Dongguan City, 523000, Guangdong Province, China.
| | - Zhen Tan
- Department of Surgery, The First Dongguan Affiliated Hospital of Guangdong Medical University, Dongguan City, 523000, Guangdong Province, China.
- Health Management Center, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Shenzhen University, Shenzhen City, 518055, Guangdong Province, China.
- General Practice Alliance, Shenzhen City, Guangdong Province, China.
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10
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Shen XF, Xu YP, Jiang YF, Gao LJ, Tong XQ, Gong J, Yang YF, Zeng RJ. Evaluating nutrient limitation in co-culture of Chlorella pyrenoidosa and Rhodobacter sphaeroides. Sci Total Environ 2024; 906:167706. [PMID: 37820812 DOI: 10.1016/j.scitotenv.2023.167706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 10/07/2023] [Accepted: 10/07/2023] [Indexed: 10/13/2023]
Abstract
The influence of nitrogen deficiency on microalgae-bacteria co-culture has been studied mostly with nitrogen-fixing bacteria. Photosynthetic bacteria (PSB), which are non-nitrogen-fixing bacteria, the impact of N deficiency on its co-culture with microalgae is unknown. In this study, Chlorella pyrenoidosa and Rhodobacter sphaeroides co-culture was cultivated photoheterotrophically with acetate. The impact of N starvation and different P supply levels on oil production were examined. When phosphorus was sufficient, N starvation increased the fatty acid methyl ester (FAME) content from 21.7 % to 28.2 %, and also increased the FAME yield (g CODFAME/g CODAcetate) from 0.17 to 0.22. However, the biomass and FAME productivities decreased. Sufficient phosphorus was also essential for a high growth rate and FAME productivity. Deficiencies in either N or P led to a decrease in the proportion of unsaturated FAMEs. iTRAQ analysis indicated N starvation promoted oil accumulation by driving the carbon flow to fatty acid synthesis in microalgae from co-culture. This study improves the understanding of biomass and lipid production via microalgae-PSB co-culture in photoheterotrophic cultivation. The mechanism of interaction between microalgae and bacteria needs further study.
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Affiliation(s)
- Xiao-Fei Shen
- School of Ecology and Environment, Anhui Normal University, Wuhu, Anhui 241000, PR China
| | - Ya-Ping Xu
- School of Ecology and Environment, Anhui Normal University, Wuhu, Anhui 241000, PR China
| | - Yi-Fan Jiang
- School of Ecology and Environment, Anhui Normal University, Wuhu, Anhui 241000, PR China
| | - Lin-Jun Gao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, PR China
| | - Xiao-Qin Tong
- School of Ecology and Environment, Anhui Normal University, Wuhu, Anhui 241000, PR China
| | - Jing Gong
- School of Ecology and Environment, Anhui Normal University, Wuhu, Anhui 241000, PR China
| | - Yan-Fang Yang
- School of Ecology and Environment, Anhui Normal University, Wuhu, Anhui 241000, PR China
| | - Raymond Jianxiong Zeng
- Center of Wastewater Resource Recovery, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, PR China.
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11
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Fricker LD. Quantitative Peptidomics: General Considerations. Methods Mol Biol 2024; 2758:89-108. [PMID: 38549010 DOI: 10.1007/978-1-0716-3646-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Peptidomics is the detection and identification of the peptides present in a sample, and quantitative peptidomics provides additional information about the amounts of these peptides. It is possible to perform absolute quantitation of peptide levels in which the biological sample is compared to synthetic standards of each peptide. More commonly, relative quantitation is performed to compare peptide levels between two or more samples. Relative quantitation can measure differences between all peptides that are detectable, which can exceed 1000 peptides in a complex sample. In this chapter, various techniques used for quantitative peptidomics are described along with discussion of the advantages and disadvantages of each approach. A guide to selecting the optimal quantitative approach is provided, based on the goals of the experiment and the resources that are available.
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Affiliation(s)
- Lloyd D Fricker
- Departments of Molecular Pharmacology and Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA.
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Liu Y, He Y, Cao J, Lu H, Zou R, Zuo Z, Li R, Zhang Y, Sun J. Correlative analysis of transcriptome and proteome in Penaeus vannamei reveals key signaling pathways are involved in IFN-like antiviral regulation mediated by interferon regulatory factor (PvIRF). Int J Biol Macromol 2023; 253:127138. [PMID: 37776923 DOI: 10.1016/j.ijbiomac.2023.127138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/02/2023]
Abstract
Interferon regulatory factors (IRFs) are crucial transcription factors that regulate interferon (IFN) induction in response to pathogen invasion. The regulatory mechanism of IRF has been well studied in vertebrates, but little has been known in arthropods. Therefore, in order to obtain new insights into the potential molecular mechanism of Peneaus vannamei IRF (PvIRF) in response to viral infection, comprehensive comparative analysis of the transcriptome and proteome profiles in shrimp infected with WSSV after knocking down PvIRF was conducted by using RNA sequencing (RNA-seq) and isobaric tags for relative and absolute quantification (iTRAQ). The sequence characterization, molecular functional evolution and 3D spatial structure of PvIRF were analyzed by using bioinformatics methods. PvIRF share the higher homology with different species in N-terminal end (containing DNA binding domain (DBD) including DNA sequence recognition sites and metal binding site) than that in C-terminal end. Within 4 IRF subfamilies of vertebrates, PvIRF had closer relationship with IRF1 subfamily. The DBD of PvIRF and C. gigas IRF1a were composed of α-helices and β-folds which was similar with the DBD structure of M. musculus IRF2. Interestingly, different from the five Tryptophan repeats highly homologous in the DBD of vertebrate IRF, the first and fifth tryptophans of PvIRF mutate to Phenylalanine and Leucine respectively, while the mutations were conserved among shrimp IRFs. RNAi knockdown of PvIRF gene by double-strand RNA could obviously promote the in vivo propagation of WSSV in shrimp and increase the mortality of WSSV-infected shrimp. It suggested that PvIRF was involved in inhibiting the replication of WSSV in shrimp. A total of 8787 transcripts and 2846 proteins were identified with significantly differential abundances in WSSV-infected shrimp after PvIRF knockdown, among which several immune-related members were identified and categorized into 10 groups according to their possible functions. Furthermore, the variation of expression profile from members of key signaling pathways involving JAK/STAT and Toll signaling pathway implied that they might participate IRF-mediated IFN-like regulation in shrimp. Correlative analyses indicated that 722 differentially expressed proteins (DEPs) shared the same expression profiles with their corresponding transcripts, including recognition-related proteins (CTLs and ITGs), chitin-binding proteins (peritrophin), and effectors (ALFs and SWD), while 401 DEPs with the opposite expression profiles across the two levels emphasized the critical role of post-transcriptional and post-translational modification. The results provide candidate signaling pathway including pivotal genes and proteins involved in the regulatory mechanism of interferon mediated by IRF on shrimp antiviral response. This is the first report in crustacean to explore the IFN-like antiviral regulation pathway mediated by IRF on the basis of transcriptome and proteomics correlative analysis, and will provide new ideas for further research on innate immune and defense mechanisms of crustacean.
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Affiliation(s)
- Yichen Liu
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Science, Tianjin Normal University, Tianjin 300387, China
| | - Yuxin He
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Science, Tianjin Normal University, Tianjin 300387, China
| | - Jinlai Cao
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Science, Tianjin Normal University, Tianjin 300387, China
| | - Hangjia Lu
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Science, Tianjin Normal University, Tianjin 300387, China
| | - Ruifeng Zou
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Science, Tianjin Normal University, Tianjin 300387, China
| | - Zhihan Zuo
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Science, Tianjin Normal University, Tianjin 300387, China
| | - Ran Li
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Science, Tianjin Normal University, Tianjin 300387, China
| | - Yichen Zhang
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Science, Tianjin Normal University, Tianjin 300387, China
| | - Jinsheng Sun
- Tianjin Key Laboratory of Animal and Plant Resistance, College of Life Science, Tianjin Normal University, Tianjin 300387, China.
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13
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Muthego D, Moloi SJ, Brown AP, Goche T, Chivasa S, Ngara R. Exogenous abscisic acid treatment regulates protein secretion in sorghum cell suspension cultures. Plant Signal Behav 2023; 18:2291618. [PMID: 38100609 PMCID: PMC10730228 DOI: 10.1080/15592324.2023.2291618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/28/2023] [Indexed: 12/17/2023]
Abstract
Drought stress adversely affects plant growth, often leading to total crop failure. Upon sensing soil water deficits, plants switch on biosynthesis of abscisic acid (ABA), a stress hormone for drought adaptation. Here, we used exogenous ABA application to dark-grown sorghum cell suspension cultures as an experimental system to understand how a drought-tolerant crop responds to ABA. We evaluated intracellular and secreted proteins using isobaric tags for relative and absolute quantification. While the abundance of only ~ 7% (46 proteins) intracellular proteins changed in response to ABA, ~32% (82 proteins) of secreted proteins identified in this study were ABA responsive. This shows that the extracellular matrix is disproportionately targeted and suggests it plays a vital role in sorghum adaptation to drought. Extracellular proteins responsive to ABA were predominantly defense/detoxification and cell wall-modifying enzymes. We confirmed that sorghum plants exposed to drought stress activate genes encoding the same proteins identified in the in vitro cell culture system with ABA. Our results suggest that ABA activates defense and cell wall remodeling systems during stress response. This could underpin the success of sorghum adaptation to drought stress.
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Affiliation(s)
- Dakalo Muthego
- Department of Plant Sciences, University of the Free State, Phuthaditjhaba, South Africa
| | - Sellwane J. Moloi
- Department of Plant Sciences, University of the Free State, Phuthaditjhaba, South Africa
| | | | - Tatenda Goche
- Department of Biosciences, Durham University, Durham, UK
- Department of Crop Science, Bindura University of Science Education, Bindura, Zimbabwe
| | | | - Rudo Ngara
- Department of Plant Sciences, University of the Free State, Phuthaditjhaba, South Africa
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Shi XF, Zhang JL, Liu K, Wang L, Wang HP, Wu HY. Detection of serum major histocompatibility complex I (HLA-1) and β2-microglobulin (β2M) in pre-eclampsia using isobaric tags for relative and absolute quantitation ( iTRAQ). Int J Gynaecol Obstet 2023. [PMID: 38149341 DOI: 10.1002/ijgo.15312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/28/2023]
Abstract
OBJECTIVE The purpose of this preliminary investigation into the pathogenesis of pre-eclampsia was to screen the differential proteins in the serum of pregnant women with normal pregnancy and early-onset pre-eclampsia using isobaric tags for relative and absolute quantitation (iTRAQ), so as to identify serum biomarkers for the early diagnosis of pre-eclampsia. METHODS We examined the peripheral serum of 58 normal pregnant women and 42 pregnant women with early-onset pre-eclampsia using iTRAQ; the differentially expressed proteins were screened for bioinformatics analysis; and the expression of candidate proteins human leukocyte antigen-1 (HLA-1) and β2-microglobulin (β2M) in placental tissues was detected using western blot. RESULTS We identified a total of 63 differential proteins in the serum of patients from the normal control group and the pre-eclampsia group, and this included 24 up-regulated proteins and 39 down-regulated proteins. The western blot results of placental tissue showed reduced HLA-1 expression (1.12 ± 0.23) in the placenta in the pre-eclampsia group as compared with the normal control group (1.34 ± 0.22). Consistent with the results observed in the serum, β2M in the placenta in the pre-eclampsia group was significantly elevated (1.05 ± 0.47) in comparison with the normal group (0.75 ± 0.33) (P < 0.05). CONCLUSION In this study, we found that iTRAQ technology was useful for identifying differentially expressed proteins in the peripheral serum of pregnant women with pre-eclampsia, and that HLA-1 and β2M, which may be involved in the occurrence of pre-eclampsia, show promise as predictive markers of pre-eclampsia.
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Affiliation(s)
- Xu-Feng Shi
- Department of Obstetrics, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Jing-Li Zhang
- Department of Obstetrics, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Kan Liu
- Department of Obstetrics, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Li Wang
- Department of Obstetrics, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Huan-Ping Wang
- Department of Obstetrics, Henan Provincial People's Hospital, Zhengzhou, Henan, China
| | - Hai-Ying Wu
- Department of Obstetrics, Henan Provincial People's Hospital, Zhengzhou, Henan, China
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15
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Li Y, Li H, Ma W, Maegele M, Tang Y, Gu Z. Proteomic profiling of serum exosomes reveals acute phase response and promotion of inflammatory and platelet activation pathways in patients with heat stroke. PeerJ 2023; 11:e16590. [PMID: 38107577 PMCID: PMC10725172 DOI: 10.7717/peerj.16590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 11/14/2023] [Indexed: 12/19/2023] Open
Abstract
Background: The pathological mechanism of heat stroke (HS) involves the acute phase response, unbalanced immunological/inflammatory reactions, and coagulation initiation, especially platelet activation. Although exosomes contain proteins involved in these biological processes, their protein cargo levels and potential roles in HS remain unknown. This study explored the serum exosome protein expression patterns after HS and their potential roles in the pathogenesis of HS. Methods: Blood samples were collected from ten patients diagnosed with HS upon admission to the intensive care unit (six with severe HS and four with mild HS). Samples from six healthy volunteers were included as control. Using ultracentrifugation, exosomes were prudently isolated, and their protein contents were profiled using liquid chromatography-tandem mass spectrometry analysis with isobaric tags for relative and absolute quantification-based proteomics. Results: Compared with healthy volunteers, patients with HS showed significant changes in the levels of 33 exosomal proteins (23 upregulated and 10 downregulated). The most upregulated proteins included serum amyloid A-1 (SAA-1), von Willebrand factor (vWF), S100A8, and histone H3. In addition, SAA-1, vWF, platelet membrane glycoprotein, S100A8, and histone H3 were more enriched in the exosomes from patients with severe HS than from those with mild HS. Gene ontology analysis revealed that the HS-modulated exosomal proteins were mostly related to inflammatory response, including the acute-phase response, platelet activation/degranulation, and innate immune response. Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed significant enrichment of proteins in the IL-17 signaling pathway, platelet activation, neutrophil extracellular trap formation, Fc epsilon RI signaling pathway, chemokine signaling pathway, and NOD-like receptor signaling pathway, among others. Several serum exosomal proteins, including SAA-1, vWF, and S100A8, which are related to the acute phase, inflammatory response, and platelet activation, were confirmed to be elevated in patients with HS, and were significantly correlated with disease severity, organ dysfunction, and death. Conclusion: Overall, this study explores the potential role of the serum exosomal proteome in the inflammatory response and platelet activation in HS, suggests the pathological mechanisms underlying HS-induced injuries, and recommends reliable exosomal biomarkers for predicting HS prognosis.
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Affiliation(s)
- Yue Li
- Academy of Orthopedics, Guangdong Province, Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Guangzhou, China
- Department of Treatment, Center for Traumatic Injuries, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
- Department of Intensive Care Unit, General Hospital of Southern Theatre Command of PLA, Guangzhou, China
- Department of Emergency Medicine, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Huan Li
- Department of ICU, Sun Yat-sen University Cancer Center, Guangzhou, China
- Sate Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wenjuan Ma
- Department of ICU, Sun Yat-sen University Cancer Center, Guangzhou, China
- Sate Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Marc Maegele
- University Witten/Herdecke (UW/H), Köln, German
- Department for Trauma and Orthopedic Surgery, Cologne-Merheim Medical Center (CMMC), University Witten/Herdecke (UW/H), Campus Cologne-Merheim, Ostmerheimerstr, Köln, Germany
| | - Youqing Tang
- Department of Emergency Medicine, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Zhengtao Gu
- Academy of Orthopedics, Guangdong Province, Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Guangzhou, China
- Department of Treatment, Center for Traumatic Injuries, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
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Jin M, Fan W, Piao J, Zhao F, Piao J. Effects of lncRNA MTC on protein expression in skin fibroblasts of Liaoning Cashmere goat based on iTRAQ technique. Anim Biotechnol 2023; 34:2817-2826. [PMID: 36093624 DOI: 10.1080/10495398.2022.2119406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Existing experiments have found a new intergenic lncRNA activated by melatonin, which is called lncRNA MTC. However, the regulatory mechanism of lncRNA MTC in Liaoning Cashmere goat skin fibroblasts has not been clarified. Specific knockdown of lncRNA MTC inhibits cell proliferation and increases apoptosis. iTRAQ reagent was used for relative and absolute quantification of proteins in lncRNA MTC-KD and NC groups to evaluate changes in protein expression during dermal fibroblast development following lncRNA MTC deletion. A total of 5931 proteins were found in Liaoning Cashmere goat skin fibroblasts, of which 123 were differentially expressed, including 32 up-regulated proteins and 91 down-regulated proteins. Of the 91 down-regulated proteins, 32 act mainly through related pathways (e.g., cell cycle, mitochondrial function, ribosomal structure, vesicular transport, cytoskeletal components and skin morphogenesis). LncRNA MTC facilitates the proliferation of Liaoning Cashmere goat skin fibroblasts by regulating ITGB5, TlN2, CTSS, POLG, RAP1B, CHAF1A, CDCA8 and other proteins involved in cell proliferation. The results of this study provide some candidate proteins for the in-depth investigation of the molecular mechanism of lncRNA MTC, which facilitates hair growth in cashmere goats and provides more insights into their regulatory networks and biochemical pathways.
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Affiliation(s)
- Mei Jin
- Department of Life Sciences, Liaoning Provincial Key Laboratory of Biotechnology and Drug Discovery, Liaoning Normal University, Dalian, China
| | - Weiyu Fan
- Department of Life Sciences, Liaoning Provincial Key Laboratory of Biotechnology and Drug Discovery, Liaoning Normal University, Dalian, China
| | - Jun Piao
- Department of Life Sciences, Liaoning Provincial Key Laboratory of Biotechnology and Drug Discovery, Liaoning Normal University, Dalian, China
| | - Fengqin Zhao
- Department of Life Sciences, Liaoning Provincial Key Laboratory of Biotechnology and Drug Discovery, Liaoning Normal University, Dalian, China
| | - Jing'ai Piao
- Department of Life Sciences, Liaoning Provincial Key Laboratory of Biotechnology and Drug Discovery, Liaoning Normal University, Dalian, China
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Chan SH, Kuo WH, Wang LH. SCEL regulates switches between pro-survival and apoptosis of the TNF-α/TNFR1/NF-κB/c-FLIP axis to control lung colonization of triple negative breast cancer. J Biomed Sci 2023; 30:93. [PMID: 38037106 PMCID: PMC10688137 DOI: 10.1186/s12929-023-00986-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 11/19/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND Patients with metastatic triple-negative breast cancer (mTNBC) have a higher probability of developing visceral metastasis within 5 years after the initial diagnosis. Therefore, a deeper understanding of the progression and spread of mTNBC is urgently needed. METHODS The isobaric tag for relative and absolute quantitation (iTRAQ)-based LC-MS/MS proteomic approach was applied to identify novel membrane-associated proteins in the lung-tropic metastatic cells. Public domain datasets were used to assess the clinical relevance of the candidate proteins. Cell-based and mouse models were used for biochemical and functional characterization of the protein molecule Sciellin (SCEL) identified by iTRAQ to elucidate its role and underlying mechanism in promoting lung colonization of TNBC cells. RESULTS The iTRAQ-based LC-MS/MS proteomic approach identified a membrane-associated protein SCEL that was overexpressed in the lung-tropic metastatic cells, and its high expression was significantly correlated with the late-stage TNBC and the shorter survival of the patients. Downregulation of SCEL expression significantly impaired the 3D colony-forming ability but not the migration and invasion ability of the lung colonization (LC) cells. Knockdown of SCEL reduced TNF-α-induced activation of the NF-κB/c-FLIP pro-survival and Akt/Erk1/2 growth signaling pathways in the LC cells. Specifically, knockdown of SCEL expression switched TNF-α-mediated cell survival to the caspase 3-dependent apoptosis. Conversely, ectopic expression of SCEL promoted TNF-α-induced activation of NF-κB/c-FLIP pro-survival and Akt/Erk1/2 pro-growth signaling pathway. The result of co-immunoprecipitation (Co-IP) and GST pull-down assay showed that SCEL could interact with TNFR1 to promote its protein stability. The xenograft mouse model experiments revealed that knockdown of SCEL resulted in increase of caspase-3 activity, and decrease of ki67 and TNFR1 expression as well as increase of tumor-associated macrophages in the metastatic lung lesions. Clinically, SCEL expression was found to be positively correlated with TNFR1 in TNBC tissues. Lastly, we showed that blocking TNF-α-mediated cell survival signaling by adalimumab effectively suppressed the lung colonization of the SCEL-positive, but not the SCEL-downregulated LC cells in the tail-vein injection model. CONCLUSIONS Our findings indicate that SCEL plays an essential role in the metastatic lung colonization of TNBC by promoting the TNF-α/TNFR1/NF-κB/c-FLIP survival and Akt/Erk1/2 proliferation signaling. Thus, SCEL may serve as a biomarker for adalimumab treatment of TNBC patients.
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Affiliation(s)
- Shih-Hsuan Chan
- School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan.
- Chinese Medicine Research Center, China Medical University, No. 91, Hsueh-Shih Road, Taichung, 40402, Taiwan.
- Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung, 40402, Taiwan.
| | - Wen-Hung Kuo
- Department of Surgery, National Taiwan University Hospital, Taipei, 100, Taiwan
| | - Lu-Hai Wang
- Chinese Medicine Research Center, China Medical University, No. 91, Hsueh-Shih Road, Taichung, 40402, Taiwan.
- Graduate Institute of Integrated Medicine, China Medical University, Taichung, Taiwan.
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18
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Liu B, Liu D, Chen T, Wang X, Xiang H, Wang G, Cai R. iTRAQ-based quantitative proteomic analysis of the antibacterial mechanism of silver nanoparticles against multidrug-resistant Streptococcus suis. Front Microbiol 2023; 14:1293363. [PMID: 38033593 PMCID: PMC10684948 DOI: 10.3389/fmicb.2023.1293363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023] Open
Abstract
Background The increase in antibiotic resistance of bacteria has become a major concern in clinical treatment. Silver nanoparticles (AgNPs) have significant antibacterial effects against Streptococcus suis. Therefore, this study aimed to investigate the antibacterial activity and mechanism of action of AgNPs against multidrug-resistant S. suis. Methods The effect of AgNPs on the morphology of multidrug-resistant S. suis was observed using scanning electron microscopy (SEM). Differentially expressed proteins were analyzed by iTRAQ quantitative proteomics, and the production of reactive oxygen species (ROS) was assayed by H2DCF-DA staining. Results SEM showed that AgNPs disrupted the normal morphology of multidrug-resistant S. suis and the integrity of the biofilm structure. Quantitative proteomic analysis revealed that a large number of cell wall synthesis-related proteins, such as penicillin-binding protein and some cell cycle proteins, such as the cell division protein FtsZ and chromosomal replication initiator protein DnaA, were downregulated after treatment with 25 μg/mL AgNPs. Significant changes were also observed in the expression of the antioxidant enzymes glutathione reductase, alkyl hydroperoxides-like protein, α/β superfamily hydrolases/acyltransferases, and glutathione disulfide reductases. ROS production in S. suis positively correlated with AgNP concentration. Conclusion The potential antibacterial mechanism of AgNPs may involve disrupting the normal morphology of bacteria by inhibiting the synthesis of cell wall peptidoglycans and inhibiting the growth of bacteria by inhibiting the cell division protein FtsZ and Chromosomal replication initiator protein DnaA. High oxidative stress may be a significant cause of bacterial death. The potential mechanism by which AgNPs inhibit S. suis biofilm formation may involve affecting bacterial adhesion and interfering with the quorum sensing system.
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Affiliation(s)
- Baoling Liu
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou, China
- College of Animal Science and Technology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Dingyu Liu
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou, China
| | - Tianbao Chen
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou, China
| | - Xiaohu Wang
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou, China
| | - Hua Xiang
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou, China
| | - Gang Wang
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou, China
| | - Rujian Cai
- Institute of Animal Health, Guangdong Academy of Agricultural Sciences, Key Laboratory of Livestock Disease Prevention of Guangdong Province, Scientific Observation and Experiment Station of Veterinary Drugs and Diagnostic Techniques of Guangdong Province, Ministry of Agriculture and Rural Affairs, Guangzhou, China
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Qianman B, Wupuer A, Jiasharete T, Luo B, Nihemaiti M, Jielile J. iTRAQ-based proteomics reveals potential markers and treatment pathways for acute Achilles tendon rupture. J Orthop Surg Res 2023; 18:852. [PMID: 37946221 PMCID: PMC10636927 DOI: 10.1186/s13018-023-04346-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/04/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Due to its limited blood supply and irregular mechanical loading, the Achilles tendon is the most frequently ruptured tendon. Despite the rising incidence of acute Achilles tendon rupture (AATR), the optimal treatment remains controversial. Missed diagnoses and delayed treatments lead to poor outcomes and limited treatment options. This study aimed to identify potential biomarkers for diagnosing and developing therapies for AATR. METHODS We employed the coupled isobaric tag for relative and absolute quantitation-liquid chromatography-electrospray ionization-tandem mass spectrometry approach to investigate protein expression in tissues from AATR patients. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted to identify differentially expressed proteins (DEPs) between AATR patients and healthy individuals. A protein-protein interaction (PPI) network of DEPs was constructed using the Search Tool for the Retrieval of Interacting Genes. The screened hub genes were selectively verified by immunohistochemical staining. RESULTS We identified 410 DEPs between AATR patients and controls. The DEPs were significantly enriched in GO terms such as the extracellular region, extracellular region part, and defense response, as well as KEGG pathways, including complement and coagulation cascades, focal adhesion, and regulation of actin cytoskeleton. The main hub nodes in the PPI network comprised fibronectin 1 (FN1), major histocompatibility complex, class I, B (HLA-B), filamin A (FLNA), heat shock 27-kDa protein 1 (HSPB1), heat shock protein family A member 5 (HSPA5), apolipoprotein A4 (APOA4), and myosin IC (MYO1C). Although APOA4 and collagens I, II, and III were detectable in healthy tendons, immunohistochemical staining confirmed higher expression of these proteins in the acutely ruptured Achilles tendon. CONCLUSIONS Our findings lay a foundation for further molecular studies of AATR. Inflammation and age-related degeneration may contribute to the pathogenesis of AATR. Moreover, the identified DEPs could be potential biomarkers for AATR diagnosis and treatment.
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Affiliation(s)
- Bayixiati Qianman
- Department of Osteopathy and Orthopedics (Ankle) Surgery, The Sixth Teaching Hospital of Xinjiang Medical University, No. 39 Wuxing South Road, Ürümqi, 830001, Xinjiang Uygur Autonomous Region, China
| | - Aikeremu Wupuer
- Department of Osteopathy and Orthopedics (Ankle) Surgery, The Sixth Teaching Hospital of Xinjiang Medical University, No. 39 Wuxing South Road, Ürümqi, 830001, Xinjiang Uygur Autonomous Region, China
| | - Tuomilisi Jiasharete
- Urumqi No.1 Middle School, No. 195, West 2nd Lane, Kanas Hubei Road, Urumqi Economic and Technological Development Zone (Toutunhe District), Ürümqi, 830015, Xinjiang Uygur Autonomous Region, China
| | - Biao Luo
- Department of Orthopaedics, Pingmei Shenma Medical Group General Hospital, No.1 South of Kuanggoong Middle Road, Xinhua District, Pingdingshan, 467000, Henan, China
| | - Meihua Nihemaiti
- Altay Traditional Chinese Medicine Hospital (Regional Kazakh Medical Hospital) in Xinjiang Uygur Autonomous Region, No. 40 Yingbin Road, Altay City, 836500, Xinjiang Uygur Autonomous Region, China
| | - Jiasharete Jielile
- Department of Osteopathy and Orthopedics (Ankle) Surgery, The Sixth Teaching Hospital of Xinjiang Medical University, No. 39 Wuxing South Road, Ürümqi, 830001, Xinjiang Uygur Autonomous Region, China.
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20
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Li X, Li M, Xue X, Wang X. Proteomic analysis reveals oxidative stress-induced activation of Hippo signaling in thiamethoxam-exposed Drosophila. Chemosphere 2023; 338:139448. [PMID: 37437626 DOI: 10.1016/j.chemosphere.2023.139448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/12/2023] [Accepted: 07/07/2023] [Indexed: 07/14/2023]
Abstract
Thiamethoxam (THIA) is a widely used neonicotinoid insecticide. However, the toxicity and defense mechanisms activated in THIA-exposed insects are unclear. Here, we used isobaric tags for relative and absolute quantitation (iTRAQ) proteomics technology to identify changes in protein expression in THIA-exposed Drosophila. We found that the antioxidant proteins Cyp6a23 and Dys were upregulated, whereas vir-1 was downregulated, which may have been detoxification in response to THIA exposure. Prx5 downregulation promoted the generation of reactive oxygen species. Furthermore, the accumulation of reactive oxygen species led to the induction of antioxidant defenses in THIA-exposed Drosophila, thereby enhancing the levels of oxidative stress markers (e.g., superoxide dismutase, glutathione S-transferase, and glutathione) and reducing catalase expression. Furthermore, the Hippo signaling transcription coactivator Yki was inactivated by THIA. Our results suggesting that Hippo signaling may be necessary to promote insect survival in response to neonicotinoid insecticide toxicity.
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Affiliation(s)
- Xiaoqin Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, Beijing, 100193, China; Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing, 100193, China
| | - Mingquan Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, Beijing, 100193, China; Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing, 100193, China
| | - Xianle Xue
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, Beijing, 100193, China
| | - Xing Wang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, Beijing, 100193, China; Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing, 100193, China.
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21
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Gao Y, Shi X, Chang Y, Li Y, Xiong X, Liu H, Li M, Li W, Zhang X, Fu Z, Xue Y, Tang J. Mapping the gene of a maize leaf senescence mutant and understanding the senescence pathways by expression analysis. Plant Cell Rep 2023; 42:1651-1663. [PMID: 37498331 DOI: 10.1007/s00299-023-03051-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/12/2023] [Indexed: 07/28/2023]
Abstract
KEY MESSAGES Narrowing down to a single putative target gene behind a leaf senescence mutant and constructing the regulation network by proteomic method. Leaf senescence mutant is an important resource for exploring molecular mechanism of aging. To dig for potential modulation networks during maize leaf aging process, we delimited the gene responsible for a premature leaf senescence mutant els5 to a 1.1 Mb interval in the B73 reference genome using a BC1F1 population with 40,000 plants, and analyzed the leaf proteomics of the mutant and its near-isogenic wild type line. A total of 1355 differentially accumulated proteins (DAP) were mainly enriched in regulation pathways such as "photosynthesis", "ribosome", and "porphyrin and chlorophyll metabolism" by the KEGG pathway analysis. The interaction networks constructed by incorporation of transcriptome data showed that ZmELS5 likely repaired several key factors in the photosynthesis system. The putative candidate proteins for els5 were proposed based on DAPs in the fined QTL mapping interval. These results provide fundamental basis for cloning and functional research of the els5 gene, and new insights into the molecular mechanism of leaf senescence in maize.
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Affiliation(s)
- Yong Gao
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xia Shi
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yongyuan Chang
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yingbo Li
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xuehang Xiong
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hongmei Liu
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Mengyuan Li
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Weihua Li
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xuehai Zhang
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhiyuan Fu
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yadong Xue
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Jihua Tang
- State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China.
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Ngo HL, Huynh TQ, Tran NBV, Nguyen NHB, Tong TH, Trinh TTL, Nguyen VD, Das PP, Lim TK, Lin Q, Nguyen TTH. Proteomic analysis of ceftazidime and meropenem-exposed Pseudomonas aeruginosa ATCC 9027. Proteome Sci 2023; 21:15. [PMID: 37770917 PMCID: PMC10537932 DOI: 10.1186/s12953-023-00217-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 09/12/2023] [Indexed: 09/30/2023] Open
Abstract
BACKGROUND Pseudomonas aeruginosa is well known for its intrinsic ability to resist a wide range of antibiotics, thus complicates treatment. Thus, understanding the response of the pathogen to antibiotics is important for developing new therapies. In this study, proteomic response of P. aeruginosa to the commonly used anti-pseudomonas antibiotics, ceftazidime (Caz) and meropenem (Mem) was investigated. METHODS P. aeruginosa ATCC 9027, an antibiotic-susceptible strain, was exposed to sub-MIC values of antibiotics either Caz or Mem for 14 days to obtain E1 strains and then cultured in antibiotic-free environments for 10 days to obtain E2 strains. Proteomes of the initial and E1, E2 strains were identified and comparatively analyzed using isobaric tags for relative and absolute quantitation (iTRAQ) in cooperation with nano LC-MS/MS. Noted up and down-regulated proteins were confirmed with quantitative reverse transcriptase PCR (qRT-PCR). RESULTS Overall, 1039 and 1041 proteins were identified in Caz and Mem-exposed strains, respectively. Upon antibiotic exposure, there were 7-10% up-regulated (Caz: 71, Mem: 85) and down-regulated (Caz: 106, Mem: 69) proteins (1.5-fold change cut-off). For both Caz and Mem, the DEPs were primarily the ones involved in metabolic process, membrane, virulence, protein synthesis, and antibiotic resistance in which proteins involved in antibiotics resistance tended to be up-regulated while proteins involved in protein synthesis and metabolic process were down-regulated. Noted proteins included beta-lactamase AmpC which was up-regulated and OprD which was down-regulated in both the antibiotic-exposed strains. Besides, biofilm formation related proteins TssC1 and Hcp1 in Caz- exposed strains and the membrane/ periplasmic proteins Azu and PagL in Mem-exposed strains were found significantly down-regulated. qRT-PCR results confirmed the expression change of AmpC, Hcp1 and OprD proteins. CONCLUSION Exposure of Pseudomonas aeruginosa to sub-MIC values of Caz and Mem resulted in around 10% change in its proteome. Not only proteins with confirmed roles in antibiotic resistance mechanisms changed their expression but also virulence- associated proteins. Both Caz and Mem response involved up-regulation of AmpC and down-regulation of OprD. While TssC1 and Hcp1 were responsible for Caz response, Azu and PagL were more likely involved in Mem response.
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Affiliation(s)
- Hong Loan Ngo
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Viet Nam National University Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Thuc Quyen Huynh
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Viet Nam National University Ho Chi Minh City, Ho Chi Minh City, Vietnam
- Research Center for Infectious Diseases, International University, Ho Chi Minh City, Vietnam
| | - Nguyen Bao Vy Tran
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Viet Nam National University Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Ngoc Hoa Binh Nguyen
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Viet Nam National University Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Thi Hang Tong
- Viet Nam National University Ho Chi Minh City, Ho Chi Minh City, Vietnam
- Research Center for Infectious Diseases, International University, Ho Chi Minh City, Vietnam
| | - Thi Truc Ly Trinh
- Viet Nam National University Ho Chi Minh City, Ho Chi Minh City, Vietnam
- Research Center for Infectious Diseases, International University, Ho Chi Minh City, Vietnam
| | - Van Dung Nguyen
- Viet Nam National University Ho Chi Minh City, Ho Chi Minh City, Vietnam
- Research Center for Infectious Diseases, International University, Ho Chi Minh City, Vietnam
| | - Prem Prakash Das
- Department of Biological Sciences, Protein and Proteomics Centre, National University of Singapore, Singapore, Singapore
| | - Teck Kwang Lim
- Department of Biological Sciences, Protein and Proteomics Centre, National University of Singapore, Singapore, Singapore
| | - Qingsong Lin
- Department of Biological Sciences, Protein and Proteomics Centre, National University of Singapore, Singapore, Singapore
| | - Thi Thu Hoai Nguyen
- School of Biotechnology, International University, Ho Chi Minh City, Vietnam.
- Viet Nam National University Ho Chi Minh City, Ho Chi Minh City, Vietnam.
- Research Center for Infectious Diseases, International University, Ho Chi Minh City, Vietnam.
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Gao X, Qian J, Zhang Y, Wang H, Cui J, Yang Y. Analysis of differential membrane proteins related to matrix stiffness-mediated metformin resistance in hepatocellular carcinoma cells. Proteome Sci 2023; 21:14. [PMID: 37740172 PMCID: PMC10517517 DOI: 10.1186/s12953-023-00216-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/01/2023] [Indexed: 09/24/2023] Open
Abstract
BACKGROUND Our previous work shows that increased matrix stiffness not only alters malignant characteristics of hepatocellular carcinoma (HCC) cells, but also attenuates metformin efficacy in treating HCC cells. Here, we identified differential membrane proteins related to matrix stiffness-mediated metformin resistance for better understand therapeutic resistance of metformin in HCC. METHODS Differential membrane proteins in HCC cells grown on different stiffness substrates before and after metformin intervention were screened and identified using isobaric tags for relative and absolute quantification (iTRAQ) labeling coupled with the liquid chromatography-tandem mass spectrometry (LC-MS/MS), then bioinformatic analysis were applied to determine candidate membrane protein and their possible signaling pathway. RESULTS A total of 5159 proteins were identified and 354 differential membrane proteins and membrane associated proteins, which might be associated with matrix stiffness-mediated metformin resistance were discovered. Then 94 candidate membrane proteins including 21 up-regulated protein molecules and 73 down-regulated protein molecules were further obtained. Some of them such as Annexin A2 (ANXA2), Filamin-A (FLNA), Moesin (MSN), Myosin-9 (MYH9), Elongation factor 2 (eEF2), and Tax1 binding Protein 3 (TAX1BP3) were selected for further validation. Their expressions were all downregulated in HCC cells grown on different stiffness substrates after metformin intervention. More importantly, the degree of decrease was obviously weakened on the higher stiffness substrate compared with that on the lower stiffness substrate, indicating that these candidate membrane proteins might contribute to matrix stiffness-mediated metformin resistance in HCC. CONCLUSIONS There was an obvious change in membrane proteins in matrix stiffness-mediated metformin resistance in HCC cells. Six candidate membrane proteins may reflect the response of HCC cells under high stiffness stimulation to metformin intervention, which deserve to be investigated in the future.
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Affiliation(s)
- Xiangyu Gao
- Department of Endocrinology, Huashan Hospital, Fudan University, 12 Middle Urumqi Road, Shanghai, 200040, PR China
| | - Jiali Qian
- Department of Endocrinology, Huashan Hospital, Fudan University, 12 Middle Urumqi Road, Shanghai, 200040, PR China
| | - Yang Zhang
- Institute of Biomedical Science, Fudan University, 131 Dong' an Road, Shanghai, 200032, PR China
| | - Heming Wang
- Department of Gastroenterology, Zhongshan Hospital, Fudan University, 136 Yi Xue Yuan Road, Shanghai, 200032, PR China
| | - Jiefeng Cui
- Liver Cancer Institute, Zhongshan Hospital, Fudan University & Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, 136 Yi Xue Yuan Road, Shanghai, 200032, PR China.
| | - Yehong Yang
- Department of Endocrinology, Huashan Hospital, Fudan University, 12 Middle Urumqi Road, Shanghai, 200040, PR China.
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Li C, Chen Z, Deng Y, Jiang S, Su Y, Yang S, Lin Y, Tian D. iTRAQ-based protein profiling and functional identification of four genes involved in rice basal resistance against Magnaporthe oryzae in two contrasting rice genotypes. Stress Biol 2023; 3:39. [PMID: 37698658 PMCID: PMC10497467 DOI: 10.1007/s44154-023-00118-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 08/22/2023] [Indexed: 09/13/2023]
Abstract
Rice blast, caused by Magnaporthe oryzae, is one of the most destructive rice diseases. Developing blast-resistant rice cultivars represents the most economical and environmentally friend strategy for managing the disease. In our previous study, an isobaric tags for relative and absolute quantitation (iTRAQ)-based comparative protein quantification was carried out to investigate the resistance gene Piz-t gene-mediated resistance response to infection in two contrasting rice genotypes of the Piz-t transgenic Nipponbare line (NPB-Piz-t) and its wild-type Nipponbare (NPB). Here, from the comparisons of differentially expressed proteins (DEPs) of NPB-Piz-t to the avirulent isolate KJ201 (KJ201-Piz-t)and the virulent isolate RB22 (RB22-Piz-t) with mock-treated NPB-Piz-t (Mock-Piz-t), NPB to the virulent isolate KJ201(KJ201-NPB) and RB22 (RB22-NPB) with mock-treated NPB (Mock-NPB), 1, 1, and 6 common DEPs were, respectively, identified at 24, 48 and 72 h post-inoculation (hpi) in the susceptible comparisons of RB22-Pizt/Mock-Piz-t, KJ201-NPB/Mock-NPB, and RB22-NPB/Mock-NPB, involving in gi|54,290,836 and gi|59,800,021 were identified in the resistance comparison KJ201-Piz-t/Mock-Piz-t at 48 and 72 hpi respectively. Moreover, four genes of Os01g0138900 (gi|54,290,836), Os04g0659300 (gi|59,800,021), Os09g0315700 (gi|125,563,186) or Os04g0394200 (gi|21,740,743) were knocked out or overexpressed in NPB using gene over-expression and CRISPR/Cas9 technology, and results verified that the Os01g0138900 obviously affected the rice blast resistance. Further, expression and targeted metabolomics analysis illuminated the resistance response of cysteine-containing substances as gi|59,800,021 under blast infection. These results provide new targets for basal resistance gene identification and open avenues for developing novel rice blast resistant materials.
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Affiliation(s)
- Chenchen Li
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, Fujian, China
- College of Agriculture, College of Life Science, Fujian Agricultural and Forestry University, Fuzhou, 350002, China
| | - Ziqiang Chen
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, Fujian, China
| | - Yun Deng
- Nanping Institute of Agricultural Sciences, Fujian, China
| | - Shuyu Jiang
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, Fujian, China
- College of Agriculture, College of Life Science, Fujian Agricultural and Forestry University, Fuzhou, 350002, China
| | - Yan Su
- Nanping Institute of Agricultural Sciences, Fujian, China
| | - Shaohua Yang
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, Fujian, China
| | - Yan Lin
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, Fujian, China
| | - Dagang Tian
- Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, Fujian, China.
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25
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Yan M, Zheng H, Yan R, Lang L, Wang Q, Xiao B, Zhang D, Lin H, Jia Y, Pan S, Chen Q. Vinculin Identified as a Potential Biomarker in Hand-Arm Vibration Syndrome Based on iTRAQ and LC-MS/MS-Based Proteomic Analysis. J Proteome Res 2023; 22:2714-2726. [PMID: 37437295 PMCID: PMC10408646 DOI: 10.1021/acs.jproteome.3c00277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Indexed: 07/14/2023]
Abstract
Local vibration can induce vascular injuries, one example is the hand-arm vibration syndrome (HAVS) caused by hand-transmitted vibration (HTV). Little is known about the molecular mechanism of HAVS-induced vascular injuries. Herein, the iTRAQ (isobaric tags for relative and absolute quantitation) followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomics approach was applied to conduct the quantitative proteomic analysis of plasma from specimens with HTV exposure or HAVS diagnosis. Overall, 726 proteins were identified in iTRAQ. 37 proteins upregulated and 43 downregulated in HAVS. Moreover, 37 upregulated and 40 downregulated when comparing severe HAVS and mild HAVS. Among them, Vinculin (VCL) was found to be downregulated in the whole process of HAVS. The concentration of vinculin was further verified by ELISA, and the results suggested that the proteomics data was reliable. Bioinformative analyses were used, and those proteins mainly engaged in specific biological processes like binding, focal adhesion, and integrins. The potential of vinculin application in HAVS diagnosis was validated by the receiver operating characteristic curve.
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Affiliation(s)
- Maosheng Yan
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
- Department
of Public Health, Guangzhou Medical University, Guangzhou, Guangdong 510000, China
| | - Hanjun Zheng
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
- Department
of Public Health, Guangzhou Medical University, Guangzhou, Guangdong 510000, China
| | - Rong Yan
- The
Centers for Disease Control and Prevention of Haizhu District, Guangzhou, Guangdong 510230, China
| | - Li Lang
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
| | - Qia Wang
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
| | - Bin Xiao
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
| | - Danying Zhang
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
| | - Hansheng Lin
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
| | - Yanxia Jia
- Department
of Public Health, Shanxi Medical University, Tai Yuan, Shanxi 030000, China
| | - Siyu Pan
- Guangdong
Province Hospital for Occupational Disease Prevention and Treatment, Guangdong Provincial Key Laboratory of Occupational
Disease Prevention and Treatment, Guangzhou, Guangdong 510230, China
- Department
of Public Health, Guangdong Pharmaceutical
University, Guangzhou, Guangdong 510230, China
| | - Qingsong Chen
- Department
of Public Health, Guangdong Pharmaceutical
University, Guangzhou, Guangdong 510230, China
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26
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Borek S, Stefaniak S, Nuc K, Wojtyla Ł, Ratajczak E, Sitkiewicz E, Malinowska A, Świderska B, Wleklik K, Pietrowska-Borek M. Sugar Starvation Disrupts Lipid Breakdown by Inducing Autophagy in Embryonic Axes of Lupin ( Lupinus spp.) Germinating Seeds. Int J Mol Sci 2023; 24:11773. [PMID: 37511532 PMCID: PMC10380618 DOI: 10.3390/ijms241411773] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
Under nutrient deficiency or starvation conditions, the mobilization of storage compounds during seed germination is enhanced to primarily supply respiratory substrates and hence increase the potential of cell survival. Nevertheless, we found that, under sugar starvation conditions in isolated embryonic axes of white lupin (Lupinus albus L.) and Andean lupin (Lupinus mutabilis Sweet) cultured in vitro for 96 h, the disruption of lipid breakdown occurs, as was reflected in the higher lipid content in the sugar-starved (-S) than in the sucrose-fed (+S) axes. We postulate that pexophagy (autophagic degradation of the peroxisome-a key organelle in lipid catabolism) is one of the reasons for the disruption in lipid breakdown under starvation conditions. Evidence of pexophagy can be: (i) the higher transcript level of genes encoding proteins of pexophagy machinery, and (ii) the lower content of the peroxisome marker Pex14p and its increase caused by an autophagy inhibitor (concanamycin A) in -S axes in comparison to the +S axes. Additionally, based on ultrastructure observation, we documented that, under sugar starvation conditions lipophagy (autophagic degradation of whole lipid droplets) may also occur but this type of selective autophagy seems to be restricted under starvation conditions. Our results also show that autophagy occurs at the very early stages of plant growth and development, including the cells of embryonic seed organs, and allows cell survival under starvation conditions.
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Affiliation(s)
- Sławomir Borek
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Szymon Stefaniak
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Katarzyna Nuc
- Department of Biochemistry and Biotechnology, Faculty of Agronomy, Horticulture and Bioengineering, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
| | - Łukasz Wojtyla
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Ewelina Ratajczak
- Institute of Dendrology, Polish Academy of Sciences, Parkowa 5, 62-035 Kórnik, Poland
| | - Ewa Sitkiewicz
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Agata Malinowska
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Bianka Świderska
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Karolina Wleklik
- Department of Plant Physiology, Faculty of Biology, Adam Mickiewicz University Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Małgorzata Pietrowska-Borek
- Department of Biochemistry and Biotechnology, Faculty of Agronomy, Horticulture and Bioengineering, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland
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Guo J, Chen N, Tan F, Zhou J, Xiang H, Luo Y, Zhou Z. iTRAQ-based proteomic analysis of imiquimod in the treatment of ulcerative colitis. Am J Transl Res 2023; 15:4454-4466. [PMID: 37560232 PMCID: PMC10408506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/07/2023] [Indexed: 08/11/2023]
Abstract
OBJECTIVE In this study, we explored the potential mechanisms and the signaling pathways involved in the treatment of Ulcerative Colitis (UC) with imiquimod (IMQ). METHODS The UC mouse model was established by treating C57BL/6J mice with 3% Dextran Sulfate Sodium (DSS). Then, the UC-related symptoms were examined. Disease Activity Index (DAI) was estimated based on weight loss, stool consistency, and occult bleeding or hematochezia. Histological changes were evaluated by Hematoxylin and Eosin (H&E) staining. Furthermore, we used multiplexed Isobaric Tagging for Relative and Absolute Protein Quantification (iTRAQ) technique coupled with high-throughput liquid chromatography tandem mass spectrometry (LC-MS/MS) to determine the differentially expressed proteins (DEPs). RESULTS Administration of 3% DSS for 7 days induced acute colitis associated with diarrhea, hematochezia, weight loss, and colon shortening. However, after IMQ administration, almost all the above symptoms were improved by different degrees. Specifically, the DAI, histological disorder, and colon shortening were attenuated. In iTRAQ analysis, a total of 4170 proteins were identified with a high confidence (≥ 95% confidence). The numbers of DEPs between the normal and UC model mice, between the normal and the IMQ-treated therapy mice, as well as between the model and the therapy mice were 317, 253, and 209, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the DEPs involved in the complement and coagulation cascades were downregulated in IMQ-treated therapy group. CONCLUSIONS IMQ might ameliorate colitis by suppressing the complement and coagulation cascades pathway, which might serve as new therapeutic strategies for the treatment of patients with UC.
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Affiliation(s)
- Jinkun Guo
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Hubei Key Laboratory of Digestive System DiseaseWuhan 430060, Hubei, China
| | - Na Chen
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Hubei Key Laboratory of Digestive System DiseaseWuhan 430060, Hubei, China
| | - Feifei Tan
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Hubei Key Laboratory of Digestive System DiseaseWuhan 430060, Hubei, China
| | - Julan Zhou
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Hubei Key Laboratory of Digestive System DiseaseWuhan 430060, Hubei, China
| | - Hongyu Xiang
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Hubei Key Laboratory of Digestive System DiseaseWuhan 430060, Hubei, China
| | - Yu Luo
- Jingmen Hospital of Traditional Chinese MedicineJingmen 448001, Hubei, China
| | - Zhongyin Zhou
- Department of Gastroenterology, Renmin Hospital of Wuhan University, Hubei Key Laboratory of Digestive System DiseaseWuhan 430060, Hubei, China
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Zhang L, Hou M, Zhang X, Cao Y, Sun S, Zhu Z, Han S, Chen Y, Ku L, Duan C. Integrative transcriptome and proteome analysis reveals maize responses to Fusarium verticillioides infection inside the stalks. Mol Plant Pathol 2023; 24:693-710. [PMID: 36938972 PMCID: PMC10257047 DOI: 10.1111/mpp.13317] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 06/11/2023]
Abstract
Fusarium stalk rot caused by Fusarium verticillioides is one of the most devastating diseases of maize that causes significant yield losses and poses potential security concerns for foods worldwide. The underlying mechanisms of maize plants regulating defence against the disease remain poorly understood. Here, integrative proteomic and transcriptomic analyses were employed to identify pathogenesis-related protein genes by comparing differentially expressed proteins (DEPs) and differentially expressed genes (DEGs) in maize stalks after inoculation with F. verticillioides. Functional enrichment analysis showed that DEGs and DEPs were mainly enriched in glutathione metabolism, starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism, linoleic acid metabolism, and phenylpropanoid biosynthesis. Fourteen DEGs and DEGs that were highly elevated after inoculation with F. verticillioides were confirmed with parallel reaction monitoring and reverse transcription-quantitative PCR, demonstrating the accountability and reliability of proteomic and transcriptomic data. We also assessed the potential roles of defence-related genes ZmCTA1, ZmWIP1, and ZmLOX2, identified from the multi-omics analysis, during the process of F. verticillioides infection through virus-induced gene silencing. The elevation of stalk rot symptomatic characteristics in the silenced plants revealed their contribution to resistance. We further functionally characterized the roles of ZmLOX2 expression in the defence response of maize plants conditioning fungal invasion via the salicylic acid-dependent pathway. Collectively, this study provides a comprehensive analysis of transcriptome and proteome of maize stalks following F. verticillioides inoculation, and defence-related genes that could inform selection of new genes as targets in breeding strategies.
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Affiliation(s)
- Lili Zhang
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
- Institute of Cereal CropsHenan Academy of Agricultural SciencesZhengzhouChina
- College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Mengwei Hou
- Institute of Cereal CropsHenan Academy of Agricultural SciencesZhengzhouChina
| | - Xingrui Zhang
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yanyong Cao
- Institute of Cereal CropsHenan Academy of Agricultural SciencesZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Suli Sun
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Zhendong Zhu
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Shengbo Han
- Institute of Cereal CropsHenan Academy of Agricultural SciencesZhengzhouChina
- College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Yanhui Chen
- College of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Lixia Ku
- College of AgronomyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Canxing Duan
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
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Hu M, Zhang H, Kong L, Ma J, Wang T, Lu X, Guo Y, Zhang J, Guan R, Chu P. Comparative proteomic and physiological analyses reveal tribenuron-methyl phytotoxicity and nontarget-site resistance mechanisms in Brassica napus. Plant Cell Environ 2023; 46:2255-2272. [PMID: 37102754 DOI: 10.1111/pce.14598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/12/2023] [Accepted: 04/18/2023] [Indexed: 06/08/2023]
Abstract
The application of herbicides is the most effective strategy for weed control and the development of herbicide-resistant crops will facilitate the weed management. The acetolactate synthase-inhibiting herbicide, tribenuron-methyl (TBM), is broadly used for weed control. However, its application in rapeseed field is restricted since rapeseed is sensitive to TBM. Herein, an integrated study of cytological, physiological and proteomic analysis of the TBM-resistant rapeseed mutant M342 and its wild-type (WT) plants was conducted. After TBM spraying, M342 showed improved tolerance to TBM, and proteins implicated in non-target-site resistance (NTSR) to herbicides had a significantly higher level in M342 as compared with the WT. Differentially accumulated proteins (DAPs) between these two genotypes were enriched in glutathione metabolism and oxidoreduction coenzyme metabolic process, which protected the mutant from oxidative stress triggered by TBM. Important DAPs related to stress or defence response were up-accumulated in M342 regardless of the TBM treatment, which might serve as the constitutive part of NTSR to TBM. These results provide new clues for further exploration of the NTSR mechanism in plants and establish a theoretical basis for the development of herbicide-resistant crops.
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Affiliation(s)
- Maolong Hu
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Centre for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, China
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Hongkun Zhang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Centre for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Lingna Kong
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Centre for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Juanjuan Ma
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Ting Wang
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Xinyu Lu
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Institute of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Yue Guo
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Jiefu Zhang
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Rongzhan Guan
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Centre for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Pu Chu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Centre for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, China
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Ma X, Wang M, Wang J, Zhang Q, Pu S, Wang R, Yu S, Wang L, Pan Y. Dynamic Changes in Proteome during Yak Oocyte Maturation Analyzed Using iTRAQ Technology. Animals (Basel) 2023; 13:2085. [PMID: 37443883 DOI: 10.3390/ani13132085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
The aim of this study was to investigate protein regulation at different time points during the in vitro maturation of yak oocytes. Yak oocytes at GV, MI, and MII stages were collected during in vitro maturation, and differential proteomics sequencing was performed using iTRAQ technology. GO functional classification indicated that the differential proteins were closely associated with biological processes such as "metabolic processes", and molecular events such as "binding" molecular-function-related categories were active. KOG analysis showed that energy-metabolism-related activities were vigorous during oocyte development from the GV phase to MI phase, and genetic material preparation activities were more active when oocytes developed from the MI stage to MII stage. KEGG pathway analysis showed that the PPAR metabolic pathway, Hippo signaling pathway, and ECM-receptor interaction and metabolic pathway were enriched from the GV to the MI stages. The PI3K-Akt, TGF-β, and phagosome pathways were enriched from the MI stage to the MII stage. These results indicate that transient dynamic changes occurred in the proteome during the maturation of yak oocytes, and the physiological functions mediated by these were also different. The accurate identification of the differential proteins in the three stages of GV, MI, and MII was helpful in further analyzing the molecular regulatory mechanism of yak oocyte maturation.
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Affiliation(s)
- Xin Ma
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Province Livestock Embryo Engineering Research Center, Lanzhou 730070, China
| | - Meng Wang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Province Livestock Embryo Engineering Research Center, Lanzhou 730070, China
| | - Jinglei Wang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Province Livestock Embryo Engineering Research Center, Lanzhou 730070, China
| | - Qian Zhang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Province Livestock Embryo Engineering Research Center, Lanzhou 730070, China
| | - Sisi Pu
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Rui Wang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
| | - Sijiu Yu
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Province Livestock Embryo Engineering Research Center, Lanzhou 730070, China
| | - Libin Wang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Province Livestock Embryo Engineering Research Center, Lanzhou 730070, China
| | - Yangyang Pan
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Province Livestock Embryo Engineering Research Center, Lanzhou 730070, China
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Yang X, Jiang Z, He J, Shen L. iTRAQ-Based Quantitative Proteomics Unveils Protein Dynamics in the Root of Solanum melongena L. under Waterlogging Stress Conditions. Life (Basel) 2023; 13:1399. [PMID: 37374181 DOI: 10.3390/life13061399] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/10/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Waterlogging poses significant abiotic stress that endangers the survival of plants, including crops. In response, plants dramatically change their physiology to enhance their tolerance to waterlogging, such as proteome reconfiguration. Here, we utilized isobaric tags for the relative and absolute quantitation (iTRAQ)-based protein labeling technique to examine the proteomic changes induced by waterlogging in the roots of Solanum melongena L., a solanaceous plant. The plants were subjected to 6, 12, and 24 h of waterlogging stress at the flowering stage. Of the 4074 identified proteins, compared to the control, the abundance of the proteins increased and decreased in 165 and 78 proteins, respectively, in 6 h of treatments; 219 and 89 proteins, respectively, in 12 h of treatments; and 126 and 127 proteins, respectively, in 24 h of treatments. The majority of these differentially regulated proteins participated in processes such as energy metabolism, amino acid biosynthesis, signal transduction, and nitrogen metabolism. Fructose-bisphosphate aldolase and three alcohol dehydrogenase genes, in particular, were up- or down-regulated in waterlogging-treated Solanum melongena roots, suggesting that some proteins related to anaerobic metabolism (glycolysis and fermentation) may play vital roles in protecting its roots from waterlogging stress to enable long-term survival. Overall, this research not only offers a comprehensive dataset of protein alterations in waterlogged Solanum melongena roots but also insights into the mechanisms by which solanaceous plants adapt to waterlogging stress.
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Affiliation(s)
- Xu Yang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Zheng Jiang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Jie He
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Lei Shen
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
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Wu L, Gui M, Liu J, Cheng J, Li Z, Bao R, Chen X, Gong Y, Du G. Comparative Proteomic Analysis of Roots from a Wild Eggplant Species Solanum sisymbriifolium in Defense Response to Verticillium dahliae Inoculation. Genes (Basel) 2023; 14:1247. [PMID: 37372425 DOI: 10.3390/genes14061247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Eggplant verticillium wilt, caused by Verticillium spp., is a severe eggplant vascular disease. Solanum sisymbriifolium, a wild species of eggplant that is resistant to verticillium wilt, will be beneficial for genetically modifying eggplants. To better reveal the response of wild eggplant to verticillium wilt, proteomic analysis by iTRAQ technique was performed on roots of S. sisymbriifolium after exposure to Verticillium dahliae, and some selected proteins were also validated using parallel reaction monitoring (PRM). After inoculation with V. dahliae, the phenylalanine ammonia lyase (PAL) and superoxide dismutase (SOD) enzymes and the malondialdehyde (MDA) and soluble protein (SP) of S. sisymbriifolium roots all exhibited an increase in activity or content compared with that of the mock-inoculated plants, especially at 12 and 24 h post-inoculation (hpi). A total of 4890 proteins (47.04% of the proteins were from S. tuberosum and 25.56% were from S. lycopersicum according to the species annotation) were identified through iTRAQ and LC-MS/MS analysis. A total of 369 differentially expressed proteins (DEPs) (195 downregulated and 174 upregulated) were obtained by comparison of the control and treatment groups at 12 hpi, and 550 DEPs (466 downregulated and 84 upregulated) were obtained by comparison of the groups at 24 hpi. The most significant Gene Ontology (GO) enrichment terms at 12 hpi were regulation of translational initiation, oxidation-reduction, and single-organism metabolic process in the biological process group; cytoplasm and eukaryotic preinitiation complex in the cellular component group; and catalytic activity, oxidoreductase activity, and protein binding in the molecular function group. Small molecule metabolic, organophosphate metabolic, and coenzyme metabolic processes in the biological process group; the cytoplasm in the cellular component group; and catalytic activity and GTPase binding in the molecular function group were significant at 24 hpi. Then, KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis was performed, and 82 and 99 pathways (15 and 17, p-value < 0.05) were found to be enriched at 12 and 24 hpi, respectively. Selenocompound metabolism, ubiquinone, and other terpenoid-quinone biosyntheses, fatty acid biosynthesis, lysine biosynthesis, and the citrate cycle were the top five significant pathways at 12 hpi. Glycolysis/gluconeogenesis, biosynthesis of secondary metabolites, linoleic acid metabolism, pyruvate metabolism, and cyanoamino acid metabolism were the top five at 24 hpi. Some V. dahliae-resistance-related proteins, including phenylpropanoid-pathway-related proteins, stress and defense response proteins, plant-pathogen interaction pathway and pathogenesis-related proteins, cell wall organization and reinforcement-related proteins, phytohormones-signal-pathways-related proteins, and other defense-related proteins were identified. In conclusion, this is the first proteomic analysis of S. sisymbriifolium under V. dahliae stress.
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Affiliation(s)
- Liyan Wu
- Horticultural Institute of Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Min Gui
- Horticultural Institute of Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Jiaxun Liu
- Horticultural Institute of Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Jie Cheng
- Horticultural Institute of Yunnan Academy of Agricultural Sciences, Kunming 650205, China
- School of Agriculture, Yunnan University, Kunming 650500, China
| | - Zhibin Li
- Horticultural Institute of Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Rui Bao
- Horticultural Institute of Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Xia Chen
- Horticultural Institute of Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Yaju Gong
- Horticultural Institute of Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Guanghui Du
- School of Agriculture, Yunnan University, Kunming 650500, China
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Kumari M, Kapoor R, Devanna BN, Varshney S, Kamboj R, Rai AK, Sharma TR. iTRAQ based proteomic analysis of rice lines having single or stacked blast resistance genes: Pi54/ Pi54rh during incompatible interaction with Magnaporthe oryzae. Physiol Mol Biol Plants 2023; 29:871-887. [PMID: 37520805 PMCID: PMC10382468 DOI: 10.1007/s12298-023-01327-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 05/12/2023] [Accepted: 06/08/2023] [Indexed: 08/01/2023]
Abstract
Deployment of single or multiple blast resistance (R) genes in rice plant is considered to be the most promising approach to enhance resistance against blast disease caused by fungus Magnaporthe oryzae. At the proteome level, relatively little information about R gene mediated defence mechanisms for single and stacking resistance characteristics is available. The overall objective of this study is to look at the proteomics of rice plants that have R genes; Pi54, Pi54rh and stacked Pi54 + Pi54rh in response to rice blast infection. In this study 'isobaric tag for relative and absolute quantification' (iTRAQ)-based proteomics analysis was performed in rice plants at 72-h post inoculation with Magnaporthe oryzae and various differentially expressed proteins were identified in these three transgenic lines in comparison to wild type during resistance response to blast pathogen. Through STRING analysis, the observed proteins were further examined to anticipate their linked partners, and it was shown that several defense-related proteins were co-expressed. These proteins can be employed as targets in future rice resistance breeding against Magnaporthe oryzae. The current study is the first to report a proteomics investigation of rice lines that express single blast R gene Pi54, Pi54rh and stacked (Pi54 + Pi54rh) during incompatible interaction with Magnaporthe oryzae. The differentially expressed proteins indicated that secondary metabolites, reactive oxygen species-related proteins, phenylpropanoid, phytohormones and pathogenesis-related proteins have a substantial relationship with the defense response against Magnaporthe oryzae. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01327-3.
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Affiliation(s)
- Mandeep Kumari
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Vanasthali, Rajasthan India
| | - Ritu Kapoor
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab India
| | - B. N. Devanna
- ICAR-National Rice Research Institute, Cuttack, Odisha India
| | - Swati Varshney
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, Delhi India
| | - Richa Kamboj
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
- Department of Bioscience and Biotechnology, Banasthali Vidyapith, Vanasthali, Rajasthan India
| | - Amit Kumar Rai
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - T. R. Sharma
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
- Division of Crop Science, Indian Council of Agricultural Research, Krishi Bhavan, New Delhi, India
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Qian Z, Cong C, Li Y, Bi Y, He Q, Li T, Xia Y, Xu L, Mickael HK, Yu W, Liu J, Wei D, Huang F. Quantification of host proteomic responses to genotype 4 hepatitis E virus replication facilitated by pregnancy serum. Virol J 2023; 20:111. [PMID: 37264422 DOI: 10.1186/s12985-023-02080-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/23/2023] [Indexed: 06/03/2023] Open
Abstract
BACKGROUND Hepatitis E virus (HEV) infection is a common cause of acute hepatitis worldwide and causes approximately 30% case fatality rate among pregnant women. Pregnancy serum (PS), which contains a high concentration of estradiol, facilitates HEV replication in vitro through the suppression of the PI3K-AKT-mTOR and cAMPK-PKA-CREB signaling pathways. However, the proteomics of the complex host responses to HEV infection, especially how PS facilitates viral replication, remains unclear. METHODS In this study, the differences in the proteomics of HEV-infected HepG2 cells supplemented with fetal bovine serum (FBS) from those of HEV-infected HepG2 cells supplemented with serum from women in their third trimester of pregnancy were quantified by using isobaric tags for relative and absolute quantification technology. RESULTS A total of 1511 proteins were identified, among which 548 were defined as differentially expressed proteins (DEPs). HEV-infected cells supplemented with PS exhibited the most significant changes at the protein level. A total of 328 DEPs, including 66 up-regulated and 262 down-regulated proteins, were identified in HEV-infected cells supplemented with FBS, whereas 264 DEPs, including 201 up-regulated and 63 down-regulated proteins, were found in HEV-infected cells supplemented with PS. Subsequently, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses revealed that in HEV-infected cells, PS supplementation adjusted more host genes and signaling pathways than FBS supplementation. The DEPs involved in virus-host interaction participated in complex interactions, especially a large number of immune-related protein emerged in HEV-infected cells supplemented with PS. Three significant or interesting proteins, including filamin-A, thioredoxin, and cytochrome c, in HEV-infected cells were functionally verified. CONCLUSIONS The results of this study provide new and comprehensive insight for exploring virus-host interactions and will benefit future studies on the pathogenesis of HEV in pregnant women.
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Affiliation(s)
- Zhongyao Qian
- Medical School, Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Chao Cong
- Medical School, Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Yi Li
- Medical School, Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Yanhong Bi
- Medical School, Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Qiuxia He
- Medical School, Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Tengyuan Li
- Medical School, Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Yueping Xia
- Medical School, Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Liangheng Xu
- Medical School, Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Houfack K Mickael
- Medical School, Kunming University of Science and Technology, Kunming, People's Republic of China
| | - Wenhai Yu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, People's Republic of China.
| | - Jiankun Liu
- 920th Hospital of Joint Logistics Support Force of PLA, Kunming, People's Republic of China.
| | - Daqiao Wei
- Medical School, Kunming University of Science and Technology, Kunming, People's Republic of China.
| | - Fen Huang
- Medical School, Kunming University of Science and Technology, Kunming, People's Republic of China.
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Jain V, Akhtar J, Priya R, Sakhuja P, Goyal S, Agarwal AK, Ghose V, Polisetty RV, Sirdeshmukh R, Siraj F, Gautam P. Tissue proteome analysis for profiling proteins associated with lymph node metastasis in gallbladder cancer. BMC Cancer 2023; 23:402. [PMID: 37142981 PMCID: PMC10161508 DOI: 10.1186/s12885-023-10840-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 04/12/2023] [Indexed: 05/06/2023] Open
Abstract
Lymph node (LN) metastasis is the earliest sign of metastatic spread and an established predictor of poor outcome in gallbladder cancer (GBC). Patients with LN positive GBC have a significantly worse survival (median survival- 7 months) than patients with LN negative disease (median survival- ~ 23 months) in spite of standard treatment which includes extended surgery followed by chemotherapy, radiotherapy and targeted therapy. This study aims at understanding the underlying molecular processes associated with LN metastasis in GBC. Here, we used iTRAQ-based quantitative proteomic analysis using tissue cohort comprising of primary tumor of LN negative GBC (n = 3), LN positive GBC (n = 4) and non-tumor controls (Gallstone disease, n = 4), to identify proteins associated with LN metastasis. A total of 58 differentially expressed proteins (DEPs) were found to be specifically associated with LN positive GBC based on the criteria of p value ≤ 0.05, fold change ≥ 2 and unique peptides ≥ 2. These include the cytoskeleton and associated proteins such as keratin, type II cytoskeletal 7 (KRT7), keratin type I cytoskeletal 19 (KRT19), vimentin (VIM), sorcin (SRI) and nuclear proteins such as nucleophosmin Isoform 1 (NPM1), heterogeneous nuclear ribonucleoproteins A2/B1 isoform X1 (HNRNPA2B1). Some of them are reported to be involved in promoting cell invasion and metastasis. Bioinformatic analysis of the deregulated proteins in LN positive GBC using STRING database identified 'neutrophil degranulation' and 'HIF1 activation' to be among the top deregulated pathways. Western blot and IHC analysis showed a significant overexpression of KRT7 and SRI in LN positive GBC in comparison to LN negative GBC. KRT7, SRI and other proteins may be further explored for their diagnostics and therapeutic applications in LN positive GBC.
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Affiliation(s)
- Vaishali Jain
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India
- Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
| | - Javed Akhtar
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India
- Jamia Hamdard-Institute of Molecular Medicine, Jamia Hamdard, New Delhi, 110062, India
| | - Ratna Priya
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India
- Jamia Hamdard-Institute of Molecular Medicine, Jamia Hamdard, New Delhi, 110062, India
| | - Puja Sakhuja
- Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, 110002, India.
| | - Surbhi Goyal
- Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, 110002, India
| | - Anil Kumar Agarwal
- Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, 110002, India
| | - Vivek Ghose
- Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
- Institute of Bioinformatics, International Tech Park, Bangalore, 560066, India
| | - Ravindra Varma Polisetty
- Department of Biochemistry, Sri Venkateswara College, University of Delhi, New Delhi, 110021, India
| | - Ravi Sirdeshmukh
- Manipal Academy of Higher Education (MAHE), Manipal, 576104, India
- Institute of Bioinformatics, International Tech Park, Bangalore, 560066, India
| | - Fouzia Siraj
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India
| | - Poonam Gautam
- ICMR-National Institute of Pathology, Safdarjung Hospital Campus, New Delhi, 110029, India.
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Guo D, Zhang B, Wu D, Hu X, Tu H. Identification of PRTN3 as a novel biomarker for the diagnosis of early gastric cance. J Proteomics 2023; 277:104852. [PMID: 36804624 DOI: 10.1016/j.jprot.2023.104852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 02/04/2023] [Accepted: 02/10/2023] [Indexed: 02/18/2023]
Abstract
Gastric cancer (GC) remains one of the most common types of cancer worldwide and has a high mortality rate. However, tools for the early detection of gastric cancer are still lacking. Isobaric tagging for relative and absolute quantitation (iTRAQ) proteomic assays were conducted to identify and quantify the differentially expressed proteins (DEPs) in the gastric mucosal tissues of GC patients at different stages. Bioinformatics analysis was used to identify the pathways enriched among the DEPs and candidate marker proteins. The expression levels and distribution of candidate proteins were confirmed by parallel reaction monitoring (PRM) analysis. In this study, by using the iTRAQ quantitative proteomic strategy, we identified 727 and 502 DEPs that were upregulated in EGC vs. PGC and EGC vs. NGC, respectively. These DEPs were mainly involved in the innate immune response and RNA binding. PRTN3 was identified as a marker of early gastric cancer by Gene Ontology enrichment analysis. Furthermore, the PRM assay confirmed the significant overexpression of PRTN3 in EGC gastric mucosa compared to PGC and NGC mucosa. Our data demonstrated that PRTN3 in the gastric mucosa could be used as a novel biomarker to identify patients with early gastric cancer via endoscopy. SIGNIFICANCE: Gastric cancer remains one of the most common types of cancer worldwide and has a high mortality rate. Patients with progressive gastric cancer and gastroesophageal junction cancer have a poor prognosis, with a 5-year relative survival rate of 6%. Therefore, early detection and diagnosis of gastric cancer is a key step toward improving the survival rate. The present study identified PRTN3 as a marker of early gastric cancer by an iTRAQ quantitative proteomic strategy. The PRM assay confirmed the significant overexpression of PRTN3 in EGC gastric mucosa compared to PGC and NGC mucosa. This study discovered that PRTN3 in the gastric mucosa could be used as a novel biomarker to identify patients with early gastric cancer via endoscopy.
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Yang J, Yuan X, Hao Y, Shi X, Yang X, Yan W, Chen L, Zhang D, Shen C, Li D, Zhu Z, Liu X, Zheng H, Zhang K. Proteins in pregnant swine serum promote the African swine fever virus replication: an iTRAQ-based quantitative proteomic analysis. Virol J 2023; 20:54. [PMID: 36978180 PMCID: PMC10043535 DOI: 10.1186/s12985-023-02004-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 03/03/2023] [Indexed: 03/30/2023] Open
Abstract
African swine fever (ASF) is a severe infectious disease caused by the African swine fever virus (ASFV), seriously endangering the global pig industry. ASFV possesses a large genome, strong mutation ability, and complex immune escape mechanisms. Since the first case of ASF was reported in China in August 2018, it has had a significant impact on social economy and food safety. In the present study, pregnant swine serum (PSS) was found to promote viral replication; differentially expressed proteins (DEPs) in PSS were screened and identified using the isobaric tags for relative and absolute quantitation technology and compared with those in non-pregnant swine serum (NPSS). The DEPs were analyzed using Gene Ontology functional annotation, Kyoto Protocol Encyclopedia of Genes and Genome pathway enrichment, and protein-protein interaction networks. In addition, the DEPs were validated via western blot and RT-qPCR experiments. And the 342 of DEPs were identified in bone marrow-derived macrophages cultured with PSS compared with the NPSS. The 256 were upregulated and 86 of DEPs were downregulated. The primary biological functions of these DEPs involved signaling pathways that regulate cellular immune responses, growth cycles, and metabolism-related pathways. An overexpression experiment showed that the PCNA could promote ASFV replication whereas MASP1 and BST2 could inhibit it. These results further indicated that some protein molecules in PSS were involved in the regulation of ASFV replication. In the present study, the role of PSS in ASFV replication was analyzed using proteomics, and the study will be provided a basis for future detailed research on the pathogenic mechanism and host interactions of ASFV as well as new insights for the development of small-molecule compounds to inhibit ASFV.
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Affiliation(s)
- Jinke Yang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730000, China
| | - Xingguo Yuan
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730000, China
| | - Yu Hao
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730000, China
| | - Xijuan Shi
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730000, China
| | - Xing Yang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730000, China
| | - Wenqian Yan
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730000, China
| | - Lingling Chen
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730000, China
| | - Dajun Zhang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730000, China
| | - Chaochao Shen
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730000, China
| | - Dan Li
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730000, China
| | - Zixiang Zhu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730000, China
| | - Xiangtao Liu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730000, China
| | - Haixue Zheng
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730000, China.
| | - Keshan Zhang
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730000, China.
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Ni F, Chenling G, Fang H, Xun L, Xiaoye W, Yinsheng T, Mingguang H, Chuanhuo H. Analysis of differential proteins between non-capacitated and capacitated boar sperm and verification of the effect of phosphofructokinase on capacitation. Theriogenology 2023; 199:19-29. [PMID: 36682265 DOI: 10.1016/j.theriogenology.2022.12.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022]
Abstract
The objective of this study was to analyze the differences in the proteins in non-capacitated and capacitated boar sperm and to identify the functions of the differential proteins and key capacitation proteins of boar sperm before and after capacitation. Transwell chambers were used to separate capacitated sperm proteins using a unique polycarbonate membrane. Meanwhile, isotopic tags for relative and absolute quantification combined with LC‒MS/MS analysis were used for quantitative determination of differential proteins. Through the comparative analysis of different databases, 475 different proteins were identified in non-capacitated sperm and capacitated sperm, of which 303 were significantly upregulated and 172 were significantly downregulated. These differentially-expressed proteins are mainly involved in redox processes, cell biosynthesis processes and cell aromatic compound metabolism biological processes. They also participate in the signaling pathways of phosphorylation, ketone synthesis and degradation, most of which interact to varying degrees. Among these differentially-expressed proteins, phosphofructokinase attracted our attention as a potential capacitated protein. We further verified that phosphofructokinase can promote boar sperm capacitation by immunoblotting.
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da Camara N, Dubery IA, Piater LA. Proteome Analysis of Nicotiana tabacum Cells following Isonitrosoacetophenone Treatment Reveals Defence-Related Responses Associated with Priming. Plants (Basel) 2023; 12:1137. [PMID: 36903995 PMCID: PMC10005295 DOI: 10.3390/plants12051137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/25/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
Proteins play an essential regulatory role in the innate immune response of host plants following elicitation by either biotic or abiotic stresses. Isonitrosoacetophenone (INAP), an unusual oxime-containing stress metabolite, has been investigated as a chemical inducer of plant defence responses. Both transcriptomic and metabolomic studies of various INAP-treated plant systems have provided substantial insight into this compound's defence-inducing and priming capabilities. To complement previous 'omics' work in this regard, a proteomic approach of time-dependent responses to INAP was followed. As such, Nicotiana tabacum (N. tabacum) cell suspensions were induced with INAP and changes monitored over a 24-h period. Protein isolation and proteome analysis at 0, 8, 16 and 24 h post-treatment were performed using two-dimensional electrophoresis followed by the gel-free eight-plex isobaric tags for relative and absolute quantitation (iTRAQ) based on liquid chromatography and mass spectrometry. Of the identified differentially abundant proteins, 125 were determined to be significant and further investigated. INAP treatment elicited changes to the proteome that affected proteins from a wide range of functional categories: defence, biosynthesis, transport, DNA and transcription, metabolism and energy, translation and signalling and response regulation. The possible roles of the differentially synthesised proteins in these functional classes are discussed. Results indicate up-regulated defence-related activity within the investigated time period, further highlighting a role for proteomic changes in priming as induced by INAP treatment.
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Xu L, He Y, Yuan X, Liu K, Cui Y, Ma H, Ma C, Yu X. iTRAQ-based proteomic analysis reveals the underlying mechanism of postmortem tenderization of refrigerated porcine Longissimus thoracis et lumborum muscle. Meat Sci 2023; 197:109068. [PMID: 36495834 DOI: 10.1016/j.meatsci.2022.109068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/20/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022]
Abstract
The isobaric tags for relative and absolute quantitation (iTRAQ) technology was used for differential proteomic analysis of refrigerated porcine Longissimus thoracis et lumborum (LTL) muscle at different time points postmortem (45 min, 4 h, 8 h, 12 h, 24 h, 48 h, 72 h and 96 h) to mechanistically elucidate the postmortem tenderization. Compared with the proteins identified in porcine LTL muscle at 45 min postmortem (control), 862 proteins were significantly expressed at 4 h, 8 h, 12 h, 24 h, 48 h, 72 h and 96 h postmortem. Moreover, clustering and path analysis showed that the quality traits of porcine LTL muscle, including pH, shear force, myofibril fragmentation index, correlated significantly with 2, 6 and 6 differentially expressed proteins, respectively, with the lowest or highest expression at 8 h or 12 h postmortem. Overall, the tenderness of refrigerated porcine LTL muscle might be significantly affected by changes in quality traits at 8 h and 12 h postmortem.
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Shi Y, Huang C, Wang X, Jin W, Wang M, Yu H. Physiological and iTRAQ-based quantitative proteomics analyses reveal the similarities and differences in stress responses between short-term boron deficiency and toxicity in wheat roots. Mol Biol Rep 2023; 50:3617-3632. [PMID: 36795283 DOI: 10.1007/s11033-022-08123-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 11/15/2022] [Indexed: 02/17/2023]
Abstract
BACKGROUND Boron (B) is a trace element that is essential for normal wheat development, such as root growth. In wheat, roots are important organs that absorb nutrients and water. However, at present, there is insufficient research on the molecular mechanism underlying how short-term B stress affects wheat root growth. METHODS AND RESULTS Here, the optimal concentration of B for wheat root growth was determined, and the proteomic profiles of roots under short-term B deficiency and toxicity were analyzed and compared by the isobaric tag for relative and absolute quantitation (iTRAQ) technique. A total of 270 differentially abundant proteins (DAPs) that accumulated in response to B deficiency and 263 DAPs that accumulated in response to B toxicity were identified. Global expression analysis revealed that ethylene, auxin, abscisic acid (ABA), and Ca2+ signals were involved in the responses to these two stresses. Under B deficiency, DAPs related to auxin synthesis or signaling and DAPs involved in calcium signaling increased in abundance. In striking contrast, auxin and calcium signals were repressed under B toxicity. Twenty-one DAPs were detected under both conditions, including RAN1 that played a core role in the auxin and calcium signals. Overexpression of RAN1 was shown to confer plant resistance to B toxicity by activating auxin response genes, including TIR and those identified by iTRAQ in this research. Moreover, growth of the primary roots of tir mutant was significantly inhibited under B toxicity. CONCLUSION Taken together, these results indicate that some connections were present between RAN1 and the auxin signaling pathway under B toxicity. Therefore, this research provides data for improving the understanding of the molecular mechanism underlying the response to B stress.
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Affiliation(s)
- Yongchun Shi
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Chenhan Huang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Xiaoran Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Weihuan Jin
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Mengqing Wang
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China
| | - Haidong Yu
- College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, Henan, China.
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Nie Z, Kang G, Yan D, Qin H, Yang L, Zeng R. Downregulation of HbFPS1 affects rubber biosynthesis of Hevea brasiliensis suffering from tapping panel dryness. Plant J 2023; 113:504-520. [PMID: 36524729 PMCID: PMC10107253 DOI: 10.1111/tpj.16063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/01/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
Tapping panel dryness (TPD) is a century-old problem that has plagued the natural rubber production of Hevea brasiliensis. TPD may result from self-protective mechanisms of H. brasiliensis in response to stresses such as excessive hormone stimulation and mechanical wounding (bark tapping). It has been hypothesized that TPD impairs rubber biosynthesis; however, the underlying mechanisms remain poorly understood. In the present study, we firstly verified that TPD-affected rubber trees exhibited lower rubber biosynthesis activity and greater rubber molecular weight compared to healthy rubber trees. We then demonstrated that HbFPS1, a key gene of rubber biosynthesis, and its expression products were downregulated in the latex of TPD-affected rubber trees, as revealed by transcriptome sequencing and iTRAQ-based proteome analysis. We further discovered that the farnesyl diphosphate synthase HbFPS1 could be recruited to small rubber particles by HbSRPP1 through protein-protein interactions to catalyze farnesyl diphosphate (FPP) synthesis and facilitate rubber biosynthesis initiation. FPP content in the latex of TPD-affected rubber trees was significantly decreased with the downregulation of HbFPS1, ultimately resulting in abnormal development of rubber particles, decreased rubber biosynthesis activity, and increased rubber molecular weight. Upstream regulator assays indicated that a novel regulator, MYB2-like, may be an important regulator of downregulation of HbFPS1 in the latex of TPD-affected rubber trees. Our findings not only provide new directions for studying the molecular events involved in rubber biosynthesis and TPD syndrome and contribute to rubber management strategies, but also broaden our knowledge of plant isoprenoid metabolism and its regulatory networks.
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Affiliation(s)
- Zhiyi Nie
- Rubber Research Institute & Key Laboratory of Biology and Genetic Resources of Rubber treesMinistry of Agriculture and Rural Affairs of the People's Republic of China, Chinese Academy of Tropical Agricultural SciencesHaikou571101HainanChina
- Key Laboratory of Materials Engineering for High Performance Natural Rubber, Hainnan ProvinceChinese Academy of Tropical Agricultural SciencesHaikou571101HainanChina
| | - Guijuan Kang
- Rubber Research Institute & Key Laboratory of Biology and Genetic Resources of Rubber treesMinistry of Agriculture and Rural Affairs of the People's Republic of China, Chinese Academy of Tropical Agricultural SciencesHaikou571101HainanChina
- Key Laboratory of Materials Engineering for High Performance Natural Rubber, Hainnan ProvinceChinese Academy of Tropical Agricultural SciencesHaikou571101HainanChina
| | - Dong Yan
- Rubber Research Institute & Key Laboratory of Biology and Genetic Resources of Rubber treesMinistry of Agriculture and Rural Affairs of the People's Republic of China, Chinese Academy of Tropical Agricultural SciencesHaikou571101HainanChina
| | - Huaide Qin
- Rubber Research Institute & Key Laboratory of Biology and Genetic Resources of Rubber treesMinistry of Agriculture and Rural Affairs of the People's Republic of China, Chinese Academy of Tropical Agricultural SciencesHaikou571101HainanChina
- Key Laboratory of Materials Engineering for High Performance Natural Rubber, Hainnan ProvinceChinese Academy of Tropical Agricultural SciencesHaikou571101HainanChina
| | - Lifu Yang
- Institute of Scientific and Technical InformationChinese Academy of Tropical Agricultural SciencesHaikou571101HainanChina
| | - Rizhong Zeng
- Rubber Research Institute & Key Laboratory of Biology and Genetic Resources of Rubber treesMinistry of Agriculture and Rural Affairs of the People's Republic of China, Chinese Academy of Tropical Agricultural SciencesHaikou571101HainanChina
- Key Laboratory of Materials Engineering for High Performance Natural Rubber, Hainnan ProvinceChinese Academy of Tropical Agricultural SciencesHaikou571101HainanChina
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Chen J, Du X, Xu X, Zhang S, Yao L, He X, Wang Y. Comparative Proteomic Analysis Provides New Insights into the Molecular Basis of Thermal-Induced Parthenogenesis in Silkworm ( Bombyx mori). Insects 2023; 14:insects14020134. [PMID: 36835703 PMCID: PMC9962255 DOI: 10.3390/insects14020134] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/14/2023] [Accepted: 01/19/2023] [Indexed: 05/27/2023]
Abstract
Artificial parthenogenetic induction via thermal stimuli in silkworm is an important technique that has been used in sericultural production. However, the molecular mechanism underlying it remains largely unknown. We have created a fully parthenogenetic line (PL) with more than 85% occurrence and 80% hatching rate via hot water treatment and genetic selection, while the parent amphigenetic line (AL) has less than 30% pigmentation rate and less than 1% hatching rate when undergoing the same treatment. Here, isobaric tags for relative and absolute quantitation (iTRAQ)-based analysis were used to investigate the key proteins and pathways associated with silkworm parthenogenesis. We uncovered the unique proteomic features of unfertilized eggs in PL. In total, 274 increased abundance proteins and 211 decreased abundance proteins were identified relative to AL before thermal induction. Function analysis displayed an increased level of translation and metabolism in PL. After thermal induction, 97 increased abundance proteins and 187 decreased abundance proteins were identified. An increase in stress response-related proteins and decrease in energy metabolism suggested that PL has a more effective response to buffer the thermal stress than AL. Cell cycle-related proteins, including histones, and spindle-related proteins were decreased in PL, indicating an important role of this decrease in the process of ameiotic parthenogenesis.
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Affiliation(s)
- Jine Chen
- Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xin Du
- Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xia Xu
- Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Sheng Zhang
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Lusong Yao
- Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Xiuling He
- Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yongqiang Wang
- Institute of Sericulture and Tea, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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Zhao C, Zheng Z, Zhu S, Zhang L, Zhang P, Xiong H, Li Y, Zhu Y, Zhao M, Li J. iTRAQ and PRM-Based Comparative Proteomic Profiling of the Hippocampus in Rat Models of Epilepsy. J Integr Neurosci 2023; 22:21. [PMID: 36722232 DOI: 10.31083/j.jin2201021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/17/2022] [Accepted: 07/18/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Epilepsy is a disease caused by paroxysmal abnormal supersynchronous electrical activity of brain neurons, and it is also one of the most common illnesses in neurology. Among the causes, hippocampal sclerosis may be one of the main causes of temporal lobe epilepsy. However, the pathogenesis of hippocampal sclerosis in epilepsy remains unclear. METHODS We established an epilepsy model by intraperitoneal injection of pentetrazol (PTZ) into Sprague-Dawley rats, and applied isobaric tags for relative and absolute quantitation (iTRAQ) technology to identify differentially expressed proteins (DEPs) in the hippocampus. We quantified a total of 3782 proteins. DEPs were defined as proteins with a fold change >1.2 (or <0.83) and a Q value (p-adjusted) <0.05. RESULTS Comparing the epilepsy group and the control group, we identified 170 DEPs, comprising 109 upregulated and 61 downregulated proteins. According to bioinformatics analysis, the DEPs were primarily involved in long-term potentiation, the calcium signalling pathway, aldosterone synthesis and secretion, carbon metabolism, and dopaminergic synapses. Four of these proteins were validated using parallel reaction monitoring (PRM), including Glud1, Atp1a2, Prkcg and Arpc3. CONCLUSIONS Our research results may provide further insight into the molecular pathology of hippocampal injury in epilepsy.
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Affiliation(s)
- Congcong Zhao
- Department of Forensic Medicine, Chongqing Medical University, 400010 Chongqing, China
| | - Zhe Zheng
- Department of Forensic Medicine, Chongqing Medical University, 400010 Chongqing, China
| | - Shisheng Zhu
- Faculty of Medical Technology, Chongqing Medical and Pharmaceutical College, 401331 Chongqing, China.,Chongqing Engineering Research Center of Pharmaceutical Sciences, 401331 Chongqing, China
| | - Li Zhang
- Department of Forensic Medicine, Chongqing Medical University, 400010 Chongqing, China
| | - Peng Zhang
- Department of Forensic Medicine, Chongqing Medical University, 400010 Chongqing, China
| | - Hongli Xiong
- Department of Forensic Medicine, Chongqing Medical University, 400010 Chongqing, China
| | - Yongguo Li
- Department of Forensic Medicine, Chongqing Medical University, 400010 Chongqing, China
| | - Ying Zhu
- Department of Forensic Medicine, Chongqing Medical University, 400010 Chongqing, China
| | - Minzhu Zhao
- Department of Forensic Medicine, Chongqing Medical University, 400010 Chongqing, China
| | - Jianbo Li
- Department of Forensic Medicine, Chongqing Medical University, 400010 Chongqing, China
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Hu S, Sun Z, Li B, Zhao H, Wang Y, Yao G, Li X, Bian X, Li TC, Vankelecom H, Sun Y. iTRAQ-based Proteomic Analysis Unveils ACSL4 as a Novel Potential Regulator of Human Endometrial Receptivity. Endocrinology 2023; 164:6991315. [PMID: 36652382 DOI: 10.1210/endocr/bqad012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 01/19/2023]
Abstract
Competent endometrial receptivity is a prerequisite for successful embryo implantation. Identification of novel key molecules involved in endometrial receptivity is essential to better interpret human implantation and improve pregnancy rates in assisted reproduction treatment. Isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomics was performed to profile the proteomes of the prereceptive (luteinizing hormone [LH] + 2, n = 4) and receptive (LH + 7, n = 4) endometrial tissues. A total of 173 differentially expressed proteins (DEPs) between LH + 2 and LH + 7 endometrial samples were identified. Integrated analysis of the proteomic data and published transcriptomic data was performed to identify the concordant DEPs with differential expression at both the messenger RNA and protein levels. Protein-protein interaction (PPI) network analysis was performed on concordant DEPs. We first identified 63 novel concordant DEPs and 5 hub proteins (ACSL4, ACSL5, COL1A1, PTGS1, and PLA2G4F) between LH + 2 and LH + 7 endometrial samples. ACSL4 was predominantly expressed in endometrial epithelial cells and its expression was significantly upregulated by progesterone in the LH + 7 endometrium and significantly downregulated in repeated implantation failure patients. Knockdown of ACSL4 in endometrial epithelial cells induced the downregulation of endometrial receptivity markers (HOXA10, COX2, and LIF) and the significant decrease of implantation rate during in vitro implantation analysis. This study provides the first gel-independent quantitative proteomes of the LH + 2 and LH + 7 human endometrium using iTRAQ technology. The identified concordant DEPs and hub proteins open a new avenue for future studies aimed at elucidating the underlying mechanisms governing endometrial receptivity. ACSL4 was identified as a novel regulatory molecule in the establishment of endometrial receptivity and might play important roles during implantation.
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Affiliation(s)
- Shuanggang Hu
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Center for Reproductive Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200135, China
| | - Zhe Sun
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Center for Reproductive Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200135, China
| | - Boyu Li
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Center for Reproductive Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200135, China
| | - Hanting Zhao
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Center for Reproductive Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200135, China
| | - Yuan Wang
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Center for Reproductive Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200135, China
| | - Guangxin Yao
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Center for Reproductive Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200135, China
| | - Xinyu Li
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Center for Reproductive Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200135, China
| | - Xuejiao Bian
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Center for Reproductive Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200135, China
| | - Tin Chiu Li
- Department of Obstetrics and Gynaecology, Chinese University of Hong Kong, Hong Kong 999077, China
| | - Hugo Vankelecom
- Department of Development and Regeneration, Cluster Stem Cell Biology and Embryology, Research Unit of Stem Cell Research, University of Leuven (KU Leuven), B-3000 Leuven, Belgium
| | - Yun Sun
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Center for Reproductive Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200135, China
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Xu Q, Nie H, Dong S, Song J, Wang Q, Yan X. iTRAQ-based proteomic analysis reveals proteins associated with cold stress response in two different populations of Manila clam (Ruditapes philippinarum). Proteomics 2023; 23:e2100396. [PMID: 36607282 DOI: 10.1002/pmic.202100396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 12/18/2022] [Accepted: 12/21/2022] [Indexed: 01/07/2023]
Abstract
Water temperature is one of the key environmental factors for marine ectotherms and a change in temperature beyond and organism's capacity limits can cause a series of changes to physiological state and damage to the organism. Understanding how organisms adapt to complex environments is a central goal of evolutionary biology and ecology. Ruditapes philippinarum is an ecologically and scientifically important marine bivalve species. To uncover the molecular mechanisms of acclimation of R. philippinarum to low-temperature stress, iTRAQ-based quantitative proteomics was conducted to compare the proteomes of the north and south populations of R. philippinarum under low-temperature stress. The results showed a total of 6355 and 6352 proteins were identified in two populations, respectively. Among these, 94 and 83 were differentially abundant proteins (DAPs), and most of DAPs were related to oxidation-process, protein binding, or an integral component of membrane. According to the results of KEGG pathway enrichment analysis, most of DAPs in both populations are involved in immune-related pathways, while other population-specific significant abundance proteins of south population and north population were enriched in biosynthesis of amino acids (Enolase, Glutamine synthetase) and unsaturated fatty acids pathways (3-ketoacyl-CoA thiolase, Stearoyl-CoA desaturase), respectively, indicating that two population of clams may have different cold-stress regulation mechanisms. Our study provides new insights into different cold stress tolerance mechanisms in northern and southern populations of R. philippinarum using iTRAQ-based proteomics. This work contributes to a better understanding of molecular basis on cold stress response and adaptations, which shed lights on evolutionary biology and general ecophysiology of R. philippinarum.
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Affiliation(s)
- Qiaoyue Xu
- Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Hongtao Nie
- Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Shasha Dong
- Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
| | - Jun Song
- College of Marine Science and Environment, Dalian Ocean University, Dalian, China
| | - Qingzhi Wang
- Liaoning Ocean and Fisheries Science Research Institute and Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Dalian, China
| | - Xiwu Yan
- Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, College of Fisheries and Life Science, Dalian Ocean University, Dalian, China
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Akhtar J, Jain V, Kansal R, Priya R, Sakhuja P, Goyal S, Agarwal AK, Ghose V, Polisetty RV, Sirdeshmukh R, Kar S, Gautam P. Quantitative tissue proteome profile reveals neutrophil degranulation and remodeling of extracellular matrix proteins in early stage gallbladder cancer. Front Oncol 2023; 12:1046974. [PMID: 36686780 PMCID: PMC9853450 DOI: 10.3389/fonc.2022.1046974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 12/13/2022] [Indexed: 01/07/2023] Open
Abstract
Gallbladder cancer (GBC) is an aggressive malignancy of the gastrointestinal tract with a poor prognosis. It is important to understand the molecular processes associated with the pathogenesis of early stage GBC and identify proteins useful for diagnostic and therapeutic strategies. Here, we have carried out an iTRAQ-based quantitative proteomic analysis of tumor tissues from early stage GBC cases (stage I, n=7 and stage II, n=5) and non-tumor controls (n=6) from gallstone disease (GSD). We identified 357 differentially expressed proteins (DEPs) based on ≥ 2 unique peptides and ≥ 2 fold change with p value < 0.05. Pathway analysis using the STRING database showed, 'neutrophil degranulation' to be the major upregulated pathway that includes proteins such as MPO, PRTN3, S100A8, MMP9, DEFA1, AZU, and 'ECM organization' to be the major downregulated pathway that includes proteins such as COL14A1, COL1A2, COL6A1, COL6A2, COL6A3, BGN, DCN. Western blot and/or IHC analysis confirmed the elevated expression of MPO, PRTN3 and S100A8 in early stage of the disease. Based on the above results, we hypothesize that there is an increased neutrophil infiltration in tumor tissue and neutrophil degranulation leading to degradation of extracellular matrix (ECM) proteins promoting cancer cell invasion in the early stage GBC. Some of the proteins (MPO, MMP9, DEFA1) associated with 'neutrophil degranulation' showed the presence of 'signal sequence' suggesting their potential as circulatory markers for early detection of GBC. Overall, the study presents a protein dataset associated with early stage GBC.
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Affiliation(s)
- Javed Akhtar
- Laboratory of Molecular Oncology, Indian Council of Medical Research (ICMR) - National Institute of Pathology, New Delhi, India,Jamia Hamdard- Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Vaishali Jain
- Laboratory of Molecular Oncology, Indian Council of Medical Research (ICMR) - National Institute of Pathology, New Delhi, India,Department (Nil), Manipal Academy of Higher Education (MAHE), Manipal, India
| | - Radhika Kansal
- Laboratory of Molecular Oncology, Indian Council of Medical Research (ICMR) - National Institute of Pathology, New Delhi, India
| | - Ratna Priya
- Laboratory of Molecular Oncology, Indian Council of Medical Research (ICMR) - National Institute of Pathology, New Delhi, India,Jamia Hamdard- Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Puja Sakhuja
- Department of Pathology, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India,*Correspondence: Poonam Gautam, ; ; Puja Sakhuja,
| | - Surbhi Goyal
- Department of Pathology, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Anil Kumar Agarwal
- Department of Pathology, Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi, India
| | - Vivek Ghose
- Department (Nil), Manipal Academy of Higher Education (MAHE), Manipal, India,Institute of Bioinformatics, International Tech Park, Bangalore, India
| | | | - Ravi Sirdeshmukh
- Department (Nil), Manipal Academy of Higher Education (MAHE), Manipal, India,Institute of Bioinformatics, International Tech Park, Bangalore, India
| | - Sudeshna Kar
- Jamia Hamdard- Institute of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Poonam Gautam
- Laboratory of Molecular Oncology, Indian Council of Medical Research (ICMR) - National Institute of Pathology, New Delhi, India,*Correspondence: Poonam Gautam, ; ; Puja Sakhuja,
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Zhou G, Wang YS, Peng H, Li SJ, Sun TL, Shi QS, Garcia-Ojalvo J, Xie XB. Proteomic signatures of synergistic interactions in antimicrobials. J Proteomics 2023; 270:104743. [PMID: 36210012 DOI: 10.1016/j.jprot.2022.104743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/12/2022] [Accepted: 10/01/2022] [Indexed: 11/06/2022]
Abstract
Mounting evidence has shown that antimicrobial agents can interfere synergistically with bacterial viability and proliferation when acting together at both the planktonic and biofilm levels without clear underlying molecular mechanisms. Here, multiplexed proteomics by iTRAQ was used to study the interplay between two biocides, the isothiazolone 1,2-benzisothiazolin-3-one (BIT) and the chelating agent disodium ethylenediaminetetraacetic acid (EDTA-2Na), employing the Citrobacter werkmanii as a model system. We first confirmed that these two biocides act synergistically on this bacterial species and then extracted the proteomic profiles of C. werkmanii cells in the presence of BIT, EDTA-2Na, and their combinations. In particular, we identified 43 core proteins that are differentially expressed in all three conditions simultaneously. Meanwhile, we found that these core proteins are consistently up-regulated when these two biocides are present, but not for single biocides, where we found a balanced mix of up- and down-regulation. Meanwhile, most of the deletion mutants of the core DEPs exhibited biofilm growth inhibition under joint biocide action, while their response was very heterogenous, with respect to the wild-type strain. Together, our results show that while BIT and EDTA-2Na act on multiple protein targets, they interact synergistically at the protein level in a very consistent manner. SIGNIFICANCE: Our preliminary experiments have demonstrated that a combination of 1,2-benzisothiazolin-3-one (BIT) and EDTA-2Na shows higher inhibitory effects on planktonic growth and biofilm formation in both C. werkmanii and Staphylococcus aureus than when these two biocides act alone. However, the mechanistic basis of such synergistic interaction is still unknown. Therefore, the key proteins involved in the above-mentioned enhanced antimicrobial synergy were elucidated using multiplexed proteomics analysis by isobaric tags for relative and absolute quantification (iTRAQ). Our results reveal that the joint action of BIT and EDTA-2Na induces consistent protein expression alteration in a set of core proteins of C. werkmanii, which underlies a strong synergistic antimicrobial effect, which increase our understanding of the action modes of BIT and EDTA-2Na as well as their combinations.
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Affiliation(s)
- Gang Zhou
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong 510070, People's Republic of China; Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Dr. Aiguader 88, Barcelona, 08003, Spain.
| | - Ying-Si Wang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong 510070, People's Republic of China
| | - Hong Peng
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong 510070, People's Republic of China
| | - Su-Juan Li
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong 510070, People's Republic of China
| | - Ting-Li Sun
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong 510070, People's Republic of China
| | - Qing-Shan Shi
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong 510070, People's Republic of China.
| | - Jordi Garcia-Ojalvo
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona Biomedical Research Park (PRBB), Dr. Aiguader 88, Barcelona, 08003, Spain.
| | - Xiao-Bao Xie
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, Guangdong 510070, People's Republic of China.
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Huo J, Hu X, Bai J, Lv A. Multiomics analysis revealed miRNAs as potential regulators of the immune response in Carassius auratus gills to Aeromonas hydrophila infection. Front Immunol 2023; 14:1098455. [PMID: 36820086 PMCID: PMC9938762 DOI: 10.3389/fimmu.2023.1098455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/11/2023] [Indexed: 02/06/2023] Open
Abstract
The gill of fish is an important immune organ for pathogen defense, but its microRNA (miRNA) expression and regulatory mechanism remain unclear. In this study, we report on the histopathological and immunohistochemical features of the gills of the crucian carp Carassius auratus challenged with Aeromonas hydrophila. Small RNA libraries of the gills were constructed and sequenced on the Illumina HiSeq 2000 platform. A total of 1,165 differentially expressed miRNAs (DEMs) were identified in gills, of which 539 known and 7 unknown DEMs were significantly screened (p < 0.05). Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that the potential target genes/proteins were primarily involved in 33 immune-related pathways, in which the inflammatory responses were focused on the Toll-like receptor (TLR), mitogen-activated protein kinase (MAPK), and nuclear factor kappa B (NF-κB) signaling pathways. Moreover, the expression levels of 14 key miRNAs (e.g., miR-10, miR-17, miR-26a, miR-144, miR-145, and miR-146a) and their target genes (e.g., TNFα, TLR4, NF-κB, TAB1, PI3K, and IRAK1) were verified. In addition, the protein levels based on isobaric tags for relative and absolute quantification (iTRAQ) were significantly associated with the results of the quantitative real-time PCR (qRT-PCR) analysis (p < 0.01). miR-17/pre-miR-17 were identified in the regulation expression of the NF-κB target gene, and the phylogenetic tree analysis showed that the pre-miR-17 of C. auratus with the closest similarity to the zebrafish Danio rerio is highly conserved in teleosts. This is the first report of the multi-omics analysis of the miRNAs and proteins in the gills of C. auratus infected with A. hydrophila, thus enriching knowledge on the regulation mechanism of the local immune response in Cyprinidae fish.
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Affiliation(s)
- Jiaxin Huo
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, China
| | - Xiucai Hu
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, China
| | - Jie Bai
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, China
| | - Aijun Lv
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, College of Fisheries, Tianjin Agricultural University, Tianjin, China
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50
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Shi H, Liu S, Tan Z, Yin L, Zeng L, Liu T, Zhang S, Zhang L. Proteomic and metabonomic analysis uncovering Enterovirus A71 reprogramming host cell metabolic pathway. Proteomics 2023; 23:e2200362. [PMID: 36254857 DOI: 10.1002/pmic.202200362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/04/2022] [Indexed: 01/19/2023]
Abstract
Enterovirus A71 (EV71) infection can cause hand, foot, and mouth disease (HFMD) and severe neurological complications in children. However, the biological processes regulated by EV71 remain poorly understood. Herein, proteomics and metabonomics studies were conducted to uncover the mechanism of EV71 infection in rhabdomyosarcoma (RD) cells and identify potential drug targets. Differential expressed proteins from enriched membrane were analyzed by isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomics technology. Twenty-six differential proteins with 1.5-fold (p < 0.05) change were detected, including 14 upregulated proteins and 12 downregulated proteins. The upregulated proteins are mainly involved in metabolic process, especially in the glycolysis pathway. Alpha-enolase (ENO1) protein was found to increase with temporal dependence following EV71 infection. The targeted metabolomics analysis revealed that glucose absorption and glycolysis metabolites were increased after EV71 infection. The glycolysis pathway was inhibited by knocking down ENO1 or the use of a glycolysis inhibitor (dichloroacetic acid [DCA]); and we found that EV71 infection was inhibited by depleting ENO1 or using DCA. Our study indicates that EV71 may reprogram glucose metabolism by activating glycolysis, and EV71 infection can be inhibited by interrupting the glycolysis pathway. ENO1 may be a potential target against EV71, and DCA could act as an inhibitor of EV71.
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Affiliation(s)
- Huichun Shi
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Siyuan Liu
- The College of Information, Mechanical and Electrical Engineering, Shanghai Normal University, Shanghai, China
| | - Zhimi Tan
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Lin Yin
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Liyan Zeng
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Tiefu Liu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Shuye Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Lijun Zhang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
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