scholarly journals Comparative Proteomic Analysis of Erythropoiesis Tissue Head Kidney Among three Antarctic Fish Species

2021 ◽  
Author(s):  
Ruonan Jia ◽  
Shaojun Huang ◽  
Wanying Zhai ◽  
Shouwen Jiang ◽  
Wenhao Li ◽  
...  
Keyword(s):  
Antarctic Fish ◽  
Head Kidney ◽  
Integrated Approach ◽  
Tandem Mass ◽  
Clear Trend ◽  
Marker Proteins ◽  
Tandem Mass Tag ◽  
Liquid Chromatography Tandem Mass ◽  
Lineage Marker ◽  
Antarctic Icefish

Abstract Antarctic icefish is the only known vertebrate species that lacks oxygen-carrying hemoglobin and functional erythrocytes. To reveal the unique hematopoietic process of icefish, we used an integrated approach including tandem mass tag (TMT) labeling and liquid chromatography-tandem mass spectrometry (LC-MS/MS) to quantify the dynamic changes in the head kidney whole proteome of a white-blooded icefish, Chionodraco hamatus, compared to those in two other red-blooded Antarctic fish, Trematomus bernacchii and Notothenia coriiceps. Of the 4,672 identified proteins, in the Antarctic ice fish head kidney, 123 proteins were significantly up-regulated and 95 proteins were down-regulated. The functional grouping of differentially expressed proteins based on KEGG pathway analysis shows that white blood fish and red blood fish have significant differences in erythropoiesis, heme biogenesis, leucocyte and platelet cell development. The proteins involved in the hematopoietic process in icefish showed a clear trend of downregulation of erythroid lineage marker proteins and upregulation of lymphoid and megakaryocytic lineage marker proteins, including CD9, ITGB2, and MTOR, which suggests a shift in hematopoiesis in the icefish head kidney due to the loss of erythrocytes. The results of the present study not only provide basic datasets for the head kidney proteins of Antarctic fishes, but also provide important references for studies on immunity and hematopoiesis in various species.

Phosphoproteome Reveals the Lactation Mechanism in Caprine Mammary Gland Tissues in Peak and Late Lactation Stages

2020 ◽  
Author(s):  
Chao Zhu ◽  
Hao Yin ◽  
Quyu Duan ◽  
Fu Li ◽  
Yue Jiang ◽  
...  
Keyword(s):  
Protein Phosphorylation ◽  
Calcium Signalling ◽  
Enrichment Analysis ◽  
Protein Translation ◽  
Integrated Approach ◽  
Rna Degradation ◽  
Signalling Pathway ◽  
Tandem Mass ◽  
Mapk Signalling Pathway ◽  
Tandem Mass Tag

Abstract Background: Protein phosphorylation plays an important role in lactation. Differentially modified modification sites between peak lactation (PL, 90 days postpartum) and late lactation (LL, 280 days postpartum) were investigated using an integrated approach, namely, liquid chromatography with tandem mass spectrometry (LC-MS/MS) and tandem mass tag (TMT) labelling, to understand the molecular biological mechanisms in goat breast tissues.Results: A total of 1,938 (1,111 up-regulated, 827 down-regulated) differentially modified modification sites of 1,172 proteins were identified (P values < 0.05 and fold change of phosphorylation ratios > 1.5). In addition, the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that ribosome (chx03010), RNA transport (chx03013), protein export (chx03060), calcium signalling pathway (chx04020), oxytocin signalling pathway (chx04921), RNA degradation (chx03018) and MAPK signalling pathway (chx04010) were enriched in relation to energy metabolism and protein translation. The results of western blot showed phosphorylation levels of ACACA, EIF4EBP1 and IRS1 increased and JUN decreased in PL compared with LL. The result was consistent with phosphoproteome. Conclusions: Overall, these data indicate that protein phosphorylation is closely related to lactation and differentially modified modification sites might have potential research value in the regulation of goat lactation.

scholarly journals Fumonisin B1-Induced Changes in Cotton Fiber Elongation Revealed by Sphingolipidomics and Proteomics

Biomolecules ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1258
Author(s):  
Li Wang ◽  
Chen Liu ◽  
Yujie Liu ◽  
Ming Luo
Keyword(s):  
Cotton Fiber ◽  
Fumonisin B1 ◽  
Tandem Mass ◽  
Fiber Elongation ◽  
Synthesis Inhibitor ◽  
Tandem Mass Tag ◽  
Liquid Chromatography Tandem Mass ◽  
Membrane Components ◽  
Induced Changes ◽  
Complex Sphingolipids

Sphingolipids are essential biomolecules and membrane components, but their regulatory role in cotton fiber development is poorly understood. Here, we found that fumonisin B1 (FB1)—a sphingolipid synthesis inhibitor—could block fiber elongation severely. Using liquid chromatography tandem mass spectrometry (LC-MS/MS), we detected 95 sphingolipids that were altered by FB1 treatment; of these, 29 (mainly simple sphingolipids) were significantly increased, while 33 (mostly complex sphingolipids) were significantly decreased. A quantitative analysis of the global proteome, using an integrated quantitative approach with tandem mass tag (TMT) labeling and LC-MS/MS, indicated the upregulation of 633 and the downregulation of 672 proteins after FB1 treatment. Most differentially expressed proteins (DEPs) were involved in processes related to phenylpropanoid and flavonoid biosynthesis. In addition, up to 20 peroxidases (POD) were found to be upregulated, and POD activity was also increased by the inhibitor. To our knowledge, this is the first report on the effects of FB1 treatment on cotton fiber and ovule sphingolipidomics and proteomics. Our findings provide target metabolites and biological pathways for cotton fiber improvement.

Proteomic Analysis of Differentially Expressed Proteins in Mycobacterium Tuberculosis- Infected Macrophages

2019 ◽  
Vol 17 ◽  
Author(s):  
Shuang Tian ◽  
Dongjun Yang ◽  
Qian Long ◽  
Min Ling
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Differentially Expressed ◽  
Tandem Mass ◽  
Differentially Expressed Proteins ◽  
Cellular Processes ◽  
Tandem Mass Tag ◽  
Proliferation And Apoptosis ◽  
Liquid Chromatography Tandem Mass ◽  
Infected Cells ◽  
Cellular Components

: Mycobacterium tuberculosis (MTB) and Mycobacterium avium (MA) belong to the intracellular parasitic bacteria. To better understand how MTB survives in macrophages and the different pathogenic mechanisms of MTB and MA, the tandem mass tag (TMT) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) were used for analysis of the differentially expressed proteins in MTB-infected macrophages and MA-infected macrophages. A total of 682 proteins were found to be differentially expressed in MTB-infected cells in comparison with MA-infected cells. Gene Ontology annotation revealed the involvement of 682 differentially expressed proteins in cellular components, biological processes and molecular functions including binding, catalytic activity, metabolic processes, cellular processes, cell part, cell proliferation and apoptosis, etc. Among these, 10 proteins (O60812, P06576, O43660-2, E9PL10, O00442, M0R050, Q9H8H0, Q9BSJ8, P41240 and Q8TD57-3) were down-regulated in MTB-infected cells. We found that M0R050, O00442, Q9H8H0, O60812 and O43660 are interactive proteins which participate in a multitude of cellular RNA processing, suggesting that these five down-regulated proteins might repress the synthesis of some resistant proteins in MTB-infected cells to promote MTB survival in macrophages.

scholarly journals Novel targets identified by integrated proteomic and phosphoproteomic analysis in spermatogenesis of swamp buffalo (Bubalus bubalis)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Yu-lin Huang ◽  
Peng-fei Zhang ◽  
Qiang Fu ◽  
Weng-tan He ◽  
Kai Xiao ◽  
...  
Keyword(s):  
Physiological Mechanism ◽  
Bubalus Bubalis ◽  
Tandem Mass ◽  
Chromatography Tandem Mass Spectrometry ◽  
Fiber Protein ◽  
Tandem Mass Tag ◽  
Tripartite Motif ◽  
Liquid Chromatography Tandem Mass ◽  
Swamp Buffalo ◽  
Reproductive Processes

Abstract To understand mechanisms of spermatogenesis, the proteome and the phosphoproteome in prepubertal and pubertal swamp buffalo (Bubalus bubalis) testes were analyzed using tandem mass tag (TMT) coupled with liquid chromatography-tandem mass spectrometry (LC–MS/MS). In prepubertal testes, 80 proteins were overexpressed, 148 proteins were underexpressed, and 139 and 142 protein sites had higher and lower phosphorylation, respectively, compared to the levels in pubertal testes. Several of these proteins were associated with reproductive processes such as sexual reproduction, spermatogenesis, fertilization, and spermatid development. In particular, outer dense fiber protein 1 (ODF1), protein maelstrom homolog (MAEL), actin-like protein 7B (ACTL7B), tyrosine-(Y)-phosphorylation regulated (CABYR), and tripartite motif containing 36 (TRIM36) were upregulated with age at both the proteome and phosphoproteome levels. Combining proteome and phosphoproteome analysis can be effectively applied to study the protein/phosphorylation patterns of buffalo testes. These data provide new regulatory candidates and evidence for a complex network in spermatogenesis in buffalo testes, and serve as an important resource for exploring the physiological mechanism of spermatogenesis in mammals.

scholarly journals Tandem Mass Tag-Based Quantitative Proteomic Analysis of Chicken Bursa of Fabricius Infected With Reticuloendotheliosis Virus

2021 ◽  
Vol 8 ◽  
Author(s):  
Dahan Yang ◽  
Xiaoping Lv ◽  
Shujun Zhang ◽  
Shimin Zheng
Keyword(s):  
Antigen Processing ◽  
Bursa Of Fabricius ◽  
Receptor Interaction ◽  
Tandem Mass ◽  
Reticuloendotheliosis Virus ◽  
Biological Regulation ◽  
Tandem Mass Tag ◽  
Before And After ◽  
Liquid Chromatography Tandem Mass ◽  
Mass Tag

Reticuloendotheliosis virus (REV) is a type C avian retrovirus that causes immunosuppression, dwarf syndrome, and lymphoma in infected hosts. In this study, we used tandem mass tag (TMT) labeling and liquid chromatography–tandem mass spectrometry (LC-MS/MS) to characterize protein alterations in chicken bursa of Fabricius, before and after REV infection at 7, 14, 21, and 28 days. Our data showed that 1,127, 999, 910, and 1,138 differentially expressed proteins were significantly altered at 7, 14, 21, and 28 days after REV infection, respectively. Morphological analysis showed that REV infection reduced in cortical lymphocytes, bursal follicle atrophy, and nuclear damage. Bioinformatics analysis indicated these proteins were mainly involved with immune responses, energy metabolism, cellular processes, biological regulation, metabolic processes, response to stimuli, and multicellular organismal process. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway cluster analysis showed that post-infection, proteins were enriched in the cell cycle, Wnt signaling, antigen processing and presentation, cytokine receptor interaction, adenosine 3′,5′-cyclic monophosphate signaling pathway, and NF-κB signaling. In addition, we observed that peroxiredoxin 4 (PRDX4), peroxiredoxin 6 (PRDX6), glutathione peroxidase 3 (GPX3), catalase (CAT), and peroxidasin (PXDN) were involved in oxidative stress. Some heat shock protein (HSP) family members such as HSPH1, DNAJA4, HSPA8, and HSPA4L also changed significantly after REV infection. These findings help clarify interactions between REV and the host and provides mechanistic insights on REV-induced host immunosuppression.

scholarly journals Tandem Mass Tag labelling quantitative acetylome analysis of differentially modified proteins during mycoparasitism of Clonostachys chloroleuca 67–1

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Na Jiang ◽  
Binna Lv ◽  
Haixia Wu ◽  
Shidong Li ◽  
Manhong Sun
Keyword(s):  
Fungal Pathogens ◽  
Molecular Mechanisms ◽  
Tandem Mass ◽  
The Novel ◽  
Post Translational Modification ◽  
Bioinformatics Analyses ◽  
Tandem Mass Tag ◽  
Liquid Chromatography Tandem Mass ◽  
Insight Into ◽  
Mass Tag

AbstractLysine acetylation (Kac) is an important post-translational modification (PTM) of proteins in all organisms, but its functions have not been extensively explored in filamentous fungi. In this study, a Tandem Mass Tag (TMT) labelling lysine acetylome was constructed, and differentially modified Kac proteins were quantified during mycoparasitism and vegetative growth in the biocontrol fungus Clonostachys chloroleuca 67–1, using liquid chromatography-tandem mass spectrometry (LC–MS/MS). A total of 1448 Kac sites were detected on 740 Kac proteins, among which 126 sites on 103 proteins were differentially regulated. Systematic bioinformatics analyses indicate that the modified Kac proteins were from multiple subcellular localizations and involved in diverse functions including chromatin assembly, glycometabolism and redox activities. All Kac sites were characterized by 10 motifs, including the novel CxxKac motif. The results suggest that Kac proteins may have effects of broadly regulating protein interaction networks during C. chloroleuca parasitism to Sclerotinia sclerotiorum sclerotia. This is the first report of a correlation between Kac events and the biocontrol activity of C. chloroleuca. Our findings provide insight into the molecular mechanisms underlying C. chloroleuca control of plant fungal pathogens regulated by Kac proteins.

scholarly journals Analysis of Differentially Expressed Proteins in Mycobacterium avium-Infected Macrophages Comparing with Mycobacterium tuberculosis-Infected Macrophages

2017 ◽  
Vol 2017 ◽  
pp. 1-9 ◽  
Author(s):  
Dongjun Yang ◽  
Xin Fu ◽  
Shiyi He ◽  
Xueping Ning ◽  
Min Ling
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Mycobacterium Avium ◽  
Biological Process ◽  
Differentially Expressed ◽  
Tandem Mass ◽  
Chromatography Tandem Mass Spectrometry ◽  
Tandem Mass Tag ◽  
Liquid Chromatography Tandem Mass ◽  
Infected Cells ◽  
Multiple Signaling

Mycobacterium avium (MA) belongs to the intracellular parasitic bacteria. To better understand how MA survives within macrophages and the different pathogenic mechanisms of MA and Mycobacterium tuberculosis (MTB), tandem mass tag (TMT) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis have been used to determine the proteins which are differentially expressed in MA-infected and MTB-infected macrophages. 369 proteins were found to be differentially expressed in MA-infected cells but not in MTB-infected cells. By using certain bioinformatics methods, we found the 369 proteins were involved in molecular function, biological process, and cellular component including binding, catalytic activity, metabolic process, cellular process, and cell part. In addition, some identified proteins were involved in multiple signaling pathways. These results suggest that MA probably survive within macrophages by affecting the expression of some crucial proteins.

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