scholarly journals Novel Proteome and N-Glycoproteome of the Thermophilic Fungus Chaetomium thermophilum in Response to High Temperature

2021 ◽  
Vol 12 ◽  
Author(s):  
Jinpeng Gao ◽  
Qingchao Li ◽  
Duochuan Li
Keyword(s):  
Liquid Chromatography ◽  
High Temperature ◽  
Protein Complexes ◽  
Differentially Expressed ◽  
Temperature Adaptation ◽  
Thermophilic Fungi ◽  
Chaetomium Thermophilum ◽  
Liquid Chromatography Tandem Mass ◽  
Underlying Basis ◽  
Related Proteins

Thermophilic fungi are eukaryotic species that grow at high temperatures, but little is known about the underlying basis of thermophily at cell and molecular levels. Here the proteome and N-glycoproteome of Chaetomium thermophilum at varying culture temperatures (30, 50, and 55°C) were studied using hydrophilic interaction liquid chromatography enrichment and high-resolution liquid chromatography–tandem mass spectroscopy analysis. With respect to the proteome, the numbers of differentially expressed proteins were 1,274, 1,374, and 1,063 in T50/T30, T55/T30, and T55/T50, respectively. The upregulated proteins were involved in biological processes, such as protein folding and carbohydrate metabolism. Most downregulated proteins were involved in molecular functions, including structural constituents of the ribosome and other protein complexes. For the N-glycoproteome, the numbers of differentially expressed N-glycoproteins were 160, 176, and 128 in T50/T30, T55/T30, and T55/T50, respectively. The differential glycoproteins were mainly involved in various types of N-glycan biosynthesis, mRNA surveillance pathway, and protein processing in the endoplasmic reticulum. These results indicated that an efficient protein homeostasis pathway plays an essential role in the thermophily of C. thermophilum, and N-glycosylation is involved by affecting related proteins. This is the novel study to reveal thermophilic fungi’s physiological response to high-temperature adaptation using omics analysis, facilitating the exploration of the thermophily mechanism of thermophilic fungi.

scholarly journals Hemocyte proteome of the Lake Baikal endemic Eulimnogammarus verrucosus (Crustacea: Amphipoda) sheds light on immune-related proteins

2021 ◽  
Vol 66 (4) ◽  
Author(s):  
Elena Zolotovskaya ◽  
Anna Nazarova ◽  
Alexandra Saranchina ◽  
Andrei Mutin ◽  
Polina Drozdova ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Immune Response ◽  
Pattern Recognition ◽  
Antimicrobial Activity ◽  
Liquid Chromatography ◽  
Lake Baikal ◽  
Tandem Mass ◽  
Chromatography Tandem Mass Spectrometry ◽  
Liquid Chromatography Tandem Mass ◽  
Related Proteins

Hemocytes are cells circulating in the hemolymph and playing an important role in crustacean immunity. These cells not only function as phagocytes but also express immune compounds to the hemolymph. Here we obtained hemocyte proteome of the endemic amphipod (Amphipoda, Crustacea) Eulimnogammarus verrucosus from Lake Baikal, the first hemocyte proteome of an amphipod, using liquid chromatography/tandem mass spectrometry (LC-MS/MS). A total of 1152 unique proteins were discovered with LC-MS/MS. We discovered both proteins directly involved in the immune response, such as pattern recognition proteins (C-type lectins), and compounds with antimicrobial activity (ctenidin and anti-lipopolysaccharide factor/scygonadin). Moreover, hemocyanins which may act as a phenoloxidase and C-type lectins were among the most diverse protein groups in the hemocyte proteome. The obtained data can be useful for further studies of immune components and mechanisms in Baikal amphipods.

scholarly journals Integrated Proteotranscriptomics of Human Myometrium in Labor Landscape Reveals the Increased Molecular Associated With Inflammation Under Hypoxia Stress

2021 ◽  
Vol 12 ◽  
Author(s):  
Lina Chen ◽  
Lele Wang ◽  
Yihong Luo ◽  
Qian Huang ◽  
Kaiyuan Ji ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Differentially Expressed ◽  
Human Myometrium ◽  
Rna Seq ◽  
Hypoxia Stress ◽  
Data Independent Acquisition ◽  
Parallel Reaction Monitoring ◽  
Liquid Chromatography Tandem Mass ◽  
Related Proteins ◽  
Physiological And Biochemical

During labor, a variety of coordinated physiological and biochemical events cause the myometrium to transition from a quiescent to contractile state; the molecular mechanisms responsible for this transition, however, remain unclear. To better understand this transition at a molecular level, the global transcriptome and proteome of human myometrial samples in labor and those not in labor were investigated through RNA sequencing (RNA-seq) and quantitative liquid chromatography–tandem mass spectrometry (LC-MS/MS) via data-independent acquisition (DIA) and parallel reaction monitoring (PRM) methods. Furthermore, an integrated proteotranscriptomic analysis was performed to explore biological processes and pathway alterations during labor; this analysis identified 1,626 differentially expressed mRNAs (1,101 upregulated, 525 downregulated) and 135 differentially expressed proteins (97 upregulated, 38 downregulated) in myometrium between nonlabor and in labor groups. The comprehensive results of these analyses showed that the upregulated mRNAs and proteins increased inflammation under hypoxia stress in the myometrium under labor, and related proteins and cytokines were validated by PRM and Luminex assays. Our study confirmed the biological process of inflammation and hypoxia in laboring myometrium at the transcriptome and proteome levels and provided recourse to discover new molecular and biological changes during labor.

scholarly journals Quantitative LC–MS/MS uncovers the regulatory role of autophagy in immune thrombocytopenia

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Rui-Jie Sun ◽  
Dong-mei Yin ◽  
Dai Yuan ◽  
Shu-yan Liu ◽  
Jing-jing Zhu ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Immune Thrombocytopenia ◽  
Differentially Expressed ◽  
Haematopoietic Stem Cell ◽  
Bone Marrow Mononuclear Cell ◽  
Protein Protein Interaction ◽  
Healthy Donors ◽  
Liquid Chromatography Tandem Mass ◽  
Pathway Analyses ◽  
Related Proteins

Abstract Background Immune thrombocytopenia (ITP) is an autoimmune haemorrhagic disease whose pathogenesis is associated with bone marrow megakaryocyte maturation disorder and destruction of the haematopoietic stem cell microenvironment. Methods In this study, we report the qualitative and quantitative profiles of the ITP proteome. Liquid chromatography–tandem mass spectrometry (LC–MS/MS) was conducted to elucidate the protein profiles of clinical bone marrow mononuclear cell (BMMC) samples from ITP patients and healthy donors (controls). Gene Ontology (GO) and Kyoto Encyclopaedia Genes and Genome (KEGG) pathway analyses were performed to annotate the differentially expressed proteins. A protein–protein interaction (PPI) network was constructed with the BLAST online database. Target proteins associated with autophagy were quantitatively identified by parallel reaction monitoring (PRM) analysis. Results Our approaches showed that the differentially expressed autophagy-related proteins, namely, HSPA8, PARK7, YWHAH, ITGB3 and CSF1R, were changed the most. The protein expression of CSF1R in ITP patients was higher than that in controls, while other autophagy-related proteins were expressed at lower levels in ITP patients than in controls. Conclusion Bioinformatics analysis indicated that disruption of the autophagy pathway is a potential pathological mechanism of ITP. These results can provide a new direction for exploring the molecular mechanism of ITP.

scholarly journals Quantitative LC-MS/MS Uncovers The Regulatory Role of Autophagy in Immune Thrombocytopenia

2020 ◽  
Author(s):  
Rui-Jie Sun ◽  
Dai Yuan ◽  
Dong-mei Yin ◽  
Shu-yan Liu ◽  
Jing-jing Zhu ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Immune Thrombocytopenia ◽  
Differentially Expressed ◽  
Bone Marrow Mononuclear Cell ◽  
Protein Protein Interaction ◽  
Parallel Reaction Monitoring ◽  
Liquid Chromatography Tandem Mass ◽  
Pathway Analyses ◽  
Haemorrhagic Disease ◽  
Related Proteins

Abstract Background: Immune thrombocytopenia (ITP) is an autoimmune haemorrhagic disease whose pathogenesis is associated with bone marrow megakaryocyte maturation disorder and microenvironment destruction of haematopoietic stem cells.Method: In this study, we report the qualitative and quantitative profile of the proteome in ITP. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was conducted to detect the protein profiles in clinical bone marrow mononuclear cell (BMMC) samples from ITP patients and healthy volunteers (controls). Gene Ontology (GO) and Kyoto Encyclopedia Genes and Genome (KEGG) pathway analyses were performed for the annotation of differentially expressed proteins. The protein-protein interaction (PPI) network was constructed with the BLAST online database. Target proteins associated with autophagy were quantitatively identified by parallel reaction monitoring (PRM) analysis.Results: Our approaches showed that of the differentially expressed autophagy-related proteins, namely, HSPA8, PARK7, YWHAH, ITGB3 and CSF1R, were the most changed. The expression of the CSF1R protein in ITP patients was higher than that in controls, while the expression of other autophagy-related proteins was lower in ITP patients than in controls.Conclusion: Bioinformatics analysis indicated that the abnormal autophagy pathway is a potential pathological mechanism of ITP. These results can provide a new direction for exploring the molecular mechanism of ITP.

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