scholarly journals TMT-based quantitative proteomics analysis reveals the key proteins related with the differentiation process of goat intramuscular adipocytes

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Yu Du ◽  
Yong Wang ◽  
Qing Xu ◽  
Jiangjiang Zhu ◽  
Yaqiu Lin
Keyword(s):  
Cholesterol Metabolism ◽  
Interaction Network ◽  
Mass Spectrometry Analysis ◽  
Signal Pathways ◽  
Differentiation Process ◽  
Spectrometry Analysis ◽  
Protein Protein Interaction ◽  
Network Analyses ◽  
Protein Factor ◽  
Tandem Mass Tag

Abstract Background Intramuscular adipocytes differentiation is a complex process, which is regulated by various transcription factor, protein factor regulators and signal transduction pathways. However, the proteins and signal pathways that regulates goat intramuscular adipocytes differentiation remains unclear. Result In this study, based on nanoscale liquid chromatography mass spectrometry analysis (LC-MS/MS), the tandem mass tag (TMT) labeling analysis was used to investigate the differentially abundant proteins (DAPs) related with the differentiation process of goat intramuscular adipocytes. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes enrichment and protein-protein interaction network analyses were performed for the characterization of the identified DAPs. The candidate proteins were verified by parallel reaction monitoring analysis. As a result, a total of 123 proteins, 70 upregulation proteins and 53 downregulation proteins, were identified as DAPs which may be related with the differentiation process of goat intramuscular adipocytes. Furthermore, the cholesterol metabolism pathway, glucagon signaling pathway and glycolysis / gluconeogenesis pathway were noticed that may be the important signal pathways for goat Intramuscular adipocytes differentiation. Conclusions By proteomic comparison between goat intramuscular preadipocytes (P_IMA) and intramuscular adipocytes (IMA), we identified a series protein that might play important role in the goat intramuscular fat differentiation, such as SRSF10, CSRP3, APOH, PPP3R1, CRTC2, FOS, SERPINE1 and AIF1L, could serve as candidates for further elucidate the molecular mechanism of IMF differentiation in goats.

scholarly journals Evidence for Direct Protein-Protein Interaction between Members of the Enterobacterial Hha/YmoA and H-NS Families of Proteins

2002 ◽  
Vol 184 (3) ◽  
pp. 629-635 ◽  
Author(s):  
J. M. Nieto ◽  
C. Madrid ◽  
E. Miquelay ◽  
J. L. Parra ◽  
S. Rodríguez ◽  
...  
Keyword(s):  
Recombinant Protein ◽  
Protein A ◽  
Nitrilotriacetic Acid ◽  
Mass Spectrometry Analysis ◽  
Spectrometry Analysis ◽  
E Coli ◽  
Protein Protein Interaction ◽  
New Family ◽  
Missense Mutant ◽  
First Time

ABSTRACT Escherichia coli nucleoid-associated H-NS protein interacts with the Hha protein, a member of a new family of global modulators that also includes the YmoA protein from Yersinia enterocolitica. This interaction has been found to be involved in the regulation of the expression of the toxin α-hemolysin. In this study, we further characterize the interaction between H-NS and Hha. We show that the presence of DNA in preparations of copurified His-Hha and H-NS is not directly implicated in the interaction between the proteins. The precise molecular mass of the H-NS protein retained by Hha, obtained by mass spectrometry analysis, does not show any posttranslational modification other than removal of the N-terminal Met residue. We constructed an H-NS-His recombinant protein and found that, as expected, it interacts with Hha. We used a Ni2+-nitrilotriacetic acid agarose method for affinity chromatography copurification of proteins to identify the H-NS protein of Y. enterocolitica. We constructed a six-His-YmoA recombinant protein derived from YmoA, the homologue of Hha in Y. enterocolitica, and found that it interacts with Y. enterocolitica H-NS. We also cloned and sequenced the hns gene of this microorganism. In the course of these experiments we found that His-YmoA can also retain H-NS from E. coli. We also found that the hns gene of Y. enterocolitica can complement an hns mutation of E. coli. Finally, we describe for the first time systematic characterization of missense mutant alleles of hha and truncated Hha′ proteins, and we report a striking and previously unnoticed similarity of the Hha family of proteins to the oligomerization domain of the H-NS proteins.

scholarly journals The Influence of Let-7b-5p Target Gene in Cholangiocarcinoma and its Bioinformatic Analysis

2021 ◽  
Vol 5 (2) ◽  
Author(s):  
Xibing Zhang ◽  
Jianghua Ran ◽  
Fang Liu ◽  
Yingpeng Zhao ◽  
Zongqiang Hu
Keyword(s):  
Protein Interaction ◽  
Protein Interaction Network ◽  
Target Gene ◽  
Interaction Network ◽  
Receptor Interaction ◽  
Pathway Enrichment Analysis ◽  
Signal Pathways ◽  
Biological Functions ◽  
Protein Protein Interaction ◽  
Protein Protein Interaction Network

Objective: To analyze the biological functions and its clinical significance of let-7b-5p target gene in cholangiocarcinoma utilizing bioinformatics. Methods: The paper focuses on the let-7b-5p target gene, and predicts its biological functions as well as related signal pathways through GO biological function and KEGG signal pathway enrichment analysis. The STRING database and Cytoscape are used to construct a protein-protein interaction network to screen core genes. Results: The results of GO analysis showed that let-7b-5p target gene was mainly enriched in biological processes such as Small GTPase binding, Rho GTPase binding, and Rac GTPase binding. The results of KEGG analysis showed that let-7b-5p target gene was significantly enriched in key signaling pathways including Focal adhesion and ECM-receptor interaction. Through protein-protein interaction network and module analysis, CXCL8 and SDC2 were screened as the core site. Conclusion: let-7b-5p can participate in the regulation of biological functions of tumor cells in cholangiocarcinoma, suggesting that it may play an important role as a tumor suppressor gene and biomarker in the occurrence and development of cholangiocarcinoma, which provides new ideas for its diagnosis and treatment.

scholarly journals Combined Transcriptome and Proteome Leukocyte’s Profiling Reveals Up-Regulated Module of Genes/Proteins Related to Low Density Neutrophils and Impaired Transcription and Translation Processes in Clinical Sepsis

2021 ◽  
Vol 12 ◽  
Author(s):  
Giuseppe Gianini Figueirêdo Leite ◽  
Bianca Lima Ferreira ◽  
Alexandre Keiji Tashima ◽  
Erika Sayuri Nishiduka ◽  
Edecio Cunha-Neto ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mononuclear Cells ◽  
Interaction Network ◽  
Low Density ◽  
Mitochondrial Translation ◽  
Peripheral Blood Mononuclear ◽  
Protein Coding ◽  
Protein Protein Interaction ◽  
Network Analyses ◽  
Host Defense System

Sepsis is a global health emergency, which is caused by various sources of infection that lead to changes in gene expression, protein-coding, and metabolism. Advancements in “omics” technologies have provided valuable tools to unravel the mechanisms involved in the pathogenesis of this disease. In this study, we performed shotgun mass spectrometry in peripheral blood mononuclear cells (PBMC) from septic patients (N=24) and healthy controls (N=9) and combined these results with two public microarray leukocytes datasets. Through combination of transcriptome and proteome profiling, we identified 170 co‐differentially expressed genes/proteins. Among these, 122 genes/proteins displayed the same expression trend. Ingenuity Pathway Analysis revealed pathways related to lymphocyte functions with decreased status, and defense processes that were predicted to be strongly increased. Protein-protein interaction network analyses revealed two densely connected regions, which mainly included down‐regulated genes/proteins that were related to the transcription of RNA, translation of proteins, and mitochondrial translation. Additionally, we identified one module comprising of up‐regulated genes/proteins, which were mainly related to low-density neutrophils (LDNs). LDNs were reported in sepsis and in COVID-19. Changes in gene expression level were validated using quantitative real-time PCR in PBMCs from patients with sepsis. To further support that the source of the upregulated module of genes/proteins found in our results were derived from LDNs, we identified an increase of this population by flow cytometry in PBMC samples obtained from the same cohort of septic patients included in the proteomic analysis. This study provides new insights into a reprioritization of biological functions in response to sepsis that involved a transcriptional and translational shutdown of genes/proteins, with exception of a set of genes/proteins related to LDNs and host‐defense system.

scholarly journals Predicting the Molecular Mechanism of “Angong Niuhuang Pills” in the Treatment of COVID-19 Based on Network Pharmacology

2021 ◽  
Vol 16 (6) ◽  
pp. 1934578X2110240
Author(s):  
Peng-yu Chen ◽  
Chen Wang ◽  
Ying Zhang ◽  
Chong Yuan ◽  
Bing Yu ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Treatment Plan ◽  
Interaction Network ◽  
Network Pharmacology ◽  
Signal Pathways ◽  
Active Components ◽  
Protein Protein Interaction ◽  
Pathway Annotation ◽  
Chinese Patent ◽  
8Th Edition

Introduction Angong Niuhuang Pills (AGNH), a Chinese patent medicine recommended in the “Diagnosis and Treatment Plan for COVID-19 (8th Edition),” may be clinically effective in treating COVID-19. The active components and signal pathways of AGNH through network pharmacology have been examined, and its potential mechanisms determined. Methods We screened the components in the Traditional Chinese Medicine Systems Pharmacology (TCMSP) via Drug-like properties (DL) and Oral bioavailability (OB); PharmMapper and GeneCards databases were used to collect components and COVID-19 related targets; KEGG pathway annotation and GO bioinformatics analysis were based on KOBAS3.0 database; “herb-components-targets-pathways” (H-C-T-P) network and protein-protein interaction network (PPI) were constructed by Cytoscape 3.6.1 software and STRING 10.5 database; we utilized virtual molecular docking to predict the binding ability of the active components and key proteins. Results A total of 87 components and 40 targets were screened in AGNH. The molecular docking results showed that the docking scores of the top 3 active components and the targets were all greater than 90. Conclusion Through network pharmacology research, we found that moslosooflavone, oroxylin A, and salvigenin in AGNH can combine with ACE2 and 3CL, and then are involved in the MAPK and JAK-STAT signaling pathways. Finally, it is suggested that AGNH may have a role in the treatment of COVID-19.

scholarly journals Mechanism Analysis of Coix Seed in Gastric Cancer Treatment Based on Biological Network Modules

2020 ◽  
Vol 15 (5) ◽  
pp. 1934578X2092752
Author(s):  
Fengbin Zhang ◽  
Xiaoyan Liu ◽  
Bingjie Huo ◽  
Bing Li ◽  
Ruixing Zhang
Keyword(s):  
Gastric Cancer ◽  
Target Genes ◽  
Biological Network ◽  
Interaction Network ◽  
Mechanism Analysis ◽  
Protein Protein Interaction ◽  
Network Analyses ◽  
Analysis Methods ◽  
Coix Seed ◽  
Modular Analysis

Coix seed, the mature seed of Coix lacryma-jobi L., is a traditional herb widely used in various cancer adjuvant treatments; however, its mechanism is unknown. The aim of this study was to reveal the multitarget mechanisms of Coix seed in the treatment of gastric cancer (GC) by biological network and modular analysis methods. Forty-one ingredients and 482 targets of Coix seed and 165 GC-related genes were obtained from databases. Twelve on-target genes ( AICDA, CASP3, EP300, ERBB2, FGFR2, IL12A, IL12B, IL1B, LOX, TJP1, TP53, and TRIB3) of Coix seed overlapped with GC-related genes. Using compound-target and protein–protein interaction network analyses, we discovered the core targets of Coix seed. Markov cluster algorithm-based modular analysis identified 5 potential module targets of Coix seed for GC. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis demonstrated the vast actions of Coix seed, which involve pathways in cancer, the cell cycle, receptor signal transduction, deoxyribonucleic acid damage response, transcriptional regulation, apoptosis, and cell connections. This study elucidated the potential mechanisms of Coix seed on GC, which may lead to the development of an effective drug. Additionally, this study showed the feasibility of network and modular analysis methods to investigate traditional Chinese medicinal herbal mechanisms and may provide a new angle for further research in the field of anticancer mechanisms and multitarget drugs.

scholarly journals Deep proteomic analysis of chicken erythropoiesis

2018 ◽  
Author(s):  
Marjorie Leduc ◽  
Emilie-Fleur Gautier ◽  
Anissa Guillemin ◽  
Cédric Broussard ◽  
Virginie Salnot ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Terminal Differentiation ◽  
Erythroid Differentiation ◽  
Absolute Quantification ◽  
Mass Spectrometry Analysis ◽  
Differentiation Process ◽  
Erythroid Cells ◽  
Spectrometry Analysis ◽  
Gata Transcription Factors ◽  
Chicken Erythrocytes

AbstractIn contrast to mammalian erythroid cells that lost their nucleus at the end of the differentiation process, circulating chicken erythrocytes, like erythrocytes of most other non-mammalian vertebrates, are nucleated although their nucleus is believed to be transcriptionally silent. This major difference suggests that the erythroid differentiation process is likely to present both similarities and differences in mammals compared to other vertebrates. Since proteins are the major cellular effectors, analysis of the proteome is more prone to reflect true differences than analysis of the pattern of mRNA expression. We have previously reported the evolution of the proteome of human erythroid cells throughout their differentiation process. Here we report the analysis of the proteome of chicken erythroblasts during their terminal differentiation. We used the T2EC cellular model that allows to obtain homogenous populations of immature erythroblasts. Induction of their terminal differentiation led to their maturation and the possibility to obtain cells at different differentiation stages. Mass spectrometry analysis of these cell populations allowed the absolute quantification of 6167 proteins throughout the terminal differentiation process. Beside many proteins with similar expression patterns between chicken and human erythroblasts, like SLC4A1 (Band3), GATA1 or CD44, this analysis also revealed that other important proteins like Kit or other GATA transcription factors exhibit fully different patterns of expression.

scholarly journals Unique Protein Interaction Networks Define The Chromatin Remodeling Module of The NuRD Complex

2021 ◽  
Author(s):  
Mehdi Sharifi Tabar ◽  
Caroline Giardina ◽  
Yue Julie Feng ◽  
Habib Francis ◽  
Hakimeh Moghaddas Sani ◽  
...  
Keyword(s):  
Chromatin Remodeling ◽  
Protein Interaction ◽  
Treatment Strategies ◽  
Interaction Network ◽  
Terminal Segment ◽  
Mass Spectrometry Analysis ◽  
Nurd Complex ◽  
Nucleosome Remodeling ◽  
Spectrometry Analysis ◽  
Underlying Mechanisms

AbstractThe combination of four proteins and their paralogues including MBD2/3, GATAD2A/B, CDK2AP1, and CHD3/4/5, which we refer to as the MGCC module, form the chromatin remodeling module of the Nucleosome Remodeling and Deacetylase (NuRD) complex, a gene repressor complex. Specific paralogues of the MGCC subunits such as MBD2 and CHD4 are amongst the key repressors of adult-stage fetal globin and provide important targets for molecular therapies in beta (β)-thalassemia. However, mechanisms by which the MGCC module acquires paralogue-specific function and specificity have not been addressed to date. Understanding the protein-protein interaction (PPI) network of the MGCC subunits is essential in defining underlying mechanisms and developing treatment strategies. Therefore, using pulldown followed by mass spectrometry analysis (PD-MS) we report a proteome-wide interaction network of the MGCC module in a paralogue-specific manner. Our data also demonstrate that the disordered C-terminal region of CHD3/4/5 is a gateway to incorporate remodeling activity into both the ChAHP (CHD4, ADNP, HP1γ) and NuRD complexes in a mutually exclusive manner. We define a short aggregation prone region (APR) within the C-terminal segment of GATAD2B that is essential for the interaction of CHD4 and CDK2AP1 with the NuRD complex. Finally, we also report an association of CDK2AP1 with the Nuclear Receptor Co-Repressor (NCOR) complex. Overall, this study provides insight into the possible mechanisms through which the MGCC module can achieve specificity and diverse biological functions.

scholarly journals High-Throughput Quality Control Assay for the Solid-Phase Syn-thesis of DNA-Encoded Libraries of Macrocycles

2020 ◽  
Author(s):  
Animesh Roy ◽  
Thomas Kodadek
Keyword(s):  
Quality Control ◽  
Control Method ◽  
Solid Phase ◽  
Mass Spectrometry Analysis ◽  
Liquid Chromatography Mass Spectrometry ◽  
Phase Synthesis ◽  
Spectrometry Analysis ◽  
Protein Protein Interaction ◽  
Classic Problem ◽  
Conformational Preferences

There is considerable interest in the development of libraries of scaffold-diverse macrocycles as a source of ligands for difficult targets, such as protein-protein interaction surfaces. A classic problem in the synthesis of high-quality macrocyclic libraries is that some linear precursors will cyclize efficiently while some will not, depending on their conformational preferences. We report here a powerful quality control method that can be employed to readily distinguish between scaffolds that do and do not cyclize efficiently during solid-phase synthesis of thioether macrocycles without the need for tedious liquid chromatography/mass spectrometry analysis. We demonstrate that this assay can be employed to identify largely linear “impurities” in a DNA-encoded library of macrocycles. We also use the method to establish a useful quality control protocol for re-synthesis of putative macrocyclic screening hits.

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