In vitro andin silico processes to identify differentially expressed proteins

PROTEOMICS ◽  
2004 ◽  
Vol 4 (8) ◽  
pp. 2333-2351 ◽  
Author(s):  
Nadia Allet ◽  
Nicolas Barrillat ◽  
Thierry Baussant ◽  
Celia Boiteau ◽  
Paolo Botti ◽  
...  
Keyword(s):  
Differentially Expressed ◽  
Differentially Expressed Proteins

scholarly journals Screening for proteins related to the biosynthesis of hispidin and its derivatives in Phellinus igniarius using iTRAQ proteomic analysis

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jinjing Guo ◽  
Xiaoxi Liu ◽  
Yuanjie Li ◽  
Hongyan Ji ◽  
Cheng Liu ◽  
...  
Keyword(s):  
Stress Responses ◽  
Biosynthetic Pathway ◽  
Multiple Reaction Monitoring ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Common Source ◽  
Differentially Expressed Proteins ◽  
Phellinus Igniarius ◽  
Chemical Structures

Abstract Background Hispidin (HIP) and its derivatives, a class of natural fungal metabolites, possess complex chemical structures with extensive pharmacological activities. Phellinus igniarius, the most common source of HIP, can be used as both medicine and food. However, the biosynthetic pathway of HIP in P. igniarius remains unclear and we have a limited understanding of the regulatory mechanisms related to HIP. In this work, we sought to illustrate a biosynthesis system for hispidin and its derivatives at the protein level. Results We found that tricetolatone (TL) is a key biosynthetic precursor in the biosynthetic pathway of hispidin and that its addition led to increased production of hispidin and various hispidin derivatives. Based on the changes in the concentrations of precursors and intermediates, key timepoints in the biosynthetic process were identified. We used isobaric tags for relative and absolute quantification (iTRAQ) to study dynamic changes of related proteins in vitro. The 270 differentially expressed proteins were determined by GO enrichment analysis to be primarily related to energy metabolism, oxidative phosphorylation, and environmental stress responses after TL supplementation. The differentially expressed proteins were related to ATP synthase, NAD binding protein, oxidoreductase, and other elements associated with electron transfer and dehydrogenation reactions during the biosynthesis of hispidin and its derivatives. Multiple reaction monitoring (MRM) technology was used to selectively verify the iTRAQ results, leading us to screen 11 proteins that were predicted to be related to the biosynthesis pathways. Conclution These findings help to clarify the molecular mechanism of biosynthesis of hispidin and its derivatives and may serve as a foundation for future strategies to identify new hispidin derivatives.

scholarly journals Proteomics variations after short-term heat shock treatment reveal differentially expressed proteins involved in early microspore embryogenesis in cabbage (Brassica oleracea)

2019 ◽  
Author(s):  
Henan Su ◽  
Guo Chen ◽  
Xing Liu ◽  
Limei Yang ◽  
Mu Zhuang ◽  
...  
Keyword(s):  
Heat Shock ◽  
In Vitro Culture ◽  
Microspore Embryogenesis ◽  
Shock Treatment ◽  
Differentially Expressed ◽  
High Temperature Treatment ◽  
Differentially Expressed Proteins ◽  
Heat Shock Treatment ◽  
Short Term

Abstract Background Microspore embryogenesis (ME) provides an efficient way to breed crops. In many cases, short-term heat shock treatment can greatly increase the embryogenesis rate of brassicas. However, its molecular mechanism is largely unclear. Results To mine for the key genes, pathways and interplay in the underlying networks, we compared the proteomes of isolated microspores with samples pre-treated at 32 °C for 24 h and 25 °C for 24 h using two cabbage accessions (Zhonggan 628 and 87-534) showing extremely different embryogenic rates. The embryo yield was 0 and 19.7 embryos/bud for Zhonggan 628 at 25 °C and 32 °C, respectively, and was 0 for 87-534 at both temperatures. Using a label-free proteomics technology, more differentially expressed proteins (DEPs) were found for Zhonggan 628 (363 DEPs, 115 upregulated and 248 downregulated) than for 87-534 (282 DEPs, 162 upregulated and 120 downregulated). 97 DEPs specially identified only in Zhonggan 628 but not in 87-534 after heat-shock treatment were the key proteins that maybe related to heat shock-induced embryogenesis in vitro culture. Those 97 DEPs were mainly enriched in carbon metabolic process and protein synthesis and degradation process. Malate dehydrogenase (mMDH), sgt1 homolog B (SGT1), heat shock 70 kDa protein 5 (HSP70), and cell division control protein 48 homolog A (CDC48) may play an important role in cabbage embryogenesis and were identified based on pathway enrichment and protein−protein interaction analyses. In addition, changes in the abundance of 9 representative DEPs were correlated with their corresponding mRNA levels using qRT-PCR. Carbohydrate metabolism supplies the energy needed for the rapid growth that occurs during embryo development, and the folding of synthesized proteins or the refolding of damaged and unstable proteins occur, which may due to the stress induced by in vitro culture. Conclusions A set of putative proteins presumably specific for microspore embryogenesis induced by high temperature treatment were identified. In isolated microspore culture of cabbage, we present the first exposition of non-embryo and the embryo (induced by 32 °C heat shock treatment 24h) changes in the expression of specific proteins.

scholarly journals Proteomic Comparative Analysis of Pregnancy Serum Facilitating Hepatitis E Virus Replication in Hepatoma Cells

2017 ◽  
Author(s):  
Yi Li ◽  
Yanhong Bi ◽  
Wenhai Yu ◽  
Chenchen Yang ◽  
Jue Wang ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Pregnant Women ◽  
Hepatitis E Virus ◽  
Hepatitis E ◽  
Hepatoma Cells ◽  
Host Cells ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Absolute Quantitation

Hepatitis E virus (HEV) is a common cause of acute hepatitis worldwide, accounting for approximately 25% of deaths among pregnant women. We previously reported that pregnancy serum facilitates HEV replication in vitro. However, the differences in host cells with HEV infection induced by pregnancy serum and fetal bovine serum (FBS) are unclear. In this study, differentially expressed proteins were identified in HEV-infected hepatoma cells (HepG2) supplemented with different sera by using isobaric tags for relative and absolute quantitation. Proteomic analysis indicated that HEV infection significantly induced 1014 differentially expressed proteins in HEV-infected HepG2 cells when supplemented with FBS compared with pregnancy serum. Further validation by Western blot confirmed that filamin A, heat-shock proteins 70 and 90, Cytochrome c, and Thioredoxin were associated with HEV infection. This comparative analysis provides an important basis to further investigate HEV pathogenesis in pregnant women and HEV replication.

scholarly journals Screening for Proteins Related to The Biosynthesis of Hispidin and Its Derivatives in Phellinus Igniarius Using iTRAQ Proteomic Analysis

2020 ◽  
Author(s):  
Jinjing Guo ◽  
Xiaoxi Liu ◽  
Yuanjie Li ◽  
Hongyan Ji ◽  
Cheng Liu ◽  
...  
Keyword(s):  
Stress Responses ◽  
Multiple Reaction Monitoring ◽  
Enrichment Analysis ◽  
Absolute Quantification ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Phellinus Igniarius ◽  
Chemical Structures ◽  
Isobaric Tags

Abstract Background: Hispidin (HIP) and its derivatives, a class of natural fungal metabolites, possess extremely complex and interesting chemical structures with extensive pharmacological activities. Phellinus igniarius, which is the most common sources of HIP, can be used as both medicine and food. The biosynthetic pasthway of HIP in P. igniarius is not yet clear and hence effective regulatory mechanism of HIP is absent.The purpose of this paper was to illustrate a biosynthesis system for hispidin and its derivatives at the protein level. Results: We found that tricetolatone (TL) is a key biosynthetic precursor in the biosynthetic pathway of hispidin and that its addition led to increased production of hispidin and various hispidin derivatives. Based on the changes in the concentrations of precursors and intermediates, key timepoints in the biosynthetic process were identified. We used isobaric tags for relative and absolute quantification (iTRAQ) to study dynamic changes of related proteins in vitro. The 270 differentially expressed proteins were determined by GO enrichment analysis to be primarily related to energy metabolism, oxidative phosphorylation, and environmental stress responses after TL supplementation. The differentially expressed proteins were related to ATP synthase, NAD binding protein, oxidoreductase, and other elements associated with electron transfer and dehydrogenation reactions during the biosynthesis of hispidin and its derivatives. Multiple reaction monitoring (MRM) technology was used to selectively verify the iTRAQ results, leading us to screen 11 proteins that were predicted to be related to the biosynthesis pathways.Conclution: These findings help to clarify the molecular mechanism of biosynthesis of hispidin and its derivatives and may serve as a foundation for future strategies to identify new hispidin derivatives.

scholarly journals Dysregulation of ferroptosis may involve in the development of non-small cell lung cancer in Xuanwei area

2020 ◽  
Author(s):  
Zhang Yang ◽  
Guangjian Li ◽  
Jiapeng Yang ◽  
Guangqiang Zhao ◽  
Zhenghai Shen ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Indoor Air Pollution ◽  
Protein Profiling ◽  
Differentially Expressed ◽  
Receptor Interaction ◽  
Differentially Expressed Proteins ◽  
Tandem Mass Tag ◽  
Differential Proteins ◽  
Local Residents

Abstract Background The Xuanwei area of Yunnan Province, China is one of the regions with the highest incidence of lung cancer in the world. Local residents use bituminous coal as fuel for cooking and heating, which causes serious indoor air pollution. After the local government carried out furnace and stove reform work, the high incidence of lung cancer in residents continued. We herein wonder if there are specific mechanisms at protein level for the development of lung cancer in the area. Methods We investigated the changes of protein profiling in tumor of the patients from Xuanwei area. Tandem Mass Tag (TMT) were employed to screen the differential proteins between carcinoma and para-carcinoma tissues. Results We identified a total of 422 differentially-expressed proteins, among which 162 proteins were significantly upregulated and 260 were downregulated compared to para-carcinoma tissues. Many of the differentially-expressed proteins were related to ECM-receptor interaction, focal adhesion, PI3K/AKT pathway and ferroptosis. Further experiments on the two differential proteins, TXN2 and HP, showed that the change of their expressions could make the lung cancer cell lines more resistant to erastin or RSL-induced ferroptosis in vitro, and promote the growth of tumor in nude mice. Conclusion This study revealed that aberrant regulation of ferroptosis may involve in the development of lung cancer in Xuanwei area.

scholarly journals Erzhi Tiangui Granules Improve In Vitro Fertilization Outcomes in Infertile Women with Advanced Age

2021 ◽  
Vol 2021 ◽  
pp. 1-7
Author(s):  
Jinlong Sun ◽  
Jing-Yan Song ◽  
Yao Dong ◽  
Shan Xiang ◽  
Qiong Guo
Keyword(s):  
Placebo Group ◽  
In Vitro Fertilization ◽  
Follicular Fluid ◽  
Differentially Expressed ◽  
Advanced Age ◽  
Differentially Expressed Proteins ◽  
High Quality ◽  
Vitro Fertilization ◽  
Infertile Women

Background. The fertility of females with advanced age declines with aging. Therefore, for medical and social reasons, it is important to establish mechanisms to protect and improve the fertility of such populations. With widespread use of traditional Chinese medicine (TCM) in in vitro fertilization (IVF), studies have evaluated their impact on improving the fertility of females with advanced age. In this study, we performed proteomic analysis of follicular fluid to reveal mechanisms of the Erzhi Tiangui (EZTG) granule (Chinese herbs for replenishing vital essence to tonify the kidney) in improving the outcomes of IVF in infertile women with advanced age. Methods. This was a randomized, double-blind, and placebo-controlled trial in which 100 patients with advanced age were divided into the EZTG group and the placebo group by the random number table plus envelope method. Both groups were subjected to controlled ovarian stimulation with a GnRH antagonist regimen. Differences between the two groups were evaluated, including the TCM syndrome score after treatment, gonadotrophin (Gn) days and Gn doses, the number of retrieved oocytes, 2 pronucleus (PN) fertilization, 2PN cleavage, and high-quality embryos. Differentially expressed proteins were identified using the LC-MS/MS method, and their functions were determined through bioinformatics analyses. Results. The number of high-quality embryos in the placebo group was significantly lower than that in the EZTG group (2.88 ± 1.85 vs. 4.13 ± 2.83, p = 0.011 ). Eleven differentially expressed proteins were identified between the two groups. Four proteins were highly expressed, whereas seven were suppressed in the control group, compared to the EZTG group. The overall trend suggested that the apoptotic effect in the follicular fluid of the EZTG group was downregulated. Conclusion. Treatment with the EZTG granule can improve embryo quality in IVF of advanced age females with both kidney Qi and Yin deficiency syndromes. The mechanism is attributed to downregulation of apoptotic-effector protein expressions in the follicular fluid. This trial is registered with ChiCTR1900025139.

scholarly journals Proteomic Analyses of Thioredoxins f and m Arabidopsis thaliana Mutants Indicate Specific Functions for These Proteins in Plants

Antioxidants ◽  
2019 ◽  
Vol 8 (3) ◽  
pp. 54 ◽  
Author(s):  
Juan Fernández-Trijueque ◽  
Antonio-Jesús Serrato ◽  
Mariam Sahrawy
Keyword(s):  
Protein Profiling ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Specific Target ◽  
Fructose 1,6 Bisphosphatase ◽  
Response To Stress ◽  
Quantitative Alteration ◽  
Hormone Signalling ◽  
Specific Target Protein

A large number of plastidial thioredoxins (TRX) are present in chloroplast and the specificity versus the redundancy of their functions is currently under discussion. Several results have highlighted the fact that each TRX has a specific target protein and thus a specific function. In this study we have found that in vitro activation of the fructose-1,6-bisphosphatase (FBPase) enzyme is more efficient when f1 and f2 type thioredoxins (TRXs) are used, whilst the m3 type TRX did not have any effect. In addition, we have carried out a two-dimensional electrophoresis-gel to obtain the protein profiling analyses of the trxf1, f2, m1, m2, m3 and m4 Arabidopsis mutants. The results revealed quantitative alteration of 86 proteins and demonstrated that the lack of both the f and m type thioredoxins have diverse effects on the proteome. Interestingly, 68% of the differentially expressed proteins in trxf1 and trxf2 mutants were downregulated, whilst 75% were upregulated in trxm1, trxm2, trxm3 and trxm4 lines. The lack of TRX f1 provoked a higher number of down regulated proteins. The contrary occurred when TRX m4 was absent. Most of the differentially expressed proteins fell into the categories of metabolic processes, the Calvin–Benson cycle, photosynthesis, response to stress, hormone signalling and protein turnover. Photosynthesis, the Calvin–Benson cycle and carbon metabolism are the most affected processes. Notably, a significant set of proteins related to the answer to stress situations and hormone signalling were affected. Despite some studies being necessary to find specific target proteins, these results show signs that are suggest that the f and m type plastidial TRXs most likely have some additional specific functions.

scholarly journals Differential Proteomic Analysis of Syncytiotrophoblast Extracellular Vesicles from Early-Onset Severe Preeclampsia, using 8-Plex iTRAQ Labeling Coupled with 2D Nano LC-MS/MS

2015 ◽  
Vol 36 (3) ◽  
pp. 1116-1130 ◽  
Author(s):  
Hongmei Li ◽  
Lei Han ◽  
Zhiling Yang ◽  
Wei Huang ◽  
Xin Zhang ◽  
...  
Keyword(s):  
Western Blot ◽  
Extracellular Vesicles ◽  
Proteomic Analysis ◽  
Early Onset ◽  
Culture Method ◽  
Explant Culture ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Go Annotation

Aims: Previous studies have revealed that the increased shedding of syncytiotrophoblast extracellular vesicles (STBM) may lead to preeclampsia (PE). We aimed to identify the proteins carried by STBM and their potential pathological roles in early-onset severe PE. Methods: In this study, we performed a differential proteomic analysis of STBM from early-onset severe PE patients, using iTRAQ isobaric tags and 2D nano LC-MS/MS. STBM were generated by the in vitro explant culture method, and then verified by electron microscopy and western blot analysis. Results: A total of 18 533 unique peptides and 3 317 proteins were identified, 3 292 proteins were quantified. We identified 194 differentially expressed proteins in STBM from early-onset severe PE patients, 122 proteins were up-regulated and 72 proteins were down-regulated. Further bioinformatics analysis revealed that mitochondrion, transmembrane transport and transmembrane transporter activity were the most abundant categories in gene ontology (GO) annotation. Glycolysis/ gluconeogenesis, citrate cycle, fatty acid elongation, steroid hormone biosynthesis and oxidative phosphorylation were the five significantly represented pathways. Four differentially expressed proteins (siglec-6, calnexin, CD63 and S100-A8) related to inflammation, coagulation or immunoregulation were independently verified using western blot. Conclusions: The identification of key proteins carried by STBM may serve not only as a basis for better understanding and further exploring the etiology and pathogenesis of PE, but also as potential biomarkers and in providing targets for future therapy in PE, especially in early-onset severe PE(sPE).

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