scholarly journals iTRAQ-Based Quantitative Proteomic Analysis of the Arabidopsis Mutant opr3-1 in Response to Exogenous MeJA

2020 ◽  
Vol 21 (2) ◽  
pp. 571 ◽  
Author(s):  
Jiayu Qi ◽  
Xiaoyun Zhao ◽  
Zhen Li
Keyword(s):  
Protein Synthesis ◽  
Proteomic Analysis ◽  
Ribosomal Proteins ◽  
Absolute Quantification ◽  
Pcr Analysis ◽  
Regulation Mechanism ◽  
Proteomic Profiling ◽  
Quantitative Proteomic Analysis ◽  
Meja Treatment ◽  
Related Proteins

Jasmonates (JAs) regulate the defense of biotic and abiotic stresses, growth, development, and many other important biological processes in plants. The comprehensive proteomic profiling of plants under JAs treatment provides insights into the regulation mechanism of JAs. Isobaric tags for relative and absolute quantification (iTRAQ)-based quantitative proteomic analysis was performed on the Arabidopsis wild type (Ws) and JA synthesis deficiency mutant opr3-1. The effects of exogenous MeJA treatment on the proteome of opr3-1, which lacks endogenous JAs, were investigated. A total of 3683 proteins were identified and 126 proteins were differentially regulated between different genotypes and treatment groups. The functional classification of these differentially regulated proteins showed that they were involved in metabolic processes, responses to abiotic stress or biotic stress, the defense against pathogens and wounds, photosynthesis, protein synthesis, and developmental processes. Exogenous MeJA treatment induced the up-regulation of a large number of defense-related proteins and photosynthesis-related proteins, it also induced the down-regulation of many ribosomal proteins in opr3-1. These results were further verified by a quantitative real-time PCR (qRT-PCR) analysis of 15 selected genes. Our research provides the basis for further understanding the molecular mechanism of JAs’ regulation of plant defense, photosynthesis, protein synthesis, and development.

scholarly journals Chromatin-Associated Proteins Revealed by SILAC-Proteomic Analysis Exhibit a High Likelihood of Requirement for Growth Fitness under DNA Damage Stress

2012 ◽  
Vol 2012 ◽  
pp. 1-12
Author(s):  
Han Wang ◽  
Pornpimol Tipthara ◽  
Lei Zhu ◽  
Suk Yean Poon ◽  
Kai Tang ◽  
...  
Keyword(s):  
Dna Damage ◽  
Proteomic Analysis ◽  
Ribosomal Proteins ◽  
Cell Extract ◽  
Label Free ◽  
High Likelihood ◽  
Nonhistone Proteins ◽  
Quantitative Proteomic Analysis ◽  
Proteomic Approach ◽  
Associated Functions

Chromatin-associated nonhistone proteins (CHRAPs) are readily collected from the DNaseI digested crude chromatin preparation. In this study, we show that the absolute abundance-based label-free quantitative proteomic analysis fail to identify potential CHRAPs from the CHRAP-prep. This is because that the most-highly abundant cytoplasmic proteins such as ribosomal proteins are not effectively depleted in the CHRAP-prep. Ribosomal proteins remain the top-ranked abundant proteins in the CHRAP-prep. On the other hand, we show that relative abundance-based SILAC-mediated quantitative proteomic analysis is capable of discovering the potential CHRAPs in the CHRAP-prep when compared to the whole-cell-extract. Ribosomal proteins are depleted from the top SILAC ratio-ranked proteins. In contrast, nucleus-localized proteins or potential CHRAPs are enriched in the top SILAC-ranked proteins. Consistent with this, gene-ontology analysis indicates that CHRAP-associated functions such as transcription, regulation of chromatin structures, and DNA replication and repair are significantly overrepresented in the top SILAC-ranked proteins. Some of the novel CHRAPs are confirmed using the traditional method. Notably, phenotypic assessment reveals that the top SILAC-ranked proteins exhibit the high likelihood of requirement for growth fitness under DNA damage stress. Taken together, our results indicate that the SILAC-mediated proteomic approach is capable of determining CHRAPs without prior knowledge.

scholarly journals iTRAQ-Based Proteomics Analysis of Autophagy-Mediated Responses against MeJA in Laticifers of Euphorbia kansui L.

2019 ◽  
Vol 20 (15) ◽  
pp. 3770
Author(s):  
Fang ◽  
Yao ◽  
Zhang ◽  
Tian ◽  
Wang ◽  
...  
Keyword(s):  
Developmental Process ◽  
Cysteine Proteinase ◽  
Defense Responses ◽  
Absolute Quantification ◽  
Pcr Analysis ◽  
Control Group ◽  
Proteomics Analysis ◽  
Meja Treatment ◽  
Euphorbia Kansui ◽  
Isobaric Tags

Autophagy is a well-defined catabolic mechanism whereby cytoplasmic materials are engulfed into a structure termed the autophagosome. Methyl jasmonate (MeJA), a plant hormone, mediates diverse developmental process and defense responses which induce a variety of metabolites. In plants, little is known about autophagy-mediated responses against MeJA. In this study, we used high-throughput comparative proteomics to identify proteins of latex in the laticifers. The isobaric tags for relative and absolute quantification (iTRAQ) MS/MS proteomics were performed, and 298 proteins among MeJA treated groups and the control group of Euphorbia kansui were identified. It is interesting to note that 29 significant differentially expressed proteins were identified and their associations with autophagy and ROS pathway were verified for several selected proteins as follows: α-L-fucosidase, β-galactosidase, cysteine proteinase, and Cu/Zn superoxide dismutase. Quantitative real-time PCR analysis of the selected genes confirmed the fact that MeJA might enhance the expression of some genes related to autophagy. The western blotting and immunofluorescence results of ATG8 and ATG18a which are two important proteins for the formation of autophagosomes also demonstrated that MeJA could promote autophagy at the protein level. Using the electron microscope, we observed an increase in autophagosomes after MeJA treatment. These results indicated that MeJA might promote autophagy in E. kansui laticifers; and it was speculated that MeJA mediated autophagy through two possible ways: the increase of ROS induces ATG8 accumulation and then aotophagosome formation, and MeJA promotes ATG18 accumulation and then autophagosome formation. Taken together, our results provide several novel insights for understanding the mechanism between autophagy and MeJA treatment. However, the specific mechanism remains to be further studied in the future.

scholarly journals Comparative Proteomic Analysis of Dipsacus asperoides Roots from Different Habitats in China

Molecules ◽  
2020 ◽  
Vol 25 (16) ◽  
pp. 3605
Author(s):  
Haijun Jin ◽  
Hua Yu ◽  
Haixia Wang ◽  
Jia Zhang
Keyword(s):  
Proteomic Analysis ◽  
Absolute Quantification ◽  
Pcr Analysis ◽  
Allene Oxide ◽  
Allene Oxide Cyclase ◽  
Protein Levels ◽  
Depth Analysis ◽  
Differential Proteins ◽  
Isobaric Tags

Dipsacus asperoides is a kind of Chinese herbal medicine with beneficial health properties. To date, the quality of D. asperoides from different habitats has shown significant differences. However, the molecular differences in D. asperoides from different habitats are still unknown. The aim of this study was to investigate the differences in protein levels of D. asperoides from different habitats. Isobaric tags for relative and absolute quantification (iTRAQ) and 2DLC/MS/MS were used to detect statistically significant changes in D. asperoides from different habitats. Through proteomic analysis, a total of 2149 proteins were identified, of which 42 important differentially expressed proteins were screened. Through in-depth analysis of differential proteins, the protein metabolism energy and carbohydrate metabolism of D. asperoides from Hubei Province were strong, but their antioxidant capacity was weak. We found that three proteins, UTP-glucose-1-phosphate uridylyltransferase, allene oxide cyclase, and isopentyl diphosphate isomerase 2, may be the key proteins involved in dipsacus saponin VI synthesis. Eight proteins were found in D. asperoides in response to environmental stress from different habitats. Quantitative real-time PCR analysis confirmed the accuracy and authenticity of the proteomic analysis. The results of this study may provide the basic information for exploring the cause of differences in secondary metabolites in different habitats of D. asperoides and the protein mechanism governing differences in quality.

scholarly journals Quantitative proteomic analysis of G-protein signalling inStagonospora nodorumusing isobaric tags for relative and absolute quantification

PROTEOMICS ◽  
2010 ◽  
Vol 10 (1) ◽  
pp. 38-47 ◽  
Author(s):  
Tammy Casey ◽  
Peter S. Solomon ◽  
Scott Bringans ◽  
Kar-Chun Tan ◽  
Richard P. Oliver ◽  
...  
Keyword(s):  
G Protein ◽  
Proteomic Analysis ◽  
Absolute Quantification ◽  
Quantitative Proteomic Analysis ◽  
G Protein Signalling ◽  
Isobaric Tags

Quantitative proteomic analysis identifying three annexins as lymph node metastasis-related proteins in lung adenocarcinoma

2010 ◽  
Vol 29 (1) ◽  
pp. 174-184 ◽  
Author(s):  
Ying-Fu Liu ◽  
Yong-Heng Chen ◽  
Mao-Yu Li ◽  
Peng-Fei Zhang ◽  
Fang Peng ◽  
...  
Keyword(s):  
Lymph Node ◽  
Lymph Node Metastasis ◽  
Lung Adenocarcinoma ◽  
Proteomic Analysis ◽  
Quantitative Proteomic Analysis ◽  
Node Metastasis ◽  
Related Proteins

scholarly journals Quantitative proteomic analysis and functional characterization of Acanthamoeba castellanii exosome-like vesicles

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Wei-Chen Lin ◽  
Chia-Yun Tsai ◽  
Jian-Ming Huang ◽  
Shang-Rung Wu ◽  
Lichieh Julie Chu ◽  
...  
Keyword(s):  
Immune Response ◽  
Proteomic Analysis ◽  
Functional Characterization ◽  
Acanthamoeba Castellanii ◽  
Host Cells ◽  
C6 Cells ◽  
Proteomic Profiling ◽  
Quantitative Proteomic Analysis ◽  
Rat Glioma

Abstract Background Pathogenic protozoans use extracellular vesicles (EVs) for intercellular communication and host manipulation. Acanthamoeba castellanii is a free-living protozoan that may cause severe keratitis and fatal granulomatous encephalitis. Although several secreted molecules have been shown to play crucial roles in the pathogenesis of Acanthamoeba, the functions and components of parasite-derived EVs are far from understood. Methods Purified EVs from A. castellanii were confirmed by electron microscopy and nanoparticle tracking analysis. The functional roles of parasite-derived EVs in the cytotoxicity to and immune response of host cells were examined. The protein composition in EVs from A. castellanii was identified and quantified by LC-MS/MS analysis. Results EVs from A. castellanii fused with rat glioma C6 cells. The parasite-derived EVs induced an immune response from human THP-1 cells and a cytotoxic effect in C6 cells. Quantitative proteomic analysis identified a total of 130 proteins in EVs. Among the identified proteins, hydrolases (50.2%) and oxidoreductases (31.7%) were the largest protein families in EVs. Furthermore, aminopeptidase activities were confirmed in EVs from A. castellanii. Conclusions The proteomic profiling and functional characterization of EVs from A. castellanii provide an in-depth understanding of the molecules packaged into EVs and their potential mechanisms mediating the pathogenesis of this parasite.

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