scholarly journals Proteomic Analysis of Rapeseed Root Response to Waterlogging Stress

Plants ◽  
2018 ◽  
Vol 7 (3) ◽  
pp. 71 ◽  
Author(s):  
Jinsong Xu ◽  
Xing Qiao ◽  
Zhitao Tian ◽  
Xuekun Zhang ◽  
Xiling Zou ◽  
...  
Keyword(s):  
Proteomic Analysis ◽  
Molecular Mechanisms ◽  
Yangtze River Basin ◽  
Reduction Process ◽  
Absolute Quantification ◽  
Brassica Napus L ◽  
Waterlogging Stress ◽  
Oxidation Reduction ◽  
Root Response ◽  
Isobaric Tags

The overall health of a plant is constantly affected by the changing and hostile environment. Due to climate change and the farming pattern of rice (Oryza sativa) and rapeseed (Brassica napus L.), stress from waterlogging poses a serious threat to productivity assurance and the yield of rapeseed in China’s Yangtze River basin. In order to improve our understanding of the complex mechanisms behind waterlogging stress and identify waterlogging-responsive proteins, we firstly conducted iTRAQ (isobaric tags for relative and absolute quantification)-based quantitative proteomic analysis of rapeseed roots under waterlogging treatments, for both a tolerant cultivar ZS9 and sensitive cultivar GH01. A total of 7736 proteins were identified by iTRAQ, of which several hundred showed different expression levels, including 233, 365, and 326 after waterlogging stress for 4H, 8H, and 12H in ZS9, respectively, and 143, 175, and 374 after waterlogging stress for 4H, 8H, and 12H in GH01, respectively. For proteins repeatedly identified at different time points, gene ontology (GO) cluster analysis suggested that the responsive proteins of the two cultivars were both enriched in the biological process of DNA-dependent transcription and the oxidation–reduction process, and response to various stress and hormone stimulus, while different distribution frequencies in the two cultivars was investigated. Moreover, overlap proteins with similar or opposite tendencies of fold change between ZS9 and GH01 were observed and clustered based on the different expression ratios, suggesting the two genotype cultivars exhibited diversiform molecular mechanisms or regulation pathways in their waterlogging stress response. The following qRT-PCR (quantitative real-time polymerase chain reaction) results verified the candidate proteins at transcription levels, which were prepared for further research. In conclusion, proteins detected in this study might perform different functions in waterlogging responses and would provide information conducive to better understanding adaptive mechanisms under environmental stresses.

scholarly journals Proteomic Analysis of Beef Tenderloin and Flank Assessed Using an Isobaric Tag for Relative and Absolute Quantitation (iTRAQ)

Animals ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 150
Author(s):  
Zhaomin Lei ◽  
Jianping Wu ◽  
Deyin Zhang ◽  
Ting Liu ◽  
Shengguo Zhao ◽  
...  
Keyword(s):  
Proteomic Analysis ◽  
Expression Patterns ◽  
Tca Cycle ◽  
Absolute Quantification ◽  
Absolute Quantitation ◽  
Oxidation Reduction ◽  
The Tca Cycle ◽  
Isobaric Tag ◽  
Isobaric Tags

Herein, we performed a proteomic analysis of tenderloin and flank steaks from Simmental cattle using the isobaric tags for a relative and absolute quantification (iTRAQ) approach. We identified 17 amino acids in both steaks, and Gly, Cys, Ile, Lys, and Pro differed most in abundance between the steak types (p < 0.05). A comparison of the expression patterns in steaks revealed 128 differentially expressed proteins (DEPs), of which 44 were up-regulated and 84 were down-regulated. Furthermore, 27 DEPs (p < 0.05) were subjected to gene ontology (GO) analysis, and many were found to be related to oxidation-reduction, metabolism, hydrogen ion transmembrane transport, transport, the tricarboxylic acid (TCA) cycle, mitochondrial electron transport, and the conversion of nicotinamide adenine dinucleotide (NADH) to ubiquinone. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis also implicated these DEPs in various signalling pathways, including oxidative phosphorylation, cardiac muscle contraction, the TCA cycle, biosynthesis, and the metabolism. These findings provide a new insight into key proteins involved in the determination of amino acid composition in beef.

scholarly journals Differential Abundance of Brain Mitochondrial Proteins in Yak and Cattle: A Proteomics-Based Study

2021 ◽  
Vol 8 ◽  
Author(s):  
Xiaoming Ma ◽  
Qiang Zhang ◽  
Yongfu La ◽  
Donghai Fu ◽  
Hiu Jiang ◽  
...  
Keyword(s):  
High Throughput Screening ◽  
Interaction Analysis ◽  
Reduction Process ◽  
Brain Mitochondria ◽  
Absolute Quantification ◽  
Mitochondrial Proteins ◽  
Oxidoreductase Activity ◽  
Coenzyme Binding ◽  
Oxidation Reduction ◽  
Isobaric Tags

The plateau adaptability and stress resistance of yaks are widely known based on their capacity to survive under severe habitat conditions. However, a few studies on brain mitochondria have characterized these adaptations at the protein level. We identified and quantified the brain mitochondrial proteins using isobaric tags for relative and absolute quantification (iTRAQ) and Proteomics. Western blotting was used to verify changes in the expression of target proteins. A total of 57 differentially abundant proteins (DAPs) were identified in the yak brain tissue. Gene Ontology (GO) analysis showed molecular functions of these DAPs including downregulated oxidoreductase activity but upregulated coenzyme binding. Significantly enriched biological processes were oxidation–reduction process (downregulated) and small molecule metabolic processes (upregulated). STRING protein interaction analysis indicated a complex interaction between dehydrogenase, transaminase, and ATP synthetase families. Reactome pathway analysis highlighted that the majority of DAPs participated in aerobic metabolic pathways such as metabolism, citric acid cycle, and respiratory electron transport. Immunoblotting confirmed that changes in FKBP4 and ATPAF2 expression were consistent with the results of mass spectrometry. We performed a high-throughput screening to identify DAPs in brain mitochondria between yak and cattle, which could explain the plateau adaptability of yaks.

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

scholarly journals Identification of differentially expressed proteins in fresh and frozen–thawed boar spermatozoa by iTRAQ-coupled 2D LC–MS/MS

Reproduction ◽  
2014 ◽  
Vol 147 (3) ◽  
pp. 321-330 ◽  
Author(s):  
Xiaoli Chen ◽  
Huabin Zhu ◽  
Chuanhuo Hu ◽  
Haisheng Hao ◽  
Junfang Zhang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Bioinformatic Analysis ◽  
Absolute Quantification ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Protein Levels ◽  
Boar Semen ◽  
Isobaric Tags ◽  
Boar Spermatozoa

Cryodamage is a major problem in semen cryopreservation, causing changes in the levels of proteins that influence the function and motility of spermatozoa. In this study, protein samples prepared from fresh and frozen–thawed boar spermatozoa were compared using the isobaric tags for relative and absolute quantification (iTRAQ) labeling technique coupled to 2D LC–MS/MS analysis. A total of 41 differentially expressed proteins were identified and quantified, including 35 proteins that were present at higher levels and six proteins that were present at lower levels in frozen–thawed spermatozoa by at least a mean of 1.79-fold (P<0.05). On classifying into ten distinct categories using bioinformatic analysis, most of the 41 differentially expressed proteins were found to be closely relevant to sperm premature capacitation, adhesions, energy supply, and sperm–oocyte binding and fusion. The expression of four of these proteins, SOD1, TPI1, ODF2, and AKAP3, was verified by western blot analysis. We propose that alterations in these identified proteins affect the quality of cryopreserved semen and ultimately lower its fertilizing capacity. This is the first study to compare protein levels in fresh and frozen–thawed spermatozoa using the iTRAQ technology. Our preliminary results provide an overview of the molecular mechanisms of cryodamage in frozen–thawed spermatozoa and theoretical guidance to improve the cryopreservation of boar semen.

scholarly journals iTRAQ-Based Analysis of Proteins Co-Regulated by Brassinosteroids and Gibberellins in Rice Embryos during Seed Germination

2018 ◽  
Vol 19 (11) ◽  
pp. 3460 ◽  
Author(s):  
Qian-Feng Li ◽  
Jin-Dong Wang ◽  
Min Xiong ◽  
Ke Wei ◽  
Peng Zhou ◽  
...  
Keyword(s):  
Seed Germination ◽  
Regulatory Network ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Higher Plants ◽  
Absolute Quantification ◽  
Rice Seed ◽  
Differentially Expressed Proteins ◽  
Search Tool ◽  
Isobaric Tags

Seed germination, a pivotal process in higher plants, is precisely regulated by various external and internal stimuli, including brassinosteroid (BR) and gibberellin (GA) phytohormones. The molecular mechanisms of crosstalk between BRs and GAs in regulating plant growth are well established. However, whether BRs interact with GAs to coordinate seed germination remains unknown, as do their common downstream targets. In the present study, 45 differentially expressed proteins responding to both BR and GA deficiency were identified using isobaric tags for relative and absolute quantification (iTRAQ) proteomic analysis during seed germination. The results indicate that crosstalk between BRs and GAs participates in seed germination, at least in part, by modulating the same set of responsive proteins. Moreover, most targets exhibited concordant changes in response to BR and GA deficiency, and gene ontology (GO) indicated that most possess catalytic activity and are involved in various metabolic processes. Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) analysis was used to construct a regulatory network of downstream proteins mediating BR- and GA-regulated seed germination. The mutation of GRP, one representative target, notably suppressed seed germination. Our findings not only provide critical clues for validating BR–GA crosstalk during rice seed germination, but also help to optimise molecular regulatory networks.

scholarly journals iTRAQ-Based Proteomics Analysis of Response to Solanum tuberosum Leaves Treated with the Plant Phytotoxin Thaxtomin A

2021 ◽  
Vol 22 (21) ◽  
pp. 12036
Author(s):  
Lu Liu ◽  
Liaoyang Hao ◽  
Ning Liu ◽  
Yonglong Zhao ◽  
Naiqin Zhong ◽  
...  
Keyword(s):  
Stress Responses ◽  
Common Scab ◽  
Reduction Process ◽  
Absolute Quantitation ◽  
Proteomics Analysis ◽  
Thaxtomin A ◽  
Oxidation Reduction ◽  
Plant Pathogen Interaction ◽  
Response To Stress ◽  
Isobaric Tags

Thaxtomin A (TA) is a phytotoxin secreted by Streptomyces scabies that causes common scab in potatoes. However, the mechanism of potato proteomic changes in response to TA is barely known. In this study, the proteomic changes in potato leaves treated with TA were determined using the Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) technique. A total of 693 proteins were considered as differentially expressed proteins (DEPs) following a comparison of leaves treated with TA and sterile water (as a control). Among the identified DEPs, 460 and 233 were upregulated and downregulated, respectively. Based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, many DEPs were found to be involved in defense and stress responses. Most DEPs were grouped in carbohydrate metabolism, amino acid metabolism, energy metabolism, and secondary metabolism including oxidation–reduction process, response to stress, plant–pathogen interaction, and plant hormone signal transduction. In this study, we analyzed the changes in proteins to elucidate the mechanism of potato response to TA, and we provided a molecular basis to further study the interaction between plant and TA. These results also offer the option for potato breeding through analysis of the resistant common scab.

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