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 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 Quantitative Analysis of Multidrug Resistance Mechanisms in Human Gastric Cancer Cells

2010 ◽  
Vol 2010 ◽  
pp. 1-11 ◽  
Author(s):  
Huai-Dong Hu ◽  
Feng Ye ◽  
Da-Zhi Zhang ◽  
Peng Hu ◽  
Hong Ren ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Multidrug Resistance ◽  
Cell Line ◽  
Molecular Mechanisms ◽  
Absolute Quantification ◽  
Differentially Expressed ◽  
Human Gastric Cancer ◽  
Differentially Expressed Proteins ◽  
Gastric Cancer Cells ◽  
Proteomic Approach

Multidrug resistance (MDR) is a major obstacle towards a successful treatment of gastric cancer. However, the mechanisms of MDR are intricate and have not been fully understood. To elucidate the molecular mechanisms of MDR in gastric cancer, we employed the proteomic approach of isobaric tags for relative and absolute quantification (iTRAQ), followed by LC-MS/MS, using the vincristine-resistant SGC7901/VCR cell line and its parental SGC7901 cell line as a model. In total, 820 unique proteins were identified and 91 proteins showed to be differentially expressed in SGC7901/VCR compared with SGC7901. Several differentially expressed proteins were further validated by western blot analysis. Furthermore, the association of MVP, one of the highly expressed proteins in SGC7901/VCR, with MDR was verified. Our study is the first application of iTRAQ technology for MDR mechanisms analysis in gastric cancer, and many of the differentially expressed proteins identified have not been linked to MDR in gastric cancer before, which showed the value of this technology in identifying differentially expressed proteins in cancer.

scholarly journals GABA-Alleviated Oxidative Injury Induced by Salinity, Osmotic Stress and their Combination by Regulating Cellular and Molecular Signals in Rice

2019 ◽  
Vol 20 (22) ◽  
pp. 5709 ◽  
Author(s):  
Mohamed S. Sheteiwy ◽  
Hongbo Shao ◽  
Weicong Qi ◽  
Yousef Alhaj Hamoud ◽  
Hiba Shaghaleh ◽  
...  
Keyword(s):  
Cell Cycle ◽  
Antioxidant Enzymes ◽  
Seed Germination ◽  
Osmotic Stress ◽  
Salinity Stress ◽  
Cell Cycle Progression ◽  
Molecular Mechanisms ◽  
Oryza Sativa L ◽  
Water Relation ◽  
Rice Seed

This study was conducted in order to determine the effect of priming with γ-aminobutyric acid (GABA) at 0.5 mM on rice (Oryza sativa L.) seed germination under osmotic stress (OS) induced by polyethylene glycol (30 g/L PEG 6000); and salinity stress (S, 150 mM NaCl) and their combination (OS+S). Priming with GABA significantly alleviated the detrimental effects of OS, S and OS+S on seed germination and seedling growth. The photosynthetic system and water relation parameters were improved by GABA under stress. Priming treatment significantly increased the GABA content, sugars, protein, starch and glutathione reductase. GABA priming significantly reduced Na+ concentrations, proline, free radical and malonaldehyde and also significantly increased K+ concentration under the stress condition. Additionally, the activities of antioxidant enzymes, phenolic metabolism-related enzymes, detoxification-related enzymes and their transcription levels were improved by GABA priming under stress. In the GABA primed-plants, salinity stress alone resulted in an obvious increase in the expression level of Calcineurin B-like Protein-interacting protein Kinases (CIPKs) genes such as OsCIPK01, OsCIPK03, OsCIPK08 and OsCIPK15, and osmotic stress alone resulted in obvious increase in the expression of OsCIPK02, OsCIPK07 and OsCIPK09; and OS+S resulted in a significant up-regulation of OsCIPK12 and OsCIPK17. The results showed that salinity, osmotic stresses and their combination induced changes in cell ultra-morphology and cell cycle progression resulting in prolonged cell cycle development duration and inhibitory effects on rice seedlings growth. Hence, our findings suggested that the high tolerance to OS+S is closely associated with the capability of GABA priming to control the reactive oxygen species (ROS) level by inducing antioxidant enzymes, secondary metabolism and their transcription level. This knowledge provides new evidence for better understanding molecular mechanisms of GABA-regulating salinity and osmotic-combined stress tolerance during rice seed germination and development.

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 Study of Hypothalamus in Pigs Exposed to Heat Stress

2020 ◽  
Author(s):  
Tianyue Yu ◽  
Yan-Hong Yong ◽  
Jun-yu Li ◽  
Biao Fang ◽  
Can-ying Hu ◽  
...  
Keyword(s):  
Body Weight ◽  
Heat Stress ◽  
Regulatory Networks ◽  
Protein Profile ◽  
Absolute Quantification ◽  
The Body ◽  
Differentially Expressed ◽  
Farm Animals ◽  
Differentially Expressed Proteins ◽  
The Brain

Abstract Background : With evidence of warming climates, it is important to understand the effects of heat stress in farm animals in order to minimize production losses. Studying the changes in the brain proteome induced by heat stress may aid in understanding how heat stress affects brain function. The hypothalamus is a critical region in the brain that controls the pituitary gland, which is responsible for the secretion of several important hormones. In this study, we examined the hypothalamic protein profile of 10 pigs (15 ± 1 kg body weight), with five subjected to heat stress (35 ± 1 °C; relative humidity = 90%) and five acting as controls (28 ± 3°C; RH = 90%). Result: The isobaric tags for relative and absolute quantification (iTRAQ) analysis of the hypothalamus identified 1710 peptides corresponding to 360 proteins, including 295 differentially expressed proteins (DEPs), 148 of which were up-regulated and 147 down-regulated, in heat-stressed animals. The Ingenuity Pathway Analysis (IPA) software predicted 30 canonical pathways, four functional groups, and four regulatory networks of interest. The DEPs were mainly concentrated in the cytoskeleton of the pig hypothalamus during heat stress. Conclusions: In this study, heat stress significantly increased the body temperature and reduced daily gain of body weight in pigs. Furthermore, we identified 295 differentially expressed proteins, 147 of which were down-regulated and 148 up-regulated in hypothalamus of heat stressed pigs. The IPA showed that the DEPs identified in the study are involved in cell death and survival, cellular assembly and organization, and cellular function and maintenance, in relation to neurological disease, metabolic disease, immunological disease, inflammatory disease, and inflammatory response. We hypothesize that a malfunction of the hypothalamus may destroy the host physical and immune function, resulting in decreased growth performance and immunosuppression in heat stressed pigs.

scholarly journals Comparative Proteomics of Schistosoma Japonicum Developed From Different Oncomelania Snails Permissive Areas

2021 ◽  
Author(s):  
Feng Miao ◽  
Yongbin Wang ◽  
Kun Yang ◽  
Wei Li ◽  
Chunrong Xiong ◽  
...  
Keyword(s):  
Absolute Quantification ◽  
Shandong Province ◽  
Receptor Expression ◽  
Differentially Expressed ◽  
Water Diversion ◽  
Differentially Expressed Proteins ◽  
Histone H4 ◽  
Intermediate Hosts ◽  
Male Adult ◽  
Isobaric Tags

Abstract Background: Schistosomiasis is an important zoonotic parasitic disease that is widely prevalent in tropical and subtropical countries and regions in the worldwide.Methods: We aimed to analyze the proteomic differences between adult S. japonicum worms in Weishan Lake of Shandong province and the Jiangsu Yangtse river. Isobaric tags for relative and absolute quantification (iTRAQ) assays were used to analyze the differential proteomic profiles between female and male adult worms.Results: A total of 2364 adult S. japonicum proteins were identified, and 1901 proteins were quantified by isobaric tags for relative and absolute quantification (iTRAQ) technology. Our results revealed 68 differentially expressed proteins (DEPs) in female adult worms and 55 DEPs in male adult worms. LC-MS/MS and bioinformatics analysis indicated that these DEPs are enriched in cellular composition, molecular function, biological function and catabolism pathways. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Domain and Clusters of Orthologous Groups (COG) analyses indicated that several groups of DEPs were involved in regulating transport, metabolism, signal transduction, energy production and conversion, defense and biosynthesis in adult S. japonicum worms. Our findings indicated that adult S. japonicum worms derived from O. hupensis that were transferred from permissive to nonpermissive areas exhibited moderate changes at the proteomic level. Moreover, snails transferred to the Weishan Lake did not change their schistosomiasis transmission ability and remained pathogenic in mice. In addition, three upregulated proteins (peptidylprolyl isomerase, heat shock protein 90α and receptor expression-enhancing protein (Q5DBJ1)) and three downregulated proteins (histone H3, histone H4 and receptor expression-enhancing protein (C1L9D7)) were found in both female and male adult worms. Conclusions: Proteomic analysis showed that differentially expressed proteins (DEPs) between adult S. japonicum worms in Weishan Lake of Shandong province and the Jiangsu Yangtse river. The results of this proteomics analysis of adult worms that hatched in two separate intermediate hosts help to improve our understanding of the growth and developmental mechanisms of S. japonicum in different environments. Under the South-to-North Water Diversion Project (SNWDP) framework, long-term surveillance is needed to prevent the diffusion of O. hupensis and to reduce the risk of schistosomiasis transmission.

scholarly journals Proteomic Study of Hypothalamus in Pigs Exposed to Heat Stress

2019 ◽  
Author(s):  
Tianyue Yu ◽  
Yan-Hong Yong ◽  
Jun-yu Li ◽  
Biao Fang ◽  
Can-ying Hu ◽  
...  
Keyword(s):  
Heat Stress ◽  
Regulatory Networks ◽  
Protein Profile ◽  
Absolute Quantification ◽  
Farm Animals ◽  
Itraq Analysis ◽  
Canonical Pathways ◽  
Brain Proteome ◽  
Isobaric Tags ◽  
The Brain

Abstract Background: With evidence of warming climates, it is important to understand the effects of heat stress in farm animals in order to minimize production losses. Study of changes in the brain proteome induced by heat stress may aid in understanding how heat stress impacts brain function. The hypothalamus is a key region in the brain that controls the pituitary gland, which is responsible for the secretion of several important hormones. Result: In this study, we examined the hypothalamic protein profile of ten pigs (30–40 kg body weight), 5 of which were subjected to heat stress (35 ± 1°C; relative humidity = 90%) and 5 acting as controls (28 ± 3°C; RH = 90%). The isobaric tags for relative and absolute quantification (iTRAQ) analysis of the hypothalamus identified 1710 peptides corresponding to 360 proteins, and 295 deferentially expressed proteins (DEPs), 148 of which were up-regulated and 147 down-regulated in heat-stressed animals. Ingenuity Pathway Analysis software predicted 30 canonical pathways, 4 functional groups, and 4 regulatory networks of interest and the DEPs mainly concentrated in the cytoskeleton of the pig hypothalamus during heat stress. Conclusions: The upstream regulators of these 295 DEPs in the hypothalamus of the pig under HS are mainly transcriptional regulators, chemical drugs, and sRNA. This study provides reference data for further study of the mechanism of HS on hypothalamic physiology and metabolism(Illustration 1).

Exogenous melatonin promotes rice seed germination under salinity through regulating antioxidants and metabolic homeostasis

2020 ◽  
Author(s):  
Liexiang Huangfu ◽  
Enying Zhang ◽  
Huimin Fang ◽  
Pengcheng Li ◽  
Yang Xu ◽  
...  
Keyword(s):  
Salt Stress ◽  
Seed Germination ◽  
Stress Responses ◽  
Molecular Mechanisms ◽  
Main Body ◽  
Rice Seed ◽  
Metabolic Homeostasis ◽  
Exogenous Melatonin ◽  
Total Antioxidant ◽  
Pre Treatment

Abstract Background Melatonin plays important roles in multiple plant developmental processes and stress responses. However, little is known about the role and putative mechanism of exogenous melatonin in regulating rice seed germination under salt stress. Main Body Here, we revealed that the exogenous application of melatonin can significantly promote rice seed germination under salinity. Its putative molecular mechanisms are further investigated through metabolomic and transcriptomic analyses. The results revealed that the phytohormone concentrations in germinating seeds are reprogrammed, the activities of superoxide dismutase (SOD), catalase (CAT), and peroxidase (POD) are enhanced, and the total antioxidant capacity under salinity is activated by exogenous melatonin. In addition, rice seeds pre-treated with melatonin exhibit higher concentrations of glycosides than non-treated seeds under salinity. Furthermore, exogenous melatonin alleviates the accumulation of fatty acids under salinity. Genome-wide transcriptomic profiling is used to identify 7160 transcripts which are differentially expressed under salt (NaCl), salt + melatonin (MT100), and control treatments. Pathway and GO enrichment analyses reveal that the genes involved in the response to oxidative stress, hormone metabolism, heme building, mitochondrion, and tricarboxylic acid transformation are altered after melatonin pre-treatment under salinity. Conclusion This study provides evidence for exogenous melatonin increasing rice seed germination under salt stress, mainly through the activation of antioxidants and modulation of metabolic homeostasis.

scholarly journals CoryneRegNet 2: An Integrative Bioinformatics Approach for Reconstruction and Comparison of Transcriptional Regulatory Networks in Prokaryotes

2006 ◽  
Vol 3 (2) ◽  
pp. 1-13 ◽  
Author(s):  
Jan Baumbach ◽  
Karina Brinkrolf ◽  
Tobias Wittkop ◽  
Andreas Tauch ◽  
Sven Rahmann
Keyword(s):  
Transcription Factor ◽  
Data Warehouse ◽  
Binding Sites ◽  
Regulatory Network ◽  
High Performance ◽  
Regulatory Networks ◽  
Transcriptional Regulatory Networks ◽  
Transcriptional Regulatory ◽  
Search Tool ◽  
Gene Regulatory

SummaryCoryneRegNet is an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. Initially, it was designed to provide methods for the analysis and visualization of the gene regulatory network of Corynebacterium glutamicum. Now we integrated the genomes and transcriptional interactions of three other corynebacteria, C. diphtheriae, C. efficiens, and C. jeikeium into CoryneRegNet; providing comparative analysis and visualization with GraphVis. We also integrated the high-performance PSSM search tool PoSSuM search to detect potential transcription factor binding sites within and across species. As an application, we reconstruct in silico the regulatory network of the iron metabolism regulator DtxR in the four corynebacteria.CoryneRegNet is freely accessible at https://www.cebitec.uni-bielefeld.de/groups/gi/software/coryneregnet/. The final slash (/) is mandatory. In order to use the GraphVis feature, Java (at least version 1.4.2) is required.

scholarly journals Local genetic context shapes the function of a gene regulatory network

2021 ◽  
Author(s):  
Anna Nagy-Staroń ◽  
Kathrin Tomasek ◽  
Caroline Caruso Carter ◽  
Elisabeth Sonnleitner ◽  
Bor Kavčič ◽  
...  
Keyword(s):  
Gene Regulatory Network ◽  
Gene Regulatory Networks ◽  
Regulatory Network ◽  
Regulatory Networks ◽  
Molecular Mechanisms ◽  
Transcriptional Unit ◽  
Regulatory Sequences ◽  
Gene Regulatory ◽  
Context Shapes ◽  
Genetic Context

Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions, such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks remains a major challenge. Here, we use a well-defined synthetic gene regulatory network to study how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one gene regulatory network with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Our results demonstrate that changes in local genetic context can place a single transcriptional unit within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual transcriptional units, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of gene regulatory networks.

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