scholarly journals Quantitative proteomic analysis of auxin signaling during seedling development

2017 ◽  
Author(s):  
Dior R. Kelley ◽  
Zhouxin Shen ◽  
Justin W. Walley ◽  
Elisabeth J. Chapman ◽  
Steven P. Briggs ◽  
...  
Keyword(s):  
Transcript Abundance ◽  
Absolute Quantification ◽  
Auxin Signaling ◽  
Data Sets ◽  
Transcriptional Responses ◽  
Downstream Signaling ◽  
Regulation Mechanisms ◽  
Isobaric Tags ◽  
Hypocotyl Tissue ◽  
Spatial Specificity

AbstractAuxin induces rapid gene expression changes throughout plant development. How these transcriptional responses relate to changes in protein abundance is not well characterized. We have identified auxin regulated proteins in whole seedlings, roots and hypocotyls and at three different time points (30 min, 120 min and 3 hours) using an iTRAQ (isobaric tags for relative and absolute quantification) based quantitative proteomics approach. These profiling experiments detected 4,701 proteins from seedling tissue, 6,740 proteins from root tissue and 3,925 proteins from hypocotyl tissue. Comparisons between the differentially expressed proteins data sets showed little overlap, suggesting that auxin proteomes exhibit both temporal and spatial specificity. Numerous proteins showed significant changes in abundance following auxin treatment independent of changes in cognate transcript abundance. This includes several well characterized proteins with various roles in auxin pathways, suggesting that complex gene regulation mechanisms follow auxin signaling events. Specifically, regulation of translation may play a role as inferred from MapMan categorization analyses and protein interaction networks comprised of auxin regulated proteins. Additionally, functional categorization of auxin regulated proteins indicates rapid and complex metabolic changes occur in both roots and hypocotyls in response to auxin which are not apparent from transcriptome analyses. Altogether these data describe novel auxin-regulated proteomes and are an excellent resource for identifying new downstream signaling components related to auxin-mediated plant growth and development.

Analysis of wound-induced gene expression in Nicotiana species with contrasting alkaloid profiles

2004 ◽  
Vol 31 (7) ◽  
pp. 721 ◽  
Author(s):  
Steven J. Sinclair ◽  
Richard Johnson ◽  
John D. Hamill
Keyword(s):  
Fold Increase ◽  
Transcript Abundance ◽  
Nicotiana Sylvestris ◽  
Nicotiana Glauca ◽  
Transcriptional Responses ◽  
Transcript Levels ◽  
Solanaceae Species ◽  
Genes Encoding ◽  
Root Tissues ◽  
Alkaloid Profiles

We determined the capacity of three Nicotiana (Solanaceae) species with very different alkaloid profiles (Nicotiana sylvestris Speg & Comes, Nicotiana alata Link & Otto and Nicotiana glauca Grah.) to increase their alkaloid contents in both leaf and root tissues following foliage damage. We also investigated the transcriptional responses of genes encoding enzymes important for alkaloid biosynthesis, namely quinolinate phosphoribosyltransferase (QPT), putrescine N-methyltransferase (PMT), ornithine decarboxylase (ODC) and the putative alkaloid biosynthetic gene A622. In response to wounding of foliage in the well studied ‘model’ species N. sylvestris, a rise, approximately 2-fold, in leaf nicotine levels was observed several days after a 4–5-fold increase in the transcript levels of all genes in the roots. In contrast, leaf tissues of the ornamental tobacco N. alata showed very low levels of any pyridine alkaloid, even when analysed 1 week after wounding, correlating with a general lack of transcript abundance representing any of these genes in leaves or roots following foliage damage. However, addition of methyl jasmonate to cultured roots of N. alata did produce elevated levels of nicotine and anatabine raising the possibility that components of the leaf–root wound signalling system in N. alata are different from those in N. sylvestris. Wounding of the tree tobacco N. glauca, was followed by a 2-fold increase in anabasine levels several days later. This increase followed a large rise in transcript levels of ODC, QPT and A622, though not PMT, in wounded leaves, but not in non-wounded leaves or roots. These data support the hypothesis that N. glauca is able to produce increased anabasine levels following wounding in its foliage, setting it apart from N. sylvestris where induced alkaloid production takes place in roots. We discuss the possibility that increased transcript levels detected by ODC and A622 probes play important roles in anabasine synthesis in N. glauca.

scholarly journals Probabilistic data integration identifies reliable gametocyte-specific proteins and transcripts in malaria parasites

2017 ◽  
Author(s):  
Lisette Meerstein-Kessel ◽  
Robin van der Lee ◽  
Will Stone ◽  
Kjerstin Lanke ◽  
David A Baker ◽  
...  
Keyword(s):  
Transcript Abundance ◽  
Data Sets ◽  
Asexual Blood Stage ◽  
Systematic Analysis ◽  
Humoral Immune ◽  
Proteomic Data ◽  
Genome Wide ◽  
Field Samples ◽  
Specific Proteins ◽  
Specific Antigens

AbstractPlasmodium gametocytes are the sexual forms of the malaria parasite essential for transmission to mosquitoes. To better understand how gametocytes differ from asexual blood-stage parasites, we performed a systematic analysis of available ‘omics data for P. falciparum and other Plasmodium species. 18 transcriptomic and proteomic data sets were evaluated for the presence of curated “gold standards” of 41 gametocyte-specific versus 46 non-gametocyte genes and integrated using Bayesian probabilities, resulting in gametocyte-specificity scores for all P. falciparum genes.To illustrate the utility of the gametocyte score, we explored newly predicted gametocyte-specific genes as potential biomarkers of gametocyte carriage and exposure. We analyzed the humoral immune response in field samples against 30 novel gametocyte-specific antigens and found five antigens to be differentially recognized by gametocyte carriers as compared to malaria-infected individuals without detectable gametocytes. We also validated the gametocyte-specificity of 15 identified gametocyte transcripts on culture material and samples from naturally infected individuals, resulting in eight transcripts that were >1000-fold higher expressed in gametocytes compared to asexual parasites and whose transcript abundance allowed gametocyte detection in naturally infected individuals. Our integrated genome-wide gametocyte-specificity scores provide a comprehensive resource to identify targets and monitor P. falciparum gametocytemia.

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

scholarly journals Monocyte Proteomics Reveals Involvement of Phosphorylated HSP27 in the Pathogenesis of Osteoporosis

2015 ◽  
Vol 2015 ◽  
pp. 1-9 ◽  
Author(s):  
Bhavna Daswani ◽  
Manoj Kumar Gupta ◽  
Shubhangi Gavali ◽  
Meena Desai ◽  
Gajanan J. Sathe ◽  
...  
Keyword(s):  
Absolute Quantification ◽  
Osteoclast Formation ◽  
Mineral Density ◽  
Monocyte Migration ◽  
Receptor Activator ◽  
Lower Chamber ◽  
Isobaric Tags ◽  
First Time ◽  
Upper Chamber ◽  
Increased Susceptibility

Peripheral monocytes, precursors of osteoclasts, have emerged as important candidates for identifying proteins relevant to osteoporosis, a condition characterized by low Bone Mineral Density (BMD) and increased susceptibility for fractures. We employed 4-plex iTRAQ (isobaric tags for relative and absolute quantification) coupled with LC-MS/MS (liquid chromatography coupled with tandem mass spectrometry) to identify differentially expressed monocyte proteins from premenopausal and postmenopausal women with low versus high BMD. Of 1801 proteins identified, 45 were differentially abundant in low versus high BMD, with heat shock protein 27 (HSP27) distinctly upregulated in low BMD condition in both premenopausal and postmenopausal categories. Validation in individual samples (n=80) using intracellular ELISA confirmed that total HSP27 (tHSP27) as well as phosphorylated HSP27 (pHSP27) was elevated in low BMD condition in both categories (P<0.05). Further, using transwell assays, pHSP27, when placed in the upper chamber, could increase monocyte migration (P<0.0001) and this was additive in combination with RANKL (receptor activator ofNFkBligand) placed in the lower chamber (P=0.05). Effect of pHSP27 in monocyte migration towards bone milieu can result in increased osteoclast formation and thus contribute to pathogenesis of osteoporosis. Overall, this study reveals for the first time a novel link between monocyte HSP27 and BMD.

scholarly journals iTRAQ-Based Comparative Proteomics Analysis of Urolithiasis Rats Induced by Ethylene Glycol

2020 ◽  
Vol 2020 ◽  
pp. 1-10
Author(s):  
Yanan Cao ◽  
Bin Duan ◽  
Xiaowei Gao ◽  
E. Wang ◽  
Zhitao Dong
Keyword(s):  
Ethylene Glycol ◽  
Kidney Stones ◽  
Enrichment Analysis ◽  
Absolute Quantification ◽  
Rat Models ◽  
Protein Protein Interaction ◽  
Parallel Reaction Monitoring ◽  
High Prevalence ◽  
Isobaric Tags ◽  
And Control

Nephrolithiasis is a frequent chronic urological condition with a high prevalence and recurrence rate. Proteomics studies on urolithiasis rat models are highly important in characterizing the pathophysiology of kidney stones and identifying potential approaches for preventing and treating kidney stones. The isobaric tags for relative and absolute quantification (iTRAQ) were performed to identify differentially expressed proteins (DEPs) in the kidney between urolithiasis rats and control rats. The results showed that 127 DEPs (85 upregulated and 42 downregulated) were identified in urolithiasis and control rats. The functions of DEPs were predicted by Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and protein–protein interaction (PPI) network analysis. The expression of four upregulated proteins (Tagln, Akr1c9, Spp1, and Fbn1) and four downregulated proteins (Hbb, Epb42, Hmgcs2, and Ca1) were validated by parallel reaction monitoring (PRM). Proteomics studies of ethylene glycol-induced urolithiasis rat models using iTRAQ and PRM helped to elucidate the molecular mechanism governing nephrolithiasis and to identify candidate proteins for the treatment of kidney stones.

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 GZFLW Induces Apoptosis of Ectopic Endometrial Stromal Cells via Promoting VPS53 Protein Stability

2018 ◽  
Vol 2018 ◽  
pp. 1-10
Author(s):  
Ziyu Zhang ◽  
Faying Liu ◽  
YunYun Xu ◽  
Huang Huang ◽  
Yang Zou ◽  
...  
Keyword(s):  
Molecular Mechanism ◽  
Stromal Cells ◽  
In Vitro Study ◽  
Absolute Quantification ◽  
Endometrial Stromal Cells ◽  
Gynecological Diseases ◽  
Isobaric Tags ◽  
Differential Expression Protein ◽  
Vacuolar Protein

Endometriosis is still a major problem in obstetrics and gynecology. While GZFLW (Gui Zhi Fu Ling Wan) has been originally used for treating gynecological diseases, however, the molecular mechanism that GZFLW acts on endometriosis is not clear. To investigate the molecular mechanism that GZFLW plays role on endometriosis, iTRAQ (isobaric tags for relative and absolute quantification) proteomics and human endometrial stromal cells (Y14) obtained from a patient with endometriosis were used in in vitro study. Our results demonstrated that GZFLW decreased Y14 cells proliferation while increased cells apoptosis. The differential expression protein VPS53 (Vacuolar protein sorting 53 homolog) was predicted by iTRAQ coupled LC-MS/MS and further identified by western blot. Besides, GZFLW induced VPS53 protein level by promoting its stabilization. Our findings highlight a novel role for VPS53 in gynecology and provide a potent therapeutic strategy against endometriosis.

Sign in / Sign up

Export Citation Format

Share Document