scholarly journals Proteome Profiling of the Mutagen-Induced Morphological and Yield Macro-Mutant Lines of Nigella sativa L.

Plants ◽  
2019 ◽  
Vol 8 (9) ◽  
pp. 321 ◽  
Author(s):  
Ambreen Asif ◽  
Mohammad Yunus K. Ansari ◽  
Abeer Hashem ◽  
Baby Tabassum ◽  
Elsayed Fathi Abd_Allah ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Seed Yield ◽  
Carbon Metabolism ◽  
Nigella Sativa ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Induced Mutagenesis ◽  
Leaf Proteome ◽  
Mutant Lines

In the present investigation, the leaf proteome profile of the macro-mutant lines of Nigella sativa L. was analyzed to identify the key proteins involved in the expression of traits associated with the morphology, seed yield, and content of thymoquinone. In our earlier study, the macro-mutants were generated with contrasting morphological traits and seed yields through induced mutagenesis, using ethyl methyl sulfonate, gamma rays, and combinations of both. Analysis of the leaf proteome of the control and macro-mutant lines of N. sativa showed that twenty-three proteins were differentially expressed. These differentially expressed proteins were sequenced through mass spectrometry and identified using the MASCOT software. On the basis of their function, these proteins were categorized into several groups. Most proteins were found in the categories of signal transduction (18%) and carbon metabolism (18%). A total of 13% of proteins belonged to the categories of energy and metabolism. Proteins in the categories of secondary plant metabolism, stress defense, cytoskeleton, and protein synthesis were also found. The polycomb group protein (FIE1), transcription factor (PRE1), and geranyl diphosphate synthase were notable proteins, in addition to some proteins of signal transduction and carbon metabolism. Expression patterns of the differentially expressed proteins were also studied at the transcript level by using qRT-PCR. Transcriptomics analysis was consistent with the proteomics data. This study shows the changes that take place at the proteomic level through induced mutagenesis, as well as the involvement of some proteins in the expression traits associated with plant height, seed yield, and the thymoquinone content of N. sativa. The identified proteins might help elucidate the metabolic pathways involved in the expression of traits, including seed yield, and the active compounds of medicinal plants.

scholarly journals LC-MS/MS analysis of lesional and normally looking psoriatic skin reveals significant changes in protein metabolism and RNA processing

2020 ◽  
Author(s):  
V.V. Sobolev ◽  
R.H. Ziganshin ◽  
A.V. Mezentsev ◽  
A.G. Soboleva ◽  
M. Denieva ◽  
...  
Keyword(s):  
Healthy Volunteers ◽  
Rna Processing ◽  
Protein Identification ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Psoriatic Skin ◽  
Differentially Expressed Proteins ◽  
Kinin System ◽  
Lesional Skin ◽  
Kallikrein Kinin System

AbstractBackgroundPlaque psoriasis is a chronic autoimmune disorder characterized by the development of red scaly plaques. To date psoriasis lesional skin transcriptome has been extensively studied, whereas only few proteomic studies of psoriatic skin are available.AimThe aim of this study was to compare protein expression patterns of lesional and normally looking skin of psoriasis patients with skin of the healthy volunteers, reveal differentially expressed proteins and identify changes in cell metabolism caused by the disease.MethodsSkin samples of normally looking and lesional skin donated by psoriasis patients (n = 5) and samples of healthy skin donated by volunteers (n = 5) were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). After protein identification and data processing, the set of differentially expressed proteins was subjected to protein ontology analysis to characterize changes in biological processes, cell components and molecular functions in the patients’ skin compared to skin of the healthy volunteers.ResultsThe performed analysis identified 405 and 59 differentially expressed proteins in lesional and normally looking psoriatic skin compared to healthy control. We discovered decreased expression of KNG1, APOE, HRG, THBS1 and PLG in normally looking skin of the patients. Presumably, these changes were needed to protect the epidermis from spontaneous activation of kallikrein-kinin system and delay the following development of inflammatory response. In lesional skin, we identified several large groups of proteins with coordinated expression. Mainly, these proteins were involved in different aspects of protein and RNA metabolism, namely ATP synthesis and consumption; intracellular trafficking of membrane-bound vesicles, pre-RNA processing, translation, chaperoning and degradation in proteasomes/immunoproteasomes.ConclusionOur findings explain the molecular basis of metabolic changes caused by disease in skin lesions, such as faster cell turnover and higher metabolic rate. They also indicate on downregulation of kallikrein-kinin system in normally looking skin of the patients that would be needed to delay exacerbation of the disease. Data are available via ProteomeXchange with identifier PXD021673.

scholarly journals Genome-Wide Identification of Long Non-coding RNA in Trifoliate Orange (Poncirus trifoliata (L.) Raf) Leaves in Response to Boron Deficiency

2019 ◽  
Vol 20 (21) ◽  
pp. 5419 ◽  
Author(s):  
Gao-Feng Zhou ◽  
Li-Ping Zhang ◽  
Bi-Xian Li ◽  
Ou Sheng ◽  
Qing-Jiang Wei ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Plant Hormones ◽  
Target Genes ◽  
Expression Patterns ◽  
Poncirus Trifoliata ◽  
Differentially Expressed ◽  
Boron Deficiency ◽  
Trifoliate Orange ◽  
Genome Wide ◽  
A Genome

Long non-coding RNAs (lncRNAs) play important roles in plant growth and stress responses. As a dominant abiotic stress factor in soil, boron (B) deficiency stress has impacted the growth and development of citrus in the red soil region of southern China. In the present work, we performed a genome-wide identification and characterization of lncRNAs in response to B deficiency stress in the leaves of trifoliate orange (Poncirus trifoliata), an important rootstock of citrus. A total of 2101 unique lncRNAs and 24,534 mRNAs were predicted. Quantitative real-time polymerase chain reaction (qRT-PCR) experiments were performed for a total of 16 random mRNAs and lncRNAs to validate their existence and expression patterns. Expression profiling of the leaves of trifoliate orange under B deficiency stress identified 729 up-regulated and 721 down-regulated lncRNAs, and 8419 up-regulated and 8395 down-regulated mRNAs. Further analysis showed that a total of 84 differentially expressed lncRNAs (DELs) were up-regulated and 31 were down-regulated, where the number of up-regulated DELs was 2.71-fold that of down-regulated. A similar trend was also observed in differentially expressed mRNAs (DEMs, 4.21-fold). Functional annotation of these DEMs was performed using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, and the results demonstrated an enrichment of the categories of the biosynthesis of secondary metabolites (including phenylpropanoid biosynthesis/lignin biosynthesis), plant hormone signal transduction and the calcium signaling pathway. LncRNA target gene enrichment identified several target genes that were involved in plant hormones, and the expression of lncRNAs and their target genes was significantly influenced. Therefore, our results suggest that lncRNAs can regulate the metabolism and signal transduction of plant hormones, which play an important role in the responses of citrus plants to B deficiency stress. Co-expression network analysis indicated that 468 significantly differentially expressed genes may be potential targets of 90 lncRNAs, and a total of 838 matched lncRNA-mRNA pairs were identified. In summary, our data provides a rich resource of candidate lncRNAs and mRNAs, as well as their related pathways, thereby improving our understanding of the role of lncRNAs in response to B deficiency stress, and in symptom formation caused by B deficiency in the leaves of trifoliate orange.

Proteomic analysis of differentially expressed proteins in the roots of Columbia-0 and Landsberg erecta ecotypes of Arabidopsis thaliana in response to aluminum toxicity

2012 ◽  
Vol 92 (7) ◽  
pp. 1267-1282 ◽  
Author(s):  
T. Karuppanapandian ◽  
S-J. Rhee ◽  
E-J. Kim ◽  
B. K. Han ◽  
O. A. Hoekenga ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Stress Responses ◽  
Proteomic Analysis ◽  
Crop Production ◽  
Aluminum Toxicity ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Monodehydroascorbate Reductase ◽  
Differentially Expressed Proteins ◽  
Al Stress

Karuppanapandian, T., Rhee, S.-J., Kim, E.-J., Han, B. K., Hoekenga, O. A. and Lee, G. P. 2012. Proteomic analysis of differentially expressed proteins in the roots of Columbia-0 and Landsberg erecta ecotypes of Arabidopsis thaliana in response to aluminum-toxicity. Can. J. Plant Sci. 92: 1267–1282. Aluminum (Al) is phytotoxic when solubilized into Al3+ in acidic soils and represents a major constraint for crop production. The present study describes Al-stress responses in roots of Al-tolerant and Al-sensitive Arabidopsis ecotypes, Columbia-0 (Col-0) and Landsberg erecta (Ler), respectively. Comparative proteomic analysis was applied to plants grown in hydroponic solution culture under acidic pH (4.2) conditions. To investigate time-dependent responses, 6-d-old seedlings were treated with 30 µM AlCl3 for 24, 48, or 72 h; total proteins were prepared from roots and separated by two-dimensional gel electrophoresis (2-DE). From 2-DE analysis, were 600 proteins were inspected, 29 proteins were differentially responsive to Al-treatment. The 2-DE patterns were compared and differentially expressed proteins identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Analysis of protein expression patterns revealed that a set of proteins is functionally associated with tricarboxylic acid (TCA) cycle and glycolysis, reactive oxygen quenching and detoxification mechanism, and signal transduction pathways, etc., could play important roles in mediating plant response to Al in Arabidopsis ecotypes. Comparison of the changes in the protein profiles revealed that Al-stress increased Al-tolerance related proteins in Al-tolerant Col-0, but only generic stress responses occurred in Al-sensitive Ler. Specifically, Al up-regulated proteins such as alcohol dehydrogenase, monodehydroascorbate reductase, GTP-binding nuclear protein Ran-2, and leucine aminopeptidase in Col-0 but not in Ler.

scholarly journals Amelioration of seed yield, oil content and oil quality through induced mutagenesis in sesame (Sesamum indicum L.)

2015 ◽  
Vol 44 (1) ◽  
pp. 15-22 ◽  
Author(s):  
Tamina Begum ◽  
Tapash Dasgupta
Keyword(s):  
Seed Yield ◽  
Fatty Acid Content ◽  
Oil Quality ◽  
Mutation Breeding ◽  
Sesamum Indicum ◽  
High Yield ◽  
Polyunsaturated Fatty Acid Content ◽  
Oil Percentage ◽  
Induced Mutagenesis ◽  
Mutant Lines

Thirty mutant lines selected from 3 widely adapted genotypes of sesame viz. Rama, SI 1666 and IC 21706 (ten from each of the three genotypes), developed by induced physical (?-rays) and chemical (EMS) mutagens, were evaluated against their respective control genotype for yield and its important attributes in M4 generation to reveal the ramification of mutagens for disclosing the magnitude of variation among mutants in advance generation and also to identify the promising positive mutants to refurbish new improved varieties of sesame. Mutants professing higher seed yield were evaluated for oil quantity and quality. All selected mutant lines evinced improved seed yield over their respective controls. Irrespective of the genotypes highest yield was recorded in the line induced by 0.5% EMS. Based on mean seed yield and its components, selected 10 superior mutants, also possessed high oil percentage with a better oil profile having relatively more polyunsaturated fatty acid content, specially linoleic acid, than the control, indicating potentiality of mutation breeding to restructure plants with high yield, improved oil percentage and quality. DOI: http://dx.doi.org/10.3329/bjb.v44i1.22718 Bangladesh J. Bot. 44(1): 15-22, 2015 (March)

scholarly journals Proteomic identification of glutamine synthetase as a differential marker for oligodendrogliomas and astrocytomas

2011 ◽  
Vol 115 (4) ◽  
pp. 789-795 ◽  
Author(s):  
Zhengping Zhuang ◽  
Meng Qi ◽  
Jie Li ◽  
Hiroaki Okamoto ◽  
David S. Xu ◽  
...  
Keyword(s):  
Glutamine Synthetase ◽  
Glial Cell ◽  
Cell Cultures ◽  
Gel Electrophoresis ◽  
Expression Patterns ◽  
Morphological Variability ◽  
Differentially Expressed ◽  
Differentially Expressed Proteins ◽  
Two Dimensional Gel Electrophoresis ◽  
Glial Cell Cultures

Object Astrocytomas and oligodendrogliomas are primary CNS tumors that remain a challenge to differentiate histologically because of their morphological variability and because there is a lack of reliable differential diagnostic markers. To identify proteins that are differentially expressed between astrocytomas and oligodendrogliomas, the authors analyzed the proteomic expression patterns and identified uniquely expressed proteins in these neoplasms. Methods Proteomes of astrocytomas and oligodendrogliomas were analyzed using 2D gel electrophoresis and subsequent computerized gel analysis to detect differentially expressed proteins. The proteins were identified using high-performance liquid chromatography accompanied by tandem mass spectrometry. To determine the role of the differentially expressed proteins in astrocytes, undifferentiated glial cell cultures were treated with dibutyryl–cyclic adenosine monophosphate (cAMP). Results Two-dimensional gel electrophoresis revealed that glutamine synthetase was differentially expressed in astrocytomas and oligodendrogliomas. Western blot and immunohistochemical analyses confirmed the increased expression of glutamine synthetase in astrocytomas compared with oligodendrogliomas. Whereas glutamine synthetase expression was demonstrated across all grades of astrocytomas (Grade II–IV [15 tumors]) and oligoastrocytomas (4 tumors), it was expressed in only 1 oligodendroglioma (6% [16 tumors]). Treatment of undifferentiated glial cell cultures with dibutyryl-cAMP resulted in astrocyte differentiation that was associated with increased levels of glial fibrillary acidic protein and glutamine synthetase. Conclusions These data indicate that glutamine synthetase expression can be used to distinguish astrocytic from oligodendroglial tumors and may play a role in the pathogenesis of astrocytomas.

scholarly journals Comparative Proteomics Reveals Cold Acclimation Machinery Through Enhanced Carbohydrate and Amino Acid Metabolism in Wucai (Brassica Campestris L.)

Plants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 474
Author(s):  
Lingyun Yuan ◽  
Shilei Xie ◽  
Libing Nie ◽  
Yushan Zheng ◽  
Jie Wang ◽  
...  
Keyword(s):  
Amino Acid ◽  
Cold Acclimation ◽  
Low Temperatures ◽  
Amino Acid Metabolism ◽  
Acid Metabolism ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Pcr Analysis ◽  
Differentially Expressed Proteins ◽  
Limited Information

Limited information is available on the cold acclimation of non-heading Chinese cabbage (NHCC) under low temperatures. In this study, the isobaric tags for relative and absolute quantification (iTRAQ) were used to illustrate the molecular machinery of cold acclimation. Compared to the control (Cont), altogether, 89 differentially expressed proteins (DEPs) were identified in wucai leaves responding to low temperatures (LT). Among these proteins, 35 proteins were up-regulated ((and 54 were down-regulated). These differentially expressed proteins were categorized as having roles in carbohydrate metabolism, photosynthesis and energy metabolism, oxidative defense, amino acid metabolism, metabolic progress, cold regulation, methylation progress, and signal transduction. The fructose, glucose, and sucrose were dramatically increased in response to cold acclimation. It was firstly reported that aspartate, serine, glutamate, proline, and threonine were significantly accumulated under low temperatures. Results of quantitative real-time PCR analysis of nine DEPs displayed that the transcriptional expression patterns of six genes were consistent with their protein expression abundance. Our results demonstrated that wucai acclimated to low temperatures through regulating the expression of several crucial proteins. Additionally, carbohydrate and amino acid conversion played indispensable and vital roles in improving cold assimilation in wucai.

scholarly journals Characterization of Seed Storage Proteins from Chickpea Using 2D Electrophoresis Coupled with Mass Spectrometry

2016 ◽  
Vol 2016 ◽  
pp. 1-6 ◽  
Author(s):  
Pramod Kumar Singh ◽  
Nidhi Shrivastava ◽  
Krishna Chaturvedi ◽  
Bechan Sharma ◽  
Sameer S. Bhagyawant
Keyword(s):  
Mass Spectrometry ◽  
Storage Proteins ◽  
Seed Storage Protein ◽  
Expression Patterns ◽  
Seed Storage ◽  
Seed Storage Proteins ◽  
Differentially Expressed ◽  
2D Electrophoresis ◽  
Differentially Expressed Proteins ◽  
Amino Acid Homology

Proteomic analysis was employed to map the seed storage protein network in landrace and cultivated chickpea accessions. Protein extracts were separated by two-dimensional gel electrophoresis (2D-GE) across a broad range 3.0–10.0 immobilized pH gradient (IPG) strips. Comparative elucidation of differentially expressed proteins between two diverse geographically originated chickpea accessions was carried out using 2D-GE coupled with mass spectrometry. A total of 600 protein spots were detected in these accessions. In-gel protein expression patterns revealed three protein spots as upregulated and three other as downregulated. Using trypsin in-gel digestion, these differentially expressed proteins were identified by matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) which showed 45% amino acid homology of chickpea seed storage proteins withArabidopsis thaliana.

scholarly journals LC-MS/MS analysis of lesional and normally looking psoriatic skin reveals significant changes in protein metabolism and RNA processing

PLoS ONE ◽  
2021 ◽  
Vol 16 (5) ◽  
pp. e0240956
Author(s):  
V. V. Sobolev ◽  
A. V. Mezentsev ◽  
R. H. Ziganshin ◽  
A. G. Soboleva ◽  
M. Denieva ◽  
...  
Keyword(s):  
Healthy Volunteers ◽  
Rna Processing ◽  
Protein Identification ◽  
Expression Patterns ◽  
Differentially Expressed ◽  
Psoriatic Skin ◽  
Differentially Expressed Proteins ◽  
Kinin System ◽  
Lesional Skin ◽  
Kallikrein Kinin System

Background Plaque psoriasis is a chronic autoimmune disorder characterized by the development of red scaly plaques. To date psoriasis lesional skin transcriptome has been extensively studied, whereas only few proteomic studies of psoriatic skin are available. Aim The aim of this study was to compare protein expression patterns of lesional and normally looking skin of psoriasis patients with skin of the healthy volunteers, reveal differentially expressed proteins and identify changes in cell metabolism caused by the disease. Methods Skin samples of normally looking and lesional skin donated by psoriasis patients (n = 5) and samples of healthy skin donated by volunteers (n = 5) were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). After protein identification and data processing, the set of differentially expressed proteins was subjected to protein ontology analysis to characterize changes in biological processes, cell components and molecular functions in the patients’ skin compared to skin of the healthy volunteers. The expression of selected differentially expressed proteins was validated by ELISA and immunohistochemistry. Results The performed analysis identified 405 and 59 differentially expressed proteins in lesional and normally looking psoriatic skin compared to healthy control. In normally looking skin of the patients, we discovered decreased expression of KNG1, APOE, HRG, THBS1 and PLG. Presumably, these changes were needed to protect the epidermis from spontaneous activation of kallikrein-kinin system and delay the following development of inflammatory response. In lesional skin, we identified several large groups of proteins with coordinated expression. Mainly, these proteins were involved in different aspects of protein and RNA metabolism, namely ATP synthesis and consumption; intracellular trafficking of membrane-bound vesicles, pre-RNA processing, translation, chaperoning and degradation in proteasomes/immunoproteasomes. Conclusion Our findings explain the molecular basis of metabolic changes caused by disease in skin lesions, such as faster cell turnover and higher metabolic rate. They also indicate on downregulation of kallikrein-kinin system in normally looking skin of the patients that would be needed to delay exacerbation of the disease. Data are available via ProteomeXchange with identifier PXD021673.

scholarly journals Quantitative proteomic analysis identified differentially expressed proteins with tail/rump fat deposition in Chinese thin- and fat-tailed lambs

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0246279
Author(s):  
Jilong Han ◽  
Tingting Guo ◽  
Yaojing Yue ◽  
Zengkui Lu ◽  
Jianbin Liu ◽  
...  
Keyword(s):  
Adipose Tissue ◽  
Expression Patterns ◽  
Fat Deposition ◽  
The Body ◽  
Differentially Expressed ◽  
Peroxisome Proliferator ◽  
Differentially Expressed Proteins ◽  
Peroxisome Proliferator Activated Receptor ◽  
Fat Accumulation ◽  
Hazardous Environments

Tail adipose as one of the important functional tissues can enhance hazardous environments tolerance for sheep. The objective of this study was to gain insight into the underlying development mechanisms of this trait. A quantitative analysis of protein abundance in ovine tail/rump adipose tissue was performed between Chinese local fat- (Kazakh, Hu and Lanzhou) and thin-tailed (Alpine Merino, Tibetan) sheep in the present study by using lable-free approach. Results showed that 3400 proteins were identified in the five breeds, and 804 were differentially expressed proteins, including 638 up regulated proteins and 83 down regulated proteins in the tail adipose tissues between fat- and thin-tailed sheep, and 8 clusters were distinguished for all the DEPs’ expression patterns. The differentially expressed proteins are mainly associated with metabolism pathways and peroxisome proliferator activated receptor signaling pathway. Furthermore, the proteomics results were validated by quantitative real-time PCR and Western Blot. Our research has also suggested that the up-regulated proteins ACSL1, HSD17β4, FABP4 in the tail adipose tissue might contribute to tail fat deposition by facilitating the proliferation of adipocytes and fat accumulation in tail/rump of sheep. Particularly, FABP4 highly expressed in the fat-tail will play an important role for tail fat deposition. Our study might provide a novel view to understanding fat accumulation in special parts of the body in sheep and other animals.

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