A comparative proteomic analysis for adventitious root formation in lotus root (Nelumbo nucifera Gaertn)

2017 ◽  
Vol 72 (5-6) ◽  
pp. 181-196
Author(s):  
Cheng Libao ◽  
Jiang Runzhi ◽  
Yang Mengli ◽  
Li Liangjun ◽  
Li Shuyan
Keyword(s):  
Molecular Mechanisms ◽  
Root Formation ◽  
Molecular Level ◽  
Adventitious Root Formation ◽  
Lotus Root ◽  
Liquid Chromatography Tandem Mass ◽  
Three Stages ◽  
Isobaric Tags ◽  
Related Proteins ◽  
Insight Into

AbstractAdventitious roots (ARs) directly affect lotus seedling growth and product quality because principal root is not well developed. However, the details of AR formation at the molecular level have not been determined in lotus. Therefore, three stages were chosen to identify the change of proteins abundant during rhizome formation, using isobaric tags for relative and absolute quantization coupled with liquid chromatography–tandem mass spectrometry to gain insight into the molecular mechanisms involved in AR formation. We totally obtained 323,375 spectra during AR formation. After filtering to eliminate low-scoring spectra, 66,943 spectra, including 53,106 unique spectra, were identified. These unique spectra matched 28,905 peptides, including 24,992 unique peptides, which were assembled into 6686 proteins. In the C0/C1 and C1/C2 stages, 66 and 32 proteins showed enhanced abundance, and 173 and 73 proteins showed decreased abundance, respectively. Seventeen important AR formation-related proteins from the three stages were identified, and the expressions of nine genes from the above-identified proteins were assessed by qRT-PCR. This article provides a comprehensive understanding of the changes in metabolism during AR formation, and is helpful to accelerate the progress of breeding in fulture in lotus root.

scholarly journals In Silico Investigation of the Anti-Tumor Mechanisms of Epigallocatechin-3-Gallate

Molecules ◽  
2019 ◽  
Vol 24 (7) ◽  
pp. 1445 ◽  
Author(s):  
Wang Wang ◽  
Xiuhong Xiong ◽  
Xue Li ◽  
Qinyang Zhang ◽  
Wentao Yang ◽  
...  
Keyword(s):  
Green Tea ◽  
Molecular Mechanisms ◽  
Protein Database ◽  
Tumor Target ◽  
Target Proteins ◽  
Pharmacological Mechanism ◽  
Putative Target ◽  
Docking Method ◽  
Related Proteins ◽  
Insight Into

The EGCG, an important component of polyphenol in green tea, is well known due to its numerous health benefits. We employed the reverse docking method for the identification of the putative targets of EGCG in the anti-tumor target protein database and these targets were further uploaded to public databases in order to understand the underlying pharmacological mechanisms and search for novel EGCG-associated targets. Similarly, the pharmacological linkage between tumor-related proteins and EGCG was manually constructed in order to provide greater insight into the molecular mechanisms through a systematic integration with applicable bioinformatics. The results indicated that the anti-tumor mechanisms of EGCG may involve 12 signaling transduction pathways and 33 vital target proteins. Moreover, we also discovered four novel putative target proteins of EGCG, including IKBKB, KRAS, WEE1 and NTRK1, which are significantly related to tumorigenesis. In conclusion, this work may provide a useful perspective that will improve our understanding of the pharmacological mechanism of EGCG and identify novel potential therapeutic targets.

scholarly journals A Novel Insight Into Mechanism of Derangement of Coagulation Balance: Interactions of Quantum Dots with Coagulation-Related Proteins

2021 ◽  
Author(s):  
Lingyan Zhang ◽  
Yingting Wu ◽  
Xingling Luo ◽  
Tianjiang Jia ◽  
Kexin Li ◽  
...  
Keyword(s):  
Quantum Dots ◽  
Active Sites ◽  
Molecular Level ◽  
Comprehensive Evaluation ◽  
Circulatory System ◽  
Electronic Products ◽  
Protein Conjugates ◽  
Related Proteins ◽  
Insight Into ◽  
Biosafety Evaluation

Abstract Background Quantum dots (QDs) have gained increased attention for their extensive biomedical and electronic products applications. Due to the high priority of QDs in contacting the circulatory system, understanding the hemocompatibility of QDs is one of the most important aspects for their biosafety evaluation. Thus far, the effect of QDs on coagulation balance haven’t been fully understood, and limited studies also have yet elucidated the potential mechanism from the perspective of interaction of QDs with coagulation-related proteins. Results QDs induced the derangement of coagulation balance by prolonging the activated partial thromboplastin time and prothrombin time as well as changing the expression levels of coagulation and fibrinolytic factors. The contact of QDs with PTM (prothrombin), PLG (plasminogen) and FIB (fibrinogen) which are primary coagulation-related proteins in the coagulation and fibrinolytic systems formed QDs-protein conjugates through hydrogen-bonding and hydrophobic interaction. The affinity of proteins with QDs followed the order of PTM>PLG>FIB, and was larger with CdTe/ZnS QDs than CdTe QDs. Binding with QDs not only induced static fluorescence quenching of PTM, PLG and FIB, but also altered their conformational structures. The binding of QDs to the active sites of PTM, PLG and FIB may promote the activation of proteins, thus interfering the hemostasis and fibrinolysis processes. Conclusions The interactions of QDs with PTM, PLG and FIB may be key contributors for interference of coagulation balance, that is helpful to achieve a reliable and comprehensive evaluation on the potential biological influence of QDs from the molecular level.

Transcriptome profiling reveals an IAA-regulated response to adventitious root formation in lotus seedling

2018 ◽  
Vol 73 (5-6) ◽  
pp. 229-240 ◽  
Author(s):  
Cheng Libao ◽  
Jiang Runzhi ◽  
Yang Jianjun ◽  
Xu Xiaoyong ◽  
Zeng Haitao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Root Formation ◽  
Molecular Level ◽  
Critical Role ◽  
Transcriptome Profiling ◽  
Adventitious Root Formation ◽  
Transcriptional Level ◽  
Comprehensive Understanding ◽  
Sequencing Technique ◽  
Indole 3 Acetic Acid

AbstractAdventitious roots (ARs) of lotus (NelumbonuciferaGaertn.) play a critical role in water and nutrient uptake. We found that exogenously applied 10-μM indole-3-acetic acid (IAA) promoted the formation of ARs, while 150-μM IAA significantly inhibited the emergence of ARs. However, little is known about these different responses to various concentrations of IAA at the molecular level. This study, therefore, examined the gene expression profiling in four libraries treated with 10- and 150-μM IAA based on the high-throughout tag sequencing technique. Approximately 2.4×107clean tags were obtained after the removal of low-quality tags from each library respectively, among which about 10% clean tags were unambiguous tag-mapped genes to the reference genes. We found that some genes involved in auxin metabolism showed a similar tendency for expression in the A/CK and C/CK libraries, while three genes were enhanced their expression only in the A/CK libraries. Two transcription factors including B3 domain-containing protein At2g36080-like and trihelix transcription factor were up-regulated for transcriptional level in the A/C libraries. The expressions of six important genes related to AR formation were significantly different in the A/CK and C/CK libraries. In summary, this study provides a comprehensive understanding of gene expression regulated by IAA involved in AR formation in lotus.

scholarly journals Integrated Proteotranscriptomics of Human Myometrium in Labor Landscape Reveals the Increased Molecular Associated With Inflammation Under Hypoxia Stress

2021 ◽  
Vol 12 ◽  
Author(s):  
Lina Chen ◽  
Lele Wang ◽  
Yihong Luo ◽  
Qian Huang ◽  
Kaiyuan Ji ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Differentially Expressed ◽  
Human Myometrium ◽  
Rna Seq ◽  
Hypoxia Stress ◽  
Data Independent Acquisition ◽  
Parallel Reaction Monitoring ◽  
Liquid Chromatography Tandem Mass ◽  
Related Proteins ◽  
Physiological And Biochemical

During labor, a variety of coordinated physiological and biochemical events cause the myometrium to transition from a quiescent to contractile state; the molecular mechanisms responsible for this transition, however, remain unclear. To better understand this transition at a molecular level, the global transcriptome and proteome of human myometrial samples in labor and those not in labor were investigated through RNA sequencing (RNA-seq) and quantitative liquid chromatography–tandem mass spectrometry (LC-MS/MS) via data-independent acquisition (DIA) and parallel reaction monitoring (PRM) methods. Furthermore, an integrated proteotranscriptomic analysis was performed to explore biological processes and pathway alterations during labor; this analysis identified 1,626 differentially expressed mRNAs (1,101 upregulated, 525 downregulated) and 135 differentially expressed proteins (97 upregulated, 38 downregulated) in myometrium between nonlabor and in labor groups. The comprehensive results of these analyses showed that the upregulated mRNAs and proteins increased inflammation under hypoxia stress in the myometrium under labor, and related proteins and cytokines were validated by PRM and Luminex assays. Our study confirmed the biological process of inflammation and hypoxia in laboring myometrium at the transcriptome and proteome levels and provided recourse to discover new molecular and biological changes during labor.

scholarly journals Differential Protein Analysis of Pecan Hardwood Cuttings

HortScience ◽  
2019 ◽  
Vol 54 (9) ◽  
pp. 1551-1557 ◽  
Author(s):  
Fan Cao ◽  
Xinwang Wang ◽  
Zhuangzhuang Liu ◽  
Yongrong Li ◽  
Fangren Peng
Keyword(s):  
Energy Metabolism ◽  
Adventitious Root ◽  
Stress Proteins ◽  
Root Formation ◽  
Signal Transmission ◽  
Adventitious Rooting ◽  
Adventitious Root Formation ◽  
Differentially Expressed Proteins ◽  
Differential Protein ◽  
Related Proteins

Pecan cuttings are difficult for rooting. This study describes the pecan hardwood rooting process based on anatomic characteristics to understand root formation mechanisms of pecan cuttings. The expressed proteins of different periods during the adventitious rooting process of pecan seedling hardwood cuttings were identified and analyzed to evaluate the rooting mechanism. The expressed proteins of pecan cutting seedlings were also compared with other cultivar cuttings during the rooting period. Pecan seedling cuttings were developed at different air and substrate temperatures to induce root formation. Adventitious root formation of pecan hardwood cuttings was described, and the phloem at the base of the prepared cuttings was selected as the sample for the differential protein analysis. The results showed that adventitious root formation of pecan hardwood cuttings was the only product of callus differentiation, which originated from the cells of the cambium or vascular ray parenchyma. Such adventitious root primordia were developed from those calluses that formed the regenerative structure, and the expressed proteins during the adventitious rooting of pecan hardwood cutting were identified and analyzed by matrix-assisted laser desorption ionization–time of flight–mass spectrometry (MALDI-TOF-MS) to evaluate the rooting mechanism. Eight differentially expressed proteins were found in the rooting periods, and 15 differential proteins were found by comparing pecan cutting types, which were analyzed by peptide mass fingerprinting homology. The results show that the primordial cells were differentiated from the meristematic cells. Furthermore, the differentially expressed proteins contained energy metabolism proteins, adversity stress proteins, and signal transmission proteins. The energy metabolism-related proteins were adenosine triphosphate (ATP) synthase, photosynthesis-related proteins, and enolase. The adversity-stress proteins containing heat shock-related proteins and signal transmission proteins were mainly cytochrome enzymes and heme-binding proteins. Adventitious root formation of pecan cultivar hardwood cuttings was difficult. More trials should be performed from the potential aspects of high defensive protection and phloem morphologic structure.

scholarly journals Intersection between ageing-related Genes and SARS-CoV-2 Interactome: Is it higher than expected?

2020 ◽  
Author(s):  
Pietro Hiram Guzzi ◽  
Elisabetta Pedace ◽  
Federico Manuel Giorgi
Keyword(s):  
Virus Infection ◽  
Severe Acute Respiratory Syndrome ◽  
Elderly Patients ◽  
Elderly People ◽  
Mechanism Of Action ◽  
Molecular Mechanisms ◽  
Molecular Level ◽  
Adverse Outcomes ◽  
Molecular Changes ◽  
Related Proteins

Abstract Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (coronavirus disease, 2019; COVID-19) is associated with adverse outcomes in patients. It has been observed that lethality seems to be related to the age of patients. Moreover, it has been demonstrated that ageing causes some modifications at a molecular level.Objective: The study aims to investigate a possible link between the increased COVID-19 lethality and the molecular changes that occur in elderly people.Methods: We considered publicly available datasets on ageing-related genes and SARS-CoV-2 interactors. Then, for each SARS-CoV-2 protein interactor, we tested for the enrichment of ageing-related proteins. Finally, we performed a network-based analysis to identify which molecular mechanisms could play a role in the SARS-CoV-2 molecular aetiology and ultimately affect COVID-19 outcome.Results: We observed a significant intersection between some SARS-CoV-2 interactors and ageing-related genes. Our analysis evidenced that virus infection particularly affects ageing molecular mechanisms centred around proteins EEF2, NPM1, HMGA1, HMGA2, APEX1, CHEK1, PRKDC, and GPX4.Conclusion: Our study generated a mechanistic framework aiming at explaining the correlation between COVID-19 incidence in elderly patients and molecular mechanisms of ageing. This will provide testable hypotheses for future investigation on the mechanism of action of coronaviruses and pharmacological solutions tailored on specific age ranges.

scholarly journals Tandem Mass Tag labelling quantitative acetylome analysis of differentially modified proteins during mycoparasitism of Clonostachys chloroleuca 67–1

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Na Jiang ◽  
Binna Lv ◽  
Haixia Wu ◽  
Shidong Li ◽  
Manhong Sun
Keyword(s):  
Fungal Pathogens ◽  
Molecular Mechanisms ◽  
Tandem Mass ◽  
The Novel ◽  
Post Translational Modification ◽  
Bioinformatics Analyses ◽  
Tandem Mass Tag ◽  
Liquid Chromatography Tandem Mass ◽  
Insight Into ◽  
Mass Tag

AbstractLysine acetylation (Kac) is an important post-translational modification (PTM) of proteins in all organisms, but its functions have not been extensively explored in filamentous fungi. In this study, a Tandem Mass Tag (TMT) labelling lysine acetylome was constructed, and differentially modified Kac proteins were quantified during mycoparasitism and vegetative growth in the biocontrol fungus Clonostachys chloroleuca 67–1, using liquid chromatography-tandem mass spectrometry (LC–MS/MS). A total of 1448 Kac sites were detected on 740 Kac proteins, among which 126 sites on 103 proteins were differentially regulated. Systematic bioinformatics analyses indicate that the modified Kac proteins were from multiple subcellular localizations and involved in diverse functions including chromatin assembly, glycometabolism and redox activities. All Kac sites were characterized by 10 motifs, including the novel CxxKac motif. The results suggest that Kac proteins may have effects of broadly regulating protein interaction networks during C. chloroleuca parasitism to Sclerotinia sclerotiorum sclerotia. This is the first report of a correlation between Kac events and the biocontrol activity of C. chloroleuca. Our findings provide insight into the molecular mechanisms underlying C. chloroleuca control of plant fungal pathogens regulated by Kac proteins.

scholarly journals Proteomic Insight Into the Molecular Principles of Grapevine Habituation

2011 ◽  
Vol 57 (4) ◽  
pp. 129-136
Author(s):  
Mária Čarná ◽  
Vladimír Repka ◽  
Ernest Šturdí
Keyword(s):  
Defense Mechanisms ◽  
Molecular Mechanisms ◽  
Protein Microarray ◽  
Molecular Evidence ◽  
Two Dimensional Gel Electrophoresis ◽  
Expression Of Genes ◽  
Differential Expression Pattern ◽  
Protein Microarray Analysis ◽  
Related Proteins ◽  
Insight Into

Proteomic Insight Into the Molecular Principles of Grapevine Habituation Two-dimensional gel electrophoresis coupled to protein microarray analysis was used to examine, for the first time, the molecular mechanisms of grapevine (Vitis vinifera L., cv. Limberger) habituation. The examination of 2-D maps derived from control and habituated cell culture revealed the presence of 55 protein spots displaying a differential expression pattern. These facts have provide a molecular evidence suggesting that the habituated cells can be used as a model for study of cell differentiation and plant defense mechanisms. Cell death, extra-cellular alkalinization and expression of genes responsible for the formation of the defense-related proteins were analyzed in suspension cultures with hormonal autonomy (habituation). Results obtained using habituated grapevine cells compared with non-habituated cells were different and strongly depended on the concentration of elicitor applied.

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