Comprehensive Phosphoproteomic Analysis of Pepper Fruit Development Provides Insight into Plant Signaling Transduction

Phosphoproteomic Analysis Indicates Phosphorylated Proteins in Response to Postharvest Blueberries Fruit Softening during Shelf Life

Postharvest blueberry fruit is prone to softening. Protein phosphorylation is an important post-translational modification that was involved in fruit softening. However, little is known about protein phosphorylation in postharvest blueberry fruit softening. The firmness, the apparent morphology, and cell structures of blueberry fruit were changed. As the decay rate of postharvest blueberry fruit increased, the soluble solid and titrable acid contents decreased significantly. Phosphoproteomic sequencing results showed that there were 4100 phosphorylated peptides, 5635 phosphorylated sites, and 1437 phosphorylated proteins and showed significant differences on 0 and 8 d. The GO database and KEGG pathway results indicated that these phosphorylated proteins were mainly involved in "biological process", "molecular function", "plant hormone signal transduction", and "metabolic pathways". Besides, a number of phosphorylated proteins were found in cell wall metabolism, plant hormone signaling, primary metabolism, energy metabolism, membrane and transport, ubiquitination-based proteins, and other metabolisms.

WTAP promotes proliferation of esophageal squamous cell carcinoma via m6A-dependent epigenetic promoting of PTP4A1

Esophageal squamous cell carcinoma (ESCC) represents a frequently seen malignancy with high prevalence worldwide. Although current studies have shown that Wilms' tumor 1-associated protein (WTAP), a major part in the methyltransferase complex, is involved in various tumor pathological processes, its specific role in ESCC remains unclear. Therefore, the present work focused on exploring WTAP's function and mechanism in ESCC progression using clinical ESCC specimens, ESCC cells, and mammalian models. Firstly, we proved WTAP was significantly upregulated within ESCC, and WTAP mRNA expression showed a good diagnostic performance for ESCC. Functionally, WTAP positively regulated in-vivo and in-vitro ESCC cells' malignant phenotype through the AKT-mTOR signaling pathway. Meanwhile, WTAP positively regulated the N6-methyladenosine (m6A) modification levels in ESCC cells. Protein tyrosine phase type IVA member 1 (PTP4A1) was confirmed to be the m6A target of WTAP, and WTAP positively regulated the expression of PTP4A1. Further study revealed that PTP4A1 showed high expression within ESCC. Silencing PTP4A1 inhibited the AKT-mTOR signaling pathway to suppress ESCC cells' proliferation. Rescue experiments showed that silencing PTP4A1 partially reversed the WTAP-promoting effect on ESCC cells' proliferation ability. Mechanistically, WTAP regulated PTP4A1 expression to activate the AKT-mTOR pathway, promoting the proliferation of ESCC cells. Our study demonstrated that WTAP regulates the progression of ESCC through the m6A-PTP4A1-AKT-mTOR signaling axis and that WTAP is a potential target for diagnosing and treating ESCC.

Quantitative Phosphoproteomic Analysis Reveals Potential Regulatory Mechanisms of Early Fruit Enlargement in Pecan (Carya illinoinensis)

Pecan (Carya illinoinensis) is a popular tree nut. Its fruit development undergoes slow growth, rapid expansion, core hardening, and kernel maturation stages. However, little is known about how pecan initiates fruit development and enlargement after pollination. In this study, we performed the first large-scale identification of potential phosphorylation sites and proteins at early development of pecan fruit by a label-free phosphoproteomic quantification technique. A total of 2155 phosphosites were identified from 1953 phosphopeptides covering 1311 phosphoproteins in unpollinated pistils and fruits at 5 and 9 weeks after pollination. Of these, 699 nonredundant phosphoproteins were differentially phosphorylated (DP). Furthermore, the phosphorylation intensity of DP proteins in brassinolide (BR) and auxin signaling were analyzed, and the function of CiBZR1 was investigated. Ectopic expression of CiBZR1 resulted in BR response phenotypes with curled leaves and fruit, while enlarged seed size in Arabidopsis. Subcellular localization and transcriptional activation activity assay demonstrated that CiBZR1 distributed in both the nucleus and cytoplasm with transcriptional activity. When two phosphosites mutated, CiBZR1^S201P,S205G moved to the nucleus completely, while the transcriptional activity remained unchanged. Taken together, our data reveal extensive phosphoproteins and lay a foundation to comprehensively dissect the potential post-translational regulation mechanism of early development of pecan fruit.

Integrative Proteomics and Phosphoproteomics Analysis of the Rat Adenohypophysis after GnRH Treatment

The regulation of mammalian reproductive activity is tightly dependent on the HPG axis crosstalk, in which several reproductive hormones play important roles. Among them, the physiological functions of gonadotropins are gradually being uncovered. However, the mechanisms by which GnRH regulates FSH synthesis and secretion still need to be more extensively and deeply explored. With the gradual completion of the human genome project, proteomes have become extremely important in the fields of human disease and biological process research. To explore the changes of protein and protein phosphorylation modifications in the adenohypophysis after GnRH stimulation, proteomics and phosphoproteomics analyses of rat adenohypophysis after GnRH treatment were performed by using TMT markers, HPLC classification, LC/MS, and bioinformatics analysis in this study. A total of 6762 proteins and 15,379 phosphorylation sites contained quantitative information. Twenty-eight upregulated proteins and fifty-three downregulated proteins were obtained in the rat adenohypophysis after GnRH treatment. The 323 upregulated phosphorylation sites and 677 downregulated phosphorylation sites found in the phosphoproteomics implied that a large number of phosphorylation modifications were regulated by GnRH and were involved in FSH synthesis and secretion. These data constitute a protein-protein phosphorylation map in the regulatory mechanism of "GnRH-FSH," which provides a basis for future studies on the complex molecular mechanisms of FSH synthesis and secretion. The results will be helpful for understanding the role of GnRH in the development and reproduction regulated by the pituitary proteome in mammals.

A Data-Driven Signaling Network Inference Approach for Phosphoproteomics

Proteins are rapidly and dynamically post-transcriptionally modified as cells respond to changes in their environment. For example, protein phosphorylation is mediated by kinases while dephosphorylation is mediated by phosphatases. Quantifying and predicting interactions between kinases, phosphatases, and target proteins over time will aid the study of signaling cascades under a variety of environmental conditions. Here, we describe methods to statistically analyze label-free phosphoproteomic data and infer posttranscriptional regulatory networks over time. We provide an R-based method that can be used to normalize and analyze label-free phosphoproteomic data using variance stabilizing normalization and a linear mixed model across multiple time points and conditions. We also provide a method to infer regulator-target interactions over time using a discretization scheme followed by dynamic Bayesian modeling computations to validate our conclusions. Overall, this pipeline is designed to perform functional analyses and predictions of phosphoproteomic signaling cascades.

Novel Translational and Phosphorylation Modification Regulation Mechanisms of Tomato (Solanum lycopersicum) Fruit Ripening Revealed by Integrative Proteomics and Phosphoproteomics

The tomato is a research model for fruit-ripening, however, its fruit-ripening mechanism still needs more extensive and in-depth exploration. Here, using TMT and LC-MS, the proteome and phosphoproteome of AC⁺⁺ (wild type) and rin (ripening-inhibitor) mutant fruits were studied to investigate the translation and post-translational regulation mechanisms of tomato fruit-ripening. A total of 6141 proteins and 4011 phosphorylation sites contained quantitative information. One-hundred proteins were identified in both omics’ profiles, which were mainly found in ethylene biosynthesis and signal transduction, photosynthesis regulation, carotenoid and flavonoid biosynthesis, chlorophyll degradation, ribosomal subunit expression changes, MAPK pathway, transcription factors and kinases. The affected protein levels were correlated with their corresponding gene transcript levels, such as NAC-NOR, MADS-RIN, IMA, TAGL1, MADS-MC and TDR4. Changes in the phosphorylation levels of NAC-NOR and IMA were involved in the regulation of tomato fruit-ripening. Although photosynthesis was inhibited, there were diverse primary and secondary metabolic pathways, such as glycolysis, fatty acid metabolism, vitamin metabolism and isoprenoid biosynthesis, regulated by phosphorylation. These data constitute a map of protein—protein phosphorylation in the regulation of tomato fruit-ripening, which lays the foundation for future in-depth study of the sophisticated molecular mechanisms of fruit-ripening and provide guidance for molecular breeding.

Plant Cell and Organism Development

Plants represent a unique and fascinating group of living organisms [...].