Plasmodium falciparum Calcium-Dependent Protein Kinase 4 is Critical for Male Gametogenesis and Transmission to the Mosquito Vector

Transmission of the malaria parasite to the mosquito vector is critical for the completion of the sexual stage of the parasite life cycle and is dependent on the release of male gametes from the gametocyte body inside the mosquito midgut. In the present study, we demonstrate that PfCDPK4 is critical for male gametogenesis and is involved in phosphorylation of proteins essential for male gamete emergence.

Reduced Membrane Cholesterol Content in Skeletal Muscle Is Not Essential for Greater Insulin-stimulated Glucose Uptake after Acute Exercise by Rats

One exercise session can elevate insulin-stimulated glucose uptake (GU) by skeletal muscle, but it is uncertain if this effect is accompanied by altered membrane cholesterol content, which is reportedly inversely related to insulin-stimulated GU. Muscles from sedentary (SED) or exercised 3hours post-exercise (3hPEX) rats were evaluated for: GU, membrane cholesterol, and phosphorylation of cholesterol regulatory proteins (pHMCGRSer872 and pABCA1Ser2054). Insulin-stimulated GU for 3hPEX exceeded SED. Membrane cholesterol, pHMCGRSer872 and pABCA1Ser2054 did not differ between groups. Novelty: Alterations in membrane cholesterol and phosphorylation of proteins that regulate muscle cholesterol are not essential for elevated insulin-stimulated GU in skeletal muscle after acute exercise.

Proteogenomic characterization of hepatocellular carcinoma

SUMMARYWe performed a proteogenomic analysis of hepatocellular carcinomas (HCCs) across clinical stages and etiologies. We identified pathways differentially regulated on the genomic, transcriptomic, proteomic and phosphoproteomic levels. These pathways are involved in the organization of cellular components, cell cycle control, signaling pathways, transcriptional and translational control and metabolism. Analyses of CNA-mRNA and mRNA-protein correlations identified candidate driver genes involved in epithelial-to-mesenchymal transition, the Wnt-β-catenin pathway, transcriptional control, cholesterol biosynthesis and sphingolipid metabolism. The activity of targetable kinases aurora kinase A and CDKs was upregulated. We found that CTNNB1 mutations are associated with altered phosphorylation of proteins involved in actin filament organization, whereas TP53 mutations are associated with elevated CDK1/2/5 activity and altered phosphorylation of proteins involved in lipid and mRNA metabolism. Integrative clustering identified HCC subgroups with distinct regulation of biological processes, metabolic reprogramming and kinase activation. Our analysis provides insights into the molecular processes underlying HCCs.

Label-Free Quantitative Phosphoproteomics of the Fission Yeast Schizosaccharomyces pombe Using Strong Anion Exchange- and Porous Graphitic Carbon-Based Fractionation Strategies

The phosphorylation of proteins modulates various functions of proteins and plays an important role in the regulation of cell signaling. In recent years, label-free quantitative (LFQ) phosphoproteomics has become a powerful tool to analyze the phosphorylation of proteins within complex samples. Despite the great progress, the studies of protein phosphorylation are still limited in throughput, robustness, and reproducibility, hampering analyses that involve multiple perturbations, such as those needed to follow the dynamics of phosphoproteomes. To address these challenges, we introduce here the LFQ phosphoproteomics workflow that is based on Fe-IMAC phosphopeptide enrichment followed by strong anion exchange (SAX) and porous graphitic carbon (PGC) fractionation strategies. We applied this workflow to analyze the whole-cell phosphoproteome of the fission yeast Schizosaccharomyces pombe. Using this strategy, we identified 8353 phosphosites from which 1274 were newly identified. This provides a significant addition to the S. pombe phosphoproteome. The results of our study highlight that combining of PGC and SAX fractionation strategies substantially increases the robustness and specificity of LFQ phosphoproteomics. Overall, the presented LFQ phosphoproteomics workflow opens the door for studies that would get better insight into the complexity of the protein kinase functions of the fission yeast S. pombe.

Mitochondrial Metabolism, Dysfunctions in Senescence Cell and the Possible Interventions through Herbal Medicines

The mitochondria are the cell`s powerhouse. They are considered ubiquitous organelles of all eukaryotic cells, being responsible for the cell’s life and death cycle. Through stimuli in the environment in which they live, mitochondria can modulate their own biogenesis as well as signal retrograde to the nucleus to modify the structure of their proteins. Since the mitochondrial genome contains only 37 genes, much of the encoding of its proteins depends on the nuclear genome. Thus, the communication between mitochondria and the nucleus seems to be a target of science in understanding the pathologies associated with this organelle. Some medicinal herbs have been shown to influence mitochondrial biogenesis, such as Gynostemma pentaphyllun (GP) and berberine, which increase the phosphorylation of proteins AMPactivated protein kinase (AMPK). Just as GP and berberine phosphorylate AMPK in signaling for mitochondrial biogenesis, the sesquiterpene beta-caryophyllene (BCP) demonstrated positive results in reorganizing mitochondrial transcription factors, being an agonist of the peroxisome proliferatoractivated alpha receptor (PPAR-α). Another plant derivative, the non-psychoactive cannabinoid known as cannabidiol (CBD), has been showing control in the metabolism of calcium in the mitochondrial matrix. In this review, we seek to get a closer look at the biochemical mechanisms of action of some of these plants, as well as their synergies in the results of different treatments. In the view of oriental medicines, the use of associated medicinal herbs has always been part of their treatment protocols. However, the effectiveness of these treatments in relation to plant synergy can be observed in future clinical trials for better understanding.

Effects of Bioflavonoids from Taxus Media var. Hicksii on Superoxide Generation, Phosphorylation of Proteins and Translocation of Cytosolic Compounds to the Cell Membrane in Human Neutrophils

In present work, the effects of bioflavonoids (ginkgetin and sciadopitysin) on stimulus-induced superoxide generation, tyrosyl and serine/threonine phosphorylation of proteins in human neutrophils, and the translocation of cytosolic compounds (p47phox, p67phox and Rac) to cell membrane were studied, which were isolated from the needles of Taxus media var. Hicksii. Meanwhile, three normal flavonoids (apigenin, quercetin and isoquercetin) were involved as contrasts. The results indicated that ginkgetin and sciadopitysin were capable of concentration-dependently inhibitory effects on the superoxide generation induced by N-formyl-methionyl-leucyl-phenylalanine (fMLP), arachidonic acid (AA) and phorbol-12-myristate 13-acetate (PMA). And they also suppressed fMLP- and AA- induced tyrosyl or PMA-induced serine/threonine phosphorylation and the translocation of cytosolic compounds (p47phox, p67phox and Rac) to cell membrane, which were in parallel with the suppression of the stimulus-induced superoxide generation. The effect of these compounds on the radical-scavenging was also investigated. Ginkgetin and sciadopitysin did not show remarkable effect on DPPH radical-scavenging activity, and they didn’t display the radical-scavenging activity on superoxide anion generated by phenagine methoxysulfate (PMS)-NADH system. Apparently, ginkgetin and sciadopitysin had great performance in pharmacological value and they are worthy of in-depth study.

Short-term High-fat Overfeeding Does Not Induce NF-κB Inflammatory Signaling in Subcutaneous White Adipose Tissue

Context It is unclear how white adipose tissue (WAT) inflammatory signaling proteins respond during the early stages of overnutrition. Objective To investigate the effect of short-term, high-fat overfeeding on fasting abdominal subcutaneous WAT total content and phosphorylation of proteins involved in nuclear factor-κB (NF-κB) inflammatory signaling, systemic metabolic and inflammatory biomarkers. Design Individuals consumed a high-fat (65% total energy from total fat), high-energy (50% above estimated energy requirements) diet for 7 days. Results Fifteen participants (aged 27 ± 1 years; body mass index 24.4 ± 0.6 kg/m2) completed the study. Body mass increased following high-fat overfeeding (+1.2 ± 0.2 kg; P < 0.0001). However, total content and phosphorylation of proteins involved in NF-κB inflammatory signaling were unchanged following the intervention. Fasting serum glucose (+0.2 ± 0.0 mmol/L), total cholesterol (+0.4 ± 0.1 mmol/L), low-density lipoprotein cholesterol (+0.3 ± 0.1 mmol/L), high-density lipoprotein cholesterol (+0.2 ± 0.0 mmol/L), and lipopolysaccharide-binding protein (LBP; +4.7 ± 2.1 µg/mL) increased, whereas triacylglycerol concentrations (−0.2 ± 0.1 mmol/L) decreased following overfeeding (all P < 0.05). Systemic biomarkers (insulin, soluble cluster of differentiation 14 [CD14], C-reactive protein, interleukin-6, tumor necrosis factor-α and monocyte chemoattractant protein-1) and the proportion and concentration of circulating CD14+ monocytes were unaffected by overfeeding. Conclusion Acute lipid oversupply did not impact on total content or phosphorylation of proteins involved in WAT NF-κB inflammatory signaling, despite modest weight gain and metabolic alterations. Systemic LBP, which is implicated in the progression of low-grade inflammation during the development of obesity, increased in response to a 7-day high-fat overfeeding period.

EMBER: Multi-label prediction of kinase-substrate phosphorylation events through deep learning

Kinase-catalyzed phosphorylation of proteins forms the backbone of signal transduction within the cell, enabling the coordination of numerous processes such as the cell cycle, apoptosis, and differentiation. While on the order of 105 phosphorylation events have been described, we know the specific kinase performing these functions for less than 5% of cases. The ability to predict which kinases initiate specific individual phosphorylation events has the potential to greatly enhance the design of downstream experimental studies, while simultaneously creating a preliminary map of the broader phosphorylation network that controls cellular signaling. To this end, we describe EMBER, a deep learning method that integrates kinase-phylogeny information and motif-dissimilarity information into a multi-label classification model for the prediction of kinase-motif phosphorylation events. Unlike previous deep learning methods that perform single-label classification, we restate the task of kinase-motif phosphorylation prediction as a multi-label problem, allowing us to train a single unified model rather than a separate model for each of the 134 kinase families. We utilize a Siamese network to generate novel vector representations, or an embedding, of motif sequences, and we compare our novel embedding to a previously proposed peptide embedding. Our motif vector representations are used, along with one-hot encoded motif sequences, as input to a classification network while also leveraging kinase phylogenetic relationships into our model via a kinase phylogeny-based loss function. Results suggest that this approach holds significant promise for improving our map of phosphorylation relations that underlie kinome signaling.Availabilityhttps://github.com/gomezlab/EMBER