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Keywords = protein kinases (PKs)

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21 pages, 2666 KiB  
Article
Metabolites from the Dendrobium Endophyte Pseudomonas protegens CM-YJ44 Alleviate Insulin Resistance in HepG2 Cells via the IRS1/PI3K/Akt/GSK3β/GLUT4 Pathway
by Luqi Qin, Yixia Zhou, Bei Fan, Jiahuan Zheng, Rao Diao, Jiameng Liu and Fengzhong Wang
Pharmaceuticals 2025, 18(6), 817; https://doi.org/10.3390/ph18060817 - 29 May 2025
Viewed by 525
Abstract
Background/Objectives: Endophytes can produce bioactive metabolites similar to their host plants. CM-YJ44 (Pseudomonas protegens CHA0, 99.24% similarity), an endophyte from Dendrobium officinale, has not yet validated hypoglycemic potential. This study aimed to evaluate its anti-insulin resistance (IR) activity and metabolite profile. [...] Read more.
Background/Objectives: Endophytes can produce bioactive metabolites similar to their host plants. CM-YJ44 (Pseudomonas protegens CHA0, 99.24% similarity), an endophyte from Dendrobium officinale, has not yet validated hypoglycemic potential. This study aimed to evaluate its anti-insulin resistance (IR) activity and metabolite profile. Methods: The fermentation broth of CM-YJ44 was separated into three fractions (CM-YJ44-1, -2, and -3) using semi-preparative high-performance liquid chromatography (pre-HPLC). An IR HepG2 cell model was constructed to evaluate their glucose uptake capacity. CM-YJ44-3 was further tested for oxidative stress, inflammatory, and insulin signaling pathway activation. Metabolites in CM-YJ44-3 were preliminarily identified using the Q Exactive Focus LC-MS system (QE), and the dendrobine content was quantified by ultra-performance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS). Molecular docking was performed to predict the binding affinities between dendrobine and target proteins. Results: Among the three fractions, CM-YJ44-3 significantly reduced nitric oxide (NO) and reactive oxygen species (ROS) levels in IR cells, enhanced glycogen synthesis, upregulated the activities of pyruvate kinase (PK) and hexokinase (HK), and suppressed the expression of inflammatory factors. Its mechanism of action was mainly through activation of the IRS1/PI3K/Akt/GSK3β/GLUT4 signaling pathway. QE analysis preliminarily identified 24 metabolites in CM-YJ44-3. Quantitative analysis by UPLC-MS/MS showed that the dendrobine content was 78.73 ± 4.29 ng/mL. Molecular docking results indicated that dendrobine exhibited binding energies below −5 kcal/mol with multiple target proteins involved in this signaling pathway, suggesting it may be a key bioactive component responsible for the anti-IR effect. Conclusions: This study provides the first evidence of hypoglycemic bioactive metabolite production by strain CM-YJ44, indicating its potential as a novel microbial candidate for alleviating IR. Full article
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16 pages, 6252 KiB  
Article
OsVPS16 Deficiency Enhances Salinity Tolerance in Rice by Regulating Ion Homeostasis, Antioxidant Activity, and Stress-Responsive Gene Expression
by Juan Liu, Mingming Tang, Yun Lu, Huimin Yan, Yang Liu, Yongrun Cao, Xiaohua Song, Qiuyuan Liu and Xin Ji
Agronomy 2025, 15(5), 1146; https://doi.org/10.3390/agronomy15051146 - 7 May 2025
Viewed by 580
Abstract
Soil salinization has emerged as a significant global threat to agricultural productivity. Rice is susceptible to salinity stress at the seedling stage. However, the mechanisms underlying rice responses to salinity stress remain incompletely characterized. In this study, we have characterized a transfer DNA [...] Read more.
Soil salinization has emerged as a significant global threat to agricultural productivity. Rice is susceptible to salinity stress at the seedling stage. However, the mechanisms underlying rice responses to salinity stress remain incompletely characterized. In this study, we have characterized a transfer DNA (T-DNA) insertion mutant line of rice, designated OsVPS16 (Os12g0594200), to elucidate its functional role in salt stress tolerance. A real-time quantitative PCR (RT-qPCR) analysis revealed that salt stress inhibited the expression of OsVPS16, with the vps16 mutant showing negligible expression levels. A phenotypic analysis showed that the loss of OsVPS16 enhanced primary root elongation, and increased the survival rate to improve salt stress tolerance. Compared to the wild type (DJ), the vps16 mutant accumulated less Na+ and more K+ in the shoots under salt stress. Furthermore, the vps16 mutant displayed decreased malondialdehyde (MDA) accumulation and enhanced the activities of superoxide dismutase (SOD) and peroxidase (POD) under salt stress. Transcriptomic profiling identified 1236 differentially expressed genes (DEGs) between vps16 and DJ roots under salt stress. A functional enrichment analysis revealed that DEGs were enriched in protein serine/threonine kinase activity, Ca2+ signal pathways, and the MAPK signaling pathway. Notably, the up-regulation of critical protein kinases (PKs) and transcription factors (TFs), including OsSRK1, OsCDPK21, and OsNAC45, probably adds to the effect of OsVPS16 mutation to account for salt stress tolerance. Collectively, comprehensive physiological and molecular analyses demonstrated that the loss of OsVPS16 improves rice salt tolerance through multiple mechanisms, including the regulation of K+/Na+ homeostasis, the modulation of antioxidant enzyme activities, and the transcriptional reprogramming of stress-responsive genes. This study not only elucidates the function of a novel salt stress response gene in rice, but also provides valuable genetic resources for developing salt-tolerant rice cultivars through molecular breeding approaches. Full article
(This article belongs to the Section Plant-Crop Biology and Biochemistry)
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27 pages, 6562 KiB  
Article
A Positive Feedback DNA-PK/MYT1L-CXCR1-ERK1/2 Proliferative Signaling Loop in Glioblastoma
by Bo Wang, Dongping Li, Yaroslav Ilnytskyy, Levon M. Khachigian, Nuanying Zhong, Rocio Rodriguez-Juarez, Igor Kovalchuk and Olga Kovalchuk
Int. J. Mol. Sci. 2025, 26(9), 4398; https://doi.org/10.3390/ijms26094398 - 6 May 2025
Cited by 1 | Viewed by 520
Abstract
Glioblastoma is the most common primary brain tumor in adults. Our previous studies revealed a functional interplay of myelin transcription factor 1-like (MYT1L) with the DNA-dependent protein kinase (DNA-PK) in the regulation of p21 transcription. However, the contributing role of this functional interplay [...] Read more.
Glioblastoma is the most common primary brain tumor in adults. Our previous studies revealed a functional interplay of myelin transcription factor 1-like (MYT1L) with the DNA-dependent protein kinase (DNA-PK) in the regulation of p21 transcription. However, the contributing role of this functional interplay in glioblastoma remains largely unknown. Here, we used cell lines with normal DNA-PK (HEK293 and M059K) or deficient DNA-PK (M059J) as a model system to demonstrate the importance of the DNA-PK-dependent activation of MYT1L in controlling the transcription of CXC chemokine receptor 1 (CXCR1) in a positive-feedback proliferative signaling loop in glioblastoma with numerous conventional techniques. In normal DNA-PK cells, MYT1L acted as an oncogene by promoting cell proliferation, inhibiting apoptosis, and shortening a cell cycle S phase. However, in DNA-PK-deficient cells, MYT1L functioned as a tumor suppressor by inhibiting cell proliferation and inducing a G1 arrest. The enforced expression of MYT1L promoted CXCR1 transcription in DNA-PK-normal cells but attenuated transcription in DNA-PK-deficient cells. Bioinformatics analysis predicted a MYT1L-binding sequence at the CXCR1 promoter. The functional dependence of MYT1L on DNA-PK in CXCR1 transcription was validated by luciferase assay. Although the expression of CXCR1 was lower in M059J cells as compared to M059K cells, it was higher than in normal brain tissue. The CXCR1 ligands interleukin 8 (IL-8) and GRO protein alpha (GROα) expressed in M059J and M059K cells may signal through the extracellular signal-regulated kinase 1/2 (ERK1/2) pathway that can be blocked by CXCR1 siRNA. Our findings demonstrate the existence of a positive feedback DNA-PK/MYT1L-CXCR1-ERK1/2 proliferation loop in glioblastoma cells that may represent a pharmacological target loop for therapeutic intervention. Full article
(This article belongs to the Section Molecular Oncology)
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13 pages, 4830 KiB  
Article
PKM2 Facilitates Classical Swine Fever Virus Replication by Enhancing NS5B Polymerase Function
by Mengzhao Song, Shanchuan Liu, Yan Luo, Tiantian Ji, Yanming Zhang and Wen Deng
Viruses 2025, 17(5), 648; https://doi.org/10.3390/v17050648 - 29 Apr 2025
Viewed by 483
Abstract
Host metabolic reprogramming is a critical strategy employed by many viruses to support their replication, and the key metabolic enzyme plays important roles in virus infection. This study investigates the role of pyruvate kinase M2 (PKM2), a glycolytic enzyme with non-canonical functions, in [...] Read more.
Host metabolic reprogramming is a critical strategy employed by many viruses to support their replication, and the key metabolic enzyme plays important roles in virus infection. This study investigates the role of pyruvate kinase M2 (PKM2), a glycolytic enzyme with non-canonical functions, in the replication of classical swine fever virus (CSFV). Using PK-15 cells and piglet models, we demonstrate that CSFV infection upregulates PKM2 expression both in vitro and in vivo, creating a proviral environment. knockdown of PKM2 by siRNA reduced CSFV proliferation, while PKM2 overexpression significantly increased virus propagation, which was evaluated by viral protein synthesis, genome replication, and progeny virion production. A direct interaction between PKM2 and CSFV NS5B protein was identified by co-immunoprecipitation and GST-pulldown assays, and PKM2 affected NS5B polymerase activity in a dual-luciferase reporter assay, with PKM2 depletion reducing RdRp function by 50%. Temporal analysis of the first viral replication cycle confirmed PKM2-dependent enhancement of CSFV RNA synthesis. These findings establish PKM2 as a proviral host factor that directly binds NS5B to potentiate RdRp activity, thereby bridging metabolic adaptation and viral genome replication. This study provides new evidence of a glycolytic enzyme physically interacting and enhancing viral polymerase function, offering new information about CSFV–host interaction. Full article
(This article belongs to the Section Animal Viruses)
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20 pages, 979 KiB  
Article
Role of Microencapsulated Essential Oil and Pepper Resin in the Diet of Cows in the Third Lactation Phase on Immunological Pathways
by Karoline Wagner Leal, Marta Lizandra do Rego Leal, Gabriel S. Klein, Andrei Lucas R. Brunetto, Guilherme Luiz Deolindo, Camila Eduarda Justen, Matheus Dellaméa Baldissera, Tainara L. Santos, Daniela Zanini, Rafael C. de Araujo and Aleksandro Schafer da Silva
Vet. Sci. 2025, 12(4), 344; https://doi.org/10.3390/vetsci12040344 - 8 Apr 2025
Viewed by 791
Abstract
The objective was to determine whether dairy cows may activate traditional and alternative inflammatory pathways by consuming a combination of a phytogenic diet (essential oil and pepper resin). Twenty pregnant Jersey cows in the final (third) lactation phase (260 days in milk) were [...] Read more.
The objective was to determine whether dairy cows may activate traditional and alternative inflammatory pathways by consuming a combination of a phytogenic diet (essential oil and pepper resin). Twenty pregnant Jersey cows in the final (third) lactation phase (260 days in milk) were divided into two groups: control, with no additive consumption, and test, with the addition of the phytogenic to the concentrate portion of the diet (150 mg/day/kg dry matter). Blood samples were collected on experimental days 1, 7, 14, 21, 28, 35, and 42 by coccygeal vein puncture to assess the complete blood count, serum biochemistry of levels of total protein, albumin, and globulin, as well as carbohydrate metabolism (glucose), lipid metabolism (cholesterol and triglycerides), protein metabolism (urea), activities of hepatic enzymes (gamma-glutamyl transferase (GGT) and aspartate aminotransferase (AST)), cytokine levels (interleukins IL-1β, IL-6, and IL-10), antioxidant response [thiobarbituric acid reactive substances (TBARS), reactive oxygen species (ROS), total thiol (PSH), and non-protein thiol (NPSH), and glutathione S(GST)], cholinergic system [total cholinesterase (ChE) and acetylcholinesterase (AChE)], purinergic signaling [NTPDase, 5′ectonucleotidase and adenosine deaminase (ADA)], and energetic metabolism enzymes [creatine kinase (CK), pyruvate kinase (PK), and adenylate kinase (AK)]. Productive performance was assessed through feed intake and milk production. The results revealed that the use of phytogenic compounds significantly influenced the cholinergic system and purinergic signaling associated with immunology. The reduction in cholinesterase (ChE) activity and the increase in acetylcholinesterase (AChE) activity in lymphocytes suggest the modulation of the cholinergic system, enhancing the immune response. Furthermore, the elevated activity of adenosine deaminase (ADA) in lymphocytes and platelets, together with increased ATP and ADP hydrolysis in platelets, indicates the beneficial regulation of purinergic signaling, potentially contributing to inflammatory modulation. These effects were accompanied by a lower production of pro-inflammatory cytokines (IL-1β and IL-6) and a higher production of IL-10, reinforcing an anti-inflammatory profile. The reduced leukocyte and lymphocyte counts may reflect a lower inflammatory demand, while the increased levels of NPSH and GST antioxidants suggest cellular protection. Despite these physiological changes, productive performance and milk quality remained unaffected. In summary and practical terms, including this additive in the cows’ diet benefits the cow’s health in the final third of gestation when the animal already has a reduced immune response due to advanced gestation. Full article
(This article belongs to the Special Issue Advancing Ruminant Health and Production: Alternatives to Antibiotics)
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23 pages, 4706 KiB  
Article
Bridging the Gap Between hiPSC-CMs Cardiotoxicity Assessment and Clinical LVEF Decline Risk: A Case Study of 21 Tyrosine Kinase Inhibitors
by Zhijie Wan, Chenyu Wang, Shizheng Luo, Jinwei Zhu, Hua He and Kun Hao
Pharmaceuticals 2025, 18(4), 450; https://doi.org/10.3390/ph18040450 - 23 Mar 2025
Viewed by 535
Abstract
Objectives: There is growing concern over tyrosine kinase inhibitor (TKI)-induced cardiotoxicity, particularly regarding left ventricular dysfunction and heart failure in clinical treatment. These adverse effects often lead to treatment discontinuation, severely impacting patient outcomes. Therefore, there is an urgent need for more [...] Read more.
Objectives: There is growing concern over tyrosine kinase inhibitor (TKI)-induced cardiotoxicity, particularly regarding left ventricular dysfunction and heart failure in clinical treatment. These adverse effects often lead to treatment discontinuation, severely impacting patient outcomes. Therefore, there is an urgent need for more precise risk assessment methods. This study aimed to assess the cardiotoxicity of TKIs, refine in vitro to in vivo extrapolation (IVIVE) methodologies to improve predictive accuracy, and identify critical in vitro parameters for assessment. Methods: By leveraging high-throughput cardiotoxicity screening with human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs), a mechanism-based toxicodynamic (TD) model for TKIs was constructed. A QSP-PK-TD model was developed by integrating pharmacokinetic (PK) and quantitative systems pharmacology (QSP) models. This model incorporates critical drug exposure factors, such as plasma protein binding, tissue–plasma partitioning, and drug distribution heterogeneity to enhance extrapolation accuracy. Results: The QSP-PK-TD model validated the reliability of IVIVE and identified the area under the curve of drug effects on mitochondrial membrane potential (AEMMP) and cardiomyocyte contractility (AEAAC) as key in vitro parameters for assessing TKI-induced cardiotoxicity. Incorporating critical drug exposure factors obviously improved qualitative and quantitative extrapolation accuracy. Conclusions: This study established a framework for predicting in vivo cardiotoxicity from in vitro parameters, enabling efficient translation of preclinical data into clinical risk assessment. These findings provide valuable insights for drug development and regulatory decision-making, offering a powerful tool for evaluating TKI-induced cardiotoxicity. Full article
(This article belongs to the Section Pharmacology)
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16 pages, 10437 KiB  
Article
Genome-Wide Identification of Peanut Pyruvate Kinase Gene Family and Their Potential Roles in Seed Germination and Drought Stress Responses
by Guanlong Chen, Shaona Chen, Zepeng Peng, Zhirou Zou, Bangyi Cheng, Xiaorong Wan, Zhao Zheng and Bin Yang
Horticulturae 2025, 11(2), 200; https://doi.org/10.3390/horticulturae11020200 - 13 Feb 2025
Viewed by 766
Abstract
Pyruvate kinase (PK), a pivotal enzyme in glycolysis, serves as a multifunctional regulator of plant growth, development, and stress adaptation. Despite its significance, the functional roles of PKs in peanut remain largely unexplored. Here, we performed a genome-wide identification and systematic characterization of [...] Read more.
Pyruvate kinase (PK), a pivotal enzyme in glycolysis, serves as a multifunctional regulator of plant growth, development, and stress adaptation. Despite its significance, the functional roles of PKs in peanut remain largely unexplored. Here, we performed a genome-wide identification and systematic characterization of PK genes in cultivated peanut, identifying 21 AhPK genes (AhPK1AhPK21). Phylogenetic classification divided these genes into two subfamilies: PKc (comprising PKc-1 and PKc-2 subgroups) and PKp (comprising PKp-α and PKp-β subgroups). AhPK members within the same subfamily shared similar motif composition patterns, while genes from different subgroups showed significantly different exon–intron organizations. Collinearity analysis indicated that segmental duplication events and purifying selection predominantly drove the expansion and evolution of the AhPK family. Evolutionary analysis further indicated closer evolutionary relationships between peanut PKs and those of Arabidopsis than with rice. Predicted protein interaction networks suggested that AhPKs can form polymeric protein complexes (e.g., PKp-α and PKp-β) or interact with some important proteins, including FBA4, F14O13.7, APY, DLD, and T16L4.190. Promoter analysis identified abundant cis-regulatory elements associated with light responses, stress responses, hormone responses, and development. Expression pattern analysis demonstrated the significant induction of multiple AhPK genes during seed germination and under polyethylene glycol (PEG)-induced drought stress or abscisic acid (ABA) treatment. Collectively, these findings provide critical insights into the functional roles of AhPK genes in seed germination and drought stress responses, establishing a foundation for future mechanistic studies. Full article
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17 pages, 1686 KiB  
Article
Multikinase Treatment of Glioblastoma: Evaluating the Rationale for Regorafenib
by Ana Maria Muñoz-Mármol, Bárbara Meléndez, Ainhoa Hernandez, Carolina Sanz, Marta Domenech, Oriol Arpí-Llucia, Marta Gut, Anna Esteve, Anna Esteve-Codina, Genis Parra, Cristina Carrato, Iban Aldecoa, Mar Mallo, Estela Pineda, Francesc Alameda, Nuria de la Iglesia, Eva Martinez-Balibrea, Anna Martinez-Cardús, Anna Estival-Gonzalez and Carmen Balana
Cancers 2025, 17(3), 375; https://doi.org/10.3390/cancers17030375 - 23 Jan 2025
Cited by 1 | Viewed by 1306
Abstract
We explored the rationale for treating glioblastoma (GBM) with regorafenib. In 103 newly diagnosed GBM patients, we assessed mutations, copy number variants (CNVs), fusions, and overexpression in 46 genes encoding protein kinases (PKs) potentially targeted by regorafenib or its metabolites and performed a [...] Read more.
We explored the rationale for treating glioblastoma (GBM) with regorafenib. In 103 newly diagnosed GBM patients, we assessed mutations, copy number variants (CNVs), fusions, and overexpression in 46 genes encoding protein kinases (PKs) potentially targeted by regorafenib or its metabolites and performed a functional enrichment analysis to assess their implications in angiogenesis. We analyzed regorafenib’s binding inhibitory activity and target affinity for these 46 PKs and focused on a subset of 18 genes inhibited by regorafenib at clinically achievable concentrations and on 19 genes involved in angiogenesis. Putative oncogenic alterations were defined as oncogenic/likely oncogenic mutations, oncogenic fusions, CNVs > 5, and/or gene overexpression. Regorafenib did not target all 46 PKs. For the 46-gene set, 40 genes (86.9%) and 73 patients (70.8%) harbored at least one alteration in genes encoding targetable PKs, but putative oncogenic alterations were present in only 34 patients (33%). In the 18-gene set, 18 genes (100%) and 48 patients (46.6%) harbored alterations, but putative oncogenic alterations were detected in only 26 patients (25.2%). Thirty patients (29.1%) had oncogenic alterations in the 18-gene set and/or in angiogenesis-related genes. Around 33% of patients had oncogenic alterations in any of the 46 potential targets. Additionally, the suboptimal dosing of regorafenib, due to its poor penetration of the blood–brain barrier, may reduce the likelihood of effectively targeting certain PKs. Future use of multi-target drugs must be guided by a thorough understanding of target presence, effective inhibition, and the drug’s ability to reach brain tumors at adequate concentrations. Full article
(This article belongs to the Section Cancer Biomarkers)
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14 pages, 286 KiB  
Article
Rice-Fish Farming Improved Antioxidant Defences, Glucose Metabolism, and Muscle Nutrient of Carassius auratus in Sichuan Province
by Tao Yan, Yun-Yi Xie, Bo Zhou, Xu Kuang, Qing-Zhi Li, Feng-Qi Zhao, Qian-Dong Li and Bin He
Metabolites 2024, 14(12), 710; https://doi.org/10.3390/metabo14120710 - 17 Dec 2024
Cited by 1 | Viewed by 1206
Abstract
Rice-fish farming is an ancient and enduring aquaculture model in China. This study aimed to assess the variations in digestive enzymes, antioxidant properties, glucose metabolism, and nutritional content between Carassius auratus reared in paddy fields and ponds. Notably, the levels of amylase and [...] Read more.
Rice-fish farming is an ancient and enduring aquaculture model in China. This study aimed to assess the variations in digestive enzymes, antioxidant properties, glucose metabolism, and nutritional content between Carassius auratus reared in paddy fields and ponds. Notably, the levels of amylase and trypsin in C. auratus from rice paddies were considerably higher compared to those from ponds. Additionally, the hepatic catalase (CAT) activity in fish from paddy (2.45 ± 0.16 U/mg) exceeded that of their pond counterparts (2.27 ± 0.25 U/mg). Regarding glucose metabolism, the activities of key enzymes such as Na+/K+-ATPase (NKA) (paddy: 82.45 ± 6.11 U/g; pond: 78.53 ± 7.18 U/g), hexokinase (HK) (paddy: 9.55 ± 0.58 U/g; pond: 8.83 ± 0.72 U/g), glucokinase (GK) (paddy: 4.09 ± 0.21 IU/g; pond: 3.44 ± 0.33 IU/g), glucose-6-phosphatase (G6Pase) (paddy: 85.71 ± 4.49 IU/g; pond: 79.12 ± 9.34 IU/g), and glucose-6-phosphate dehydrogenase (G6PDH) (paddy: 47.23 ± 3.22 U/g; pond: 42.31 ± 4.93 U/g) were significantly elevated in rice paddy-cultured fish compared to those in ponds. Conversely, phosphor-pyruvate kinase (PK) (paddy: 418.15 ± 31.89 U/g; pond: 570.16 ± 56.06 U/g) activity was markedly reduced in the paddy group. Hepatic glycogen content (paddy: 15.70 ± 0.98 ng/g; pond: 14.91 ± 1.24 ng/g) was also substantially higher in fish from paddy, although no significant differences in muscle glycogen content (paddy: 7.14 ± 0.59 ng/g; pond: 6.70 ± 0.52 ng/g) were observed between the two environments. In terms of nutritional composition, fish raised in paddy exhibited higher crude protein (paddy: 18.46 ± 0.47 g/100 g muscle; pond: 15.57 ± 0.25 g/100 g muscle) and crude ash (paddy: 1.19 ± 0.02 g/100 g muscle; pond: 0.97 ± 0.02 g/100 g muscle) than those in ponds, whereas the crude fat (paddy: 0.87 ± 0.04 g/100 g muscle; pond: 1.66 ± 0.04 g/100 g muscle) was notably lower in paddy fish. Furthermore, fish from rice paddies had a greater total content of monounsaturated fatty acids (MUFA) (paddy: 4.25 ± 0.24 g/100 g muscle; pond: 6.73 ± 0.27 g/100 g muscle), non-essential amino acids (NEAA) (paddy: 9.04 ± 0.3 g/100 g muscle; pond: 7.19 ± 0.21 g/100 g muscle), and delicious amino acids (DAA) (paddy: 7.11 ± 0.2 g/100 g muscle; pond: 5.45 ± 0.19 g/100 g muscle) compared to those from pond cultures. These findings suggest that rice-fish co-culture systems can yield healthier and more environmentally sustainable aquatic products by improving feed digestion and optimizing nutrient metabolism. Full article
(This article belongs to the Special Issue Metabolism and Nutrition in Fish)
33 pages, 4009 KiB  
Review
Cyclic Peptides as Protein Kinase Modulators and Their Involvement in the Treatment of Diverse Human Diseases
by Lorena Martínez-Alcantar, Laura Hernández-Padilla, Alma Laura Díaz-Pérez, Lizbeth Guadalupe Villalón-Magallán, Mayra Xóchitl Durán-Maldonado, César Díaz-Pérez, Marlene E. Campos-Morales, Citlali Figueroa-Guzmán and Jesús Campos-García
Kinases Phosphatases 2024, 2(4), 346-378; https://doi.org/10.3390/kinasesphosphatases2040023 - 12 Dec 2024
Cited by 1 | Viewed by 3908
Abstract
Protein kinases (PKs) are an important and very popular family of enzymes that play a vital role in regulating cellular processes via the phosphorylation of targets. Nevertheless, modifications in the expression due to mutations or their dysregulation can lead to diseases, including autoimmune [...] Read more.
Protein kinases (PKs) are an important and very popular family of enzymes that play a vital role in regulating cellular processes via the phosphorylation of targets. Nevertheless, modifications in the expression due to mutations or their dysregulation can lead to diseases, including autoimmune disorders, cardiovascular problems, diabetes, neurological diseases, and cancers. Cyclic ultra-short peptides are amazing structures with unique properties. The cyclicity of cyclic peptides (CPs) can mimic the interactions between PKs and natural substrates, influencing the enzyme activity essential in health and disease physiology. Our review summarized that interference in the signal transduction mechanism of the PKs by CPs implies the inhibition of substrate phosphorylation at the level of the active site, similar to anti-neoplastic drugs. The remarkable capacity of CPs to interact with targets positions them as promising candidates for developing protein kinase inhibitors in treating diseases. This review offers new insights for CPs in molecular mechanisms, cytotoxicity, target selectivity, and the possibility of designing more effective and safe therapeutic agents. Full article
(This article belongs to the Special Issue Human Protein Kinases: Development of Small-Molecule Therapies)
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22 pages, 7524 KiB  
Article
The Molecular Mechanism of Farnesoid X Receptor Alleviating Glucose Intolerance in Turbot (Scophthalmus maximus)
by Gaochan Qin, Mingzhu Pan, Dong Huang, Xinxin Li, Yue Liu, Xiaojun Yu, Kangsen Mai and Wenbing Zhang
Cells 2024, 13(23), 1949; https://doi.org/10.3390/cells13231949 - 23 Nov 2024
Cited by 1 | Viewed by 1039
Abstract
To explore the molecular targets for regulating glucose metabolism in carnivorous fish, the turbot (Scophthalmus maximus) was selected as the research object to study. Farnesoid X receptor (FXR; NR1H4), as a ligand-activated transcription factor, plays an important role in glucose metabolism [...] Read more.
To explore the molecular targets for regulating glucose metabolism in carnivorous fish, the turbot (Scophthalmus maximus) was selected as the research object to study. Farnesoid X receptor (FXR; NR1H4), as a ligand-activated transcription factor, plays an important role in glucose metabolism in mammals. However, the mechanisms controlling glucose metabolism mediated by FXR in fish are not understood. It was first found that the protein levels of FXR and its target gene, small heterodimer partner (SHP), were significantly decreased in the high-glucose group (50 mM, HG) compared with those in the normal glucose group (15 mM, CON) in primary hepatocytes of turbot. By further exploring the function of FXR in turbot, the full length of FXR in turbot was cloned, and its nuclear localization function was characterized by subcellular localization. The results revealed that the FXR had the highest expression in the liver, and its capability to activate SHP expression through heterodimer formation with retinoid X receptor (RXR) was proved, which proved RXR could bind to 15 binding sites of FXR by forming hydrogen bonds. Activation of FXR in both the CON and HG groups significantly increased the expression of glucokinase (gk) and pyruvate kinase (pk), while it decreased the expression of cytosolic phosphoenolpyruvate carboxykinase (cpepck), mitochondrial phosphoenolpyruvate carboxykinase (mpepck), glucose-6-phosphatase 1 (g6pase1) and glucose-6-phosphatase 2 (g6pase2), and caused no significant different in glycogen synthetase (gs). ELISA experiments further demonstrated that under the condition of high glucose with activated FXR, it could significantly decrease the activity of PEPCK and G6PASE in hepatocytes. In a dual-luciferase reporter assay, the FXR could significantly inhibit the activity of G6PASE2 and cPEPCK promoters by binding to the binding site ‘ATGACCT’. Knockdown of SHP after activation of FXR reduced the inhibitory effect on gluconeogenesis. In summary, FXR can bind to the mpepck and g6pase2 promoters to inhibit their expression, thereby directly inhibiting the gluconeogenesis pathway. FXR can also indirectly inhibit the gluconeogenesis pathway by activating shp. These findings suggest the possibility of FXR as a molecular target to regulate glucose homeostasis in turbot. Full article
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36 pages, 37425 KiB  
Article
Cocaine-Induced DNA-Dependent Protein Kinase Relieves RNAP II Pausing by Promoting TRIM28 Phosphorylation and RNAP II Hyperphosphorylation to Enhance HIV Transcription
by Adhikarimayum Lakhikumar Sharma, Priya Tyagi, Meenata Khumallambam and Mudit Tyagi
Cells 2024, 13(23), 1950; https://doi.org/10.3390/cells13231950 - 23 Nov 2024
Viewed by 1634
Abstract
Drug abuse continues to pose a significant challenge in HIV control efforts. In our investigation, we discovered that cocaine not only upregulates the expression of the DNA-dependent protein kinase (DNA-PK) but also augments DNA-PK activation by enhancing its phosphorylation at S2056. Moreover, DNA-PK [...] Read more.
Drug abuse continues to pose a significant challenge in HIV control efforts. In our investigation, we discovered that cocaine not only upregulates the expression of the DNA-dependent protein kinase (DNA-PK) but also augments DNA-PK activation by enhancing its phosphorylation at S2056. Moreover, DNA-PK phosphorylation triggers the higher localization of the DNA-PK into the nucleus. The finding that cocaine increases the nuclear localization of the DNA-PK provides further support to our observation of enhanced DNA-PK recruitment at the HIV long terminal repeat (LTR) following cocaine exposure. By activating and facilitating the nuclear localization of the DNA-PK, cocaine effectively orchestrates multiple stages of HIV transcription, thereby promoting HIV replication. Additionally, our study demonstrates that the cocaine-induced DNA-PK promotes the hyper-phosphorylation of the RNA polymerase II (RNAP II) carboxyl-terminal domain (CTD) at Ser5 and Ser2 sites, enhancing both the initiation and elongation phases, respectively, of HIV transcription. The cocaine-mediated enhancement of transcriptional initiation is supported by its activation of cyclin-dependent kinase 7 (CDK7). Additionally, the induction of transcriptional elongation is marked by higher LTR recruitment and the increased phosphorylation of CDK9, which indicates the stimulation of positive transcriptional elongation factor b (P-TEFb). We demonstrate for the first time that cocaine, through DNA-PK activation, promotes the specific phosphorylation of TRIM28 at serine 824 (p-TRIM28, S824). This modification converts TRIM28 from a transcriptional inhibitor to a transactivator for HIV transcription. Additionally, we observed that the phosphorylation of TRIM28 (p-TRIM28, S824) promotes the transition from the pausing phase to the elongation phase of HIV transcription, thereby facilitating the production of full-length HIV genomic transcripts. This finding corroborates the previously observed enhanced RNAP II CTD phosphorylation at Ser2, a marker of transcriptional elongation, following cocaine exposure. Accordingly, upon cocaine treatment, we observed the elevated recruitment of p-TRIM28-(S824) at the HIV LTR. Overall, our results unravel the intricate molecular mechanisms underlying cocaine-induced HIV transcription and gene expression. These findings hold promise for the development of highly targeted therapeutics aimed at mitigating the detrimental effects of cocaine in individuals living with HIV. Full article
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21 pages, 2042 KiB  
Review
Emerging Functions of Protein Tyrosine Phosphatases in Plants
by Jing Xin, Chuanling Li, Xiaoqian Liu, Xueke Shi, Yu Sun and Jian-Xiu Shang
Int. J. Mol. Sci. 2024, 25(22), 12050; https://doi.org/10.3390/ijms252212050 - 9 Nov 2024
Viewed by 1393
Abstract
Reversible protein phosphorylation, known as the “switch” of the cell, is controlled by protein kinases (PKs) and protein phosphatases (PPs). Based on substrate specificity, PPs are classified into protein serine/threonine phosphatases and protein tyrosine phosphatases (PTPs). PTPs can dephosphorylate phosphotyrosine and phosphoserine/phosphothreonine. In [...] Read more.
Reversible protein phosphorylation, known as the “switch” of the cell, is controlled by protein kinases (PKs) and protein phosphatases (PPs). Based on substrate specificity, PPs are classified into protein serine/threonine phosphatases and protein tyrosine phosphatases (PTPs). PTPs can dephosphorylate phosphotyrosine and phosphoserine/phosphothreonine. In plants, PTPs monitor plant physiology, growth, and development. This review summarizes an overview of the PTPs’ classification and describes how PTPs regulate various plant processes, including plant growth and development, plant hormone responses, and responses to abiotic and biotic stresses. Then, future research directions on the PTP family in plants are discussed. This summary will serve as a reference for researchers studying PTPs in plants. Full article
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15 pages, 5731 KiB  
Article
Disruption of RNA Splicing Increases Vulnerability of Cells to DNA-PK Inhibitors
by Anastasia P. Kovina, Artem V. Luzhin, Victor V. Tatarskiy, Dmitry A. Deriglazov, Natalia V. Petrova, Nadezhda V. Petrova, Liya G. Kondratyeva, Omar L. Kantidze, Sergey V. Razin and Artem K. Velichko
Int. J. Mol. Sci. 2024, 25(21), 11810; https://doi.org/10.3390/ijms252111810 - 3 Nov 2024
Viewed by 1861
Abstract
DNA-dependent protein kinase (DNA-PK) is a key effector of non-homologous end joining (NHEJ)-mediated double-strand break (DSB) repair. Since its identification, a substantial body of evidence has demonstrated that DNA-PK is frequently overexpressed in cancer, plays a critical role in tumor development and progression, [...] Read more.
DNA-dependent protein kinase (DNA-PK) is a key effector of non-homologous end joining (NHEJ)-mediated double-strand break (DSB) repair. Since its identification, a substantial body of evidence has demonstrated that DNA-PK is frequently overexpressed in cancer, plays a critical role in tumor development and progression, and is associated with poor prognosis in cancer patients. Recent studies have also uncovered novel functions of DNA-PK, shifting the paradigm of the role of DNA-PK in oncogenesis and renewing interest in targeting DNA-PK for cancer therapy. To gain genetic insight into the cellular pathways requiring DNA-PK activity, we used a CRISPR/Cas9 screen to identify genes in which defects cause hypersensitivity to DNA-PK inhibitors. We identified over one hundred genes involved in DNA replication, cell cycle regulation, and RNA processing that promoted cell survival when DNA-PK kinase activity was suppressed. This gene set will be useful for characterizing novel biological processes that require DNA-PK activity and identifying predictive biomarkers of response to DNA-PK inhibition in the clinic. We also validated several genes from this set and reported previously undescribed genes that modulate the response to DNA-PK inhibitors. In particular, we found that compromising the mRNA splicing pathway led to marked hypersensitivity to DNA-PK inhibition, providing a possible rationale for the combined use of splicing inhibitors and DNA-PK inhibitors for cancer therapy. Full article
(This article belongs to the Section Molecular Biology)
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19 pages, 5336 KiB  
Article
Research on Function of Ribosomal Protein S6 Kinases, 1α and β, Based on Molecular Cloning and siRNA-Based Interference in Juvenile Blunt Snout Bream (Megalobrama amblycephala)
by Jiaze Gu, Haifeng Mi, Mingchun Ren, Dongyu Huang, Ahmed Mohamed Aboseif, Hualiang Liang and Lu Zhang
Biology 2024, 13(11), 875; https://doi.org/10.3390/biology13110875 - 28 Oct 2024
Viewed by 1181
Abstract
The aim of this study was to investigate the effects of S6K1α and β on the expression of glycolysis- and gluconeogenesis-related genes in juvenile blunt snout bream. Two isoforms, α and β, of ribosomal protein S6 kinase 1 in blunt snout bream were [...] Read more.
The aim of this study was to investigate the effects of S6K1α and β on the expression of glycolysis- and gluconeogenesis-related genes in juvenile blunt snout bream. Two isoforms, α and β, of ribosomal protein S6 kinase 1 in blunt snout bream were cloned and characterized, and their expression patterns were examined in vivo. The sequence analysis showed that s6k1α and s6k1β contain open reading frames of 2217 and 1497 bp, encoding 738 and 498 amino acids, respectively. Both S6K1α and S6K1β consist of an S_TKc domain and an extended S_TK_X domain. s6k1α and s6k1β were abundantly expressed in the heart and gonads. siRNAs were designed, and the experiment showed that α-siRNA inhibited s6k1α and s6k1β expression, but β-siRNA exclusively inhibited s6k1α expression (p < 0.05). α-siRNA upregulated the expression levels of gk and pk, while β-siRNA upregulated pepck and g6p expression (p < 0.05). The expression of g6pdh was found to be downregulated, but the gs mRNA level was overexpressed after treatment with α-siRNA and β-siRNA (p < 0.05). In the present experiment, S6K1α was more intimately involved in the regulation of gluconeogenesis when only S6K1α was inhibited, whereas the inhibition of both S6K1α and S6K1β collectively co-regulated glycolysis. Full article
(This article belongs to the Section Biochemistry and Molecular Biology)
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