Search Results (351)

The stress response is essential for cellular and organismal survival as it acts as a protective and adaptive mechanism to maintain homeostasis. At the organismal level, physical stressors induce responses in mammals that are mediated primarily by the hypothalamic–pituitary–adrenal (HPA) axis, which regulates glucocorticoid secretion. The HPA axis functions as a circadian-regulated, multi-oscillator system, in which the paraventricular nucleus, the pituitary, and the adrenal gland exhibit intrinsic rhythmicity while remaining coordinated by the output from the suprachiasmatic nucleus. Glucocorticoids act both as stress effectors and systemic zeitgebers that synchronize peripheral clocks. At the cellular level, cellular stressors are sensed by four protein kinases of eukaryotic translation initiation factor 2α (eIF2α) and activate the evolutionarily conserved integrated stress response (ISR), which converges on phosphorylation of Serine 51 on eIF2α. ISR signaling is temporally regulated by the circadian clock and controls time-of-day-dependent protein synthesis. In parallel, ISR pathways feed back onto the circadian clock through transcriptional, translational and epigenetic mechanisms, directly influencing core clock gene expression and stability of circadian oscillations. Physiological ISR activity supports circadian robustness and resetting, whereas excessive ISR activation dampens rhythmic gene expression and destabilizes behavioral rhythms. The current review summarizes recent advances in our understanding of the crosstalk mechanisms between the HPA axis, ISR, and the circadian clock to provide new insights into disease mechanisms and inform chronotherapeutic strategies to target dysregulated HPA and ISR activities and restore temporal homeostasis. Full article

Eukaryotic genomes are organized into chromatin, a highly compact structure in which DNA is packaged into nucleosomes. Nucleosome formation, where DNA is wrapped around histone proteins, is essential for genome stability. This compaction protects DNA from damage and regulates accessibility of genes. Nucleosomes must be disassembled and reassembled during DNA replication and repair. These processes require precise regulation of histone folding, transfer, and deposition by a diverse network of histone chaperones. Chromatin assembly factor 1 (CAF-1) is a conserved histone chaperone that specifically deposits newly synthesized histones during replication-coupled and repair-coupled nucleosome assembly. The sliding clamp proliferating cell nuclear antigen (PCNA) serves as a regulatory scaffold during these processes by recruiting CAF-1 and many other proteins to sites of DNA replication and repair. Recent structural and biochemical studies have revealed increasingly complex mechanisms underlying PCNA-mediated CAF-1 recruitment, involving multiple protein interaction motifs, DNA-binding domains, and regulatory mechanisms that ensure efficient nucleosome assembly. This review summarizes current advances in understanding the molecular mechanisms by which human and yeast CAF-1 complexes are recruited to sites of DNA synthesis and how CAF-1 function is coordinated with other histone chaperones during replication and repair. These studies have provided important insights into how cells coordinate DNA metabolism with epigenome maintenance to preserve genome integrity. Full article

Background: Opioid use during pregnancy is linked to preterm birth, fetal growth restriction, and Neonatal Opioid Withdrawal Syndrome. While the placenta is the primary regulator of the uterine environment, the precise molecular mechanisms by which opioids dismantle placental function remain poorly defined. Methods: The transcriptomic landscape of opioid-exposed human placentas from a unique Hawai’i-based cohort was characterized. Results: Transcriptional signatures were defined by genes involved in translational inhibition and metabolic attenuation. Integrative network modeling predicted a prominent stress-signaling hub centered on p38 Mitogen-Activated Protein Kinase and Extracellular Signal-Related Kinase 1/2, paralleling a broad suppression of ribosomal protein transcripts (Ribosomal Protein 27S, -29, and -39). This response was further characterized by the inhibition of the Myelecytomatosis Proto-Oncogene regulatory hub, predicting a loss of mitochondrial phosphate transport through associated genes (via Solute Carrier Family 25A3) and cell-cycle progression (via S-Phase Kinase-Associated Protein 1). Additionally, the genes in this model suggested upregulation of antisense regulatory brakes, such as RAP2C Antisense RNA 1, which might further reinforce this inhibitory state. Conclusion: The findings suggest that prenatal opioid exposure is associated with the disruption of placental homeostasis. This may be coordinated by protein synthesis and bioenergetic flux, as inferred from the modeled eukaryotic Translation Initiation Factor-mediated Integrated Stress Response. These findings establish a localized, clinical baseline of human placental stress, highlighting candidate molecular regulatory nodes to guide future mechanistic studies and biomarker discovery in exposed pregnancies. Full article

Chronic pain is a major global health burden and often remains difficult to treat with current therapies, which frequently provide incomplete relief and may cause systemic side effects. As essential organelles in eukaryotic cells, mitochondria facilitate ATP synthesis and serve as key regulators of calcium homeostasis and apoptosis. Evidence points to mitochondrial dysfunction not merely as a result of trauma, but as a fundamental factor in why pain becomes persistent. On the other hand, the endoplasmic reticulum (ER) is more than just a structural component of the cell; it is a multi-functional organelle responsible for protein quality control, including folding and degradation, as well as lipid production and calcium signaling. ER dysfunction is a primary driver of various pathologies, such as cardiovascular disease, cancer, and neurodegenerative disorders. The organelle’s ability to execute its vital functions is strictly dependent on sufficient levels of ATP. Because mitochondrial and ER functions are closely interconnected through calcium exchange, ATP-dependent protein homeostasis, oxidative stress, and mitochondria-associated ER membranes, their dysfunction may act together to amplify nociceptive sensitization and pain chronification. In this review, we summarize current evidence linking mitochondrial dysfunction, ER stress, and ER-mitochondrial crosstalk to the pathogenesis of chronic pain and discuss their potentials as therapeutic targets. Full article

During protein synthesis, ribosome stalling, collision, and aberrant elongation can lead to the accumulation of defective nascent polypeptides and compromise cellular homeostasis. To counteract such translational disturbances, eukaryotic cells have evolved a highly conserved translational quality control network, in which the ribosome-associated quality control (RQC) pathway plays a central role in the recognition and elimination of aberrant translation complexes. Zinc Finger Protein 598 (ZNF598), a key E3 ubiquitin ligase in mammalian cells, functions as an essential factor in the early recognition and signal transduction steps of the RQC pathway. Accumulating evidence indicates that ZNF598 senses aberrant translational states, and particularly in the context of ribosome collision, mediates site-specific ubiquitination of 40S ribosomal proteins, thereby promoting ribosome splitting, nascent chain clearance, and subsequent processing of defective mRNAs. Beyond its canonical role in RQC, ZNF598 has also been implicated in the translational repression of defective mRNAs, regulation of inflammatory signaling, antiviral responses, and control of toxic translation products associated with neurodegenerative disorders. In this review, we summarize the structural features, molecular mechanisms, regulatory networks, and physiological as well as pathological functions of ZNF598. We also discuss current controversies and future directions in the field, with the aim of providing a broader framework for understanding translational quality control and its therapeutic potential. Full article

The yeast metabolic cycle (YMC) in Saccharomyces cerevisiae provides a tractable model for examining how mitochondrial respiration, redox timing, and metabolic phase shape transcriptome abundance and fidelity. Ribosomal-RNA-depleted whole-transcriptome RNA sequencing (WRS) and RNA-seq-derived mismatch analyses were performed across low-dissolved-oxygen (Low-DO)/high-respiration and high-dissolved-oxygen (High-DO)/lower-respiration phases. Among 1505 phase-differentially expressed genes, Low DO was enriched for ribosome biogenesis, rRNA processing, translation, sulfur metabolism, and protein synthesis, whereas High DO was enriched for oxidant detoxification, oxidoreductase activity, and redox-buffering-related pathways. Generalized linear mixed models identified a substitution-class-dependent Low-DO-associated RNA-seq mismatch response. The strongest mismatch-level increase occurred in the collapsed C > T/G > A-compatible class, whereas C > A/G > T did not increase. This pattern was not consistent with a simple single-lesion model and instead supported a mixed Low-DO-associated RNA-seq sequence-discordance landscape. Variant-rate modeling additionally detected T > C/A > G and T > A/A > T increases, indicating that multiple biological and technical processes may contribute to the observed spectrum. Recurrence analysis showed that most called variants were sample-specific, supporting a transient RNA-seq mismatch landscape rather than stable DNA mutation. These findings establish the YMC as a reductionist eukaryotic framework for studying how metabolic phase and redox state shape transcriptome fidelity. Full article

This article proposes three possible explanations that relate to the process of eukaryotic translation initiation. These explanations suggest mechanisms as to how concentrations of initiation factors (by mass or by posttranslational modification) can influence start site selection, how regulation of translation by 4E-BP (an inhibitor of m⁷G cap-dependent translation) can be explained by “eIF4F disassembly” and how the scanning mechanism might involve initiation factor binding at the 5′ end of the mRNA to provide for apparent unidirectional Brownian movement to locate the initiating AUG. These represent testable models, although the experiments would not be simple. It is hoped that the insights provided will assist researchers in defining the precise steps and mechanisms of the complex initiation process. It is noted that the better this process is understood, the easier it will be to understand how this process is regulated under a wide variety of biological situations, such as nutritional deprivation, heat shock, cell growth, or disease. Additionally, as initiation is the rate-limiting step in translation, a better understanding of this process should also suggest new avenues to treat various diseases, especially conditions of unrestricted growth. Full article

Ribosome-inactivating proteins are a class of toxins that target eukaryotic ribosomes, inhibit protein synthesis, and ultimately induce cell death. Several of these toxins pose significant clinical and public health threats. Among these, ricin, derived from the castor bean plant (Ricinus communis), is a highly potent biotoxin with recognized bioterrorism potential. Other ribosome-inactivating proteins, including Shiga toxin produced by pathogenic Shigella and Escherichia coli, as well as mucoricin from Mucorales fungi, contribute to disease severity and can lead to life-threatening complications. Despite these risks, no approved therapeutics are currently available. The development of effective inhibitors depends on robust and well-defined strategies to identify and validate small molecules that disrupt toxin–ribosome interactions. Efforts to target the catalytic active site have met with limited success, largely due to its broad, shallow, and highly polar architecture, which is not conducive to high-affinity binding by drug-like molecules. In contrast, the ribosome-binding interface represents a more tractable target, as it is essential for toxin recruitment and offers more structurally defined and druggable features. Inhibitors targeting this interface can also exert allosteric effects by disrupting long-range conformational coupling between the ribosome-binding region and the active site, thereby attenuating catalytic activity without directly engaging the catalytic pocket. In this review, we compile and evaluate biophysical and biochemical assays for the discovery and characterization of small-molecule inhibitors that target toxin–ribosome interactions. We examine in vitro binding approaches, including surface plasmon resonance-based fragment screening and fluorescence anisotropy assays for ranking inhibitory activity. We further review biochemical and molecular assays that assess ribosome protection from toxin-mediated depurination, along with complementary cell-based assays that evaluate functional rescue in cellular systems. Collectively, this review consolidates current screening methodologies and highlights opportunities to refine assay strategies, thereby supporting the advancement of targeted therapeutics. Full article

Quantum dots such as CdS QDs have been extensively studied using human cells, plants, and unicellular eukaryotes such as Saccharomyces cerevisiae, whereas ZnS QDs—considered low-toxicity alternatives to cadmium-based nanomaterials—remain comparatively underexplored. Following preliminary analyses of ZnS QDs’ effects on wild-type S. cerevisiae BY4742 growth, the Yeast Knock-Out collection, comprising ~4600 haploid mutants deleted in non-essential genes, was screened in the presence of ZnS QDs. Sensitive mutants were predominantly associated with mitochondrial functions, prompting further characterization of sod1Δ, glr1Δ, and of the hypersensitive mutant pos5Δ. This last mutant, which lacks a mitochondrial NADH kinase, showed hypersensitivity specific to ZnS QDs but not to CdS QDs or zinc sulfate (ZnSO₄). Flow cytometry analysis of the wild-type strain and the pos5Δ mutant detected no significant increase in reactive oxygen species after ZnS QD treatment. RNA-sequencing analyses of the wild-type strain and the pos5Δ mutant exposed to ZnS QDs (or ZnSO₄) revealed that ZnS QD exposure selectively modulated genes encoding mitochondrial proteins, metal-binding factors, and intracellular trafficking components. Comparison with published data on CdS QDs identified specific mechanisms involving protein synthesis and degradation. Saccharomyces cerevisiae once again proved its versatility for studying engineered nanomaterial interactions with biological systems. Full article

Objectives: The study aimed to evaluate the effects of full-fat rice bran (FFRB; Tainung No. 81, Taiwan) at various doses on insulin resistance, muscle atrophy, and gut microbiota composition in middle-aged ovariectomized (OVX) mice fed a high-fat diet (HFD), using young sham-operated mice as a life-stage reference group. Methods: Thirty-six female ICR mice were assigned to six groups, including OVX mice fed HFD with or without 5%, 10%, or 20% FFRB. Results: Compared with HFD-fed OVX controls, 20% FFRB reduced body weight gain by 43%, decreased visceral fat mass, and improved insulin resistance (homeostasis model assessment of insulin resistance, HOMA-IR reduced by 65%, P_trend = 0.001). FFRB attenuated the decline in relative grip strength (forelimb, P_trend = 0.013; four-limb, P_trend < 0.001), and upregulated muscle protein synthesis genes, including insulin receptor substrate 1 (IRS-1), mammalian target of rapamycin (mTOR), eukaryotic translation initiation factor 4E binding protein 1 (eIF-4EBP1), while downregulating forkhead box protein O1 (FOXO1), muscle RING-finger protein-1 (MuRF-1), and interleukin (IL)-6. FFRB was also associated with higher fecal acetate levels (P_trend < 0.001), upregulated colonic tight junction genes (occludin and zonula occludens (ZO)-1), and greater relative abundance of g_Muribaculum. Correlation analyses revealed positive associations between short-chain fatty acids (SCFAs) and muscle strength, muscle anabolic markers, genus Lachnospiraceae_UCG_001, and Muribaculum. Conclusions: Dietary inclusion of FFRB was associated with favorable metabolic and muscle-related parameters in HFD-fed middle-aged OVX mice, with potential involvement of gut microbiota and SCFA alterations. Full article

An eight-week feeding trial was conducted to investigate methionine and lysine supplementation on the growth performance, body composition, antioxidant index and protein synthesis-related gene expression of the FFCR No. 2 strain common carp (Cyprinus carpio). The experiment included five groups: the CON group (basal diet), CM group (supplemented with 0.6% crystalline methionine), CML group (supplemented with 0.6% crystalline methionine and 0.3% crystalline lysine), HM group (supplemented with 0.6% coated methionine), and HML group (supplemented with 0.6% coated methionine and 0.3% coated lysine). The results showed that the WG (weight gain), SGR (specific growth rate) and CF (condition factor) of the HML group were significantly increased (p < 0.05), and the activities of amylase, lipase, and protease in the intestine of those belonging to the HML group were significantly higher than those in the CON group (p < 0.05). The whole-body crude lipid, SOD (superoxide dismutase), GOT (glutamic oxaloacetic transaminase) activity, and BUN (urea nitrogen) levels in serum were reduced significantly in the HM and HML groups than in the CON group (p < 0.05). Additionally, in the HML group the gene expression levels of IGF-1 (insulin-like growth factor-1), IGFBP (insulin-like growth factor binding protein), 4EBP1(recombinant eukaryotic translation initiation factor 4E binding protein 1), and S6K1 (ribosomal protein s6 kinase 1) in the muscle were significantly higher than those in the CON group. In summary, supplementing coated methionine and lysine improved amino acid utilization, enhanced growth performance, and upregulated the expression of genes associated with growth and protein synthesis. Full article

The discovery of melatonin as a multifunctional free radical scavenger and its possible synthesis in the mitochondrial matrix of peripheral eukaryotic somatic cells highlights a critical new perspective on the importance of this indole. Experimental evidence supporting these findings is substantial, but there are still lingering questions whether melatonin is a direct radical scavenger in vivo and whether it is synthesized in the mitochondrial matrix. We systematically analyze the innovative experimental approaches that support melatonin’s radical scavenging actions and assess the compelling data supporting its production in mitochondria. Melatonin concentrations are reportedly higher in this organelle than in other cellular compartments. Proteins for the enzymes required to convert serotonin to melatonin are present in the mitochondrial matrix and purified mitochondria synthesize melatonin. In the mitochondrial matrix, melatonin is likely located within the “damage radius” of highly reactive oxygen species. We also summarize novel actions of melatonin associated with its regulation of membrane fluidity, determine the molecular composition of membrane lipid rafts, and modulate liquid–liquid phase separation and biomolecular condensates intracellularly. If the findings discussed herein continue to be validated, melatonin would be in an optimal position to function as an antioxidant and may be a key driver in the context of preserving mitochondrial redox homeostasis and disease mitigation. Full article

The eukaryotic translation initiation factor 4E (eIF4E) family plays a dual role in plants, regulating cap-dependent protein synthesis and mediating susceptibility to viruses in the family Potyviridae. In cowpea (Vigna unguiculata (L.) Walp.), an economically important legume cultivated worldwide, the structural determinants of these isoforms remain largely unexplored. This study characterizes the genomic organization, evolutionary history, and conformational dynamics of eIF4E, eIF(iso)4E, and nCBP in cowpea using a multi-omics approach. Genome mining identified three paralogous genes located on chromosomes 4, 6, and 7, showing high synteny with Phaseolus vulgaris. Phylogenetic analysis confirmed nCBP as the ancestral Class I lineage, distinct from the Class II eIF4E and eIF(iso)4E clades. Theoretical models for the isoforms were generated and subsequently validated by molecular dynamics simulations, revealing that while all isoforms preserve the canonical tertiary architecture and an electropositive cap-binding pocket, eIF(iso)4E exhibits superior structural compactness and hydrogen-bond stability. These biophysical features highlight their role as a stable anchor for viral VPg proteins. By elucidating the atomic-level landscape of these factors, we provide a robust structural framework to guide allele mining and genome-editing strategies aiming to engineer virus-resistant cowpea cultivars without compromising agronomic performance. Full article

Chlorinated paraffins (CPs) are widely used, structurally complex mixtures of chlorinated alkanes whose ecological risks in aquatic ecosystems have raised increasing concern. However, the toxic effects and molecular mechanisms of CPs on primary aquatic producers remain poorly understood. In this study, we used the eukaryotic green algae Chlorella sp. and the prokaryotic cyanobacterium Microcystis aeruginosa (M. aeruginosa) as test organisms to systematically investigate the effects of CPs with different carbon chain lengths, namely short-chain CPs (SCCPs), medium-chain CPs (MCCPs), and long-chain CPs (LCCPs), on algal growth, photosynthetic pigment content, antioxidant systems, cellular ultrastructure, and the underlying molecular responses. Our results showed that CPs toxicity to algae is significantly dependent on both CPs carbon-chain length and algal species. Exposure to 1.0 mg/L SCCPs for 96 h produced a growth inhibition of Chlorella sp. of 14.45%. CPs’ exposure significantly altered algal Chl-a content and elicited antioxidant defense responses, and affected the synthesis and extracellular release of MC-RR and MC-LR in M. aeruginosa. Ultrastructural observations revealed cell surface wrinkling and deformation in both Chlorella sp. and M. aeruginosa. Chlorella sp. additionally exhibited thylakoid disintegration and plasmolysis. Transcriptomic analysis indicated that CPs with different chain lengths significantly downregulated genes in Chlorella sp. associated with DNA replication and mismatch repair, suggesting impairment of replication initiation and elongation and compromised genome stability. Concurrently, genes encoding photosynthetic antenna proteins and carbon fixation were upregulated. In M. aeruginosa, CPs exposure markedly disturbed energy metabolism pathways, including glycolysis/gluconeogenesis and oxidative phosphorylation, which were generally downregulated. This study provides a comparative assessment of CPs’ toxicity between the eukaryotic algae Chlorella sp. and the prokaryotic algae M. aeruginosa, revealing that toxicity is co-determined by carbon chain length and algal species. Additionally, it provides critical toxicological data and establishes a theoretical foundation for the scientific assessment of the aquatic ecological risks posed by CPs with different carbon chain lengths. Full article

The mitogen-activated protein kinase (MAPK) cascade constitutes a core component of signal transduction pathways in eukaryotic organisms. With its precise, efficient, and specific mechanism of action, this cascade pathway integrates, amplifies, and rapidly transmits signals. Among them, the specificity and functional diversity of the MPK3 cascade depend on the phosphorylation interaction between MKK and MPK3, as well as the specific interaction between MPK3 and its substrates. MPK3 targets an extremely diverse array of substrates, including transcription factors, RNA-binding proteins, enzymes, and transporters. The summary of the regulatory role of the MPK3 signal mainly focuses on three functional mechanisms: The most well-known regulatory mechanism is to recognize and phosphorylate substrate proteins or transcription factors, thereby affecting the stability and transcriptional activity of downstream substrates, and thus regulating the transcriptional regulatory activity and expression of downstream genes. MPK3 can also participate in downstream functional regulation by triggering the MAPKKK-MKK4/5-MPK3/6 signaling pathways or feedback mechanisms. MPK3 can exert regulatory effects independently or together with MPK6. The redundancy of the MPK3/6 function is related to the synergistic effect of the component cascade reaction, as well as the dose-dependent activation effect. This article presents a comprehensive synthesis of the latest research progress on the regulatory role of MPK3, in plant growth, development, and stress adaptation and defence. Moreover, it provides critical evaluations and forward-looking perspectives on the future investigation of the underlying molecular mechanisms governing MPK3-mediated regulation. Full article