Search Results (914)

Translation of mRNAs is a tightly regulated process in gene expression. In mRNA, the 5′ untranslated region (5′ UTR) controls ribosome recruitment and frequently contains structured elements that modulate translation efficacy. This study investigates stable structural motifs within the 5′ UTR of DDX23 mRNA, encoding a protein relevant for anticancer therapy, as potential regulators and targets for antisense oligonucleotides (ASOs). Despite bioinformatic predictions and transcriptomic validations suggesting RNA G-quadruplex (rG4) formation, comprehensive structural analysis using a light-up assay and CD, UV, and NMR spectroscopy revealed that most putative rG4-forming sequences do not fold into stable rG4 structures, although one of them exists in an equilibrium between rG4 and an alternative, likely hairpin, conformation. Reporter assays using a robust G4 stabilizer also argue against the significant regulatory role of rG4s in DDX23 mRNA translation. Instead, we identified and characterized a stable hairpin structure with potential regulatory function. Based on these findings, we designed fully locked nucleic acid (LNA)-modified ASOs to target this hairpin and regions flanking the upstream open reading frame (uORF) and start codon of the coding sequence. A reporter assay demonstrated that cap-proximal targeting achieved robust translation inhibition up to 80%. In contrast, targeting the efficiently translated uORF was ineffective, presumably due to steric hindrances from the ribosomal complex. The study yields crucial design principles for translation-regulating ASOs: avoid targeting regions shielded by efficient uORF translation and carefully tune ASO-RNA duplex stability to surpass endogenous structures without disrupting regulatory mechanisms. These findings provide insights into the regulation of DDX23 expression and establish a framework for developing ASO-based therapeutics with broad implications for mRNA targeting in anticancer applications. Full article

Background: Mitoxantrone (MX) is regularly used to treat several cancers. Despite its long history in the clinic, recent studies continue to unveil novel protein targets. These targets may contribute to the cytotoxic effects of the drug, as well as potential non-canonical antitumor activity. A better understanding of MX’s cellular targets is required to fully comprehend the molecular consequences of treatment and to interpret MX sensitivity in homologous recombination (HR)-deficient cancer. Methods: Here, we evaluated MX activity in HR-deficient UWB1.289 (BRCA1−) ovarian cancer cells and surveyed the binding profile of MX using TMT-labeled quantitative proteomics and chemoproteomics. Results: Mass spectrometry (MS) analysis of cellular extracts from MX-treated BRCA1−UWB1.289 cells revealed unique downregulation of pathways instrumental in maintaining genomic stability, including single-strand annealing. Moreover, the BRCA1− cells exhibited a significant upregulation of proteins involved in ribosome biogenesis and RNA processing. Additional MS analyses following affinity-purification using a biotinylated-mitoxantrone probe corroborated these findings, which showed considerable targeting of proteins involved in genome maintenance and RNA processing. Conclusions: Our results suggest that an interplay of both canonical and non-canonical MX-antitumor activity overwhelms the BRCA1− UWB1.289 cells. Furthermore, this study characterizes the target landscape of MX, providing insights into off-target effects and MX action in HR-deficient cancer. Full article

Background/Objectives: Osteoporosis is caused by excessive osteoclast activation via the receptor activator nuclear factor kappa B ligand (RANKL), which is released from osteoblasts or osteocytes. RANKL regulates osteoclast activity by binding to the receptor activator of nuclear factor kappa B (RANK) in the canonical pathway or leucine-rich repeat-containing G protein-coupled receptor 4 (LGR4) in the non-canonical pathway. In this study, we attempted to develop an intact small-fragment protein based on RANKL by removing the RANK-binding site and transforming the amino acid residues at crucial sites to inhibit osteoclast activity and treat osteoporosis. Methods: We expressed a small-fragment variant of RANKL as a soluble glutathione S-transferase (GST) or 6x histidine (His)-tagged fusion protein using a GST- or His-binding domain tag expression vector system. To generate an intact form of small-fragment RANKL, ribosome-inactivating protein–His-fusion RANKL was purified using HisTrap affinity chromatography and treated with tobacco etch virus nuclear inclusion endopeptidase to remove the His-tag fusion protein. Tartrate-resistant acid phosphatase (TRAP) and bone resorption pit formation assays were performed to analyze the inhibitory effects on osteoclast differentiation and activation. Results: The intact forms of 225RANKL295P and 225RANKL295A showed the strongest inhibitory effects on TRAP activity and bone resorption pit formation. Conclusions: Using an optimal construct design, a large and diverse range of small RANKL fragments could be generated. This suggests that the generation of small-fragment RANKL provides a promising avenue for the advancement of novel therapeutic approaches to osteoporosis. Full article

Background/Objectives: The butterfish Stromateus stellatus is undervalued and usually discarded as bycatch, leading to an inefficient and unsustainable use of marine biomass. Overall, although Stromateus is the type genus of the family Stromateidae, its species are less studied than more economically important fishes. Methods: In this study, we determined and analyzed the complete mitochondrial genome sequence of S. stellatus. Furthermore, we performed maximum likelihood and Bayesian inference analyses to infer the phylogenetic relationships among 21 species of the order Scombriformes. Results: Using next-generation sequencing (NGS) and de novo assembly, a circular mitochondrial genome of 16,509 bp was obtained, exhibiting the typical vertebrate mitochondrial structure comprising 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. Three intergenic regions were identified, including the control region and the origin of light-strand replication, along with several gene overlaps. The heavy strand nucleotide composition was determined to be 28.79% A, 27.84% C, 16.32% G, and 27.05% T, with a GC content of 44.16%. The three Peprilus and five Pampus species formed a clade together with S. stellatus, supported by high bootstrap and posterior probability values, confirming the monophyly of Stromateidae. Conclusions: The gene order and content are consistent with those reported for other Stromateidae species and correspond to the typical arrangement observed in most bony fishes. This mitochondrial genome represents the first one reported for the genus Stromateus, providing valuable insights into the genetic makeup of S. stellatus, contributing to a better understanding of marine biodiversity. Additionally, these data will support future research on pelagic fish evolution and assist in sustainable fisheries management. Full article

Background/Objectives: Cardiovascular disease (CVD) is the leading cause of mortality in patients with rheumatoid arthritis (RA), not fully explained by traditional risk factors and disease activity alone. This study explored the relationship between circulating monocyte subsets, inflammatory cytokine profiles, and Mammalian Target of Rapamycin Complex (mTORC) signaling in RA patients with and without a history of CVD. Methods: Peripheral blood mononuclear cells from 9 RA patients with prior CVD, 9 carefully matched RA controls without CVD, and 6 healthy controls were analyzed by flow cytometry. Matching was rigorously conducted across clinically relevant variables, including age, sex, blood pressure, lipid profile, smoking status, RA duration, disease activity, Disease-Modifying Anti-Rheumatic Drug (DMARD) failures, and steroid use. Monocyte subsets were classified as inflammatory (CD14⁺HLA-DR⁺CCR2⁺) and non-inflammatory (CD14⁺CD163⁺CCR2⁻). Results: RA-CVD⁺ patients exhibited higher frequencies of inflammatory monocytes and elevated intracellular levels of Interleukin 1 β (IL-1β) and Interleukin 6 (IL-6) compared to RA-CVD⁻ patients and healthy controls. mTORC activation, assessed by phosphorylation of S6 Ribosomal Protein (S6Rp), was significantly increased in inflammatory monocytes from RA-CVD⁺ patients. Conclusions: S6Rp correlated with IL-1β and IL-6 levels only in the RA-CVD⁺ group, suggesting a link between mTORC activity and inflammatory monocyte function. Notably, these inflammatory features did not correlate with disease activity scores or disease duration. We observed increased mTORC1 signaling in inflammatory monocytes in RA-CVD⁺ patients, suggesting a potential association with cardiovascular comorbidity. Full article

Positive (+) sense RNA viruses include many important pathogens that exploit noncanonical translation mechanisms to express their genomes within the host cells. Unlike DNA or negative (−) sense RNA viruses, (+) sense RNA viruses can directly function as mRNAs, even though they lack typical features of host mRNAs, such as the 5′ cap structure required for canonical translation initiation. Instead, they exploit structured RNA elements to recruit host translational machinery without the 5′ cap, bypassing the canonical translation initiation mechanism. Prominent examples include internal ribosome entry sites (IRESs) and 3′ cap-independent translation enhancers (3′ CITEs). These RNA modules facilitate translation initiation by recruiting the ribosomal subunits, either directly or through initiation factors, and mediating long-range RNA-RNA interactions. Other regulatory motifs, such as frameshifting signals, allow the ribosome to shift reading frames to regulate protein output. All these RNA elements function through RNA-protein interactions and often utilize host and virus-encoded proteins to hijack the host’s translational apparatus. Over the past several years, various structural biology approaches, including biochemical and enzymatic probing, X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryogenic electron microscopy (cryo-EM), have revealed the unique structural roles of these viral RNA elements and their protein complexes. Although a few structures of IRES and CITE domains have been solved through these methods, the structures of these RNA elements and their structure-function relationship have remained largely unknown. This review discusses the current understanding of translation-related RNA structures in (+) sense RNA viruses, the critical RNA-protein interactions they mediate, and various structural biology approaches used to study them. Since the genome of these viruses serves as a template for two mutually exclusive virological processes, namely genome translation and replication, the review also discusses how viruses can utilize RNA structure-based strategies to regulate the switch between genome translation and replication, highlighting future directions for exploring these fundamental virological processes to develop antiviral therapeutics able to combat diseases caused by these pathogens. Full article

Ribosome hibernation is a conserved translational stress response in bacteria, regulated by the hibernation-promoting factor (HPF). Plastid-specific ribosomal protein 1 (PSRP1) is the chloroplast ortholog of bacterial HPF. Although bacterial HPFs have been extensively characterized, both structurally and mechanistically, the physiological roles and mechanisms of PSRP1 in plant chloroplasts remain unclear. Here, we aimed to clarify the role of PSRP1 in chloroplast ribosome hibernation by examining its function under dark-stress conditions in the moss Physcomitrium patens. The PSRP1 knockout mutant exhibited moderate but statistically significant growth defects under both long- and short-day conditions compared to those of the wild-type plants. Moreover, the mutant displayed pronounced growth delay when co-cultured with wild-type plants, indicating a competitive disadvantage. Under dark conditions, wild-type plants exhibit increased PSRP1 protein accumulation, whereas the knockout mutant displayed reduction in chloroplast rRNA content. Notably, although PSRP1 is capable of inducing 100S dimers, we detected no chloroplast 100S dimers either in vivo or in vitro, suggesting a chloroplast-specific ribosome protection mechanism distinct from that of bacteria. These findings reveal PSRP1-mediated chloroplast ribosome protection and could provide new insights into plant stress tolerance. Full article

A reassessment of the risk-benefit balance of the two lipid nanoparticle (LNP)-based vaccines, Pfizer’s Comirnaty and Moderna’s Spikevax, is currently underway. While the FDA has approved updated products, their administration is recommended only for individuals aged 65 years or older and for those aged 6 months or older who have at least one underlying medical condition associated with an increased risk of severe COVID-19. Among other factors, this change in guidelines reflect an expanded spectrum and increased incidence of adverse events (AEs) and complications relative to other vaccines. Although severe AEs are relatively rare (occurring in <0.5%) in vaccinated individuals, the sheer scale of global vaccination has resulted in millions of vaccine injuries, rendering post-vaccination syndrome (PVS) both clinically significant and scientifically intriguing. Nevertheless, the cellular and molecular mechanisms of these AEs are poorly understood. To better understand the phenomenon and to identify research needs, this review aims to highlight some theoretically plausible connections between the manifestations of PVS and some unique structural properties of mRNA-LNPs. The latter include (i) ribosomal synthesis of the antigenic spike protein (SP) without natural control over mRNA translation, diversifying antigen processing and presentation; (ii) stabilization of the mRNA by multiple chemical modification, abnormally increasing translation efficiency and frameshift mutation risk; (iii) encoding for SP, a protein with multiple toxic effects; (iv) promotion of innate immune activation and mRNA transfection in off-target tissues by the LNP, leading to systemic inflammation with autoimmune phenomena; (v) short post-reconstitution stability of vaccine nanoparticles contributing to whole-body distribution and mRNA transfection; (vi) immune reactivity and immunogenicity of PEG on the LNP surface increasing the risk of complement activation with LNP disintegration and anaphylaxis; (vii) GC enrichment and double proline modifications stabilize SP mRNA and prefusion SP, respectively; and (viii) contaminations with plasmid DNA and other organic and inorganic elements entailing toxicity with cancer risk. The collateral immune anomalies considered are innate immune activation, T-cell- and antibody-mediated cytotoxicities, dissemination of pseudo virus-like hybrid exosomes, somatic hypermutation, insertion mutagenesis, frameshift mutation, and reverse transcription. Lessons from mRNA-LNP vaccine-associated AEs may guide strategies for the prediction, prevention, and treatment of AEs, while informing the design of safer next-generation mRNA vaccines and therapeutics. Full article

Grain amaranths are recalcitrant to conventional in vitro plant regeneration by organogenesis de novo or through somatic embryogenesis. Consequently, floral organogenesis by these methods, representing the culminating developmental point in angiosperms, is rarely achieved. In the present study, the manipulation of in vitro flowering was explored as part of a strategy designed to overcome grain amaranth’s regeneration recalcitrance. It led to an efficient and reproducible in vitro protocol in which half-longitudinally dissected zygotic embryos generated fully developed Amaranthus hypochondriacus (Ah) plants. The use of high-irradiance illumination with LED lamps with a 3:1 red–blue irradiance ratio was a critical factor, leading to a 70% rate of early flowering events under flowering-inhibiting long-day photoperiod conditions. Contrariwise, no flowering was induced under LED white lights. All in vitro flowering Ah plants yielded viable seeds. To understand the basic molecular mechanisms of the phenomenon observed, gene expression patterns and principal component analysis of key flowering-related genes were analyzed after cultivation in vitro for 4, 8, and 12 weeks under both lighting regimes. These coded for photoreceptors, photomorphogenetic regulators, embryogenic modulators, and flowering activators/repressors. The results highlighted the upregulation of key flowering-regulatory genes, including CONSTANS, FLOWERING LOCUS T, and LEAFY, together with the downregulation of the floral repressor TERMINAL FLOWER1. Ribosome biogenesis- and seed-development-related genes were also differentially expressed, supporting a key role in this process for protein synthesis and embryogenesis. A model is proposed to explain how this light-regulated molecular framework enables in vitro flowering and seed production in Ah plants kept under long-day photoperiods. Full article

Here, 18S-rDNA sequences of Blastocystis sp., previously documented from symptomatic (cases) and asymptomatic (controls) carriers, were analyzed to determine their population structure, predict their secondary structure, and examine their interactions with ribosomal proteins (Bud23, RPS5, and RPS18). Phylogenetic and population differentiation analyses were performed using STRUCTURE software V2.3.4. Moreover, an analysis of the rRNA secondary structure and folding of each sequence was performed, and their probability of interaction with ribosomal proteins was determined. Phylogenetic and haplotype analyses sorted the sequences into genetic subtypes ST1, ST2, and ST3, while the population structure showed each cluster as a differentiated subpopulation, suggesting incipient speciation or cryptic species differentiation. Furthermore, the analysis of the secondary structure of rRNA exhibited specific arrangements for each subtype. In addition, the probability of interaction between 18S-rRNA sequences of Blastocystis from cases and controls with RPS5 and RPS18 was significant, matching the biological plausibility of the previously documented finding that control isolates had a lower generation time than isolates obtained from cases. These findings reinforce the hypothesis that ribosomal subtypes ST1–ST3 of Blastocystis represent evolutionarily distinct lineages with the potential to be recognized as future species. Furthermore, they underscore the functional relevance of 18S-rRNA sequences from clinical isolates of Blastocystis. Full article

A pathogenic fungus was isolated from the leaves of strawberry black spot in Zhengzhou China. Based on morphological and phylogenetic analysis, the isolate was identified as Alternaria alstroemeriae. Hybrid sequencing and assembly yielded a high-quality 38.7 Mb genome with 12,781 predicted genes and 99.6% Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness. Functional annotation revealed enrichment in carbohydrate metabolism, secondary metabolite biosynthesis, and virulence-associated genes. Strain L6 harbored 45 biosynthetic gene clusters(BGCs), including 12 clusters for terpenes, 7 for non-ribosomal peptide synthetases, and 7 for polyketide synthases. Six BGCs showed high similarity to known pathways producing alternariol (phytotoxic/mycotoxic compound), alternapyrone (phytotoxin), choline (osmoprotectant), terpestacin (anti-angiogenic agent), clavaric acid (anticancer terpenoid), and betaenone derivatives (phytotoxins). CAZyme analysis identified 596 carbohydrate-active enzymes, aligning with L6’s biotrophic lifestyle. Additionally, 996 secreted proteins were predicted, of which five candidate effectors contained the conserved RxLx [EDQ] host-targeting motif, suggesting potential roles in virulence. This genome resource highlights L6’s exceptional secondary metabolites (SMs) diversity, featuring both plant-pathogenic toxins and pharmacologically valuable compounds, indicating that this endophytic fungus is a potential producer of metabolites meriting further exploration and development. Full article

Escherichia coli displays strong adaptability for growth and reproduction at low temperatures, with ribosome biogenesis being a critical process for its growth in cold environments. The cold-shock proteins (CSPs) encompass a protein family that can assist bacterial growth at low temperatures by acting as molecular chaperones. In this study, we investigated whether CSP CspA, CspE, and CspI affect ribosomal RNA (rRNA) transcription. Deletion of the single genes encoding these proteins had only a very marginal effect on cellular growth at low temperatures, and rRNA synthesis was hardly affected. Double and triple deletion of the genes encoding these proteins resulted in a much stronger phenotype providing evidence that CspA, CspE, and CspI play an essential role in maintaining 16S rRNA synthesis and enabling optimal cellular growth at low temperatures. These findings suggest the existence of efficient backup mechanisms able to compensate for the absence of a single CSP. Full article

Background: Using fish collagen supplements in daily nutrition may positively influence health and healthy aging. However, their systemic, molecular-level effects on humans are not well characterized. Therefore, given the scarcity of proteomic data, this study aimed to assess the serum proteomic changes during the fish collagen supplementation in healthy women. Methods: This was a crossover interventional study. Thirty healthy women received either 5 mL of fish gel collagen (from silver carp: Hypophthalmichthys molitrix) supplementation with 200 mL of pure water for 40 days or 200 mL of pure water for 40 days only. The washout between the fish collagen and pure water supplementation was 40 days. The nutritional status and dietary intake were assessed. Proteome analyses were conducted using a MALDI-TOF mass spectrometer in a positive linear mode in the m/z 1000–10,000 range. Results: The diet of the women in this study was not well-balanced. Supplementation did not affect nutritional status. Only water content significantly increased. During the fish collagen supplementation, the following discriminative proteins were identified: Filamin-A, Filamin-B, actin, Vimentin, Tropomyosin beta chain, 40S ribosomal protein S8, ATP-dependent RNA helicase DHX8, and FERM domain-containing protein 4A. Conclusions: Changes in serum proteins may reflect broader cytoskeletal remodeling and cellular adaptation resulting from collagen intake. Full article

Ribosomal proteins have long been recognized as vital components of ribosomes that are involved in protein synthesis. However, emerging evidence indicates that some ribosomal proteins exhibit extraribosomal functions. In this study, we investigated the role of the ribosomal protein S4 X-linked (RPS4X) in the regulation of the Skp1–Cullin1–F-box (SCF) ubiquitin ligase complex and apoptosis. We found that RPS4X expression interfered with SCF complex formation by disrupting the interaction between Cullin1 and Skp1. This disruption suppressed ubiquitination of multiple SCF complex substrates, including the anti-apoptotic proteins myeloid cell leukemia 1 (MCL1) and HS1-associated protein X1 (HAX1). Stabilization of MCL1 and HAX1 by RPS4X led to increased resistance of HeLa cells to doxorubicin-induced apoptosis. These findings suggest that RPS4X contributes to the regulation of protein homeostasis and apoptotic pathways by modulating SCF complex activity, providing new insights into the extraribosomal roles of ribosomal proteins. Full article

White-lipped tree frogs, Polypedates braueri, are currently included in the list of terrestrial wildlife with important ecological, scientific, and social value in China. Understanding the structure and characteristics of the mitochondrial genome provides essential information for resource conservation and phylogenetic analyses of P. braueri. While the complete mitochondrial genomes serve as important molecular markers for phylogenetic and genetic studies, the mitochondrial genome of P. braueri has received little attention. In this paper, we analyzed the characterization of the mitochondrial genome of P. braueri and investigated the phylogenetic relationships of Rhacophoridae. The complete mitochondrial genome of P. braueri was 20,254 bp in length, containing thirty-six genes (twelve protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), twenty-two transfer RNA genes (tRNAs)), three non-coding regions for the origin of light strand (O_L), and two control regions (CR). There were six overlapping regions and seventeen intergenic spacer regions in the mitogenome. The mitogenome also showed a bias towards A + T content (61.87%) and had negative AT-skew (−0.039) and GC-skew (−0.209). All the PCGs employed the ATG, ATA, or ATT as the start codon and TAA, TAG, AGG, or single T as the stop codon. Additionally, all of the tRNAs displayed a typical cloverleaf secondary structure, except trnS1, which lacked the D arm. The phylogenetic analysis, based on the maximum likelihood (ML) and Bayesian inference (BI) methods, revealed that Rhacophoridae could be classified into four monophyletic genera. The phylogenetic status of P. braueri was closely related to that of Polypedates megacephalus and Polypedates leucomystax. Additionally, selective pressure analysis suggested that COX1 and ND1 were highly efficient for discriminating closely related species in the genus Polypedates, while ND4L was the most appropriate marker for population-level genetic analyses. The diversification of the Polypedates commenced during the Late Oligocene and extended into the Miocene. The present study provides valuable genomic information on P. braueri and new insights into the phylogenetic relationships of Rhacophoridae. Full article