bims-ribost Biomed News
on Ribostasis and translation stress
Issue of 2026–10–18
73 papers selected by
Cédric Chaveroux, CNRS



  1. RNA Biol. 2026 Dec;23(1): 1-22
      The proteostasis network maintains cell function by safeguarding the proteome through the coordinated actions of protein synthesis, quality control, and degradation machinery including chaperones and the ubiquitin-proteasome system. Proteostasis collapse and activation of the integrated stress response (ISR) occur in ageing and neurodegeneration. Upon proteotoxic stress, translation suppression during the ISR drives the assembly of non-translating mRNAs into biomolecular condensates called stress granules. Stress granules act as a double-edged sword in the proteostasis network, serving beneficial or detrimental roles through their effects on translation, protein quality control, and protein aggregation. In this review, we discuss how protein synthesis, quality control, and degradation factors regulate stress granule dynamics, and conversely how stress granules impact proteostasis. While stress granules may initially protect cells by sequestering misfolded, aggregation-prone proteins and regulating translation, they may evolve into sites of pathological aggregation. Clarifying these intersections may reveal therapeutic strategies for neurodegeneration and other disease processes.
    Keywords:  Proteostasis; integrated stress response; protein quality control; stress granules; translation
    DOI:  https://doi.org/10.1080/15476286.2026.2731904
  2. Semin Hematol. 2026 Sep 16. pii: S0037-1963(26)00087-9. [Epub ahead of print]
      Translational control has emerged as a critical layer of gene expression reprogramming in cancer, with the ribosome functioning as a central regulatory node rather than a passive protein synthesis machinery. This review provides an integrated overview of how defects in ribosomes and translational regulation contribute to the pathogenesis of lymphoid leukemias and lymphomas. We focus on 3 major axes: mutations in ribosomal proteins, alterations in ribosomal RNA, and dysregulation of translation initiation mediated by the eukaryotic initiation factor 4F complex. Recurrent mutations in ribosomal proteins, such as RPL10 in T-cell acute lymphoblastic leukemia and RPS15 in chronic lymphocytic leukemia, alter ribosome function, leading to selective changes in mRNA translation, impaired translational fidelity, and increased oxidative stress that promotes genomic instability. In parallel, emerging evidence indicates that alterations in ribosomal RNA, including changes in ribosomal DNA copy number, biogenesis, and epigenetic modifications, contribute to ribosome heterogeneity and oncogenic transformation, although their precise roles in hematologic malignancies remain incompletely understood. Furthermore, aberrant activation of translation initiation pathways-often driven by the AKT/mTOR/MYC signaling axis-enhances both global protein synthesis and selective translation of oncogenic transcripts, reinforcing malignant phenotypes. Together, these ribosome-intrinsic and -extrinsic defects converge to reprogram the translatome, promote tumor progression, and create therapeutic vulnerabilities. Targeting translational control mechanisms therefore represents a promising strategy for the treatment of lymphoid malignancies.
    Keywords:  Chronic lymphocytic leukemia; Ribosomal protein mutations; Ribosome biogenesis; T-cell acute lymphoblastic leukemia; eIF4F; rRNA
    DOI:  https://doi.org/10.1053/j.seminhematol.2026.09.002
  3. Cell Rep. 2026 Oct 13. pii: S2211-1247(26)01204-0. [Epub ahead of print]45(10): 118125
      Various ribosome-associated quality control pathways safeguard translation fidelity by detecting and resolving aberrant translation events. Recently, a pathway that senses stalled ribosomes with an occluded A-site has been described. The small molecules NVS1.1 and ternatin-4 induce ribosome stalling by trapping eukaryotic release factor 1 (eRF1) and elongation factor 1A1 (eEF1A1), respectively, within the ribosomal A-site, thereby promoting their ubiquitination and proteasomal degradation. Additionally to the previously identified factors GCN1, RNF14, and RNF25, we identify here the deubiquitinase USP9X as a regulator of this pathway. In the absence of USP9X deubiquitinase activity, eRF1 is still ubiquitinated but fails to undergo efficient degradation. However, compared with wild-type cells, K6-linked ubiquitin chains accumulate on eRF1 in cells lacking USP9X activity, suggesting that USP9X trims K6-linked ubiquitin chains during a late step of substrate processing. Furthermore, clearance of trapped eRF1 engages a feedback mechanism involving 4EHP and the integrated stress response (ISR) to suppress translation, whereas impaired degradation prevents translational shutdown.
    Keywords:  CP: molecular biology; K6-linked ubiquitination; USP9X; deubiquitination; eEF1A1; eRF1; proteasomal degradation; ribosome; ribosome quality control; translation; ubiquitination
    DOI:  https://doi.org/10.1016/j.celrep.2026.118125
  4. Anim Genet. 2026 Oct;57(5): e70223
      Bovine mastitis is a heterogeneous inflammatory disease that compromises milk production, animal welfare and dairy sustainability. Despite extensive transcriptomic and epigenomic research, a PubMed search completed in September 2026 identified only 12 primary studies addressing epitranscriptomic regulation in bovine mastitis, representing approximately 0.1% of indexed publications. This review critically evaluates N6-methyladenosine (m6A), the most extensively studied RNA modification in bovine mastitis, its regulatory machinery and effects on mammary immunity, while identifying m5C and A-to-I editing as priorities for mechanistic investigation. Current evidence identifies transcript-specific RNA stability as the best-supported mechanism and provides a foundation for investigating m6A-dependent translation. Functional studies of ALKBH5-LOC4191, YTHDF2-IER3, YTHDF2-associated CCL20 and CCL5 regulation, m6A-regulated LncRNA7825 and FTO-FN1 demonstrate that m6A reshapes inflammatory signalling, mitochondrial stress, epithelial-barrier integrity, cell survival and bacterial control. Synthesizing these findings, we propose a context-dependent RNA-fate checkpoint model in which biological effects depend on the modified transcript, effector protein, pathogen, cellular context and infection phase. The FTO-FN1 axis shows that bacterial control and tissue protection can diverge, establishing them as complementary outcomes. Future studies should test whether m6A provides an early post-transcriptional response layer and whether pathogens manipulate it, using time-resolved multi-omics, nucleotide-specific perturbation, primary cells, mammary organoids and longitudinal cattle samples. Parallel profiling of non-m6A modifications should define interacting regulatory layers. These approaches should establish causal modification sites, resolve pathogen-specific regulation, connect molecular mechanisms with disease trajectories, and support validated milk-based biomarkers, mammary-targeted interventions and prioritization of stable genetic variants for breeding mastitis-resistant cattle.
    Keywords:  N6‐methyladenosine; RNA modification; bovine mastitis; epitranscriptomics; translational biomarkers
    DOI:  https://doi.org/10.1002/age.70223
  5. Front Genet. 2026 ;17 1856671
       Introduction: Heat shock protein 70 (HSP70) is a central molecular chaperone that maintains proteostasis by supporting protein folding, preventing protein aggregation, and coordinating cellular stress responses. Dysregulation of HSP70 has been associated with cancer progression, neurodegenerative disorders, and aging-related proteotoxicity. However, many experimental approaches rely on chemical inhibition or stress-inducing conditions that may introduce additional confounding effects. This study aimed to investigate the proteostatic consequences of HSP70 depletion in the absence of stress-inducing chemical inhibitors.
    Methods: A rapid, quantitative workflow was developed to assess chaperone function and proteostasis in cultured cells. HSP70 was depleted in HeLa cells using siRNA-mediated gene silencing. Knockdown efficiency was evaluated at the transcript and protein levels using quantitative polymerase chain reaction (qPCR) and Western blotting, respectively. Flow cytometry was used to quantify ProteoStat-detected misfolded/aggregated protein burden and total cellular fluorescence from a G3BP1-GFP reporter.
    Results: siRNA-mediated HSP70 depletion resulted in a greater than 90% reduction in HSP70 transcript and protein levels. HSP70-depleted cells exhibited a 1.8-fold increase in ProteoStat fluorescence, indicating an increased burden of misfolded/aggregated proteins, and a 2.9-fold increase in total cellular G3BP1-GFP fluorescence. Because flow cytometry does not resolve intracellular localization or puncta formation, the increased G3BP1-GFP fluorescence should be interpreted as a surrogate reporter response and does not constitute direct evidence of stress granule biogenesis.
    Discussion: These findings are consistent with impaired proteostasis following acute HSP70 depletion and demonstrate the potential utility of an inhibitor-independent workflow for evaluating cellular responses associated with targeted chaperone depletion. Orthogonal spatial validation using immunofluorescence or confocal microscopy is required to determine G3BP1 localization and confirm stress granule formation. In addition, experiments using multiple independent siRNA duplexes will be necessary to establish target specificity and strengthen the mechanistic interpretation of the observed proteostatic response.
    Keywords:  HeLa cells; Ras GTPase-activing protein-binding protein 1; heat shock protein 70; molecular chaperones; protein aggregation; proteostasis; small interfering RNA
    DOI:  https://doi.org/10.3389/fgene.2026.1856671
  6. Sci Adv. 2026 Oct 16. 12(42): eaef7741
      Ribosomal RNA modification enzymes increase cellular fitness, but it's little known whether this benefit arises from rRNA modification or a chaperone function of the modification enzyme. Here, we show that E. coli methyltransferase RsmB chaperones the initial recruitment of ribosomal proteins to the 16S 3' domain rRNA, a key step in assembly of the 30S subunit. Real-time single-molecule assembly experiments show that the RsmB product, 16S m5C967, has little effect on the rRNA affinity for ribosomal proteins. Instead, RsmB facilitates stable recruitment of primary protein uS7 during transcription while blocking the addition of secondary protein uS19. Completion of the methyltransferase cycle promotes RsmB release, allowing assembly to continue. Dimethyl sulfate footprinting of trapped RsmB-rRNA complexes revealed that RsmB restructures a critical rRNA helix junction. Our results illustrate how an RNA modification enzyme favors the proper sequence of protein addition by temporarily reshaping the energy landscape of co-transcriptional rRNA folding.
    DOI:  https://doi.org/10.1126/sciadv.aef7741
  7. Wiley Interdiscip Rev RNA. 2026 Sep-Oct;17(5):17(5): e70065
      RNA-binding proteins (RBPs) regulate RNA processing, localization, translation, and decay, yet similar perturbations can have different consequences across cells and tissues. RNA-protein reciprocity relates this variation to the balance between the binding sites presented by RNA and the protein available to regulate them. Regulation can remain stable while sufficient RBP is available, but become sensitive to small changes as that reserve narrows. The biological consequence depends on which transcripts lose regulation and how strongly the cell depends on their products. Examples from endogenous regulatory RNAs, repeat-expansion diseases, viral infection, and cancer show that RNA-dependent RBP redistribution can preserve cellular function or contribute to its failure. Binding affinity, partner proteins, autoregulation, and RNA-dependent assembly shape these responses. This Perspective develops the framework and proposes experiments to connect changes in local RNA demand and RBP supply with target binding and biological output. The aim is to identify when a modest molecular perturbation has a disproportionate functional effect, and when restoring the RNA-protein balance can recover regulation.
    Keywords:  RNA regulation; RNA‐binding proteins; RNA–protein stoichiometry; alternative polyadenylation; binding‐site competition; biomolecular condensates; post‐transcriptional regulation
    DOI:  https://doi.org/10.1002/wrna.70065
  8. Oxid Med Cell Longev. 2026 ;2026(1): e8809922
      Cells are continuously exposed to oxidative and proteotoxic stress that disrupt redox balance and protein homeostasis. Two major cytoprotective systems-the nuclear factor erythroid 2-related factor 2 (NRF2) pathway and the heat shock response (HSR) mediated by heat shock factor 1 (HSF1) and heat shock proteins (HSPs)-form an interconnected stress-adaptation network that coordinates redox defense, proteostasis, and cellular survival. Although historically viewed as largely independent pathways, accumulating evidence demonstrates extensive bidirectional and context-dependent crosstalk through transcriptional coregulation, protein-protein interactions, posttranslational mechanisms, and shared molecular hubs, including p62/SQSTM1 and the ubiquitin-proteasome system. This network integrates antioxidant defense with protein quality control, mitochondrial homeostasis, and inflammatory and metabolic signaling; however, NRF2 and HSR responses can also become functionally uncoupled under specific biochemical and metabolic conditions. This review critically examines the molecular mechanisms underlying NRF2-HSP crosstalk and its functional consequences in neurodegeneration, cancer, ischemia-reperfusion (I/R) injury, aging, and tumor immunity. Particular attention is given to the dual role of this axis: transient activation promotes cytoprotection, proteostasis, and tissue recovery, whereas chronic or constitutive activation can support tumor metabolism, immune evasion, and therapeutic resistance. In I/R injury, endoplasmic reticulum (ER) stress (ERS)-induced XBP1-HRD1 signaling may impose an additional constraint on NRF2 activity, highlighting an important limitation of endogenous cytoprotection. Finally, we discuss therapeutic strategies targeting NRF2, HSF1, and HSPs, emphasizing the challenges of systemic pathway modulation, the importance of pharmacodynamic biomarkers and molecular stratification, and the potential of rational combination approaches. A context-, tissue-, and cell-specific understanding of NRF2-HSP signaling will be essential for translating this complex stress-response network into precision therapeutic strategies.
    Keywords:  HSF1; NRF2; cellular stress response; heat shock proteins; proteostasis; redox homeostasis; tumor immunity
    DOI:  https://doi.org/10.1155/omcl/8809922
  9. Front Cell Dev Biol. 2026 ;14 1935788
      Mitochondrial dysfunction is a hallmark of Parkinson's disease (PD), but how impaired mitochondrial homeostasis drives the selective death of dopaminergic neurons is still poorly understood. At the center of this problem lies the mitochondrial protein import machinery-the TOM and TIM23 translocases-which doubles as a stress-sensing hub that coordinates two distinct quality control pathways. When import is compromised, the kinase PINK1 accumulates on the mitochondrial surface, recruits Parkin to ubiquitinate outer membrane proteins, and triggers mitophagy. Meanwhile, the stress sensor DELE1 is cleaved and released to the cytosol, where it activates the HRI kinase to phosphorylate eIF2α and engage the integrated stress response (ISR). These two pathways are not independent. Recent work shows they engage in antagonistic crosstalk: the DELE1-HRI-ISR axis suppresses PINK1/Parkin-dependent mitophagy by preserving mitochondrial import efficiency, acting as a molecular brake on organelle clearance. The balance between these pathways is governed by the SIFI E3 ubiquitin ligase complex, which targets both DELE1 and HRI for degradation. Disruption of SIFI causes progressive neurodegeneration in humans. Here we synthesize the structural, biochemical, and genetic evidence that defines the TOM/TIM-PINK1/Parkin-DELE1/HRI signaling axis, examine how its dysregulation contributes to dopaminergic neuron vulnerability, and evaluate therapeutic strategies targeting mitochondrial import stress in PD.
    Keywords:  DELE1; HRI; PINK1; Parkinson’s disease; integrated stress response; mitochondrial protein import; mitophagy; parkin
    DOI:  https://doi.org/10.3389/fcell.2026.1935788
  10. J Mol Biol. 2026 Oct 12. pii: S0022-2836(26)00438-9. [Epub ahead of print] 170065
      Ribosome biogenesis is a highly coordinated pathway that involves the assembly of ribosomal RNAs (rRNAs) with ribosomal proteins (r-proteins) to generate functional ribosomal subunits (r-subunits). The Saccharomyces cerevisiae (yeast) large 60S r-subunit consists of three rRNA molecules and 46 r-proteins. The contributions of nearly all r-proteins of the yeast large r-subunit have been characterized; however, a few non-essential proteins remain poorly understood. Although non-essential, human eL22 has been identified as a key player in p53 regulation during ribosomal stress and as a highly mutated target in cancers. Despite this function, the role of eL22 in ribosome maturation is still ill-defined. In this study, we characterized yeast eL22 r-protein, which is encoded by two paralogous genes that exhibit markedly different expression levels. Our results show that eL22 assembles into intermediate nucleolar pre-60S ribosomal particles. Loss of eL22 impairs cell growth and reduces 60S r-subunit accumulation, phenotypes that are exacerbated at low temperatures. Analysis of pre-rRNA processing by pulse-chase labeling, northern blot hybridization, and primer extension reveals a defect in 27S pre-rRNA maturation, specifically at the level of 27SB pre-rRNA processing. Consequently, nuclear export of eL22-deficient pre-60S particles is mildly impaired. Furthermore, we identify genetic interactions between eL22 and neighboring r-proteins, eL38 and eL31. We conclude that eL22 assembly is required for optimal pre-60S maturation during middle nucleolar stages, particularly at low temperatures, a function likely supported by the cooperative action of other r-proteins associated with common elements of 25S rRNA.
    Keywords:  60S ribosomal subunit; eL31; eL38; nucleolus; rRNA processing; ribosomal RNA domain III; ribosome assembly; yeast
    DOI:  https://doi.org/10.1016/j.jmb.2026.170065
  11. Mol Plant. 2026 Oct 13. pii: S1674-2052(26)00342-4. [Epub ahead of print]
      Rising global temperatures and increasingly frequent heat events pose a major threat to crop productivity and food security. Heat stress disrupts plant physiological and metabolic processes, compromising growth, development, and ultimately yield (Lesk et al. 2021). Understanding the molecular mechanisms that allow plants to withstand elevated temperatures is therefore increasingly important for improving crop resilience. Post-transcriptional regulation provides plants with a rapid means of reshaping gene expression during stress. RNA modifications can influence mRNA stability, translation, and localization, including partitioning into stress granules (SGs) - dynamic biomolecular condensates that rapidly assemble when cells experience adverse conditions (Arango et al. 2018; Kudrin et al. 2024; Kearly et al. 2024; Shen 2025). Recent work showed that N4-acetylcytidine (ac4C)-modified RNAs are preferentially enriched in SGs, raising the intriguing possibility that RNA modifications contribute to determining SG composition (Kudrin et al. 2024). Zhang et al. (Zhang et al. 2026) now provide a mechanistic and physiological framework for this idea in plants, connecting RNA acetylation, selective mRNA partitioning into SGs, transcript protection, and heat-stress tolerance.
    DOI:  https://doi.org/10.1016/j.molp.2026.10.003
  12. Cells. 2026 Sep 30. pii: 1794. [Epub ahead of print]15(19):
      Glioblastoma, isocitrate dehydrogenase (IDH)-wildtype (GBM), remains one of the most aggressive primary brain tumors, and its proteostasis machinery represents a potential therapeutic target. Here we identify HSP27 as a key regulator-associated proteostasis in glioblastoma, IDH-wildtype, where it is linked to protein synthesis, folding, stress-granule dynamics and ubiquitin-mediated turnover. Ribo-seq showed HSP27 depletion reduced global protein synthesis, while TME labeling coupled to mass spectrometry revealed increased accumulation of unfolded proteins, indicating proteotoxic stress. Proteomic analysis of isolated stress granules (SGs) revealed enhanced sequestration of translational regulators, including EIF4E, mTOR, EIF3M and QKI, into stress granules (SGs), thereby reinforcing translational repression. Ubiquitinome profiling further revealed increased ubiquitination and proteasome-dependent loss of oncogenic and translational regulators, including AKT2, PARP1, EIF4G1, EIF4A3, and DDX5. Functionally, targeting HSP27 inhibits tumor growth and sensitizes glioblastoma to translational blockade. In orthotopic models, antisense oligonucleotide targeting HSP27 in combination with Didemnin B suppressed tumor progression and prolonged survival compared with either single agent. These findings associate HSP27 with proteostasis in glioblastoma, IDH-wildtype, and suggest HSP27-dependent proteostasis buffering as a therapeutic vulnerability.
    Keywords:  HSP27; glioblastoma; proteostasis; stress granule; translation
    DOI:  https://doi.org/10.3390/cells15191794
  13. Mol Cancer. 2026 Oct 14. pii: 241. [Epub ahead of print]25(1):
      The dynamic and reversible N6-methyladenosine (m6A) RNA modification has emerged as a pivotal layer of epitranscriptomic regulation in cancer, governing RNA metabolism and function. Concurrently, deubiquitylating enzymes (DUBs), key components of the post-translational modifications (PTMs) system, orchestrate protein stability and signaling pathways crucial for tumorigenesis. Recent evidence reveals extensive and intricate crosstalk between these two regulatory systems, forming a complex network that can influence cancer progression. This review systematically explores the bidirectional interplay between DUBs and m6A modification. On one hand, specific DUBs can deubiquitinate and stabilize core m6A "writers" (methyltransferases), "erasers" (demethylases), or "readers" (recognition proteins), thereby influencing RNA metabolism and downstream gene expression. On the other hand, m6A modification can regulate the expression of certain DUBs, either by influencing the stability and translation of their mRNAs or by controlling associated regulatory factors. This reciprocal regulation profoundly impacts key oncogenic processes, including cell proliferation, metastasis, metabolic reprogramming, and therapy resistance. By integrating current findings, this review highlights the significance of the DUB-m6A axis as a critical regulatory hub in cancer biology. Deciphering this crosstalk not only provides novel insights into tumor mechanisms but also unveils promising therapeutic targets for overcoming drug resistance and developing innovative anti-cancer strategies.
    Keywords:  Cancer; Deubiquitinases; Epitranscriptomic modification; N6-methyladenosine; Post-translational modification
    DOI:  https://doi.org/10.1186/s12943-026-02808-1
  14. bioRxiv. 2026 Sep 28. pii: 2026.09.25.754245. [Epub ahead of print]
      Endoplasmic reticulum (ER) stress is associated with many human diseases, but current understanding of how ER stress responses reshape the stressed proteome over time is still emerging. Specifically, how organellar protein quality control and clearance pathways coordinate to maintain proteostasis in early and prolonged ER stress is unclear. Here we describe a spatiotemporal proteomic strategy termed simultaneous proteome localization and turnover analysis with time resolution (SPLAT-TR) to interrogate the synthesis, degradation, and localization changes of over 4,000 proteins in early (1-4 hours) and prolonged (16-24 hours) ER stress. As ER stress progresses, each time point is distinguished by distinct protein translocation and clearance regulations, coupled to differential organellar proteostasis and usage of protein degradation pathways. Mitochondria show a bimodal response, with a shift from early activation of respiratory protein towards protein quality control pathways in prolonged stress, coinciding with energetics decline. In the Golgi, the increased clearance of collagen proteins is paradoxically coupled to an increased synthesis of secretory pathway components, suggesting removal by secretion. In the ER, the proteome remodels under prolonged stress via increased synthesis of UFMylation and ER-phagy-related proteins coupled to the selective degradation of ER membrane and microdomain proteins. Inhibition of UFMylation alters ER-phagy receptor usage and synergistically induces stress-induced cell death. These results present a systematic delineation of cell compartment proteostasis under unfolded protein response and highlight the utility of SPLAT-TR to investigate time-dependent cellular events.
    DOI:  https://doi.org/10.64898/2026.09.25.754245
  15. Methods Mol Biol. 2027 ;3081 419-433
      DEAD-box RNA helicases are widespread ATP-driven enzymes that reshape RNA structures and RNA-protein complexes during many steps of RNA metabolism. In bacteria, DEAD-box RNA helicases support cellular growth and responses to stress by contributing to ribosome biogenesis, RNA degradation, and translation initiation. Growing evidence indicates that several DEAD-box RNA helicases can also form liquid-liquid phase-separated condensates that concentrate RNA and partner proteins. This behavior adds a new layer of control to RNA regulation, although the molecular factors that promote or tune liquid-liquid phase separation (LLPS) are still unclear. Here, we describe an in vitro microscopy-based assay to characterize the LLPS behavior of bacterial DEAD-box RNA helicases. The protocol includes step-by-step procedures to evaluate condensate formation, salt sensitivity and dissolution, RNA dependency and specificity, and ATP effects. We further provide detailed instructions for quantitative analysis of microscope images, including size and assessment of protein enrichment within condensates. Altogether, this workflow enables systematic dissection of key physicochemical parameters governing DEAD-box helicase LLPS and provides a standardised framework for comparative studies across bacterial DEAD-box proteins or variants.
    Keywords:  DEAD-box proteins; Image analysis; Intrinsically disordered region (IDR); Liquid–liquid phase separation (LLPS); Microscopy; RNA helicase
    DOI:  https://doi.org/10.1007/978-1-0716-5571-9_20
  16. J Exp Biol. 2026 Oct 13. pii: jeb.252969. [Epub ahead of print]
      Despite a likely role in setting stress tolerance limits, food ration has received limited attention as an ecological factor affecting the cellular stress response (CSR). To study the interactive effects of food and temperature on the proteomic heat shock response, we acclimated intertidal mussels (Mytilus californianus) to four combinations of nearshore (low) and aquaculture (high) phytoplankton levels, combined with low (20 °C) and high (30 °C) aerial temperatures during daytime low tides. Mussels were then exposed to an acute (6 h), aerial heat stress (33 °C) and allowed to recover for 1 h and 25 h in pre-exposure conditions. Proteomic changes in the gill before and after heat shock were measured using label-free liquid-chromatography-mass spectrometry. Compared to other acclimation treatments, low-food-low-temperature (LTLF) mussels modified more splicing factors, heterogeneous nuclear ribonucleoproteins, ribosomal proteins, and translation initiation and elongation factors, suggesting systemic changes to RNA processing, selection, and translation. LTLF mussels also increased chaperones of the actin- and microtubule-associated cytoskeleton and proteins that mature along the endoplasmic reticulum to Golgi secretory pathway. Simultaneously, actin stress fiber formation at focal adhesions and the extracellular matrix, along with anchoring of microtubule-associated cilia, indicate a possible system-wide mechanical breakdown of the cytoskeleton. Signaling proteins causing cytoskeletal changes varied mainly in LTLF mussels and suggest a food-dependent role for prostaglandin synthesis. Overall, the acclimation-dependent proteomic changes show how thermal conditioning and food ration together will shape the CSR of mussels during heat waves.
    Keywords:   Mytilus ; Cellular signaling; Cytoskeleton; MRNA processing; Proteomics; Proteostasis; Translation
    DOI:  https://doi.org/10.1242/jeb.252969
  17. bioRxiv. 2026 Sep 28. pii: 2026.09.25.754444. [Epub ahead of print]
      Chemical modifications of RNA provide an additional regulatory layer essential for development. N6-methyladenosine (m6A) is the most abundant internal mRNA mark, but how site specificity, stoichiometry, and cellular context together determine mRNA fate remains unclear. Here, we define these rules in cardiogenesis by combining single-molecule nanopore direct RNA sequencing (DRS) with a CRISPR-dCas13 epitranscriptomic editing platform in human induced pluripotent stem cells and a conditional Mettl14 cardiac knockout in mice, integrated with multi-omics, to map m6A sites and quantify stoichiometry. We uncover a bimodal m6A code in which low versus high modification ratios are associated with opposite mRNA and protein outcomes. We further show that Mettl14 loss causes developmental cardiomyopathy and embryonic lethality by disrupting the glycolysis-to-oxidative phosphorylation (OXPHOS) metabolic switch, and identify an m6A-YY1 (Yin Yang 1) axis that post-transcriptionally controls OXPHOS genes. Finally, targeted installation of m6A at defined sites using CRISPR-dCas13 reveals that m6A effects on YY1 are strongly locus- and context-dependent. Together, these findings establish m6A as a site- and stoichiometry-dependent regulatory code interpreted by cellular context to direct cardiac metabolic maturation. These principles are likely to extend to other developmental and physiological contexts in which precise control of metabolic state and gene dosage is required.
    DOI:  https://doi.org/10.64898/2026.09.25.754444
  18. Plants (Basel). 2026 Sep 22. pii: 2896. [Epub ahead of print]15(19):
      Daily supplements have emerged as a compelling strategy for heavy metal detoxification (e.g., Hg and Pb), given that conventional chelation therapy lacks chronic exposure data and is heavily reliant on the doctor's experience. Among such natural agents, Chlorella vulgaris (C. vulgaris), a commercially available supplement, is known for its notable heavy metal-binding capacity and ancillary benefits. Yet, the detoxification mechanisms of action of C. vulgaris have remained largely unexplored. In this study, our transcriptomic and signaling analyses demonstrated that the chemically characterized aqueous extract of C. vulgaris may have attenuated Hg2+-induced mitotic catastrophe in HEK-293 cells and was predicted to activate AKT signaling and modulate the expression of zinc finger protein-related genes. Furthermore, in corresponding DMT1-overexpressing cells, the protective effects of the extract were associated with the modulation of translation and ubiquitination pathways. These changes may coincide with the partial recovery of the two major ribosomal stress surveillance pathways. Intriguingly, under conditions in which Hg2+ did not provoke the more severe ribotoxic stress response, the C. vulgaris extract appeared to alleviate Hg2+-induced ribosomal stress by engaging both ribosomal quality control and the integrated stress response, particularly the response of GCN2 to amino acid deficiency. Ultimately, these findings suggest the protective effect of C. vulgaris extract against Hg2+ toxicity is associated with DMT1 at the transcriptome level, warranting further experimental investigation of its potential as a nutraceutical adjuvant in mercury detoxification.
    Keywords:  DMT1; algal aqueous extract; heavy metal; mitotic catastrophe; network pharmacology; ribosomal stress surveillance
    DOI:  https://doi.org/10.3390/plants15192896
  19. Methods Mol Biol. 2027 ;3081 217-248
      Internal ribosome entry sites (IRES) are structured RNA elements that facilitate cap-independent translation initiation. IRES activity is regulated by its interactions with host and viral RNA-binding proteins (RBPs), collectively known as IRES trans-acting factors (ITAFs), which modulate RNA folding, ribosome recruitment, and translation efficiency. Characterizing these RNA--protein interactions provides valuable insights into the mechanisms that regulate IRES activity. Hepatitis E virus (HEV), is a positive-sense, single-stranded RNA virus. Our earlier study discovered an IRES-like (IRESl) element in the genotype 1-HEV (g1-HEV), which mediated translation of the open reading frame four (ORF4). This chapter describes our stepwise protocol to identify host proteins that associate with the HEV-IRESl using two independent methods: the yeast three-hybrid (Y3H) assay and the RNA-protein interaction detection (RaPID) assay. The Y3H assay enables genetic screening of host cDNA libraries to identify RBPs that bind to an RNA sequence in vivo, while the RaPID assay employs proximity-dependent biotinylation to capture transient interactions in mammalian cells. Together, these methods offer a robust approach for identifying the dynamic network of IRES-associated RBPs.
    Keywords:  Hepatitis E virus; IRES-like element; Internal ribosome entry site; RNA–protein interaction; RNA–protein interaction detection; Yeast three-hybrid
    DOI:  https://doi.org/10.1007/978-1-0716-5571-9_9
  20. Proc Natl Acad Sci U S A. 2026 Oct 20. 123(42): e2607201123
      Molecular chaperones interact with non-native proteins, playing crucial roles in preventing misfolding and in enabling efficient folding in the cellular environment. Trigger factor is a bacterial chaperone that binds to ribosomes, interacting with nascent polypeptides emerging from the ribosome and guiding their early folding steps. In contrast to the central role of the chaperone in promoting folding of newly synthesized proteins, its dynamic interactions with nascent chains emerging from the ribosome remain poorly understood. Here, we use single-molecule fluorescence and optical tweezers approaches to directly observe and characterize trigger factor interactions with a ribosome-bound client protein at increasing chain lengths. We find that trigger factor dwell times on ribosome-nascent chain complexes increase non-monotonically with nascent chain length, and that binding to nascent proteins is best described by a combination of multiple weak, dynamic interactions that are established after the chaperone docks onto the ribosome and evolve during polypeptide elongation. Application of mechanical force perturbs trigger factor binding, supporting a multivalent interaction model. This binding mode may help to stabilize nascent proteins against misfolding while allowing them to dynamically sample conformational space in search of their native structures.
    Keywords:  molecular chaperones; protein synthesis; ribosome; single-molecule fluorescence; single-molecule spectroscopy
    DOI:  https://doi.org/10.1073/pnas.2607201123
  21. J Biol Chem. 2026 Oct 14. pii: S0021-9258(26)02517-2. [Epub ahead of print] 113645
      Dietary methionine restriction improves metabolic health and has therapeutic potential in multiple disease contexts. Methionine metabolism regulates transmethylation reactions, including N6-methyladenosine (m6A) RNA methylation, by modulating availability of S-adenosyl methionine (SAM). Both m6A methylation and methionine metabolism have separately been linked to circadian regulation, but whether dietary methionine influences circadian rhythms through m6A remains unknown. Here we show that short-term methionine deprivation induces diurnal variation in serum methionine and SAM and reprograms diurnal expression of m6A writers, erasers, and readers in mouse liver. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) at two timepoints (ZT9, ZT21) revealed that a methionine-deficient (MD) diet was associated with a roughly 10-fold increase in differentially methylated m6A peaks between timepoints relative to control, despite no change in methylation at core clock transcripts. These diet-induced oscillations arose at sites already methylated under the control diet, indicating that methionine restriction alters the rhythmicity of existing m6A marks rather than inducing new methylation, and were enriched in transcripts involved in RNA processing, translation, ubiquitination, and mTORC1 signaling. Integrating RNA-seq and proteomics, we found that a subset of these m6A changes co-occurred with altered mRNA and/or protein abundance, indicating gene-specific rather than global effects. Notably, reduced m6A methylation of Mat2a and Cbs, encoding enzymes central to methionine homeostasis, was associated with increased MAT2A and decreased CBS protein levels, respectively. These findings identify diet-induced, diurnally rhythmic m6A methylation as a candidate mechanism linking methionine metabolism to circadian biology and nominate specific m6A sites and pathways for future investigation.
    Keywords:  circadian oscillation; m6A RNA methylation; metabolism; methionine restriction
    DOI:  https://doi.org/10.1016/j.jbc.2026.113645
  22. Methods Mol Biol. 2027 ;3081 435-453
      Stress granules (SGs) are cytoplasmic, membrane-less ribonucleoprotein (RNP) granules that form in response to cellular stress following the inhibition of translation initiation. Their assembly, composition, and crosstalk with processing bodies (P-bodies) are mediated by protein-protein, RNA-protein, and RNA-RNA interactions. DEAD/DEAH-box RNA helicases are key regulators of stress granules. Here, we present standardized protocols for (i) immunofluorescence of stress granule and P-body scaffold proteins and helicases, (ii) single-molecule RNA fluorescence in situ hybridization (smRNA FISH), and (iii) quantitative image analysis using Imaris software, including single-cell and nuclear segmentation, stress granule and P-body surface rendering, docking interaction analysis, and RNA spot detection.
    Keywords:  Microscopy; P-body; RNA; RNA helicase; RNA–RNA interactions; RNP granules; Stress granule; smRNA FISH
    DOI:  https://doi.org/10.1007/978-1-0716-5571-9_21
  23. Proc Natl Acad Sci U S A. 2026 Oct 20. 123(42): e2604945123
      It is well established in yeast and animal system that the level of uridine thiolation at position 34 of tRNA anticodon loops can impact the decoding potential of the corresponding codons. Using Arabidopsis thaliana, we confirm that the ability of the plant ribosome to decode AAA, GAA, and CAA codons is impaired when this thiol group is lost, leading to a reduction in protein production, especially for genes enriched in these codons. Interestingly, we observed that loss of tRNA thiolation results in variations in the levels of numerous proteins involved in sulfur-compound metabolism and amino acid biosynthesis. These variations, in turn, affect the accumulation of several sulfur-containing metabolites and amino acids, suggesting that the level of tRNA thiolation has a direct and profound impact on plant metabolism. We also demonstrate that U34 thiolation is essential for adjusting plant growth in response to sulfur limitation and that its absence directly affects the plant's interaction with bacteria, including both pathogens and beneficial organisms. Our results support the hypothesis that the level of tRNA thiolation can be used in plant to link nutritional status to translation.
    Keywords:  epitranscriptomics; plant nutrition; plant-bacteria interactions; ribosome dynamics; tRNA
    DOI:  https://doi.org/10.1073/pnas.2604945123
  24. Photobiomodul Photomed Laser Surg. 2026 Oct 12. 25785478261493763
       BACKGROUND: Energy-based aesthetic devices alter tissue temperature across defined spatial and temporal distributions, producing biological effects commonly described as collagen contraction, neocollagenesis, elastogenesis, adipocyte injury, or tissue tightening. These clinical labels encompass distinct processes including protein damage, cellular stress adaptation, inflammation, cell death, extracellular matrix turnover, and long-term remodeling. Heat-shock proteins (HSPs) and mammalian cold-shock proteins provide a mechanistic framework for interpreting these responses.
    OBJECTIVE: To evaluate the roles of heat- and cold-responsive proteins in energy-based aesthetic medicine and propose a temperature-time-depth framework linking device-specific tissue exposure to molecular, histological, and clinical responses.
    MATERIALS AND METHODS: A structured narrative review was conducted using targeted PubMed searches and examination of reference lists from pivotal mechanistic and human-tissue studies. Literature through August 2026 was considered. Priority was given to studies reporting tissue-temperature measurements, human skin biopsies, spatial histology, protein or RNA measurements, controls, serial assessments, and late clinical or structural outcomes.
    RESULTS: Heat activates heat-shock factor 1 and induces HSP70, HSP27, HSP90, and other chaperones. HSP47 (SERPINH1) is particularly relevant to dermal remodeling because it is an endoplasmic reticulum collagen chaperone required for procollagen folding, trafficking, and secretion. Human studies of fractional laser and radiofrequency, together with emerging microfocused ultrasound histology, support a sequence in which early stress and inflammatory responses precede HSP47-positive fibroblast recruitment and matrix remodeling. However, HSP induction alone does not establish durable clinical tightening, and excessive thermal exposure may cause necrosis, fibrosis, scarring, dyschromia, or injury to nerves and fat. Mammalian cold adaptation involves cold-inducible RNA-binding protein (CIRBP/CIRP) and RNA-binding motif protein 3 (RBM3), best characterized during sustained mild hypothermia near 32°C-34°C. These proteins regulate RNA stability, translation, metabolism, and cell survival. Their adaptive intracellular functions must be distinguished from profound cold injury and extracellular CIRP-mediated inflammation. Direct evidence linking aesthetic cooling to CIRBP- or RBM3-mediated dermal neocollagenesis remains insufficient.
    CONCLUSIONS: Mechanistic interpretation should be based on measured biological dose, tissue compartment, and response timing rather than console temperature, surface temperature, or device category alone. Heat-shock mechanisms are supported for several thermal modalities, whereas cold-shock-mediated aesthetic neocollagenesis remains a translational hypothesis requiring direct molecular, histological, and clinical validation.
    Keywords:  CIRBP; CIRP; HSP47; HSP70; RBM3; aesthetic medicine; cold-shock protein; collagen; cryolipolysis; fibroblast; heat-shock protein; laser; microfocused ultrasound; radiofrequency
    DOI:  https://doi.org/10.1177/25785478261493763
  25. Biochem Biophys Res Commun. 2026 Oct 08. pii: S0006-291X(26)01471-3. [Epub ahead of print]839 154705
      P-bodies and the RNA-induced silencing complex (RISC) are vital in regulating post-transcriptional gene expression, with their association contributing to mRNA regulation in a context-dependent manner in cells. RISC is responsible for microRNA (miRNA)-guided target detection and translational repression, while P-bodies are versatile cytoplasmic RNA granules involved in storing, repressing translation, and degrading mRNA. Some studies show that the spatial relationship between the components of RISC and P-bodies is dynamic and context-dependent, shifting in response to specific cellular environments or stress states. This mini-review examines the context-dependent relationship between P-bodies and the RISC in regulating mRNA stability and fate, including degradation, translational repression, and long-term storage or decay under stress. It also covers recent discoveries regarding biomolecular condensates and the role of the RISC and P-body components in cancer and viral infections. Examining how the relationship between RISC and P-bodies may clarify how spatial organisation and mRNA regulatory pathways influence transcript fate.
    Keywords:  AGO2; P-bodies; RISC machinery; RNAi; SND1; miRNAs
    DOI:  https://doi.org/10.1016/j.bbrc.2026.154705
  26. Cell Chem Biol. 2026 Oct 15. pii: S2451-9456(26)00325-9. [Epub ahead of print]33(10): 1353-1355
      Endoplasmic-reticulum-associated ribosome quality control (ER-RQC) requires ubiquitin-fold modifier 1 (UFM1) for UFMylation of the ribosomal protein RPL26. In the August 6 issue of Molecular Cell, Mao et al.1 identify an ER-associated complex (UFSP2/ODR4) as critical for deUFMylation of RPL26 and uncover a critical physiologic role for UFSP2 in neuronal proteostasis.
    DOI:  https://doi.org/10.1016/j.chembiol.2026.08.015
  27. Phys Chem Chem Phys. 2026 Oct 12.
      Protein aggregation is widely associated with neurodegenerative disorders, but increasing evidence suggests that similar misfolding phenomena also contribute to cancer. Although p53 aggregation is commonly associated with oncogenic mutations, wild-type p53 can also misfold under cellular stress. Here, we show that the endogenous polyanion polyphosphate regulates the phase behaviour and aggregation of wild-type p53 in a pH-dependent manner. Using thioflavin T kinetics together with optical and electron microscopy, we demonstrate that acidic conditions promote polyphosphate-driven coacervation of p53, leading to the formation of multicoacervate condensates. These protein-rich condensates locally concentrate p53 and accelerate fibril nucleation and maturation into dense fibrillar networks. In contrast, at neutral pH, p53 remains soluble and non-amyloidogenic, consistent with the absence of phase separation. Together, our findings reveal a phase separation-assisted pathway for p53 fibrillization under acidic stress and highlight polyphosphate as an important regulator of p53 aggregation.
    DOI:  https://doi.org/10.1039/d6cp02900k
  28. Front Microbiol. 2026 ;17 1957771
      The genomes of positive-strand RNA [(+)ssRNA] viruses function as dynamic RNA molecules that participate in multiple, sometimes competing, processes during infection, including translation, genome replication, subgenomic RNA (sgRNA) transcription, and genome packaging. These distinct processes require viral RNAs to adopt different conformational states, which are influenced by RNA-RNA interactions and associated viral or host factors. Therefore, understanding how viral RNAs undergo structural remodeling in space and time, and how they transition between different functional states, represents a central question in the regulation of positive-strand RNA virus gene expression. Recent studies of diverse plant positive-strand RNA viruses have revealed that long-distance RNA-RNA interactions (LDRIs) serve as important regulatory mechanisms that shape viral RNA higher-order structures and functional states. This review summarizes recent advances in understanding how LDRI-mediated RNA conformational transitions contribute to the formation of higher-order viral RNA structures and support diverse viral RNA functions. We propose that LDRIs should be viewed not only as physical connections between distant RNA regions, but also as dynamic structural elements embedded within viral RNA folding landscapes, where they contribute to transitions between alternative RNA conformations and functional states.
    Keywords:  RNA structural remodeling; dynamic RNA structure; gene expression and replication; long-distance RNA–RNA interactions (LDRIs); plant positive-strand RNA viruses
    DOI:  https://doi.org/10.3389/fmicb.2026.1957771
  29. Res Sq. 2026 Oct 01. pii: rs.3.rs-10284597. [Epub ahead of print]
      Cells that lose adhesion to their native extracellular matrix must either adapt to impaired adhesion signaling or undergo anoikis. How cells convert loss of adhesion into translational stress responses and survival signaling remains incompletely understood. Here, we define adhesion stress as a cellular stress state triggered by impaired adhesion signaling and show that this state induces stress granule (SG) assembly as an adaptive survival mechanism. We modeled adhesion stress through cell detachment, reduced adhesion strength, and pharmacologic inhibition of focal adhesion kinase (FAK). Across these models, adhesion stress activated a RhoA-ROCK-PERK-eIF2α signaling pathway that drove SG assembly. PERK was the principal eIF2α kinase required for this adhesion-stress response. Proteomic profiling further showed that adhesion-stress SGs represent a previously unrecognized SG subtype characterized by a Rho GTPase-associated protein signature and selective enrichment of CASP4, an inflammatory caspase linked to cell-death signaling. Functionally, SG assembly limited CASP4 activation and reduced apoptotic signaling during FAK inhibitor-induced adhesion stress. In parallel, PERK contributed to sustained AKT-mTOR survival signaling during anoikis. Genetic loss of SG assembly or pharmacologic inhibition of G3BP-dependent SG formation increased anoikis sensitivity and sensitized cancer cells to multiple FAK inhibitors. SGs were also enriched in invading cancer cells in human breast tumors, consistent with a role for adhesion-stress adaptation in invasive tumor contexts. Together, these findings identify adhesion-stress SGs as a RhoA-ROCK-PERK-driven survival program that limits anoikis and enables anchorage-independent cancer cell survival.
    DOI:  https://doi.org/10.21203/rs.3.rs-10284597/v1
  30. Mol Microbiol. 2026 Oct 11.
      The mechanistic target of rapamycin (mTOR) signaling pathway is a central regulator of nutrient sensing, metabolism, growth, and stress adaptation in most eukaryotes. Malaria parasites of the genus Plasmodium, however, lack identifiable orthologues of mTOR kinase and its associated signaling complexes, raising the question of how these organisms coordinate environmental sensing with developmental progression and proliferation. Here, we discuss emerging evidence suggesting that Plasmodium has evolutionarily replaced the canonical mTOR signaling axis with a distributed regulatory architecture composed of parasite-specific nutrient sensors, kinase-based signaling pathways, translational repression mechanisms, and unconventional autophagy processes. Components such as KIN, PI3K, eIF2α kinases, eIF4E-interacting protein DOZI, and Maf1 collectively preserve many hallmark outputs of mTOR signaling, including metabolic adaptation, stress tolerance, developmental plasticity, and reversible quiescence. In addition, malaria parasites interact with host mTOR pathways during infection, potentially exploiting host-derived anabolic signaling environments to support intracellular development. These findings suggest that Plasmodium exemplifies an extreme case of signaling plasticity in eukaryotic evolution, demonstrating how essential mTOR-associated functions can be maintained despite the apparent loss of the pathway itself.
    Keywords:   Plasmodium ; kinase network; malaria; mechanistic target of rapamycin; nutrient sensing; stress adaptation
    DOI:  https://doi.org/10.1111/mmi.70123
  31. Methods Mol Biol. 2027 ;3081 473-489
      RNA helicase DHX9 is a multi-functional protein governing transcriptional modulation, RNA processing, R-loop balance, and genome stability. SUMOylation is a post-translational modification that adds a critical regulatory layer to protein function by diversifying subcellular localization, stability, enzymatic activity, and protein-protein interactions. This protocol describes a basic but detailed approach for the analysis of DHX9 SUMOylation. We demonstrate that accurate site identification, specifically at Lysine 120 (K120), is the prerequisite for defining the molecular mechanism of this modification. Identifying the K120 acceptor site enables the generation of specific mutants to dissect how DHX9 SUMOylation orchestrates the protein interactions necessary to preserve genomic integrity. Furthermore, this protocol provides a versatile framework for characterizing the SUMOylation of other RNA helicases involved in RNA regulation.
    Keywords:  DHX9; R-loop; SUMO; SUMOylation
    DOI:  https://doi.org/10.1007/978-1-0716-5571-9_23
  32. Front Cell Dev Biol. 2026 ;14 1949071
      Intervertebral disc degeneration (IDD) is the fundamental pathological process underlying low back pain, a major cause leading to disability worldwide. As the most prevalent methylation modification in eukaryotic RNA molecules, N6-methyladenosine (m6A) is involved in various diseases and cellular processes by regulating RNA fate. Methyltransferase-like protein 3 (METTL3) is the sole catalytic component of the methyltransferase complex and mediates m6A deposition on target RNAs. METTL3 is ubiquitously expressed and modulated by a variety of factors at the transcriptional and post-transcriptional levels. METTL3 expression is significantly increased in degenerative nucleus pulposus tissue and shows a positive correlation with degeneration degree. Importantly, recent studies have demonstrated that METTL3-mediated m6A modification is able to promote the progression of IDD through multiple approaches, including extracellular matrix metabolism imbalance, inflammatory response, nucleus pulposus cell senescence and apoptosis, and mitochondrial dysfunction. Thus, METTL3 could represent a promising therapeutic target for IDD. This review systematically summarizes the latest advances regarding the role of METTL3 in IDD and underlying molecular mechanisms, and also highlights its potential translational implications.
    Keywords:  IDD; METTL3; apoptosis; cell senescence; extracellular matrix; m6A
    DOI:  https://doi.org/10.3389/fcell.2026.1949071
  33. J Cell Sci. 2026 Oct 01. pii: jcs264879. [Epub ahead of print]139(19):
      Glioblastoma is the most aggressive and lethal malignancy of the central nervous system and exhibits a complex interplay with endoplasmic reticulum (ER) stress (ERS). The multifunctional ER is the primary site of the unfolded protein response (UPR), which is activated under conditions of ERS to enhance protein-folding capacity and promote cell survival. However, persistent ERS can trigger apoptosis. Despite extensive research over the past decades, the mechanistic insights into the impact of ERS and the UPR on glioblastoma pathogenesis and progression remain unclear. The UPR operates through three canonical signaling pathways: inositol-requiring enzyme 1 (IRE1), PKR-like ER kinase (PERK, also known as EIF2AK3) and activating transcription factor 6 (ATF6). These pathways regulate glioblastoma development through both independent and synergistic mechanisms. In this Review, we discuss the current state of research on the role of the UPR in glioblastoma and delineate the distinct mechanisms of each signaling pathway. Furthermore, we evaluate the challenges associated with UPR-targeting therapeutic agents and propose possible treatment strategies to leverage the regulatory mechanisms of the different UPR pathways to overcome these limitations.
    Keywords:  Apoptosis induction; Drug resistance; Glioblastoma; Targeted therapy; Unfolded protein response
    DOI:  https://doi.org/10.1242/jcs.264879
  34. Mol Cells. 2026 Oct 14. pii: S1016-8478(26)00098-1. [Epub ahead of print] 100407
      Ribosome collisions during aberrant translation activate ribosome-associated quality control (RQC) to resolve stalled ribosome complexes and triage incomplete nascent chains. How this co-translational surveillance is coordinated with other ribosome-associated activities remains unclear. Here, we identify the ribosome-associated Hsp40 chaperone DNAJC2 that restrains translational flux and limits RQC engagement during collision-prone translation. Genetic epistasis analysis revealed that DNAJC2 titrates the flux of aberrant translation intermediates through the canonical RQC pathway, from the collision-sensing RQC factor ZNF598 to the downstream NEMF-LTN1 E3 ligase complex for proteasomal degradation. DNAJC2 depletion further sensitized cells to collision-induced ribotoxic stress response (RSR), indicating increased vulnerability to global translation stress. Mechanistically, loss of DNAJC2 accelerated translation elongation, thereby promoting ribosome collisions and ZNF598-dependent ribosome disassembly. Accordingly, reducing translational flux with the translation inhibitor homoharringtonine or a huntingtin upstream ORF rescued DNAJC2-depletion phenotypes during RQC-sensitive poly(A)-mediated translational stalling. Together, we propose that DNAJC2 acts as a translational rheostat to buffer ribosome collisions, prevent RQC overload, and set the threshold for RSR activation.
    Keywords:  DNAJC2; Ribosome-associated quality control (RQC); ribosome-associated complex (RAC); ribotoxic stress response (RSR); translational flux
    DOI:  https://doi.org/10.1016/j.mocell.2026.100407
  35. Cancers (Basel). 2026 Sep 26. pii: 3120. [Epub ahead of print]18(19):
      Over the past three decades, the biology of EIF3E (int6) has emerged as far more complex than originally anticipated. Initially identified as a common integration site of Mouse Mammary Tumor Virus (MMTV) and subsequently recognized as a component of the eukaryotic translation initiation factor 3 (eIF3) complex, EIF3E is now understood as a multifunctional regulator involved in selective mRNA translation, proteostasis, genome stability, cellular stress responses, and tissue homeostasis. Recent studies have further extended this framework by demonstrating that conditional Eif3e deficiency promotes lymphoma susceptibility in mice, providing in vivo evidence linking EIF3E-dependent translational regulation to immune homeostasis and cancer development. This focused review retraces the scientific journey of EIF3E from its discovery as int6 to the progressive definition of its diverse biological functions and context-dependent roles in cancer. Particular attention is given to the historical relationship between int6 (EIF3E) and int7 (RSPO2), whose unexpected reunion in recurrent EIF3E::RSPO2 fusions in human solid tumors provides a unique bridge between classical retroviral insertional mutagenesis and contemporary cancer genomics. While transcriptional activation of RSPO2 through EIF3E regulatory elements represents the established oncogenic mechanism of the fusion, whether disruption of one EIF3E allele exerts additional biological effects remains unknown. Together, these observations highlight EIF3E as a nexus between selective translation, cellular homeostasis, and cancer, while emerging links between epigenomic, epitranscriptomic, and translational regulation open new perspectives for understanding its context-dependent functions in tumorigenesis.
    Keywords:  DNA repair; EIF3E; EIF3E::RSPO2 fusion; cancer; int6; lymphoma susceptibility; proteostasis; selective translation
    DOI:  https://doi.org/10.3390/cancers18193120
  36. Sci Adv. 2026 Oct 16. 12(42): eaee5884
      In most cells, Malat1 long noncoding RNA localizes to the nucleus where it affects splicing and chromatin function. In mouse neurons, Malat1 is exported to the cytoplasm where it is translated to generate the M1 micropeptide. Here, we characterize an internal ribosome entry site (IRES) required for M1 translation that is sufficient to induce cap-independent expression of a downstream open reading frame. In vivo chemical probing and structural modeling defined a three-stem-loop RNA secondary structure that encompasses the active IRES segment and coincides with a mouse B1 SINE (short interspersed element) repetitive element. In affinity purification experiments, a minimal IRES/B1 RNA selectively bound ribosomal subunits, translation factors, and the known IRES cofactors Rack1 and hnRNP A2/B1. Depletion of Rack1 and hnRNP A2/B1 inhibited IRES-dependent translation of the reporter and expression of the endogenous M1 peptide. Our study identifies an unexpected functional unit hidden within a widely studied long noncoding RNA.
    DOI:  https://doi.org/10.1126/sciadv.aee5884
  37. Nucleic Acids Res. 2026 Oct 13. pii: gkag966. [Epub ahead of print]54(19):
      The promyelocytic leukemia protein (PML) is a stress-response factor that assembles into PML nuclear bodies, dynamic subnuclear compartments involved in tumor suppression and antiviral defense. The most abundant isoform, PML-1, has been linked to transcriptional regulation, genome stability, and antiviral responses, yet the molecular basis of these functions remains unclear and is generally attributed to proteins associated with PML nuclear bodies. Here, we report that PML-1 itself harbors a previously structurally uncharacterized nucleic acid-binding domain. The domain, termed PXL, is encoded by exon 9 of the PML gene and is unique to isoform 1. Its structure reveals an exonuclease III fold, but lacks the catalytic residues required for activity, defining PXL as a pseudo-exonuclease. Biochemical, structural, mutational, and cellular analyses demonstrate that PXL specifically binds G-rich oligonucleotides implicated in G-quadruplex formation and displays a strong in vitro preference for polyUG RNA. Furthermore, deletion of the PXL domain significantly decreases PML colocalization with G-quadruplexes in cells, downregulates genomic maintenance pathways, and modulates the expression of E2F target and interferon-α response genes. These findings provide a molecular basis for previous observations implicating PML in nucleic acid-associated functions and establish a mechanistic framework for future studies of PML-mediated stress responses, nuclear organization, and gene regulation.
    DOI:  https://doi.org/10.1093/nar/gkag966
  38. Proc Natl Acad Sci U S A. 2026 Oct 20. 123(42): e2621525123
      The bacterial RNA degradosome is a central mediator of RNA turnover, yet how its components are organized and regulated in living cells remains unclear. Using live-cell single-molecule imaging, we quantified the spatial distribution and dynamics of the four major Escherichia coli degradosome components: RNase E, RhlB, PNPase, and enolase. These proteins occupied distinct membrane-associated and cytoplasmic pools whose relative abundance varied among proteins and changed with physiological state. In particular, PNPase underwent pronounced redistribution between membrane-associated and cytoplasmic states in response to altered RNA availability and growth conditions, whereas RNase E and RhlB remained largely membrane associated. To determine the functional consequences of this organization, we examined the degradation of lacZ reporter transcripts with different translation initiation strengths. PNPase and RhlB preferentially promoted degradation of weakly translated transcripts, whereas strongly translated transcripts were largely insensitive to their loss. Together, these results reveal that the bacterial RNA degradosome is not a static, uniformly assembled molecular machine. Instead, RNA decay is organized through dynamic intracellular partitioning of degradosome components, linking physiological state and translation status to transcript degradation.
    Keywords:  RNA degradation; biomolecular stoichiometry; post-transcriptional gene regulation; single-molecule microscopy
    DOI:  https://doi.org/10.1073/pnas.2621525123
  39. Molecules. 2026 Sep 22. pii: 3360. [Epub ahead of print]31(19):
      Prolidase (PEPD) is a metalloproteinase that hydrolyzes imidodipeptides containing proline or hydroxyproline at the C-terminus and also participates in the non-catalytic regulation of cellular stress responses and p53 availability. Here, we characterized population-level responses associated with transient CRISPR/Cas9-directed targeting of PEPD in heterogeneous MCF7 breast cancer cultures using three independent sgRNAs. PEPD enzymatic activity was quantified in three independent biological experiments, whereas PEPD and p53/apoptosis-related proteins were examined by representative Western blotting and exploratory immunofluorescence microscopy. All three PEPD-targeting constructs were associated with reduced population-average PEPD activity, and representative immunoblots showed directionally concordant reductions in PEPD protein signal. Representative protein analyses additionally revealed a qualitative pattern involving p53, MDM2, cleaved caspase-9, cleaved caspase-7, and cleaved PARP-1. These protein observations were not supported by independent biological replication suitable for inferential analysis and are therefore interpreted descriptively. Editing of the endogenous PEPD locus was not directly confirmed or quantified by genomic analysis. During prolonged puromycin selection, the persistence of adherent PEPD-targeted cells decreased under the conditions tested; however, this experiment was qualitative and was not designed as a formal viability or rescue assay. Collectively, the data demonstrate a replicated population-level reduction in PEPD enzymatic activity following PEPD-directed CRISPR/Cas9 perturbation and identify an associated exploratory p53/MDM2- and apoptosis-related protein pattern. A contribution of Cas9-mediated DNA-damage signaling to the latter cannot be excluded.
    Keywords:  CRISPR/Cas9; MCF7; MDM2; PEPD; apoptosis; p53; prolidase
    DOI:  https://doi.org/10.3390/molecules31193360
  40. Proc Natl Acad Sci U S A. 2026 Oct 20. 123(42): e2608103123
      Neural crest cells, a multipotent vertebrate stem cell population, undergo a tightly regulated epithelial-mesenchymal transition (EMT) to delaminate from the neural tube and initiate migration. Neural crest EMT is controlled by a transient pulse of Draxin, which acts as a molecular rheostat of canonical Wnt signaling, and is then rapidly downregulated by unknown mechanisms. To address this, here we use in vivo reporter assays and live RNA imaging to show that Draxin mRNA is rapidly degraded posttranscriptionally via its 3' untranslated region. We found that Draxin transcripts are targeted to cytoplasmic processing bodies (P-bodies), which are membrane-less sites of RNA processing and decay. Disruption of P-bodies by CRISPR/Cas9-mediated depletion of the RNA helicase DDX6 prevented posttranscriptional downregulation of Draxin and impaired neural crest EMT in vivo. These findings parallel observations in human patients carrying DDX6 mutations, who exhibit defects in P-body assembly and craniofacial abnormalities associated with neural crest dysfunction. Together, our results identify P-bodies as regulators of Draxin mRNA decay and reveal a spatially organized mechanism of RNA turnover that controls neural crest EMT during vertebrate development.
    Keywords:  EMT; P-bodies; epithelial to mesenchymal transition; neural crest; posttranscriptional regulation
    DOI:  https://doi.org/10.1073/pnas.2608103123
  41. Methods Mol Biol. 2027 ;3081 1-17
      Cellular RNAs depend on proteins for efficient folding to specific functional structures and for transitions between functional structures. This dependence arises from intrinsic properties of RNA structure. Specifically, RNAs possess stable local structure, largely in the form of helices, and there are abundant opportunities for RNAs to form alternative helices and tertiary contacts and therefore to populate alternative structures. Proteins with RNA chaperone activity, either ATP-dependent or ATP-independent, can promote structural transitions by interacting with single-stranded RNA (ssRNA) to compete away partner interactions and then release ssRNA so that it can form new interactions. In this chapter, we review the basic properties of RNA and the proteins that function as chaperones and remodelers. We then use these properties as a foundation to explore key points for the design and interpretation of experiments that probe RNA rearrangements and their acceleration by proteins.
    Keywords:  ADP-BeF3; AMP-PNP; ATP analogs; Helicases; RNA folding; RNA remodeling
    DOI:  https://doi.org/10.1007/978-1-0716-5571-9_1
  42. Free Radic Biol Med. 2026 Oct 15. pii: S0891-5849(26)01214-1. [Epub ahead of print]
      Aging progressively impairs skeletal muscle function, leading to sarcopenia, frailty, and loss of independence. Although oxidative stress has long been considered a central driver of muscle aging, increasing evidence indicates that reactive oxygen species (ROS) also serve essential signaling functions that coordinate mitochondrial remodeling, proteostasis, metabolism, and tissue repair. Consequently, age-related muscle dysfunction is increasingly understood as reflecting impaired adaptive redox signaling rather than excessive oxidant production alone. In this review, we propose the concept of redox resilience as an integrative framework describing the capacity of skeletal muscle to preserve structural integrity and functional performance through the dynamic regulation of oxidant production, antioxidant defenses, and redox-sensitive signaling in response to physiological challenges. We discuss how aging disrupts this resilience through impaired redox-sensitive signaling, including the attenuation of exercise-induced Nrf-2 activation, together with alterations in the multicellular organization of skeletal muscle. Recent advances in single-cell and single-nucleus transcriptomics have revealed that muscle aging involves profound remodeling of specialized myonuclear populations, stromal cells, immune cells, and intercellular communication networks, highlighting the multicellular complexity of skeletal muscle aging and providing a framework to investigate how redox-dependent processes may interact with tissue-wide signaling networks. We further examine how regular physical exercise reinforces redox resilience by promoting transient ROS-mediated signaling through NADPH oxidases, activation of Nrf-2 and PGC-1α-dependent pathways, mitochondrial quality control, and metabolic remodeling. These adaptations enhance the capacity of skeletal muscle to respond to physiological stress while preserving tissue homeostasis. Finally, we discuss future perspectives for targeting adaptive redox networks to promote healthy muscle aging and propose that restoring redox resilience may preserve physiological ROS signaling while strengthening endogenous antioxidant responses and limiting excessive oxidative damage, thereby contributing to the maintenance of muscle function and health span.
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2026.10.023
  43. Methods Mol Biol. 2027 ;3081 267-277
      RNA helicases play a critical role in RNA biogenesis by modulating RNA-protein interactions in an ATP-dependent manner. Although many RNA helicases function by unwinding RNA secondary structures or displacing proteins from RNA, a subset of RNA helicases facilitates the loading of their interacting proteins onto RNA. Here, I present an in vitro method for analyzing the formation of the uridine-rich small nuclear RNA (U snRNA) export complex, for which the involvement of RNA helicases was previously unknown. This method can be used to determine whether complex formation is ATP-dependent and identify RNA helicases that facilitate the loading of the U snRNA export factor onto RNA. This approach can identify RNA helicases involved in protein loading onto various RNA-protein complexes.
    Keywords:  RNA export; RNA helicase; RNA–protein complex; U snRNA; UV crosslinking
    DOI:  https://doi.org/10.1007/978-1-0716-5571-9_11
  44. Toxicol Mech Methods. 2026 Oct 15. 1-32
      Hexavalent chromium [Cr(VI)] is a recognized environmental and occupational carcinogen associated with an increased risk of lung cancer. The nuclear factor erythroid 2-related factor 2 (NRF2)-Kelch-like ECH-associated protein 1 (KEAP1) pathway regulates cellular responses to oxidative and electrophilic stress and may influence cell survival following Cr(VI) exposure. Under basal conditions, KEAP1 promotes NRF2 ubiquitination and proteasomal degradation. Oxidative or electrophilic stress can impair this process, allowing NRF2 to accumulate and activate genes involved in antioxidant defense, detoxification, and cellular redox regulation, including HMOX1, NQO1, and GCLC. Although these responses can protect normal cells from acute stress, persistent NRF2 activity has also been associated with metabolic adaptation, resistance to apoptosis, and tumor-promoting phenotypes in several cancer models.However, the extent to which NRF2-KEAP1 signaling directly contributes to Cr(VI)-induced lung carcinogenesis remains incompletely established. Many studies on Cr(VI) have investigated oxidative stress, inflammation, genotoxicity, and cellular transformation. In contrast, relatively few have directly tested whether NRF2 activation is causally involved in tumor initiation or progression in chromium-exposed lung models. This review examines the relationship among Cr(VI) exposure, redox imbalance, and NRF2-KEAP1 signaling, distinguishing findings from chromium-specific experimental systems from mechanisms inferred from broader lung cancer research. It also discusses downstream processes relevant to carcinogenesis, occupational exposure, and risk assessment, as well as potential preventive or therapeutic strategies. The available evidence supports NRF2-KEAP1 signaling as an important component of the cellular response to Cr(VI)-associated stress, but further mechanistic studies are needed to establish its specific causal contribution to chromium-induced lung carcinogenesis.
    Keywords:  Chromium toxicity; KEAP1; Lung carcinogenesis; NRF2; metabolic reprogramming; oxidative stress
    DOI:  https://doi.org/10.1080/15376516.2026.2750969
  45. bioRxiv. 2026 Sep 22. pii: 2026.09.18.752750. [Epub ahead of print]
      Translation reprogramming is central to cancer cell plasticity under stress. However, the molecular players coordinating translation and epitranscriptomic rewiring to determine adaptive responses to mitotic stress remain elusive. Here, we found that microtubule targeting agent (MTA)-induced CDK1 blocks global translation while it phosphorylates and degrades TACC3, a multifunctional adaptor, releasing eIF4A/eIF4E/eIF4G2 initiation factors. This promotes selective m 7 G cap-dependent translation of mRNAs with 'MTAup' motif that are functionally required for apoptosis by disrupting proteostasis, promoting MTA-sensitivity. On the other hand, selectively translated TACC3 interacts with eIF3d/eIF4G1 and the m 6 A writer METTL3, mediating switch to m 6 A methylation and m 7 G cap-independent translation of mRNAs with hnRNPC-motif involved in chromosome segregation, driving MTA tolerance. TACC3 inhibition overcomes MTA resistance via restoring translation reprogramming. These findings demonstrate that TACC3 is a pivotal coordinator of translation/epitranscriptomic reprogramming and a therapeutic target in MTA-refractory cancers.
    Highlights: MTA-induced CDK1 blocks global translation while increasing selective translationCap-dependent translation of mRNAs with MTAup motif leads to MTA-induced apoptosis TACC3 fuels m 6 A methylation/switch to cap-independent translation and MTA tolerance TACC3 serves as a potential therapeutic target to overcome MTA resistance.
    DOI:  https://doi.org/10.64898/2026.09.18.752750
  46. Microbiol Mol Biol Rev. 2026 Oct 14. e0034625
      SUMMARYProtein synthesis by ribosomes proceeds through the sequential stages of initiation, elongation, termination, and ribosome recycling. In most bacteria, coupled transcription-translation enhances the efficiency of transcription but limits opportunities to repair or eliminate faulty mRNAs, thereby increasing the likelihood that ribosomes encounter incomplete or damaged transcripts. Furthermore, mRNA integrity can be compromised by transcriptional errors, abortive transcription, nucleolytic cleavage, or chemical damage. Translation of such defective transcripts, as well as other hard-to-translate mRNAs, can impede elongation or termination, resulting in stalled ribosome complexes that sequester ribosomes and tRNAs, thereby reducing their availability for subsequent rounds of translation. To maintain translation capacity, bacteria employ dedicated ribosome rescue and quality control pathways that resolve stalled complexes and promote the turnover of aberrant mRNAs and nascent polypeptides. Here, we summarize the molecular mechanisms underlying bacterial ribosome stalling, describe the pathways that rescue stalled ribosomes, and discuss current technologies for detecting ribosome stalling. We also highlight the physiological roles of programmed ribosome stalling and explore the potential of ribosome rescue pathways as druggable sites.
    Keywords:  ABCF; RQC; Ribo-seq; antibiotic; ribosome collision; ribosome profiling; ribosome stalling; tmRNA; translation arrest
    DOI:  https://doi.org/10.1128/mmbr.00346-25
  47. Virulence. 2026 Dec;17(1): 2748149
      Akabane virus (AKAV) initiates transcription in the cytoplasm via the cap-snatching mechanism. Cytoplasmic host mRNAs act as the primary cap donors, whereas the impact of their subcellular localization on the cap-snatching process remains unclear. Herein, we demonstrate that the AKAV-induced disassembly of polysomes, stress granules (SGs), and processing bodies (PBs) collectively facilitates viral cap-snatching. Mechanistically, AKAV infection activates the PKR-eIF2α signaling axis, leading to the disassembly of polysomes and subsequent translational shutoff. Intriguingly, the viral N protein disassembles SGs and PBs by competing for sequestered RNAs within these granules, whereas mutations of its RNA-binding residues abolish this activity. Moreover, PKR-eIF2α inhibition impairs AKAV replication and cap-snatching efficacy. In contrast, inhibition of SGs via G3BP1 knockdown or chemical agents significantly enhances viral replication and cap-snatching efficiency, indicating that polysomes and SGs disassembly favor caps acquisition. Additionally, N protein-mediated PBs disassembly protects mRNA from degradation, and PBs inhibition enhances cap-snatching. Taken together, AKAV has evolved a sophisticated strategy to reprogram mRNA distribution to create an optimal cellular environment for viral cap-snatching.
    Keywords:  AKAV; PBs; SGs; cap-snatching; polysomes
    DOI:  https://doi.org/10.1080/21505594.2026.2748149
  48. Sci China Life Sci. 2026 Oct 08.
      Ribosome, the universally conserved cellular machinery, orchestrates protein synthesis across all organisms. Ribosome-associated factors that regulate translation during biogenesis and stress adaptation remain underexplored in archaea due to limited structural data. Here we present eight cryogenic electron microscopy (cryo-EM) structures of the archaeal 50S ribosomal subunit at resolutions of 2.07-3.26 Å, revealing a previously uncharacterized cystathionine β-synthase (CBS) domain-containing protein positioned above the peptidyl transferase center, with an extended loop that inserts deeply into the peptide exit tunnel. Intriguingly, distinct adenosine derivatives occupy the ligand-binding pocket of the CBS protein in different structural states of the 50S subunit. Molecular dynamics simulations indicate that ATP binding induces a more contracted conformation of the extended loop, suggesting that nucleotide occupancy may modulate this protein's ribosome-association mode. Biochemical and bioinformatic analyses reveal that the extended loop is predominantly found in archaea, suggesting lineage-specific adaptations of ribosome-associated CBS proteins. Furthermore, the relatively sparse and dispersed distribution of rRNA modifications likely reflects organism-specific adaptations. Collectively, this work provides a structural framework for understanding how CBS-family proteins engage the archaeal ribosome and how their association may be tuned by cellular nucleotide status, offering insights into the molecular diversity of ribosome-associated factors and their roles in stress adaptation.
    Keywords:  CBS domain-containing protein; adenosine derivatives; archaeal ribosome; cryo-electron microscopy; rRNA chemical modification
    DOI:  https://doi.org/10.1007/s11427-026-3481-3
  49. Methods Mol Biol. 2027 ;3081 145-161
      The 3'→5' RNA helicase YTHDC2 is a posttranscriptional regulator of gene expression in reproductive cells, where it is essential for the progression of meiosis. But a detailed understanding of its molecular mechanism is currently lacking. Cross-linking and immunoprecipitation (CLIP) followed by high-throughput sequencing is a well-established method for transcriptome-wide identification of the positions of protein-RNA interactions and has played a critical role in studies of RNA-binding proteins. In this chapter, we present an optimized protocol for performing YTHDC2 CLIP in mouse testes to identify YTHDC2-RNA interactions, from harvesting testis tissue, through isolation of cross-linked YTHDC2-RNA complexes, to the preparation of sequencing libraries.
    Keywords:  CLIP; Meiosis; RNA helicase; Spermatogenesis; Testis; YTHDC2; m6A
    DOI:  https://doi.org/10.1007/978-1-0716-5571-9_6
  50. Int J Mol Sci. 2026 Oct 07. pii: 8892. [Epub ahead of print]27(19):
      Unc-51-like autophagy-activating kinase 1 (ULK1), a serine/threonine kinase, is the central regulator of autophagy initiation and plays a crucial role in cellular homeostasis, metabolic adaptation, and stress responses. We performed a large-scale phosphoproteomic data analysis of ULK1 by systematically integrating and analyzing 891 profiling and 245 differential human phosphoproteomic datasets. S450, S623, and S638 emerged as the predominant phosphosites in ULK1, with the highest frequency of detection across multiple cellular phosphoproteomics datasets. Conservation analysis showed that these phosphosites are conserved across mammalian species and human ULK1 and ULK2 (Unc-51-like autophagy-activating kinase 2). The co-regulatory networks associated with these phosphosites, including interacting proteins, upstream kinases, and downstream substrates, were systematically analyzed. The phosphosite co-regulated ULK1 interactome revealed a network of associations linking ubiquitin-dependent cargo recognition to autophagosome biogenesis, trafficking, and maturation, indicating that ULK1 phosphoregulation may extend beyond its established role in autophagy initiation and be associated with multiple stages of selective autophagy. Notably, ULK1 phosphosites were linked to key metabolic enzymes in glycogen, sphingolipid, phospholipid, and glycolytic pathways, as well as classical lipolysis. Protein-normalized analysis across 12 cancer cohorts showed significant upregulation of the predominant ULK1 phosphosites, most frequently at S450 and S623. Comparative analysis with an independent ULK1/2 knockout phosphoproteomic dataset further supported the relevance of these identified co-regulated protein phosphosites. Collectively, this study provides a phosphosite-resolved view of ULK1 regulation and identifies candidate phosphosites and associated proteins for future functional and mechanistic studies.
    Keywords:  ULK1; autophagy; lipolysis; metabolic enzymes; phospho-regulatory network
    DOI:  https://doi.org/10.3390/ijms27198892
  51. Expert Rev Mol Med. 2026 Oct 15. 28 e45
       BACKGROUND: Immune-related diseases contribute substantially to global morbidity and mortality. CD8+ T cells play a critical role in adaptive immunity by eliminating virus-infected and malignant cells. The biology of CD8+ T cells is governed by tightly regulated gene expression programs, and disruption of these programs can lead to diverse immunopathologies and malignancies. This article evaluates our current understanding of post-transcriptional and translational regulation of gene expression in CD8+ T cells by RNA-binding proteins.
    METHODS: Relevant and up-to-date literature was critically analysed to gain mechanistic insights into the roles of RNA-binding proteins in CD8+ T cell biology and to identify key knowledge gaps and future directions, with particular emphasis on therapeutic implications.
    RESULTS: RNA-binding proteins regulate diverse aspects of CD8+ T cell biology, including differentiation, cytokine production, stress adaptation and proliferation. Recent studies further reveal how dysregulated expression and function of RNA-binding proteins contribute to hyperinflammation and haematological malignancies.
    CONCLUSIONS: RNA-binding proteins are emerging as key post-transcriptional and translational checkpoint regulators of CD8+ T cell biology and represent promising therapeutic targets for immune-related diseases; however, substantial mechanistic and disease-specific studies, as well as rigorous translational validation, are required before RNA-binding protein-targeted therapeutic strategies can be safely and effectively advanced into clinical practice.
    Keywords:  CAR-T cell immunotherapy; CD8+ T cells; RNA-binding proteins; immunological memory; post-transcriptional regulation of gene expression; tumour-infiltrating lymphocytes
    DOI:  https://doi.org/10.1017/erm.2026.10075
  52. bioRxiv. 2026 Sep 28. pii: 2026.09.26.754687. [Epub ahead of print]
      Ribosome malfunction has toxic consequences, but how mammalian cells select ribosomal subunits for degradation remains poorly understood. Here, we develop a pulse-chase CRISPR screening strategy to identify regulators of ribosome turnover and uncover that loss of protein UFMylation promotes ribosome degradation. Normal UFMylation releases the 60S subunit from the endoplasmic reticulum (ER) translocon. Without UFMylation, single-molecule tracking and optogenetic proximity labeling reveal accumulation of ER-associated 60S subunits and their specific degradation. This translocon-associated large subunit degradation (TLSD) is independent of the lysosome and, in our human cell model, is only active in nondividing, contact-inhibited cells. Degradation requires the poorly characterized protein R3HDM4, which we term TLSD1. Upon UFMylation loss, TLSD1 redistributes to the ER and promotes 60S degradation. These findings identify a cell-state-dependent pathway for clearing ER-retained 60S subunits. We propose translocon release acts as a checkpoint for ribosome function, explaining TLSD1's genetic links to neuronal health and erythropoiesis.
    DOI:  https://doi.org/10.64898/2026.09.26.754687
  53. Int J Mol Sci. 2026 Sep 24. pii: 8526. [Epub ahead of print]27(19):
      Encoding genetic information involves both structure and sequence. Non-protein-coding (NCR) RNAs modulate host immune responses by guiding and assembling stress-specific protein effectors, with flipons enabling dynamic transitions between states. Small NCRs transcribed by both RNA Polymerases 2 and 3 normally modulate these pathways. The miRNAs, tRNA fragments, mitrons, piRNAs, and endo-small-interfering RNA products target the guide effector complexes to their targets. These NCRs filter the subset of RNAs that are translated, a process modulated by other NCRs that fine-tune RNA stability, localization, and kinetics through the modifications they direct. When these RNAs, or their targets, are dysregulated, host interferon responses are activated through the accumulation of uncapped triphosphorylated RNAs, dsRNAs, or flipon-encoded Z-RNAs. These responses are initially suppressed to avoid attacks on self-RNAs, but above a threshold, highly immunogenic pathways are unleashed. These same responses resist viral and other infections without pathogen-specific effectors or prior exposure. They also eliminate dysfunctional cells. These universal responses, when unresolved, contribute to a range of pathologies, increasing cancer, inflammatory diseases, and senescence. The review focuses on recent findings showing how these integrated host responses are driven by, and exploit, the retrotransposon invasion of animal genomes.
    Keywords:  Z-RNA; argonaute; cancer; dsRNA; endogenous retroelements; flipons; immunity; infection; interferon; lupus; noncoding RNA; reverse transcription
    DOI:  https://doi.org/10.3390/ijms27198526
  54. J Virol. 2026 Oct 13. e0102526
      mRNA capping is a co-transcriptional, nuclear process in eukaryotes that adds a cap onto the 5' end of RNA to confer stability, efficient translation, and nuclear export. Viruses have evolved diverse strategies by mimicking or subverting host pathways to install an mRNA cap for efficient gene expression and evasion of the host innate immune response. The conventional mRNA capping pathway, employed by many RNA and DNA viruses, is mediated by dedicated RNA 5'-triphosphatase, guanylyltransferase, and methyltransferase enzymes. In contrast, many RNA viruses utilize unconventional capping mechanisms that diverge from the canonical pathway, offering unique opportunities to develop virus family-specific antiviral therapeutics. Among negative-sense RNA viruses, members of the order Mononegavirales harbor a unique capping domain, polyribonucleotidyltransferase (PRNTase), embedded within the viral RdRp large (L) protein. Unlike the conventional guanylyltransferase-mediated mechanism, PRNTase catalyzes mRNA capping through the formation of a covalent L-pRNA intermediate rather than the canonical GMP-enzyme intermediate. The HR motif in PRNTase, involved in covalent linking to mRNA, is highly conserved in non-segmented negative-strand RNA viruses. This review focuses on structural and functional insights into Mononegavirales capping, highlighting the conserved motifs and domain architecture that make it a promising therapeutic target.
    Keywords:  Mononegavirales; PRNTase; RNA capping; antiviral target; paramyxovirus
    DOI:  https://doi.org/10.1128/jvi.01025-26
  55. Ren Fail. 2026 Dec;48(1): 2729639
      Podocyte injury is a convergent driver of glomerular disease progression, yet the genetic determinants that govern podocyte vulnerability to oxidative stress remain incompletely defined. Here, we performed genome-wide CRISPR-Cas9 knockout screens in differentiated human podocytes exposed to two complementary injury models: Adriamycin (ADR), a clinically relevant inducer of podocyte damage, and hydrogen peroxide (H2O2), a direct oxidative stress challenge. Human podocytes were transduced with a genome-wide sgRNA library, differentiated under non-permissive conditions and subjected to optimized stress conditions that imposed selective pressure while preserving library complexity. Across five independent replicates per condition, sequencing-based sgRNA profiling demonstrated high reproducibility, balanced library representation and clear treatment-specific selection. The ADR screen identified 819 depleted and 456 enriched genes, whereas the H2O2 screen identified 277 depleted and 215 enriched genes. Integrated analysis revealed both model-specific dependencies and 27 shared depleted genes across the two injury conditions, implicating stress adaptation, chromatin regulation, mitochondrial metabolism, inflammatory signaling and cytoskeletal organization as candidate processes required for podocyte survival. These genome-wide screens provide a functional framework for prioritizing genes that regulate podocyte resilience to oxidative injury and offer a resource for mechanistic studies of glomerular disease.
    Keywords:  ADR; Podocyte; chronic kidney disease; genome-wide CRISPR knockout screening; oxidative stress
    DOI:  https://doi.org/10.1080/0886022X.2026.2729639
  56. Biochem J. 2026 Nov 04. 483(11): 2123-2138
      Biomolecular condensates, formed through phase separation of multivalent biomolecules, play essential roles in cellular processes such as stress response, RNA processing, transcriptional control, and genome organization. Nucleic acids are increasingly recognized as important drivers and regulators of condensate formation and dynamics. This review examines recent advances in coarse-grained molecular simulations of dynamic nucleic acids and their phase transitions. We survey established computational frameworks validated against experimental data and discuss emerging applications that address increasingly complex systems. Existing studies reveal that base-mediated interactions emerge as dominant drivers in homotypic nucleic acid condensation and that simulation resolution fundamentally determines which physical phenomena are accessible and observable. We underscore that different modeling approaches at various resolutions provide complementary insights into nucleic acid condensation mechanisms and the driving forces. We emphasize the opportunities and challenges in extending these frameworks to capture the complexity of nucleic acid-mediated phase separation in biological contexts, while identifying important gaps in current modeling capabilities. Overall, molecular simulations at multiple scales have proven to be powerful tools for elucidating the mechanistic principles underlying nucleic acid condensates and their cellular functions.
    Keywords:  coarse-graining; dynamic structure; ion coordination; molecular simulation; phase transition
    DOI:  https://doi.org/10.1042/BCJ20260251
  57. EMBO J. 2026 Oct 10.
      The transcription factor Bicoid (Bcd) protein guides early Drosophila patterning and is the best-characterised morphogen. The source of the morphogen, bcd mRNA, is maternally deposited during oogenesis and localised to the anterior pole. When and where Bcd protein is produced and how this protein gradient is dynamically shaped remains contentious. Here, we use the SunTag reporter system to quantitatively examine the spatiotemporal profile of bcd mRNA translation in vivo. We show that association with Processing bodies (P bodies) in mature oocytes prevent premature bcd mRNA translation. Following egg activation, bcd mRNA dissociates from P bodies and translation is observed at the anterior pole. Translation remains largely restricted to the anterior domain throughout early development. At cellularisation, translation ceases and the remaining bcd mRNA associates with reformed P bodies, which appear to block any further translation. We use these observations to create a new modified synthesis-diffusion-degradation model of Bcd gradient, which is consistent with experimental measurements. Overall, our study reveals that bcd mRNA translation is tightly controlled in space and time during oogenesis and early embryogenesis.
    DOI:  https://doi.org/10.1038/s44318-026-00927-5
  58. Nucleic Acids Res. 2026 Oct 13. pii: gkag969. [Epub ahead of print]54(19):
      By mapping ribosome-protected fragments genome-wide, ribosome profiling (Ribo-seq) has uncovered extensive translation beyond conventional coding sequences, revealing non-canonical ORFs (ncORFs) with roles in diverse biological processes. However, robust ncORF identification remains challenging when Ribo-seq datasets exhibit attenuated periodicity. Protocol-induced biases during library construction is an important contributor to this loss, yet most ORF callers do not explicitly model these distortions. Here, we present RiboBA, a bias-aware probabilistic framework for robust ORF identification from Ribo-seq data. RiboBA combines a generative module that jointly infers protocol-induced biases and codon-level ribosome occupancy with a supervised module that identifies translated ORFs and initiation sites from the bias-adjusted profiles. In simulations with known P-site positions, RiboBA improved exact nucleotide- and codon-level P-site assignment relative to a conventional fixed-offset approach. Across simulations and diverse empirical Ribo-seq datasets, together with orthogonal immunopeptidomics evidence, RiboBA accurately recovers protocol-induced parameters and improves ncORF identification, with pronounced advantages for RNase I libraries with attenuated periodicity, and for MNase and nuclease P1 datasets, while maintaining competitive runtimes. In a Drosophila case study, RiboBA identified candidate ncORFs with coding potential, including recurrent upstream translation in ThrRS and Mettl2, linking ncORF translation to threonine-related translational regulation.
    DOI:  https://doi.org/10.1093/nar/gkag969
  59. Trends Plant Sci. 2026 Oct 14. pii: S1360-1385(26)00303-1. [Epub ahead of print]
      Protein synthesis rate is distinct from steady-state protein abundance and must be measured independently to understand how cells regulate protein levels and respond to environments. Technologies used to predict or directly quantify protein synthesis include ribosome profiling, radioactive and stable isotope labelling, and bioorthogonal noncanonical amino acid tagging (BONCAT). Here, we emphasise BONCAT's potential in plants, which, when combined with click-chemistry, enables the detection, enrichment, and characterisation of newly synthesised proteins themselves. We summarise lessons from BONCAT applications in cell-free systems, microbes, mammalian cells, and animals and evaluate its potential in plants. Establishing robust BONCAT approaches in plants can advance studies in proteome regulation, stress responses, development, circadian biology, and plant-microbe interactions.
    Keywords:  BONCAT; noncanonical amino acid; plant nascent protein labelling; proteostasis
    DOI:  https://doi.org/10.1016/j.tplants.2026.09.009
  60. Cancers (Basel). 2026 Oct 08. pii: 3232. [Epub ahead of print]18(19):
      Gliomas are the most prevalent and aggressive primary tumors of the central nervous system (CNS), with glioblastoma demonstrating particularly poor survival rates despite multimodal treatment approaches. The extensive molecular heterogeneity and resistance to conventional therapies highlight the urgent need for novel biomarkers and therapeutic targets. Non-coding RNAs (ncRNAs), transcripts that do not encode proteins, have emerged as crucial regulators of gene expression and cellular homeostasis in both normal and malignant contexts. Their dysregulation contributes to key oncogenic processes, including uncontrolled proliferation, apoptosis, evasion, invasion, and therapeutic resistance. Small and intermediate-sized are strong candidates for biomarkers due to their high abundance and relative stability. Previous reviews on ncRNAs highlight the numerous roles of microRNAs, long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) in gliomas. Here, we focus specifically on small and intermediate-length non-coding RNAs, including transfer RNAs (tRNAs) and tRNA-derived fragments (tRFs or tsRNAs), small nucleolar RNAs (snoRNAs), vault RNAs (vRNAs or vtRNAs), small nuclear RNAs (snRNAs) and mitochondrial tRNAs (mt-tRNAs). Recent studies suggest that these various non-coding RNAs participate in diverse aspects of glioma biology, including regulation of gene expression and modulation of metabolic and immune pathways, and correlate with tumor grade and molecular subtype. In this review, we summarize current evidence regarding the expression profiles and functional roles of small and intermediate-length non-coding RNAs in glioma tumorigenesis, progression, and therapeutic response. The differential expression of many of these ncRNAs in gliomas implies their involvement in both tumor-suppressive and oncogenic processes. A deeper understanding of these molecules may provide valuable insights into glioma biology and reveal novel biomarkers for diagnosis, prognosis, and treatment.
    Keywords:  cancer; glioblastoma; glioma; intermediate-sized non-coding RNA; small non-coding RNA; tumorigenesis
    DOI:  https://doi.org/10.3390/cancers18193232
  61. Cell Chem Biol. 2026 Oct 15. pii: S2451-9456(26)00357-0. [Epub ahead of print]33(10): 1443-1458
      Arginine methylation is a post-translational modification found on many proteins, including RNA-binding proteins, signaling molecules, histones, and heat shock proteins, where it can alter protein-protein and protein-nucleic acid interactions. Arginine methylation regulates many cellular pathways, including RNA metabolism, signal transduction, gene expression, cellular stress responses, DNA repair, and, more recently, innate immune sensing. Here, we discuss recent advances in innate immune sensing and the emerging role of arginine methylation in suppressing tumor immune visibility. We describe current knowledge of protein arginine methyltransferase (PRMT) inhibitors and degraders and their use from preclinical models to clinical trials, alone or in combination with other therapies, to reduce tumor progression and enhance the effectiveness of cancer immunotherapy.
    Keywords:  CD8(+) T cells. immunotherapy; PRMTs; RLR pathway; arginine methylation; cGAS-STING pathway; dsRNA sensors; interferon; viral mimicry
    DOI:  https://doi.org/10.1016/j.chembiol.2026.09.010
  62. MicroPubl Biol. 2026 ;2026
      RNA-binding proteins (RBPs) undergo regulated phase transitions during oogenesis that are critical for maternal mRNA regulation. In C. elegans , the CCT chaperonin prevents ectopic condensation of RBPs in maturing oocytes, including MEX-3 and CAR-1 . Here, we show that CCT differentially affects oocyte RBP condensation depending on protein identity and cellular context. Depletion of CCT did not cause ectopic condensation of the P-granule proteins GLH-1 and PGL-1 . During heat stress, CCT depletion reduced MEX-3 and CAR-1 condensation, opposite from the phenotype in normally maturing oocytes. These findings reveal CCT as a context-dependent regulator of RBP phase transitions in oocytes.
    DOI:  https://doi.org/10.17912/micropub.biology.002420
  63. Plants (Basel). 2026 Sep 30. pii: 2995. [Epub ahead of print]15(19):
      Plants coordinate their growth and developmental programs through dynamic communication in the core of the nucleus, enabling them to adapt to persistently high-temperature environments. Upon heat stress, plants primarily perceive and transduce thermal signals between the nucleus and other organelles, a process defined as nuclear-organellar communication. The published research on plants in response to heat environments mainly focuses on sensing heat physical signals from the plasma membrane (PM)/cytosol to the nucleus, eliciting nuclear transcriptional reprogramming and decoding organelle-derived retrograde signals to the nucleus. Consequently, plants have evolved sophisticated systems to decode adverse temperature signals relying on efficient nuclear-organellar coordination. This review summarizes how plants maintain cellular homeostasis via nuclear crosstalk. Heat signals are initially perceived, which triggers the production of secondary messengers including phosphatidic acid (PA), calcium ions (Ca2+) and reactive oxygen species (ROS). In addition, proteins also deliver thermal signals to the nucleus. As the central signaling hub, the nucleus orchestrates global transcriptional reprogramming predominantly through the Heat Shock Transcriptional Factors (HSFs)-heat shock proteins (HSPs) regulatory module, and sends instructions to the endoplasmic reticulum (ER), chloroplasts and mitochondria. Conversely, organelle-derived retrograde signals coordinate stress adaptation: the unfolded protein response relieves ER stress, and heat stress activates ROS-mediated chloroplast-to-nucleus and mitochondria-to-nucleus feedback pathways. We further outline candidate thermosensing proteins residing in different organelles, and highlight major unsolved issues. Critical knowledge gaps include the intrinsic thermosensing capacity of chloroplasts and mitochondria, inter-organellar coordination of second-messenger dynamics, specific organelle functions, and the biological roles of membrane contact sites. Further mechanistic insights will facilitate the application of genome editing, synthetic biology and artificial-intelligence-aided design to breed heat-tolerant crops without yield penalties.
    Keywords:  chloroplasts; endoplasmic reticulum; heat stress; mitochondria; nuclear-organellar communication; nucleus; plasma membrane
    DOI:  https://doi.org/10.3390/plants15192995
  64. Bone Res. 2026 Oct 16. pii: 106. [Epub ahead of print]14(1):
      Collagen X, encoded by the Col10a1 gene, is expressed specifically by hypertrophic chondrocytes (HCs) in the cartilage. Mutations of the Col10a1 gene in humans, which increase the endoplasmic reticulum (ER) stress in HCs, lead to metaphyseal chondrodysplasia type Schmid (MCDS). However, the mechanism of how HCs respond to ER stress to affect bone development and growth is not entirely understood. In this study, we generated a new mouse model harboring a 13 bp deletion (13del) in the endogenous Col10a1 gene. These 13del-MCDS mice display all the known clinical characteristics of human MCDS, as well as the molecular and cellular changes within the growth plate cartilage. For the first time, we found that triggering ER stress leads to activation of hypoxia and HIFs pathways in vivo, promoting cellular survival in HCs of the 13del-MCDS mice. To test whether the activated hypoxia and HIFs pathways are triggered by ER stress or extrinsic factors, we generated WT/GFP-MCDS chimera mice. Our findings showed that the activation of hypoxia and the hypoxic pathway is an intrinsic response to ER stress, which may partly occur through activation of ATF4 in HCs of mice. In parallel, p53 pathway changes and autophagy-associated protein-quality-control responses were observed in spatial association with altered chondrocyte differentiation and survival. These findings reveal coordinated engagement of multiple stress-response pathways during the adaptive response of hypertrophic chondrocytes to chronic ER stress.
    DOI:  https://doi.org/10.1038/s41413-026-00587-5
  65. Neurosci Lett. 2026 Oct 14. pii: S0304-3940(26)00262-4. [Epub ahead of print] 138762
       BACKGROUND: RNA editing is an epitranscriptomic mechanism that shapes transcriptome diversity and fine-tunes neuronal function. While adenosine-to-inosine (A-to-I) editing by ADAR enzymes has been extensively studied in neurodegenerative disorders, the role of cytidine-to-uridine (C-to-U) editing catalyzed by APOBEC1 remains largely unexplored.
    METHODS: We investigated the impact of APOBEC1 on RNA editing homeostasis and prion disease progression using complementary in vitro and in vivo models. Global RNA editing and gene expression profiles were established in non-infected N2A and prion-infected sc-N2A murine neuroblastoma cells, under control conditions or following APOBEC1 depletion. APOBEC1 was silenced by shRNA-mediated knockdown to assess its regulatory contribution. In vivo disease progression was assessed in Apobec1 knockout mice subjected to RML prion infection to evaluate survival outcomes.
    RESULTS: Prion infection was associated with a global increase in RNA editing and an expanded repertoire of edited transcripts in sc-N2A cells. APOBEC1 depletion markedly reduced the overall editing levels, affecting both A-to-I and C-to-U editing events, reshaping editing patterns in transcripts associated with RNA and protein transport, cellular stress responses, synaptic signaling, and neuroimmune interactions. Consistently, Apobec1 KO mice exhibited accelerated body weight loss and significantly shortened survival following RML prion challenge.
    CONCLUSIONS: These findings support APOBEC1 as a contributor to RNA editing homeostasis and suggest that APOBEC1 loss reduces resilience to prion-induced neurodegenerative stress. APOBEC1 deficiency was associated with altered editome profiles in prion-infected cells and accelerated disease progression in the RML prion model.
    Keywords:  Apobec1; Apobec1 knockdown; Neurodegeneration; Prion diseases; RNA editing
    DOI:  https://doi.org/10.1016/j.neulet.2026.138762
  66. Nucleic Acids Res. 2026 Oct 13. pii: gkag970. [Epub ahead of print]54(19):
      Entry into M-phase requires mRNA translation, but whether mitotic and meiotic divisions share a conserved translational programme and which newly synthesized proteins promote Cdk1 activation remain unclear. We developed Attribute Network-based Ranking (ANeR), a multi-objective network-based method that ranks mRNAs according to their proximity to a training group across heterogeneous two-condition omics datasets. Applied to 30 datasets covering mitotic and meiotic divisions, ANeR identified a conserved M-phase translational fingerprint. Benchmarking ANeR predictions against independent mitotic datasets, together with experimental validation in Xenopus oocytes, confirmed that ANeR prioritizes proteins whose accumulation increases during both mitotic and meiotic M-phases. Application of ANeR to the meiotic translational programme identified Fam76b and Cdca3 as previously unrecognized translationally activated regulators required for timely Cdk1 activation, demonstrating that ANeR can uncover new regulators of meiotic M-phase. Analysis of the oocyte translational programme established how broadly CPE/PAS regulatory rules apply, identified transcripts that do not conform to these rules, and experimentally validated their translational activation. Together, these findings establish that vertebrate mitotic and meiotic transitions share a conserved programme of translationally regulated transcripts and demonstrate that ANeR can identify new regulators of cell division. Broadly, ANeR provides a flexible framework for investigating diverse biological questions using a collection of two-condition datasets.
    DOI:  https://doi.org/10.1093/nar/gkag970
  67. Int J Mol Sci. 2026 Sep 30. pii: 8773. [Epub ahead of print]27(19):
      More than three decades have passed since the discovery of miRNAs in human cells, yet many of their biological properties remain poorly understood. The aim of this study was to investigate whether miRNAs can interact with target gene mRNAs through fully complementary base pairing. Using the MirTarget program, we demonstrated that all nucleotides of miRNAs can form fully complementary interactions with nucleotides of target gene mRNAs. A total of 1036 miRNAs, which were identified by Backes et al. and we designated as BmiRNAs and mRNAs from 17,508 human genes, were analyzed, revealing several important characteristics. The vast majority of BmiRNAs were found to bind fully complementarily to the 3'-untranslated regions (3'UTRs) of target gene mRNAs. Many mRNAs contained binding sites (BSs) for multiple BmiRNAs, forming binding site clusters in which BmiRNAs may compete for interaction with the same mRNA. We also identified identical groups of up to four BmiRNAs capable of binding to the mRNAs of different genes. In addition, genes whose mRNAs contained up to eight BmiRNA binding sites were identified. These findings broaden our understanding of the mechanisms by which BmiRNAs regulate human gene expression at the mRNA translation stage and provide new insights into their potential role in post-transcriptional gene regulation.
    Keywords:  human genes; mRNA; miRNA; miRNA-mRNA interaction
    DOI:  https://doi.org/10.3390/ijms27198773
  68. Methods Mol Biol. 2027 ;3081 381-397
      DEAD-box RNA helicases (DDXs) are a family of enzymes that participate in nearly all aspects of cellular RNA metabolism by remodeling RNA structures. Among them, DDX3X plays key roles in diverse physiological processes, including the translational regulation of gene expression, and its malfunction is frequently associated with the onset of disease. To elucidate the molecular mechanisms of DDX3X, solution nuclear magnetic resonance (NMR) spectroscopy provides unique insights into its RNA-binding properties, dynamic behavior, and intermolecular interactions, complementing conventional structural approaches aimed at determining high-resolution atomic models. In this chapter, we present a detailed protocol for preparing isotopically labeled proteins for NMR analysis, using the minimal functional core region of DDX3X as an example. The presented protocol enables the production of large amounts of purified protein, which can also be adapted for other in vitro structural and biochemical experiments used to characterize helicase function.
    Keywords:  Bacterial protein expression; DDX3X; Intermolecular interaction; Nuclear magnetic resonance; Protein dynamics; Stable isotope labeling; Structural biology
    DOI:  https://doi.org/10.1007/978-1-0716-5571-9_18
  69. Plant Genome. 2026 Dec;19(4): e70327
      5-Methylcytidine (m5C) modifications play a critical role in RNA metabolism. TRM4B (tRNA-specific methytransferase 4B) is the only known component of the plant m5C machinery that mediates mRNA (messenger RNA) methylation. To date, no regulators governing site-specific m5C modifications have been identified, apart from several degenerated sequence motifs. Drawing on relevant findings in animals, we investigated the involvement of AGO1 (Argonaute 1) in m5C regulation using an ago1 mutant of Arabidopsis. m5C-RIP-seq (m5C RNA immunoprecipitation followed by deep sequencing) identified high-confidence 5981 and 4559 m5C peaks in WT (wild type) and ago1, respectively. A substantial proportion of these peaks overlapped between WT and ago1, indicating their high gene specificity. Compared to WT, ago1 exhibited 366 hyper-methylated and 168 hypo-methylated peaks. While both hyper- and hypo-methylation could correlate with either up- or down-regulated gene expression, actively transcribed genes with relatively complex structures were preferentially targeted by m5C modification. A significant fraction of m5C-associated genes are functionally involved in mRNA surveillance and ribosome biogenesis. Intriguingly, over 60% of m5C peaks identified in WT were associated with the miRNA (microRNA) binding sites. Furthermore, AGO1 binding signals could be detected on the corresponding transcripts for >40% of the m5C peaks based on the AGO1-RIP-seq experiment. Immunoprecipitation coupled to mass spectrometry validated the interaction between TRM4B and TRANSPORTIN1 (TRN1)-a known AGO1-interacting protein that is also implicated in the miRNA pathway. These findings support a model in which the miRNA-guided AGO1 complex plays a critical role in mediating site-specific m5C modifications.
    DOI:  https://doi.org/10.1002/tpg2.70327
  70. Nat Commun. 2026 09 10. pii: 10711. [Epub ahead of print]17(1):
      Biomolecular condensates are membraneless compartments, crucial for organising and regulating diverse cellular processes. Current approaches to study condensate biology either use simplified recombinant protein systems with limited physiological relevance, or complex live-cell models with restricted experimental control and scalability. Here, we present ExVivo PhaseScan, a droplet microfluidics platform that couples mammalian lysate-based reconstitution with scalable analysis to generate high-resolution phase diagrams of compositionally complex protein condensates. We apply this approach to study two multicomponent condensate systems, stress granules and nucleoli, and dissect the physicochemical interactions that influence their stability. We further developed a machine learning pipeline to analyse condensate morphology which we use to reveal how mutations in the amyotrophic lateral sclerosis (ALS)-linked protein Fused in Sarcoma (FUS) remodels condensate properties. We identify liquid-to-solid transitions of mutant FUS within stress granules and nucleoli, and show that these transitions can be reversed by RNA aptamer-based interventions. Together, these findings establish ExVivo PhaseScan as a versatile tool for dissecting the physicochemical and pathological regulation of condensates, with potential to inform therapeutic strategies for diseases driven by aberrant phase transitions.
    DOI:  https://doi.org/10.1038/s41467-026-77696-6
  71. Hum Cell. 2026 Oct 11. pii: 148. [Epub ahead of print]39(10):
      TXNDC11 is an endoplasmic reticulum-associated redox protein involved in protein quality control, but its relevance in acute myeloid leukemia remains incompletely understood. This study examined the expression pattern, prognostic value, and stress-related functional role of TXNDC11 in acute myeloid leukemia using public transcriptomic datasets and experimental validation. Bioinformatic analyses were used to evaluate TXNDC11 expression, survival association, protein interaction networks and pathway enrichment. Loss-of-function experiments were performed in acute myeloid leukemia cell lines to assess cell viability, oxidative stress status, endoplasmic reticulum stress signaling, and responses to the chemical chaperone 4-phenylbutyric acid. TXNDC11 expression was relatively elevated in acute myeloid leukemia samples and higher expression was associated with shorter overall survival. Protein interaction and enrichment analyses connected TXNDC11-associated networks with endoplasmic reticulum-associated degradation, unfolded protein response, endomembrane organization, and apoptosis-related pathways. In THP-1 and HL-60 cells, TXNDC11 knockdown reduced cellular viability and was accompanied by increased reactive oxygen species and malondialdehyde levels, decreased ATP content, reduced glutathione availability, and a lower GSH/GSSG ratio, indicating disruption of redox homeostasis. At the molecular level, TXNDC11 depletion increased GRP78/BiP, p-eIF2α/eIF2α, ATF4, p-IRE1α/IRE1α, cleaved ATF6 p50/full-length ATF6, DDIT3/CHOP mRNA, XBP1s mRNA, HSPA5/BiP mRNA, and cleaved caspase-3, supporting activation of multiple UPR-associated signals and apoptosis-associated marker expression. Treatment with 4-phenylbutyric acid partially attenuated these stress-related molecular and redox changes. Repeated local si-TXNDC11 administration suppressed AML xenograft growth and reduced TXNDC11 expression in endpoint tumor tissues. These findings suggest that TXNDC11 is linked to adverse prognosis in acute myeloid leukemia and may support leukemic cell stress adaptation by limiting endoplasmic reticulum stress-associated redox imbalance and apoptotic signaling.
    Keywords:  Acute myeloid leukemia; Apoptosis; Endoplasmic reticulum stress; Oxidative stress; TXNDC11
    DOI:  https://doi.org/10.1007/s13577-026-01460-7
  72. mBio. 2026 Oct 14. e0224726
      Variable phytoplankton resource demands can buffer productivity to climate-driven declines in nutrient supply, but the extent of this buffering depends on limits to cellular elemental plasticity. Elemental plasticity is driven by a combination of genomic adaptation and physiological regulation, but their mechanistic links remain unresolved. Here, we combine continuous culture experiments with proteomics and elemental analyses to determine how genomic diversity shapes nutrient stress plasticity in six strains of the globally distributed cyanobacterium Synechococcus. By maintaining fixed growth rates in chemostats under nitrogen- or phosphorus-limiting conditions, we disentangle lineage-specific resource demands from growth effects. All strains show conserved induction of nutrient acquisition pathways, yet strain identity explains most pan-proteome variance, and variation in non-core protein expression predicts deviations in elemental plasticity. Strains from oligotrophic compared to mesotrophic regions exhibit broader proteomic adjustments and wider C:P and N:P ranges. Our findings show that genomic diversity expressed through pan-proteome regulation amplifies physiological plasticity and increases phytoplankton nutrient stress buffering capacity under future climate conditions.IMPORTANCEMarine cyanobacteria are among the most abundant microbes on Earth and play central roles in global nutrient cycling, yet the molecular mechanisms that determine how they respond to nutrient stress remain poorly understood. Here, we show that genomic diversity within the marine cyanobacterium Synechococcus translates into differences in protein expression and cellular resource allocation. Combining chemostat experiments and proteomics across multiple strains, we demonstrate that variation in the non-core genome shapes how lineages regulate nutrient acquisition pathways and adjust cellular C:N:P stoichiometry under nitrogen or phosphorus stress. These results reveal how pan-genome diversity generates physiological plasticity within microbial populations, providing a mechanistic link between microbial genomic variation and ecosystem-level nutrient cycling in the ocean.
    Keywords:  cyanobacteria; genome analysis; marine microbiology; proteomics; stress adaptation
    DOI:  https://doi.org/10.1128/mbio.02247-26
  73. Mol Biol Rep. 2026 Oct 16. pii: 1738. [Epub ahead of print]53(1):
       BACKGROUND: Trastuzumab resistance remains a major challenge in the clinical management of gastric cancer (GC), and effective strategies to overcome resistance are still limited. NEK2 has been implicated in GC progression and therapeutic resistance in several tumor types; however, its role in trastuzumab resistance in GC and the underlying mechanisms remain unclear.
    METHODS AND RESULTS: Trastuzumab-resistant NCI-N87/TR cells were established from parental NCI-N87 cells by stepwise exposure to increasing concentrations of trastuzumab. NEK2 was markedly upregulated in trastuzumab-resistant GC cells. Silencing NEK2 attenuated trastuzumab resistance, as evidenced by decreased cell viability and DNA replication and increased apoptosis, whereas NEK2 overexpression enhanced resistance to trastuzumab. Mechanistically, NEK2 promoted FN1 expression and activated PI3K/AKT signaling, while exogenous FN1 partially rescued the inhibitory effect of NEK2 knockdown on trastuzumab resistance. RNA immunoprecipitation, MeRIP-qPCR, and dual-luciferase reporter assays analyses further showed that WTAP-dependent N6-methyladenosine (m6A) modification at nucleotide 5882 of FN1 mRNA, followed by YTHDF1 recognition, enhanced FN1 mRNA stability and protein expression. Moreover, overexpression of either WTAP or YTHDF1 restored FN1 expression, AKT phosphorylation, and trastuzumab resistance in NEK2-silenced cells.
    CONCLUSION: NEK2 promotes trastuzumab resistance in GC by enhancing WTAP/YTHDF1-dependent m6A regulation of FN1, thereby activating PI3K/AKT signaling. These findings suggest that NEK2 may represent a potential therapeutic target for overcoming trastuzumab resistance in GC.
    Keywords:  FN1; Gastric cancer; NEK2; Trastuzumab resistance; m6A
    DOI:  https://doi.org/10.1007/s11033-026-12927-z