bims-ribost Biomed News
on Ribostasis and translation stress
Issue of 2026–07–12
76 papers selected by
Cédric Chaveroux, CNRS
  1. Wanted and unwanted modifications of mRNA, and their effect on gene expression and signaling.
  2. Profiling of terminating ribosomes reveals translational control at stop codons.
  3. NEPRO forms fibrous scaffolds in the nucleolus to maintain nucleolar integrity and orchestrate ribosome biogenesis.
  4. Single-nucleotide RNA m6A mapping in bovine preimplantation development reveals site-specific regulation of RPL12 at zygotic genome activation.
  5. Evolution of the ribosomal exit tunnel through the eyes of the nascent chain.
  6. From ribosomopathies to therapeutic targets: ribosomal alterations in pediatric leukemogenesis and tumorigenesis.
  7. Illuminating ribosome biogenesis disorders through structural biology.
  8. Noncanonical caps, m6A, and Ψ RNA modifications in plant and animal development.
  9. Exploring the functions of Ded1/DDX3 proteins in plants.
  10. Molecular mechanism of IF1- and IF2-driven translation initiation in bacteria.
  11. Interleukin-6 is critical in the development of pulmonary vascular disease in Gcn2-deficient mice.
  12. Reading another hidden message in the genetic code.
  13. A novel method for the identification and quantification of N6-methyladenosine motifs in RNA transcripts.
  14. Riboregulation in bacteria: From simple switches to complex regulatory networks
  15. The sRNA LhrC5 and Hfq post-transcriptionally regulate ferritin expression in Listeria monocytogenes.
  16. The role of mitochondrial proteases in inflammation and immunity.
  17. Insights into the regulatory roles of LIKE-HETEROCHROMATIN PROTEIN 1 and its targeting to different nuclear compartments modulated by NLS and the conserved domains in the moss Physcomitrium patens.
  18. m6A-Mediated Regulation of p63 by the METTL16-IGF2BP2 Axis Governs Epithelial Stem Cell Function and Epidermal Development.
  19. Mitochondrial membrane remodeling in stress adaptation: Lipid control of organelle quality.
  20. METTL13 at the interface of translational control, protein methylation, and disease biology.
  21. Broad Roles of Endoplasmic Reticulum Stress Sensors Activated by Diverse Pathophysiological Stimuli.
  22. C9orf72-associated poly-GR in skeletal muscle leads to neuromuscular junction deficits and muscle atrophy.
  23. Elongationless start-stop elements are stress-resilient translation gates that are more repressive than uTranslons.
  24. Divergent CRD-dependent mechanisms govern RAS isoform-selective recruitment of CRAF and ARAF.
  25. Global stabilization of the mitochondrial proteome is associated with extreme anoxia tolerance in Austrofundulus limnaeus WS40NE cells.
  26. MicroRNA-mediated regulation of cell wall dynamics and intercellular communication under stress.
  27. PDD-mediated mitochondrial and chloroplast tRNA modifications regulate cellular protein synthesis by shaping the genome-wide translational landscape in rice.
  28. RVB-1 and RVB-2 are stress responsive proteins in Neurospora crassa and RVB-1 interacts with the centromeric Shugoshin (SGO-1) protein.
  29. Compressive stress inhibits proliferation in AsPC-1 pancreatic cancer cells and reduction of Myc protein.
  30. AUA codon decoding by preferential use of tRNAIle(UAU) in Lactobacillus casei.
  31. Partial base pairing between 5' and 3' UTRs artificially regulates IVT mRNA expression levels.
  32. Epithelial and microenvironmental mosaicism under stress: a two-compartment model for lung cancer development in never-smokers.
  33. Stress granules as RNA triage hubs suppress extracellular vesicle secretion under oxidative stress in cancer.
  34. Intrinsically disordered regions in eukaryotic mRNA decay pathways.
  35. Ribosome RNA Extraction and RNase R Treatment.
  36. Integrated multi-omics analysis reveals a pH-driven metabolic and translational switch in Ureaplasma parvum.
  37. Translation accuracy in E. coli.
  38. Mitochondrial Hsp60/10 Client Protein Decline Reveals Braak/Tau- and Cognition-Linked Proteostasis Vulnerabilities in Alzheimer's Disease.
  39. Rethinking PINK1/Parkin-mediated mitophagy in Parkinson's disease: functional continuity and activation-clearance uncoupling.
  40. METTL3-Mediated m6A Modification Stabilizes COL1A1 mRNA to Promote Extracellular Matrix Accumulation in Keloids.
  41. Network-level reprogramming of cell death pathways in colorectal cancer cells by combined thymoquinone and 5-fluorouracil treatment.
  42. mRNA and protein expression of fetal insulin receptor in breast cancer cell lines and tissues.
  43. Autophagy in the liver.
  44. The p53 - CerS6 interaction on the ER integrates p53 and sphingolipid signaling pathways in metabolic stress response.
  45. QutRNA2: robust tRNA modification discovery from Nanopore direct tRNA sequencing.
  46. Local translation controls early reactive changes in perisynaptic astrocyte processes at pre-symptomatic stages of Alzheimer's disease.
  47. FGF21 connects ER stress to sulfide signaling to enhance cellular resilience.
  48. ELAVL1 and ELAVL4 are required for Musashi-dependent translational activation.
  49. IGF2BP3 mediates the mRNA upregulation of NLRP3 to promote parathyroid cell proliferation in chronic kidney disease via an m⁶A-dependent manner.
  50. Inhibition of SIK2 and SIK3 induces adaptive ER-phagy and creates a therapeutic vulnerability in ovarian cancer.
  51. Mechanosensing at the endoplasmic reticulum by IRE1.
  52. Resolving cellular signaling in space and time: From organelle proteomics to spatial phosphoproteomics.
  53. Enterovirus RNase L inhibiting RNAs are highly conserved with limited phylogenetic distribution.
  54. Phosphate Starvation Shapes M6A Modification and Poly(A) Tails to Regulate mRNA Decay in Rice.
  55. Yippee-like protein Moh1 links gene expression to metabolism and selective stress resistance in Saccharomyces cerevisiae.
  56. Proteome-scale quantification of the interactions driving condensate formation of intrinsically disordered proteins.
  57. Naturally occurring mutations in replication proteins of a small RNA virus that alter the number, sizes, and relative abundances of subgenomic RNAs.
  58. Ribosome hibernation in zinc-starved Mycobacterium abscessus confers amikacin tolerance.
  59. Mechanistic insights into the role of PEDF-R (PNPLA2) in photoreceptors.
  60. Protein Turnover in Plants - Cost of Synthesis, Repair and Crop Engineering Opportunities.
  61. seq2ribo: structure-aware integration of machine learning and simulation to predict ribosome location profiles from RNA sequences.
  62. Mechanism of Ribosomal A1493 in Stabilizing and Rigidly Supporting the Codon-Anticodon Helix During tRNA Recognition.
  63. Ginsenoside Rk1 inhibits EMT and the metastasis of hepatocellular carcinoma by affecting the m6A modification of mRNA.
  64. The RNA-binding protein Pumilio limits polymodal nociception in Drosophila larvae.
  65. Translation initiation by the Kozak mRNA sequence is based on a conformational readout on the ribosome.
  66. The R120G Knock-in Mutation in αB-Crystallin is Insufficient to Induce Cardiomyopathy in Mice.
  67. Integrative multi-omics analyses reveal nuclear noncoding RNA-mediated regulatory landscape in Alzheimer's disease.
  68. Threonine Phosphorylation Is a Bioreversible Surrogate of Proline Hydroxylation in a Collagen Triple Helix.
  69. Pterostilbene in Oxidative Stress-Related Diseases: Context-Dependent Regulation of Redox Homeostasis and Translational Challenges.
  70. RACK1 in host immune response to infections: molecular mechanisms and therapeutic potentials.
  71. Control theory analysis of dynamic metabolic response elucidates mitochondrial-cytoplasmic coupling and nutrient partitioning.
  72. The Power of Nup85: Controlling Molecular Traffic and Cellular Fate.
  73. Translation-dependent retrograde signaling coordinates high-light acclimation in plants.
  74. Phase separation and protein aggregation in neurodegenerative diseases.
  75. Antisense Oligonucleotide-Mediated Chimeric RNA Knockdown.
  76. RNA activation in insects: From emerging evidence to molecular applications.
  1. J Biol Chem. 2026 Jul 06. pii: S0021-9258(26)02186-1. [Epub ahead of print] 113314
    Wanted and unwanted modifications of mRNA, and their effect on gene expression and signaling.
    Ankanahalli N Nanjaraj Urs, Animesh Dali, Hani S Zaher.
      RNA plays essential roles in transmitting and decoding genetic information, as well as carrying out enzymatic functions during transcription and translation. The function of the polymer is determined by the unique structures of its four nucleobases, which dictate how the molecule interacts with itself, other RNAs, and proteins. As a result, modifications to the bases often impact RNA function by altering these interactions. While we have known for decades that tRNA, rRNA and mRNA are modified, recent research has shed more light on the functional importance of these internal modifications in mRNAs. In addition to enzyme-mediated modifications, mRNA is also susceptible to damage-induced alterations. These arise from endogenous and exogenous alkylating, oxidizing, and cross-linking agents, as well as exposure to UV radiation. Many of these modifications severely disrupt tRNA-mRNA interactions, often leading to ribosome stalling. An integrating theme of this review is that both enzymatic and damage-induced modifications are actively sensed by the cell, with damage-induced modifications in particular engaging dedicated quality control pathways and stress-response programs that regulate gene expression and cellular fate. We begin this review by discussing the most abundant enzymatic mRNA modifications and focus on their impact on translation before turning to damage-induced lesions and the ribosome-based quality control machinery that resolves them. We conclude by discussing the remarkable discovery that damaged mRNA, through its impact on ribosome collisions, activates the integrated stress response (ISR) and ribotoxic stress response (RSR) to reprogram gene expression and, under severe conditions, determine cell fate.
    Keywords:  RNA damage; collided ribosomes; gene expression; mRNA modification; ribosome; ribosome quality control; ribotoxic stress signaling; the integrated stress response; translation; translational control
    DOI:  https://doi.org/10.1016/j.jbc.2026.113314
  2. Elife. 2026 07 07. pii: RP109257. [Epub ahead of print]14
    Profiling of terminating ribosomes reveals translational control at stop codons.
    Longfei Jia, Yuanhui Mao, Saori Uematsu, Xinyi Ashley Liu, Leiming Dong, Leonardo Henrique França de Lima, Shu-Bing Qian.
      Accurate termination of protein synthesis is paramount for the integrity of the cellular proteome, yet the dynamics and fidelity of ribosome termination remain poorly understood. Here, we establish a profiling strategy to capture terminating ribosomes in mammalian cells and reveal a substantial heterogeneity in ribosome pausing at individual stop codons. We identify a sequence motif upstream of the stop codon that promotes termination pausing, a finding supported by massively parallel reporter assays. Unexpectedly, reduced termination pausing increases the likelihood of stop codon slippage, giving rise to proteins with heterogeneous C-terminal extensions. Mechanistically, we show that sequence-dependent termination pausing is consistent with post-decoding mRNA scanning by the 3' end of 18 S rRNA. We further uncover tissue-specific patterns of termination pausing that correlate with the stoichiometry of Rps26, which potentially modulates mRNA:rRNA interactions. Together, these results suggest termination pausing as a distinct translational signature shaped by mRNA sequence contexts, ribosome heterogeneity, and cell type-specific translational control.
    Keywords:  biochemistry; chemical biology; human; ribosome; stop codon; translation
    DOI:  https://doi.org/10.7554/eLife.109257
  3. Protein Sci. 2026 Aug;35(8): e70710
    NEPRO forms fibrous scaffolds in the nucleolus to maintain nucleolar integrity and orchestrate ribosome biogenesis.
    Abhishek Kumar, Shailesh Kumar Gupta, Yogendra Pratap Mathuria, Buddhi Prakash Jain, Debasish Kumar Ghosh.
      The nucleolus is a dynamic, membrane-less organelle whose sub-compartmentalization regulates ribosome biogenesis, RNA processing, and stress signaling. While Nucleolus and Neural Progenitor protein (NEPRO) has been classified as a nucleolar protein involved in ribosomopathy, its intra-nucleolar organization, structural features, and functional contributions have remained less understood. Here, we show that NEPRO localizes predominantly to the edges of the nucleolar boundary, forming distinct pools that do not localize to the canonical nucleolar subdomains. NEPRO assembles into elongated fibers in nucleolus. Recombinant NEPRO self-polymerizes into fibrils under mildly acidic conditions, and these fibers also contour the periphery of the dense fibrillar component of nucleolus. NEPRO depletion disrupted nucleolar integrity. NEPRO harbors an arginine-rich nucleolar localization signal (NoLS: 442-460 amino acid region), and interaction of the NoLS of NEPRO with GNL3's acidic C-terminal region nucleates and concentrates NEPRO, lowering its fibrillation threshold and promoting pH-dependent fibrillar assembly in nucleolus. Affinity pulldown of NEPRO's N-terminal coiled-coil domain identified nucleolar interacting proteins enriched in ribosomal and rRNA-processing factors. NEPRO knockdown impaired 40S/60S/80S ribosome assembly, induced G0/G1 arrest, and cell senescence. Collectively, our data define NEPRO as a structural scaffold protein that orchestrates nucleolar structural organization and ribosome biogenesis through formation of fibrous structures, with its dysfunction leading to nucleolar stress and cell-cycle arrest.
    Keywords:  NEPRO; fibrous structure; nucleolar integrity; nucleolar protein; ribosome biogenesis; scaffold structure
    DOI:  https://doi.org/10.1002/pro.70710
  4. Cell Rep. 2026 Jul 06. pii: S2211-1247(26)00713-8. [Epub ahead of print]45(7): 117635
    Single-nucleotide RNA m6A mapping in bovine preimplantation development reveals site-specific regulation of RPL12 at zygotic genome activation.
    Rajan Iyyappan, Yichi Niu, Yang Li, Hao Ming, Kinga Pajdzik, Noah R Rakestraw, Piyush K Jain, Chuan He, Chenghang Zong, Zongliang Jiang.
      RNA N6-methyladenosine (m6A) is a key regulator of gene expression during early embryogenesis. Using SAC-seq (m6A-selective allyl chemical labeling and sequencing), an antibody-independent m6A profiling method, we generated the first single-nucleotide-resolution m6A map of bovine oocytes and preimplantation embryos. We observed both coordinated and uncoupled relationships between m6A modification and expression of protein-coding and noncoding genes. Integrative analysis of the transcriptome, m6A epitranscriptome, and translatome revealed dynamic m6A remodeling, particularly in ribosomal protein genes. Functional interrogation of a specific m6A site within the RPL12 transcript demonstrated that loss of this modification reduces protein synthesis, disrupts translation-related gene expression, impairs zygotic genome activation, and compromises blastocyst formation. Notably, supplementation with wild-type RPL12 mRNA failed to rescue developmental arrest, suggesting that m6A regulates RPL12 function beyond transcript abundance. Overall, these findings provide a valuable single-nucleotide-resolution resource of m6A dynamics in mammalian embryogenesis and uncover a site-specific mechanism by which m6A regulates translation and developmental competence in early embryos.
    Keywords:  CP: Developmental biology; CP: Genomics; RPL12; SAC-seq; ZGA; bovine; m(6)A; preimplantation development
    DOI:  https://doi.org/10.1016/j.celrep.2026.117635
  5. Nucleic Acids Res. 2026 Jul 03. pii: gkag689. [Epub ahead of print]54(13):
    Evolution of the ribosomal exit tunnel through the eyes of the nascent chain.
    Tomasz Włodarski.
      The exit tunnel is a universally conserved feature of the ribosome that directs the nascent polypeptide into the cellular environment and is involved in co-translational folding, stalling, and antibiotic binding. While cryogenic electron microscopy has revealed variations in ribosome structure, tunnel definition and comparative analyses have largely relied on geometric algorithms. Here, we present a functional, nascent chain (NC)-centric characterization of the exit tunnel across the tree of life, derived from molecular dynamics simulations of 64 cytoplasmic ribosome structures. By mapping steric accessibility through the "eyes" of the NC at five distinct stages of translation, we reveal a topological and stage-dependent complexity invisible to geometric approaches, demonstrating how tunnel accessibility dynamically changes during biosynthesis. We identify transient, bacteria-specific lateral branches that, in archaeal and eukaryotic ribosomes, are structurally occluded by the eL39 protein and N-terminal extensions of the uL24 protein. These evolutionary "plugs" seal the tunnel wall and decrease its functional width. Collectively, our results demonstrate that the ribosome exit tunnel has a branched, lineage-specific topology where accessibility is temporally gated by NC length. This functional definition provides a new framework for understanding how ribosomal architecture modulates the early stages of protein biogenesis.
    DOI:  https://doi.org/10.1093/nar/gkag689
  6. Front Oncol. 2026 ;16 1832877
    From ribosomopathies to therapeutic targets: ribosomal alterations in pediatric leukemogenesis and tumorigenesis.
    Michalina Horochowska, Ewa Jakubczyk, Marek Ussowicz.
      Ribosomes are central to cellular growth and proteome maintenance, and cancer cells frequently depend on increased ribosome biogenesis and altered translation to sustain proliferation, stress tolerance, and metabolic rewiring. Paradoxically, inherited "ribosomopathies" caused by germline defects in ribosomal proteins or ribosome biogenesis factors present with tissue hypoplasia and bone marrow failure early in life, yet confer substantially increased lifetime risk of myelodysplastic syndrome (MDS), acute myeloid leukemia (AML), and selected solid tumors. In parallel, somatic alterations affecting ribosomal proteins and ribosome regulatory pathways recur across malignancies, including hematologic cancers such as T-cell acute lymphoblastic leukemia (T-ALL), and in pediatric solid tumors. Mechanistically, oncogenic ribosome disturbances can reprogram translation toward specific mRNA subsets, alter translational fidelity, trigger nucleolar/ribosomal stress signaling via the 5S ribonucleoprotein (5S RNP)-MDM2-p53 axis, and enable selection for compensatory or cooperating lesions (notably TP53 pathway alterations). Clinically, these insights support diagnostics and surveillance of inherited ribosome-related cancer predisposition syndromes, therapeutic targeting of ribosome biogenesis and translational control, including RNA polymerase I inhibition, and the eIF4 translation-initiation machinery. Here, we present current evidence linking constitutional and acquired ribosomal dysfunction to leukemogenesis and tumorigenesis, highlight disease- and context-specific mechanisms, and outline priorities for translational research and precision therapy.
    Keywords:  Diamond–Blackfan anemia; leukemia predisposition; medulloblastoma; neuroblastoma; nucleolar stress; p53; ribosomal proteins; ribosome biogenesis
    DOI:  https://doi.org/10.3389/fonc.2026.1832877
  7. RNA Biol. 2026 Jul 08.
    Illuminating ribosome biogenesis disorders through structural biology.
    Sameer Singh, Denis L J Lafontaine.
      Ribosomes are essential nanomachines responsible for synthesizing all cellular proteins. Their production, known as ribosome biogenesis, is a highly complex and energy-intensive process that requires the coordinated action of hundreds of proteins and RNA-based trans-acting factors to assemble and mature the functional ribosomal components. Ribosome biogenesis is increasingly recognized as a key contributor to human disease: excessive ribosome production can fuel tumorigenesis, while insufficient or defective ribosome production is observed in a group of tissue-specific disorders known as ribosomopathies. Although the basis of this tissue specificity remains poorly understood, the most commonly affected systems are the blood, brain, and bones. Recent advances in structural biology have yielded high-resolution snapshots of precursor (pre-) ribosomes at various stages of maturation, offering new insights into how pathogenic variants of ribosomal proteins or assembly factors disrupt critical molecular interactions. In this review, we highlight selected examples where structural information is beginning to illuminate the molecular basis of ribosomopathies.
    Keywords:  RNA modification; RNA processing; Ribosome biogenesis disease; Ribosomopathy; nucleolus
    DOI:  https://doi.org/10.1080/15476286.2026.2701521
  8. Dev Cell. 2026 Jul 08. pii: S1534-5807(26)00197-8. [Epub ahead of print]61(7): 1446-1470
    Noncanonical caps, m6A, and Ψ RNA modifications in plant and animal development.
    Xuemei Chen, Hao Hu, Guifang Jia, Chengqi Yi, Danmeng Zhu.
      RNA modifications constitute a dynamic layer of gene regulation during development. Among them, noncanonical caps, N6-methyladenosine (m6A), and pseudouridine (Ψ) represent three major classes of chemical marks. Noncanonical caps diversify the 5' end of RNA, whereas m6A and Ψ act as internal modifications that modulate RNA structure and RNA-protein interactions. Through these molecular effects, noncanonical caps, m6A, and Ψ influence RNA processing, localization, and function, thereby governing RNA fate in response to developmental and environmental cues. Advances in detection, quantification, and transcriptome-wide profiling have greatly expanded our understanding of these modifications, while revealing important technical challenges. In this review, we discuss how these three major RNA modifications regulate developmental programs in plants and animals, with emphasis on their molecular mechanisms and biological functions. We further highlight their potential relevance for therapeutic strategies in human diseases and agricultural approaches for crop improvement under climate change.
    DOI:  https://doi.org/10.1016/j.devcel.2026.05.013
  9. J Exp Bot. 2026 Jul 10. pii: erag220. [Epub ahead of print]
    Exploring the functions of Ded1/DDX3 proteins in plants.
    Isabel C Okeke, René Toribio, M Mar Castellano, Alfonso Muñoz.
      DEAD-box RNA helicases of the Ded1/DDX3 sub-family are essential regulators of cellular proteostasis. The functions of these proteins have been extensively studied in mammals and yeast. In these organisms, Ded1/DDX3 proteins play key roles in both canonical and non-canonical translation initiation and translation-related processes. Moreover, they also participate in different processes related to RNA metabolism. Plant homologues, although less studied, have revealed both conserved and unique functions compared with other eukaryotes. Members of this sub-family in plants play important roles in plant defence by regulating translation initiation of upstream open reading frames associated with stem loops situated downstream of their start codons during immune activation, as well as in loading small RNAs into extracellular vesicles. Additionally, these proteins have been associated with abiotic stress adaptation and with non-sense-mediated RNA decay, although the functional relevance of the latter remains unclear. This review provides an overview of the current knowledge about the structure, biochemical, and biological functions of Ded1/DDX3 sub-family members in both plant and non-plant eukaryotes, highlighting the peculiarities of plant Ded1/DDX3 members, and the major gaps that remain in understanding this protein sub-family in plants.
    Keywords:  DDX3; DEAD-box helicases; Ded1; RNA secondary structure; protein synthesis; stress response
    DOI:  https://doi.org/10.1093/jxb/erag220
  10. bioRxiv. 2026 Jun 29. pii: 2026.06.26.734871. [Epub ahead of print]
    Molecular mechanism of IF1- and IF2-driven translation initiation in bacteria.
    Gabriel Soares Guerra, Hassan Zafar, Xueliang Ge, Ritwika S Basu, Chenhui Huang, Ahmed H Hassan, Nicolette A Valdez, Sylva Brabencova, Lucie Slamova, Chandra Sekhar Mandava, Howard Gamper, Ya-Ming Hou, Matthieu G Gagnon, Suparna Sanyal, Gabriel Demo.
      Bacterial translation initiation is a highly regulated process essential for accurate start codon selection and the assembly of an elongation-competent ribosome. Two initiation factors, 1 (IF1) and 3 (IF3), contribute to quality control for formation of 30S preinitiation complex (30S PIC), while the GTPase IF2 facilitates stable initiator tRNA binding and promotes subunit association. However, the molecular mechanism of IF1 action and the regulatory role of IF2-mediated GTP hydrolysis and inorganic phosphate (Pi) release remain poorly understood. Using ensemble cryo-EM integrated with fast-kinetics, we delineate the translation initiation pathway involving IF1 and IF2. We show that IF1 transiently associates with the 30S subunit and interferes with the formation of multiple inter-subunit bridges. IF2 promotes subunit association by stabilizing the 30S PIC through interactions mediated by its N-terminal domains. IF1 departure happens after or concomitant with GTP hydrolysis, following which the inter-subunit bridges establish. Then Pi release triggers remodeling of IF2 followed by its departure from the 70S initiation complex. These findings reveal how the coordinated interplay of IF1 and IF2 with the ribosome ensures translational fidelity and plays crucial role for formation of elongation-competent 70S.
    DOI:  https://doi.org/10.64898/2026.06.26.734871
  11. Proc Natl Acad Sci U S A. 2026 Jul 14. 123(28): e2531623123
    Interleukin-6 is critical in the development of pulmonary vascular disease in Gcn2-deficient mice.
    Max Schwiening, Qingyue Gao, Mark Southwood, Alexi Crosby, Stephen Moore, Jose A Valer, Niki Veale, Benjamin J Dunmore, Paul D Upton, A A Roger Thompson, Nicholas W Morrell, Stefan J Marciniak, Elaine Soon.
      Biallelic mutations in EIF2AK4, encoding Eukaryotic Translation Initiation Factor 2α kinase 4 or General Control Nonderepressible 2 (GCN2), cause pulmonary veno-occlusive disease (PVOD), a fatal form of pulmonary hypertension. The mechanisms linking GCN2 deficiency with pulmonary vascular pathology are poorly understood. To investigate this, we developed two mouse models: genetic ablation of Gcn2, to mirror GCN2-mutation positive PVOD, and a pharmacological model using mitomycin C, a drug which can cause PVOD as an idiosyncratic drug reaction. Both models were phenotyped, and lungs from wild-type and Gcn2-deficient mice were analyzed using single-cell RNA sequencing. We show that homozygous loss of Gcn2 is sufficient to induce mild pulmonary hypertension in mice. Single-cell transcriptomic profiling identified adventitial fibroblasts as the cell population exhibiting the most Gcn2-dependent transcriptional changes. Pathway analysis revealed upregulation of inflammatory signaling in Gcn2-/- adventitial fibroblasts. Consistent with this, we demonstrate a proinflammatory phenotype in Gcn2-/- mouse fibroblasts and in Gcn2-/- mice. Using a mitomycin C-induced murine model, genetic deletion of interleukin-6 (Il6) rescued the pulmonary vascular phenotype. Furthermore, chronic lipopolysaccharide exposure exaggerated pulmonary hypertension in Gcn2-/- mice, and Il6 ablation rescued both baseline and lipopolysaccharide-exacerbated disease. Pharmacological inhibition or genetic ablation of the Integrated Stress Response, which can be driven by GCN2-activation, phenocopies Gcn2 deficiency. Therefore, we establish a regulatory effect of an intact GCN2-Integrated Stress Response on IL-6 signaling. Together, we show that interleukin-6 is a critical mediator of both Gcn2 deficiency-associated and mitomycin C-triggered pulmonary vascular disease in mice and highlight IL-6-dependent pathways as potential therapeutic targets.
    Keywords:  GCN2; interleukin-6; pulmonary veno-occlusive disease
    DOI:  https://doi.org/10.1073/pnas.2531623123
  12. Trends Genet. 2026 Jul 06. pii: S0168-9525(26)00149-6. [Epub ahead of print]
    Reading another hidden message in the genetic code.
    Yuichiro Mishima.
      The genetic code determines not only the amino acid sequences of proteins but also mRNA stability. How is this hidden message read? Hia and colleagues have now identified human DHX29 as a reader of the mRNA stability code carried by codons, providing new mechanistic insights into translation-coupled gene regulation.
    Keywords:  mRNA decay; ribosome; synonymous codons; translation
    DOI:  https://doi.org/10.1016/j.tig.2026.06.006
  13. Mol Biol Rep. 2026 Jul 08. pii: 1119. [Epub ahead of print]53(1):
    A novel method for the identification and quantification of N6-methyladenosine motifs in RNA transcripts.
    Neha Choudhari, H S Anirudh Srinivas, Praneeth Sai Tadepalli, Rounak Roy, Souvik Dey.
       BACKGROUND: N6-methyladenosine profiles of mRNA transcripts regulate their translocation from the nucleus to the cytosol, stability, and translational efficiency; hence, they have been implicated in gene expression and disease progression. The m6A-methylation is widely associated with various cancers and neurological, cardiovascular, and developmental disorders, which demand early diagnosis. A robust m6A-motif prediction is necessary to enable us to identify the regulatory nucleic acid sequences that determine mRNA fate in normal and diseased conditions.
    METHODS AND RESULTS: We have developed a transcript-aware computational pipeline, termed m6A Functional Index in Transcription (m6A-FINDiT), that can identify potential m6A sites on mRNA transcripts, considering molecular intricacies associated with their secondary structure. This tool can separately identify m6A motifs within the coding sequences as well as in non-translatable regions, i.e., 5'UTR and 3'UTR, of mRNA transcripts. Parallelly, another technique was developed that quantifies specific m6A methylation motifs through a probe-based ELISA process, MAQ-G. This second method successfully validated the N⁶-methyladenosine motifs predicted by the initially developed motif-finder program.
    CONCLUSION: This integrated m6A-FINDiT and MAQ-G, coupled with a real-time qPCR assay, could correlate the methylation profiles of N6-methyladenosine motifs with the expression and stability contours of a gene. To establish the physiological implications of these techniques, we chose three tumour-suppressor genes, viz., IRF8, RB1, and TP53 mRNA transcripts, which may undergo m6A methylation at certain DRACH motifs. The m6A-FINDiT pipeline could successfully predict the specific m6A motifs, and the MAQ-G confirmed the methylation profile of the latter. These duo techniques hold potential for use in clinical settings for early cancer detection.
    Keywords:  Early cancer detection; Probe-based ELISA; Tumor suppressor gene; m6A-methylation; m6A-motif prediction; mRNA stability
    DOI:  https://doi.org/10.1007/s11033-026-12270-3
  14. Postepy Biochem. 2026 06 07. 72(2): 85-98
    Riboregulation in bacteria: From simple switches to complex regulatory networks
    Paulina Lipska, Julia Konarska, Adrianna Raczkowska, Karolina Jaworska.
      Riboregulation is a key component of bacterial adaptation, as regulatory RNAs enable rapid and precise control of gene expression in response to stress and fluctuating environmental conditions. This control is exerted at the levels of transcription, translation, and mRNA stability, allowing the cell to efficiently adjust gene expression without the need to produce additional protein regulators. Regulation involves both locally acting elements (including riboswitches, thermosensors, and antisense RNAs) and in trans acting molecules primarily sRNAs which form extensive networks affecting the expression of many genes simultaneously. The multilayered nature of these systems is further enhanced by sRNA-binding proteins and RNA sponges, which modulate the availability of regulators and shape complex gene expression control networks. Modern methods like Hfq-CLASH enable better identification of these interactions in vivo. In parallel, applied research leverages these mechanisms in synthetic biology and against antibiotic resistance.
    DOI:  https://doi.org/10.18388/tkbrr231
  15. Front Microbiol. 2026 ;17 1771046
    The sRNA LhrC5 and Hfq post-transcriptionally regulate ferritin expression in Listeria monocytogenes.
    Patrycja Gomza, Katarzyna Ścibek, Magdalena Ładziak, Michał Burmistrz, Eva M S Lillebaek, Birgitte H Kallipolitis, Agata Krawczyk-Balska.
      The RNA chaperone Hfq facilitates base-pairing interactions between small regulatory RNAs (sRNAs) and their target mRNAs in Gram-negative bacteria. In Gram-positive species, however, its analogous matchmaker function remains poorly defined, with the notable exception of the Hfq-dependent sRNA LhrA in the pathogen Listeria monocytogenes. This bacterium also encodes the LhrC family of homologous sRNAs, which typically repress gene expression by base-pairing near ribosome-binding sites of target mRNAs. Although LhrC1-5 bind Hfq, their previously characterized regulatory functions are Hfq-independent. Here, we focus on LhrC5, which is uniquely encoded within the operon of ferritin (Fri), an iron-storage protein critical for virulence and stress adaptation. We used a combination of in vitro and in vivo methods including co-immunoprecipitation, northern blot, EMSA, RNA structure probing, in vitro translation, Hfq overexpression, and RNA stability analysis. The fri gene is transcribed from one σB-dependent and two σA-dependent promoters. We demonstrate that Hfq specifically promotes the binding of LhrC5-but not the homologous LhrC4-to the ribosome-binding site of the σA1-derived fri mRNA, resulting in reduced translation in vitro. No interaction between LhrC5 and transcripts originating from the σA2 or σB promoters was detected. Consistent with this specificity, cellular analyses show that LhrC5, but not LhrC1-4, selectively destabilizes the σA1-derived fri mRNA under osmotic stress conditions, thereby fine-tuning its expression. However, Hfq was not required for this LhrC5-dependent regulation of fri mRNA stability under physiological conditions. Notably, Hfq overexpression during σA1-to-σB switching of the fri promoter leads to accelerated decay of both σA1- and σB-derived fri mRNAs, consistent with the involvement of Hfq in post-transcriptional downregulation of fri expression. Collectively, this study identifies fri as a new regulatory target of the LhrC sRNA family member LhrC5 and reveals a previously unrecognized role of Hfq in LhrC5-dependent control. These findings uncover additional complexity in riboregulation in this pathogen, with potential implications for iron homeostasis.
    Keywords:  Hfq protein; Listeria monocytogenes; ferritin; post-transcriptional regulation; sRNAs
    DOI:  https://doi.org/10.3389/fmicb.2026.1771046
  16. Front Immunol. 2026 ;17 1761658
    The role of mitochondrial proteases in inflammation and immunity.
    Anna Rebeka Oliveira Ferreira, Emily A Day.
      The global rise in chronic inflammatory and autoimmune disorders has intensified research to understand cellular stress response pathways that drive immune dysregulation. Mitochondria have emerged not only as central hubs of cellular metabolism but also as active modulators of immunity and inflammation. Mitochondrial proteases are essential regulators of mitochondrial protein quality control, dynamics, and stress responses. By selectively degrading misfolded or damaged proteins, they maintain mitochondrial function and bioenergetic capacity. Beyond housekeeping roles, mitochondrial proteases also influence immune signaling by modulating mitochondrial stress pathways, reactive oxygen species production, and the release of mitochondrial-derived danger signals. Dysregulation of these proteases has been linked to chronic inflammation and contributes to the pathogenesis of inflammatory diseases. This review summarizes current knowledge on the role of mitochondrial proteases CLPXP, LONP1, i-AAA, m-AAA, as well as processing peptidase OMA1, in immune cells and inflammatory pathologies. We explore the molecular mechanisms by which these mitochondrial proteases regulate immune signaling, integrating the results from immune cells as well as other non-immune cell types, including those involved in cancer, neurodegeneration, renal injury, and other inflammatory pathologies. We explore mitochondrial proteases function as context-dependent regulators of immunometabolic signaling, with effects shaped by cell type, metabolic state, and stress conditions. Finally, we discuss emerging small molecules and drugs targeting mitochondrial proteases to highlight their potential therapeutic role in modulating inflammation. By situating mitochondrial proteases at the crossroads of immunometabolism and therapeutic intervention, this review underscores their untapped potential in the development of innovative anti-inflammatory strategies.
    Keywords:  MAVS; cGAS-STING; immune cells; inflammatory disease; innate immunity; macrophages; mitochondrial dysfunction; mtDNA
    DOI:  https://doi.org/10.3389/fimmu.2026.1761658
  17. Plant J. 2026 Jul;127(1): e71032
    Insights into the regulatory roles of LIKE-HETEROCHROMATIN PROTEIN 1 and its targeting to different nuclear compartments modulated by NLS and the conserved domains in the moss Physcomitrium patens.
    Bhawana Goel, Sanjay Kapoor, Meenu Kapoor.
      LIKE-HETEROCHROMATIN PROTEIN 1 (LHP1) is a polycomb group protein that exists in shared multiprotein complexes that harbor core PRC1 and PRC2 proteins. We previously characterized LHP1 in the moss Physcomitrium patens and showed that its function is closely linked with regulation of RNA metabolic processes and the protein is distributed in the nucleoplasm, subnuclear foci, and the nucleolus. To gain mechanistic insight into PpLHP1-mediated gene regulation, in the present study genome-wide changes in transcript profiles of genes affected by loss-of-PpLHP1 function were studied using pplhp1 mutants. RNA-seq analysis reveals a key role for PpLHP1 in regulating energy metabolic processes, ribosome-related pathways, stress signaling/responsive pathways, DNA transcription, etc. ChIP using H3K27me3 coupled with qRT-PCR shows that PpLHP1 suppresses transcription at 5S rRNA promoters and the untimely activation of genes regulating developmental transition by PRC2-dependent and independent mechanisms. To study how PpLHP1 finds its targets in different nuclear compartments and the roles of the multiple NLSs and the conserved domains in guiding the protein, FRAP and deletion studies were performed. These show that PpLHP1 is a mobile protein that diffuses freely in the nucleoplasmic space showing different retention times in the nucleolus, nucleoplasm, and the subnuclear foci indicating its differential affinity for targets at these sites. Expression of PpLHP1 fragments in protonema cells and its subsequent visualization under confocal microscope shows that localization of PpLHP1 to different subnuclear compartments is guided by the monopartite NLS2, CD, and CSD that also play a key role in promoting subnuclear foci formation in the nucleoplasm.
    Keywords:  LHP1; chromo domain; chromo shadow domain; moss; nuclear localization; polycomb; transcriptome
    DOI:  https://doi.org/10.1111/tpj.71032
  18. FASEB J. 2026 Jul 15. 40(13): e72115
    m6A-Mediated Regulation of p63 by the METTL16-IGF2BP2 Axis Governs Epithelial Stem Cell Function and Epidermal Development.
    Hanjing Song, Jiani Zhang, Suman Huo, Xian Xu, Caiyan Huang, Lin Chen, Xueqin Yang, Yeqing Qian, Xiao-Jing Zhu.
      The transcription factor p63 is indispensable for epithelial stem cell proliferation/differentiation and epidermal development, with alterations in the p63 pathway underlying a subset of ectodermal dysplasias. Despite its critical role, the mechanisms regulating p63 expression remain poorly understood. Here, we identify an m6A-mediated posttranscriptional mechanism controlling the expression of ΔNp63, the predominant functional p63 isoform in epidermal basal cells. We found that Cre-mediated conditional deletion of Mettl16, encoding a conserved m6A methyltransferase, in mouse epithelial basal cells caused severe skin developmental abnormalities, reminiscent of human ectodermal dysplasias. RNA sequencing revealed significant downregulation of ΔNp63 and its target genes in Mettl16-deficient skin, which linked METTL16 to p63 pathways. Mechanistically, we demonstrated that METTL16 directly binds to ΔNp63 mRNA to mediate its m6A modification; this modified ΔNp63 mRNA is subsequently recognized by the m6A reader IGF2BP2, which stabilizes ΔNp63 mRNA and thereby modulates its protein levels. Critically, restoration of ΔNp63 expression mitigated the epidermal defects in Mettl16-deficient mice. Collectively, our findings uncover a novel METTL16-m6A-IGF2BP2-ΔNp63 regulatory axis governing epidermal development, providing insights into the etiology of ectodermal dysplasias.
    Keywords:  METTL16; RNA methylation; epithelial development; epithelial stem cells; m6A modification; p63
    DOI:  https://doi.org/10.1096/fj.202504248RR
  19. Protein Sci. 2026 Aug;35(8): e70703
    Mitochondrial membrane remodeling in stress adaptation: Lipid control of organelle quality.
    Lena J Reichert, F-Nora Vögtle, Carlotta Peselj.
      Mitochondria respond to proteotoxic stress through the mitochondrial unfolded protein response, traditionally viewed as a transcriptional program that restores proteostasis by inducing chaperones and proteases. Emerging evidence indicates that mitochondrial membrane remodeling constitutes an additional adaptive component of this response. Regulated changes in mitochondrial lipid composition, particularly involving the signature phospholipid cardiolipin, support mitochondrial function during stress by stabilizing protein import machineries, promoting mitochondrial protein biogenesis, and facilitating recovery from dysfunction. In addition, stress originating in other organelles, especially the endoplasmic reticulum, reshapes mitochondrial membranes through altered lipid biosynthesis, inter-organelle lipid trafficking, and stress signaling pathways. These findings suggest that mitochondrial membrane remodeling represents a regulatory layer of organelle quality control integrated within interconnected stress response networks and may provide new opportunities to enhance mitochondrial resilience in disease.
    Keywords:  ER–mitochondria crosstalk; cardiolipin; mitochondrial membrane remodeling; mitochondrial protein biogenesis; mitochondrial unfolded protein response (UPRmt); organelle stress signaling
    DOI:  https://doi.org/10.1002/pro.70703
  20. Exp Mol Pathol. 2026 Jul 10. pii: S0014-4800(26)00043-2. [Epub ahead of print]147 105064
    METTL13 at the interface of translational control, protein methylation, and disease biology.
    Jiejie He, Yongli Yang, Yan Li.
      Methyltransferase-like 13 (METTL13) is a member of the methyltransferase-like (METTL) family characterized by two conserved seven-beta-strand(7BS) catalytic domains. Current evidence identifies METTL13 primarily as a dual protein methyltransferase that modifies the translation elongation factor 1 A(eEF1A), including Lys55 dimethylation and N-terminal methylation. Through this best-established mechanism, METTL13 enhances eEF1A GTPase activity, reshapes translation elongation and codon-specific translational output, and promotes protein production in cells. In multiple cancer settings, METTL13 and the eEF1A-K55 methylation axis are associated with increased translational demand, tumor progression, and Ras-driven tumorigenesis. At the same time, accumulating studies indicate that METTL13 functions are strongly context dependent. Beyond its canonical eEF1A-centered role, METTL13 has been linked to additional regulatory programs, including the c-Cbl/SERCA2a axis, RNA-associated pathways, and disease-specific signaling networks, although these noncanonical mechanisms remain less well defined. Intriguingly, METTL13 may also exert protective or tumor-suppressive effects in selected contexts, such as ischemic heart failure, hereditary deafness, and clear cell renal cell carcinoma. In this narrative review, we summarize the structural and functional features of METTL13, its regulatory network, and current evidence for its roles in malignant and non-malignant diseases. By integrating structural features, molecular modification mechanisms, translational control, disease pathophysiology, and early clinical-translation evidence, this review reframes METTL13 as a context-dependent regulator of proteome adaptation and highlights unresolved mechanistic questions regarding substrate specificity, microenvironment-dependent functional outputs, and context-specific intervention strategies.
    Keywords:  Cancer; Epigenetic regulation; METTL13; Protein methylation; RNA methylation; Translational control; eEF1A; m(6)A
    DOI:  https://doi.org/10.1016/j.yexmp.2026.105064
  21. Front Biosci (Landmark Ed). 2026 Jun 25. 31(6): 50701
    Broad Roles of Endoplasmic Reticulum Stress Sensors Activated by Diverse Pathophysiological Stimuli.
    Kenshiro Fujise, Himari Kimura, Tomoki Tsuji, Yasunao Kamikawa, Kazunori Imaizumi, Atsushi Saito.
      The endoplasmic reticulum (ER) stress response is a critical cellular program that maintains proteostasis and membrane homeostasis through the activation of the ER stress sensor proteins inositol-requiring enzyme 1 (IRE1), protein kinase R-like ER kinase (PERK), activating transcription factor 6 (ATF6), and old astrocyte specifically induced substance (OASIS) family proteins. These sensors, canonically understood as transducers of the unfolded protein response (UPR), respond to the accumulation of misfolded proteins in the ER lumen as a result of ER luminal Ca2+ depletion, defective disulfide bond formation, dysregulated glycosylation, or inhibition of ER-associated degradation. However, recent conceptual advances have reshaped understanding of these classical mechanisms, by revealing multiple non-canonical pathways that operate independently of luminal proteotoxicity. Emerging evidence highlights the roles of ER stress sensors in integrating diverse stimuli, including the integrated stress response, lipid bilayer stress, mitochondria-ER contact, and the DNA damage response. Herein, we discuss how these ER stress sensors function as multidimensional signaling hubs for proteotoxic, metabolic, and genomic stresses, and consequently modulate pathophysiological cellular outcomes. Finally, we examine current knowledge regarding both canonical and non-canonical modes of ER stress sensor activation, and we discuss how these mechanisms expand the functional scope of ER stress signaling in physiological regulation and diseases.
    Keywords:  ER stress sensors; endoplasmic reticulum (ER); unfolded protein response (UPR)
    DOI:  https://doi.org/10.31083/FBL50701
  22. Mol Ther. 2026 Jul 09. pii: S1525-0016(26)00567-8. [Epub ahead of print]
    C9orf72-associated poly-GR in skeletal muscle leads to neuromuscular junction deficits and muscle atrophy.
    Xinyi Tan, Shuangshuang Sun, Yuqing Yan, Wei Li, Ning Ding, Lin Xu, Liying He, Yuhao Zhang, Wenbing Chen, Yongjun Zheng, Lei Li.
      Hexanucleotide repeat expansions in C9orf72 produce dipeptide repeat (DPR) proteins that are widely expressed, including the nervous system and skeletal muscle. Among these DPRs, arginine-containing proteins, poly-GR and poly-PR are toxic in the nervous system, but whether DPRs in skeletal muscle contribute to ALS pathogenesis is unclear. Here, we show that muscle-restricted expression of poly-GR drives motor deficits in mice, including muscle atrophy and neuromuscular junction (NMJ) deficits. Poly-GR in muscle interacted with the NMJ key organizer MuSK and promoted MuSK degradation, disrupting postsynaptic structure and impairing neuromuscular transmission. Importantly, a MuSK agonist antibody (X-17) stabilized NMJs and rescued neuromuscular transmission. Moreover, poly-GR in muscle activated the integrated stress response (ISR), elevating eIF2α phosphorylation and broadly suppressing protein translation. ISR inhibition with ISRIB restored translation and MuSK protein levels, and ameliorated both muscle atrophy and NMJ deficits. These findings demonstrate that skeletal muscle actively contributes to C9orf72-ALS pathology. Targeting muscle with ISRIB offers a therapeutic strategy to preserve motor function in C9orf72-ALS.
    DOI:  https://doi.org/10.1016/j.ymthe.2026.07.002
  23. Nucleic Acids Res. 2026 Jul 03. pii: gkag627. [Epub ahead of print]54(13):
    Elongationless start-stop elements are stress-resilient translation gates that are more repressive than uTranslons.
    Justin Rendleman, Solomon A Haizel, Shaohuan Wu, Laurelle Lee Young, Junjie Liu, Xinyi Ge, Huijing Zou, Mahabub Pasha Mohammad, Matthew Pressler, Shuvadeep Maity, Vladislava Hronová, Zhaofeng Gao, Anna Herrmannová, Anna Smirnova, Amy Lei, Kristina Allgoewer, Daniel Sultanov, Will Edward Hinckley, Ziyue Cheng, Lauren Shelby, Tanubrata Dey, Krzysztof J Szkop, Ivan Topisirovic, Ola Larsson, Maria Hatzoglou, Leoš Shivaya Valášek, Christine Vogel.
      Start-stop elements are translation regulatory elements in 5' untranslated regions (UTR) of eukaryotic transcripts, consisting of a start codon immediately followed by a stop codon. In contrast to canonical upstream Translons (uTranslons), they exclude elongation which creates unique properties. We conducted a comprehensive, carefully controlled comparison of human start-stop elements and uTranslons both at a genome-wide level and with targeted reporter assays. We found that start-stops and uTranslons were similar with respect to their presence in the 5' UTRs of hundreds of genes, in particular transcription factors and signaling molecules, the low transcript levels of the corresponding genes, short RNA half-lives, and the negative effect on downstream translation. However, start-stop containing genes were translationally even more repressed than genes with uTranslons. Analysing the start-stop architecture and diverse ribosome footprinting datasets, we found evidence for a start-stop-specific mechanism that involves repeat cycling between initiation, termination, ribosome splitting, and 60S rejoining-a process possibly modulated by ASCC3 and eIF1. This cycling explained increased ribosome retention at start-stops and was-in contrast to ribosome retention at uTranslons-independent of the global initiation state. Finally, we showed that the start-stop element in human ATF4 augments the core regulatory model by controlling translation of the uTranslons.
    DOI:  https://doi.org/10.1093/nar/gkag627
  24. Protein Sci. 2026 Aug;35(8): e70687
    Divergent CRD-dependent mechanisms govern RAS isoform-selective recruitment of CRAF and ARAF.
    Shrhea Banerjee, Sravani Malasani, Shriti Banerjee, Maria Celeste López Vásquez, Shane McSorley, Zhihong Wang.
      RAF kinases interpret signals from the three major RAS isoforms to initiate MAPK pathway activation, yet the molecular logic that governs isoform-specific RAS recruitment and the early events that relieve RAF autoinhibition are not yet fully understood. In particular, how the modular N-terminal regulatory architecture of CRAF and ARAF, anchored by the multifunctional cysteine-rich domain (CRD), discriminates among HRAS, KRAS, and NRAS has remained a central unresolved question. Here, we combine quantitative biophysical measurements with structural and dynamic analyses to define how RAS isoform identity and CRD engagement shape the earliest steps of RAF activation. These studies reveal unexpectedly divergent modes of RAS recognition between CRAF and ARAF and expose previously unappreciated functions of the CRD in modulating RAS affinity and intramolecular regulatory contacts. We further identify a direct link between RAS binding and destabilization of RAF autoinhibition, suggesting a mechanism by which RAS engagement facilitates the transition from an inactive monomer to an activation-competent assembly. Finally, we show that emerging KRAS inhibitors variably perturb KRAS-CRAF interactions, offering insight into how these therapeutics influence early RAS-RAF signaling events. Together, this work uncovers distinct biophysical principles that govern RAS-RAF selectivity and reveals a regulatory role for the CRD that reframes our understanding of RAF activation and its dysregulation in RAS-driven cancers.
    Keywords:  ARAF; CRAF; HDX‐MS; KRAS, HRAS, NRAS; RAS inhibitors; RAS–RAF signaling; cystine‐rich domain (CRD)
    DOI:  https://doi.org/10.1002/pro.70687
  25. BMC Biol. 2026 Jul 06.
    Global stabilization of the mitochondrial proteome is associated with extreme anoxia tolerance in Austrofundulus limnaeus WS40NE cells.
    Chelsea Hughes, Meranda M Corona, Dietmar Kültz, Jason E Podrabsky.
       BACKGROUND: Austrofundulus limnaeus is an extremophile vertebrate native to small temporary ponds of Venezuela. Embryos of A. limnaeus must survive variable and often extreme conditions, including long periods of anoxia. Neuroepithelial cells derived from these embryos, WS40NE cells, provide a unique tool to understand how the proteome changes in response to anoxic stress.
    RESULTS: Using label-free proteomics, 19,604 peptides and 3487 proteins were quantified in normoxic, 4d anoxic, and 24 h recovery WS40NE cells. Of these, 2612 proteins (74.9%) were statistically significantly differentially abundant in at least one comparison: 1988 comparing normoxia to 4 days anoxia (57.0%), 923 comparing 4 days anoxia to 24 h recovery (26.5%), and 1814 comparing normoxia to 24 h recovery (52.0%). Further, interaction networks of proteins with similar expression patterns suggest that relative mitochondrial capacity may increase during anoxia, including upregulation and/or preferred stabilization of proteins involved in mitochondrial metabolism and mitochondrial transcription and translation. This is in sharp contrast to trends in proteins that support cytoplasmic translation.
    CONCLUSIONS: These data support an active role for mitochondria in mediating the survival of the anoxia-tolerant WS40NE cell line and highlight the value of this non-traditional vertebrate model for uncovering novel mechanisms of cellular resilience.
    Keywords:  Anoxia; Anoxia recovery; Anoxia tolerance; Mitochondrial metabolism; Proteomics; Stress tolerance
    DOI:  https://doi.org/10.1186/s12915-026-02674-9
  26. Front Plant Sci. 2026 ;17 1871374
    MicroRNA-mediated regulation of cell wall dynamics and intercellular communication under stress.
    Ana Belén Mendoza-Soto, Katia Aviña-Padilla.
      MicroRNAs (miRNAs) are short endogenous non-coding RNAs that regulate gene expression at the post-transcriptional level through mRNA cleavage or translational repression. In plants, miRNAs play pivotal roles in a wide range of biological processes, including development, growth, and responses to biotic and abiotic stresses. Central to these processes is the plant cell wall, a dynamic structure that not only provides mechanical support but also functions as the first line of defense against environmental challenges and pathogen attack. The plant cell wall must maintain a fine balance between rigidity and plasticity, enabling rapid remodeling in response to developmental cues and stress signals. This remodeling process requires tight and coordinated regulation of genes involved in cell wall biosynthesis, modification, and degradation. Emerging evidence indicates that miRNAs are key regulators of these processes, modulating the expression of transcription factors, enzymes, and signaling components associated with cell wall dynamics. In addition to their intracellular roles, miRNAs can also function as mobile signals, linking cell wall remodeling with intercellular communication through plasmodesmata and coordinating responses at the tissue level. Furthermore, recent studies suggest that pathogen-derived small RNAs may contribute an additional regulatory layer by targeting host genes associated with cell wall structure and connectivity. In this review, we summarize recent advances in the identification and functional characterization of miRNAs involved in the regulation of plant cell wall responses. We highlight their regulatory implications, target genes, and roles in integrating developmental, stress-related, and intercellular communication pathways. Understanding the RNA-mediated control of cell wall dynamics provides new insights into plant adaptability and resilience, with potential applications in crop improvement and stress tolerance engineering.
    Keywords:  cell wall remodeling; microRNAs; plant cell wall; post-transcriptional regulation; stress response
    DOI:  https://doi.org/10.3389/fpls.2026.1871374
  27. J Adv Res. 2026 Jul 04. pii: S2090-1232(26)00533-3. [Epub ahead of print]
    PDD-mediated mitochondrial and chloroplast tRNA modifications regulate cellular protein synthesis by shaping the genome-wide translational landscape in rice.
    Lu Sun, Xiangchao Kong, Yibin Wang, Hui Liu, Xiaohong Zhu, Pingli Lu.
      Stable tRNA modifications regulate developmental processes by ensuring efficient protein synthesis across different organisms. However, our understanding of tRNA-modification enzymes in plant organelles remains relatively limited. Previously, natural variants of rice PDD (PLEIOTROPIC DEVELOPMENTAL DEFECTS) were shown to disrupt chloroplast tRNA mnm5s2U modification and cause growth defects. Here, we identified three critical residues (positions 145, 191, and 376) in PDDOL essential for PDD function. We found that the pleiotropic developmental defects in the NIL-PDDOL were associated with abnormal mitochondrial development, indicating that PDD also plays an essential role in mitochondria. Biochemical analyses confirmed that PDD dysfunction significantly reduced mitochondrial complex enzyme activities and substantially decreased mitochondrial protein accumulation. Ultra-high-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) revealed that PDD regulates τm5U, τm5s2U and mnm5s2U modifications in both mitochondrial and chloroplast tRNAs. RNA-seq and Ribo-seq analyses revealed that these modification deficiencies caused codon-specific translation stalling in mitochondrial and chloroplast genes, impairing translation efficiency and reducing protein levels. Additionally, the transcription and translation of numerous nuclear genes are altered in NIL-PDDOL via retrograde regulation, with a significant up-regulation of genes involved in cytoplasmic mRNA transcription and translation processes. Our work demonstrates that a dual-targeting organelle tRNA modification enzyme regulates cellular protein synthesis by orchestrating translation of organelle genomes and nuclear genomes. These findings provide a foundation for studying translational control in organelles and highlight the functional integration of organelle activity with plant growth and development.
    Keywords:  Chloroplast; Mitochondria; Retrograde regulation; Translation efficiency; tRNA modification
    DOI:  https://doi.org/10.1016/j.jare.2026.07.015
  28. FEBS J. 2026 Jul 06.
    RVB-1 and RVB-2 are stress responsive proteins in Neurospora crassa and RVB-1 interacts with the centromeric Shugoshin (SGO-1) protein.
    Jonatas Erick Maimoni Campanella, Paula Aboud Barbugli, Antoniel Augusto Severo Gomes, Fernanda Zanolli Freitas, Iran Malavazi, Maria Célia Bertolini.
      The Neurospora crassa RVB-1 and RVB-2 proteins belong to the AAA+ (ATPases Associated with various cellular Activities) superfamily and are organized in a hetero-hexameric complex essential for multiple cellular processes. Although they have been described as associated with cancer, new molecular functions have recently been described for them. Here, we investigate their participation in the fungus stress response, and our results support that they are components of the regulatory mechanism involved in the cellular stress response. Results of gene and protein expression, as well as cellular localization, revealed that their expression and location are modulated under stressing conditions, such as temperature, salt, and light. Furthermore, they are components of cytoplasmic granules induced by stress. Through immunoprecipitation assays followed by mass spectrometry, we identified many RVB-1 interactors, including components of chromatin remodeling complexes, some of which showed to be involved in stress response. New RVB-1 partners were identified, such as proteins participating in carbohydrate and cell wall metabolism, cell signaling, among other processes. One such new partner is shugoshin (SGO-1), a pericentromeric protein described as a regulator of chromosomal segregation during meiosis. Using genetic and biochemical approaches, we demonstrate the RVB-1 and SGO-1 interaction, and the structural aspects were analyzed by AlphaFold3. This interaction reveals a new RVB-1 function as a protein likely important for the maintenance of the centromeric region. Our findings confirm the relevant function of RVBs as stress sensors in N. crassa and reveal new interactors, highlighting their importance in the context of cellular metabolism.
    Keywords:  Neurospora crassa; RVB‐1; RVB‐2; protein interaction; shugoshin; stress response
    DOI:  https://doi.org/10.1111/febs.70643
  29. PLoS One. 2026 ;21(7): e0352769
    Compressive stress inhibits proliferation in AsPC-1 pancreatic cancer cells and reduction of Myc protein.
    Fuko Miyake, Seiichiro Ishihara, Naomi Ando, Shoichiro Tange, Atsushi Enomoto, Hisashi Haga.
      Cancer cells grow in confined tumor microenvironments and push the surrounding tissue, which reacts and exposes them to compressive stress. Previous studies have revealed that compressive stress inhibits proliferation in breast and colorectal cancer cells. It has been reported that pancreatic tumors accumulate compressive stress in vivo, but it is not well understood whether compressive stress regulates proliferation in pancreatic cancer cells. Therefore, the effect of compressive stress on the proliferation of human pancreatic cancer cells was investigated in this study. We found that the growth of compressed AsPC-1 human pancreatic cancer cells was slower than that of uncompressed cells. Furthermore, the protein expression of Myc was reduced in compressed cells, which inhibited their proliferation. In addition, the expression of Snail, which is correlated with poor prognosis in pancreatic cancer patients, was promoted by compressive stress and the inhibition of Myc. These results suggest that compressive stress inhibits proliferation and triggers Snail expression via the reduction of Myc protein in AsPC-1 pancreatic cancer cells.
    DOI:  https://doi.org/10.1371/journal.pone.0352769
  30. RNA. 2026 Jul 08. pii: rna.081092.126. [Epub ahead of print]
    AUA codon decoding by preferential use of tRNAIle(UAU) in Lactobacillus casei.
    Chie Tomikawa, Satoshi Okura, Gakuto Uesugi, Kodai Toda, Kazuyuki Takai.
      Modified nucleosides at the first (wobble) position of tRNA anticodons play critical roles in accurate decoding of the genetic code. In bacteria, the isoleucine AUA codon is typically decoded by tRNAIle(LAU), in which lysidine (L) at the wobble position of tRNAIle with a CAU anticodon ensures discrimination from the methionine AUG codon. However, some bacteria, such as Mycoplasma mobile, lack tRNAIle(LAU) and instead utilize tRNAIle(UAU). In this organism, the unmodified uridine at the wobble position is thought to enable specific decoding of AUA while avoiding AUG recognition. In our previous study, we identified a lactic acid bacterium in which both tRNAIle(LAU) and tRNAIle(UAU) coexist. Here, we show that tRNAIle(LAU) is scarcely aminoacylated in vivo, whereas tRNAIle(UAU) is efficiently aminoacylated. Notably, the presence of 4-thiouridine (s4U) at position 8 inhibits IleRS-dependent aminoacylation of tRNAIle(UAU) in vitro, suggesting a regulatory role of tRNA modification in this process. Moreover, tRNAIle(LAU) exhibits incomplete discrimination between AUA and AUG codons and binds to AUG in the ribosomal A-site binding assays. In contrast, tRNAIle(UAU) containing N 6-threonylcarbamoyladenosine (t6A) at position 37 showed a tendency toward improved discrimination between AUA and AUG codons and preferentially recognized AUA at the ribosomal A site. These results indicate that AUA decoding is predominantly mediated by preferential use of tRNAIle(UAU) rather than canonical tRNAIle(LAU), revealing an alternative mechanism of codon decoding based on differential utilization of tRNA isoacceptors, and providing an additional layer of translational control in bacteria.
    Keywords:  codon decoding; isoleucine AUA codon; lysidine; noncanonical translation; tRNA modification
    DOI:  https://doi.org/10.1261/rna.081092.126
  31. Nucleosides Nucleotides Nucleic Acids. 2026 Jul 08. 1-18
    Partial base pairing between 5' and 3' UTRs artificially regulates IVT mRNA expression levels.
    Nao Hosoda, Atsushi Takasu, Kohei Nakanishi, Kentaro Hayashi, Shunsuke Saito, Naoyuki Yamada, Kenji Tsuge.
      Eukaryotic mature mRNAs possess a 5' cap and a 3' polyadenylate tail (poly(A)), both of which are essential for regulating mRNA expression levels. This regulation is structurally based on the circularization of mRNA, mediated by physical interactions among the 5' cap-binding protein eIF4E, the 3' poly(A)-binding protein PABPC1, and the translation initiation factor eIF4G, which bridges eIF4E and PABPC1. Here, we demonstrate that partial base pairing between the 5' and 3' untranslated regions (UTRs) of in vitro-transcribed (IVT) mRNAs promotes circularization and artificially boosts the expression levels. The expression levels of IVT mRNAs are influenced by the patterns formed by the lengths of the complementary and non-complementary regions between the UTRs. Moreover, we observed a sigmoidal relationship between the expression levels and Gibbs free energy changes resulting from 5'-3' UTR pairing. Collectively, these findings provide a novel framework for the rational design of 5' and 3' UTRs in IVT mRNAs and for predicting their expression levels based on thermodynamic parameters.
    Keywords:  Gibbs free energy change; IVT mRNA; circularization; eukaryote; translation
    DOI:  https://doi.org/10.1080/15257770.2026.2698790
  32. Front Cell Dev Biol. 2026 ;14 1891974
    Epithelial and microenvironmental mosaicism under stress: a two-compartment model for lung cancer development in never-smokers.
    Risa Burr.
      The somatic mutation theory frames cancer initiation as the consequence of accumulating driver mutations. However, the widespread presence of oncogenic mutations in normal tissues and the rarity with which these clones progress to malignancy suggest that mutation alone is insufficient. Non-small-cell lung cancer in never-smokers exemplifies this paradox, as tumors often arise in the context of low mutational burden. Here, I integrate insights from developmental mosaicism and stress biology to propose a two-compartment model of cancer development. I argue that epithelial and microenvironmental genetic mosaicism establish latent initiated fields of susceptibility, while environmental and intrinsic stressors-particularly those engaging the integrated stress response-act as selective filters that determine which clones expand, adapt, or remain latent. In this framework, cancer development reflects the convergence of permissive epithelial clones, a supportive or altered microenvironment, and sustained stress. This perspective extends classical somatic evolution and field cancerization models by emphasizing the role of stress-mediated selection across interacting tissue compartments, with implications for early detection and prevention.
    Keywords:  cancer predisposition; clonal selection; genetic mosaicism; integrated stress response (ISR); lung cancer in never-smokers; tumor microenvironment
    DOI:  https://doi.org/10.3389/fcell.2026.1891974
  33. Proc Natl Acad Sci U S A. 2026 Jul 14. 123(28): e2533990123
    Stress granules as RNA triage hubs suppress extracellular vesicle secretion under oxidative stress in cancer.
    Yue Dong, Takeshi Yoshida, Mitsuyo Maeda, Haruki Adachi, Asami Eguchi, Emi Mishiro-Sato, Daisuke Okuzaki, Yosky Kataoka, Takuya Yoshida, Chitose Oneyama.
      Cancer cells confronting oxidative stress must coordinate their extracellular vesicle (EV) secretion to balance intercellular signaling with the intracellular programs required for survival, yet how these decisions are integrated remains poorly understood. Here, we identify a stress-adaptive mechanism in which stress granules (SGs) selectively suppress CD63+ EV release. Using a bioluminescent EV-reporter screen, we found that the clinical compound YM155 selectively inhibits CD63+ EV secretion across diverse tumor cells. Mechanistically, YM155 rapidly inactivates the antioxidant transcription factor FOXO3a, diminishing expression of key detoxifying enzymes and leading to delayed but sustained accumulation of reactive oxygen species (ROS). Elevated ROS drives SG formation, and these SGs function not as passive storage sites but as RNA triage hubs that exclude and destabilize a subset of transcripts. Among them, Rab27A mRNA-encoding a GTPase essential for multivesicular-body docking to the plasma membrane-is selectively excluded and degraded, resulting in loss of Rab27A protein and suppression of CD63+ EV secretion. Forced Rab27A expression restores EV release but paradoxically reduces proliferation under oxidative stress, indicating that EV suppression is prosurvival. The same FOXO3a-ROS-SG-Rab27A axis operates during physiological glucose deprivation and is evident in vivo, where SGs form in xenograft tumors and circulating CD63+ EVs decline. Pancancer transcriptomic analyses further show that Rab27A expression correlates with FOXO3a-dependent antioxidant programs, underscoring clinical relevance. These findings reveal that SGs actively reprogram RNA fate to tune vesicle output, establishing a redox-responsive mechanism by which cancer cells transiently suppress EV secretion to enhance survival.
    Keywords:  Rab27A; cancer progression; extracellular vesicle; reactive oxygen species; stress granule
    DOI:  https://doi.org/10.1073/pnas.2533990123
  34. Trends Biochem Sci. 2026 Jul 07. pii: S0968-0004(26)00178-7. [Epub ahead of print]
    Intrinsically disordered regions in eukaryotic mRNA decay pathways.
    Sarah Lewandowski, Lea Sophie Pommerening, Sutapa Chakrabarti.
      Regulation of gene expression in cells is mediated by RNA-binding proteins (RBPs), which act as adaptors connecting messenger RNA (mRNA) to enzymatic and structural components to achieve a distinct functional outcome. RBPs are enriched in intrinsically disordered regions (IDRs). These regions mediate multivalent interactions that lead to the expansion of a physical and functional network in cells and, therefore, play a pivotal role in mRNA processing. In this review, we highlight the role of IDRs in eukaryotic mRNA decay. IDRs drive the assembly of transient mRNA-protein complexes essential for mRNA degradation and regulate the catalytic activities of enzymes involved therein. Beyond these functions, IDRs connect different pathways of targeted mRNA decay, building a global functional network that dictates gene expression.
    Keywords:  CCR4–NOT; Dcp2; SLiMs; UPF1; conformational flexibility; networks
    DOI:  https://doi.org/10.1016/j.tibs.2026.06.002
  35. Methods Mol Biol. 2026 ;3024 109-115
    Ribosome RNA Extraction and RNase R Treatment.
    Qiong Wang, Yiwei Wang, Hui Li.
      Chimeric RNAs can exert biological functions in various ways, and their biological functions often depend on their RNA sequences or their potential protein-coding ability. Here, we introduce two relatively mature experimental methods. One method is to extract ribosomes followed by PCR to determine whether the chimeric RNA has the ability to bind to ribosomes, thereby preliminarily evaluating its potential to code for proteins. The other method is to verify whether the chimeric RNA is resistant to RNase R, thereby preliminarily evaluating whether it has a circular RNA structure.
    Keywords:  Chimeric RNA; Chimeric circular RNA; RNase R; Ribosome pull-down
    DOI:  https://doi.org/10.1007/978-1-0716-5202-2_11
  36. Microbiol Spectr. 2026 Jul 10. e0346325
    Integrated multi-omics analysis reveals a pH-driven metabolic and translational switch in Ureaplasma parvum.
    Hiroaki Hase, Yukiko Nakura, Yuki Shimada, Atsuko Nishino, Michiko Kodama, Itaru Yanagihara.
      Human ureaplasmas are minimal-genome bacteria and pathobionts of the urogenital tract. They must adapt to fluctuating pH conditions despite the absence of canonical transcriptional regulatory systems. However, the mechanisms underlying these responses remain unclear. This study aimed to construct a system-level model of pH adaptation in this minimal pathogen. We used an integrated multi-omics platform combining proteomics, metabolomics, and RNA modification profiling to construct a system-level model of pH adaptation. The results revealed a bifurcated strategy governed by the differential activation of preexisting, co-regulated functional modules. Under neutral pH conditions (pH 7), Ureaplasma parvum activated energy metabolism and upregulated ATP synthesis while forming a stress-counteracting proteostasis pathway. This may suggest a biological energy state under high stress conditions. Conversely, under acidic stress (pH 5), it activated biosynthesis/translation, showing significant upregulation of ribosomal proteins and accumulation of translation precursors and the polyamine spermidine. This may represent a state of expanded translational capacity. This adaptive switch is accompanied by dynamic reorganization of the epitranscriptome, highlighting the importance of post-transcriptional regulation. This study suggests mechanisms by which minimal organisms achieve adaptive plasticity through sophisticated post-transcriptional and metabolic control, providing a new framework for understanding Ureaplasma physiology and the biology of genome-reduced organisms.IMPORTANCEMinimal bacteria challenge canonical views of cellular regulation. In organisms with radically reduced genomes and sparse transcription factors, how adaptive plasticity is achieved remains a core question. Our study proposes a model in which a simple physicochemical cue-extracellular pH-selects among prewired cellular programs, while post-transcriptional and epitranscriptomic layers fine-tune execution. The findings of this study suggest a multi-omics scheme for how organisms adapt to environmental changes and ensure survival without inducing new circuits or complex transcriptional regulation. Conceptually, it proposes regulation via RNA modifications in processes, such as metabolism, proteostasis, and translation. This framework may be generalizable to other genome-reduced microorganisms. Beyond microbiology, it provides design principles for synthetic biology and offers a mechanistic interpretation of phenotypic tolerance to stress factors. It may encourage the use of pH-linked epitranscriptome signals as measurable indicators of cellular state.
    Keywords:  RNA modification; Ureaplasma parvum; metabolomics; multi-omics; pH stress; proteomics
    DOI:  https://doi.org/10.1128/spectrum.03463-25
  37. Nucleic Acids Res. 2026 Jul 03. pii: gkag674. [Epub ahead of print]54(13):
    Translation accuracy in E. coli.
    Ryan Stikeleather, Farhan Ali, Wei-Chin Ho, Tim Licknack, Michael Lynch.
      Translation is a fundamental process of life, yet methods to systematically investigate its fidelity have been limited. Most previous estimates of translation-error rates have relied on reporter assays that evaluate only a single codon and fail to capture the full spectrum of translation errors. Here, we present a proteome-wide analysis of mass spectrometry data that directly estimates nearly all pairwise amino-acid substitution rates, revealing mistranslation rates and spectra per amino acid and per codon. Applying this method to ribosomal variants of Escherichia coli reported to differ in translation fidelity, we found no significant differences among their overall error rates, estimated here at 2 per 1000 amino acids. Instead, each variant exhibited unique mistranslation profiles; the putative error-prone variant preferentially misread near-cognate codons at the third position, with a bias that likely led to prior overestimates of its error rate. We also tested the translational-accuracy hypothesis of codon usage, which predicts that codons enriched in highly expressed genes are selected for translational accuracy. Contrary to that prediction, codons favored in highly expressed genes are not translated more accurately. These results underscore the necessity of proteome-wide measures of translation accuracy and highlight the limitations of single-codon approaches for characterizing translation fidelity.
    DOI:  https://doi.org/10.1093/nar/gkag674
  38. bioRxiv. 2026 Jun 30. pii: 2026.06.25.734545. [Epub ahead of print]
    Mitochondrial Hsp60/10 Client Protein Decline Reveals Braak/Tau- and Cognition-Linked Proteostasis Vulnerabilities in Alzheimer's Disease.
    Ashlyn Sloane, Varunya M Kattunga, Julie K Andersen.
       Background: Alzheimer's disease (AD) is classically defined by amyloid and tau pathology and is accompanied by broad disruptions in proteostasis. Heat shock proteins (HSPs) help maintain proteostasis, yet mitochondrial chaperone systems remain comparatively underexplored in AD. Hsp60 and Hsp10 form a mitochondrial chaperonin complex that folds dozens of AD-implicated mitochondrial proteins, but this client network has not been evaluated as an integrated proteostasis axis in AD. It remains unknown whether Hsp60/10 client proteins are selectively vulnerable across AD severity.
    Methods: We analyzed transcriptomic, proteomic, neuropathological, and cognitive data from the Religious Order Study and Memory and Aging Project (ROSMAP) to evaluate Hsp60/10 client proteins in AD. We compared Hsp60/10 clients with abundance-matched non-client mitochondrial proteins and tested differences across AD diagnostic groups and associations with Braak/tau burden, cognitive outcomes, and network centrality. These evidence layers were integrated into a candidate prioritization framework.
    Results: Hsp60/10 client abundance declined more strongly at the protein level than at the RNA level in late-stage AD. Compared with abundance-matched non-client mitochondrial proteins, Hsp60/10 clients showed stronger late-stage protein abundance decline. Greater late-stage client decline was associated with higher Hsp60/10 network centrality, defining a selectively vulnerable client subnetwork. Lower client abundance was associated with greater Braak/tau burden and greater cognitive impairment. Integrated prioritization nominated mitochondrial translation and TCA/pyruvate/redox clients as high-priority candidates for mechanistic follow-up.
    Conclusions: Together, these findings identify an Hsp60/10 client-centered mitochondrial proteostasis axis spanning mitochondrial translation and TCA/pyruvate/redox metabolism that is associated with AD severity. These findings identify a novel potential axis warranting further investigation as a mechanistic link between mitochondrial dysfunction, proteostasis, and AD.
    DOI:  https://doi.org/10.64898/2026.06.25.734545
  39. Front Aging Neurosci. 2026 ;18 1865383
    Rethinking PINK1/Parkin-mediated mitophagy in Parkinson's disease: functional continuity and activation-clearance uncoupling.
    Lingzhe Wang, Bin Xu.
      Mitochondrial dysfunction is a central feature of Parkinson's disease (PD) and contributes to the selective vulnerability of nigral dopaminergic (DA) neurons. Among the pathways that maintain mitochondrial integrity, PINK1/Parkin-mediated mitophagy has been extensively characterized as a stress-responsive mechanism for the recognition and removal of damaged mitochondria. However, despite robust activation of this pathway in experimental systems, translation of these findings into effective disease-modifying strategies has remained limited. Here, we propose that a conceptual distinction may help account for this gap. Current research has largely focused on pathway activation as a surrogate for functional recovery, yet mitochondrial quality control depends on the maintenance of functional continuity across multiple sequential steps, from damage recognition and ubiquitin signaling to autophagosome formation and lysosomal degradation. Disruption at any of these stages may compromise overall pathway output. Accumulating evidence suggests that, under PD-relevant conditions, upstream signaling and downstream mitochondrial clearance can become partially uncoupled, such that activation of the PINK1/Parkin pathway does not necessarily ensure effective completion of mitophagy. Within this framework, mitochondrial dysfunction interacts with α-synuclein (α-syn) accumulation, lysosomal impairment, and neuroinflammatory signaling to form a self-reinforcing pathological network. This perspective provides a mechanistic basis for understanding why strategies that enhance upstream signaling alone have shown limited translational success. Finally, we discuss key challenges for therapeutic development, including the need for readouts that distinguish pathway engagement from pathway completion, the limitations of current model systems, and the importance of aligning patient stratification and intervention timing with pathway biology. We suggest that restoring functional continuity across the mitophagic process, rather than focusing exclusively on increasing pathway activation, may offer a more productive conceptual basis for targeting mitochondrial dysfunction in PD.
    Keywords:  PINK1; Parkin; Parkinson’s disease; functional uncoupling; lysosomal dysfunction; mitochondrial quality control; mitophagy; neuroinflammation
    DOI:  https://doi.org/10.3389/fnagi.2026.1865383
  40. Exp Cell Res. 2026 Jul 06. pii: S0014-4827(26)00240-5. [Epub ahead of print] 115123
    METTL3-Mediated m6A Modification Stabilizes COL1A1 mRNA to Promote Extracellular Matrix Accumulation in Keloids.
    Yanbin Zhai, Xiaofei Wang, Wanli Guo, Xiaobin Chen.
      Keloids are pathological scars characterized by excessive collagen deposition and fibroblast hyperactivity, yet effective therapies remain limited due to incomplete understanding of their molecular drivers. Emerging evidence implicates N6-methyladenosine (m6A) RNA modification in fibrotic diseases, but its role in keloid pathogenesis is unclear. Here, we investigated the function and mechanism of the m6A methyltransferase METTL3 in keloid fibrosis. RNA sequencing of human keloid and normal skin tissues revealed significant upregulation of METTL3 and enrichment of extracellular matrix-related pathways. METTL3 was consistently overexpressed in keloid tissues and primary keloid fibroblasts (KF), which exhibited enhanced proliferation, migration, and resistance to apoptosis. Knockdown of METTL3 in KF suppressed these pro-fibrotic phenotypes and markedly reduced expression of α-SMA, TGF-β1, and collagen type I alpha 1 chain (COL1A1). Mechanistically, METTL3 deposited m6A modifications on the coding sequence of COL1A1 mRNA, enhancing its stability. YTHDF1 recognized these m6A marks and promoted COL1A1 mRNA translation. RNA pull-down and gene-specific m6A-PCR confirmed direct binding of YTHDF1 to m6A-modified COL1A1; loss of YTHDF1 reduced COL1A1 protein levels without affecting its mRNA abundance. Rescue experiments in which COL1A1 overexpression restored the fibrotic phenotypes suppressed by METTL3 knockdown established COL1A1 as a critical downstream effector of METTL3. Importantly, intradermal delivery of METTL3 shRNA in a rat tension-driven excisional scar model significantly attenuated scar formation, collagen accumulation, and fibrotic marker expression. Our findings establish METTL3 as a central epitranscriptomic regulator of keloid fibrosis by stabilizing COL1A1 mRNA and enabling YTHDF1-mediated translational enhancement, forming an m6A-YTHDF1-COL1A1 axis, highlighting its potential as a novel therapeutic target for pathological scarring.
    Keywords:  COL1A1; METTL3; YTHDF1; fibrosis; keloid; m(6)A methylation
    DOI:  https://doi.org/10.1016/j.yexcr.2026.115123
  41. Front Mol Biosci. 2026 ;13 1864680
    Network-level reprogramming of cell death pathways in colorectal cancer cells by combined thymoquinone and 5-fluorouracil treatment.
    Natalia Kurowska, Celina Kruszniewska-Rajs, Barbara Strzałka-Mrozik.
       Introduction: Colorectal cancer remains a leading cause of cancer-related mortality, with resistance to 5-fluorouracil (5-FU) posing a major therapeutic challenge. Thymoquinone (TQ), a bioactive compound derived from Nigella sativa, exhibits anticancer activity; however, its system-level effects in colorectal cancer are not fully understood.
    Methods: RKO colorectal cancer cells were treated with TQ, 5-FU, or their combination for 24 h, followed by genome-wide transcriptomic profiling using oligonucleotide microarrays. Drug interaction effects were assessed using a deviation-from-additivity model. Selected genes were validated by RT-qPCR and Western blotting, and functional relevance was evaluated using bioinformatics analyses.
    Results: Combined treatment induced extensive network-level reprogramming of pathways associated with apoptosis, cellular stress response, and proliferation. Although no classical transcriptional synergy was observed, the interaction between TQ and 5-FU resulted in coordinated modulation of overlapping signaling networks. Key regulatory genes, including FAS and CYLD, were linked to enhanced pro-apoptotic signaling, whereas BIRC3 and EIF2AK3 were associated with adaptive or resistance-related responses.
    Conclusion: TQ acts as a context-dependent modulator of chemotherapy response, reshaping cell death and stress-related signaling networks rather than directly enhancing cytotoxicity. These findings highlight the potential of TQ to influence therapeutic responses in fluoropyrimidine-based treatment of colorectal cancer and support further functional and in vivo validation.
    Keywords:  5-fluorouracil; cell death pathways; colorectal cancer; drug combination; signaling networks; stress response; thymoquinone; transcriptomic profiling
    DOI:  https://doi.org/10.3389/fmolb.2026.1864680
  42. Breast Cancer Res Treat. 2026 Jul 08. pii: 2. [Epub ahead of print]218(1):
    mRNA and protein expression of fetal insulin receptor in breast cancer cell lines and tissues.
    Xihong Zhang, Albert Barrios, LeeAnn Higgins, Todd Markowski, Kevin Murray, Bruce Witthuhn, Tzu-Yi Yang, Douglas Yee.
       BACKGROUND: The insulin receptor (IR) is expressed in breast cancer cells and plays a role in regulating tumor biology. There are two IR isoforms generated from the same gene. Alternate splicing with exclusion or inclusion of exon 11 accounts for the two isoforms. The exon 11 excluded isoform (IR-A) is expressed during fetal development while the full-length adult IR (IR-B) is the primary form expressed during adult life. This splice variant results in a 12 amino acid variation in peptide sequence. Breast cancer cells overexpress IR-A with an increased IR-A: IR-B ratio. Most of these data were obtained by examining mRNA expressions.
    METHODS: In this work, we examined over 40 breast cancer cell lines and patient tumor samples for mRNA expression of the IR isoforms. Further we used mass spectrometry to evaluate IR-A protein expression.
    RESULTS: Most breast cancer cell lines and tissues overexpress IR-A compared to IR-B. Mass spectrometry analysis demonstrated IR-A protein expression in the Du4475 cell line which has a high level of IR-A mRNA expression.
    CONCLUSION: IR-A mRNA is frequently expressed in breast cancer cells. To our knowledge, this is the first demonstration of IR-A protein expression. Thus, IR-A mRNA and protein expression demonstrate a potential role for this insulin receptor isoform in breast cancer biology.
    Keywords:  Adult form of insulin receptor; Breast cancer; Fetal form of insulin receptor; Insulin receptor; Mass spectrometry; mRNA expression
    DOI:  https://doi.org/10.1007/s10549-026-08018-z
  43. Autophagy Rep. 2026 ;5(1): 2698350
    Autophagy in the liver.
    Elijah Burks, Jenna Copes, Kelly Nguyen, Albert Tawil-Brown, Shengmin Yan.
      The liver plays a dynamic role in maintaining whole-body homeostasis through its control of nutrient metabolism, detoxification, and immune regulation. Autophagy, a conserved lysosomal degradation pathway, is central to these functions, enabling hepatocytes to adapt to fluctuations in nutrient availability, hormonal signals, and cellular stress. Hepatic autophagy is tightly regulated by nutrient and energy-sensing pathways, including AMPK, mTOR, the coordinated actions of insulin and glucagon, and transcriptional regulators TFEB, FOXO proteins, PPAR isoforms, FXR, and NRF2. Epigenomic mechanisms, chromatin remodeling complexes, and post-transcriptional regulators, such as microRNAs (miRNAs), RNA-binding proteins (RBPs), and liquid-liquid phase separation (LLPS), further refine autophagy gene expression and autophagosome formation. In physiological conditions, autophagy maintains hepatocyte integrity by supporting lipid, carbohydrate, and protein turnover and by clearing damaged or excess organelles through selective pathways such as mitophagy, lipophagy, pexophagy, ER-phagy, and xenophagy. Autophagy dysfunction contributes to the development of various liver diseases, including metabolic dysfunction-associated steatotic liver disease (MASLD), alcohol-associated liver disease (ALD), cholestatic liver disease, liver fibrosis, and hepatocellular carcinoma (HCC). Understanding the diverse regulatory networks governing hepatic autophagy, along with the roles of autophagy in liver homeostasis, provides new opportunities for therapeutic intervention. This review summarizes existing findings on the role of autophagy in the liver, focusing on recent advances in the regulation of hepatic autophagy. It also highlights unresolved mechanisms and discusses how targeting autophagy may offer novel strategies for treating liver diseases.
    Keywords:  Autophagy; liver disease; liver homeostasis; macroautophagy; metabolism
    DOI:  https://doi.org/10.1080/27694127.2026.2698350
  44. J Lipid Res. 2026 Jul 09. pii: S0022-2275(26)00127-6. [Epub ahead of print] 101097
    The p53 - CerS6 interaction on the ER integrates p53 and sphingolipid signaling pathways in metabolic stress response.
    Madeline S Childress, Kristen A Jeffries, David A Horita, Sergey A Krupenko, Natalia I Krupenko.
      Ceramides, a diverse class of bioactive sphingolipids, play a pivotal role in cellular stress response. We have previously reported a novel mechanism by which a particular member of this class, C16-ceramide, activates death pathways in cancer cells. In this mechanism, C16-ceramide, generated by ceramide synthase 6 (CerS6), binds directly to the tumor suppressor p53 and protects it from MDM2-mediated degradation, thereby promoting a stress response. In the present study, we investigated the mechanism by which p53 acquires ceramide, a highly hydrophobic molecule. Using bimolecular fluorescence complementation, we show that in cells under metabolic stress, p53 is recruited to the cytoplasmic surface of the ER by CerS6, the ER resident enzyme generating C16-ceramide. The direct contact between the two proteins enables the transfer of C16-ceramide from CerS6 to the DNA-binding domain (DBD) of p53. Domain deletion experiments and pulldown assays with purified recombinant cytoplasmic fragments of CerS6 showed that the p53 physically interacts with the two large cytoplasmic loops of CerS6, forming a complex on the surface of the ER membrane. The interaction between p53 and CerS6 strictly requires the presence of C16-ceramide in the catalytic site of the enzyme. Substitution of the CerS6 lumenal loop, which defines enzyme's acyl chain specificity, with the corresponding loop of CerS2, which generates very-long-chain ceramides, abolished the interaction with p53. Our results uncover a previously unknown process, the direct C16-ceramide transfer to the p53 DBD at the ER-surface, which is a mechanism regulating activation of this tumor suppressor. The findings that this mechanism is triggered upon metabolic stress induction by specific chemotherapeutics, as well as by nutrient and growth factor deprivation, highlight it as a promising target for cancer treatment.
    Keywords:  CerS6; MTX; ceramides; endoplasmic reticulum; p53 activation; sphingolipid signaling
    DOI:  https://doi.org/10.1016/j.jlr.2026.101097
  45. NAR Genom Bioinform. 2026 Sep;8(3): lqag065
    QutRNA2: robust tRNA modification discovery from Nanopore direct tRNA sequencing.
    Michael Piechotta, Wei Guo, Isabel S Naarmann-de Vries, Felix Kallenborn, Swastik Mishra, Francesca Tuorto, Bertil Schmidt, Christoph Dieterich.
      Transfer RNAs (tRNAs) are essential for protein synthesis and are extensively modified to ensure their structure and function. Direct RNA sequencing with Oxford Nanopore Technologies enables positional modification analysis but is challenged by tRNAs' short length, redundancy, and dense modifications. We present QutRNA2, a scalable workflow that includes GPU-accelerated local alignment, statistical filtering, pairwise error profile comparison, and customizable visualization. Achieving up to 25-fold speed gains over CPU methods, QutRNA2 identifies enzyme-dependent modifications in nuclear- and mitochondrial-encoded tRNAs, demonstrated in high-volume human and mouse samples. This open-source solution provides a comprehensive, multiplexing-compatible framework for tRNA analysis, addressing a key gap in current tools. QutRNA2 is released under Apache-2.0 license and is available at https://github.com/dieterich-lab/QutRNA2.
    DOI:  https://doi.org/10.1093/nargab/lqag065
  46. Neurobiol Dis. 2026 Jul 09. pii: S0969-9961(26)00273-1. [Epub ahead of print] 107528
    Local translation controls early reactive changes in perisynaptic astrocyte processes at pre-symptomatic stages of Alzheimer's disease.
    Katia Avila-Gutierrez, María Ángeles Carrillo de Sauvage, Noémie Depret, Marc Oudart, Robin Thompson, Rodrigo Alvear-Perez, Yiannis Poulot-Becq-Giraudon, Esther Kozlowski, Heloïse Monnet, Philippe Mailly, Valentin Garcia, Laurent Jourdren, Alexandre Lucas, Alexis Bemelmans, Helene Hirbec, Carole Escartin, Martine Cohen-Salmon.
      Early synaptic dysfunction is a hallmark of Alzheimer's disease (AD), yet the astrocytic mechanisms underlying these alterations remain poorly defined. Here, we identify astrocyte perisynaptic processes (PAPs) as subcellular hotspots of early translational dysregulation in AD. Soluble Aβ₁-₄₂ rapidly enhanced global and local protein synthesis in primary astrocytes. In 5.5-month-old APP/PS1-dE9 (APP) mice, translating ribosome affinity purification (TRAP) revealed widespread remodeling of the PAP translatome, while whole-astrocyte translation remained largely unchanged. Dysregulated mRNAs were linked to neuroinflammation, synaptic remodeling, and endoplasmic reticulum stress, and alterations emerged prior to amyloid plaque deposition. Among them, Serpina3n encoding α1-antichymotrypsin exhibited increased mRNA abundance in PAPs, uncovering spatially restricted translational control. Mechanistically, early Serpina3n upregulation was partially driven by JAK-STAT3 signaling, with preferential effects in astrocyte processes. These findings provide a conceptual advance by demonstrating that local translation in astrocyte PAPs is an early and compartment-specific mechanism that may contribute to synaptic dysfunction and disease initiation in AD.
    Keywords:  Alzheimer's disease; Astrocyte reactivity; Astrocytes; FISH; Glia; Inflammation; JAK-STAT3; Local translation; Neurodegenerative disorders; Perisynaptic astrocyte process; SOCS3; Serpina3n; Synapse; TRAP; mRNA distribution
    DOI:  https://doi.org/10.1016/j.nbd.2026.107528
  47. Cell Metab. 2026 Jul 07. pii: S1550-4131(26)00235-4. [Epub ahead of print]38(7): 1255-1257
    FGF21 connects ER stress to sulfide signaling to enhance cellular resilience.
    Sarah Hatem, András K Ponti, Christopher Hine.
      Fibroblast growth factor 21 (FGF21) is a stress-induced endocrine hormone that regulates metabolism. Grandl et al. show that FGF21, through its receptor β-klotho (KLB), enhances sulfide signaling and hydrogen sulfide production, strengthening the unfolded protein response and integrated stress response to promote stress resilience, metabolic adaptation, and potentially healthy aging.
    DOI:  https://doi.org/10.1016/j.cmet.2026.06.009
  48. bioRxiv. 2026 Jul 02. pii: 2026.07.01.735911. [Epub ahead of print]
    ELAVL1 and ELAVL4 are required for Musashi-dependent translational activation.
    Katherine Bronson, Milla M Reddick, Kenzie B MacNicol, Cole Bolen, Linda Hardy, Alex Lagasse, Angela K Odle, Gwen V Childs, Melanie C MacNicol, Angus M MacNicol.
      The RNA-binding proteins Musashi1 and Musashi2 (MSI1 and MSI2) regulate stem cell function and tissue plasticity by modulating mRNA translation. While typically known as translational repressors, the MSI1 and MSI2 proteins can also act as context-dependent activators of mRNA translation, although the mechanism of MSI-mediated translational activation are unknown. Here, we identify Embryonic Lethal Abnormal Vision-like (ELAVL) proteins as essential co-regulators of MSI1-dependent translational activation. In Xenopus laevis oocytes, antisense oligonucleotide knockdown of Elavl4 inhibited progesterone-stimulated maturation and blocked polyadenylation and translation of key MSI target mRNAs, including the Mos and Cyclin B5 mRNAs. Exogenous expression of ELAVL4 rescued these defects, confirming its necessity for maturation and cell cycle progression. Mechanistically, we determined that the ELAVL4 C-terminal domain interacts with the N-terminal RNA recognition motifs of MSI1 in an RNA-independent manner. Mass spectrometry and functional assays revealed this interaction is evolutionarily conserved: mouse ELAVL1 interacts with MSI1 in the pituitary, and human ELAVL1 rescues Elavl4 -depleted Xenopus oocytes. Furthermore, knockdown of Elavl1 in a mammalian cell line abrogated MSI-dependent translational activation of a pituitary Prop1 3' UTR mRNA reporter. Our results establish a conserved mechanism where ELAVL family members interact with MSI to promote MSI-dependent mRNA translational activation.
    DOI:  https://doi.org/10.64898/2026.07.01.735911
  49. Endocrine. 2026 Jul 10. pii: 223. [Epub ahead of print]91(1):
    IGF2BP3 mediates the mRNA upregulation of NLRP3 to promote parathyroid cell proliferation in chronic kidney disease via an m⁶A-dependent manner.
    Sen Kan, BianJie Zhao, Long Miao, ZhengJie Han, QinJun Li, Yu Wu, Ling Wang.
       OBJECTIVE: To investigate the underlying mechanism of NLRP3 in the pathogenesis of parathyroid hyperplasia.
    METHODS: Parathyroid glands (PGs) (n = 35) were obtained from 10 maintenance hemodialysis patients undergoing parathyroidectomy. A secondary hyperparathyroidism (SHPT) model was induced in rats by 5/6 nephrectomy followed by a high‑phosphate diet. Serum levels of calcium, phosphorus, creatinine, blood urea nitrogen (BUN), and intact parathyroid hormone (PTH) were measured. The expression of IGF2BP3 and NLRP3 was evaluated using quantitative reverse‑transcription polymerase chain reaction and Western blotting. NLRP3 mRNA stability was examined through RNA decay assays, and its translation was assessed by polysome profiling. RNA immunoprecipitation was performed to confirm the binding of IGF2BP3 to NLRP3 mRNA, while N⁶‑methyladenosine (m⁶A) modification levels in NLRP3 mRNA were measured via m⁶A‑RIP.
    RESULTS: NLRP3 expression was detected in pathological parathyroid tissues from chronic kidney disease patients with SHPT. Compared with less severe diffuse hyperplastic nodules, NLRP3 expression was significantly higher in nodular hyperplastic PG tissues. In SHPT rats, both IGF2BP3 and NLRP3 were upregulated in PG tissues. Knockdown of IGF2BP3 or NLRP3 reduced serum PTH levels and suppressed PG hyperplasia in SHPT rats. IGF2BP3 regulated NLRP3 expression in PGs through m⁶A‑dependent mechanisms by modulating NLRP3 mRNA stability and translation. NLRP3 overexpression reversed the phenotypic effects of IGF2BP3 knockdown in PG tissues of SHPT rats.
    CONCLUSION: IGF2BP3 enhances NLRP3 mRNA stability and translation via m⁶A modification, thereby aggravating SHPT and parathyroid hyperplasia.
    Keywords:  IGF2BP3; NLRP3; Parathyroid hyperplasia; Secondary hyperparathyroidism; m⁶A modification
    DOI:  https://doi.org/10.1007/s12020-026-04702-8
  50. Res Sq. 2026 Jul 01. pii: rs.3.rs-9933879. [Epub ahead of print]
    Inhibition of SIK2 and SIK3 induces adaptive ER-phagy and creates a therapeutic vulnerability in ovarian cancer.
    Zhen Lu, Rumeysa Ozyurt, Gamze Bildik, Weiqun Mao, Hailing Yang, Robert Bast.
      Cancer cells depend on protein quality control pathways to survive intrinsic and microenvironmental stress. Endoplasmic reticulum (ER)-selective autophagy (ER-phagy) maintains ER homeostasis by eliminating damaged ER and misfolded protein aggregates during ER stress. How ER stress-induced ER-phagy is regulated in cancer remains poorly understood. Salt-inducible kinases SIK2 and SIK3 (SIK2/3) are serine/threonine kinases implicated in metabolic regulation and cancer cell survival, but their roles in ER stress signaling and ER-phagy have not previously been studied. Here, we show that genetic or pharmacologic inhibition of SIK2/3 induces proteotoxic stress and activates the unfolded protein response through the PERK and IRE1 pathways, with predominant engagement of PERK and its downstream effector ATF4. SIK2/3 inhibition promotes ER-phagy by upregulating the ER-phagy receptor CCPG1 in an ATF4-dependent manner and increasing autophagic flux, thereby enabling cancer cell survival under stress. Disruption of this adaptive response results in the accumulation of polyubiquitinated protein aggregates, induction of CHOP, and apoptotic cell death in ovarian cancer cells. Importantly, combined treatment with the dual SIK2/3 inhibitor GRN-300 and the autophagy inhibitor chloroquine synergistically enhanced proteotoxic stress, reduced cell viability (combination index < 0.9), and triggered CHOP-dependent apoptosis. In ovarian cancer xenograft models, GRN-300 plus chloroquine markedly suppressed tumor growth and significantly prolonged survival compared with either monotherapy. Together, these findings identify SIK2/3 as key regulators of ER stress-induced ER-phagy and reveal a targetable stress-adaptation pathway that can be exploited therapeutically in ovarian cancer.
    DOI:  https://doi.org/10.21203/rs.3.rs-9933879/v1
  51. Res Sq. 2026 Jul 01. pii: rs.3.rs-10144286. [Epub ahead of print]
    Mechanosensing at the endoplasmic reticulum by IRE1.
    Hesso Farhan, Michaela Mayr, Luiz Garcia-Souza, Murphy McDermott, Utku Horzum, Yannick Frey, Margot Haun, Stephan Geley, Chao Jiang, Mattias Luber, Anush Bakunts, Camilla Pirolo, Alesia Yakimchyk, Klaus Liedl, Wylie Stroberg, Timo Betz, Liam Holt.
      Sensing and integration of mechanical forces in eukaryotic cells have largely been attributed to the plasma membrane and the nucleus. Here, we identify the endoplasmic reticulum (ER) as an autonomous mechanosensitive organelle and uncover IRE1 as an ER-resident mechanosensor. We show that applying mechanical forces to ER membranes increases lateral tension, which is sensed by the transmembrane domain of IRE1. Mechano-activation of IRE1 was unrelated to its canonical role in the unfolded protein response and occurred independently of nuclear mechanosensing. Instead, mechanically activated IRE1 triggered JNK signaling and increased global protein synthesis independently of XBP1 splicing. In engineered skeletal muscle tissue, both electrical stimulation and passive stretch similarly activated IRE1, increased translation, and contributed to training-induced increases in contractile force. Collectively, our results uncover a non-canonical role for IRE1 as an ER-based mechanosensor that couples mechanical forces to the regulation of protein translation.
    DOI:  https://doi.org/10.21203/rs.3.rs-10144286/v1
  52. Curr Opin Chem Biol. 2026 Jul 09. pii: S1367-5931(26)00073-6. [Epub ahead of print]94 102724
    Resolving cellular signaling in space and time: From organelle proteomics to spatial phosphoproteomics.
    Alejandro Matía, Ruth Hüttenhain.
      Cellular signaling is inherently organized in space and time, requiring coordinated control of protein localization, molecular interactions, and enzymatic activity across subcellular compartments. Recent advances in chemical biology, protein engineering, and quantitative proteomics have made it possible to interrogate these dimensions in an integrated manner. Here, we highlight emerging strategies to resolve signaling organization across three interconnected dimensions: organelle-resolved proteome mapping to define spatial context, proximity labeling to capture local protein interaction networks, and spatially resolved phosphoproteomics to quantify signaling outputs. Developments in proximity labeling, including split, conditionally activated and light-gated enzymes, enable temporally controlled, context-dependent profiling of transient protein assemblies in living cells. Advances in high-throughput and low-input phosphoproteomics, together with improved computational frameworks for kinase activity inference and subcellular enrichment strategies, are enabling spatially resolved measurement of signaling activity. Together, these approaches are shifting the field from static localization maps toward dynamic models of signaling networks.
    DOI:  https://doi.org/10.1016/j.cbpa.2026.102724
  53. bioRxiv. 2026 Jun 30. pii: 2026.06.29.735259. [Epub ahead of print]
    Enterovirus RNase L inhibiting RNAs are highly conserved with limited phylogenetic distribution.
    Samantha I Zangari, Madeline E Sherlock, Jeffrey S Kieft.
      RNA molecules form specific 3D structures that facilitate a variety of functions through interactions with other macromolecules. Many RNA viral genomes maintain these structures to interact with and evade host immunity machinery. One such element, the competitive inhibitor RNA (ciRNA), discovered in the protein coding region of the poliovirus serotype 1 (PV1) genome, inhibits a host antiviral protein, ribonuclease L (RNase L). Although some functionally essential structural motifs of the PV1 ciRNA have been studied, the extent of its evolutionary conservation and other structural requirements remained unexplored. Here we combined bioinformatic and biochemical techniques to further define the requirements of a functional ciRNA and assess its phylogenetic distribution. We systematically mutated ciRNA structural features, verifying that ciRNA inhibitory activity requires a conserved loop E motif and a long-range base-pairing interaction, but its peripheral stems are dispensable and in fact a circularly permuted version maintains function. A structure-based homology search identified potential ciRNAs across the Picornaviridae family, but only a subset of those tested were functional-all are in Enterovirus coxsackiepol . When structural features needed for function were transposed from PV1 ciRNA to an RNA unable to inhibit RNase L, the chimeric RNAs did not gain wild-type function, and chemical probing data revealed that these nonfunctional RNAs are unable to form the correct secondary structure. Overall, the dual constraints of encoding a protein and forming a specific functional structure appear to not only limit the sequence diversity, but also the phylogenetic distribution, of ciRNAs.
    DOI:  https://doi.org/10.64898/2026.06.29.735259
  54. Plant Cell Environ. 2026 Jul 09.
    Phosphate Starvation Shapes M6A Modification and Poly(A) Tails to Regulate mRNA Decay in Rice.
    Wang Chen, Yanhua Zhu, Ziqi Zhang, Zhujun Wang, Hudong Kuang, Zhaowan Yang, Chenxinyu Tan, Honghui Lin, Jian Yang.
      Phosphorus is essential for plant growth and reproduction. Plants have evolved diverse strategies to adapt to fluctuations in inorganic phosphate (Pi) availability by reprogramming gene expression. In addition to transcriptional regulation, RNA decay plays a crucial role in mRNA metabolism. In this study, we investigated whether RNA decay influences mRNA stability and whether m6A and m5C modifications and poly(A) tails are involved in this process, using Direct RNA sequencing for detection. We successfully established a genome-wide mRNA decay assay in rice and found that mRNA decay rates are primarily determined by G/C content in the 5' UTR, G/C content and RNA secondary structures in the CDS, m6A and m5C modifications in the 3' UTR, as well as the number of introns and the length of poly(A) tails. Both phosphate-starvation-induced (PSI) and phosphate-starvation-downregulated (PSD) genes decay faster than non-responsive genes, likely due to their higher CDS G/C content, fewer introns, and lower m6A modification rates. Pi starvation accelerated the decay of PSI genes but slowed the decay of PSD genes. Nanopore Direct RNA sequencing revealed that m6A modification and poly(A) tail length, rather than m5C modification, play central roles in regulating mRNA decay under Pi starvation. Furthermore, overexpression of the m6A reader OsYTH10 protected m6A-modified transcripts of OsPT2 and OsPAP21b from degradation, thereby enhancing Pi accumulation in rice. Collectively, our findings demonstrate that phosphate starvation remodels m6A methylations and poly(A) tails to modulate mRNA stability and shape the gene expression landscape in rice.
    Keywords:  RNA decay; m5C; m6A; poly(A) tails; rice
    DOI:  https://doi.org/10.1111/pce.70694
  55. Microb Cell. 2026 ;13 261-281
    Yippee-like protein Moh1 links gene expression to metabolism and selective stress resistance in Saccharomyces cerevisiae.
    Çağla Ece Olgun, Gizem Turan Duman, Gizem Güpür, Hamit İzgi, Mariam Huda, Demet Çetin, Zekiye Suludere, Fatma Küçük Baloğlu, Ayşe Koca Çaydaşı, Mesut Muyan.
      The Yippee-like (YPEL) proteins are a evolutionarily conserved eukaryotic family implicated in proliferation, senescence, and stress adaptation, yet their molecular functions remain poorly defined. Humans possess five paralogs (YPEL1-YPEL5), while the budding yeast S. cerevisiae contains a single ortholog, MOH1, previously linked to stress responses but with an unclear cellular role. Here, we investigated the function of MOH1 in S. cerevisiae. MOH1 deletion resulted in stress-specific phenotypes, including increased sensitivity to sodium azide and sulfuric acid, but enhanced resistance to hydrogen peroxide and acetic acid. Moh1 protein levels were dynamically regulated, decreasing upon hydrogen peroxide treatment and increasing in response to sulfuric acid. Morphological analyses including SEM revealed that moh1 Δ cells are rounder, form aggregates, and exhibit altered surface architecture independently of stress. RNA profiling and FTIR spectroscopy uncovered transcriptional reprogramming and metabolic remodeling, including alterations in lipid, protein, and cell wall polysaccharide levels and composition. Functional analyses showed that increased resistance to hydrogen peroxide is not due to altered mitochondrial ROS production but rather to reduced intracellular ROS accumulation. This effect is attributed to decreased cellular uptake resulting from altered permeability, supported by resistance to Congo red and sensitivity to SDS, consistent with cell envelope remodeling. Collectively, our findings identify Moh1 as a regulatory factor linking gene expression to metabolism and cellular architecture, thereby influencing cell envelope permeability and conferring selective stress resistance in S. cerevisiae.
    Keywords:  FTIR; MOH1; RNA-Seq; S. cerevisiae; SEM; stress response
    DOI:  https://doi.org/10.15698/mic2026.06.881
  56. Nat Commun. 2026 Jul 09.
    Proteome-scale quantification of the interactions driving condensate formation of intrinsically disordered proteins.
    Rasmus K Norrild, Sören von Bülow, Baptiste Zanchet, Einar Halldórsson, Kresten Lindorff-Larsen, Joseph M Rogers, Alexander K Buell.
      Cellular organization in the form of biomolecular condensates is a fundamental regulatory mechanism across all forms of life. Formation of condensates relies on multivalent interactions that are often weak and transient, making them challenging to study experimentally. We have developed Condensate Partitioning by mRNA-Display (CPmD) to measure these interactions from the partition free energies of peptides and nucleic acids into reconstituted condensates. CPmD increases experimental throughput by several orders of magnitude, and we apply it to reveal the interactions driving condensate formation of intrinsically disordered proteins. We show that the partition free energies of about one hundred thousand peptides derived from the disordered proteome into a model condensate directly reflect their intrinsic propensity to form condensates. We reveal that amino acid content, linked to hydrophobicity, is the primary determinant of phase behavior. Additionally, CPmD uniquely resolves subtle sequence-dependent contributions that can encode specificity. CPmD thus provides a powerful tool to decipher how weak interactions between protein and RNA regulate biological function through condensate formation.
    DOI:  https://doi.org/10.1038/s41467-026-74825-z
  57. PLoS Pathog. 2026 Jul;22(7): e1013842
    Naturally occurring mutations in replication proteins of a small RNA virus that alter the number, sizes, and relative abundances of subgenomic RNAs.
    Camila Perdoncini Carvalho, Deya Wang, Junping Han, Khwannarin Khemsom, Hanqiao Chen, Yizhi Tao, Feng Qu.
      Many positive-strand (+) RNA viruses produce subgenomic RNAs (sgRNAs) in infected cells. sgRNAs are synthesized by virus-encoded replication proteins (RPs), but whether RPs regulate the number and sizes of sgRNAs remains largely unknown. We report multiple naturally occurring mutations within the RPs of turnip crinkle virus (TCV) that alter the number, sizes, and relative abundances of TCV sgRNAs. TCV is a (+) RNA virus that normally produces two sgRNAs: the 1,724-nucleotide (nt) sgRNA1 expressing movement proteins, and the 1,449-nt sgRNA2 expressing capsid protein. A single amino acid change, A113V, within a region shared by TCV RPs p28 and p88, diminished sgRNA1 levels and delayed viral systemic spread. Interestingly, three second-site RP mutations emerged in infected plants that, alone or in combination with A113V, resulted in over-production of sgRNA1 or accumulation of two alternative sgRNAs of 1,876 and 1,601 nt, and rescued A113V defects. The alternative sgRNAs originated from nearly identical recombination events, their size difference reflecting varying 5' extensions. They may have accumulated to high levels through selective stabilization of their (-)-strand intermediates that were in turn derived from transcriptional pausing and recombination. Our findings reveal previously unrecognized constraints on viral RPs that ensure production of sgRNAs with precise sizes and abundances.
    DOI:  https://doi.org/10.1371/journal.ppat.1013842
  58. Microbiol Spectr. 2026 Jul 06. e0037826
    Ribosome hibernation in zinc-starved Mycobacterium abscessus confers amikacin tolerance.
    Ryan Z Treen, Austin J Fox, Yunlong Li, Kelley Hurst-Hess, Nilesh K Banavali, Pallavi Ghosh, Rajendra K Agrawal, Anil K Ojha.
      Intrinsic and acquired antibiotic resistance in Mycobacterium abscessus present unique challenges in treatment of its infections, which are rapidly emerging as a significant public health threat. The majority of clinically relevant antibiotics used against M. abscessus infections target the ribosome, which undergoes remodeling and hibernation in Mycobacterium smegmatis and Mycobacterium tuberculosis in response to zinc-limiting conditions. Ribosome remodeling involves replacement of multiple zinc-binding C+ ribosomal proteins with a CXXC motif by their respective C- paralogs lacking the motif, whereas ribosome hibernation involves recruitment of mycobacterial protein Y (Mpy) to the mRNA decoding center on the 30S subunit. Here, we report that zinc-responsive ribosome remodeling and hibernation are conserved in M. abscessus. We further demonstrate that Mpy binding suppresses translation and preserves ribosome abundance under zinc-limited conditions, while conferring tolerance to the aminoglycoside amikacin. Systematic biochemical analyses demonstrate that amino acid residues of Mpy that are critical for its interaction with the ribosome are also essential for Mpy stability in the cytosol. Together, these findings demonstrate amikacin tolerance as an important outcome of ribosome hibernation in M. abscessus.
    IMPORTANCE: Mycobacterium abscessus causes life-threatening infections in people with underlying health conditions. The treatment regimens for M. abscessus infections are months-long and include several ribosome-targeting antibiotics, such as amikacin. The long regimens are primarily attributed to intrinsic drug resistance in the pathogen. However, mechanisms of resistance for several of the antibiotics remain unclear. Here, we show that ribosome hibernation in M. abscessus by Mpy under zinc-starved conditions, which likely prevail in hosts, is a key determinant of amikacin tolerance. Thus, Mpy is a potential target for potentiating amikacin activity against M. abscessus.
    Keywords:  Mycobacterium abscessus; NTM; antibiotic tolerance; ribosome remodeling
    DOI:  https://doi.org/10.1128/spectrum.00378-26
  59. Biosci Rep. 2026 Jul 22. pii: BSR20250121. [Epub ahead of print]46(7):
    Mechanistic insights into the role of PEDF-R (PNPLA2) in photoreceptors.
    S Patricia Becerra.
      Photoreceptors are highly specialized neurons that depend on continuous membrane renewal and tightly regulated lipid homeostasis to maintain their visual function. Age-associated disruptions of these processes increase cellular stress and contribute to photoreceptor degeneration. Pigment epithelium-derived factor (PEDF) is a potent neuroprotective factor in the retina, and the identification of its receptor, PEDF-R (PNPLA2), has provided key mechanistic insight into how PEDF signaling is coupled to lipid metabolism. The present review examines the molecular and cellular mechanisms underlying PEDF-R function in photoreceptors and the retinal pigment epithelium (RPE). PEDF-R acts as a multifunctional enzyme with phospholipase and lipase activities that link extracellular PEDF binding to intracellular lipid remodeling. Through these activities, PEDF-R has been associated with processes essential for photoreceptor survival such as membrane phospholipid turnover, mitochondrial integrity, calcium homeostasis, and redox balance. In addition, PEDF-R contributes to retinoid metabolism and lipid processing associated with outer-segment renewal in the RPE. We further discuss how disruption of the PEDF-PEDF-R pathway impairs lipid homeostasis, promotes oxidative and inflammatory stress, and increases susceptibility to age-related retinal degeneration. These insights position PEDF-R as a key contributor to photoreceptor homeostasis and a potential therapeutic target for preserving retinal function in aging and disease.
    Keywords:  PEDF-R; PNPLA2; lipids; neuroprotection; phospholipases; photoreceptors
    DOI:  https://doi.org/10.1042/BSR20250121
  60. Plant Physiol. 2026 Jul 08. pii: kiag481. [Epub ahead of print]
    Protein Turnover in Plants - Cost of Synthesis, Repair and Crop Engineering Opportunities.
    Anastasia J I Högerl, Sudarshan Gnanamani, Ulschan Bathe.
      Protein lifespan is shaped by plant developmental stage and cellular requirements; both are fairly well understood processes. Beyond regulated degradation, chemical damage is another major cause of protein turnover, yet it is an understudied area in plant biology and crop engineering. The associated respiratory costs limit harvestable crop yield because the degradation and resynthesis of inactivated proteins consume carbon that then cannot be used for biomass production. Approximately half of the carbon fixed by plants is lost through respiration; of that protein turnover makes ∼25-40%. In this review, we examine the importance of spontaneous protein modifications arising under both optimal and environmental stress conditions; the latter can elevate protein turnover costs, negatively impacting crop yield. While homeostasis of most proteins following damage is likely maintained via de novo synthesis, some molecular mechanisms exist in cells to prevent and repair protein damage. They offer a substantial energetic advantage over resynthesis. We illustrate these benefits with specific examples and quantify their associated costs. Finally, understanding the causes, energetic consequences, and repair mechanisms of protein damage can inform strategies to improve crop performance. We suggest potential protein targets and synthetic biology approaches to be exploited for future crop engineering.
    Keywords:  Protein turnover; crop engineering; protein damage; protein damage repair; respiration
    DOI:  https://doi.org/10.1093/plphys/kiag481
  61. Bioinformatics. 2026 Jul 01. pii: btag296. [Epub ahead of print]42(Supplement_1):
    seq2ribo: structure-aware integration of machine learning and simulation to predict ribosome location profiles from RNA sequences.
    Gün Kaynar, Carl Kingsford.
       MOTIVATION: Ribosome dynamics are vital in the process of protein expression. Current methods rely on ribosome profiling (Ribo-seq), RNA-seq profiles, and full genomic context. This restricts their use in de novo sequence design, like messenger RNA (mRNA) vaccines. Simulation-only approaches like the Totally Asymmetric Simple Exclusion Process (TASEP) oversimplify translation by focusing solely on codon elongation times.
    RESULTS: We present seq2ribo, a hybrid simulation and machine learning framework that predicts ribosome A-site locations using only an mRNA sequence as input. Our method first employs a novel structure-aware TASEP (sTASEP), which models translation using a comprehensive set of fitted parameters that include codon wait times and structural features, such as local angles, base-pairing, and discrete positional buckets. The ribosome locations generated by sTASEP are then processed by a polisher model, which learns to refine the simulated ribosome distributions. seq2ribo provides high-fidelity predictions of ribosome locations across diverse cell types (iPSC, HEK293, LCL, and RPE-1), significantly outperforming baselines. seq2ribo is the first method to achieve meaningful positional correlation with observed ribosome profiles from sequence alone, reaching transcript-level Pearson correlations up to 0.920 and within-transcript shape correlations up to 0.186, where all baselines yield near-zero values on these metrics. seq2ribo also reduces elementwise error by up to 37.7% relative to the sequence-only Translatomer baseline. By adding a task-specific head, seq2ribo achieves Pearson correlations up to 0.732 with experimental translation efficiency (TE) across several cell lines, and up to 0.903 with measured protein expression. By operating from sequence alone, seq2ribo provides a new tool for synthetic biology, enabling the rational design and optimization of mRNA sequences without the need for expression-level data or genomic context.
    AVAILABILITY: seq2ribo is available at https://github.com/Kingsford-Group/seq2ribo.
    DOI:  https://doi.org/10.1093/bioinformatics/btag296
  62. J Phys Chem B. 2026 Jul 10.
    Mechanism of Ribosomal A1493 in Stabilizing and Rigidly Supporting the Codon-Anticodon Helix During tRNA Recognition.
    Shuhao Zhang, Zhen Wang, Jie Qiao, Wenbing Zhang.
      The ribosome ensures translational accuracy by monitoring codon-anticodon interactions at the A site decoding center, yet the mechanism of conserved nucleotides contributing to this process remains controversial. Here, we performed molecular dynamics simulations based on a tRNA recognition intermediate that reflects the ribosomal state during ongoing tRNA recognition. We systematically investigated the coupling between the stability of the first codon-anticodon base pair and the conformational dynamics of A1493 in both cognate and near-cognate tRNA systems. Our results show that A1493 stabilizes the codon-anticodon helix through an entropic mechanism and functions as a "wedge" to provide rigid support for it. The correct flipping of A1493 is facilitated by van der Waals interactions with the residue at position 37 of tRNA, highlighting the crucial role of steric complementarity in the decoding center. However, the flipping of A1493 lacks specificity for different tRNAs due to conformational changes of A1913, suggesting that the large ribosomal subunit may also participate in tRNA recognition. We also explored changes in codon-anticodon stability during translocation. Together, these findings refine the mechanism by which conserved ribosomal nucleotides participate in decoding.
    DOI:  https://doi.org/10.1021/acs.jpcb.6c02011
  63. Phytomedicine. 2026 Jun 29. pii: S0944-7113(26)00765-8. [Epub ahead of print]159 158532
    Ginsenoside Rk1 inhibits EMT and the metastasis of hepatocellular carcinoma by affecting the m6A modification of mRNA.
    Huanyan Wu, Yuan Liu, Chenhui Zhu, Zhiguang Duan, Linlin Qu, Rongzhan Fu.
       BACKGROUND: N6-methyladenosine (m6A) is a crucial messenger RNA (mRNA) modification that plays a significant role in tumor development and metastasis. Ginsenoside Rk1 possesses notable anticancer activity; however, its effects on m6A modification have not yet been elucidated.
    HYPOTHESIS/PURPOSE: In this study, the aim is to investigate the role of ginsenoside Rk1 in the regulation of m6A modification and its effect on hepatocellular carcinoma (HCC) metastasis.
    METHODS: The construction of in vitro and in vivo lung metastasis models was used to investigate the effect of ginsenoside Rk1 on lung metastasis of HCC. RNA sequencing, m6A sequencing, siRNA cell transfection, western blotting and quantitative real-time PCR (qRT-PCR) were performed to investigate the effect of ginsenoside Rk1 on m6A modification and its mechanism of action in inhibiting lung metastasis through modulation of m6A modification.
    RESULTS: Ginsenoside Rk1 demonstrated dose-dependent inhibition of HCC metastasis both in vivo and in vitro. Mechanistically, it suppressed the expression of Fat mass and obesity-associated protein (FTO), an m6A demethylase, thereby enhancing m6A modification in HCC cells. Specifically, ginsenoside Rk1 significantly increased the m6A modification of Block of proliferation 1 (BOP1) mRNA, leading to prolonged mRNA half-life. Furthermore, ginsenoside Rk1-mediated knockdown of BOP1 expression inhibited Epithelial-mesenchymal transition (EMT) pathway-related proteins (e.g., Vimentin, matrix metalloproteinase-2 (MMP2), and matrix metalloproteinase-9 (MMP9)), thus attenuating the metastatic potential of HCC cells. These findings highlighted the therapeutic potential of ginsenoside Rk1 in mitigating HCC aggressiveness through its dual role in modulating the FTO-m6A-BOP1 axis and inhibiting the EMT pathway.
    CONCLUSION: Ginsenoside Rk1 inhibits the migration and invasion of HCC by enhancing FTO-mediated m6A modification of BOP1 mRNA. Ginsenoside Rk1 has the potential to act as an m6A methylation regulator inhibitor, offering a novel approach for targeting m6A modification in the treatment of HCC metastasis.
    Keywords:  BOP1; EMT; FTO; Ginsenoside Rk1; Hepatocellular carcinoma; Lung metastasis
    DOI:  https://doi.org/10.1016/j.phymed.2026.158532
  64. PeerJ. 2026 ;14 e21481
    The RNA-binding protein Pumilio limits polymodal nociception in Drosophila larvae.
    Sara Palega, Hannah Davenport, Rebeccah K Stewart, Jessica Horton, Andrew Bellemer.
      Nociception is the process by which the nervous system detects and processes information about potentially harmful environmental stimuli to generate behavioral and physiological responses. The process of nociception undergoes plasticity in response to injury, inflammation, and infection to shape the sensitivity of nociceptive circuits and the behavioral responses they control. We are increasingly aware that post-transcriptional regulation of gene expression shapes the sensitivity and plasticity of nociceptive sensory neurons and nociceptive behavior. In Drosophila, the Pumilio RNA-binding protein interacts with diverse target mRNAs to regulate their abundance and translation in a wide range of contexts including the establishment of embryonic polarity, maintenance of the germline, regulation of neural morphology, and homeostatic control of neural excitability. In this study, we find that Pumilio acts to limit nociceptive sensitivity through its activity in nociceptive sensory neurons. Larvae with nociceptor-specific pumilio knockdown show enhanced nocifensive responses to noxious thermal, mechanical, and chemical stimuli, while larvae with nociceptor-specific overexpression of pumilio show blunted responses to noxious thermal and mechanical sensitivity. Furthermore, we find that Pumilio is required in the nociceptors for larvae to expression nociceptive sensitization following injury, suggesting a role for Pumilio in nociceptor plasticity. These observations may be explained by regulation of neuronal excitability, dendrite morphology, and cell signaling by Pumilio, and future studies will elucidate these mechanisms.
    Keywords:  Drosophila; Gene regulation; Nociception; Pumilio
    DOI:  https://doi.org/10.7717/peerj.21481
  65. Nat Commun. 2026 Jul 08.
    Translation initiation by the Kozak mRNA sequence is based on a conformational readout on the ribosome.
    Ottilie von Loeffelholz, Charles Barchet, Samuel Holvec, Aida Abou Ramadan, Cristina Protuc, Anne Maglott-Roth, S Nimali T de Silva, Isabelle Hazemann, Bruno P Klaholz.
      The recognition mechanism of Kozak mRNA, typically comprising purines in the -3 and +4 positions flanking the AUG start codon, has remained enigmatic for decades. To address this fundamental function in eukaryotes during translation initiation, we analysed several cryo-EM structures of human 48S preinitiation complexes with mRNA sequences differing in Kozak activity revealing distinct modes of recognition. The pre-codon triplet forms a fan-like intercalation into the 18S ribosomal RNA (rRNA), while a -3 pyrimidine destabilizes ternary complex positioning. Specificity towards the +4 purine is achieved beyond a single residue recognition by mutual conformational adaptations of eIF1A, mRNA and rRNA that involve the insertion of a reading head in which decoding residue A1825 (rRNA) stacks with the A-site codon to stabilize the fully accommodated state. Hence, instead of relying on base pairing as in bacteria, the specific recognition of the Kozak sequence on eukaryotic ribosomes is based on an induced-fit mechanism that triggers a conformational readout of the mRNA.
    DOI:  https://doi.org/10.1038/s41467-026-73969-2
  66. Am J Physiol Heart Circ Physiol. 2026 Jul 07.
    The R120G Knock-in Mutation in αB-Crystallin is Insufficient to Induce Cardiomyopathy in Mice.
    Justin M Quiles, Rishith Ravindran, Samantha Ivezich, Liguo Chi, Rita Najor, Åsa B Gustafsson.
      Alpha B-crystallin (CryAB) is a small heat-shock protein highly expressed in cardiac tissue, where it functions as a molecular chaperone that helps prevent protein aggregation, particularly under stress conditions. A missense mutation in CryAB (R120G) causes autosomal dominant cardiomyopathy in humans and is characterized by extensive protein aggregation in cardiomyocytes. To better understand the pathogenic mechanisms underlying CryABR120G-associated cardiomyopathy, appropriate in vivo models are essential. Genetic mouse models are valuable tools for investigating disease pathogenesis and evaluating potential therapeutic strategies. In this study, we characterized a homozygous CryABR120G knock-in (KI) mouse model to assess the impact of this mutation on cardiac function. CryABR120G KI mice exhibited no overt changes in cardiac structure and function up to 12 months of age, with minimal changes in cardiac and proteotoxic stress markers, except for an increased atrial natriuretic peptide expression at 12 months. Protein quality control pathways remained largely unchanged. Although mitochondrial respiration was normal in young CryABR120G KI mice, it was reduced at 12 months of age. Despite the presence of insoluble protein aggregates, homozygous CryABR120G KI mice did not develop overt structural or functional cardiomyopathy through 12 months of age. These findings indicate that, within the age range examined, the CryABR120G KI model does not reproduce the overt cardiomyopathic phenotype associated with the CRYABR120G mutation in patients.
    Keywords:  autophagy; cardiomyopathy; mitochondria; protein aggregation; αB-Crystallin
    DOI:  https://doi.org/10.1152/ajpheart.00364.2026
  67. Arch Pharm Res. 2026 Jul 11.
    Integrative multi-omics analyses reveal nuclear noncoding RNA-mediated regulatory landscape in Alzheimer's disease.
    Sumin Yang, Sung-Hyun Kim, Jeonghyeon Choi, Yeyoung Lee, Jeehye Jung, Jae-Yeol Joo.
      Alzheimer's disease (AD) progression involves complex molecular mechanisms underlying neuronal dysfunction. While emerging evidence on long noncoding RNAs (lncRNAs) is accumulating, the relevance of nuclear noncoding RNAs (ncRNAs) to neurodegenerative diseases remains poorly understood. Small Cajal body-specific RNA 13 (scaRNA13) is a nuclear ncRNA implicated in RNA species regulation, which remains insufficiently characterized in neuronal systems and AD pathogenesis. Here, we performed integrative analyses of human postmortem brain transcriptomes and AD mouse models to examine scaRNA13 expression across disease stages, sex, and brain regions. RNA-seq and proteomic analyses were used to assess scaRNA13-associated changes in gene expression, splicing, and RNA-protein interactions. Functional assays in neuronal cells were conducted to evaluate the effects of scaRNA13 perturbation on RNA processing, protein synthesis, and tau-related pathology. scaRNA13 was aberrantly upregulated in AD patient brains with a pronounced elevation observed in female patients at advanced stages. Perturbation of scaRNA13 altered splicing patterns and global translational capacity, accompanied by altered tau aggregation- and phosphorylation-related phenotypes in neuronal cell systems. These findings support scaRNA13 as an AD-associated nuclear ncRNA candidate and suggest that scaRNA13 perturbation is associated with changes in RNA processing, translational regulation, and tau-related cellular phenotypes in neuronal cell systems.
    Keywords:   scaRNA13 ; Alzheimer’s disease; NcRNA; Neurodegeneration; Tau pathology
    DOI:  https://doi.org/10.1007/s12272-026-01629-6
  68. J Am Chem Soc. 2026 Jul 09.
    Threonine Phosphorylation Is a Bioreversible Surrogate of Proline Hydroxylation in a Collagen Triple Helix.
    Isabella M B Pearl, Ronald T Raines.
      Collagen, the most abundant protein in the human body and structural foundation of connective tissue, derives its remarkable stability from repeating (Xaa-Yaa-Gly)n sequences rich in (2S)-proline (Pro) and (2S,4R)-4-hydroxyproline (Hyp), the product of a post-translational modification. Here, we demonstrate that another such modification, phosphorylation, yields a bioreversible mimic of Hyp. Using synthetic collagen-mimetic peptides, we substituted the Xaa or Yaa position of a central Pro-Hyp-Gly triplet with (2S)-serine (Ser), (2S,3R)-threonine (Thr), or their O-phosphorylated derivatives, pSer or pThr. All substitutions were destabilizing─except pThr in the Yaa position, which preserved the triple-helical stability conferred by Hyp. Moreover, pThr within a collagen triple helix is a substrate for a mammalian secretory phosphatase. Notably, Thr is enriched at the Yaa position in mammalian fibrillar collagens, consistent with pThr being a linchpin of collagen remodeling in the extracellular matrix. Thus, the phosphorylation of threonine (which is bioreversible) mimics the hydroxylation of proline (which is not), enabling dynamic modulation of collagen architecture in development and disease.
    DOI:  https://doi.org/10.1021/jacs.5c19090
  69. Drug Des Devel Ther. 2026 ;20 608538
    Pterostilbene in Oxidative Stress-Related Diseases: Context-Dependent Regulation of Redox Homeostasis and Translational Challenges.
    Yuyao Zhang, Yingying Yu, Zhengrong Xiong, Wenying Bin, Yuxuan Yao, Huan Liu.
      This narrative review synthesizes current evidence on pterostilbene in oxidative stress-related diseases, focusing on its chemical and pharmacokinetic basis, redox-related signaling responses, disease-specific evidence, and translational challenges. Most available evidence comes from preclinical models and suggests that the biological effects of pterostilbene cannot be explained solely by direct reactive oxygen species (ROS) scavenging. Instead, pterostilbene is associated with several redox-sensitive processes, including Nrf2-related antioxidant responses, redox-inflammatory crosstalk, mitochondria-associated stress responses, metabolic regulation, and cell death-related pathways. Evidence from osteoarthritis, neurodegenerative and cognitive dysfunction models, ischemia-reperfusion injury, metabolic diseases, and cancer indicates that these effects vary substantially across pathological contexts. In non-malignant degenerative, ischemic, and metabolic models, pterostilbene is generally associated with attenuation of oxidative stress-, inflammation-, or cellular stress-related injury markers, whereas in selected cancer models it may disrupt redox-adapted tumor-cell stress tolerance and promote apoptosis- or pyroptosis-related responses. Important translational barriers remain, including incomplete direct target validation, heterogeneous dosing and intervention designs, reliance on static oxidative stress endpoints, limited clinical validation, and insufficient integration of negative or context-dependent findings. By applying a redox homeostasis-centered framework, this review clarifies the contexts in which pterostilbene effects have been reported and identifies the evidence needed before disease-specific translational positioning can be established.
    Keywords:  NF-κB; Nrf2/Keap1; cancer; ischemia–reperfusion injury; metabolic diseases; mitochondria-associated stress; oxidative stress; pterostilbene; redox homeostasis
    DOI:  https://doi.org/10.2147/DDDT.S608538
  70. Front Immunol. 2026 ;17 1859544
    RACK1 in host immune response to infections: molecular mechanisms and therapeutic potentials.
    Zhenglin He, Yishuo Ji, Hanming Hao, Kai Zhao, Shangwei Ji, Liang Han, Yue Hu.
      The global healthcare system faces increasing threats from emerging and re-emerging pathogens. Current understanding of host-pathogen interactions and underlying immune mechanisms remains incomplete, which hinders the development of effective diagnostic tools and therapeutic strategies. The receptor for activated C kinase 1 (RACK1) is a multifunctional scaffolding protein that integrates diverse signaling pathways, modulates translation, and regulates key cellular processes. Despite accumulating evidence implicating RACK1 in host immune response to infections, its multifaceted roles and mechanisms remain poorly defined. Hence, this review systematically discusses the involvement of RACK1 in host defense against bacterial and viral pathogens, with a focus on its regulation of inflammatory signaling, inflammasome activation, hormone-mediated immune regulation, reactive oxygen species production, adaptive immunity, and different pathogen infections. Together, current evidence suggests that RACK1 links signaling and translation to shape immune responses in different infectious settings and may provide a basis for host-directed therapeutic strategies.
    Keywords:  RACK1; adaptive Immunity; host-pathogen interaction; innate immunity; scaffolding protein; signal transduction; translational control
    DOI:  https://doi.org/10.3389/fimmu.2026.1859544
  71. bioRxiv. 2026 Jul 01. pii: 2026.06.28.735091. [Epub ahead of print]
    Control theory analysis of dynamic metabolic response elucidates mitochondrial-cytoplasmic coupling and nutrient partitioning.
    Xingbo Yang, Daniel J Needleman.
      Cells adjust their internal circuits in response to changes in their environment. Hence, exposing cells to changing conditions provides a way to probe the intrinsic dynamics of cellular internal circuits. Metabolic networks are examples of such circuits since metabolic fluxes dynamically adjust when environmental conditions are transiently altered. Most existing theoretical frameworks focus on cellular metabolic steady states and do not consider the dynamics of changes in metabolic fluxes. In this work, we applied transfer function analysis from control theory to analyze the changes of NADH oxidative fluxes in the mitochondria and cytoplasm in mouse oocytes in response to dynamical perturbations of oxygen depletion and recovery. We observed an overshoot of NADH oxidative flux in the cytoplasm upon oxygen recovery which is absent in the mitochondrial NADH oxidative flux. Metabolic perturbation experiments and transfer function analysis indicate that this cytoplasmic NADH overshoot results from the coupling of the mitochondrial and cytoplasmic NADH cycles. The degree of overshoot is determined by competing timescales associated with the exchange rates of lactate and pyruvate with the media and their interconversion rates catalyzed by lactate dehydrogenase. Applying control theory to the data enables the inference of the exchange and conversion rates of pyruvate and lactate, allowing predictions of the contribution of lactate to mitochondrial respiration. Our work indicates that the oocytes maintain a homeostatic respiration rate across nutrient conditions by modulating the contribution of lactate to mitochondrial respiration.
    DOI:  https://doi.org/10.64898/2026.06.28.735091
  72. Traffic. 2026 Sep;27(3): e70044
    The Power of Nup85: Controlling Molecular Traffic and Cellular Fate.
    Fatma A Abouelnazar, Ying Chu, Yongmin Yan, Donglin Hao.
      Nucleocytoplasmic transport is a fundamental process that maintains cellular homeostasis, mediated by the nuclear pore complex (NPC), a highly organized macromolecular assembly embedded in the nuclear envelope (NE). Among its structural components, nucleoporin 85 (Nup85) is a core element of the evolutionarily conserved Nup107-160 (Y-) complex, where it plays a central role in maintaining NPC architecture and function. This review provides a comprehensive overview of current knowledge on Nup85, integrating its structural organization, molecular interactions, and functional roles across diverse eukaryotic systems. Nup85 is characterized by an α-helical solenoid architecture within the ancestral coatomer element (ACE1) family and forms critical interactions with multiple nucleoporins, including Seh1, Nup43, Nup120, and Sec13, thereby contributing to NPC assembly and stability. Furthermore, Nup85 extends beyond a scaffolding role to regulate mRNA export, nucleocytoplasmic transport, gene expression, and cell cycle progression. Studies across model organisms highlight its conserved roles in processes such as stress signaling, development, mitosis, and metabolic regulation. Importantly, dysregulation or mutation of Nup85 has been associated with a range of human pathologies, including kidney disease, neurodevelopmental disorders, cancer progression, inflammatory conditions, and infectious diseases. This review aims to identify key gaps in the current understanding of Nup85, highlight its importance, and provide a basis for future research directions.
    Keywords:  Nup85; cellular homeostasis; disease mechanisms; nuclear pore complex; nucleocytoplasmic transport
    DOI:  https://doi.org/10.1111/tra.70044
  73. Mol Plant. 2026 Jul 07. pii: S1674-2052(26)00221-2. [Epub ahead of print]
    Translation-dependent retrograde signaling coordinates high-light acclimation in plants.
    Marten Moore, Aaron B Smith, Melanie Wegener, Pravin B Khambalkar, Rebeccah Victoria Tyrrell, Brea Camille Watts, Samuel J Nix, Hong Ting Tsang, Mohammad A Farooq, Diep R Ganguly, Robert T Furbank, Maria Ermakova, Barry J Pogson, Karl-Josef Dietz.
      Canonical chloroplast retrograde signaling is typically defined as chloroplast-initiated signaling circuits that regulate nuclear transcription for acclimation. This study reveals that high light (HL) also initiates translation-dependent retrograde signaling pathways (TraDeRS), which bifurcate to increase translation of chloroplast-targeted proteins and nuclear transcription factors thereby enhancing photosynthesis and reducing photoinhibition. Reprogramming of translation within 10 min of HL predominates over transcriptional regulation, evidenced by global downregulation of translation based both on ribosomal footprints (RPF) and polysome profiles in Arabidopsis. RPF-seq reveal four distinct subsets of transcripts for ribosome-mediated regulation: two subsets showing changes in ribosomal association only, and two showing combined changes of ribosomal association and transcript abundance. The 'increased translation' subset is enriched for chloroplast-targeted photosynthetic proteins containing evolutionarily-conserved 5'-UTR mRNA motifs. The motifs bind and release an RNA-binding protein, Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), in a HL and co-factor dependent manner. The motifs were sufficient to increase reporter gene translation and Rieske protein expression in vitro and in Setaria viridis. This light intensity-dependant, redox-regulated switch responds to pharmacological treatments that perturb photosynthesis and retrograde signaling, but not a generic abiotic stress, namely heat. It promotes the translation of photosynthesis proteins and HL-responsive transcription factors, such as Stress-associated proteins (SAPs), creating a rapidly responsive feed-forward loop to amplify known retrograde transcriptional responses, thereby reducing photoinhibition. The functional conservation of the GAPDH-motif interaction in Setaria viridis foreshadows new strategies for improving photosynthesis and expands our understanding of translational control mechanisms in response to chloroplast communication.
    Keywords:  High light; chloroplast; retrograde signaling; stress acclimation; transcriptome; translational control
    DOI:  https://doi.org/10.1016/j.molp.2026.07.002
  74. Biophys Chem. 2026 Jul 04. pii: S0301-4622(26)00111-0. [Epub ahead of print]338 107678
    Phase separation and protein aggregation in neurodegenerative diseases.
    Hortense de La Seiglière, Ænora Letourneur, François Ichas, Francesca De Giorgi.
      Neurodegenerative diseases such as Alzheimer's, Parkinson's, frontotemporal dementia, and ALS are characterized by amyloid protein aggregation involving intrinsically disordered proteins that are also capable of liquid-liquid phase separation (LLPS). LLPS, known to drive the formation of dynamic membraneless organelles essential for cellular functions, can play a role in limiting fibrillation process or aberrantly transition into solid aggregates under pathological conditions. Here we review how mutations, post-translational modifications, and environmental factors can modulate LLPS of proteins like Tau, TDP-43, FUS, and α-synuclein, potentially regulating amyloid aggregation. We also examine the interplay of these proteins exploring how LLPS and condensate maturation could impinge on the emergence of co-pathologies contributing to disease progression. Finally we discuss emerging therapeutic strategies, aimed at modulating phase separation dynamics.
    Keywords:  Amyloid formation; Intrinsically disordered proteins; Liquid-liquid phase separation; Neurodegenerative diseases; Protein aggregation
    DOI:  https://doi.org/10.1016/j.bpc.2026.107678
  75. Methods Mol Biol. 2026 ;3024 131-140
    Antisense Oligonucleotide-Mediated Chimeric RNA Knockdown.
    Anam Tajammal, Katie Do, Hui Li.
      Knockdown assays aim to silence the expression of a target gene. By reducing expression of a gene, researchers can investigate the gene's function in biological processes. Common knockdown assays use RNA interference (RNAi) to reduce gene expression by degrading its mRNA. However, RNAi requires the use of double-stranded RNA to target mature mRNA transcripts. Antisense oligonucleotides (ASO) offer an alternative pathway to knocking down gene expression by allowing the use of single-stranded DNA or RNA to target pre-mRNA, mature mRNA, long non-coding RNAs or DNA. Here, we have provided guidelines and procedures for ASO knockdown, application to chimeric RNAs, and necessary controls for a successful experiment.
    Keywords:  Antisense oligonucleotide; Chimeric RNA; Interfering RNA (RNAi); Knockdown
    DOI:  https://doi.org/10.1007/978-1-0716-5202-2_13
  76. Insect Mol Biol. 2026 Jul 09.
    RNA activation in insects: From emerging evidence to molecular applications.
    Sassan Asgari.
      RNA interference is commonly used as a reverse genetics tool to investigate gene function. In insects, this is achieved by introducing double-stranded RNA or synthetic short-interfering RNAs (siRNAs). However, RNA activation (RNAa) is less frequently utilised in these studies. RNAa can be achieved by targeting a gene's promoter with antisense RNA, which triggers endogenous transcription. Unlike the siRNA mechanism, which is well characterised, the RNAa mechanism is less well known. In the literature, 'RNAa' has been adopted to describe diverse small RNA-mediated upregulation mechanisms that may not necessarily function through the canonical RNAa mechanism described in mammals, which involves interaction of the small RNA with the promoter region. Although the outcomes of RNAi and RNAa differ, some components are shared between their pathways, such as Argonaute proteins. In this minireview, RNAa, its canonical and non-canonical mechanisms, and applications in insect research are examined with the aim of encouraging its use as a tool in Insect Molecular Biology.
    Keywords:  RNA activation; RNA biology; RNA interference; RNAa; RNAi; gene expression; insects
    DOI:  https://doi.org/10.1111/imb.70058
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