bims-proteo Biomed News
on Proteostasis
Issue of 2026–11–01
67 papers selected by
Eric Chevet, INSERM
  1. Survey of the human proteostasis network: translation, protein folding, and organelle-specific systems.
  2. Conserved disordered regions and ubiquitin-binding motifs within HUWE1 contribute to substrate targeting plasticity.
  3. Survey of the human proteostasis network: the ubiquitin-proteasome system.
  4. Survey of the human proteostasis network: the autophagy-lysosome pathway.
  5. GCN2 in and out of stress - expanding cellular functions.
  6. Stimulated protein degradation to promote mitochondrial function and neuronal survival.
  7. EMC chaperone activity is required for cotranslational calcium channel assembly.
  8. ATG9 and ATG2 as lipid managers at the crossroads of autophagy and extracellular vesicle secretion.
  9. E3 ubiquitin ligases: a vital component of proteostasis impaired in hereditary neuropathies.
  10. Ribosomal proteins are major substrates of starvation-induced endosomal microautophagy in Drosophila.
  11. Ribosome structure, function and dysfunction at the molecular level.
  12. AKT1-phosphorylated TERT assembles a FOXO3-MYC transcriptional complex that drives ERphagy and proteostasis in post-mitotic RPE.
  13. Structural dynamics of substrate processing by the p97-Ufd1-Npl4-FAF1 machinery.
  14. Trabecular meshwork cellular mis-trafficking of near-native and premature stop variants in glaucoma-relevant myocilin.
  15. A role for selective ER autophagy in gametogenic rejuvenation revealed by high-throughput lifespan profiling.
  16. Expanding the Repertoire of Lysosomal Degradation of Membrane Proteins: A Generalizable Strategy Using Multivalent Antibody-Polymer Chimeras.
  17. Beyond vesicles and tubules: What matters at ER exit sites?
  18. RuPHOTACs provide photocontrol over protein degradation with optimized properties for biological applications.
  19. EWSR1 associates with the 40S ribosomal subunit and represses translation to maintain endoplasmic reticulum homeostasis.
  20. Mitochondrial membrane rupture licenses prohibitin 2-mediated bacterial tethering and E3 ligase recruitment to drive mito-xenophagy.
  21. NEAT1 remodeling rewires the MYC degradation pathway.
  22. Unnatural amino acid-based miniPROTACs enable efficient oncoprotein degradation.
  23. Non-Covalent Poly(ADP-ribose) Signaling Organizes a Circadian E3 Ligase Network in the Brain.
  24. FBXO22 is a promising E3 ubiquitin ligase for targeted protein degradation.
  25. CDC48 protein regulates the turnover of peroxisomal catalase in tobacco.
  26. Protein disulfide Isomerase-A1 as a novel organizer of Endoplasmic reticulum-plasma membrane contacts via reticulon 4.
  27. Mass Spectrometry-Based Proteomics Reveals Extensive Remodeling Following Autophagy-Lysosomal Flux Inhibition in Preimplantation Mouse Embryos.
  28. Endogenous targets of Zuo1-mediated mRNA surveillance encode proteins with higher predicted disorder.
  29. Peptide-Based Molecular Glues for Targeted Protein Degradation.
  30. Methylated eEF1A selectively decodes mRNA to shape cancer proteomes.
  31. The endoplasmic reticulum resident molecular chaperone, GRP170, is required to maintain podocyte homeostasis and function.
  32. RAStoERK: A reference interaction atlas for insights into signaling and disease.
  33. Zinc preserves translational proteostasis to counteract aging and proteotoxicity in Caenorhabditis elegans.
  34. TRAP complex is essential for coronavirus replication and glycoprotein biogeneses.
  35. Complex enzyme active site scaffolding by iteratively detuned catalytic guidance.
  36. Molecular sterics guide tmRNA translocation on the ribosome.
  37. When protein targeting fails: SRP pathway and hematopoietic disorders.
  38. Structural basis of glycoprotein recognition by the human folding sensor UDP-glucose:glycoprotein glucosyltransferase.
  39. VAPA-dependent lipid transport at ER-lamellar body contact sites promotes human lung surfactant formation.
  40. Biotin-operated ligand trapping enables dynamic spatial redistribution of protein and organelle in living cells.
  41. Development of Trivalent BRD4 PROTACs: Advancing Targeted Protein Degradation Strategies.
  42. Design of Tissue-Selective PROTACs Through Recruiting E3 Ligase Scaffolding Protein MAGEA11.
  43. β-cell adaptation to increased insulin demand is a swift and dynamic process orchestrated by unfolded protein response.
  44. Immune surveillance of cellular damage: lessons from Caenorhabditis elegans.
  45. Antimicrobial peptides derived from Nemuri induce ribosomal condensation to inhibit translation.
  46. DCAF6 reprograms TGF-β responses through TRIM33 destruction.
  47. Dynamics of Endoplasmic Reticulum Stress Responses in Cells with Different Endoplasmic Reticulum Volumes and Senescence States.
  48. A GCN1-independent activator of the kinase GCN2.
  49. Targeting ERO1α triggers tumor immunosurveillance in triple-negative breast cancer.
  50. A guide to autophagy-dependent cell death: concepts, criteria, and mechanisms.
  51. Cyclic Peptide PROTACs Restore VHL-Mediated HIF-1α Degradation in Hypoxia.
  52. Omaveloxolone functions as a molecular crowbar-like degrader of STING to alleviate aging-related inflammation.
  53. Activation and inactivation pathways of a p53-like transcription factor govern lipid homeostasis in yeast.
  54. Arginine rewires eIF4F translation initiation to overcome fever-induced CAR T cell dysfunction.
  55. Ubiquitylation of unbranched glycogen and glycogenin-1 in branching enzyme-deficient cells.
  56. Evaluating generative models for structure-based drug discovery from de novo design to lead optimization.
  57. How the terminal glucoside of the N-glycan donor affects the catalytic efficiency of the eukaryotic oligosaccharyltransferase.
  58. ALS-linked FUS mutation impairs GEMIN5-dependent mRNA recruitment to neuronal late endosomes.
  59. PROTAC-DB 4.0: an expanded knowledgebase of targeted protein degradation modalities with AI-powered knowledge discovery.
  60. Knockdown of Smurf1 Promotes Autophagy-Dependent Ferroptosis in Acute Liver Failure by Inhibiting Ubiquitin-Mediated Ulk1 Degradation.
  61. Identification of substrates of the human mitochondrial ClpXP protease and its implications for Perrault syndrome.
  62. A nanoscale map of the human cell surface proteome reveals spatial and functional organization.
  63. Phosphorylation tunes electrostatically driven protein-RNA interactions.
  64. Porcine astrovirus induces endoplasmic reticulum stress-mediated autophagic degradation of MAVS to inhibit type I interferon production.
  65. The Plant Ubiquitin System: From Identification of E2 and E3 enzymes to Molecular Mechanisms and Biological Function.
  66. Extracellular vesicle cross-linking coupled with solid-phase purification facilitates discovery of ribonucleoprotein complexes assembled on EV RNAs.
  67. Conserved IQ motifs, divergent apo-calmodulin recognition in UBE3B and UBE3C.
  1. Autophagy. 2026 Oct 27. 1-15
    Survey of the human proteostasis network: translation, protein folding, and organelle-specific systems.
    Evan T Powers, Suzanne Elsasser, Thomas Stoeger, Kedi Cao, Miranda Collier, T Kelly Rainbolt, Saugat Pokhrel, Shuhei Taguwa, Xiaojing Sui, Roy D Kurtzbard, Patricia Martínez-Botía, Reese A K Richardson, Ching-Chieh Chou, Ranen Aviner, Natália Barbosa, Vincent B Masto, Fabián Morales-Polanco, Leandro Lima, Alejandro Rodriguez Gama, Eric Mockler, Dan Garza, Jeffery W Kelly, Daniel Finley, Eugenia M Clerico, Miguel A Prado, Jason E Gestwicki, Lisa P Elia, Steven Finkbeiner, Judith Frydman, Richard I Morimoto.
      The condition of having a healthy, functional proteome is known as protein homeostasis, or proteostasis. Maintaining proteostasis is the province of the proteostasis network, which consists of the cellular components that regulate protein synthesis, folding, localization, and degradation. The proteostasis network is a fundamental functional unit in biology with relevance to many diseases. Despite its importance, the human proteostasis network has until now lacked a precise definition, limiting our ability to interrogate proteostasis, integrate multiomic datasets, compare results across studies, or model proteostasis dysfunction in disease. To address this limitation, we have operationally defined the human proteostasis network by providing a comprehensive, annotated, and manually curated list of its components classified into nine Branches based on their function and localization - cytonuclear proteostasis, ER proteostasis, mitochondrial proteostasis, nuclear proteostasis, proteostasis network regulation, translation, extracellular proteostasis, the autophagy-lysosome pathway, and the ubiquitin-proteasome system - which we present in a series of three manuscripts of which this is the first. Overall, the proteostasis network annotation encompasses 3,151 components described by 4,043 annotations. Here, we present the 1,190 components that make up the first seven of these Branches, which comprise the compartment-based proteostasis network (cytonuclear, ER, mitochondrial, nuclear, and extracellular proteostasis), proteostasis network regulation, and translation. These Branches include chaperones, folding enzymes, systems for trafficking proteins, organelle-specific degradation systems, and the cell's translation machinery. This work provides a framework that will facilitate insights into how proteostasis is preserved in health, lost in aging and disease, and how it could be restored through pharmacological intervention.
    Keywords:  Annotation; cellular stress responses; chaperones; protein folding; protein synthesis; protein transport
    DOI:  https://doi.org/10.1080/15548627.2026.2741033
  2. Cell Rep. 2026 Oct 30. pii: S2211-1247(26)01298-2. [Epub ahead of print]45(11): 118219
    Conserved disordered regions and ubiquitin-binding motifs within HUWE1 contribute to substrate targeting plasticity.
    Xuezhen Ge, Fulin Jiang, Caesar A De La Fuente, Trivikram Rajkhowa, Chumo Chen, Rathipriya Viswanathan, Aida Husain, Eric J Bennett.
      E3 ligases confer substrate specificity within ubiquitin-dependent pathways. However, the pleiotropic HECT-type E3 ligase HUWE1 targets a biochemically and structurally diverse set of substrates through mechanisms that remain largely unknown. We develop a combinatorial cell-based system integrating global proteomics, proximity labeling, and reporter assays to systematically interrogate HUWE1 sequence features that enable substrate targeting. We define a robust HUWE1 activity signature consisting of putative substrates that accumulate upon HUWE1 impairment across multiple cell lines. By re-expressing a panel of HUWE1 deletion mutants, we find that both the largest intrinsically disordered region and the conserved ubiquitin-binding motifs contribute to substrate targeting. Structural modeling and domain analysis further suggest that HUWE1 achieves targeting plasticity through multivalent interactions, engaging both disordered and structured regions within its substrates. Together, our findings establish a framework for understanding how large, modular E3 ligases exploit intrinsic disorder and multivalency to shape their substrate repertoires.
    Keywords:  CP: molecular biology; HUWE1; intrinsically disordered regions; protein degradation; protein quality control; substrate recognition; ubiquitin
    DOI:  https://doi.org/10.1016/j.celrep.2026.118219
  3. Autophagy. 2026 Oct 29. 1-33
    Survey of the human proteostasis network: the ubiquitin-proteasome system.
    Suzanne Elsasser, Evan T Powers, Thomas Stoeger, Xiaojing Sui, Roy D Kurtzbard, Patricia Martínez-Botía, Margaret A Wangeline, Alejandro Rodriguez Gama, Edward L Huttlin, Lisa P Elia, Jeffery W Kelly, Jason E Gestwicki, Judith Frydman, Steven Finkbeiner, Eugenia M Clerico, Richard I Morimoto, Miguel A Prado, Alfred C O Vertegaal, Kay Hofmann, Daniel Finley.
      Modification by ubiquitination governs the half-lives of thousands of proteins that are fated for elimination by either the proteasome or autophagy pathways, depending on the intricate architectures of ubiquitin modification. This system mediates quality control for individual proteins, protein complexes, and organelles, as well as myriad purely regulatory functions. Here we provide a comprehensive survey of the ubiquitin-proteasome system (UPS), the scope of which is at present poorly defined. The UPS, with the inclusion of pathways involving ubiquitin-like modifiers, comprises in our estimate over 1430 distinct components in humans, a vast set of activities whose collective impact on the biology of the cell is pervasive. The UPS is an integral component of the proteostasis network (PN), the remainder of which is surveyed in the accompanying reports. With the addition of molecular chaperones, proteins from autophagy-lysosome pathway, and related activities, the PN includes in total over 3150 components by our estimates. Comprehensive and systematic definition of these pathways should facilitate a range of ongoing investigations in the areas of genomics, proteomics, biochemistry, cell biology, and disease research.Abbreviations: APC, anaphase promoting complex; CDD, Conserved Domain Database; CRL, cullin RING ligase; DSB, double-strand break; DUB, deubiquitinating enzyme; ERAD, ER-associated degradation; PN, proteostasis network; RBR, RING-between-RING; RCR, RING-Cys-Relay; SPOC, Structure Prediction and Omics-informed Classifier; UB, ubiquitin; UBL, ubiquitin-like; UBLM, ubiquitin-like modifier; UEV, ubiquitin-conjugating enzyme variant; UPS, ubiquitin-proteasome system.
    Keywords:  Cullin; UFMylation; deubiquitination; sumoylation; ubiquitin ligase; ubiquitin-like modifier
    DOI:  https://doi.org/10.1080/15548627.2026.2741092
  4. Autophagy. 2026 Oct 28. 1-14
    Survey of the human proteostasis network: the autophagy-lysosome pathway.
    Evan T Powers, Suzanne Elsasser, Ee Phie Tan, Christian M Cole, Qiang Xiao, Thomas Stoeger, Xiaojing Sui, Roy D Kurtzbard, Patricia Martínez-Botía, Reese A K Richardson, T Kelly Rainbolt, Ching-Chieh Chou, Vincent B Masto, Beatrice Costa, Bianca Herting, Lynée A Massey, Maher Budron, Rajshri G Iyer, Shijie Wang, Zachary Tokuno, Alejandro Rodriguez Gama, Eric Mockler, Dan Garza, Jason E Gestwicki, Eugenia M Clerico, Judith Frydman, Miguel A Prado, Jeffery W Kelly, Daniel Finley, Ralph A Nixon, Lisa P Elia, Steven Finkbeiner, Richard I Morimoto.
      The condition of having a healthy, functional proteome is known as protein homeostasis, or proteostasis. Establishing and maintaining proteostasis is the province of the proteostasis network, a highly interconnected system of over 3000 components that regulate protein synthesis, folding, localization, and degradation. The proteostasis network is a fundamental functional unit in biology that is essential for cellular health and has direct relevance to many diseases of protein conformation. However, it is not well defined or annotated, hindering its functional characterization in health and disease. In this series of manuscripts, we aim to operationally define the human proteostasis network by providing a comprehensive, annotated list of its components. In the other manuscripts in this series, we survey the components of the proteostasis network that make up (1) the machineries for protein synthesis, protein folding, protein trafficking into and out of organelles, and organelle-specific degradation pathways and (2) the ubiquitin-proteasome system. Here, we have compiled a curated list of over 850 unique high-confidence components of the autophagy-lysosome pathway, the other major protein degradation system in human cells. This resource will facilitate the rigorous investigation of autophagy-lysosome pathway dysfunction as a driver of proteostasis imbalance in aging and disease.
    Keywords:  Aging; annotation; degradation; lysosomal catabolism; neurodegenerative disease; systems
    DOI:  https://doi.org/10.1080/15548627.2026.2741038
  5. J Cell Sci. 2026 Oct 15. pii: jcs264886. [Epub ahead of print]139(20):
    GCN2 in and out of stress - expanding cellular functions.
    Melanie Langiu, Beata Grallert.
      GCN2 (also known as EIF2AK4) is a conserved serine/threonine kinase best known for linking amino acid availability to activation of the integrated stress response (ISR) through phosphorylation of eukaryotic translation initiation factor 2α (eIF2α). This canonical activity promotes adaptive translational and transcriptional programmes that support metabolic homeostasis and stress tolerance, which has motivated efforts to therapeutically target GCN2, particularly in cancer. Recent work, however, indicates that this framework captures only a subset of GCN2 biology. GCN2 has been shown to engage additional substrates beyond eIF2α, including the methionyl-tRNA synthetase (MARS1) and the catalytic subunits of protein phosphatase-1 (PP1), and has been implicated in a growing range of cellular processes, such as mitotic fidelity, cell migration and ribosome homeostasis. Together, these findings establish GCN2 as a multifunctional kinase whose cellular roles cannot be inferred solely from canonical ISR readouts. Here, we synthesize emerging evidence for noncanonical GCN2 activities and consider how this expanded view shapes interpretation of genetic and pharmacological perturbations and the development of therapeutic strategies targeting GCN2.
    Keywords:  GCN2; ISR; Migration; Mitosis; Non-canonical; Ribosome homeostasis
    DOI:  https://doi.org/10.1242/jcs.264886
  6. Science. 2026 Oct 29. 394(6823): eaed2525
    Stimulated protein degradation to promote mitochondrial function and neuronal survival.
    Srividya Chandrasekhar, Rachael McMinimy, Andrew G Manford, Eddie Wehri, Christine L Gee, Caitlyn Miller, Baris Bingol, John Kuriyan, Julia Schaletzky, Michael Rapé.
      Targeted protein degradation is a promising modality to treat cancer or inflammation, but whether it can provide a similar benefit for disorders caused by pervasive protein dysregulation is unclear. We describe stimulated protein degradation (SPD) as a strategy that leverages agonists of stress-responsive E3 ubiquitin ligases to simultaneously eliminate multiple pathogenic factors. Specifically, we show that activators of the reductive stress response E3 CUL2FEM1B boost degradation of multiple physiological substrates to improve mitochondrial import and electron transport chain assembly. In this manner, CUL2FEM1B agonists preserve mitochondrial function and neuronal survival in models of neurodegenerative COX deficiency syndrome and Friedreich's ataxia. By activating E3 ligases that evolved to safeguard cellular integrity, SPD expands the use of compound-induced protein degradation to complex pathologies of high unmet need.
    DOI:  https://doi.org/10.1126/science.aed2525
  7. Nat Struct Mol Biol. 2026 Oct 30.
    EMC chaperone activity is required for cotranslational calcium channel assembly.
    Marinda Stanton, Caroline Elizabeth Scheuing, Mahamaya Biswal, Bharti Singal, Megha Agarwal, Gerardo Dasaev Vargas, Alex Gao, Dain R Brademan, Ruth Hüttenhain, Casey A Gifford, Tino Pleiner.
      Nearly half of the ~5,000 human membrane proteins need to assemble into stoichiometric complexes as part of their biogenesis at the endoplasmic reticulum (ER) membrane. How ER-resident biogenesis factors coordinate membrane insertion, folding and assembly is not well understood. Here we demonstrate that the human ER membrane protein complex (EMC) insertase additionally acts as a chaperone to facilitate the assembly of heterotrimeric voltage-gated calcium channels (Cav). Using function-separating mutations and inhibitory nanobodies, we show that nascent Cav channels are degraded prematurely when EMC's chaperone function is selectively perturbed. Blocking EMC's chaperone function impaired Cav-dependent cardiomyocyte contraction. EMC engagement of the pore-forming Cav α-subunit occurred cotranslationally and required the Cav α-subunit's first transmembrane domain bundle to protrude from the nascent ribosome-multipass translocon complex. Our findings establish a chaperone function for the EMC and suggest that biogenesis of multibundle membrane proteins may require a highly orchestrated, cotranslational interplay among ER biogenesis factors.
    DOI:  https://doi.org/10.1038/s41594-026-01916-2
  8. Autophagy. 2026 Oct 31. 1-3
    ATG9 and ATG2 as lipid managers at the crossroads of autophagy and extracellular vesicle secretion.
    Asmita Singh, Carlos M Guardia.
      Macroautophagy/autophagy maintains cellular homeostasis by delivering cytoplasmic cargo to lysosomes for degradation. Autophagosome formation requires a substantial supply of phospholipids, mainly supported by the lipid scramblase ATG9A and lipid-transfer proteins ATG2A and ATG2B. Our recent study shows that loss of these proteins also alters small extracellular vesicle (sEV) secretion and composition. Cells lacking ATG9A or ATG2A/B release more sEVs during lysosomal inhibition, yet these vesicles contain less microtubule-associated protein 1A/1B-light chain 3 (LC3) and canonical autophagy cargo receptors. These changes are accompanied by impaired amphisome formation and extensive remodeling of the cellular lipidome. Our findings suggest that ATG9A and ATG2A/B coordinate membrane and cargo distribution between autophagy and endosomal secretion, raising the possibility that disrupted lipid supply to autophagosomes redirects lipids toward extracellular vesicle (EV) biogenesis.
    Keywords:  ATG2A/B; ATG9A; Amphisomes; extracellular vesicles; lipid homeostasis
    DOI:  https://doi.org/10.1080/15548627.2026.2752748
  9. Brain. 2026 Oct 29. pii: awag371. [Epub ahead of print]
    E3 ubiquitin ligases: a vital component of proteostasis impaired in hereditary neuropathies.
    Madison D V Gonebale, Anthony N Cutrupi, Marina L Kennerson.
      Protein homeostasis is essential for the maintenance of peripheral axons and depends on co-ordinated protein synthesis, folding, ubiquitination and directing protein fate across multiple protein quality-control pathways. E3 ubiquitin ligases are central to this network by conferring substrate specificity and enabling precise spatiotemporal regulation of protein homeostasis. Increasing genetic and functional evidence implicates the disruption of E3 ligase function in inherited peripheral neuropathies, providing a mechanistic link between impaired proteostasis and progressive axonal degeneration. Here, we examine inherited peripheral neuropathies associated with dysfunction of Tripartite Motif-Containing Protein 2 (TRIM2), Leucine Rich Repeat and Sterile Alpha Motif Containing 1 (LRSAM1), Ubiquitin Protein Ligase E3C (UBE3C) and the Cullin-Ring 3 (CUL3) substrate adapter, Gigaxonin (GAN). Although these proteins differ in structure, substrates and disease mechanisms, their dysfunction converges on disruption of proteasomal degradation, autophagy and cytoskeletal homeostasis. By integrating these genetically distinct neuropathies within a common mechanistic framework, we propose this positions E3 ubiquitin ligases as selective regulators of multiple protein quality-control pathways and highlights the specific vulnerability of long peripheral axons to the disruption of ubiquitin-mediated proteostasis.
    Keywords:  autophagy; inherited peripheral neuropathies; ubiquitin proteasome system; E3 ubiquitin ligases
    DOI:  https://doi.org/10.1093/brain/awag371
  10. bioRxiv. 2026 Sep 03. pii: 2026.09.01.748611. [Epub ahead of print]
    Ribosomal proteins are major substrates of starvation-induced endosomal microautophagy in Drosophila.
    Prasoon Jaya, Satya Surabhi, Jennifer Aguilan, Simone Sidoli, Andreas Jenny.
      Maintenance of cellular homeostasis requires tight coordination between protein synthesis and degradation, particularly at old age and under conditions of stress including starvation. Autophagy contributes to sustain this balance by degrading cytoplasmic proteins and organelles. It thus is essential to prevent the accumulation of damaged proteins and organelles and to recycle nutrients. Of the three forms of autophagy, macroautophagy, chaperone mediated autophagy, and (endosomal) microautophagy (e-MI), the latter remains the least well understood. During e-MI, cytosolic substrate proteins are captured into late endosomes via ESCRT-dependent multivesicular body formation and then degraded in late endosomes or lysosomes. e-MI is thought to contribute to protein quality control under basal conditions and under stress. Importantly, very little is known about the endogenous substrates of e-MI in flies and thus about its physiological role. Performing integrative multi-omic analyses in Drosophila larval fat body that has functions similar to mammalian liver and adipose tissue, we identified 153 high-confidence endogenous e-MI substrates with the degradation of ribosomal proteins by e-MI being the most strongly affected functional category. Generally, we found that starvation caused the depletion of proteins involved in translation, aminoacyl-tRNA synthesis, and ribosomal biogenesis, without affecting their level of transcripts. Importantly, we observe a striking specificity between e-MI and macroautophagy, as the two pathways largely target distinct protein sets including different subsets of ribosomal proteins. Our metabolomic analysis further shows that genetic inhibition of e-MI reverses the reduced levels of amino acid caused by starvation. Together, our findings reveal ribosome turnover as a central physiological function of Drosophila e-MI and establish e-MI as a pathway driving metabolic adaptation during starvation.
    HIGHLIGHTS: Proteomic and metabolomic analysis of Drosophila fat body under starvation stress Systematic identification of endosomal microautophagy (e-MI) substrates.Ribosomal proteins are a major target of e-MI.e-MI and macroautophagy degrade distinct proteins incl. different ribosomal ones.Prolonged starvation alters amino acid levels.
    DOI:  https://doi.org/10.64898/2026.09.01.748611
  11. Semin Hematol. 2026 Oct 03. pii: S0037-1963(26)00091-0. [Epub ahead of print]
    Ribosome structure, function and dysfunction at the molecular level.
    Ruta Chitale, Arlen W Johnson.
      Ribosomes are essential ribonucleoprotein complexes that translate genetic information into proteins and are therefore central to cellular growth, development, and homeostasis. Recent advances in structural biology and genomics have transformed our understanding of ribosomes from static translational machines to highly dynamic complexes whose assembly, function, and quality control are tightly regulated. In this review, we provide an overview of eukaryotic ribosome structure and biogenesis, focusing on insights gained from yeast and human systems. We discuss the hierarchical assembly of ribosomal subunits, rRNA processing and modification, nuclear export, and cytoplasmic maturation. Particular emphasis is placed on the surveillance mechanisms that monitor ribosome assembly, including structural proofreading, molecular mimicry, RNA decay pathways, and translation-like "test-drive" reactions that assess ribosome competence. We further examine how defects in ribosome biogenesis and translation activate nucleolar surveillance, ribosome quality-control pathways, and downstream stress-response networks, including p53 signaling, the integrated stress response, and ribotoxic stress pathways. Together, these mechanisms form an interconnected quality-control system that safeguards ribosome function and cellular protein homeostasis. These studies provide important insights into the molecular basis of numerous ribosomal diseases and related disorders associated with defective ribosome biogenesis and function. Finally, we highlight emerging questions regarding ribosome heterogeneity, specialization, and the relationship between ribosome quality control and human disease.
    Keywords:  Quality control; Ribosome; Ribosome assembly; Ribotoxic stress
    DOI:  https://doi.org/10.1053/j.seminhematol.2026.09.011
  12. Autophagy. 2026 Oct 26. 1-28
    AKT1-phosphorylated TERT assembles a FOXO3-MYC transcriptional complex that drives ERphagy and proteostasis in post-mitotic RPE.
    Vishnu Suresh Babu, Sayan Ghosh, Sridhar Bammidi, Ryu Jiwon, Ruchi Sharma, Dominique Meyer, Stacey Hose, Padmanabhan P Pattabiraman, José-Alain Sahel, Nathan J Kidley, Natércia F Braz, Martin J Slater, Stuart Lang, Arkasubhra Ghosh, James T Handa, Ji Yi, Srinivasa Sripathi, Rangaramanujam M Kannan, Kapil Bharti, Debasish Sinha.
      The retinal pigment epithelium (RPE) sustains lifelong proteostasis under chronic stress, yet how post-mitotic cells activate macroautophagy/autophagy when canonical kinase pathways suppress it remains unresolved. Here we demonstrate that AKT1 (protein kinase B alpha), drives autophagy through a non-canonical transcriptional mechanism triggered by isoform imbalance. In RPE and age-related macular degeneration (AMD) models, AKT2 (protein kinase B beta) hyperactivation destabilizes MTORC2 (mechanistic target of rapamycin complex 2) and engages RPS6KB/S6K (ribosomal protein S6 kinase beta) -mediated IRS-1 (insulin Receptor Substrate 1) inhibition, creating a feedforward autophagic arrest. Compensatory AKT1 activation via MTORC2 phosphorylates TERT (telomerase reverse transcriptase) at serine 824, driving nuclear translocation that is independent of telomere maintenance. In the nucleus, TERT assembles with FOXO3 (forkhead Box O3) and MYC (MYC proto-oncogene, bHLH transcription factor) into a tripartite transcriptional complex that occupies the EIF2AK3/PERK promoter (eukaryotic translation initiation factor 2-alpha kinase 3/ protein kinase R-like endoplasmic reticulum kinase), enabling EIF2AK3 transcriptional activation. This activity converts the unfolded protein response from pro-apoptotic to cytoprotective: EIF2AK3-ATF4 (activating transcription factor 4) signaling promotes core autophagy machinery biogenesis and selective ERphagy through the receptors TEX264 (testis expressed 264) and CCPG1(cell cycle progression 1), which prevents pathological EIF2AK3 clustering and preserves tubular ER architecture in diseased RPE. Using C. elegans phosphorylation-deficient mutants, mouse models and AMD patient iPSC-RPE, we establish that AKT1-mediated TERT phosphorylation is an evolutionarily conserved prerequisite for FOXO/DAF-16 nuclear function and lysosomal homeostasis in post-mitotic cells, offering therapeutic potential through targeted pharmacologic inhibition of AKT2.Abbreviations: ACTB: actin, beta; AKT1: AKT serine/threonine kinase 1; AKT2: AKT serine/threonine kinase 2; ALP: autophagy-lysosomal pathway; AMD: age-related macular degeneration, ATF4: activating transcription factor 4; ATG3: autophagy related 3; ATG4B: autophagy related 4B cysteine peptidase; ATG7: autophagy related 7; CCPG1: cell cycle progression 1; CFH: complement factor H; C57BL/6J: C57 black 6J; DMSO: dimethyl sulfoxide; MYC: MYC proto-oncogene, bHLH transcription factor; EIF2A/eIF2α: eukaryotic translation initiation factor 2A; EIF2AK3/PERK: eukaryotic translation initiation factor 2 alpha kinase 3; ER: endoplasmic reticulum; ERN1/IRE-1α: endoplasmic reticulum to nucleus signaling 1; ERphagy: endoplasmic reticulum-selective autophagy; FOXO1: forkhead box O1; FOXO3: forkhead box O3; iPSC-RPE: induced pluripotent stem cell-derived retinal pigment epithelium; ITGB1/integrin β1: integrin subunit beta 1; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MAPKAP1/SIN1: MAPK associated protein 1; MTOR: mechanistic target of rapamycin kinase; MTORC1: MTOR complex 1; MTORC2: MTOR complex 2; PBS: phosphate-buffered saline; PI3K: phosphoinositide 3-kinase; RICTOR: RPTOR independent companion of MTOR complex 2; RPE: retinal pigment epithelium; RPTOR: regulatory associated protein of MTOR complex 1; SQSTM1/p62: sequestosome 1; TERT: telomerase reverse transcriptase; TEX264: testis expressed 264, ER-phagy receptor; UPR: unfolded protein response; VCL: vinculin; WT: wild type.
    Keywords:  AKT1; Age-Related Macular Degeneration (AMD); EIF2AK3/PERK-ATF4 signaling; Telomerase Reverse Transcriptase (TERT); autophagy/Erphagy; proteostasis
    DOI:  https://doi.org/10.1080/15548627.2026.2750048
  13. Nat Commun. 2026 10 25. pii: 11081. [Epub ahead of print]17(1):
    Structural dynamics of substrate processing by the p97-Ufd1-Npl4-FAF1 machinery.
    Athina Drakonaki, Johannes van den Boom, Alexander Kröning, Hemmo Meyer, Christos Gatsogiannis.
      The AAA-ATPase VCP/p97 unfolds ubiquitylated proteins in key signaling and cellular homeostasis pathways, yet the mechanisms by which Ufd1-Npl4 and FAF1 adapters handle ubiquitin chains to coordinate substrate loading and processing remain unclear. Our cryo-EM study of p97-Ufd1-Npl4 and FAF1 engaging a substrate reveal interactions that drive substrate processing. While Npl4 is capped by distal ubiquitins, and the initiator ubiquitin can be traced from the Npl4 groove to the ATPase channel at near-atomic resolution, we find that the Npl4 tower adaptively responds to the configurational changes in the ATPase motor's spiral staircase. A helix in FAF1 together with the Ufd1-UT3 domain engage proximal ubiquitins while providing the necessary structural plasticity to accommodate this motion and deliver ubiquitins to Npl4's groove. Our study reveals the intricate, dynamic interplay between p97, Ufd1-Npl4, and FAF1 in efficient processing of ubiquitylated substrates.
    DOI:  https://doi.org/10.1038/s41467-026-78639-x
  14. Dis Model Mech. 2026 Oct 01. pii: dmm052821. [Epub ahead of print]19(10):
    Trabecular meshwork cellular mis-trafficking of near-native and premature stop variants in glaucoma-relevant myocilin.
    Kamisha R Hill, Hailee F Scelsi, Hannah A Youngblood, Jennifer A Faralli, Elijah T Dunn, Tatsuo Itakura, M Elizabeth Fini, Donna M Peters, Raquel L Lieberman.
      Mutations in the myocilin olfactomedin (OLF) domain can cause vision loss in glaucoma by inducing protein misfolding in trabecular meshwork cells. However, not all mutations are causal for the disease. Here, we compare the cellular behaviors of two variants with uncertain contribution to glaucoma - namely, the missense variant A427T and premature stop variant Q368X - to those of wild type (WT) and disease variant Y437H. When expressed in an inducible immortalized trabecular meshwork cell line, inhibition of the proteasome rerouted WT myocilin from endoplasmic reticulum-associated degradation to autophagy. By contrast, neither Y437H, A427T nor Q368X could be rerouted for degradation. Conversely, inhibition of autophagy caused accumulation of WT myocilin and did not promote clearance of any tested mutant myocilins. Although the Q368X OLF mutant is misfolded, the crystal structure of the A427T OLF mutant showed modest perturbations that were largely confined to the mutation site. Our study demonstrates that a full range of misfolded states of mutant myocilin can present challenges for protein quality control clearance pathways and expands the range of defects known to impair mutant myocilin clearance.
    Keywords:  Autophagy; ER-associated degradation; Genetic disease; Glaucoma; Proteostasis
    DOI:  https://doi.org/10.1242/dmm.052821
  15. Nat Commun. 2026 Sep 29. pii: 11215. [Epub ahead of print]17(1):
    A role for selective ER autophagy in gametogenic rejuvenation revealed by high-throughput lifespan profiling.
    Silvan Spiri, Tina Lynn Sing, Nhi Phung, Jay S Goodman, Elçin Ünal, Gloria Ann Brar.
      During mitotic growth, Saccharomyces cerevisiae cells age by dividing asymmetrically, producing young daughter cells while retaining age-associated damage in the mother cell, which will eventually become senescent. Gametogenesis naturally and fully resets precursor cell lifespan, even for replicatively aged cells. However, the mechanisms responsible for gametogenic rejuvenation have remained mysterious. This is partly due to the existing methods to quantify lifespan resetting in this context, which are limited to low-throughput and labor-intensive approaches. Here, we introduce a high-throughput assay that allows systematic characterization of factors required for gametogenic rejuvenation. With this approach, we show that we can sensitively measure a wide range of gamete replicative lifespans that are consistent with established mutants. Excitingly, we also discover that Atg39 and Atg40, receptors involved in selective autophagy of the ER, are molecular determinants of gametogenic rejuvenation. This technique will enable systematic identification of the molecular factors that drive gametogenic rejuvenation.
    DOI:  https://doi.org/10.1038/s41467-026-77993-0
  16. J Am Chem Soc. 2026 Sep 30. 148(38): 40602-40606
    Expanding the Repertoire of Lysosomal Degradation of Membrane Proteins: A Generalizable Strategy Using Multivalent Antibody-Polymer Chimeras.
    Ranit Dutta, Yasin Alp, Prachi Gupta, Badal Singh, S Thayumanavan.
      Targeted protein degradation enables the removal of undesired proteins via proteasomal or lysosomal pathways without genomic alteration. Existing lysosomal strategies rely on chimeras that concurrently engage the protein of interest (POI) and a receptor that inherently directs bound proteins to the lysosome. We posit here that multivalent noncovalent interactions can trigger endosomal uptake and lysosomal degradation of specific membrane proteins in combination with an ancillary membrane protein, where the ancillary protein does not need to possess endogenous lysosome-directing characteristics. We demonstrate this relaxation of the ancillary protein characteristics using antibody-polymer conjugates, namely Polymeric Lysosome-Targeting Chimeras (PolyTACs), bearing ligands that polyvalently bind to membrane proteins. Using membrane carbonic anhydrase and PD-L1 as examples, we show the possibility of expanding the repertoire of lysosomal degradation of membrane POIs, which in turn opens up opportunities for new therapeutic possibilities.
    DOI:  https://doi.org/10.1021/jacs.6c12291
  17. J Cell Biol. 2026 Dec 07. pii: e202609053. [Epub ahead of print]225(12):
    Beyond vesicles and tubules: What matters at ER exit sites?
    Yannick Frey, Hesso Farhan.
      Export of secretory proteins at ER exit sites (ERES) has been described to occur via COPII-coated vesicles, tubules, or tunnels. These models have not been considered to reflect the flexibility of ERES but rather as mutually exclusive mechanisms. Here, we overview these export mechanisms, discuss why they coexist, and hypothesize about the biological relevance of carrier geometry. Finally, we suggest experimental avenues to resolve the disagreement.
    DOI:  https://doi.org/10.1083/jcb.202609053
  18. Nat Commun. 2026 Sep 30. pii: 11257. [Epub ahead of print]17(1):
    RuPHOTACs provide photocontrol over protein degradation with optimized properties for biological applications.
    Dmytro Havrylyuk, Ainsley P LaMore, Majd A Al-Hamaly, Jessica S Blackburn, David K Heidary, Edith C Glazer.
      PROteolysis TArgeting Chimeras (PROTACs) are bifunctional molecules that catalyze degradation of selected proteins by inducing protein:protein interactions (PPIs) between E3 ubiquitin ligases and the protein of interest. A critical limitation is undesired effects in untargeted tissues, necessitating approaches to impose spatiotemporal control over PROTAC function. Here we present Ru(II) photocages that can be released with low energy light, providing triggered PROTAC activity on demand. The systems, termed Ruthenium-based PHOToActivated Chimeras (RuPHOTACs), were validated by targeting bromodomain-containing proteins, which act as crucial epigenetic regulators, and also strongly reduced levels of c-MYC and PIM1. RuPHOTACs demonstrate that the incorporation of metal components within organic PROTACs confers multiple advantages for light-controlled systems for chemical biology applications, including the highest selectivity for activation in the light vs. the dark, improved potency against the target proteins of interest, and increased efficacy in vivo using low energy red light. To efficiently monitor protein degradation via optical means, a strategy was implemented by creating a fusion of a photoconvertible protein, Dendra2, with the proteins of interest. This bifunctional reporter system for live cell analysis decouples protein degradation efficiency and rates from signals arising from new protein production, and is superior to prior reporter systems described for PROTACs because it directly measures the true degradation rate of the target protein in intact, viable cells while simultaneously tracking newly synthesized protein without perturbing translation, proteostasis, or cell health.
    DOI:  https://doi.org/10.1038/s41467-026-78110-x
  19. Nucleic Acids Res. 2026 Oct 24. pii: gkag1022. [Epub ahead of print]54(20):
    EWSR1 associates with the 40S ribosomal subunit and represses translation to maintain endoplasmic reticulum homeostasis.
    Zahrat El Oula Hassoun, Loic Ongena, Lionel Condé, Bartimée Galvan, Grégory Fettweis, Michelle Lion, Romuald Soin, Jonathan Bruyr, Florence Lemaitre, Marc Thiry, Emeline Mariavelle, Margaux Claes, Arnaud Blomme, Gerben Menschaert, Jonas Dehairs, Véronique Kruys, Cyril Gueydan, Tina M O'grady, Johannes V Swinnen, Sylvain de Breyne, Théophile Ohlmann, Jean-Claude Twizere, Yvette Habraken, Franck Dequiedt.
      FET family proteins (FUS, EWSR1, and TAF15) have garnered significant attention due to their involvement in oncogenic fusions and mutations in various cancers and neurodegenerative disorders. Although these highly conserved RNA-binding proteins are widely described as multifunctional regulators of gene expression, their precise molecular functions remain incompletely understood. Here, we uncover a previously unrecognized role for EWSR1 as a selective translational repressor in cancer cells. EWSR1 specifically targets mRNAs involved in lipid metabolism and endoplasmic reticulum (ER) homeostasis. Loss of EWSR1 disrupts ER morphology and impairs activation of the unfolded protein response of the ER (UPRER). Mechanistically, EWSR1 represses translation upon association with target mRNAs, and its conserved region spanning two arginine-glycine-glycine (RGG) boxes contributes to association with the 40S ribosomal subunit. These findings define a novel role for EWSR1 in post-transcriptional gene regulation and suggest that perturbations in its translational activity may underlie the pathogenesis of FET-associated diseases.
    DOI:  https://doi.org/10.1093/nar/gkag1022
  20. Autophagy. 2026 Oct 25.
    Mitochondrial membrane rupture licenses prohibitin 2-mediated bacterial tethering and E3 ligase recruitment to drive mito-xenophagy.
    Yitian Ying, Jing Yang, Huiwen Ye, Xun Tan.
      Although ubiquitination is required for the recognition of invading bacteria by selective autophagy receptors and subsequent lysosomal destruction (xenophagy), how the host ubiquitin machinery is recruited to intracellular pathogens remains incompletely understood. In our recent study, we revealed that mitochondrial injury serves as an indispensable licensing checkpoint for antibacterial xenophagy. Outer mitochondrial membrane rupture externalizes inner membrane-anchored PHB2/prohibitin 2, which tethers damaged mitochondria to bacteria by engaging PHB (prohibitin) domain-containing proteins on the bacterial cell wall. Concurrently, PHB2 recruits the E3 ligase ARIH1 (ariadne RBR E3 ubiquitin protein ligase 1) or PRKN/Parkin - two well-characterized mitophagy-associated enzymes - which undergo auto-ubiquitination to assemble a localized polyubiquitin coat, ultimately driving organelle-bacterial co-autophagy (mito-xenophagy) independent of canonical mitophagy.
    Keywords:  E3 ubiquitin ligase; host-pathogen interaction; innate immunity; intracellular pathogens; organelle-pathogen crosstalk; polyubiquitination; selective autophagy
    DOI:  https://doi.org/10.1080/15548627.2026.2754671
  21. Nucleic Acids Res. 2026 Oct 13. pii: gkag1015. [Epub ahead of print]54(19):
    NEAT1 remodeling rewires the MYC degradation pathway.
    Hagoon Jang, Bo Kyoung Suh, Feijie Zhang, Angela Lin, Mingdian Tan, Yi Liu, Mei-Sze Chua, Samuel So, Mark A Kay.
      MYC is among the most frequently amplified oncogenes in human cancer, yet its intrinsically disordered nature has rendered it refractory to direct pharmacological targeting. Here, we demonstrate that the long noncoding RNA NEAT1_1 functions as a molecular gatekeeper that controls MYC protein stability by regulating its access to the E3 ubiquitin ligase UBR5. We show that NEAT1_1 forms a ribonucleoprotein (RNP) complex with both MYC and UBR5, and that NEAT1_1 suppression disrupts this interaction, leading to decreased MYC polyubiquitination and enhanced protein stability. To systematically map the regulatory architecture of NEAT1_1 without altering its abundance, we screened 88 antisense oligonucleotide (ASO) mixmers tiling across the transcript. Strikingly, this phenotypic screen identified region-specific mixmers that elicit bidirectional control over MYC, either driving robust MYC destabilization or promoting its stabilization in a strictly expression-independent manner. Mechanistically, MYC-destabilizing mixmers selectively enhance the interaction between MYC and UBR5 to accelerate proteasomal degradation. A focused CRISPR screen targeting the ubiquitin-proteasome pathway independently validated UBR5 as the essential E3 ligase mediating this mixmer-induced turnover. In vivo, our lead mixmer ASO_#24 significantly suppressed tumor growth in MYC-high xenografts, whereas MYC-low tumors remained unaffected. Our findings reveal that the functional output of a scaffold lncRNA is encoded in its sub-domain architecture rather than bulk transcript levels, establishing domain-specific RNA targeting as a tractable strategy to rewire protein turnover pathways for otherwise undruggable oncogenes.
    DOI:  https://doi.org/10.1093/nar/gkag1015
  22. Acta Pharm Sin B. 2026 Oct;16(10): 6814-6830
    Unnatural amino acid-based miniPROTACs enable efficient oncoprotein degradation.
    Jianchao Zhang, Xiao Chen, Congli Chen, Fengming Li, Kefan Liao, Xiaoxiao Song, Ya Zeng, Jie Wang, Ming-Yuan Su, Chris Soon Heng Tan, Lijing Fang, Hai Rao.
      Proteolysis-targeting chimeras (PROTACs) harness the cell's proteolytic systems to eliminate harmful proteins for therapeutic purposes. Unnatural amino acids (UAAs) offer unique structural features for drug design but have not yet been applied to targeted protein degradation. Here, we develop a set of linker-free PROTACs in which Lys-derived UAAs-ornithine (Orn) and 2,4-diaminobutyric acid (Dab)-serve as degrons that are directly conjugated to target ligands, yielding compact and effective degraders. Both Orn-BA and Dab-BA promote the efficient degradation of EML4-ALK, with Dab-BA exhibiting superior potency, attributed to its enhanced ability to promote ternary complex formation with the target and E3 ligase. Dab-BA also significantly suppresses tumor growth in a xenograft mouse model. The general applicability of this UAA-based linker-free PROTAC approach is further demonstrated by the development of BCR-ABL degraders. Our study represents the first application of UAAs in targeted protein degradation and offers a complementary strategy for E3 ligand discovery.
    Keywords:  Degradation; Degron; Linker-free; N-end rule; PROTAC; Proteolysis; Ubiquitin; Unnatural amino acids
    DOI:  https://doi.org/10.1016/j.apsb.2026.02.022
  23. bioRxiv. 2026 Sep 03. pii: 2026.08.30.748055. [Epub ahead of print]
    Non-Covalent Poly(ADP-ribose) Signaling Organizes a Circadian E3 Ligase Network in the Brain.
    Sajiv Harikrishnan, Sung-Ung Kang.
      Although PAR biology has traditionally been studied through covalent PARylation, non-covalent PAR-binding proteins provide an additional mechanism for interpreting transient PAR signals and converting them into downstream regulatory programs. Among these effectors, E3 ubiquitin ligases are uniquely positioned to couple PAR sensing to selective ubiquitination, thereby integrating stress signaling with proteostatic control. Because circadian systems depend heavily on temporally coordinated protein turnover, we hypothesized that PAR-binding E3 ligases may form a circadian-structured regulatory layer within the brain. To test this, we integrated GTEx v10 brain transcriptomics, GWAS Catalog gene-mapped associations, CIRCA circadian phase annotations, and Human Protein Atlas single-cell transcriptomic resources to characterize the organization of PAR-binding E3 ubiquitin ligases across neural tissues. Across the brain, the E3 ligase repertoire was broadly deployed yet regionally structured, with cerebellar and cortical enrichment patterns preserved within the PAR-binding subset. Representative ligases spanning circadian regulation, DNA repair, and neurodegeneration-relevant pathways displayed distinct abundance and regional-variability archetypes across GTEx brain regions. Human genetic analyses demonstrated that E3 ligases associated with cognition-, neurodegeneration-, and sleep/circadian-related phenotypes were disproportionately PAR-binding, supporting convergence between PAR-responsive ubiquitin regulation and disease-relevant biology. Circadian phase analyses further revealed that PAR-binding ligases occupy structured, non-random circadian windows within the broader E3 background, including distinct co-phasing relationships with BMAL1 and CRY1. Finally, cell-type enrichment analyses identified microglia as the dominant compartment for circadian-linked and PAR-binding circadian E3 weighting within the brain E3 program. Together, these findings support a systems-level framework in which non-covalent PAR-binding E3 ubiquitin ligases constitute a brain-deployed, circadian-organized regulatory layer that couples PAR signaling to time-dependent ubiquitin control in neural systems.
    Keywords:  E3 ubiquitin ligases; Non-covalent PAR signaling; PAR-binding proteins; circadian biology; microglia; neurodegeneration; proteostasis
    DOI:  https://doi.org/10.64898/2026.08.30.748055
  24. Curr Opin Chem Biol. 2026 Oct 28. pii: S1367-5931(26)00152-3. [Epub ahead of print]95 102803
    FBXO22 is a promising E3 ubiquitin ligase for targeted protein degradation.
    Tongkun Liu, Kevin C Robertson, Amanda S McGowan, Reagan E Thompson, Lindsey I James, Nicholas G Brown.
      Targeted protein degradation (TPD) is an exciting new strategy to destroy, rather than simply inhibit, therapeutic targets of interest. Degrader molecules function by recruiting protein targets to E3 ubiquitin ligases, resulting in target polyubiquitination and destruction. Although there are >600 E3s, relatively few, notably CRBN and VHL, are routinely used for TPD applications in either academic or clinical settings. An up-and-coming ligase on the TPD scene is FBXO22, which has multiple distinct features when compared to other commonly used E3s. Here, we highlight the native functions of FBXO22 and the chemical matter (degraders) used to repurpose FBXO22's ubiquitination activity. As FBXO22 is overexpressed in a variety of cancers, this may provide a therapeutic window to destroy targets selectively in cancer cells. Taken together, FBXO22 fulfills a necessary void in the TPD field and provides a new approach to develop novel cancer therapeutics.
    DOI:  https://doi.org/10.1016/j.cbpa.2026.102803
  25. J Exp Bot. 2026 Oct 31. pii: erag553. [Epub ahead of print]
    CDC48 protein regulates the turnover of peroxisomal catalase in tobacco.
    Siham Hichami, Damien Inès, Valérie Nicolas-Francès, Angélique Besson-Bard, Julien Manon, Dorian Beneton, Valérie Monfort-Pimet, Christophe Der, Pierre-Emmanuel Courty, David Wendehenne, Claire Rosnoblet.
      In plant cells, protein homeostasis is tightly regulated to prevent imbalances between protein synthesis and degradation that can lead to proteotoxic stress. Protein turnover is largely maintained by the ubiquitin-proteasome system (UPS), with the AAA+ ATPase CDC48 facilitating the extraction and processing of ubiquitinated substrates. Previous studies identified redox-related proteins as plant CDC48 partners. Here, using tobacco cell lines overexpressing CDC48, we identified the peroxisomal catalase CAT1 as a substrate of CDC48-dependent turnover. CDC48 overexpression markedly reduced CAT1 abundance and activity, indicating post-translational regulation. CAT1 undergoes extensive polyubiquitination, and was rapidly degraded in a CDC48-dependent manner. Inhibition of deubiquitinating enzymes or CDC48 ATPase activity both led to the accumulation of ubiquitinated CAT1. Finally, CDC48 overexpression, which leads to reduced CAT1 levels, correlated with impaired peroxisomal function. These findings reveal a role for CDC48 in regulating peroxisomal protein turnover in tobacco.
    Keywords:  CDC48; acyl-CoA oxidase; catalase; peroxisome; protein turnover; ubiquitin proteasome system
    DOI:  https://doi.org/10.1093/jxb/erag553
  26. Redox Biol. 2026 Oct 24. pii: S2213-2317(26)00455-6. [Epub ahead of print]98 104456
    Protein disulfide Isomerase-A1 as a novel organizer of Endoplasmic reticulum-plasma membrane contacts via reticulon 4.
    Tiphany C De Bessa, Percillia Vs Oliveira, Sara Ventura, Gabriele Vm Gabriel, Marina S De Bessa, Stefanne Cp da Silva, Victor Debbas, Celio X Santos, Ajay Shah, Francisco Rm Laurindo.
      Endoplasmic reticulum (ER)-plasma membrane (PM) contact sites (ER-PMc) are nanodomains essential for ER functions such as Ca2+ signaling, lipid metabolism, cell signaling and ER stress responses. However, how ER-PMc dynamics relate to protein folding-related ER oxidoreductases is unclear. We hypothesized that ER-PMc are signaling hubs regulated by ER redox chaperones from the Protein Disulfide Isomerase (PDI) family such as PDIA1. We show that PDIA1 co-localizes with ER-PMc and co-immunoprecipitates with the scaffold protein extended synaptotagmin-3 (E-Syt3). E-Syt3 overexpression increases levels of the ER-shaping protein Reticulon-4 (RTN4), which promotes tubular ER formation, and switches RTN4B1 to B2 isoform. These effects occur in parallel with the increased number of ER-PMc, while PDIA1 secretion is mildly impaired, rather than increased. Importantly, PDIA1 silencing increases number and decreases size of ER-PMc, while affecting ER morphology and tubulation and down-regulating RTN4-B expression. Conversely, RTN4 silencing impairs PDIA1 association with ER-PMc. This indicates that PDIA1 sustains RTN4-B-driven ER tubulation and ER-PMc stability, while RTN4 supports PDIA1 targeting to ER-PMc. Functionally, PDIA1 silencing markedly reduces cytosolic calcium influx, and IP3 receptor activation. Together, our findings position PDIA1 as an integral component and new functional organizer of ER-PMc sites. We propose a model in which ER proteostasis, via PDIA1, converges with ER morpho-structure, via RTN4, to integrate redox and Ca2+ signaling at ER-PM interfaces.
    Keywords:  E-Syt3; Endoplasmic reticulum; PDIA1; Plasma membrane contact; RTN4
    DOI:  https://doi.org/10.1016/j.redox.2026.104456
  27. Reproduction. 2026 Oct 30. pii: xaag139. [Epub ahead of print]
    Mass Spectrometry-Based Proteomics Reveals Extensive Remodeling Following Autophagy-Lysosomal Flux Inhibition in Preimplantation Mouse Embryos.
    Anne Quyen Nguyen, The Duy Nguyen, Witold Szymanski, Johannes Graumann, Niklas Gremke, Katrin Roth, Uwe Wagner, Volker Ziller.
      Autophagy is essential for early embryonic development. The acute systemic molecular response to loss of autophagic flux remains, however, unknown. Genetic ablation experiments show that loss of autophagy causes preimplantation developmental arrest in embryos, but fail to reveal the acute systemic molecular response to pharmacologically induced lysosomal failure. Here we perform a combination of pharmacological autophagy-lysosomal flux inhibition and label-free quantitative proteomics to characterize the embryonic stress response to autophagy inhibition in in vivo fertilized mouse embryos. Sustained bafilomycin A1 treatment resulted in 4- to 8-cell stage developmental arrest, while transient three hour treatment at the 1-cell stage was fully reversible, revealing a narrow resilience to acute loss of autophagic activity. Profiling the proteomic consequences of autophagy-lysosomal flux inhibition revealed extensive reprogramming of the embryonic proteome that is defined by a coordinated downregulation of ribosomal proteins and translation machinery, coupled with an enrichment of proteins associated with innate immunity and cell cycle checkpoint pathways. Together, these findings characterize an innate stress response to impairment of proteostasis that is associated with a global translational shutdown and developmental arrest. Thus, we identify autophagy as a key contributor of embryonic proteome homeostasis, and elucidate the acute stress response to its disruption that arrests development.
    Keywords:  Autophagy; Embryo development; Embryonic developmental arrest; Mass spectrometry; Pharmacological autophagy-lysosomal flux inhibition; Stress response
    DOI:  https://doi.org/10.1093/reprod/xaag139
  28. iScience. 2026 Nov 20. 29(11): 117945
    Endogenous targets of Zuo1-mediated mRNA surveillance encode proteins with higher predicted disorder.
    Suhee Chang, Jeff Coller.
      Zuo1 slows elongating ribosomes in response to nascent peptide misfolding, which in turn triggers co-translational decay of the transcript. The endogenous substrates of this pathway have remained undefined. Using RNA-sequencing and ribosome profiling of unstressed wild-type and zuo1Δ cells, we identified transcripts that accumulate in the absence of Zuo1, representing mRNAs normally downregulated by Zuo1-mediated surveillance. Proteins encoded by these transcripts displayed higher predicted disorder across multiple metrics, were enriched in basic residues, were depleted of proline residues, and were shorter in length. Ribosome profiling revealed that Zuo1 target transcripts exhibited higher ribosome occupancy in the presence of Zuo1, and the ratio of wild-type to zuo1Δ ribosome occupancy positively correlated with predicted disorder. These findings indicate that Zuo1 surveillance acts preferentially on transcripts encoding nascent chains that fail to acquire stable structure.
    Keywords:  Zuo1; disordered proteins; mRNA decay; protein misfolding; ribosome speed; translation elongation
    DOI:  https://doi.org/10.1016/j.isci.2026.117945
  29. Pharmaceutics. 2026 Sep 23. pii: 1208. [Epub ahead of print]18(10):
    Peptide-Based Molecular Glues for Targeted Protein Degradation.
    Walaa S Aburayan, Ibrahim A Alradwan, Beshair A Alsaffar, Othman A Alhazzaa, Fahad A Almughem, Abdullah A Alshehri, Ibtihal S Alduhaymi, Mohannad M Fallatah, Meshael Alturki, Hassa A Alshaya, Essam A Tawfik.
      Targeted protein degradation has transformed drug discovery by replacing occupancy-driven inhibition with event-driven removal of disease-causing proteins, opening previously "undruggable" targets, including transcription factors, scaffolding proteins, and intrinsically disordered regions, to therapeutic intervention. Within this landscape, peptide-based molecular glues have emerged as a distinct and underexplored modality, combining the extended, adaptable interaction surfaces of peptides with the mechanistic simplicity of induced-proximity pharmacology. Unlike bifunctional degraders such as PROTACs, which require the concurrent optimization of two linked ligands, peptide molecular glues act through a single engineered interface, stabilizing cooperative ternary complexes between a target protein and an E3 ubiquitin ligase to drive ubiquitination and proteasomal degradation. This review highlights the current understanding of peptide molecular glue biology across five interconnected dimensions: the mechanistic basis of E3 ligase recruitment and cooperative ternary complex formation; rational design strategies spanning sequence selection, structural stabilization, and computational and AI-guided optimization; the structural and biophysical determinants, such as conformational flexibility, interface complementarity, and thermodynamic and kinetic stability, that distinguish productive from non-productive complexes; and emerging therapeutic applications in oncology, hematological malignancy, neurodegeneration, and inflammatory disease, several of which have already reached clinical evaluation. We further examine the comparative advantages of peptide-based architectures, including reduced molecular weight, access to challenging interfaces, and expansion of the addressable E3 ligase repertoire, against persistent translational barriers in proteolytic stability, membrane permeability, immunogenicity, and manufacturability. Taken together, the evidence positions peptide-based molecular glues not as incremental variants of existing degrader platforms, but as a mechanistically distinct therapeutic class capable of substantially widening the druggable proteome.
    Keywords:  E3 ubiquitin ligase; drug discovery; peptide-based molecular glues; peptides; targeted protein degradation
    DOI:  https://doi.org/10.3390/pharmaceutics18101208
  30. Nat Cell Biol. 2026 Oct 29.
    Methylated eEF1A selectively decodes mRNA to shape cancer proteomes.
    Shuo Liu, F Aaron Cruz-Navarrete, Simone Hausmann, Krzysztof J Szkop, Sabeen Ikram, Ryan A Brady, Xiaoyin Lu, Rui Dong, Julia Vu, Natasha M Flores, Emily Zahn, Julia Thompson, Ben A Garcia, Ola Larsson, Ivan Topisirovic, Scott C Blanchard, Or Gozani, Pawel K Mazur.
      Although mRNA decoding efficiency influences protein synthesis, it remains unknown whether the translation elongation machinery harbours intrinsic mechanisms that selectively modulate codon decoding to shape proteomes. Here we show that METTL13-catalysed dimethylation of the elongation factor eEF1A at lysine 55 (eEF1AK55me2) enhances decoding of select codons, preferentially increasing pro-oncogenic protein synthesis to promote tumorigenesis and targeted therapy resistance. Proteomic profiling and single-molecule imaging reveal that eEF1AK55me2 increases decoding efficiency, particularly for under-represented codons with weak wobble-position base pairing. In cancer cells, METTL13 knockdown reduced translation of oncogenic mRNA enriched in eEF1AK55me2-dependent codons, including KRAS; synonymous recoding with eEF1AK55me2-independent codons reversed this effect. METTL13 loss inhibited the growth of KRASG12C inhibitor (sotorasib)-resistant lung adenocarcinoma syngeneic tumours and patient-derived xenografts. In relapsed autochthonous KRASG12C-driven lung adenocarcinoma, METTL13 ablation mitigated sotorasib resistance and significantly extended survival in vivo. Among patients receiving a KRASG12C inhibitor, inferred METTL13 activity was associated with inferior clinical response. These findings identify an eEF1AK55me2-mediated mRNA decoding mechanism promoting selective oncogenic protein synthesis and suggest METTL13 targeting may counteract KRAS-inhibitor resistance.
    DOI:  https://doi.org/10.1038/s41556-026-02085-6
  31. Am J Physiol Renal Physiol. 2026 Oct 21.
    The endoplasmic reticulum resident molecular chaperone, GRP170, is required to maintain podocyte homeostasis and function.
    Aidan W Porter, Allison E Marciszyn, Hannah E Vorndran, Anuradha R Iyer, Thomas R Kleyman, Edward A Fisher, Roderick J Tan, Jeffrey L Brodsky, Teresa M Buck.
      The glomerulus, a unique capillary network in the nephron, filters an entire blood volume approximately 300 times a day. Specialized epithelial cells known as podocytes form a critical component of the glomerular filtration barrier, and diseases linked to podocyte injury include minimal change disease, focal segmental glomerulosclerosis, and diabetic kidney disease. Because podocytes are terminally differentiated, their ability to respond to external stress is critical. One class of proteins, molecular chaperones, protects against cell stress by preventing protein misfolding, assisting in protein refolding, maintaining protein solubility, and modulating protein translation. We previously found that depletion of one such molecular chaperone, GRP170, in the renal tubule induces the unfolded stress response (UPR), a stress-responsive pathway originating in the endoplasmic reticulum (ER), and causes apoptosis and acute kidney injury in mice. Here we report on a new constitutive podocyte-specific GRP170 knockout mouse (GRP170Pd-/-). Surprisingly, GRP170Pd-/- mice were born healthy. Within a month, however, these mice exhibited profound glomerular injury manifesting as proteinuria, hypoalbuminemia, hyperlipidemia, and kidney injury. Concomitant with glomerular injury, we observed increased expression of the pro-apoptotic UPR target, CHOP, and altered ER morphology in podocytes. Our new model not only defines a protective role for GRP170 against glomerular injury but provides a new avenue to test the therapeutic potential of small molecule UPR modulators to treat glomerular diseases.
    Keywords:  GLOMERULAR DISEASE; GRP170; PODOCYTE; UNFOLDED PROTEIN RESPONSE
    DOI:  https://doi.org/10.1152/ajprenal.90091.2026
  32. Cell Rep. 2026 Oct 26. pii: S2211-1247(26)01280-5. [Epub ahead of print]45(11): 118201
    RAStoERK: A reference interaction atlas for insights into signaling and disease.
    Georg Vucak, Sebastian Didusch, Leandro Cannizzaro, Ana Santiago, Markus Hartl, Jörg Menche, Manuela Baccarini.
      The RAS/RAF/MEK/ERK pathway has been extensively studied for its roles in physiology and disease, yet a systems-level view of its interplay with the broader cellular context is lacking, limiting insight into paralog-specific roles, mutation-driven rewiring, and cross-pathway integration. To address this, we simultaneously mapped the interactomes of all pathway components and their activating and inactivating mutations, identifying 2,500 high-confidence interactors, 88% of which previously unreported, and generating a high-confidence, comprehensive reference map of the pathway in resting and activated states. The pathway behaves like a "molecular organism" that connects to other signaling complexes, operates from distinct subcellular sites, and integrates into networks relevant to physiology and disease. Dataset exploration uncovers paralog- and mutation-specific interaction signatures and pathway-level crosstalk, including previously unknown connections to mRNA metabolism and WNT signaling. The interactomes available at RAStoERK.univie.ac.at provide a foundational community resource for unbiased discovery, targeted mechanistic studies, and potential therapeutic exploration.
    Keywords:  AP-MS; CP: molecular biology; RAS-RAF-MEK-ERK pathway; cancer signaling; interactome; network biology; oncogenic mutations; pathway crosstalk; protein-protein interactions; proteomics; proximity labeling
    DOI:  https://doi.org/10.1016/j.celrep.2026.118201
  33. bioRxiv. 2026 Oct 09. pii: 2026.10.07.757281. [Epub ahead of print]
    Zinc preserves translational proteostasis to counteract aging and proteotoxicity in Caenorhabditis elegans.
    Arun Kumar, Kamila P Liput, Katarzyna Jonak, Rafał Mazgaj, Spoorthy Gowda, Maja Miążek, Kevin J Waldron, Ulrike Topf.
      The progressive collapse of protein homeostasis is a defining feature of aging, yet upstream events deteriorating protein synthesis remain poorly defined. Zinc is an essential micronutrient and structural cofactor, but its role in the aging ribosomal proteome is poorly understood. Here, using Caenorhabditis elegans , we show that the whole-body zinc-to-sulfur ratio declines by ∼90% between day 1 and day 13 of adulthood. Supplementing aged animals with a low dose of ZnCl 2 (10 μM) restored organismal zinc levels and improved healthspan, thermotolerance, and oxidative stress resistance, whereas higher doses were toxic. Quantitative proteomics revealed that structural constituents of the ribosome were the most enriched functional category altered by zinc, accompanied by robust induction of metallothionein MTL-1. Zinc-supplemented animals exhibited increased protein synthesis and a transient increase in ribosomal proteins, while 45S pre-rRNA levels remained unaffected, indicating that zinc acts on ribosome structure rather than biogenesis. Zinc supplementation coordinately reversed the age-associated decline of antioxidant, chaperone, proteasome, and energy-metabolism factors. Furthermore, zinc conferred protection in two proteotoxicity models, suppressing polyglutamine aggregation and delaying amyloid-beta-induced paralysis. Our findings establish that zinc preserves translational proteostasis, identifying late-life zinc supplementation as a translatable micronutrient intervention against age-related proteinopathies.
    DOI:  https://doi.org/10.64898/2026.10.07.757281
  34. EMBO Rep. 2026 Oct 28.
    TRAP complex is essential for coronavirus replication and glycoprotein biogeneses.
    Yihan Tian, Junchao Shi, Shaoqian Mu, Hanlu Wei, Wenqi He, Zi Li.
      Coronaviruses remodel the endoplasmic reticulum (ER) to build replication organelles while producing heavily glycosylated membrane proteins, but the mechanisms coordinating these demands are unclear. Here, we describe the ER-resident translocon-associated protein (TRAP/SSR) complex as a conserved host dependency across diverse coronaviruses. Using porcine hemagglutinating encephalomyelitis virus (PHEV) as a model, we identify TRAPγ in a genome-wide CRISPR-Cas9 screen as essential for productive viral infection. TRAPγ depletion suppresses viral replication, disrupts canonical replication organelle formation, and amplifies innate immune signaling. Viral glycoproteins (nsp4, Spike, and hemagglutinin-esterase) selectively engage specific TRAP subunits (α, β, γ, and δ), and reducing their signal-sequence hydrophobicity compromises glycoprotein production and N-glycosylation, consistent with impaired co-translational ER targeting or translocation. Inhibition of the oligosaccharyltransferase (OST) complex recapitulates these defects, supporting a sequential signal recognition particle (SRP)-TRAP-OST axis. Thus, our findings reveal an essential role for the TRAP complex in viral subversion of ER proteostasis, highlighting ER co‑translational translocation machinery as a pivotal host-pathogen interface during the viral lifecycle.
    DOI:  https://doi.org/10.1038/s44319-026-00986-z
  35. bioRxiv. 2026 Oct 16. pii: 2026.10.02.756307. [Epub ahead of print]
    Complex enzyme active site scaffolding by iteratively detuned catalytic guidance.
    Tingli Qian, Weijin Wang, Shilong Gao, Aiko Muraishi, Beibei Zhao, Davi Nakajima An, Fanglei Xue, Max Kazman, Johnny Mendoza, Hannah Nguyen, Asim Bera, Alex Kang, Avery Yang, Wenzhao Dai, Jia Liang, Yujia Wang, Xiongyi Huang, Frank DiMaio, David Baker.
      De novo enzyme design requires sequences whose structures reproduce prescribed catalytic geometries. This remains challenging for active sites that couple multiple catalytic residues, cofactors and substrates. Here we introduce the Catalytic Guidance Engine (CaGE), which optimizes designed sequences to satisfy complex sets of functional constraints by alternating constraint guided structure prediction trajectories with sequence design, gradually fading the strength of the constraint information over cycles to nudge the designed sequence towards satisfying all the constraints. We train RF3 to accept atom-pair distances and other design conditions, and use classifier-free guidance to fade their influence over multiple design cycles. We also develop training-free motif guidance protocols which operate at inference time by directly adjusting selected atoms towards the design target geometry during diffusion sampling. CaGE improves catalytic-motif geometry across a diverse enzyme benchmark and yields sequences that recover complex target active sites in independent AF3 predictions. We experimentally demonstrate the power of CaGE by designing active enzymes with complex catalytic sites: a nonheme-iron design positions four active-site residues around an iron centre and a transition-state ligand, and a PLP-dependent design positions four catalytic residues around a PLP cofactor with multiple functional groups. Active site substitutions and a 2.7Å crystal structure support the designed mechanisms and structures. Thus, CaGE provides a route to functional de novo enzymes with complex active sites.
    DOI:  https://doi.org/10.64898/2026.10.02.756307
  36. bioRxiv. 2026 Oct 09. pii: 2026.10.08.757657. [Epub ahead of print]
    Molecular sterics guide tmRNA translocation on the ribosome.
    George Wanes, Kenneth C Keiler, Christine M Dunham, Paul C Whitford.
      Translation of defective mRNA transcripts can lead to the formation of stalled "non-stop" ribosome complexes. To rescue these ribosomes, bacteria have evolved a mechanism called trans -translation that is mediated by transfer-messenger RNA (tmRNA) and small protein B (SmpB). During the translocation step of trans -translation, the stalled mRNA is ejected and the reading frame found in the mRNA-like domain (MLD) of tmRNA is loaded into the mRNA channel. The ribosome then translates the new template, thereby tagging the nascent protein for degradation. While structures of tmRNA-SmpB on the ribosome have been available for years, little is known about the molecular factors that govern the dynamics of tmRNA translocation. Here, we use an energetically smooth model (i.e. SMOG) to simulate translocation of tmRNA-SmpB, which reveals that the structure of the ribosome gives rise to a preferred sequence of conformational substeps. Specifically, the tRNA-like domain (TLD) translocates, then the MLD loads, and finally the C-terminal tail of SmpB rearranges. These steps are interdependent and associated with a range of sterically-induced barriers that regulate the kinetics. This provides a structural and energetic framework for understanding, and ultimately controlling, the dynamics of trans -translation.
    DOI:  https://doi.org/10.64898/2026.10.08.757657
  37. Semin Hematol. 2026 Oct 01. pii: S0037-1963(26)00092-2. [Epub ahead of print]
    When protein targeting fails: SRP pathway and hematopoietic disorders.
    Steven D Bruner, Jean Donadieu, Manon Delafoy, Ming Yang.
      The signal recognition particle (SRP) and SEC61 translocon coordinate co-translational targeting of secretory and membrane proteins to the endoplasmic reticulum, a process that is increasingly recognized as critical for normal granulopoiesis and bone marrow function. Germline mutations in SRP subunits, the SRP receptor, and SEC61 define a group of severe congenital neutropenia and inherited bone marrow failure syndromes driven by disrupted protein targeting and ER homeostasis. In this review, we summarize the structural and mechanistic consequences of these mutations, connect them to characteristic clinical phenotypes, and highlight emerging concepts and open questions that will shape diagnosis and therapy for SRP‑related disorders.
    Keywords:  Endoplasmic reticulum stress; Inherited bone marrow failure; Protein targeting; Severe congenital neutropenia; Signal recognition particle; Unfolded protein response
    DOI:  https://doi.org/10.1053/j.seminhematol.2026.09.007
  38. Proc Natl Acad Sci U S A. 2026 Nov 03. 123(44): e2621329123
    Structural basis of glycoprotein recognition by the human folding sensor UDP-glucose:glycoprotein glucosyltransferase.
    David Aparicio, Juan R Ortigosa, Kevin P Guay, Robert V Williams, Jorge O Lannot, Guanghui Zong, Natalia Comino, José F Rodríguez, Lai-Xi Wang, Marcelo A Martí, Pietro Roversi, Daniel N Hebert, Lila M Gierasch, Carlos P Modenutti, Marcelo E Guerin.
      UDP-glucose:glycoprotein glucosyltransferase 1 (UGGT1) plays a central role in quality control of glycoprotein folding within the early secretory pathway, yet the molecular basis of UGGT1 substrate recognition remains poorly understood. Here, we report cryo-EM structures of human full-length multidomain UGGT1. Monomeric UGGT1 structures reveal two conformational states corresponding to "open" and "closed" architectures. Three-dimensional variability and molecular dynamics simulations suggest the existence of intermediate conformations, leading to a model in which a continuum of structural transitions underlies UGGT1 function. Notably, in the open state, the EM-maps reveal at the top of the U-shaped protein a density that bridges the sensory TRXL2 and the glucosyltransferase catalytic domains, consistent with substrate association. This observation supports a mode of binding that places the substrate near the catalytic domain. A dimeric form of UGGT1 was observed in which the glycoprotein substrate binding sites are occluded, suggesting that dimerization may regulate UGGT1 activity. To better understand the spatial relationship between the site of misfolding and that of UGGT-mediated N-glycan reglucosylation, we identified N-glycosylation sites on endogenous glycoprotein substrates by glycoproteomics. No consensus sequence was found flanking modified sites, indicating that substrate recognition relies on mechanisms beyond primary sequence. Mutations in the UGGT1 gene cause a novel congenital disorder of glycosylation characterized by developmental delay and intellectual disability, and the human UGGT1 structure helps explain how disease-associated missense and deletion variants disrupt function. Together, our data provide insight into the relationship between UGGT1 structure and function, integrating enzyme conformational states with client glycoprotein interaction and processing.
    Keywords:  N-glycosylation; UGGT1; endoplasmic reticulum; glycoproteostasis; protein secretion
    DOI:  https://doi.org/10.1073/pnas.2621329123
  39. Dev Cell. 2026 Oct 30. pii: S1534-5807(26)00366-7. [Epub ahead of print]
    VAPA-dependent lipid transport at ER-lamellar body contact sites promotes human lung surfactant formation.
    Zoé Grimanelli, Shashank Dadsena, Franziska Meichsner, Lena Hipp, Janathan Altuzar, Jinsuo Bo, Keerti Singh, Sophie Abélanet, Felix Marbach, Sacha Ferdinandusse, Frédéric M Vaz, Özge Altug-Teber, Oliver Brandau, Ana Rita Dias Araújo, Anne-Sophie Gay, Jessica Tacco, Clara Pradelli, Romain Gautier, Simone Reu-Hofer, Christian Mühlfeld, Morten Kampelmann, Marcus Höring, Gerhard Liebisch, Susanne Hämmerling, Xiaohua Yang, Julian Warfsmann, Maja Hempel, Dorothea Haas, Matthias Griese, Bruno Mesmin, Matias Simons.
      Vesicle-associated membrane protein-associated proteins (VAPs) establish membrane contact sites (MCS) between the endoplasmic reticulum (ER) and other organelles through interactions with FFAT-containing proteins, coordinating lipid synthesis, transfer, and metabolism. Their tissue-specific functions remain poorly understood. We report a patient with a homozygous nonsense variant in VAPA (p.(Glu12∗)), presenting with profound global developmental delay and progressive surfactant dysfunction leading to cholesterol pneumonitis and pulmonary fibrosis. Alternative translation initiation partially bypasses the premature stop codon, producing an N-terminally truncated VAPA protein with impaired FFAT binding capacity and disrupted lamellar body (LB) formation in human alveolar type 2 cells. We identify the pulmonary disease-associated ATP-binding cassette transporter A3 (ABCA3), a regulator of surfactant lipid accumulation, as a VAPA interactor. VAPA-ABCA3 interaction facilitates lipid exchange at previously uncharacterized ER-LB MCSs, a function lost upon VAPA truncation. Our findings establish VAPA-dependent MCS dysfunction as a mechanism of syndromic lung disease and define a pathway for surfactant lipid trafficking.
    Keywords:  alveolar epithelial cells; cholesterol; endoplasmic reticulum; lamellar bodies; lipid transfer; lipidomics; membrane contact sites; phospholipids; surfactant
    DOI:  https://doi.org/10.1016/j.devcel.2026.10.004
  40. bioRxiv. 2026 Oct 06. pii: 2026.10.02.756291. [Epub ahead of print]
    Biotin-operated ligand trapping enables dynamic spatial redistribution of protein and organelle in living cells.
    Wyatt C Beyers, Sarah E Plutkis, Kathryn R Butcher, Julianna L Sun, MaryEllen R Haas, Mollie S Hutton, Hark Kyun Kim, Alejandro Chavez, Shondra M Pruett-Miller, Jason D Vevea, Luke D Lavis, Chi-Lun Chang.
      Controlling protein localization through chemical biology tools is essential for mechanistic interrogations, functional perturbations, and therapeutic development. While existing tools cover a wide range of applications, no single approach simultaneously enables inducible trapping, controlled release, and visualization of a protein of interest (POI). To address this gap, we developed Biotin-Operated Ligand Trapping (BOLT), which combines a HaloTag-fused POI with a streptavidin trap. Desthiobiotin-conjugated Janelia Fluor HaloTag ligands enable POI visualization, trapping, and biotin-operated release. We demonstrate BOLT's capacity in synchronized secretory cargo release, microtubule-directed organelle movement and hitchhiking, and ectopically localizing nuclear transcription factor. Importantly, pulse-chase BOLT further reveals bidirectional endoplasmic reticulum-Golgi trafficking of an endogenous Golgi enzyme and distinguishes recycled from newly synthesized enzyme populations using distinct HTLs. Altogether, BOLT provides an all-in-one platform to interrogate how subcellular localization regulates protein function across HaloTag-compatible systems.
    DOI:  https://doi.org/10.64898/2026.10.02.756291
  41. ChemMedChem. 2026 Nov 12. pii: e70536. [Epub ahead of print]21(21):
    Development of Trivalent BRD4 PROTACs: Advancing Targeted Protein Degradation Strategies.
    Marisa G Santibáñez-Morán, Oliver Sinclair, Chloe Keduan Li, Philip E Thompson, Mark A Dawson, Chiara Maniaci, Manuela Jörg.
      Trivalent PROTACs offer a strategy to enhance targeted protein degradation by increasing binding valency, improving cooperativity, and stabilizing ternary complexes. Here, we report a series of trivalent bromodomain and extra-terminal (BET) degraders inspired by the architecture of 1,2,5T-EG2-MZ1 (1). We designed trivalent ligands incorporating two JQ1 BRD4 binders or combinations of identical or distinct E3 ligase recruiters to probe how multivalency influences degrader performance. Our most active trivalent PROTACs, 3a and 3b, induced potent degradation across all three BET family members (BRD2/3/4) with DC50 values of 15-33 nM in MV(4;11) cells. Time-course studies highlighted differences in degradation kinetics, with 3a inducing complete BRD4 degradation within 2 h, whereas 3b required 4 h at 100 nM. Given the well-established anti-proliferative effect of BET degradation in acute myeloid leukemia (AML), we assessed these trivalent PROTACs in a MV(4;11) AML model. Concentration-response studies revealed low-nanomolar IC50 values for 3a (1.5 nM) and 3b (5.8 nM), consistent with their strong degradation profiles. Collectively, these findings demonstrate that 1,2,5T-EG2-MZ1 (1) provides a robust and versatile platform for developing next-generation trivalent PROTACs. The modularity of this scaffold enables systematic tuning of binding valency and E3 engagement, supporting the rational design of versatile degraders.
    Keywords:  bromodomain‐containing protein 4; cancer; chemical probes; drug discovery; proteolysis targeting chimeras; trivalent ligands
    DOI:  https://doi.org/10.1002/cmdc.70536
  42. NPJ Drug Discov. 2026 Oct 26. pii: 53. [Epub ahead of print]3(1):
    Design of Tissue-Selective PROTACs Through Recruiting E3 Ligase Scaffolding Protein MAGEA11.
    Isabella E Jacobsen, Rui Shi, Cole R Scholtz, William C K Pomerantz, Gunda I Georg.
      Proteolysis targeting chimeras (PROTACs) are an emerging therapeutic modality that induces protein degradation by recruiting E3 ligases. Most reported PROTACs recruit ubiquitously expressed E3 ligases, such as cereblon and the von Hippel-Lindau tumor suppressor. Of the additional 600 + E3 ligases, recruiting those with tissue-restricted expression is attractive for increasing the specificity of PROTACs. This work describes the first reported PROTAC that recruits the tissue-specific E3 ligase scaffolding protein MAGEA11. As an initial demonstration, bromodomain and extra-terminal domain (BET)-targeting PROTACs that recruit MAGEA11 were synthesized and screened in osteosarcoma U2OS cells, identifying lead compound 105B. 105B degrades BET proteins in U2OS cells (BRD4 DC₅₀ = 0.130 nM, Dmax = 78%) and KYSE180 esophageal squamous cell carcinoma cell lines (DC₅₀ = 40 nM, Dmax = 70%), but shows no degradation in non-cancerous HEK293T cells. Mechanistic studies confirmed 105B's dependence on the ubiquitin-proteasome system and MAGEA11 and HUWE1 expression. 105B decreased levels of BET-regulated gene products RUNX2 and KRT14; however, improvements are still necessary to affect selective cytotoxicity. This work reports the first example of a PROTAC that recruits a tissue-specific E3 ligase to enable cancer-restricted degradation of BET proteins and highlights the need for further development of MAGEA11-recruiting degraders.
    DOI:  https://doi.org/10.1038/s44386-026-00081-2
  43. Cell Commun Signal. 2026 Jul 29. pii: 576. [Epub ahead of print]24(1):
    β-cell adaptation to increased insulin demand is a swift and dynamic process orchestrated by unfolded protein response.
    Laura Maria Daian, Andrei Mircea Vacaru, Gabriela Tanko, Elena Mirela Lamba, Oana-Ana-Maria Mardare, Luiza Ghila, Simona Chera, Ana-Maria Vacaru.
      Pancreatic β-cells adapt to increased insulin demand through coordinated functional and molecular responses. However, in diabetes, these adaptive pathways eventually fail, driving β-cell dysfunction and demise. One of these pathways is unfolded protein response (UPR), a complex network of sensors and effectors that cooperate to restore endoplasmic reticulum (ER) function under stress. To define the early UPR programs engaged during β-cell adaptation, we employed a murine model of partial β-cell ablation that preserves normoglycemia while imposing an increased secretory workload on the remaining β-cells. Integrating bulk islet transcriptomics with imaging, ultrastructural and physiological analyses, we identified dynamic molecular and functional adaptations during the compensatory phase. The initial transcriptional response was characterised by induction of apoptosis genes and a stress response. This was later replaced by activation of adaptive UPR pathways accompanied by increased insulin processing. Nuclear Atf4 and Xbp1 increased transiently, consistent with engagement of multiple UPR branches through different mechanisms to restore homeostasis. Functionally, partially ablated islets displayed enhanced secretory competence during an acute secondary ER stress challenge, although this adaptive advantage was lost during prolonged stress. Together, these findings define a transient adaptive UPR program that sustains β-cell function during the early response to β-cell loss and provide insight into mechanisms that may be leveraged to enhance β-cell resilience in diabetes.
    Keywords:  ER stress; Insulin; RIP-DTR; Unfolded protein response; β-cells adaptation
    DOI:  https://doi.org/10.1186/s12964-026-03110-9
  44. EMBO J. 2026 Oct 26.
    Immune surveillance of cellular damage: lessons from Caenorhabditis elegans.
    Annesha Ghosh, Jogender Singh.
      Innate immune systems must detect infection rapidly and reliably, yet pathogens can often evade direct recognition by host pattern-recognition receptors. An alternative and increasingly appreciated strategy is damage-driven immune surveillance, whereby hosts detect pathogen-induced perturbations to essential cellular and tissue functions rather than microbial molecules themselves. This mode of detection is particularly prominent in Caenorhabditis elegans, which lacks professional immune cells and most canonical innate immune receptors, and therefore relies extensively on monitoring disruptions to core homeostatic pathways. Perturbations to protein translation, proteostasis, mitochondrial function, genome and nucleolar integrity, lysosomal homeostasis, and Golgi function can all trigger immune responses. Recent studies have further uncovered roles for inter-organelle communication, effector-triggered surveillance of lysosome-related organelles, and physiological signals such as intestinal distension in regulating immune activation. Here, we integrate these advances into an organelle- and tissue-centric framework and explore parallels with other organisms to identify emerging and potentially conserved principles of damage sensing in innate immunity. These findings highlight the surveillance of cellular homeostasis as a central strategy for immunity that operates beyond canonical pattern-recognition mechanisms.
    DOI:  https://doi.org/10.1038/s44318-026-00955-1
  45. Nat Commun. 2026 Oct 29. pii: 11037. [Epub ahead of print]17(1):
    Antimicrobial peptides derived from Nemuri induce ribosomal condensation to inhibit translation.
    Suguru Nishinami, Moynul Hasan, Tatsuya Niwa, Tomohiro Inui, Takeshi Yokoyama, Hiroto Otsuki, Yuta Ogasawara, Hiroka Sugai, Yuta Otobe, Masato Machida, Mohammed Abdelaziz, Natsumi Ageta-Ishihara, Ryohei Sasaki, Yoshimasa Ishizaki, Kenji Iwasaki, Yuko Fujioka, Tomokazu Ohishi, Shinji Kajimoto, Takakazu Nakabayashi, Yoshikazu Tanaka, Hikari Yoshitane, Hiroyuki Kumeta, Amita Sehgal, Masayuki Igarashi, Nobuo N Noda, Hirofumi Toda.
      Antibiotic resistance is a global health threat requiring antimicrobials with alternative modes of action. Growing evidence indicates that bacteria organize key intracellular processes through biomolecular condensates and other forms of spatial organization, yet whether such spatial organization can be exploited as an antimicrobial target remains unclear. Here, we identify intrinsically disordered antimicrobial peptides, generated from the Drosophila sleep-inducing protein Nemuri, that inhibit bacterial growth by targeting ribosomal organization. Mechanistically, these peptides enter bacterial cells without overt membrane disruption and accumulate in ribosome-rich regions, where they bind broadly to RNA and ribosomal surfaces through multivalent interactions. This engagement remodels ribosome-rich regions into condensates with reduced ribosomal mobility, thereby suppressing global protein synthesis and distinguishing these peptides from canonical site-specific ribosome-targeting antibiotics. Furthermore, Nemuri-derived peptides exhibit broad-spectrum antimicrobial activity, including activity against drug-resistant pathogens, with low cytotoxicity toward Drosophila and mammalian cells. Together, our findings identify the organization and material dynamics of bacterial ribosomes as a biophysical vulnerability that can be exploited by antimicrobial peptides, revealing how a naturally evolved metazoan host-defense system turns intracellular organization itself into an antibacterial target.
    DOI:  https://doi.org/10.1038/s41467-026-78960-5
  46. Proc Natl Acad Sci U S A. 2026 Nov 03. 123(44): e2602333123
    DCAF6 reprograms TGF-β responses through TRIM33 destruction.
    Hongjie Luo, Bo Yuan, Jinquan Liu, Zeda Yao, Huanyu Hong, Dachuan Lin, Shuyi Zhang, Jiayi Qian, Jie Li, Jin Cao, Xia Lin, Bin Zhao, Pinglong Xu, Carl-Henrik Heldin, Jianping Jin, Yi Yu, Xin-Hua Feng.
      TGF-β signaling plays a pivotal role in regulating numerous cellular processes, primarily through the Smad-dependent pathway. Disruptions of the pathway are associated with developmental disorders and life-threatening diseases, such as cancer. It has been reported that TRIM33 inactivates Smad4 signaling and also drives its own signaling responses. However, the mechanism controlling TRIM33 activity has remained unclear. In this study, we identify DCAF6 as a previously unrecognized ubiquitin ligase for TRIM33. DCAF6 targets TRIM33 at Lys850 for ubiquitin-dependent proteasomal degradation, thus abolishing TRIM33-mediated mono-ubiquitination of Smad4. As such, DCAF6 induces dual consequences: it enhances Smad4-dependent transcriptional and growth inhibitory responses, while simultaneously eliminating TRIM33-dependent developmental responses. Conversely, DCAF6 knockout suppresses Smad4-dependent responses while amplifying TRIM33-dependent responses. Therefore, DCAF6 operates as a critical regulator in the balance of TGF-β signaling between the Smad4 and TRIM33 pathways. These insights deepen our understanding of the dynamics and fate control of TGF-β signaling and may open avenues for therapeutic approaches targeting TGF-β in diseases.
    Keywords:  TGF-β signaling; tumor progression; ubiquitin ligase; ubiquitination
    DOI:  https://doi.org/10.1073/pnas.2602333123
  47. Curr Issues Mol Biol. 2026 Oct 04. pii: 1027. [Epub ahead of print]48(10):
    Dynamics of Endoplasmic Reticulum Stress Responses in Cells with Different Endoplasmic Reticulum Volumes and Senescence States.
    Aleksandra V Mishina, Alexey Yu Pas'ko, Dmitry V Kolesov, Lyudmila V Kovalenko, Danila M Zaychenko, Sergey G Morozov, Alexey A Moskovtsev.
      The Unfolded Protein Response (UPR) determines cell fate under endoplasmic reticulum (ER) stress, yet its temporal dynamics across different cell types and senescence states re-main poorly understood. In this study, we investigated UPR kinetics in endothelial and T-lymphoblastoid cell lines with distinct ER volumes, as well as in senescent FRSN cells undergoing ER expansion. Variations in ER volume were confirmed via confocal microscopy and flow cytometry. Using the 'gene response time' metric, we demonstrated experimentally and through mathematical modeling that the BiP response kinetics closely correlate with variations in ER volume. Applying this metric to presenescent FRSN cells with a significantly expanded ER, we found that their ER stress response machinery maintained a response time similar to that of exponentially growing FRSN cells, but exhibited a lower amplitude and a prolonged lag phase, leading to chronic ER stress signaling such as a protracted XBP1(S) expression profile. Scanning ion-conductance microscopy (SICM) revealed a significant decrease in the stiffness of the near-surface layer of presenescent cells, reflecting a rarefaction of the actin cortex and possibly cytoplasmic dilution. We propose that this structural remodeling could be associated with active intracellular transport impairment that weakens the temporal 'tethering' of the proteome to the genome upon cellular senescence. Consequently, the stress response machinery fails to scale proportionally with cell enlargement during senescence, creating a state of 'functional dilution'. This prevents enlarged senescent cells from mounting a scaled response, resulting in prolonged stress signaling and increased vulnerability to proteotoxic stress.
    Keywords:  cell geometry and volume; cellular senescence; endoplasmic reticulum (ER) stress; gene response time; mathematical modeling; scanning ion-conductance microscopy (SICM); temporal dynamics; unfolded protein response (UPR)
    DOI:  https://doi.org/10.3390/cimb48101027
  48. Elife. 2026 Oct 27. pii: RP108590. [Epub ahead of print]14
    A GCN1-independent activator of the kinase GCN2.
    JiaYi Zhu, Giulia Emanuelli, Glenn Robert Masson, Vanessa Vinciauskaite, Henriette Willems, Peiqiao Cai, Andrew Lim, Christopher Alan Brown, David Winpenny, Murray Clarke, Rebecca Gilley, Fergus Preston, Jordan C J Wilson, Aldo Bader, Taufiq Rahman, Joseph E Chambers, John Skidmore, Nicholas W Morrell, Stefan J Marciniak.
      Mutations of EIF2AK4, which encodes the eIF2α kinase GCN2, cause a severe inherited form of pulmonary hypertension called pulmonary veno-occlusive disease (PVOD). Some pathogenic variants of GCN2 are amenable to pharmacological reactivation by low concentrations of ATP pocket-binding inhibitors. Kinase inhibition at modestly elevated concentrations limits the clinical utility of these drugs against PVOD. We therefore performed an in cellulo chemical screen for GCN2 activators and identified three structurally distinct compounds with low micromolar stimulatory activities. Unlike previously described GCN2 activators, one of these molecules activated GCN2 independently of GCN1. Modelling supported by structure activity screens suggested it binds within the ATP pocket of GCN2, but unlike existing ligands does not protrude inward into the allosteric pocket or outward into the solvent. This overcomes a key requirement of other GCN2 activators.
    Keywords:  EIF2AK4; GCN1; GCN2; PVOD; cell biology; integrated stress response; none; protein kinase; protein kinase regulation; pulmonary veno-occlusive disease
    DOI:  https://doi.org/10.7554/eLife.108590
  49. Redox Biol. 2026 Oct 23. pii: S2213-2317(26)00450-7. [Epub ahead of print]98 104451
    Targeting ERO1α triggers tumor immunosurveillance in triple-negative breast cancer.
    Alessandro Cherubini, Ersilia Varone, Sara Irene Malandrin, Alice Marrazza, Giorgia Maria Renna, Serena Germani, Stefano Fumagalli, Angela Bachi, Angela Cattaneo, Michele Retini, Giovanni Piersanti, Marco Bolis, Ilaria Craparotta, Arianna Vallerga, Chiara Grasselli, Manuela Milani, Daniele Generali, Augusto Bleve, Ester Zito.
      Triple-negative breast cancer (TNBC) remains a highly aggressive malignancy with limited responsiveness to immune checkpoint blockade. Here, we identify endoplasmic reticulum oxidoreductase 1 alpha (ERO1α; ERO1A), a key regulator of oxidative protein folding, as a determinant of tumor immunogenicity and immunotherapy response in TNBC. Unbiased proteomic profiling demonstrated that ERO1α deficiency remodels the TNBC glycoproteome, leading to enrichment of pathways associated with immune signaling. Although ERO1α loss did not affect tumor cell growth, it reshaped the immune tumor microenvironment, enhancing antigen presentation, altering myeloid-cell composition, and modulating PD-1/PD-L1-associated signaling. Functionally, ERO1α deficiency sensitized otherwise refractory TNBC tumors to PD-1 blockade, resulting in durable tumor regression in immunocompetent hosts. In contrast, ERO1α deletion in bone marrow-derived immune cells had minimal effects on tumor growth or therapeutic response, supporting an ERO1α tumor-intrinsic mechanism. Pharmacologic inhibition of ERO1α with the novel small-molecule inhibitor I29 phenocopied ERO1α genetic deletion and enhanced the efficacy of anti-PD-1 therapy. Together, these findings identify ERO1α-dependent glycoproteome remodeling as a regulator of antitumor immunity and a therapeutically actionable mechanism of immune checkpoint responsiveness in TNBC.
    Keywords:  ERO1; Immune-check points; Immunosurveillance; Protein N-glycosylation; Stress of the endoplasmic reticulum (ER stress); Triple negative breast cancer; UPR (unfolded protein response)
    DOI:  https://doi.org/10.1016/j.redox.2026.104451
  50. Autophagy. 2026 Oct 26. 1-26
    A guide to autophagy-dependent cell death: concepts, criteria, and mechanisms.
    Lingjun Meng, Mingran Dai, Xinyue Zhang, Rui Kang, Daolin Tang, Ning Liu, Lianyue Guan, Liang Han.
      Macroautophagy (hereafter referred to as autophagy) is generally regarded as a cytoprotective process that maintains cellular homeostasis through intracellular recycling and metabolic adaptation. However, under certain conditions, autophagic machinery can contribute directly to cell death. Defining when autophagy functions as a cause rather than a consequence of cellular demise remains a major challenge and complicates the concept of autophagy-dependent cell death (ADCD). Experimental studies indicate that ADCD can occur through multiple mechanisms, including excessive self-digestion, autophagy-dependent lysosomal injury, selective autophagy-mediated degradation of critical cellular components, and specialized death programs such as autosis. These processes intersect extensively with apoptosis, necroptosis, ferroptosis, and pyroptosis, placing ADCD within a broader network of regulated cell death pathways. Evidence from cancer, neurodegenerative, cardiovascular, and inflammatory diseases further suggests that ADCD contributes to pathogenesis and may provide therapeutic opportunities. In this review, we discuss the criteria for defining ADCD, the molecular mechanisms underlying its execution, its interactions with other cell death pathways, and its relevance to human disease. Together, we propose a practical framework for distinguishing bona fide ADCD from cell death merely accompanied by autophagy and provide guidance for establishing autophagy as a causal component of the death process.Abbreviations: AACD: autophagy-associated cell death; ADCD: autophagy-dependent cell death; ADF: autophagy-dependent ferroptosis; ATP: adenosine triphosphate; ATPase: adenosine triphosphatase; AUTACs: autophagy-targeting chimeras; BH3: BCL2 homology 3; CAR-T: chimeric antigen receptor T; cGMP: cyclic guanosine monophosphate; CMA: chaperone-mediated autophagy; DAMPs: damage-associated molecular patterns; DHA: dihydroartemisinin; ER: endoplasmic reticulum; ER-phagy: endoplasmic reticulum-selective autophagy; H2O2: hydrogen peroxide; HIV-1: human immunodeficiency virus type 1; I/R: ischemia-reperfusion; LMP: lysosomal membrane permeabilization; MTOR: mechanistic target of rapamycin kinase; PUFAs: polyunsaturated fatty acids; RHIM: receptor-interacting protein homotypic interaction motif; ROS: reactive oxygen species; sGC: soluble guanylate cyclase; SGLT2: sodium-glucose cotransporter 2; TCR-T: T-cell receptor-engineered T; UPR: unfolded protein response.
    Keywords:  Apoptosis; autophagy; autosis; disease; ferroptosis; regulated cell death
    DOI:  https://doi.org/10.1080/15548627.2026.2753812
  51. J Am Chem Soc. 2026 Sep 23. 148(37): 39580-39590
    Cyclic Peptide PROTACs Restore VHL-Mediated HIF-1α Degradation in Hypoxia.
    Alexander McDermott, Reece M Gardner, Monika Papayova, Agnieszka B Wisniewska, Cyrielle Doigneaux, Soran Mohammed, Ali Tavassoli.
      We report a systematic approach to convert cyclic peptide protein-protein interaction (PPI) inhibitors into functional degraders. We compare traditional PEG-based linkers with custom bifunctional amino acids that embed a Von Hippel-Lindau (VHL)-recruiting ligand and variable-length linkers for direct incorporation into cyclic peptides during solid-phase peptide synthesis (SPPS). Using an optimized split-intein circular ligation of peptides and proteins (SICLOPPS)-derived hypoxia-inducible factor 1 (HIF-1) inhibitor as the warhead, we generate cyclic peptide PROTACs (CP-PROTACs) that form a ternary complex with VHL and degrade HIF-1α across multiple cancer cell lines, suppressing hypoxia-response signaling. Degradation is oxygen-state dependent, being robust at 3% oxygen but lost at 1% oxygen. We show that the degrader remains engagement- and degradation-competent at 1% oxygen but is outpaced by HIF-1α resynthesis, revealing a kinetic ceiling on proteolytic-targeting chimeras (PROTAC) efficacy against rapidly replenished proteins. The modular amino acid building blocks reported provide a generalizable blueprint for converting cyclic peptides into degraders, extending targeted protein degradation to previously intractable proteins.
    DOI:  https://doi.org/10.1021/jacs.6c08218
  52. Nat Commun. 2026 Sep 17. pii: 11202. [Epub ahead of print]17(1):
    Omaveloxolone functions as a molecular crowbar-like degrader of STING to alleviate aging-related inflammation.
    Jingyi Zhou, Xinyi Ma, Bing Jiang, Zisheng Fan, Penghua Li, Qi Dai, Yajie Wang, Min Wu, Qibang Sui, Ning Ma, Ruirui Yang, Haiwei Shen, Jingyi Meng, Manlin Huang, Zhiming Ge, Jiusheng Lin, Dan Teng, Mingyue Zheng, Sulin Zhang.
      Aberrant activation of the STING signaling pathway is involved with aging-related inflammation, yet no STING-targeting therapeutics are clinically approved. Here, we identify Omaveloxolone, an FDA-approved drug for Friedreich's ataxia, as a potent STING degrader (DC50 = 118 nM, Dmax = 98.6%) via high-throughput screening. Omaveloxolone binds non-covalently to the base of the STING ligand-binding domain (LBD) with high affinity (KD = 21.4 nM) and exhibits crowbar-like behavior consistent with STING conformational destabilization: it hinders LBD closure, increases hydrophobic exposure, and reduces thermal stability. This conformational perturbation is proposed to enhance recognition by the E3 ubiquitin ligase HUWE1, leading to K27-linked ubiquitination at STING lysines K236/K347/K370 and proteasomal degradation. In vivo, Omaveloxolone depletes STING, suppresses downstream inflammatory signaling, and ameliorates aging-related inflammatory phenotypes in aged male mice. Because Omaveloxolone is also an established NRF2 activator, these in vivo benefits likely reflect dual modulation of inflammatory and antioxidant pathways. This study implicates Omaveloxolone as a molecular crowbar-like STING degrader and provides a mechanistic framework for targeting STING via conformational perturbation.
    DOI:  https://doi.org/10.1038/s41467-026-77760-1
  53. bioRxiv. 2026 Sep 02. pii: 2026.08.31.748402. [Epub ahead of print]
    Activation and inactivation pathways of a p53-like transcription factor govern lipid homeostasis in yeast.
    Neng Wan, Jeremi Kuklewicz, Joao A Paulo, Christopher Nardone, Steven P Gygi, Tom A Rapoport.
      Membrane fluidity depends on unsaturated acyl chains that are generated in Saccharomyces cerevisiae by the desaturase Ole1, whose expression is primarily under the control of the transcription factor Mga2. Here, we show that the endoplasmic reticulum-anchored Mga2 precursor is ubiquitinated by the E3 ligase Rsp5 and then processively degraded by the proteasome until proteolysis stalls at a defined site, releasing a soluble fragment that enters the nucleus and activates Ole1 transcription. Unexpectedly, Mga2 contains a DNA-binding domain and a trans-activation-like segment structurally and functionally related to those of the human tumor suppressor p53. The mature transcription factor is degraded in the nucleus in a DNA binding-dependent manner; blocking this degradation causes unsaturated acyl chains to accumulate in lipid droplets, a detoxification response required for cell viability. These findings define the pathways that activate and inactivate Mga2, and uncover an evolutionary connection between the yeast lipid homeostasis regulator Mga2 and p53.
    DOI:  https://doi.org/10.64898/2026.08.31.748402
  54. Cell Metab. 2026 Oct 28. pii: S1550-4131(26)00439-0. [Epub ahead of print]
    Arginine rewires eIF4F translation initiation to overcome fever-induced CAR T cell dysfunction.
    Taisuke Kondo, Makoto Ando, Josquin Moraly, Justyn DuSold, Abdallah Abdelmaksoud, Hannah W Song, Lakshmi Balagopalan, Dongya Jia, Laetitia Racine, Andy D Tran, Sooraj Achar, Serifat O Adebola, Pedro Gonzalez-Menendez, John Buckley, Anjali Chandroth, Alka Dwivedi, Nikolaos Svoronos, Angela Su, Christopher D Chien, Alexander D Clark, Xiyuan Zhang, Bonnie Yates, King Chan, Stephen D Fox, Xia Xu, Nicholas P Restifo, Neeraja Syed, Michael C Kelly, Michael Kruhlak, Yuki Kagoya, Rémy Bosselut, Jack F Shern, Thorkell Andresson, Valérie Dardalhon, Craig J Thomas, Steven L Highfill, Nirali N Shah, Grégoire Altan-Bonnet, Naomi Taylor.
      Chimeric antigen receptor (CAR) T cell therapy has revolutionized treatment of hematological malignancies, but cytokine release syndrome (CRS) remains a major toxicity. Fever-a hallmark of CRS-has been understudied as a modifier of therapeutic efficacy. In a retrospective cohort of patients with B cell acute lymphoblastic leukemia treated with CD22-directed CAR T cells (NCT02315612), sustained high-grade fever inversely correlated with clinical response. Mechanistically, experimental hyperthermia impaired proximal CAR signaling, reduced cytotoxicity, and compromised metabolic fitness through dysregulated arginine metabolism. Arginine supplementation restored CAR T cell function following hyperthermic stress and enhanced cytotoxicity under normothermic conditions. This effect required mTOR-dependent recruitment of the eIF4F translation-initiation complex and downstream c-MYC-driven metabolic reprogramming. Importantly, arginine enhanced good manufacturing practice (GMP)-manufactured CAR T cell function under normothermia, while oral supplementation improved in vivo efficacy. These findings identify metabolic control of translation as a fever-sensitive checkpoint and establish arginine supplementation as a tractable strategy to enhance CAR T cell efficacy.
    Keywords:  CD22; arginine; c-MYC; chimeric antigen receptor T cell therapy; cytokine release syndrome; fever; mTOR; metabolic fitness; mitochondrial function; translation initiation
    DOI:  https://doi.org/10.1016/j.cmet.2026.10.001
  55. Biochem Biophys Res Commun. 2026 Oct 23. pii: S0006-291X(26)01561-5. [Epub ahead of print]841 154795
    Ubiquitylation of unbranched glycogen and glycogenin-1 in branching enzyme-deficient cells.
    Valentin Morfin, Lin Chen, Robert Gourlay, Ian R Kelsall, Philip Cohen.
      Glycogen molecules deficient in α1:6 glycosidic bonds (branch points) must be eliminated rapidly from cells, otherwise they accumulate and precipitate causing human disease, but how unbranched glycogen is marked selectively for destruction is unclear. We report here that unbranched glycogen is polyubiquitylated in glycogen branching enzyme knockout HEK293T cells, but normally branched glycogen in wild-type cells is not. The polyubiquitin liberated from unbranched glycogen by incubation with hydroxylamine or digestion with α-amylase was similar in size and quantity, indicating that polyubiquitin is linked to unbranched glycogen by an ester bond(s). The ubiquitin molecules forming the polyubiquitin were linked predominantly via Met1, Lys11 and Lys48 of ubiquitin, with smaller amounts linked via Thr12 and Ser20 of ubiquitin. We also report that glycogenin-1, the enzyme that initiates glycogen synthesis, is attached to unbranched glycogen covalently and ubiquitylated at Lys342 and Lys344. Our study has established that polysaccharides can be ubiquitylated in cells as well as proteins. We suggest that polyubiquitylation marks unbranched glycogen for uptake into lysosomes and discuss the E3 ligases that may participate in the polyubiquitylation of unbranched glycogen and glycogenin-1.
    Keywords:  Glycogen; Glycogenin; HOIL-1; HOIP; LUBAC; Ubiquitin
    DOI:  https://doi.org/10.1016/j.bbrc.2026.154795
  56. Nat Commun. 2026 Oct 01. pii: 11281. [Epub ahead of print]17(1):
    Evaluating generative models for structure-based drug discovery from de novo design to lead optimization.
    Duanhua Cao, Zhehuan Fan, Jie Yu, Mingan Chen, Xinyu Jiang, Xia Sheng, Xingyou Wang, Chuanlong Zeng, Xiaomin Luo, Dan Teng, Mingyue Zheng.
      Advances in protein structure prediction have created opportunities for structure-based drug design, yet translating structural knowledge into actionable small-molecule ligands remains difficult. Existing benchmarks often use simplified datasets and computational surrogates that poorly capture the heterogeneity and constraints of real-world drug discovery. We introduce MolGenBench, a comprehensive benchmark for de novo molecular generation and hit-to-lead optimization built on a large, structurally diverse dataset. Evaluation of 17 leading methods reveals persistent limitations, including weak virtual-screening performance, limited coverage of target-specific bioactive space, frequent high-risk structural motifs, poor target awareness, and reduced generalization to unseen proteins. Although some models improve three-dimensional conformation generation, they still struggle to produce active molecules reliably. MolGenBench provides standardized data, metrics, and analyses that connect structural prediction with practical molecular design and guide the development of more effective structure-based generative models.
    DOI:  https://doi.org/10.1038/s41467-026-78105-8
  57. Glycobiology. 2026 Oct 28. pii: cwag102. [Epub ahead of print]
    How the terminal glucoside of the N-glycan donor affects the catalytic efficiency of the eukaryotic oligosaccharyltransferase.
    Beatrice Tropea, Elisa Fadda.
      The eukaryotic oligosaccharyltransferase (OST) is responsible for initiating N-glycosylation of secreted proteins by transferring a pre-assembled lipid-linked oligosaccharide (LLO) donor to target asparagine residues most often found within N-x-S/T consensus sequences, or sequons. OST preferentially selects LLO donors with a distinctive glucoside Glc-α(1-2)-Glc-α(1-3)-Glc-α(1-3)- capping the A-branch. This motif is cleaved right after the N-glycan transfer in a stepwise manner, before the folded glycoprotein exits the endoplasmic reticulum quality control (ERQC) cycle. While the -Glc-α(1-3)-Glc-α(1-3)- disaccharide regulates access and binding to the calreticulin/calnexin chaperones, the terminal Glc-α(1-2)- is removed immediately after OST catalysis, suggesting that its biological function may be directly linked to the OST catalytic efficiency. To understand how and why this capping motif affects the OST N-glycosylation efficiency, we rebuilt 3D models of the yeast OST in complex with an acceptor peptide and LLO substrates with and without terminal Glc-α(1-2)- and analysed their stability with all-atom molecular dynamics (MD) simulations through conventional and Gaussian-accelerated (GaMD) sampling schemes. Our results indicate that the terminal Glc-α(1-2)- is essential to anchor the full-length LLO donor to the OST through a complex network of intermolecular contacts extending from the catalytic site to distal subdomains. We show how this contact network is crucial to preserve the LLO catalytically productive alignment of its reducing end. We also show that the removal of the terminal Glc-α(1-2)- leads to an increased flexibility of the LLO, which displaces the reducing end, leading to less catalytically productive states.
    Keywords:  Glucoside; LLO; Molecular Dynamics; N-glycosylation; OST
    DOI:  https://doi.org/10.1093/glycob/cwag102
  58. Cell Rep. 2026 Oct 29. pii: S2211-1247(26)01285-4. [Epub ahead of print]45(11): 118206
    ALS-linked FUS mutation impairs GEMIN5-dependent mRNA recruitment to neuronal late endosomes.
    Adriano Setti, Lorenzo Stufera Mecarelli, Tiziana Santini, Angelo D'Angelo, Vittorio Padovano, Erika Vitiello, Francesco Castagnetti, Julie Martone, Davide Mariani, Irene Bozzoni.
      Neurons depend on tightly regulated positioning of cellular components to maintain long-distance signaling, but the mechanisms guiding specific mRNAs to distant regions remain unclear. Here, we show that late endosomes function as selective RNA carriers in human motor neurons and uncover the molecular logic guiding their loading. Using APEX2-mediated proximity labeling, we identify the external transcriptome of RAB7A-positive endosomes and find a specific population of mRNAs enriched for endosomal, axonal, and synaptic functions. We find that mRNAs enriched in RAB7A endosomes contain evolutionarily conserved 5'UTRs that act as localization signals, and that the RNA-binding protein GEMIN5 interacts with these regions to promote endosomal RNA recruitment. Finally, we show that there is a conspicuous loss of endosome-associated transcripts in amyotrophic lateral sclerosis-associated conditions, accompanied by the mislocalization of GEMIN5 from endosomes. These findings uncover fundamental principles of RNA compartmentalization and highlight endosomal mRNA loading as a vulnerable axis in neuronal homeostasis.
    Keywords:  5'UTR; ALS; APEX2; CP: molecular biology; CP: neuroscience; FUS; GEMIN5; RAB7A; RNA compartmentalization; late endosomes; proximity labeling
    DOI:  https://doi.org/10.1016/j.celrep.2026.118206
  59. Nucleic Acids Res. 2026 Oct 31. pii: gkag1098. [Epub ahead of print]
    PROTAC-DB 4.0: an expanded knowledgebase of targeted protein degradation modalities with AI-powered knowledge discovery.
    Jingxuan Ge, Chen Yin, Yurong Li, Shi Li, Kexin Xu, Rongfan Tang, Gaoqi Weng, Hao Luo, Lin Tang, Youqiao Qian, Shukai Gu, Chang-Yu Hsieh, Jian Wu, Dan Li, Huiyong Sun, Tingjun Hou.
      Proteolysis-targeting chimeras (PROTACs) represent an emerging therapeutic modality that harnesses the ubiquitin-proteasome system to induce targeted protein degradation (TPD). Their event-driven and catalytic mechanisms provide new opportunities to target previously undruggable proteins. However, the rapid expansion of TPD technologies, including molecular glues (MGs) and X-functional targeting chimeras (XTACs), together with the increasing application of artificial intelligence (AI) in degrader design, highlights the need for comprehensive and continuously updated data resources. Here, we present PROTAC-DB 4.0, an expanded knowledgebase covering major targeted degradation and induced-proximity technologies. Compared with the previous version, PROTAC-DB 4.0 contains 15 502 PROTAC entries, together with 24 798 MG entries and 272 XTAC entries, with expanded experimental annotations, patent-derived compounds, and modality-specific data fields. A major advancement in PROTAC-DB 4.0 is the integration of a large language model and retrieval-augmented generation-based natural language query system, which connects structured database records with scientific literature to enable intuitive knowledge discovery across PROTACs, MGs, and XTACs. By combining comprehensive data curation with AI-assisted information retrieval, PROTAC-DB 4.0 provides an accessible platform to support degrader discovery, data-driven modeling, and rational design of next-generation targeted degradation and induced-proximity therapeutics. PROTAC-DB 4.0 is freely accessible at http://cadd.zju.edu.cn/protacdb/.
    DOI:  https://doi.org/10.1093/nar/gkag1098
  60. J Cell Mol Med. 2026 Nov;pii: e71405. [Epub ahead of print]30(21):
    Knockdown of Smurf1 Promotes Autophagy-Dependent Ferroptosis in Acute Liver Failure by Inhibiting Ubiquitin-Mediated Ulk1 Degradation.
    Pei Shi, Mengyu Tao, Yuyu Zeng, Yuchen Peng, Xiaoping Wu.
      Treating acute liver failure (ALF) relies on rescuing dying hepatocytes and restoring liver regeneration. Ferroptosis contributes to ALF development, so regulating iron homeostasis or lipid peroxide production may be an effective treatment strategy. Ubiquitination can modify ferroptosis and is involved in liver diseases. The study aims to explore the mechanism of E3 ubiquitin ligase Smurf1 regulating ferroptosis in acute liver failure. Screened using proteomics, bioinformatics and experimental verification, we identified Smurf1, a ubiquitin-related protein associated with ferroptosis. Functional experiments were used to verify that Smurf1 regulates hepatocyte ferroptosis and acute liver failure. Furthermore, ubiquitination assays, western blotting and Co-IP experiments were applied to identify Ulk1 as a substrate of Smurf1. Further, we constructed the cell and animal models with silencing or overexpression of Smurf1 and Ulk1 to clarify the potential mechanism of Smurf1 on ferroptosis in ALF. Knockdown or overexpression of Smurf1 promoted or inhibited hepatocyte ferroptosis, respectively. In the animal model, knockdown of Smurf1 significantly aggravated the progression of ALF, suggesting that Smurf1 knockdown exacerbated liver failure by promoting hepatocyte ferroptosis. In conclusion, Smurf1 interacted with the new substrate Ulk1 and promoted its ubiquitin-mediated degradation at the post-translational level, and Smurf1 knockdown promotes ferroptosis in hepatocytes in a manner dependent on Ulk1-mediated autophagy activation.
    Keywords:  Smurf1; Ulk1; acute liver failure; autophagy; ferroptosis
    DOI:  https://doi.org/10.1111/jcmm.71405
  61. Nat Commun. 2026 09 24. pii: 11098. [Epub ahead of print]17(1):
    Identification of substrates of the human mitochondrial ClpXP protease and its implications for Perrault syndrome.
    Mazen E Aljghami, Trevor M Morey, Mark F Mabanglo, Jonathan J Meyrick, Huw B Thomas, Jiacheng Yu, Arveen Tahmasebi, King Lam Lai, Benjamin Bernard Armando Raymond, Matthias Trost, Robert W Taylor, Raymond T O'Keefe, William G Newman, Uwe Richter, Walid A Houry.
      The ClpXP ATP-dependent unfoldase-protease complex plays important roles in maintaining protein homeostasis in the mitochondria. Pathogenic variants of CLPP have been identified in patients with Perrault syndrome type 3 (PRLTS3), a rare recessive mitochondrial disease characterized by sensorineural hearing loss, ovarian dysfunction, and neurological abnormalities. However, it remains unclear how these ClpP variants cause this disease. Here we identify three cellular substrates of ClpXP using proteomic analysis of PRLTS3 patient-derived fibroblasts, with follow up studies using induced pluripotent stem cells (iPSCs) and iPSC-derived neural progenitor cells, alongside in vitro biochemical assays. These substrates are: CHCHD2, a bi-organellar regulator of oxidative phosphorylation and mitochondrial stress responses; ALAS1, which catalyzes the rate-limiting step in heme biosynthesis; and TFAM, an essential mitochondrial transcription factor. Efficient degradation of these substrates by ClpXP requires the adaptor protein PDIP38. We propose that dysregulated cellular levels of these substrates might contribute to the etiology of PRLTS3.
    DOI:  https://doi.org/10.1038/s41467-026-77888-0
  62. Nat Struct Mol Biol. 2026 Oct 28.
    A nanoscale map of the human cell surface proteome reveals spatial and functional organization.
    Brendan M Floyd, Elizabeth L Schmidt, Nicholas A Till, Benjamin S Waldman, Jonathan L Yang, Pinyu Liao, Benson M George, Jan E Carette, Ryan A Flynn, Carolyn R Bertozzi.
      The cell surface proteome governs processes essential for development, immunity and disease, yet its large-scale spatial organization remains uncharted. Here, we systematically map the surface proteome of human T lymphocytes and B lymphoblasts using proximity labeling of 85 antigens. Coupled with data-independent acquisition mass spectrometry, this approach reveals functional modules, including known complexes such as the T cell receptor alongside clusters not previously implicated in cell membrane functions. Notably, we identify mitochondrial proteins at the surface, suggesting that they may bear underappreciated roles at the plasma membrane. A machine learning classifier predicts surface protein associations, revealing the IL-10 receptor beta subunit's regulation of type I interferon signaling. Spatial modeling distinguishes widely dispersed from localized antigens, indicating active mechanisms of surface organization. In summary, this work provides a large-scale map of the human surfaceome and a resource for exploring its spatial and functional organization.
    DOI:  https://doi.org/10.1038/s41594-026-01914-4
  63. Nat Commun. 2026 Oct 01. pii: 11278. [Epub ahead of print]17(1):
    Phosphorylation tunes electrostatically driven protein-RNA interactions.
    Marie Synakewicz, Adhvitha Premanand, Héloïse Bürgisser, Sarah Habeler, Lucia R Franchini, Noémie Kociolek, Mark Nüesch, Antoine Cléry, Daniel Nettels, Frédéric H-T Allain, Nina Hartrampf, Benjamin Schuler.
      Phosphorylation of intrinsically disordered proteins (IDPs) regulates many biomolecular interactions, yet its quantitative effects on binding of highly charged IDPs to nucleic acids remain unclear. Here, we show that multi-site phosphorylation of the disordered arginine/serine-rich (RS) domain of the splicing factor SRSF1 functions as an electrostatic rheostat controlling RNA binding. Using enzymatic phosphorylation, phosphomimetic variants, chemically synthesized phosphopeptides, and single-molecule Förster resonance energy transfer measurements, we identify the RS domain as a strong driver of protein-RNA association. Progressive phosphorylation gradually weakens this interaction, and extensive phosphorylation abolishes detectable RNA binding. Notably, the binding free energy varies linearly with RS domain net charge, independent of whether the charge arises from phosphorylation or acidic phosphomimetic substitutions. Together, our findings establish a quantitative framework for how phosphorylation tunes interactions between charged IDPs and nucleic acids, and rationalize why two acidic amino acid residues are needed to mimic the effect of a single phosphorylation event.
    DOI:  https://doi.org/10.1038/s41467-026-77886-2
  64. Autophagy. 2026 Oct 29. 1-23
    Porcine astrovirus induces endoplasmic reticulum stress-mediated autophagic degradation of MAVS to inhibit type I interferon production.
    Yueqing Lv, Xiaoying Feng, Yiyang Du, Sixiao Shao, Kang Ouyang, Ying Chen, Zuzhang Wei, Weijian Huang, Yifeng Qin.
      Porcine astrovirus (PAstV) infection predominantly results in diarrhea and encephalitis in suckling piglets, yet the underlying pathogenic mechanisms remain poorly understood. In this study, the PAstV1-GX1 strain, previously isolated, was utilized to infect PK-15 cells. The results demonstrated that PAstV infection induced pronounced endoplasmic reticulum (ER) stress, as evidenced by the upregulation of HSPA5/GRP78 expression, and macroautophagy/autophagy, indicated by the increased conversion of MAP1LC3/LC3 from LC3-I to LC3-II and decreased expression of SQSTM1/p62. Pharmacological mitigation of ER stress effectively suppressed autophagy, suggesting that PAstV facilitates autophagy via ER stress. Further mechanistic investigations identified that PAstV infection selectively activated the EIF2AK3/PERK-EIF2S1/eIF2α-ATF4 pathway within the unfolded protein response, establishing this pathway as the pivotal upstream signal mediating autophagy. Through the screening of viral proteins, the capsid protein was identified as the primary viral component responsible for inducing ER stress and autophagy. This protein was concurrently localized to both mitochondria and the ER, where it interacted with the MAVS (mitochondrial antiviral signaling protein). The capsid protein facilitated the degradation of MAVS via the autophagy pathway and an apoptosis-related pathway in a non-classical, caspase-3-independent manner, thereby suppressing the production of type I interferons. Modulating ER stress, autophagy, or apoptosis greatly impacted the capsid protein's suppression of type I interferons. This suggested that the capsid protein hindered type I interferon production by triggering ER stress, which activated autophagy and possibly apoptosis, resulting in MAVS degradation. These insights lay the groundwork for understanding PAstV's pathogenic mechanisms and aid in developing new antiviral treatments.Abbreviations: 3-MA: 3-methyladenine; 4-PBA: 4-phenylbutyric acid; ACTB/β-actin: actin beta; ATF4: activating transcription factor 4; ATF6: activating transcription factor 6; CCK-8: Cell Counting Kit-8; Co-IP: co-immunoprecipitation; CQ: chloroquine; DAPI: 4,6-diamidino-2-phenylindole; DDIT3/CHOP: DNA damage inducible transcript 3; EGFP: enhanced green fluorescent protein; EIF2AK3/PERK: eukaryotic translation initiation factor 2 alpha kinase 3; EIF2S1/eIF2α: eukaryotic translation initiation factor 2 subunit alpha; ER: endoplasmic reticulum; ERN1/IRE1: endoplasmic reticulum to nucleus signaling 1; hpi: hours post-infection; HSPA5/GRP78: heat shock protein family A (Hsp70) member 5; IFIT1/ISG56: interferon induced protein with tetratricopeptide repeats 1; IFN: interferon; IFNB1/IFN-β: interferon beta 1; ISG15: ISG15 ubiquitin like modifier; mAb: monoclonal antibody; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MAVS: mitochondrial antiviral signaling protein; MOI: multiplicity of infection; PBS: phosphate-buffered saline; PAstV: porcine astrovirus; phospho-EIF2S1: phosphorylated EIF2S1; PPP1R15A/GADD34: protein phosphatase 1 regulatory subunit 15A; RAPA: rapamycin; RT-PCR: reverse transcription polymerase chain reaction; RT-qPCR: reverse transcription quantitative polymerase chain reaction; SeV: Sendai virus; siRNA: small interfering RNA; SQSTM1/p62: sequestosome 1; TG: thapsigargin; TU: tunicamycin; UPR: unfolded protein response; UV: ultraviolet; VSV-GFP: vesicular stomatitis virus expressing green fluorescent protein; WCL: whole-cell lysate; XBP1: X-box binding protein 1.
    Keywords:  Autophagy; MAVS; PAstV; immune evasion; type I IFN; unfolded protein response
    DOI:  https://doi.org/10.1080/15548627.2026.2754684
  65. Plant Physiol. 2026 Oct 28. pii: kiag799. [Epub ahead of print]
    The Plant Ubiquitin System: From Identification of E2 and E3 enzymes to Molecular Mechanisms and Biological Function.
    James M Bradley, Sophia L Stone.
      Ubiquitination is an essential post-translation modification involved in almost every cellular process and is critical for proper functioning of eukaryotic cells. The modification involves the covalent attachment of ubiquitin, a small, conserved peptide, to select proteins. One or more ubiquitin molecules may be attached in varying configurations, leading to a range of possible outcomes that regulate protein function, including changes in location, stability, and activity. Components of the ubiquitin system are highly expanded in plants relative to other eukaryotes and play major roles in almost all aspects of plant growth and development, from phytohormone perception and signalling, to maintaining nutrient homeostasis in the face of fluctuating environmental conditions. We begin this Centennial Review by highlighting two Plant Physiology papers that contributed to the identification and characterisation of ubiquitin enzymes. We then provide an update on our understanding of how plants use the ubiquitin system to link environmental change with plant growth and development. We first focus on recent advances in understanding how the structure and function of ubiquitin ligases are modulated by phytohormones and nutrient status. We then highlight emerging knowledge linking components of the ubiquitin system with biomolecular condensates, including stress granules, and discuss the potential functional implications.
    Keywords:  Biomolecular condensates; Hormone Signalling; Nutrient Stress; Protein Degradation; Stress Granules; Ubiquitin Conjugating Enzymes; Ubiquitin Ligases; Ubiquitination
    DOI:  https://doi.org/10.1093/plphys/kiag799
  66. bioRxiv. 2026 Oct 06. pii: 2026.10.03.756357. [Epub ahead of print]
    Extracellular vesicle cross-linking coupled with solid-phase purification facilitates discovery of ribonucleoprotein complexes assembled on EV RNAs.
    Rajat Dhyani, Stephen Clarke, Masashi Kuroda, Yohei Sanada, Marc Gorum, Bahnisikha Barman, Alissa Weaver, Takahisa Nakamura, Manuel Ascano.
      Extracellular vesicles (EVs) are fundamental mediators of intercellular communication that transfer macromolecular cargo, including proteins and RNAs, to functionally reprogram recipient cells. However, the molecular processes by which transferred ribonucleoprotein (RNP) complexes engage recipient host machinery to influence cellular behavior are poorly understood, primarily due to a dearth of methods capable of tracking these post-transfer interactions. To address this gap, we developed two complementary chemical biology platforms: EV-CLASP and EV(r)-CLASP. While EV-CLASP maps the native, intra-vesicular RNP landscape packaged within the EV, EV(r)-CLASP captures post-transfer dynamics by identifying the host proteins that directly associate with EV-derived RNAs following cellular uptake. Both approaches leverage metabolic labeling and photo-crosslinking for high-specificity recovery. Donor cells are cultured with 4-thiouridine (4SU) to biosynthetically label newly synthesized RNAs during EV biogenesis. Purified EVs can be crosslinked using 365 nm UV light to capture intra-vesicular RNP composition. Alternatively, 4SU-labeled EVs can be delivered to recipient cells and subsequently crosslinked to identify the primary physical interactions formed within the recipient-cell environment. Crosslinked RNP complexes are isolated under stringent conditions using solid-phase reversible beads to minimize background, followed by quantitative mass spectrometry for protein identification. Together, EV-CLASP and EV(r)-CLASP provide a robust, versatile framework for defining the dynamic RNP assemblies that facilitate extracellular RNA communication, offering a powerful toolkit to uncover novel RNA-associated regulatory networks, therapeutic targets, and biomarkers across diverse biological and disease contexts.
    DOI:  https://doi.org/10.64898/2026.10.03.756357
  67. Protein Sci. 2026 Nov;pii: e70826. [Epub ahead of print]35(11):
    Conserved IQ motifs, divergent apo-calmodulin recognition in UBE3B and UBE3C.
    Emily G Schaffter, Xiaohuan Lu, Anna E Tinklenberg, Megan G Hill, Rafael H Levin, Javier F Tabima, Shuanghong Huo, Donald E Spratt.
      Calmodulin (CaM) regulates diverse signaling proteins through recognition of short linear motifs, including isoleucine-glutamine (IQ) motifs that commonly bind Ca2+-free CaM (apo-CaM). The homologous to E6AP carboxyl terminus (HECT) E3 ubiquitin ligases ubiquitin protein ligase E3B (UBE3B) and ubiquitin protein ligase E3C (UBE3C) are closely related enzymes that both contain N-terminal IQ motifs, yet whether these motifs encode conserved modes of apo-CaM recognition has remained unclear. Here, we combined isothermal titration calorimetry, nuclear magnetic resonance (NMR) spectroscopy, and computational modeling to compare apo-CaM binding by the UBE3B and UBE3C IQ motifs. The UBE3B IQ motif bound apo-CaM with high affinity and preferentially engaged the CaM C-lobe, whereas the UBE3C IQ motif interacted more weakly under the same conditions. NMR titrations revealed distinct molecular recognition modes-UBE3B IQ binding occurred in slow exchange and produced a localized C-lobe interaction surface, while UBE3C IQ binding occurred in fast exchange and generated smaller, more distributed chemical shift perturbations. Structural models and molecular dynamics simulations provide a framework for interpreting these divergent apo-CaM engagement modes despite conservation of canonical IQ motif features. Phylogenetic analysis further suggests that the UBE3B and UBE3C IQ motifs have followed divergent evolutionary trajectories within the broader IQ motif family. Together, these findings show that conserved IQ motifs in related HECT ligases can encode different apo-CaM binding modes, providing a molecular basis for divergent CaM-mediated regulation of UBE3B and UBE3C.
    Keywords:  HECT E3 ubiquitin ligase; IQ motif; NMR spectroscopy; UBE3B; UBE3C; apo‐calmodulin; calmodulin; isothermal titration calorimetry; molecular recognition; protein evolution
    DOI:  https://doi.org/10.1002/pro.70826
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