bims-proteo Biomed News
on Proteostasis
Issue of 2026–06–07
sixty-two papers selected by
Eric Chevet, INSERM
  1. TRIM21 induces selective autophagy of viruses and bacteria.
  2. Reticulophagy limits Alzheimer's disease pathology through FAM134B-dependent APP clearance.
  3. LASER couples damage sensing to ESCRT assembly for lysosome repair.
  4. Ubiquitin-conjugating enzyme membrane anchor Cue1 confers resistance to hygromycin B in Saccharomyces cerevisiae.
  5. Faf1 accelerates p97-mediated protein unfolding by promoting ubiquitin engagement.
  6. Linker-Driven Sampling of PROTAC-Induced Ternary Complexes.
  7. A conserved antioxidant defense at the endoplasmic reticulum membrane.
  8. Coordinated expression and assembly of BiP, p58IPK, and ER chaperone complexes maximize proinsulin folding in pancreatic β cells.
  9. Genomic insights into the tunicamycin-induced endoplasmic reticulum stress response in peripheral blood mononuclear cells: A comprehensive RNA sequencing analysis.
  10. Cytosolic and ER-associated ribosomes share rRNA 2'-O-methylation landscapes across human cell types.
  11. Non-enzymatic RNA Glycation is a Metabolic Sensor of Cellular Stress.
  12. GPLD1 is a scavenger carrier mediating lysosomal degradation of extracellular aberrant proteins.
  13. FBXL21 regulates diurnal proteostasis and stress response by targeting DNAJB6 and client proteins.
  14. AMC-F1 regulates mitochondria-autophagy crosstalk independent of nutrient stress.
  15. The ER anchoring and abundance of the EEF1B complex is affected by tissue-specific alternative EEF1D splicing.
  16. Ubiquitination of secretory granules promotes their crinophagic degradation in Drosophila.
  17. Site-specific combinatorial ubiquitination drives the targeted degradation of plasma membrane proteins.
  18. Fasting disrupts the InsP₆-HDAC3 axis to drive ER stress-mediated clearance of DNA-damaged cells and enforce tissue quality control.
  19. Intramolecular Interactions between Folded and Disordered Regions Shape Ubiquilin Structure and Function.
  20. Consequences of defective mitochondrial protein import: From targeting signals to pathology.
  21. Nucleophagy removes cytotoxic trapped PARP1.
  22. Structure of the E3 ligase CRL2ZYG11B with substrates reveals the molecular basis for N-degron recognition and ubiquitination.
  23. Heat shock-induced zinc efflux repurposes Arabidopsis E3 ligase EMR as a molecular chaperone.
  24. SCM-1/SCAMP Maintains Microdomain Boundaries and Cargo Sorting within the Endosomal System.
  25. Targeted extracellular degradation of LRP8 promotes ferroptosis in cancer cells.
  26. Nanometer-scale RNA protein clusters (RPCs) Foster Helicase Activity of DEAD-box eIF4A.
  27. The mannosyltransferase DPM1 regulates the activity of ER-stress sensor IRE1 in colorectal cancer.
  28. Improving protein and protein interactions using pseudo-dimers derived from monomeric proteins.
  29. LCK-targeting molecular glues overcome resistance to inhibitor-based therapy in T-cell acute lymphoblastic leukemia.
  30. GPI‑anchored protein nanoclusters license migrasome expansion and serve as exocytic platforms for migrasome.
  31. The C-terminal region of TENT5 proteins drives ER-associated mRNA polyadenylation via FNDC3 interaction.
  32. Prevalent gut phages encode modular adhesins mediating epithelial binding and endoplasmic reticulum trafficking.
  33. WNT2B impairs endosomal trafficking via WASHC5 to inhibit autophagy: a novel non-secretory WNT pathway.
  34. Structural Basis for Mechanical Coupling in Hsp90: Hinge Flexibility Coordinates ATP Gate Closure and β-Strap Release.
  35. A cross-vertebrate brain protein interaction map identifies conserved neural and non-neural complexes.
  36. Structural insights into predicted protein-protein interactions and protein complexes in the human proteome.
  37. Intrinsically disordered regions facilitate Mlp1-Nab2 recognition in mRNA quality control.
  38. Mitochondrial C3aR and endoplasmic reticulum C5aR orchestrate calcium imbalance during oxidative stress in retinal pigment epithelial cells.
  39. A cytosolic IF1 reporter enables real-time visualization of severe mitochondrial membrane damage.
  40. ProtAttn-QuadNet: An attention-based deep learning framework for protein-protein interaction prediction using ProtBERT embeddings.
  41. DCAF8 binds DDB1 via an N-terminal helix-loop-helix motif to assemble CRL4 and promote cell cycle progression.
  42. Deep learning-driven decoding of ubiquitination: from regulatory mechanisms to targeted protein degradation.
  43. An image-based CRISPR screen reveals splicing-mediated control of HP1α condensates.
  44. Molecular insights into protein disulfide isomerase antagonism by punicalagin.
  45. Cell autonomous inflammation in VEXAS is mediated by cGAS-STING.
  46. Dissociation of UPR signaling and ER ultrastructure during 4-PBA therapy in shunt-driven pulmonary hypertension.
  47. Nascent protein retention at polysomes reduces kinetic barriers to self-assembly.
  48. TSC2 is a stress granule suppressor.
  49. Structural Pockets and Interacting RNA-Associated Ligands (SPIRAL): A DSSR-enabled Meta-Analysis of RNA-Small Molecule Recognition.
  50. Ribosome impairment, tau alternative splicing, and stress granules: a convergent axis of neuronal vulnerability driving Alzheimer's disease.
  51. Adhesion-derived condensates control component availability to regulate adhesion dynamics.
  52. AE-PocketMiner Uses Attention to Simultaneously Predict Cryptic Pockets and Their Allosteric Coupling.
  53. Beyond Inhibition: Rebalancing the Hsp90 Chaperone Network as a Therapeutic Strategy for Alzheimer's Disease.
  54. Mapping the interactome of human tRNA methyltransferase TRMT1 using dual proximity labeling.
  55. Progerin-induced nuclear envelope remodeling is shaped by cell division and NUP153.
  56. Proteostasis driven redox adaptation in ferroptosis: the p62-Keap1-Nrf2 axis.
  57. Neutrophils repurpose the nucleolus as a cytokine reservoir and secretory organelle.
  58. Inhibiting glycan degradation prevents HIV-induced inflammaging and cognitive impairment.
  59. Deubiquitinases at organelle quality control bottlenecks in neurodegeneration.
  60. Stress granule phase separation in stress-responsive cytosolic extract-in-oil droplets.
  61. UCHL3 Regulates Subgenomic Flaviviral RNA Condensates to Promote Virus Propagation.
  62. Endothelial cell RpL17-dependent translational control mediates intima-media thickening in response to disturbed flow.
  1. Mol Cell. 2026 Jun 04. pii: S1097-2765(26)00285-6. [Epub ahead of print]
    TRIM21 induces selective autophagy of viruses and bacteria.
    Tyler Rhinesmith, Anna Albecka, Marina Vaysburd, Claudia Puri, Jakub Luptak, Jerome Boulanger, Quynh-Mai Nguyen Le, Matthew J Gratian, Kevin O'Connell, Lara Few, Mark Donaldson-Wing, Patrycja Kozik, David C Rubinsztein, Leo C James.
      TRIM21 is an exceptionally versatile ubiquitin ligase that can be directed by antibodies to target oligomeric protein scaffolds, viral capsids, and proteopathic aggregates for intracellular degradation. How the cell degrades these typically resistant substrates remains poorly understood. To address this, we used TRIM21 viral restriction to create a genome-wide phenotypic screen for antibody-dependent capsid degradation. We identify an antimicrobial selective macroautophagy pathway in mammalian cells, which we term "antibody-directed xenophagy" (ADX). We show that this mechanism restricts structurally diverse pathogens, including adenovirus and Salmonella. Using quantitative microscopy, we demonstrate that TRIM21 rapidly intercepts antibody-pathogen complexes, leading to ubiquitin ligase activation. Following this, selective autophagy adaptors are recruited, and viral cargoes are delivered to lysosomes. This process reduces Salmonella pathology and bacterial tissue invasion in mice. We propose that TRIM21 evolved through competition with pathogens to induce autophagy of diverse and complex substrates, potentially explaining its versatility for targeted protein degradation.
    Keywords:  antibody; antimicrobial response; antiviral immunity; autophagy; innate immunity; protein degradation; targeted protein degradation; ubiquitin ligase; ubiquitin proteasome system; xenophagy
    DOI:  https://doi.org/10.1016/j.molcel.2026.04.031
  2. Autophagy. 2026 Jun 03.
    Reticulophagy limits Alzheimer's disease pathology through FAM134B-dependent APP clearance.
    Yuting Zhang, Jun Sun, Yixian Cui.
      Selective autophagy maintains organelle and proteome homeostasis through receptor-mediated degradation of damaged membranes and aggregation-prone proteins. Although autophagy dysfunction and endoplasmic reticulum (ER) abnormalities are prominent features of Alzheimer's disease (AD), whether reticulophagy directly contributes to amyloid precursor protein (APP) turnover has remained unclear. We identify FAM134B/RETREG1 as a specific receptor that recognizes ER-localized APP and promotes its lysosomal degradation through LC3-dependent reticulophagy. In AD patient samples and 5XFAD mice, epigenetic repression of FAM134B limits TFEB/TFE3-dependent transcription, resulting in impaired ER turnover, APP accumulation, and exacerbated amyloid pathology. Restoration of wild-type, but not LIR-mutant, FAM134B rescues reticulophagy, reduces APP and Aβ accumulation, preserves neuronal integrity, and improves cognition in 5XFAD mice. These findings establish impaired reticulophagy as an upstream pathogenic mechanism in AD and highlight FAM134B-mediated ER turnover as a potential therapeutic strategy for limiting amyloidogenic APP accumulation.
    Keywords:  5XFAD mice; FAM134B/RETREG1; MAP1LC3B/LC3B; TFE3; TFEB; amyloid beta precursor protein; autophagy; epigenetic modification; lysosome; receptor
    DOI:  https://doi.org/10.1080/15548627.2026.2684514
  3. Nature. 2026 Jun 03.
    LASER couples damage sensing to ESCRT assembly for lysosome repair.
    Claire S Goul, Aakriti Jain, Samira Yitiz, Zahra E Soltani, Serim Yang, Simon Rapp, Martina Spacci, Scot Federman, James Sacco, Huinan Li, Lauren D Enriquez, Nalan Liv, Laralynne Przybyla, Roberto Zoncu.
      Lysosomal membrane integrity is essential for cell survival, but how damage sensing is spatiotemporally coupled to repair remains poorly understood. Recruitment and assembly of endosomal sorting complex required for transport (ESCRT) I-III rapidly counteracts membrane damage, but it is unclear how ESCRT-I recognizes defective lysosomal membranes. Here, leveraging genome-wide CRISPRi screens in a damage-sensitized genetic background, we identified LC3/GABARAP-assisted stimulator for ESCRT recruitment (LASER), a multicomponent protein assembly that forms rapidly upon calcium release from damaged lysosomes and couples sensing of lysosomal membrane damage to ESCRT-dependent repair. At the core of LASER is TFG, an endoplasmic reticulum exit-site-resident protein that translocates to damaged lysosomes by binding to ATG8 family proteins (LC3 and GABARAP) conjugated to lysosomal phospholipids. ATG8-bound TFG forms oligomeric assemblies that directly recruit the essential ESCRT-I subunit TSG101 via conserved motif recognition enhanced by avidity-driven interactions. TFG binding to TSG101 stimulates sequential ESCRT-I-II-III polymerization and promotes membrane repair. TFG mutations that drive hereditary spastic paraplegia disrupt its oligomerization and impair lysosomal ESCRT recruitment and membrane resealing, implicating defective repair as a driver of TFG-associated neurodegeneration. Thus, LASER promotes ESCRT polymerization at damaged lysosomes and couples damage sensing to membrane repair.
    DOI:  https://doi.org/10.1038/s41586-026-10604-6
  4. MicroPubl Biol. 2026 ;2026
    Ubiquitin-conjugating enzyme membrane anchor Cue1 confers resistance to hygromycin B in Saccharomyces cerevisiae.
    James A Avaala, Melissa Palackel, Ian M Tesch, Joseph Gumina, Chance S Creviston, Jason D True, Justin J Crowder, Eric M Rubenstein.
      Aberrant and excess proteins are destroyed by compartment-specific protein quality control mechanisms. In Saccharomyces cerevisiae , endoplasmic reticulum (ER)-associated degradation (ERAD) and inner nuclear membrane (INM)-associated degradation (INMAD) require the Ubc6 and Ubc7 ubiquitin-conjugating enzymes. Ubc6 is an integral membrane protein. By contrast, Ubc7 is a soluble protein tethered to the ER and INM membranes by the transmembrane protein Cue1. Here, we assessed the requirement of Cue1 in resisting proteotoxic stress. CUE1 loss sensitized cells to hygromycin B to a similar extent as UBC7 deletion, consistent with a shared role for Cue1 and Ubc7 in ER and INM protein quality control.
    DOI:  https://doi.org/10.17912/micropub.biology.002032
  5. Cell Rep. 2026 Jun 02. pii: S2211-1247(26)00471-7. [Epub ahead of print]45(6): 117393
    Faf1 accelerates p97-mediated protein unfolding by promoting ubiquitin engagement.
    Zengwei Liao, Connor Arkinson, Andreas Martin.
      P97/VCP is a protein unfoldase of the AAA+ ATPase family that plays essential roles in numerous processes, including ER-associated degradation and DNA replication. For unfolding of proteins modified with K48-linked ubiquitin chains, p97 works with the heterodimeric cofactor Ufd1-Npl4, and the cofactor Faf1 was shown to enhance this activity during replisome disassembly by unknown mechanisms. Here, we employ an in vitro reconstituted system with human components for biochemical experiments, FRET-based assays, and cryo-EM structure determination to reveal that Faf1 generally accelerates ubiquitin-dependent substrate processing by promoting the unfolding of an initiator ubiquitin and its engagement by the ATPase. Faf1 thereby uses its p97-bound C-terminal UBX domain to anchor a long helix that braces Ufd1's UT3 domain and stabilizes Ufd1-Npl4 for ubiquitin unfolding. Our findings demonstrate how p97 works simultaneously with several cofactors to facilitate the unfolding of ubiquitinated proteins, indicating more complex regulatory mechanisms than for the simpler yeast Cdc48.
    Keywords:  CP: Molecular biology; Faf1; Faf2; Ufd1/Npl4; initiator ubiquitin; p97; ubiquitin-dependent protein unfolding
    DOI:  https://doi.org/10.1016/j.celrep.2026.117393
  6. J Med Chem. 2026 Jun 03.
    Linker-Driven Sampling of PROTAC-Induced Ternary Complexes.
    Hongtao Zhao, Stefan Schiesser, Christian Tyrchan, Werngard Czechtizky.
      Proteolysis-targeting chimeras (PROTACs) are heterobifunctional molecules that recruit an E3 ligase to a protein of interest, thereby promoting ubiquitin transfer and subsequent proteasomal degradation. Formation of the ternary complex is a key step in PROTAC-induced degradation, and structural insight into these complexes is important for rational PROTAC design. Here, we present a computational approach for sampling PROTAC-induced ternary complexes by reducing the search space to the conformational degrees of freedom of the linker. Evaluated on 40 cocrystal ternary complex structures, the method achieved retrospective success rates of 97% and 50% at Cα-RMSD thresholds of 10 and 4 Å from the crystal structures, respectively. Using unbound protein structures as input, the predicted ternary complexes remained within 7 Å of the experimental structures across six WDR5-PROTAC-VHL complexes. Our open-source software, TERNIFY, enables ternary-complex modeling in a standalone workflow without separate protein-protein docking and linker-sampling steps.
    DOI:  https://doi.org/10.1021/acs.jmedchem.6c00527
  7. Cell Rep. 2026 Jun 04. pii: S2211-1247(26)00567-X. [Epub ahead of print]45(6): 117489
    A conserved antioxidant defense at the endoplasmic reticulum membrane.
    Zhijian Ji, Henry de Belly, Taruna Pandey, Bingying Wang, Yao Tang, Jingxuan Yao, Shiya Xu, Kathy Li, Yanchang Bian, Shouhong Guang, Zhiyong Lou, Al Burlingame, Orion D Weiner, Thomas D Goddard, Dengke K Ma.
      Oxidative protein folding in the endoplasmic reticulum (ER) is essential for eukaryotic cells yet generates hydrogen peroxide (H2O2), a reactive oxygen species. The ER-transmembrane protein that supports ER proteostasis and guards the cytosol for antioxidant defense remains unidentified. Here, we combine AlphaFold2 and functional screens in C. elegans to discover a previously uncharacterized and evolutionarily conserved protein ERGU-1 that fulfills these roles. Deleting ERGU-1 upregulates H2O2 and NRF2/SKN-1-dependent gene expression. ERGU-1 deficiency also impairs organismal reproduction and behavioral responses to H2O2. Both C. elegans ERGU-1 and human homolog TMEM161B localize to ER membranes, forming reticular networks. Human and Drosophila homologs of ERGU-1 rescue C. elegans mutant phenotypes, demonstrating ancient and conserved functions. In addition, purified ERGU-1 and TMEM161B exhibit redox-modulated oligomeric states. Together, our results reveal an ER-membrane-specific machinery, suggesting a conserved mechanism for maintaining ER redox homeostasis and proteostasis in animal cells.
    Keywords:  AlphaFold2; CP: molecular biology; ER membrane proteostasis; ER redox homeostasis; ERGU-1; SKN-1/NRF2 signaling; TMEM161B; antioxidant defense; conserved transmembrane oxidoreductase; hydrogen peroxide; oxidative protein folding
    DOI:  https://doi.org/10.1016/j.celrep.2026.117489
  8. Proc Natl Acad Sci U S A. 2026 Jun 09. 123(23): e2533617123
    Coordinated expression and assembly of BiP, p58IPK, and ER chaperone complexes maximize proinsulin folding in pancreatic β cells.
    Insook Jang, Alec Duffey, Pamela Itkin-Ansari, Peter Arvan, Randal J Kaufman.
      Proper proinsulin folding in the endoplasmic reticulum (ER) is prerequisite to producing bioactive insulin, and proinsulin misfolding causing β cell ER stress accompanies pancreatic β cell dysfunction in type 2 diabetes (T2D). How (and which) ER chaperones coordinate to prevent proinsulin misfolding is largely unknown other than an unspecified dependence on the hsp70 member, BiP. A genetically engineered mouse enables efficient, specific pulldown of endogenous islet β cell BiP (GRP78, the major HSP70 ER chaperone) in complexes with client proteins. We demonstrate that BiP assembles in various protein complexes (including cochaperones p58IPK, GRP170, ERdj3, and oxidoreductases PDIA1 and PDIA6) that specifically bind to nonnative proinsulin. BiP requires p58IPK for productive proinsulin folding, whereas nonstoichiometric BiP excess actually hinders proinsulin folding. Coordinated and dyscoordinated BiP/cochaperone assembly in response to demand for proinsulin highlights physiologic and pathophysiologic conditions, respectively, offering a potential check point for therapeutic intervention.
    Keywords:  chaperones; endoplasmic reticulum; proinsulin folding; type 2 diabetes; β cell function
    DOI:  https://doi.org/10.1073/pnas.2533617123
  9. Biochem Biophys Rep. 2026 Jun;46 102640
    Genomic insights into the tunicamycin-induced endoplasmic reticulum stress response in peripheral blood mononuclear cells: A comprehensive RNA sequencing analysis.
    Laura S Mahl, Axel H Meyer.
      Tunicamycin induces endoplasmic reticulum (ER) stress by inhibiting N-glycosylation of newly synthesized proteins, leading to accumulation of misfolded proteins in the ER. This activates the unfolded protein response (UPR), a conserved adaptive pathway aimed at restoring proteostasis. A key mediator of this response is the kinase PERK which activates a signal cascade that leads to a global reduction in translation, while selectively enhancing the expression of stress-associated genes. This PERK-mediated response also constitutes a major arm of the integrated stress response (ISR). Under persistent ER stress, these response pathways may trigger pro-apoptotic programs in addition to adaptive responses. In this study, we used next-generation RNA sequencing to profile transcriptional changes in peripheral blood mononuclear cells (PBMCs) after 24 h of tunicamycin exposure, alone or with the PERK inhibitor GSK2606414 or the eIF2B activator ISRIB, to assess stress responses at distinct regulatory points within the PERK-ISR pathway. Key findings were validated by qRT-PCR, and pathway enrichment analysis was performed using the Gene Ontology Resource and the Reactome database. ER stress altered gene expression, with 4.80% of genes upregulated and 12.67% downregulated. GSK2606414 suppressed a broader subset of tunicamycin-induced genes than ISRIB. However, both inhibitors effectively reversed upregulation of the top two stress-responsive genes, TNC and WNT5A. Pathway enrichment analysis revealed overrepresentation of pathways related to ER stress responses, unfolded protein homeostasis, ER chaperone complex assembly, amino acid biosynthesis and interconversion, and aminoacyl-tRNA synthetase-mediated protein translation. These findings provide mechanistic insights into chronic ER stress in PBMCs and identify WNT5A and TNC as candidate biomarkers, pending further validation.
    Keywords:  ER stress; ISR; PBMCs; PERK; Transcriptomics; Tunicamycin; UPR; eIF2α
    DOI:  https://doi.org/10.1016/j.bbrep.2026.102640
  10. RNA. 2026 Jun 02. pii: rna.081054.126. [Epub ahead of print]
    Cytosolic and ER-associated ribosomes share rRNA 2'-O-methylation landscapes across human cell types.
    Ülkü Uzun, Anders H Lund.
      Ribosome heterogeneity arising from variable rRNA 2'O methylation (2'O Me) has been proposed as a potential mechanism for translational specialization, but whether such heterogeneity contributes to compartment specific translation remains unknown. Here, we systematically compare the 2'O Me landscapes of cytosolic and endoplasmic reticulum (ER)-associated ribosomes across three human cell types: HEK293 cells, H9-derived neural progenitor cells (NPCs), and neurons differentiated from these NPCs. Using detergent-based fractionation combined with RiboMeth-seq, we generate site-resolved rRNA methylation profiles for each compartment. Within each cell type, cytosolic and ER-associated ribosomes display highly similar 2'O Me patterns, with only modest compartment-specific differences observed at 18S:462 in NPCs and 28S:2043 in neurons. Across all samples, differences in 2'O Me patterns are more pronounced between cell types than between compartments. Together, these findings indicate that 2'O Me does not establish a broad ER-specific methylation signature and is unlikely to be a major determinant of ribosome localization or function at the ER.
    Keywords:  Local translation; Neuronal translation; RiboMeth-seq; Ribosome heterogeneity; rRNA 2′O-methylation
    DOI:  https://doi.org/10.1261/rna.081054.126
  11. bioRxiv. 2026 May 19. pii: 2026.05.18.725511. [Epub ahead of print]
    Non-enzymatic RNA Glycation is a Metabolic Sensor of Cellular Stress.
    Anna Knörlein, Kaila Nishikawa, Naoya Kitamura, Reena Kumari, Shino Murakami, Ankita Shrivastava, Malina Doynova, Nicolae Ciobu, Nicole Walker, Xiaohan Mei, Abdul Vehab Dozic, Jahan Rahman, Yang Xiao, Chiara Evans, Xuejing Yang, Michael G Kharas, Omar Abdel-Wahab, Francois Fuks, Kamini Singh, Samie Jaffrey, Viraj R Sanghvi, James J Galligan, Yael David.
      Non-enzymatic RNA modifications expand the epitranscriptome, encoding a rapid and chemistry-driven response to cellular stress. While methylglyoxal, a reactive glycolytic byproduct of metabolic stress, has been shown to modify proteins and DNA, its impact on RNA has remained unexplored. Here, we identify mRNA as a dynamic substrate of MGO, whose modification is actively regulated by DJ-1 and the glyoxalase detoxification system. We show that mRNA glycation impairs translation and engages both the integrated stress response and the ribotoxic stress pathway, culminating in compromised pancreatic β-cell function and reduced insulin secretion. Notably, this phenotype is alleviated by the frontline antihyperglycemic agent metformin. Together, our findings position mRNA as a direct sensor of metabolic stress and establish RNA glycation as a mechanistic link between glycolytic imbalance, translational stress and disease.
    DOI:  https://doi.org/10.64898/2026.05.18.725511
  12. Life Sci Alliance. 2026 Aug;pii: e202603717. [Epub ahead of print]9(8):
    GPLD1 is a scavenger carrier mediating lysosomal degradation of extracellular aberrant proteins.
    Mizuki Tsuchiya, Yoichiro Yagishita, Eisuke Itakura.
      Loss of proteostasis leads to the accumulation of aberrant proteins, including aggregated proteins and amyloid fibrils, contributing to various diseases. Protein quality control systems are essential for maintaining proteostasis. Although intracellular mechanisms are well characterized, pathways responsible for the degradation of aberrant proteins outside the cell remain poorly understood. We previously identified the chaperone/carrier- and receptor-mediated extracellular protein degradation pathway, in which the extracellular chaperone clusterin binds misfolded proteins and the resulting complex is delivered to lysosomes via endocytosis. However, it remains unclear whether other factors are involved in this pathway. To identify novel regulators, plasma factors binding serum amyloid A1 were investigated. Glycosylphosphatidylinositol-specific phospholipase D1 (GPLD1) was found to directly bind serum amyloid A1 and promote its lysosomal degradation. This activity was independent of GPLD1's cleavage activity for GPI-anchored proteins. Furthermore, GPLD1 mediates lysosomal degradation of misfolded proteins, with cell surface heparan sulfate acting as its receptor. Our data demonstrate that GPLD1 is a novel scavenger carrier with substrate specificity distinct from clusterin, responsible for degrading extracellular aberrant proteins.
    DOI:  https://doi.org/10.26508/lsa.202603717
  13. bioRxiv. 2026 May 22. pii: 2026.05.20.726545. [Epub ahead of print]
    FBXL21 regulates diurnal proteostasis and stress response by targeting DNAJB6 and client proteins.
    Ji Ye Lim, Jaebok Wi, Marvin Wirianto, Chorong Han, Sun Young Kim, Jane Nguyen, Sehyun Jung, Kristin Eckel-Mahan, Sung Yun Jung, Karyn A Esser, Zheng Chen, Seung-Hee Yoo.
      Circadian regulation of proteostasis, a key determinant of muscle health, remains poorly understood. Here, we identified DNAJB6, an Hsp40 (DnaJ) co-chaperone, as a substrate of the circadian E3 ligase FBXL21. FBXL21 mediated the ubiquitination-dependent proteasomal degradation of both DNAJB6 and its client proteins including Desmin; causative mutations of DNAJB6 in myopathies, however, rendered resistance to FBXL21-directed degradation. Fbxl21 KO C2C12 cells displayed aberrant accumulation of Desmin, and showed aggravated cytoplasmic accumulation of TDP-43, another DNAJB6 client protein, in heat shock response. Under timed exercise as a physiological stressor, WT mice displayed robust diurnal rhythms in the levels of stress granule markers (G3BP1 and FUS) and TDP-43 as a function of exercise timing. In contrast, the Fbxl21 hypomorph Psttm mutant mice showed elevated expression of these proteins without exercise, which was exacerbated under exercise-induced stress conditions; importantly, these abnormalities were rescued by skeletal muscle-specific FBXL21 expression. Our study elucidates a novel diurnal regulatory mechanism of skeletal muscle proteostasis via FBXL21 as a chaperone-linked E3 ligase, highlighting the FBXL21-DNAJB6 axis as a potential therapeutic target for myopathies.
    DOI:  https://doi.org/10.64898/2026.05.20.726545
  14. Nat Commun. 2026 Jun 05.
    AMC-F1 regulates mitochondria-autophagy crosstalk independent of nutrient stress.
    Yuqin Wang, Raksha K Rao, Trung Vu, Ayano Sekine, Zhengmei Mao, Nami McCarty.
      Mitochondria and autophagy are fundamental yet distinct regulators of cellular homeostasis. Here, we identify AMC-F1 (Autophagy-Mitochondria Coupling Factor 1; formerly TRIM44) as a central integrator of mitochondrial bioenergetics and autophagy. Using Amcf1 knockout and knock-in mouse models, we demonstrate that AMC-F1 bidirectionally regulates these pathways: its loss reduces mitochondrial respiration and autophagic flux, whereas its overexpression promotes mitochondrial elongation and increases autophagy independently of nutrient stress. Transcriptomic analyses reveal AMC-F1-dependent regulation of mitochondrial biogenesis programs that engage autophagy, involving mitochondrial respiratory chain complex genes under basal conditions and mitochondrial organization factors under starvation-induced autophagy. Although dispensable under homeostasis, this coupling becomes essential during stress adaptation. In an acute liver-injury model, Amcf1 knock-in mice were fully protected, exhibiting elevated OPA1, reduced caspase-3 and PARP activation, and preserved Beclin 1. This functional duality reflects AMC-F1's ability to modulate the mitochondrial integrated stress response (mtISR), enabling adaptive ATF4 signaling while preventing maladaptive responses when stress exceeds a threshold. Autophagy upregulation by AMC-F1 is critical for fine-tuning the ISR and preserving cellular resilience. Together, our findings position AMC-F1 as a stress-responsive gatekeeper and a novel coordinator of mitochondrial-autophagy crosstalk, defining a cellular state primed for stress adaptation.
    DOI:  https://doi.org/10.1038/s41467-026-73841-3
  15. Life Sci Alliance. 2026 Aug;pii: e202503513. [Epub ahead of print]9(8):
    The ER anchoring and abundance of the EEF1B complex is affected by tissue-specific alternative EEF1D splicing.
    Muhammad Jamous, Masaki Hosogane, Xiaoxin Huang, Mikiko Suzuki, Atsushi Hatano, Yuichi Shichino, Shintaro Iwasaki, Kazutaka Murayama, Masaki Matsumoto, Keiko Nakayama.
      The EEF1B complex plays a central role in translation elongation by reactivating EEF1A for the delivery of aminoacyl-tRNAs to the ribosome. Among its components, EEF1D undergoes alternative splicing to produce one long and several short isoforms, each with distinct N-terminal domains and tissue-specific expression patterns. Although the short isoforms are broadly expressed, their physiological functions remain poorly characterized. In this study, we show that short EEF1D isoforms containing exon 5 interact with the ER-resident scaffold protein KTN1 and RRBP1, thereby anchoring the EEF1B complex to the ER. Mass spectrometry analyses of FLAG-tagged EEF1D identified these interactions, and deletion of exon 5 disrupted ER anchoring, resulting in diffuse cytoplasmic localization of the EEF1B complex. In exon 5 KO mice, this altered localization was accompanied by a reduction in EEF1B subunit abundance in multiple tissues, including the liver, although global protein synthesis rates remained unchanged. Together, these findings uncover an ER-anchoring mechanism controlled by alternative splicing that shapes the spatial organization and abundance of the elongation machinery in vivo.
    DOI:  https://doi.org/10.26508/lsa.202503513
  16. FEBS Lett. 2026 May 31.
    Ubiquitination of secretory granules promotes their crinophagic degradation in Drosophila.
    Tamás Csizmadia, Anna Dósa, Asha Kiran Maddali, András Jipa, Hajnalka Laczkó-Dobos, Péter Lőw, Gábor Juhász.
      Gland cells dynamically regulate their secretory granule content via balancing synthesis, maturation, secretion, and lysosomal degradation (crinophagy). However, the signal(s) leading to crinophagic breakdown of secretory granules are unknown. Here, we show that ubiquitination of unreleased or low-grade glue-containing secretory granules marks these vesicles for crinophagy in larval salivary gland cells of Drosophila. We identify the ubiquitin ligase Cnot4 as a key mediator of glue granule ubiquitination. Loss of Cnot4 prevents ubiquitination and impairs granule fusion with lysosomes. Overexpression of Cnot4 induces premature crinophagy via ectopic ubiquitination of granules. Our work establishes that Cnot4-dependent ubiquitination of secretory granules is a key trigger of crinophagy in Drosophila, paving the way for further analysis of this barely characterized degradation route in metazoans.
    Keywords:  Cnot4; K63‐linked polyubiquitin; crinophagy; glue granule; lysosome; quality control
    DOI:  https://doi.org/10.1002/1873-3468.70376
  17. bioRxiv. 2026 May 27. pii: 2026.05.23.727405. [Epub ahead of print]
    Site-specific combinatorial ubiquitination drives the targeted degradation of plasma membrane proteins.
    Niclas Olsson, Aleksandr Gaun, Sammy Villa, Katrina Jackson, Mark E Fitzgerald, Fiona E McAllister, David Stokoe, Aaron H Nile, Kirill Bersuker.
      Cullin-RING E3 ligases (CRLs) ubiquitinate their substrates by recruiting them to complexes containing ubiquitin-conjugating enzymes (UCEs). Ubiquitination proceeds through the transfer of ubiquitin from UCEs to substrate lysines, but the specificity of lysine ubiquitination has not been widely investigated in cells. In this study, we use global ubiquitination profiling to identify sites in the kinase domains of receptor tyrosine kinases (RTKs), EGFR and Her2, that undergo CRL-mediated ubiquitination in cells treated with heterobifunctional degrader molecules. We find that VHL- and Cereblon-dependent degraders trigger the ubiquitination of a common subset of accessible lysines. Using mutagenesis, we show that the number of available ubiquitination sites specifies the extent of RTK degradation. Furthermore, introduction of non-native sites mostly fails to rescue clearance of lysine-deficient RTK mutants. These results highlight the specificity with which UCEs ubiquitinate their substrates and suggest that the ubiquitination of multiple sites governs the efficacy of degraders targeting plasma membrane proteins.
    DOI:  https://doi.org/10.64898/2026.05.23.727405
  18. bioRxiv. 2026 May 27. pii: 2026.05.24.727426. [Epub ahead of print]
    Fasting disrupts the InsP₆-HDAC3 axis to drive ER stress-mediated clearance of DNA-damaged cells and enforce tissue quality control.
    Sujan Chetterjee, Zachary Sin, Richard A Van, Nguyen Tran, Tam Tran, Anuj Shukla, Lucile Marie-Paule Jeusset, George Koshkaryan, Kevin Saldana, Rayan Muneer, Loretta Viera Preval, Lingkun Gu, Faizan Bhat, Kevin Ritter, Katherine Huang, Kayci Huff-Hardy, Richard Rood, Anas Gremida, Martin Gregory, Chien Huan Chen, Mo Weng, Frank J Dekker, Parakkal Deepak, Henning J Jessen, Kirk James McManus, Mira V Han, Prasun Guha.
      Fasting drives metabolic adaptation but also elicits acute cellular stress. How this stress shapes tissue integrity is unknown. Here, we show that in the intestine, fasting depletes growth factor signaling, which triggers cellular stress. This response functions as a tissue quality-control checkpoint that selectively eliminates pre-existing DNA-damaged cells while sparing healthy counterparts. A short-term fast diminishes TGF-β signaling and elicits endoplasmic reticulum (ER) stress, driving DNA-damaged intestinal cells beyond an apoptotic threshold, thereby reducing the inflammatory burden. Mechanistically, loss of TGF-β signaling triggers FBXO22-Cullin1-mediated degradation of the inositol kinase IPMK, leading to depletion of inositol hexaphosphate (InsP₆). InsP₆ loss attenuates HDAC3 activity and initiates coordinated epigenetic and post-translational reprogramming, thereby increasing CDK5RAP3 abundance. Elevated CDK5RAP3 inhibits ribosomal RPL26 UFMylation, thereby amplifying ER stress and selectively licensing apoptosis in DNA-damaged cells. Collectively, fasting disrupts a TGF-β-InsP 6 -HDAC3 axis to drive ER stress-dependent clearance of DNA-damaged cells, enforcing tissue quality control.
    DOI:  https://doi.org/10.64898/2026.05.24.727426
  19. Adv Sci (Weinh). 2026 Jun 02. e75904
    Intramolecular Interactions between Folded and Disordered Regions Shape Ubiquilin Structure and Function.
    Jessica K Niblo, Nirbhik Acharya, Maxwell B Watkins, Carlos A Castañeda, Shahar Sukenik.
      Multidomain proteins consist of folded domains connected by intrinsically disordered regions. The flexibility afforded by the disordered regions, coupled to the structure and surface chemistry of folded regions, allows for unique structural and functional features in these proteins. Yet, how intramolecular interactions between disordered regions and folded domains affect multidomain protein structure and function remains poorly understood. Here, we use a range of biophysical and computational approaches to measure the intramolecular interactions between the folded domains and disordered regions of ubiquilins (UBQLNs), essential components of protein quality control that shuttle poly-ubiquitinated client proteins to proteasomal degradation or autophagy. Starting with the yeast UBQLN homolog Dsk2, we find that interactions between two folded domains located at the opposite ends of UBQLN bring about a closed topology. The prevalence of this closed topology, however, is modulated by intramolecular interactions involving the disordered regions and folded STI1 domain at the center of the protein. Simulations and analysis of UBQLN homologs across multiple eukaryotic lineages reveal that these disordered:folded domain interactions exist in some UBQLN homologs but are absent in others, indicating possible fundamental differences in function among proteins with the same multidomain architecture.
    Keywords:  IDR:folded domain interactions; NMR; SAXS; Ubiquilin; coarse grain models; intramolecular interactions; intrinsically disordered proteins; molecular dynamics simulations; multidomain proteins
    DOI:  https://doi.org/10.1002/advs.75904
  20. Biochim Biophys Acta Biomembr. 2026 Jun 03. pii: S0005-2736(26)00049-0. [Epub ahead of print] 184546
    Consequences of defective mitochondrial protein import: From targeting signals to pathology.
    Maya Cielo Cornejo, Sandy Che-Eun S Lee, Shaya Smith, Carla M Koehler.
      Cellular organelles are uniquely specialized membrane-bound structures that enable cells to organize and coordinate biochemical processes. Specifically, mitochondria are essential organelles for cellular metabolism, coordinating energy production, and connecting signaling networks for cellular homeostasis. 99% of mitochondrial proteins are encoded by nuclear genes that require precise and efficient translation and import into mitochondria for biological processes. This process is mediated by coordinated pathways involving the mitochondrial specific translocation complexes, chaperones, and specialized targeting routes. Tight regulation of these import mechanisms allows for proper protein localization, folding, and assembly. Disruptions in the mitochondrial protein import pathway compromise organelle homeostasis and activate proteostatic stress and quality control pathways. Such defects have been observed in a wide range of pathophysiological conditions, including cardiovascular disease, neurodegeneration, and cancer. The import defects destabilizing mitochondrial proteins can impair oxidative phosphorylation and metabolic signaling. In sum, defects to mitochondrial function can highlight a central role of mitochondrial protein import beyond maintaining cellular function and how defects at distinct stages of import contribute to disease, underscoring opportunities for therapeutic intervention targeting mitochondrial proteostasis.
    Keywords:  Mitochondria; Mitochondrial disorders; Mitochondrial protein import; Mitochondrial protein processing; Mitochondrial targeting sequence; Proteostasis; TIM23 complex; TOM complex
    DOI:  https://doi.org/10.1016/j.bbamem.2026.184546
  21. Nat Cell Biol. 2026 Jun 02.
    Nucleophagy removes cytotoxic trapped PARP1.
    Gwendoline Hoslett, Sara Tribble, Pauline Lascaux, Stelios Koukouravas, Ignacio Torrecilla, Wei Song, Cynthia X Hou, Junyi Li, Martín González-Fernández, Giuliana De Gregoriis, Rebecca A Dagg, Darragh O'Brien, Andrea Pierangelini, Thibaud Martial, Alvin Wei Tian Ng, Nuno Raimundo, Ira Milosevic, Raimundo Freire, Yuliang Li, Sven Rottenberg, Dragomir B Krastev, Christopher J Lord, Madalena Tarsounas, Kristijan Ramadan.
      Poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi) induce cytotoxicity in homologous recombination repair (HR)-deficient (HRD) cancers by trapping PARP1 on chromatin, thereby causing irreparable replication-associated DNA damage. Although increased clearance of trapped PARP1 from chromatin reduces the sensitivity of cancer cells to PARPi, details surrounding this process remain unclear. PARPi exposure is known to cause increased autophagy flux, whereas autophagy inhibition can hypersensitize cells to PARPi. Our study reveals that trapped PARP1 is cleared via nucleophagy, with the selective autophagy receptor TEX264 and its partner segregase p97 (also known as VCP) orchestrating this process. TEX264 interacts directly with trapped PARP1, linking it to the autophagosomal protein LC3 for degradation. Disrupting this pathway, either chemically or genetically, increases PARP1 trapping, resulting in protein aggregates, DNA damage and cell lethality, ultimately re-sensitizing PARPi-resistant cells. We conclude that nucleophagy serves a cytoprotective role by targeting PARPi-induced trapped PARP1 for degradation.
    DOI:  https://doi.org/10.1038/s41556-026-01961-5
  22. Cell Rep. 2026 Jun 01. pii: S2211-1247(26)00479-1. [Epub ahead of print]45(6): 117401
    Structure of the E3 ligase CRL2ZYG11B with substrates reveals the molecular basis for N-degron recognition and ubiquitination.
    Xi Liu, Yang Li, Lennice K Castro, Zanlin Yu, Yifan Cheng, Matthew D Daugherty, John D Gross.
      ZYG11B is a substrate specificity factor for the cullin-2-RING ubiquitin ligase (CRL2), which plays a critical role in the recognition and degradation of Gly/N-degrons. Yet, how ZYG11B assembles with CRL2, and how ZYG11B couples specific substrate recognition to CRL2-mediated ubiquitination, is unknown. We present the cryo-electron microscopy (cryo-EM) structures of the CRL2ZYG11B holoenzyme alone and in complex with a Gly/N-peptide from the inflammasome-forming pathogen sensor NLRP1. The structures indicate that ZYG11B folds into a leucine-rich repeat followed by two armadillo repeat domains that promote assembly with CRL2 and specific recognition of the NLRP1 Gly/N-degron that is revealed by viral protease cleavage. Our structural and functional data indicate that blocking ZYG11B recognition of the NLRP1 Gly/N-degron inhibits NLRP1 inflammasome activation by a viral protease. Overall, we show how the CRL2ZYG11B E3 ligase complex recognizes Gly/N-degron substrates, including those that are involved in viral protease-mediated activation of the NLRP1 inflammasome.
    Keywords:  CP: immunology; CP: molecular biology; Gly/N-degron; NLRP1; ZYG11B; cryo-EM
    DOI:  https://doi.org/10.1016/j.celrep.2026.117401
  23. Mol Plant. 2026 Jun 02. pii: S1674-2052(26)00191-7. [Epub ahead of print]
    Heat shock-induced zinc efflux repurposes Arabidopsis E3 ligase EMR as a molecular chaperone.
    Ho Byoung Chae, Su Bin Bae, Joung Hun Park, Seol Ki Paeng, Seong Dong Wi, Meiai Zhao, Min Gab Kim, Woe-Yeon Kim, Sang Yeol Lee.
      EMR, an Endoplasmic Reticulum Associated Degradation (ERAD)-Mediating RING finger E3 ligase initially identified as an ER-resident protein, was unexpectedly detected in the cytoplasm under ER stress conditions. This unanticipated subcellular distribution prompted us to explore the uncharacterized functions of cytoplasmic EMR. Using an integrated approach that combines bioinformatics, biochemical, and physiological analyses, we show that EMR also acts as a specific heat-responsive regulator. Heat exposure causes Zn2+ to dissociate from the RING finger domain of EMR, triggering a conformational change from monomeric to oligomeric form driven by increased hydrophobicity. This structural reorganization, mediated by Zn2+ coordination, transforms EMR's function from an E3 ligase to a molecular chaperone. Importantly, this functional switch contributes significantly to plant thermotolerance, as EMR's chaperone activity effectively prevents heat-induced protein unfolding and aggregation of vital cellular proteins. Consequently, transgenic Arabidopsis lines overexpressing EMR in an EMR-null-mutant (emr) background, 35S:EMR, showed significantly improved thermotolerance compared to wild-type and emr plants. The critical role of EMR's chaperone activity in conferring heat stress resistance was further substantiated by the observation that 35S:EMR(C/S) plants, in which EMR(C/S) primarily retains chaperone function, exhibited heat stress tolerance comparable to that of 35S:EMR plants. Proteomic profiling after heat shock identified candidate client substrates of EMR's chaperone activity, which are mainly involved in critical cellular processes such as protein translation and energy metabolism, highlighting EMR's broad cytoprotective role. Overall, these results demonstrate that the bifunctional properties of EMR are essential for environmental stress recognition and adaptive signaling, thereby driving thermotolerance in plants.
    Keywords:  E3 ligase; Heat stress perception; Molecular chaperone; Thermotolerance; Zn(2+)-mediated structural and functional switching
    DOI:  https://doi.org/10.1016/j.molp.2026.05.024
  24. bioRxiv. 2026 May 20. pii: 2026.05.20.726532. [Epub ahead of print]
    SCM-1/SCAMP Maintains Microdomain Boundaries and Cargo Sorting within the Endosomal System.
    Kam Shan Hu, Anne Norris, Wilmer Rodriguez-Polanco, Collin McManus, Inna A Nikoronova, Geoffrey G Hesketh, Anne-Claude Gingras, Maureen M Barr, Barth D Grant.
      After endocytosis, transmembrane cargo reaches sorting endosomes where it is partitioned into physically distinct recycling or degradative microdomains. While the J-domain protein RME-8/DNAJC13 is known to maintain these boundaries by actively removing degradative machinery from the recycling microdomain, other factors that contribute to this spatial organization remain poorly defined. Here, we identify the conserved tetraspan protein SCM-1/SCAMP as a key microdomain organizer, discovered through RME-8 proximity-dependent biotinylation screens in C. elegans and human cells. Leveraging the large endosomes of C. elegans coelomocytes, we show that SCM-1 is selectively enriched within the recycling microdomain. In scm-1 mutants, recycling and degradative microdomains still assemble but fail to remain spatially distinct, resulting in inappropriate microdomain overlap. This loss of boundary integrity occurs without increasing the recruitment of sorting machineries, indicating a mechanism distinct from the RME-8-mediated uncoating pathway. scm-1 mutants exhibit significant sorting defects, including misrouting of recycling cargo MIG-14/Wls and v-SNARE SNB-2/VAMP3 to late endosomes and lysosomes. We find that snb-2 mutants themselves missort MIG-14 to late endosomes and lysosomes, suggesting that SNB-2 sorting is key for recycling function. Our data suggest that both microdomains lose efficiency in scm-1 mutants, as cargo missorted into late endosomes and lysosomes is not depleted overall, and degradation of an independent ESCRT-dependent cargo is delayed. We conclude that SCM-1 ensures endosomal sorting fidelity by stabilizing microdomain boundary integrity, a process required for efficient recycling and degradation of transmembrane cargo.
    DOI:  https://doi.org/10.64898/2026.05.20.726532
  25. bioRxiv. 2026 May 18. pii: 2026.05.16.725645. [Epub ahead of print]
    Targeted extracellular degradation of LRP8 promotes ferroptosis in cancer cells.
    Fangzhu Zhao, Alex Inague, Trenton M Peters-Clarke, Yifei Chen, Snehal D Ganjave, Yun Zhang, Kun Miao, Zi Yao, Yan Wu, Madison K C Seto, Kevin K Leung, James A Olzmann, James A Wells.
      Tumor reliance on antioxidant defenses creates a vulnerability to ferroptosis, yet strategies to therapeutically disable these systems remain limited. Here, we identify targeted degradation of the selenium uptake receptor LRP8 as an effective approach to decrease the abundance of the ferroptosis-protective enzyme glutathione peroxidase 4 (GPX4). Using bispecific cytokine receptor-targeting chimeras (KineTACs) that couple LRP8 to cytokine receptor internalization pathways, we selectively direct LRP8 to the lysosome for degradation. LRP8 degradation reduces the abundance of several selenoproteins, including GPX4, lowering the cellular threshold for lipid peroxidation and sensitizing cancer cells to ferroptosis. These findings establish receptor-mediated selenium uptake as a critical, targetable node in ferroptosis resistance and demonstrate that extracellular protein degradation can be leveraged to reprogram intracellular translational dependencies in cancer cells. More broadly, this work provides a framework for exploiting nutrient acquisition pathways to overcome therapy resistance.
    DOI:  https://doi.org/10.64898/2026.05.16.725645
  26. bioRxiv. 2026 May 25. pii: 2026.05.23.727435. [Epub ahead of print]
    Nanometer-scale RNA protein clusters (RPCs) Foster Helicase Activity of DEAD-box eIF4A.
    Him Shweta, Masaaki Sokabe, Nancy Villa, Christopher S Fraser, Yale E Goldman.
      DEAD-box RNA helicases are central regulators of RNA metabolism, employing ATP-dependent mechanisms to remodel RNA structure and RNA-protein interactions, yet how helicase catalysis is coordinated with multi-subunit interactions between RNA and protein remains unresolved. Translation initiation helicase, eukaryotic initiation factor 4A (eIF4A), which acts as an intrinsically non-processive enzyme, is essential for unwinding structured mRNAs, relies on cofactors to achieve physiological activity. Here we uncover an unexpected RNA-helicase state of eIF4A, demonstrating that eIF4A forms nanometer-scale RNA-protein clusters (RPCs) of ∼2-5 MDa in presence of its physiological cofactors eIF4B and eIF4G, RNA and ATP under near-physiological concentrations. Using a single molecule approach, we directly resolve the formation of discrete clusters that recruit multiple copies of proteins with RNA upon ATP addition and show that RPC formation correlates with helicase activity in vitro . Further, we find eIF4B as a key determinant of this multi-subunit assembly. Its intrinsically disordered regions (IDRs) together with structured RNA-recognition motifs (RRMs) drive multivalent RNA-dependent clustering, critical for efficient helicase activity. Disrupting eIF4B-RNA interactions through a targeted point mutation (F139A) in the RRM reduces both the cluster size and the helicase activity, further establishing a functional link between cluster formation and catalytic activity. Consistent with these findings, in-cell diffusion measurements reveal markedly slower diffusion of wild-type eIF4B compared with the RNA-binding-deficient mutant, indicative of RPC formation within the cellular environment. Together, our results reveal regulated helicase clustering as a previously unrecognized characteristic of the translation initiation machinery, linking ATP-dependent DEAD-box helicase activity to nanometer-scale RNA-protein clusters and translation initiation regulation.
    DOI:  https://doi.org/10.64898/2026.05.23.727435
  27. Nat Commun. 2026 Jun 03.
    The mannosyltransferase DPM1 regulates the activity of ER-stress sensor IRE1 in colorectal cancer.
    Hussein Issaoui, Lina Zawil, Lola Bellone, Diogo Goncalves, Rachel Paul, Léa Di Mascio, Sonia Núñez-Vázquez, Sandrine Marchetti, Johanna Chiche, Nicolas Nottet, Simon Le Goupil, Hadrien Laprade, Lucile Bansard, Yourae Hong, Rebecca Wall, Sabine Tejpar, Caroline Truntzer, François Ghiringhelli, Suresh Poudel, Helen M Beere, Douglas R Green, Julie Pannequin, Eric Chevet, Jean-Ehrland Ricci.
      Most colorectal cancer (CRC) patients exhibit resistance to immune checkpoint blockade (ICB), limiting treatment efficacy. Activating the unfolded protein response sensor IRE1α in cancer cells can induce anticancer immune responses, yet its regulation remains unclear. Here we identify Dolichyl-Phosphate Mannosyltransferase 1 (DPM1) as a regulator of IRE1 expression and activity using BioID screen. Analysis of CRC patient RNA-sequencing data reveals that low DPM1 expression correlates with an IRE1-dependent transcriptional signature, increased immune infiltration, and improved ICB responses. Mechanistically, DPM1 ablation reduces protein glycosylation, causing chronic IRE1 activation in cancer cells and enhanced cytotoxic T cell-mediated immunosurveillance. Inhibition or knock-out of IRE1 reverses this effect. These findings establish DPM1 as a modulator of IRE1 activity that influences tumor immunogenicity, suggesting its potential as a therapeutic target to improve cancer immunotherapy outcomes.
    DOI:  https://doi.org/10.1038/s41467-026-73942-z
  28. Nat Commun. 2026 May 30.
    Improving protein and protein interactions using pseudo-dimers derived from monomeric proteins.
    Hao Du, Xinzhe Zheng, Yuchen Ren, He Huang, Xinqi Gong, Wanli Ouyang, Yang Zhang, Yan Lu.
      Accurately predicting protein-protein interactions (PPIs) in dimeric complexes remains a fundamental challenge in computational biology. Although existing PPIs prediction models, such as AlphaFold-Multimer (AF-Multimer) and AlphaFold3 (AF3), have achieved impressive performance, they still suffer from unsatisfactory accuracy due to the limited availability of protein dimer structures, whose collection is both expensive and labor-intensive. Here, we introduce a simple yet effective pre-training method, termed split and merge proxy (SMP), that leverages abundant monomeric proteins to simulate various PPIs tasks for the first time. Specifically, SMP constructs pseudo-dimers by splitting monomer data into two subunits, referred to as pseudo-receptors and pseudo-ligands, and trains models to merge them back by predicting their pseudo interactions (e.g., contact or docking). This proxy task enables large-scale pre-training without additional cost. Models pre-trained with SMP and subsequently fine-tuned on real protein dimer datasets demonstrate consistently improved accuracy and generalization across multiple benchmarks, surpassing strong baselines. Notably, SMP delivers more accurate structure predictions than both AF-Multimer and AF3 on several CASP15 dimer targets. Our findings highlight SMP as a scalable strategy for harnessing monomeric data to advance protein complex modeling, providing insights into the linkage between monomers and multimers.
    DOI:  https://doi.org/10.1038/s41467-026-73885-5
  29. Blood. 2026 Mar 12. pii: blood.2025031127. [Epub ahead of print]
    LCK-targeting molecular glues overcome resistance to inhibitor-based therapy in T-cell acute lymphoblastic leukemia.
    Jun J Yang, Satoshi Yoshimura, Marisa Actis, Justin T Seffernick, Logan McGrath, Jamie Jarusiewicz, Anup Aggarwal, Angelina Li, Yong Li, DongGeun Lee, Lei Yang, Anand Mayasundari, Zoran Rankovic, Marcus Fischer, Gisele Nishiguchi.
      Drug resistance is a major challenge in cancer therapy, especially in hematologic malignancies where kinase inhibitors have transformed treatment yet are frequently undermined by drug resistance. While targeted protein degradation (TPD) offers a mechanistically distinct mode of action compared to inhibition-based therapeutic therapies, the potential value of TPD in drug-resistant blood cancer remains unclear. Here, we report the discovery of cereblon-recruiting molecular glue degraders (MGDs) targeting LCK, an oncogenic kinase in T-cell acute lymphoblastic leukemia (T-ALL). By high-throughput screening and medicinal chemistry optimization, we developed a series of MGDs that induced CRBN-dependent degradation of LCK as well as potent cytotoxicity in T-ALL in vitro. Structure-activity relationship analysis and ternary complex modeling revealed a non-canonical degron at the LCK-CRBN interface involving the G-loop, whose mutation disrupts this interaction. Unlike inhibitors and inhibitor-based PROTACs, these MGDs engage LCK in regions distal to the ATP binding site and thus their activities in T-ALL are not affected by gate-keeper LCK mutations that drive resistance to inhibitor-based therapeutics. Taken together, our data highlights the potential of LCK-targeting MGDs as a strategy to overcome kinase inhibitor resistance in T-ALL, offering a framework for targeting kinase dependencies in drug-refractory hematologic malignancies more broadly.
    DOI:  https://doi.org/10.1182/blood.2025031127
  30. Nat Commun. 2026 Jun 04.
    GPI‑anchored protein nanoclusters license migrasome expansion and serve as exocytic platforms for migrasome.
    Xiaopeng Li, Ying Li, Renxiang Xie, Haifeng Jiao, Li Yu.
      Migrasomes are dynamic organelles that form on migrating cells and mediate intercellular communication through secretory cargo release. Expansion of migrasomes has classically been attributed to tetraspanin-enriched microdomains (TEMs). Here we show that nanoclusters of glycosylphosphatidylinositol-anchored proteins (GPI-APs) act upstream to license expansion, while TEMs provide the stabilizing scaffold. We find that GPI-AP biosynthesis is important for migrasome formation, and that insertion of the GPI anchor alone is sufficient to drive precursor expansion, producing unstable migrasomes that retract. Stimulated emission depletion (STED) microscopy resolves a meshwork of GPI-AP nanoclusters interlocked with, yet largely segregated from, tetraspanin domains in stable migrasomes. Exocytic machinery localizes to GPI-AP regions, where secretion occurs. In cells that naturally generate unstable migrasomes, elevated tetraspanin levels convert them into stable vesicles. We propose a two-module architecture generating unstable, secretion-specialized migrasomes in some cells and stable migrasomes as extracellular extensions of the secretory pathway in others.
    DOI:  https://doi.org/10.1038/s41467-026-73674-0
  31. Cell Rep. 2026 Jun 04. pii: S2211-1247(26)00579-6. [Epub ahead of print]45(6): 117501
    The C-terminal region of TENT5 proteins drives ER-associated mRNA polyadenylation via FNDC3 interaction.
    Lisa Viviani, Daniel Lacidogna, Sara Pennacchio, Maria Vittoria Mengozzi, Ugo Orfanelli, Leone Giordano, Tommaso Perini, Simone Cenci, Enrico Milan.
      Spatial regulation of mRNA polyadenylation emerges as a key mechanism shaping cellular function. The TENT5/FAM46 family comprises four non-canonical poly(A) polymerases that stabilize transcripts encoding ER-targeted proteins, with mutations linked to diseases of professional secretory cells. Using transcriptomic and proteomic profiling with systematic mutagenesis, we show how paralog-specific divergence drives distinct localization, interactions, and functions. TENT5D, the most ER-associated member, remodels the proteome, enhancing the expression of ER, ERGIC, Golgi, and lysosomal proteins. In contrast, TENT5B lacks ER targeting and regulates proteins involved in cell division. A member-specific C-terminal region that binds ER-transmembrane FNDC3 proteins is necessary and sufficient for ER localization. Mutations in this region of TENT5C, found in multiple myeloma, impair FNDC3 binding or stability, reducing immunoglobulin production and tumor-suppressive activity. Overall, we define a domain-encoded mechanism linking TENT5 localization to transcript selectivity and secretory output, with direct implications for compartmentalized mRNA regulation and development of RNA-based therapeutic strategies.
    Keywords:  CP: molecular biology; FAM46; FNDC3; TENT5; endoplasmic reticulum; multiple myeloma; polyadenylation; secretion
    DOI:  https://doi.org/10.1016/j.celrep.2026.117501
  32. Nat Commun. 2026 Jun 04.
    Prevalent gut phages encode modular adhesins mediating epithelial binding and endoplasmic reticulum trafficking.
    Gábor Apjok, Tóbiás Sári, Orsolya Méhi, András Asbóth, Lilla Barna, Dóra Sala, Ilona Gróf, Bálint Márk Vásárhelyi, Szilvia Juhász, Csaba Pál, Péter Horváth, Ede Migh, György Schneider, Colin Hill, Mária Deli, Andrey Shkoporov, Bálint Kintses.
      Bacteriophages are crucial components of the human microbiome and hold promise as therapeutic agents. Yet, their physical interactions with mammalian cells remain poorly understood. Here, we developed a high-throughput platform to identify phages that adhere to epithelial layers and the proteins that mediate this interaction. The identified phages encode immunoglobulin (Ig)-like domain-containing proteins that, when displayed on a non-adherent phage, confer epithelial binding and internalization in vitro, and increased phage retention in the mouse gut in vivo. Phages encoding these adhesins are among the most abundant and prevalent human gut phages, including crAss-like phages and myoviruses closely related to the recently proposed Flandersviridae family. Domain sequence variation alters epithelial interaction profiles, and internalized phages traffic to the endoplasmic reticulum through the Golgi apparatus, suggesting access to non-degradative internalization pathways. These findings reveal widespread phage-human interactions in the human viral community, with potential impacts on health and implications for next-generation phage therapeutics.
    DOI:  https://doi.org/10.1038/s41467-026-74031-x
  33. Autophagy. 2026 Jun 03. 1-31
    WNT2B impairs endosomal trafficking via WASHC5 to inhibit autophagy: a novel non-secretory WNT pathway.
    Danqiong Liu, Yanling Cheng, Chuxiang Huang, Kang Xie, Jianan Jie, Qingqing Zhang, Lin Lan, Peiyu Chen, Jing Xie, Hongli Wang, Lu Ren, Huiwen Li, Lanlan Geng, Sitang Gong, Yun Zhu, Yang Cheng.
      WNT2B is canonically characterized as a secreted WNT-family ligand, which is transported to the extracellular space via the endoplasmic reticulum (ER)-Golgi pathway and binds to cell surface FZDs (frizzled class receptors) to trigger downstream signaling cascades. Here, we identify a previously unrecognized non-secretory intracellular function of WNT2B in impairing endosomal trafficking to inhibit macroautophagy/autophagy, as well as a non-canonical LC3B-II-dependent autophagic secretion mechanism for WNT2B. Specifically, the non-secretory intracellular pool of WNT2B via its conserved middle domain (MD) binds to the spectrin repeat domain (SRD) of WASHC5, competitively displacing WASHC1 and thereby disrupting WASH complex assembly and inhibiting WASHC1-mediated actin polymerization on early endosomes. This disruption impairs endosomal cargo trafficking, including the core autophagy protein ATG9A, leading to defective autophagy initiation and subsequent accumulation of pro-inflammatory and pro-fibrotic factors in fibroblasts. We validated this mechanism in vivo using a TNBS-induced mouse model of chronic colitis. Fibroblast-specific wnt2b deletion restores autophagy, reduces pro-inflammatory cytokine secretion, and ameliorates intestinal fibrosis. Consistently, in Crohn disease (CD) patient tissues, elevated WNT2B in fibrotic regions negatively correlates with autophagy activity, and positively correlates with pro-fibrotic phenotypes, and clinical disease severity. Moreover, we identify a novel LC3B-II-dependent autophagic secretion pathway for WNT2B, which is distinct from the conventional ER-to-Golgi-dependent protein secretion. Collectively, our study delineates a novel non-canonical WNT2B-WASH complex-ATG9A regulatory axis through which WNT2B impairs endosomal trafficking and disrupts autophagy, ultimately amplifying inflammation and fibrosis. This study suggests that WNT2B may serve as a promising therapeutic target for CD and autophagy-associated fibrotic disorders.Abbreviations: 3-MA: 3-methyladenine; AAV: adeno-associated virus; ACTA2: actin alpha 2, smooth muscle; ARPC2: actin related protein 2/3 complex subunit 2; ATG: autophagy related; CCN3: cellular communication network factor 3; CD: Crohn disease; CK666: 2-fluoro-N-[2-(2-methyl-1H-indol-3-yl)ethyl]benzamide; COL1A1: collagen type I alpha 1 chain; Co-IP: co-immunoprecipitation; CTNNB1: catenin beta 1; DBcAMP: dibutyryl cyclic adenosine monophosphate; DPT: dermatopontin; EEA1: early endosome antigen 1; EGFR: epidermal growth factor receptor; ELISA: enzyme-linked immunosorbent assay; ER: endoplasmic reticulum; ESCRT: endosomal sorting complexes required for transport; EV: extracellular vesicle; FRAP: fluorescence recovery after photobleaching; FL: full length; FZD: frizzled class receptor; GST: glutathione S-transferase; HIF: human intestinal fibroblast; HMGB1: high mobility group box 1; IKBKB: inhibitor of nuclear factor kappa B kinase subunit beta; IL6: interleukin 6; LDELS: LC3-dependent EV loading and secretion; LPS: lipopolysaccharide; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MD: middle domain; MEFs: mouse embryonic fibroblasts; MTOR: mechanistic target of rapamycin kinase; MVB: multivesicular body; NFKB: nuclear factor kappa B; NFKBIA: NFKB inhibitor alpha; PDCD6IP: programmed cell death 6 interacting protein; PLA: proximity ligation assay; RELA/p65: RELA proto-oncogene, NF-kB subunit; SAFB: scaffold attachment factor B; SES-CD: Simple Endoscopic Score for Crohn disease; SIM: super-resolution structured illumination microscopy; SMAD3: SMAD family member 3; SQSTM1/p62: sequestosome 1; SRD: spectrin repeat domain; TEM: transmission electron microscopy; TFRC: transferrin receptor; TGFB1: transforming growth factor beta 1; TGOLN2: trans-golgi network protein 2; TNBS: 2,4,6-trinitrobenzenesulfonic acid; TNF: tumor necrosis factor; VCA: Verprolin homology, Central and Acidic; WASHC: WASH complex subunit; WLS: Wnt ligand secretion mediator; WCL: whole cell lysates; WNT: Wnt family member; WT, wild type.
    Keywords:  ATG9A trafficking; Crohn disease; WASH complex; WNT-family protein; autophagic secretion; fibrosis
    DOI:  https://doi.org/10.1080/15548627.2026.2674714
  34. Biochemistry. 2026 Jun 03.
    Structural Basis for Mechanical Coupling in Hsp90: Hinge Flexibility Coordinates ATP Gate Closure and β-Strap Release.
    Breanna Magnan, Paul LaPointe, Leo Spyracopoulos.
      Heat shock protein 90 (Hsp90) is an essential molecular chaperone that relies on coordinated, high-energy, ATP-driven conformational rearrangements to remodel a diverse array of client proteins. A central requirement of the Hsp90 catalytic cycle is the structural coupling between the ATP gate and the N-terminal β-strap. Here, we identify the C-terminal hinge of the ATP gate (G123) as a critical mechanical element mediating this coordination. Using site-specific backbone restriction, 19F nuclear magnetic resonance spectroscopy, and molecular dynamics simulations, we show that hinge plasticity is indispensable for the transition to the closed state and facilitates a primed gate conformation that precedes β-strap release. Restricting hinge flexibility mechanically decouples the β-strap from the ATP gate, trapping Hsp90 in a conformation that precludes chaperone closure. Furthermore, our studies of asymmetric heterodimers demonstrate that hinge rigidity dictates the direction of intersubunit activation or repression across the dimer interface. These findings reveal that the ATP gate hinge functions as a mechanical switch that governs the global conformational state of the Hsp90 complex. These results define a structural basis for Hsp90 activation and highlight how local backbone dynamics drive long-range regulation of the Hsp90 dimer.
    DOI:  https://doi.org/10.1021/acs.biochem.6c00292
  35. Cell Rep. 2026 Jun 04. pii: S2211-1247(26)00500-0. [Epub ahead of print]45(6): 117422
    A cross-vertebrate brain protein interaction map identifies conserved neural and non-neural complexes.
    Vy Dang, Brittney Voigt, David Yang, Gabriel Hoogerbrugge, Muyoung Lee, Rachael M Cox, Ophelia Papoulas, Claire D McWhite, Raksha Pradeep, Janelle C Leggere, Benjamin A Neely, Ryan S Gray, Edward M Marcotte.
      Protein-protein interactions underlie core brain functions, including neurotransmitter release, receptor activation, and intracellular signaling. Here, we present a compendium of protein-protein interactions conserved across vertebrate brains, spanning over 300 million years of evolution. From 2,197 biochemical fractions across five vertebrate species, we identify over 81,000 high-confidence interactions among 6,108 conserved proteins. This interaction map (VerteBrain) reveals both regulatory and structural complexes, including extensive synaptonemal protein associations likely involved in inter-neuronal coordination. Conservation across species underscores essential roles in neuronal and glial function, as well as in additional tissues for more widely expressed complexes. The VerteBrain dataset uncovers candidate disease mechanisms, including roles for ARHGEF1 in short stature syndromes, synaptic vesicle trafficking complexes in epilepsy, and RELCH (Rab11-binding and LisH domain, coiled-coil and HEAT repeat-containing) in congenital deafness. VerteBrain provides a resource for investigating brain protein interactions and their relevance to human neurological disorders.
    Keywords:  CP: neuroscience; comparative proteomics; deafness; developmental and epileptic encephalopathy; mass spectrometry; neurodevelopmental disorders; neuroproteomics; protein-protein interactions
    DOI:  https://doi.org/10.1016/j.celrep.2026.117422
  36. Sci Rep. 2026 Jun 04.
    Structural insights into predicted protein-protein interactions and protein complexes in the human proteome.
    Jimin Pei, Jing Zhang, Qian Cong.
      Large-scale computational predictions of human protein-protein interactions (PPIs) have recently enabled systematic mapping of the human interactome at near-atomic resolution. In our previous work, we reported nearly 18,000 high-confidence predicted PPIs, along with selected examples that demonstrated the ability of these predictions to reveal both pairwise associations across diverse pathways and multi-subunit complex organization. Here, we extend that study by presenting additional examples of biological and biomedical interest. We highlight novel PPIs across DNA repair, mitochondrial function, and biogenesis of cilia and other organelles, where predicted interfaces provide mechanistic hypotheses for protein function and pathway crosstalk. We also illustrate how binary predictions can be assembled into models of higher-order assemblies, uncovering new candidate subunits and organizational principles for multi-protein complexes. Importantly, we integrate structural mapping of disease-associated mutations, many of which lie directly within predicted interaction interfaces, thereby offering explanations for how genetic variation may disrupt protein networks and contribute to pathology. Together, these case studies underscore how large-scale computational predictions can be distilled into detailed mechanistic insights, generating hypotheses for functional studies and expanding the structural and functional annotation of the human interactome.
    Keywords:  AlphaFold; Ciliopathies; DNA repair pathways; Disease-associated mutations; Human interactome; Mitochondrial function; Multi-subunit complexes; Protein-protein interactions (PPIs); Structural modeling
    DOI:  https://doi.org/10.1038/s41598-026-54567-0
  37. Nucleus. 2026 Dec;17(1): 2680376
    Intrinsically disordered regions facilitate Mlp1-Nab2 recognition in mRNA quality control.
    Mohammad Soheilypour, Mohaddeseh Peyro, Hengameh Shams, Mohammad R K Mofrad.
      Quality control of mRNAs ensures that only properly processed transcripts are exported from the nucleus. Myosin-like protein 1 (Mlp1), plays a central role in this process by interacting with RNA-binding proteins (RBPs), including Nab2. While previous studies identified Phe73 in Nab2 as critical for Mlp1 binding, the molecular mechanism remains unclear. Here, we employed a computational approach to develop a mechanistic model of Mlp1-Nab2 interaction. Our results suggest that Phe73 does not act through direct contacts with Mlp1, but instead stabilizes intramolecular interactions between Nab2 helices that promote a compact conformation. F73A disrupted this helix-helix stabilization and weakened binding, whereas F73W enhanced the interaction. Our findings support a binding mechanism in which the structural flexibility of Mlp1's disordered domain enables adaptive recognition of Nab2. This mechanism may represent a general strategy by which the nuclear basket inspects mRNPs, highlighting the importance of flexible protein-protein recognition in mRNA quality control.
    Keywords:  RNA-binding proteins (RBPs); intrinsically disordered proteins; mRNA export; mRNA quality control; molecular dynamics simulations; nuclear basket; nuclear pore complex (NPC)
    DOI:  https://doi.org/10.1080/19491034.2026.2680376
  38. Mitochondrion. 2026 Jun 03. pii: S1567-7249(26)00062-0. [Epub ahead of print] 102172
    Mitochondrial C3aR and endoplasmic reticulum C5aR orchestrate calcium imbalance during oxidative stress in retinal pigment epithelial cells.
    Masaaki Ishii, Bärbel Rohrer.
      Although C3a and C5a are classically recognized as extracellular anaphylatoxins, we previously identified mitochondrial C3a receptors (mt-C3aR) in stressed RPE cells, where its activation enhanced Ca2+ uptake and inhibited oxidative phosphorylation (OXPHOS). Here, we demonstrate a second intracellular anaphylatoxin receptor, C5aR, localized to the endoplasmic reticulum (ER) by confocal and immuno-electron microscopy. ER-C5aR activation increased SERCA-dependent Ca2+ uptake and, together with mt-C3aR, facilitated ER-to-mitochondria Ca2+ transfer at mitochondria-endoplasmic reticulum contact sites (MERCS). Moreover, oxidative stress induced Gα16 redistribution, enabling its interaction with ER-C5aR. These findings reveal a novel mechanism by which intracellular anaphylatoxin receptors shape Ca2+ homeostasis and cellular stress responses.
    Keywords:  Anaphylatoxin; Calcium; Endoplasmic reticulum; Intracellular complement signaling; mitochondria-ER contacts
    DOI:  https://doi.org/10.1016/j.mito.2026.102172
  39. J Cell Biol. 2026 Aug 03. pii: e202511088. [Epub ahead of print]225(8):
    A cytosolic IF1 reporter enables real-time visualization of severe mitochondrial membrane damage.
    Erqing Gao, Liwei Guan, Kehang Zhang, Shuze Qi, Jingxiu Xu, Jie Zhang, Tianyi Zhu, Bing Yang, Chonglin Yang, Eric Miska, Mao Zhang, Suhong Xu.
      Maintenance of mitochondrial integrity is fundamental for cellular survival, yet how cells recognize catastrophic mitochondrial membrane damage remains unknown. Here, we identify MAI-1 as the first genetically encoded reporter of severe mitochondrial membrane damage. MAI-1 is a Caenorhabditis elegans homolog of the ATP synthase inhibitor IF1 that lacks a mitochondrial targeting sequence, resides in the cytosol under basal conditions, but rapidly and irreversibly translocates to severely damaged mitochondria within milliseconds. We validate MAI-1 across diverse injury paradigms and demonstrate that cytosolic IF1 variants from other species exhibit conserved damage-induced recruitment. Mechanistically, MAI-1 recruitment requires the presence of an intact ATP synthase complex. Using MAI-1 as a sensor, we uncover that these severely damaged mitochondria are cleared through the LGG-1-mediated, PINK1/PARKIN-independent lysosomal pathway. Together, our findings establish a powerful tool for visualizing severe mitochondrial membrane damage and reveal a surveillance mechanism dedicated to structural integrity control.
    DOI:  https://doi.org/10.1083/jcb.202511088
  40. PLoS One. 2026 ;21(6): e0349433
    ProtAttn-QuadNet: An attention-based deep learning framework for protein-protein interaction prediction using ProtBERT embeddings.
    Md Shahidul Islam, Md Muhtasim Rahman Mim, Md Raihan Kabir.
      Protein-protein interactions (PPIs) form the backbone of most cellular processes, governing signal transduction, gene regulation, and metabolic control. However, experimental approaches to identifying PPIs remain expensive, laborious, and often incomplete. Recent advances in protein language models (PLMs) have transformed sequence-based PPI prediction by enabling deep contextual encoding of biochemical and structural information directly from amino acid sequences. Building upon this progress, we present ProtAttn-QuadNet, an attention-based deep learning framework that leverages ProtBERT embeddings to model reciprocal dependencies between protein pairs. The proposed model employs a quad-stream attention mechanism that integrates individual protein features, synergistic interactions, and complementary differences through multi-level self- and cross-attention layers. This architecture enables the discovery of fine-grained relational patterns while ensuring balanced bidirectional modeling of interacting proteins. Evaluated on the independent test set of a large-scale dataset from UniProt, ProtAttn-QuadNet achieves 97.16% accuracy (AUC-ROC 99.00%) on balanced data and 99.19% accuracy (AUC-ROC 99.76%) on oversampled datasets, surpassing several recent state-of-the-art PPI prediction methods. Statistical validation using the Chi-square and Wilcoxon signed-rank tests confirms the model's predictive significance and reliability. ProtAttn-QuadNet offers a powerful computational framework for large-scale PPI prediction.
    DOI:  https://doi.org/10.1371/journal.pone.0349433
  41. Cell Rep. 2026 Jun 02. pii: S2211-1247(26)00580-2. [Epub ahead of print]45(6): 117502
    DCAF8 binds DDB1 via an N-terminal helix-loop-helix motif to assemble CRL4 and promote cell cycle progression.
    Miaomiao Shen, Hang Zhang, Min Chen, Jiaqi Yang, Zhiguang Yuchi, Huawei Zhang, Liren Liu.
      Cullin-RING ligase 4 (CRL4) complexes achieve substrate specificity through DDB1-CUL4-associated factors (DCAFs), yet how individual DCAFs engage the adaptor protein DDB1 remains incompletely understood. Here, we report the cryo-electron microscopy structure of DCAF8 in complex with DDB1 (2.53 Å) and define the molecular determinants underlying CRL4DCAF8 assembly and cell cycle progression. Our structure reveals that DCAF8 associates with DDB1 primarily through an N-terminal helix-loop-helix (HLH) motif that inserts into a conserved pocket formed by the BPA and BPC domains of DDB1. Disruption of this interface impairs complex assembly, attenuates CDC25A ubiquitination, and results in cell cycle defects. In contrast, residues within the conserved double DxR box of DCAF8 are positioned away from the DDB1 interface and are dispensable for adaptor binding. Together, these findings define a DCAF8-specific recruitment mechanism within CRL4 ubiquitin ligase assemblies.
    Keywords:  CDC25A; CP: molecular biology; CRL4 ubiquitin ligase; DCAF8-DDB1 complex; cell cycle; cryo-EM
    DOI:  https://doi.org/10.1016/j.celrep.2026.117502
  42. Biol Direct. 2026 Jun 01.
    Deep learning-driven decoding of ubiquitination: from regulatory mechanisms to targeted protein degradation.
    Jiaqi Zhang, Boyu Xia, Zhe Wang, Zhixiong Wang, Yanmei Sun, Han Wang, Xinhao Li, Xin Gao, Weijie Zhao, Yunxin Li, Feilong Zhou, Tianyi Chen, Zonghan Shi, Junxian Lv, Ruowei Yang, Yewei Zhang.
       BACKGROUND: Ubiquitination is a highly dynamic post-translational modification that plays central roles in protein homeostasis, signal transduction, immune regulation, and cell fate control. Through the coordinated actions of E3 ubiquitin ligases and deubiquitinating enzymes, ubiquitination shapes the ubiquitin-proteasome system and influences a wide range of physiological and pathological processes. Dysregulation of this system is closely associated with cancer, neurodegenerative disorders, immune dysfunction, and metabolic disease. However, a comprehensive understanding of ubiquitination remains limited because of incomplete annotation, context-dependent regulation, transient molecular interactions, and highly complex many-to-many regulatory networks.
    MAIN BODY: In this review, we summarize how deep learning is reshaping ubiquitination research at multiple levels. First, we outline the major deep learning architectures applied in this field, including convolutional neural networks, recurrent neural networks, Transformers, protein language models, graph neural networks, generative models, and reinforcement learning. Second, we review recent progress in predicting ubiquitination sites and ubiquitin chain-related features, with emphasis on sequence-based, structure-informed, and multimodal representation learning strategies. Third, we discuss how deep learning contributes to mechanistic decoding of ubiquitination specificity, including substrate recognition by E3 ubiquitin ligases and deubiquitinating enzymes, degron identification, and the organization of ubiquitination regulatory networks. Fourth, we highlight the translational relevance of these approaches in biomarker discovery, targeted protein degradation, molecular glue discovery, degrader optimization, and ubiquitin-centered therapeutic design. Collectively, these advances show that deep learning is not only improving predictive accuracy, but also enhancing mechanistic interpretability and enabling rational molecular design.
    CONCLUSION: Deep learning is driving ubiquitination research from descriptive prediction toward mechanistic understanding and therapeutic application. Future progress will depend on developing more interpretable models, integrating physiological context, and strengthening experimental validation. Such efforts will accelerate the translation of ubiquitin biology into clinically useful biomarkers, precision diagnostics, and targeted therapies.
    Keywords:  Deep learning; Degron; E3 ubiquitin ligase; Molecular design; Protein language model; Targeted protein degradation; Ubiquitination; Ubiquitin–proteasome system
    DOI:  https://doi.org/10.1186/s13062-026-00848-7
  43. bioRxiv. 2026 May 28. pii: 2025.09.21.676939. [Epub ahead of print]
    An image-based CRISPR screen reveals splicing-mediated control of HP1α condensates.
    Matthew Man-Kin Wong, Shaopu Zhou, Chris Carpenter, Raeline Valbuena, Monika Priyadarshini, Aishwarya Arya, Aoon Rizvi, Catherine Carswell-Crumpton, Amelie Wileveau, Gabriel Lopez-Lopez, Josh Tycko, David Yao, Kaitlyn Spees, Jason C Maynard, Michael C Bassik, Hani Goodarzi, Serena Sanulli.
      Heterochromatin Protein 1α (HP1α) is a fundamental component of constitutive heterochromatin, forming subnuclear condensates whose regulation and function remain poorly understood. Here, we present an image-based CRISPR screen targeting nuclear factors that identifies splicing as a pivotal pathway regulating HP1α condensates. We discovered that unspliced intronic RNA modulates HP1α condensates by interacting co-transcriptionally with HP1α. By modulating the intron content, RNA processing restricts HP1α-RNA interactions at chromatin, thus enabling heterochromatin organization. Disruption of HP1α condensates due to enhanced interactions with unspliced RNA leads to loss of heterochromatin and the activation of stress response protective genes. We propose that RNA is a central component of heterochromatin that modulates HP1α condensates, and that RNA processing enzymes act as a surveillance mechanism for condensates by dynamically regulating the network of multi-valent interactions between RNA and chromatin factors. This model underscores the crosstalk between chromatin organization, transcription, and RNA processing, potentially governing broader nuclear functions.
    DOI:  https://doi.org/10.1101/2025.09.21.676939
  44. bioRxiv. 2026 May 03. pii: 2026.04.29.721714. [Epub ahead of print]
    Molecular insights into protein disulfide isomerase antagonism by punicalagin.
    Osamede C Owegie, Quinn P Kennedy, Ivan Hancco Zirena, Oren Levy, Pavel Davizon-Castillo, Moua Yang.
      Punicalagin, an ellagic acid polyphenol from pomegranate, has been proposed as an antagonist of protein disulfide isomerase (PDI) and endoplasmic reticulum resident protein 57 (ERp57), thiol oxidoreductases that regulate protein folding and extracellular thrombotic signaling. Here, biochemical oxidase and reductase assays on PDI show that punicalagin inhibits both activities with micromolar potency, thereby extending earlier work that described only disulfide reductase inhibition. In parallel, thiol labeling of catalytic cysteines revealed no change in the redox state, supporting a noncovalent, allosteric of inhibition. Molecular docking and molecular dynamics simulations showed that punicalagin binds stably and preferentially to defined sites on the N⍰terminal domains of PDI through extensive hydrogen bonding and van der Waals contacts, which is an alternative binding mode to previously reported C-terminal binding. Finally, artificial intelligence-driven network analysis identified PDI as a high-confidence target of punicalagin and related galloylated polyphenols, alongside additional signaling proteins. Together, these findings provide further mechanistic framework for punicalagin-mediated antagonism of PDI and highlight galloylated polyphenols as promising scaffolds for protein disulfide isomerase-targeted therapeutics.
    Highlights: Punicalagin, a galloylated polyphenol, antagonizes not only the reductase activity but also the oxidase activity of protein disulfide isomeraseProtein disulfide isomerase inhibition by punicalagin is through N-terminal bindingPunicalagin inhibits conformationally rather than catalytic cysteine modificationArtificial intelligence network analysis reveals pathway inhibition by punicalagin.
    DOI:  https://doi.org/10.64898/2026.04.29.721714
  45. bioRxiv. 2026 May 29. pii: 2026.05.26.727520. [Epub ahead of print]
    Cell autonomous inflammation in VEXAS is mediated by cGAS-STING.
    Samuel J Magaziner, Jason C Collins, Brecca Miller, Patrick Zheng, Amy K Wang, Jerome Hadjadj, Juan Carlos Baladrán, Maria Sirenko, Maya English, James Bertlin, Rebecca Murray, Peter H Whitney, Tania J González-Robles, Deborah Rivera, Yan Wang, Duy T Tran, Zulfeqhar A Syed, Valentina Baena, Timothee Lionnet, Kelly V Ruggles, Iannis Aifantis, Dan A Landau, Achim Werner, David B Beck.
      VEXAS (vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic) is a severe adult-onset inflammatory disease caused by somatic mutations that reduce cytoplasmic activity of UBA1, the primary initiating enzyme for ubiquitylation. How this hypomorphic state drives cell-intrinsic immune activation in mature myeloid cells is unknown. Using unbiased multi-omic, biochemical, and cell biological analyses of model systems and patient-derived cells, we show that loss of cytoplasmic UBA1 activity convergently disrupts endoplasmic reticulum- associated degradation (ERAD) and mitochondrial homeostasis. ERAD failure arises from preferential under-charging of ERAD E2 enzymes, explaining hallmark VEXAS features, including ER-derived vacuoles and unfolded protein response activation, and promotes accumulation of the ERAD substrate STING. Simultaneously, mitochondrial dysfunction drives cytosolic leakage of mitochondrial DNA, inducing cGAS-dependent STING signaling and inflammatory cytokine production. STING inhibition or reversal of mitochondrial DNA leakage resolves multi-cytokine inflammation in VEXAS models and patient myeloid cells, establishing the cGAS-STING pathway as a therapeutically actionable vulnerability.
    DOI:  https://doi.org/10.64898/2026.05.26.727520
  46. Am J Hypertens. 2026 Jun 03. pii: hpag052. [Epub ahead of print]
    Dissociation of UPR signaling and ER ultrastructure during 4-PBA therapy in shunt-driven pulmonary hypertension.
    X R Xu, L Chen, K Y Sun, X B Qin, C Y Zhang, J Li, B Tang, F Li, J G Wang.
       BACKGROUND: Pulmonary arterial hypertension associated with congenital heart disease (PAH-CHD) arises from chronic left-to-right shunting and high-flow exposure, leading to pulmonary vascular remodelling and right-heart dysfunction. Whether high-flow shunting induces branch-selective unfolded protein response (UPR) activation and endoplasmic reticulum (ER) structural adaptation in pulmonary vascular smooth muscle remains incompletely defined.
    METHODS: Rats underwent right pulmonary artery ligation combined with left common carotid artery-external jugular vein shunting (RPAL/LCS), with or without 4-phenylbutyric acid (4-PBA) treatment. Hemodynamics, right-heart function, vascular remodeling, UPR signaling, transcriptomic profiles, apoptosis, and ER ultrastructure were assessed in vivo or in HPASMC gain- and loss-of-function experiments.
    RESULTS: RPAL/LCS increased RVSP from 22.46 ± 1.68 to 59.66 ± 7.06 mmHg, whereas 4-PBA reduced RVSP to 38.24 ± 1.71 mmHg. The wall area/total vessel area ratio increased from 46.88 ± 1.69% to 77.89 ± 3.08% after RPAL/LCS and decreased to 47.19 ± 2.00% after 4-PBA treatment. Lung immunoblotting showed increased p-IRE1α/IRE1α, whereas p-PERK/PERK and ATF6N/ATF6 did not differ significantly; these proximal UPR markers were not reduced by 4-PBA at the endpoint. In HPASMCs, ATF4 and ATF6N overexpression enriched apoptosis-related programs and induced ER swelling and fragmentation, whereas XBP-1s overexpression maintained organized ER cisternae and XBP-1s knockdown disrupted ER ultrastructure with increased Annexin V-positive apoptotic cells.
    CONCLUSIONS: This study suggests that the IRE1α-XBP1s axis supports adaptive ER proteostasis and structural organization in shunt-driven pulmonary hypertension, whereas 4-PBA improves disease features without measurable suppression of canonical UPR branch activation markers.
    Keywords:  4-PBA; IRE1α; XBP-1s; endoplasmic-reticulum stress; pulmonary arterial hypertension; unfolded protein response
    DOI:  https://doi.org/10.1093/ajh/hpag052
  47. bioRxiv. 2026 May 19. pii: 2026.05.17.725791. [Epub ahead of print]
    Nascent protein retention at polysomes reduces kinetic barriers to self-assembly.
    Shriram Venkatesan, Alex Von Schulze, Jeffrey J Lange, Jacob Jensen, Lexie E Berkowicz, Dai Tsuchiya, Ning Zhang, Jennifer Gardner, Scott McCroskey, Ying Zhang, Selene Swanson, Yan Hao, Malcolm Cook, Tong Shu, Liam J Holt, Laurence Florens, Jay R Unruh, Randal Halfmann.
      Living proteomes are necessarily far from equilibrium. It is paradoxical, then, that reducing the translation of new proteins -- which should promote equilibration -- instead prolongs life. We investigated the impact of translational flux to nucleation barriers that preserve the solubility of proteins destined to form amyloids or other assemblies. By manipulating translation initiation rates directly or indirectly, across yeast and human cells, and across a variety of supersaturable proteins, we find that accelerating translation initiation broadly accelerates nucleation irrespective of their global concentrations. We showed that this effect was confined to polysomes and was enhanced by N-terminal placement or other features that retained the nascent aggregating domain at polysomes. Finally, we show that intrinsically disordered regions with high tendencies to self-associate are specifically positioned to do so co-translationally, providing evidence that cotranslational nucleation has shaped proteome evolution.
    DOI:  https://doi.org/10.64898/2026.05.17.725791
  48. bioRxiv. 2026 May 24. pii: 2026.05.21.726761. [Epub ahead of print]
    TSC2 is a stress granule suppressor.
    Yizhe Ma, Natalie G Farny.
      Stress granules (SGs) are dynamic, membrane-less ribonucleoprotein assemblies that form through liquid-liquid phase separation to prioritize stress-survival proteostasis. Through reanalysis of a Drosophila genome-wide RNAi screen, we identified a set of conserved SG suppressor genes and validated the top candidate, Tsc2, in both mouse and human cell lines. We illustrate that the complete loss of Tsc2 leads to spontaneous, canonical, and translation-dependent SGs driven by mTORC1 hyperactivation in mouse embryonic fibroblasts (MEFs). In addition, the Tsc2 -deficient MEFs also sensitized to endoplasmic reticulum stress, delaying SG clearance. In human cell lines, the siRNA-mediated partial reduction of TSC2 in U2OS cells, and in human tuberous sclerosis patient fibroblasts, does not induce spontaneous SGs. Instead, the sensitivity to ER stress, translation perturbation, and delay in clearance correlate with the remaining levels of TSC2, suggesting that TSC2 functions as a threshold-dependent regulator of SG assembly. Together, our findings provide a comprehensive list of novel conserved SG regulators and establish TSC2 as a key regulator of SG dynamics.
    DOI:  https://doi.org/10.64898/2026.05.21.726761
  49. bioRxiv. 2026 May 21. pii: 2026.05.19.726393. [Epub ahead of print]
    Structural Pockets and Interacting RNA-Associated Ligands (SPIRAL): A DSSR-enabled Meta-Analysis of RNA-Small Molecule Recognition.
    Xiang-Jun Lu, Yaqiang Wang.
      Small molecules that target structured RNA hold therapeutic promise across a wide range of diseases, yet the structural principles governing RNA-ligand recognition remain poorly defined. Here we present SPIRAL (Structural Pockets and Interacting RNA-Associated Ligands), a curated database of 1,098 RNA-small molecule structures from the Protein Data Bank covering 1,137 ligand-binding events across six functional RNA categories: riboswitches, ribozymes, synthetic aptamers, G-quadruplexes, ribosomal RNA, and regulatory RNA motifs. A customized pipeline built on DSSR (Dissecting the Spatial Structure of RNA) extracts structural interaction parameters from each complex, capturing stacking geometry, hydrogen-bond topology by RNA moiety, backbone contacts, groove engagement, and tertiary motif context. Unsupervised clustering of these fingerprints resolves six mechanistically distinct binding modes whose distribution is strongly governed by RNA functional class, demonstrating that different RNA categories engage small molecules through fundamentally different chemical strategies. To enable category-independent comparison of interaction quality across these mechanistically diverse modes, we introduce the Composite Binding Quality Score (CBQS), a seven-metric framework that ranks riboswitches highest and regulatory RNA motifs lowest among the six categories, while ribozymes, synthetic aptamers, and G-quadruplexes achieve statistically equivalent intermediate scores through three distinct recognition strategies. Analysis of 275 non-redundant affinity-characterized entries identifies C2'-endo sugar pucker count and total buried contact surface area as the dominant independent predictors of binding affinity. Both predictors are enriched at junction loops, pseudoknots, and base multiplet networks, the same tertiary structural sites most under engaged by current regulatory RNA motif binders, suggesting that ligands designed to contact these sites would improve both potency and selectivity simultaneously.
    DOI:  https://doi.org/10.64898/2026.05.19.726393
  50. Eur J Pharmacol. 2026 Jun 04. pii: S0014-2999(26)00515-7. [Epub ahead of print] 179033
    Ribosome impairment, tau alternative splicing, and stress granules: a convergent axis of neuronal vulnerability driving Alzheimer's disease.
    Mirco Masi, Chiara Oliviero, Stefano Govoni, Benjamin Wolozin, Marco Racchi, Erica Buoso.
      Alzheimer's disease (AD) is a multifactorial neurodegenerative disorder characterized by the pathological aggregation and deposition of amyloid-β (Aβ) plaques and tau neurofibrillary tangles. However, accumulating evidence points at the disruption of RNA metabolism and translational control as central players in the disease progression. Emerging studies suggest that pathogenic mechanisms previously considered separately - namely ribosome biogenesis impairment, dysregulation of tau alternative splicing, and persistent stress granule (SG) formation - could be components of an integrated axis of neuronal vulnerability contributing to early AD pathogenesis. In AD, ribosomal loss and rDNA transcriptional silencing correlate with tau hyperphosphorylation and tau-ribosome interaction, while SG-mediated sequestration of splicing factors may exacerbate 3R/4R tau imbalance, promoting aggregation-prone isoforms. These processes appear to mutually reinforce through neuroinflammation and chronic translational stress, driving progressive proteostatic failure and cognitive decline. Converging evidence across systems (histopathological, in vivo and in vitro models) strongly suggest the existence of a ribosome-tau splicing-SG axis that operates at a pre-aggregative phase of the disease. In this context, this early disruption of translational homeostasis may trigger neuronal vulnerability decades before Aβ and tau aggregation as well as symptomatic disease. In this review, we synthesize current evidence supporting a stepwise, feed-forward model that links ribosome dysfunction, splicing alterations, and chronic SG persistence in AD. Our hypothesized integrated framework highlights potential pharmacological routes each capable of targeting distinct pathogenic nodes of the axis to restore translational homeostasis and reduce neuronal vulnerability, thus outlining potential upstream intervention strategies beyond the traditional Aβ- and tau-centric therapeutic approaches.
    Keywords:  RNA-binding protein (RBPs); liquid-liquid phase separation (LLPS); nucleolar stress response; proteostasis; rDNA silencing; tau 3R/4R ratio
    DOI:  https://doi.org/10.1016/j.ejphar.2026.179033
  51. Nat Commun. 2026 Jun 05.
    Adhesion-derived condensates control component availability to regulate adhesion dynamics.
    Michal Dibus, Megan R Chastney, Giray Enkavi, Gautier Follain, Omkar Joshi, Ilpo Vattulainen, Johanna Ivaska.
      Integrin adhesion complexes mediate dynamic cell-matrix interactions to regulate cell adhesion, migration and invasion. While increasing evidence suggests that adhesion components can undergo liquid-liquid phase separation, the functional relevance of adhesion-derived condensates remains elusive. Here, we demonstrate that tensin 1 (TNS1), a multidomain adaptor protein linking active integrins with the actin cytoskeleton, forms condensates in cells to regulate adhesion component availability. We show that endogenous TNS1 condensates are formed upon focal adhesion disassembly or limited integrin-extracellular matrix engagement, acting as reversible reservoirs for unphosphorylated adhesion proteins. We identify the TNS1 intrinsically disordered region as governing TNS1 condensation and condensate biophysical properties. We further demonstrate a negative regulatory role for phosphorylation on condensate assembly upon stress-responsive kinase activation. Finally, we confirm the functional effects of TNS1 condensation on adhesion dynamics and cell migration, identifying a feedback loop acutely regulating kinase-mediated adhesion turnover upon integrin activation.
    DOI:  https://doi.org/10.1038/s41467-026-74001-3
  52. bioRxiv. 2026 May 23. pii: 2026.05.21.726899. [Epub ahead of print]
    AE-PocketMiner Uses Attention to Simultaneously Predict Cryptic Pockets and Their Allosteric Coupling.
    Si Zhang, Prajna Mishra, Devin Kelly, Rachit Kumar, Gregory R Bowman.
      Finding and targeting cryptic pockets could dramatically expand the druggable proteome. However, discovering these sites remains challenging since they are only open a fraction of the time. It is also difficult to predict the functional relevance of a cryptic site as this often requires insight into allostery. Here we introduce attention enabled (AE-)PocketMiner, an artificial intelligence (AI) method that uses a graph neural network with an attention mechanism to simultaneously predict the locations of cryptic pockets and their allosteric coupling to the rest of the protein from a single input structure. We show that AE-PocketMiner outperforms past methods for identifying cryptic pockets and recapitulates known allosteric interactions. Moreover, we experimentally confirm newly predicted cryptic pockets and mutations that allosterically control pocket opening. AE-PocketMiner thus provides a powerful framework for multiple steps of the drug discovery process-including pocket identification, prioritization, and assay design-that will help expand the druggable proteome.
    DOI:  https://doi.org/10.64898/2026.05.21.726899
  53. Drug Des Devel Ther. 2026 ;20 602287
    Beyond Inhibition: Rebalancing the Hsp90 Chaperone Network as a Therapeutic Strategy for Alzheimer's Disease.
    Zhikang Tang, Haiyu Xie, Yongxing Xu, Zhenhong Zhou, Feng Lu, Qiaozhen Wu, Weidong Liang, Maolin Zhong, Shihong Li.
      Alzheimer's disease (AD) is characterized by the pathological accumulation of misfolded amyloid-β (Aβ) and tau, driven by dysfunction of the proteostasis network in which the molecular chaperone heat shock protein 90 (Hsp90) is a central regulator. Here, we propose a shift from pan-inhibition of Hsp90 to rebalancing: selectively normalizing pathological co-chaperone assemblies while preserving homeostatic chaperone functions. We first summarize how specific co-chaperones (eg, FK506-binding protein 51 (FKBP51), activator of Hsp90 ATPase homolog 1 (Aha1), cell division cycle 37(Cdc37)) shift Hsp90 toward tau stabilization, whereas others (eg, C-terminus of Hsc70-interacting protein (CHIP), FK506-binding protein 52 (FKBP52)) promote tau clearance, and we outline Hsp90's context-dependent effects on Aβ. We then trace the evolution of therapeutic strategies from N-terminal ATPase inhibitors, which have shown limited clinical efficacy, to precision approaches including allosteric C-terminal modulators, co-chaperone-selective protein-protein interaction (PPI) inhibitors, induction-based microglial clearance strategies, and epichaperome disruptors. We conclude by critically discussing translational challenges, including blood-brain barrier (BBB) penetration, isoform selectivity, biomarker development, and long-term safety, noting that most current evidence remains preclinical. Rebalancing the Hsp90 chaperone network, rather than inhibiting it indiscriminately, offers a mechanistically grounded yet experimentally early avenue to disease-modifying therapy for AD.
    Keywords:  Alzheimer’s disease; heat shock protein 90; molecular chaperones; proteostasis; tauopathy
    DOI:  https://doi.org/10.2147/DDDT.S602287
  54. bioRxiv. 2026 May 19. pii: 2026.05.18.725941. [Epub ahead of print]
    Mapping the interactome of human tRNA methyltransferase TRMT1 using dual proximity labeling.
    Angel D'Oliviera, Sophie Olson, Harrison Bernhard, Yanbao Yu, Jeffrey S Mugridge.
      Transfer RNA methyltransferase 1 (TRMT1) installs N2-methylguanosine and N2,N2-dimethylguanosine modifications at position 26 of mammalian tRNAs, supporting tRNA structure, translation, and cellular response to redox stress. However, the local environment and interactome of TRMT1 in the cell is poorly defined. Here, we use APEX2-based proximity labeling of the N- and C-terminus of TRMT1, coupled with label-free quantitative proteomics to map candidate TRMT1-proximal proteins in HEK293T cells. Mass spectrometry data was acquired using both data-independent acquisition (DIA) and data-dependent acquisition (DDA) methods, and it was found that DIA substantially increased proximity proteome coverage, reproducibility, and the number of significantly enriched candidate hits compared to the DDA method. N- and C-terminal APEX2-TRMT1 constructs captured largely overlapping proteomes, suggesting the dual-labeling strategy provides a robust map of proximal proteins. Analysis of the significant TRMT1-proximal proteins reveals enrichment in RNA processing and ribonucleoprotein-associated factors, in addition to hits connected to tRNA modification, tRNA biogenesis, and redox-associated biology. These data provide a proteome-scale view of TRMT1-associated cellular proteins and environments, and lay the groundwork for future validation of functional TRMT1 interaction networks.
    Significance: Fusing APEX2 enzyme to both N-terminal and C-terminal of the bait enhanced the sensitivity for identification of protein interactions.Combining APEX2-based endogenous labeling with DIA mass spectrometry increases reproducibility and depth of proximity proteome.The study provides a rich source of potential interacting or proximally close proteins to TRMT1, which warrants further validation studies.
    DOI:  https://doi.org/10.64898/2026.05.18.725941
  55. J Cell Sci. 2026 Jun 04. pii: jcs.264678. [Epub ahead of print]
    Progerin-induced nuclear envelope remodeling is shaped by cell division and NUP153.
    Ayse Mubine Turkmen, Jing Wang, Adam Frost, Katharine S Ullman.
      The nuclear envelope (NE) undergoes dynamic remodeling during both physiological and pathological processes. Nuclei in cells from patients with accelerated aging diseases and from elder individuals are often lobular and convoluted. Despite extensive study, the steps of phenotype acquisition and the co-factors required are not yet fully understood. Here, we focused on progerin, a mutant form of lamin A that causes Hutchinson Gilford Progeria Syndrome (HGPS). Using an inducible cell-based system, we characterized two distinct stages of NE remodeling. Correlative light and electron microscopy of interphase-arrested cells showed that prior to cell division, progerin primarily affects the inner nuclear membrane (INM), inducing focal expansion, invagination, and the formation of multi-membranous structures, while the outer nuclear membrane remains largely unaffected. These focal regions of progerin accumulation are enriched for specific INM proteins and the nucleoporin NUP153 but largely exclude nuclear pore complexes. Live and fixed image analysis demonstrated that, upon cell division and NE reassembly, progerin-expressing cells develop pronounced nuclear lobulations characteristic of HGPS. Appreciation of this stepwise development of phenotype lends insight into cellular manifestations of aging in mitotic versus post-mitotic cell types and provides a system in which to study factors that contribute to these distinct stages in the disruption of nuclear morphology. Depletion of NUP153 reduced NE foci formation in interphase-arrested cells expressing GFP-progerin, suggesting NUP153 promotes or stabilizes INM invagination. Aberrant nuclear architecture is just one cellular feature that changes during normal and accelerated aging but its etiology provides a critical framework for understanding accompanying consequences on chromatin packaging, DNA damage, and the ER stress response.
    Keywords:  Hutchinson-Gilford progeria syndrome; NUP153; Nuclear envelope remodeling; Nuclear membrane deformation; Nuclear morphology; Progerin
    DOI:  https://doi.org/10.1242/jcs.264678
  56. Prog Biophys Mol Biol. 2026 Jun 03. pii: S0079-6107(26)00039-8. [Epub ahead of print]
    Proteostasis driven redox adaptation in ferroptosis: the p62-Keap1-Nrf2 axis.
    Nilufer Ercin, Merve Beker, Nail Besli, Ulkan Celik.
      Ferroptosis is an iron dependent form of regulated cell death driven by excessive lipid peroxidation and implicated in numerous pathological conditions. While current research has largely focused on lipid metabolism and antioxidant systems, the contribution of upstream disturbances in protein homeostasis remains insufficiently integrated into ferroptosis frameworks. p62 is a multifunctional adaptor protein involved in ubiquitin mediated proteostasis, selective autophagy, and redox signaling. Emerging evidence indicates that alterations in p62 turnover occur under cellular stress conditions associated with ferroptosis and influence the Keap1-Nrf2 (NFE2L2) signaling axis, thereby linking proteostasis imbalance to redox regulation. However, the functional implications of this interaction remain fragmented across experimental systems. In this review, we integrate recent findings on the p62-Keap1-Nrf2 pathway in ferroptosis related processes, emphasizing its roles in redox buffering, autophagic flux, and cellular stress adaptation. Rather than directly executing ferroptosis, the p62-Keap1-Nrf2 axis is better understood as a regulatory system linking proteostasis to redox balance. We propose a conceptual framework in which ferroptosis emerges from a dynamic balance between proteostasis integrity, redox buffering capacity, iron metabolism, and lipid oxidative stress.
    Keywords:  Autophagy; Keap1-Nrf2 axis; ferroptosis; p62; proteostasis; redox regulation
    DOI:  https://doi.org/10.1016/j.pbiomolbio.2026.05.007
  57. bioRxiv. 2026 May 21. pii: 2026.05.18.726057. [Epub ahead of print]
    Neutrophils repurpose the nucleolus as a cytokine reservoir and secretory organelle.
    Shuying Xu, Asya Smirnov, Rachel L Kinsella, Ananda Rankin, Ashley D Wise-Mitchell, Jessica M Alexander, Benjamin Patty, Sophie M Mikhail, Rachel M Bello, Darren Kraemalmeyer, Sebastian Boluarte, Aamir Khan, Benjamin L Allsup, Sheikh Mahmud, Bryan D Bryson, Joshua T Mattila, Eric L Greer, Siyuan Ding, Regina A Clemens, Andrew J Monteith, Eliezer Calo, Christina L Stallings.
      Type I interferons (IFN-I) are critical for antiviral defense but can drive severe pathology when dysregulated. Excess IFN-I is associated with prominent neutrophil accumulation; however, the contribution of neutrophils to IFN-I overproduction remains underexplored. In all cell types previously studied, IFN-I is synthesized de novo following sensing of microbial or host-derived inflammatory stimuli. Contrary to this paradigm, we find that neutrophils express IFNα during development and store it in the nucleolus, a membrane-less intranuclear condensate classically functioning in ribosome biogenesis. TLR-mediated bacterial sensing induces a nucleolar stress response in neutrophils that triggers rapid release of nucleoli-stored IFNα independent of de novo protein synthesis. These findings reveal that neutrophils have repurposed the nucleolus as a cytokine storage and secretory organelle, identify the first naturally occurring immunoregulatory function of nucleolar stress, and provide insight into the relationship between detrimental IFN-I levels and neutrophil accumulation.
    DOI:  https://doi.org/10.64898/2026.05.18.726057
  58. Med. 2026 Jun 05. pii: S2666-6340(26)00178-9. [Epub ahead of print] 101175
    Inhibiting glycan degradation prevents HIV-induced inflammaging and cognitive impairment.
    Leila B Giron, Alejandra Borjabad, Eran Hadas, Janeway Granche, Erika G Marques de Menezes, Thomas A Premeaux, Hongxia He, Stephen T Yeung, Shalini Singh, Courtney Friday, Joshua Glover, Eric Balboa, Derrick Dopkin, Michelle Burrows, Anthony Secreto, Nicolas Skuli, Hiroaki Tateno, Paul W Denton, Frank Palella, Michael J Corley, Lishomwa C Ndhlovu, Philip J Norris, Katherine Tassiopoulos, David J Volsky, Mohamed Abdel-Mohsen.
       BACKGROUND: Cognitive impairment is a frequent outcome of chronic viral infections linked to premature aging, including HIV. The mechanisms underlying this decline remain poorly understood. Here, we identify pro-inflammatory glycan degradation, characterized by loss of sialic acid and galactose, both hallmarks of premature aging, as a key contributor to HIV-associated cognitive impairment (HIV-CI).
    METHODS: We analyzed two cohorts of people with HIV, with and without HIV-CI, and tested causality through intervention studies in two complemetary mouse models of virally mediated inflammation and cognitive deceline.
    FINDINGS: Degradative glycomic changes were enriched in people with HIV with cognitive impairment, particularly females, and correlated with worse cognitive performance. In both a humanized mouse model of HIV and EcoHIV model, a complementary model that enables cognitive testing, pharmacological inhibition of glycan degradation with sialidase inhibitors prevented virally induced inflammation, immune activation, accelerated aging, and memory deficits.
    CONCLUSIONS: These findings implicate glycan degradation as a contributor to inflammation and cognitive impairment in HIV and highlight glycan preservation as a promising strategy to mitigate inflammation, premature aging, and cognitive decline during viral infections.
    FUNDING: This study was funded by the National Institutes of Health (NIH).
    Keywords:  HIV-CI; HIV-associated cognitive impairment; biological aging; glycosylation; neuroinflammation; sialidase inhibitors; translation to patients
    DOI:  https://doi.org/10.1016/j.medj.2026.101175
  59. Trends Mol Med. 2026 Jun 04. pii: S1471-4914(26)00115-2. [Epub ahead of print]
    Deubiquitinases at organelle quality control bottlenecks in neurodegeneration.
    Lisa M Ellerby, Avraham Ashkenazi.
      Neurodegenerative diseases with prominent motor symptoms converge on mitochondrial and lysosomal bottlenecks in selectively vulnerable neurons. Deubiquitinases regulate ubiquitin-dependent organelle fate at these decision points. Emerging evidence suggests that modulating deubiquitinase activity can restore organelle quality control and represents a promising therapeutic strategy.
    Keywords:  Parkinson’s disease; polyglutamine expansion diseases; proteostasis; ubiquitin enzymes
    DOI:  https://doi.org/10.1016/j.molmed.2026.05.006
  60. Nat Commun. 2026 Jun 05. pii: 5011. [Epub ahead of print]17(1):
    Stress granule phase separation in stress-responsive cytosolic extract-in-oil droplets.
    Aline Lieber, Oskar Staufer, Zhaozhi Sun, Ulrike Engel, Charlotte Flory, Nathan Mikhaylenko, Kevin Jahnke, Katja Kopp, Philipp Klein, Sarah Hofmann, Oliver T Fackler, Pavel Ivanov, Ilia Platzman, Pietro Scaturro, Joachim P Spatz, Alessia Ruggieri.
      Stress granules (SGs) are biomolecular condensates that form transiently in the cytosol of mammalian cells in response to stress. Dysregulation of their assembly or disassembly is implicated in human age-related diseases. While phase separation is the key process underlying SG assembly, understanding of their function, composition and regulation in response to physiological stimuli is limited. This knowledge gap reflects the challenge of gaining comprehensive and quantitative insights into the dynamic regulation of the complex composition of SGs at the single-cell level. Here we present an emulsion-based microfluidics method to overcome this limitation. "Cytosolic extracts-in-oil droplets" (CEODs) recreate a confined active cytosolic milieu that undergoes phase separation and SG formation in response to stress under physiological conditions. This approach led to the discovery of seven previously unrecognised SG components involved in signalling pathways. CEODs provide a versatile and cost-effective screening platform for future mechanistic and therapeutic studies.
    DOI:  https://doi.org/10.1038/s41467-026-73936-x
  61. Adv Sci (Weinh). 2026 Jun 03. e21781
    UCHL3 Regulates Subgenomic Flaviviral RNA Condensates to Promote Virus Propagation.
    Oscar Trejo-Cerro, Anna Beekmayer-Dhillon, Qi Wen Teo, Lewis Siu, Ming Yuan Li, Kate J Heesom, Adán Pinto-Fernández, Sumana Sanyal.
      Flavivirus subgenomic RNAs (sfRNAs) antagonise antiviral defences, yet how sfRNAs are organized and maintained in cells remains poorly understood. Here we identify ubiquitin C-terminal hydrolase L3 (UCHL3) as a post-translational regulator of flavivirus sfRNA stability and function. Using activity-based protein profiling during ZIKV and DENV infections, we discovered that UCHL3 is activated upon flavivirus infection. CRISPR-Cas9 knockout of UCHL3 significantly impaired viral replication and reduced viral protein expression across multiple cell models; reconstitution with wild-type UCHL3 rescued these defects, whereas a catalytically inactive mutant (C95A) failed to restore replication, confirming the requirement for deubiquitylase activity. Through a proximity-biotinylation sfRNA-interactome capture assay, we show that UCHL3 physically interacts with sfRNA complexes. Importantly, UCHL3 deletion accelerates RNase L activation, causing enhanced sfRNA relocalization from protective P-bodies to PABPC1-positive RNase L-induced bodies (RLBs), resulting in viral RNA decay. RNase L knockdown restores viral replication in UCHL3-deficient cells, confirming RNase L-dependent antiviral effects. This pro-viral effect of UCHL3 operates through interferon-independent mechanisms, as replication defects persist despite exogenous interferon treatment. This work therefore identifies UCHL3 as a regulator of sfRNA fate between pro-viral and antiviral RNA condensates, identifying a post-translational mechanism governing viral RNA stability and a potential therapeutic target for flavivirus infections.
    Keywords:  Zika; biomolecular condensates; dengue; deubiquitylases; sfRNA
    DOI:  https://doi.org/10.1002/advs.202521781
  62. bioRxiv. 2026 May 25. pii: 2026.05.21.726977. [Epub ahead of print]
    Endothelial cell RpL17-dependent translational control mediates intima-media thickening in response to disturbed flow.
    Mary Wines-Samuelson, Sayantani Chowdhury, Sharon Senchanthisai, Michal Shaposhnikov, Mark Sowden, Bradford C Berk.
       Background: Carotid intima-media thickening (IMT) is a major risk factor for cardiovascular disease (CVD). The large ribosomal subunit protein 17 (Rpl17) was recently reported as a CVD-associated gene; however, ribosomal mutations generally are not associated with vascular dysfunction. We have created a novel genetic model of decreased RpL17 in endothelial cells (EC) to determine how changes in endothelial ribosome expression cause IMT.
    Methods: EC-restricted RpL17 heterozygous mice (Cdh5-Cre; RpL17 fl/wt , or Rpl17-Het), were generated and subjected to sham or partial carotid ligation (PCL) surgery of the left artery to induce acute disturbed (d)-flow in vivo . Carotids were harvested on day 14 for quantitative tissue immunostaining. Purified mouse and human EC in vitro were exposed to steady (s)-flow or d-flow using cone viscometry, and collected for flow cytometry, protein expression, electron microscopy, or purification of ribosomes. Human carotid samples from healthy and endarterectomy patients were used for tissue analysis.
    Results: Carotids from RpL17-Het mice with PCL-induced d-flow showed increased IMT relative to RpL17-WT controls. In addition, RpL17 protein levels were decreased in regions of d-flow compared to s-flow. Increased levels of ER stress markers were observed by carotid immunostaining, as well as activation of the integrated stress response (ISR) in RpL17-Het EC. Analysis of mRNAs bound to polysomes vs. monosomes in EC-RpL17-Het revealed increased translational efficiency of key regulators of glycolysis, redox, inflammation, matrix, and endothelial-to-mesenchymal transition (EndMT). Metabolic profiling by Seahorse assay showed enhanced anaerobic glycolysis and decreased oxidative respiration in RpL17-Het EC, consistent with the translational efficiency data. Immunostaining of carotids identified upregulated EC inflammation and EndMT.
    Conclusions: Our data support RpL17 as a key mediator of EC phenotypic modulation that causes IMT in response to d-flow. We show a novel pathway for d-flow-mediated IMT: endoplasmic reticulum stress and activation of the ISR. These changes alter translational efficiency and reprogram EC cell cycle, metabolism, and redox state in the presence of d-flow to cause IMT, a precursor to cardiovascular pathology.
    DOI:  https://doi.org/10.64898/2026.05.21.726977
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