bims-proteo Biomed News
on Proteostasis
Issue of 2026–04–26
68 papers selected by
Eric Chevet, INSERM
  1. Identification of novel ubiquitin receptors on the 26S proteasome by photo-crosslinking mass spectrometry.
  2. Proximity Binding Assay for PROTAC Ternary Complex Analysis.
  3. Disruption of the SAGA CORE triggers collateral degradation of KAT2A.
  4. Structural basis of NSD2 degradation via targeted recruitment of SCF-FBXO22.
  5. Interplay between proteostasis pathways and innate immune responses in Caenorhabditis elegans.
  6. Redirecting TRIM21 with TRIMTACs for the targeted degradation of multimeric proteins.
  7. Zinc-redox crosstalk regulates proteostasis in the endoplasmic reticulum.
  8. Differential regulation of p62-ubiquitin conjugates in neurons versus astrocytes during cellular stress.
  9. The regulation, function and disease relevance of cytoplasmic tRNAs.
  10. The Human DBR1 Interactome Reveals Coupling Between Intron Lariat Turnover, Pre-mRNA Splicing and RNA Quality Control Pathways.
  11. An inhibitor of GCN2 and the integrated stress response directly targets ZAK protein kinase to limit cytotoxicity.
  12. Selective autophagy receptors: Multifunctional regulators of organelle turnover.
  13. rRNA expansion segments mediate ribosome dimerization as a conserved stress response.
  14. Stress Tested: Aging Rewires Tumors for Metastatic Spread Through Activation of the Integrated Stress Response.
  15. The ubiquitin ligase RNF115 is required for the clearance of damaged lysosomes.
  16. Quantitative analysis of autophagic flux reveals radiation-induced activation of SQSTM1-mediated degradation of protein aggregates and ER-phagy.
  17. Ubiquitination of glycogen and metabolites in cells and tissues.
  18. DNA-Encoded Libraries for the Discovery of E3 Ligase Ligands.
  19. Depletion of TECPR2 leads to mitochondrial failure associated with neurodegeneration.
  20. Bacteria use P-body condensates to attenuate host translation during infection.
  21. The transcription factor Rlm1 couples the MAPK Slt2/ERK1 pathway to the IRE1-driven unfolded protein response.
  22. Post-translational Modification that Shines in the Age of Viruses: ISGylation from a Structural Perspective.
  23. Oxidative stress causes a reversible decrease of deubiquitylases activity in old vertebrate brains.
  24. The Ubiquitin Script: writing protein fates in chains.
  25. GRP78 Selective Inhibitors From a Direct-to-Biology Strategy.
  26. PKR condensation at viral replication complexes initiates its activation.
  27. An in vitro approach for simulating divergent Golgi O-glycosylation of tumor-associated MUC1 from normal MUC1.
  28. Targeted delivery of glucocerebrosidase to lysosomes: The LYSOTAC (LYSOsome-TArgeting Chimera) technology.
  29. Long-Term Stress Adaptation as a Highly-Conserved Key Factor in Yeast Aging.
  30. Conserved and divergent features of human mRNA decapping revealed by biochemical reconstitution.
  31. The unfolded protein response and its activation by insulin in muscle are not altered by obesity or type 2 diabetes.
  32. Comprehensive RNA-binding protein analyses and deep learning uncover genetic constraints and disease associations in protein-RNA interfaces.
  33. Using experimental results of protein design to guide biomolecular energy-function development.
  34. mtHsp70 overexpression enhances neuroprotection through ATF5-dependent UPRmt signaling after traumatic brain injury.
  35. The E3 ligase β-TRCP1 earmarks OTUD3 for destruction to fine-tune cGAS activation.
  36. A conserved E3 ubiquitin ligase rewires carotenoid, sterol, and lipid metabolism in Xanthophyllomyces dendrorhous.
  37. Localized phosphoinositide metabolism regulates STIM1/ORAI1 fast inactivation.
  38. Multimodal profiling reveals cell type-specific pseudouridine modification and density-dependent translational regulation.
  39. Subcellular mRNA localization patterns across tissues resolved with spatial transcriptomics.
  40. Pyrazolylpyrimidinamines Decorated via Petasis Reaction as Small-Molecule Activators of the RNA-Degrading Ribonuclease IRE1α.
  41. The vault associates with membranes in situ.
  42. Simple biological controllers drive the evolution of soft modes.
  43. SMG7 and eIF4A constitute a homeostatic module controlling P-body condensation and function of meiotic bodies.
  44. Reprogramming Disulfide Reduction in Endoplasmic Reticulum Uncouples Immune Evasion of Pancreatic Cancer.
  45. Cell-internal autocrine receptor inactivation supports maintenance of mating-type identity in yeast.
  46. A landscape analysis of human SUMOylation.
  47. SEC62-mediated ER-Phagy activation alleviates Alzheimer's disease pathology and restores cognitive function in 5×FAD mice.
  48. A CRISPR-Cas9 screen identifies LAPTM4A (lysosomal protein transmembrane 4 alpha) as a key host barrier against PRRSV infection.
  49. Protocol for SUMOylome analysis using a SUMO-T86K mutant combined with Lys-C digestion.
  50. Lysosomal accumulation of Masitinib alters autophagy via pH-dependent trapping.
  51. Proteostasis at the mitochondrial outer membrane: Quality control of mitochondrial protein transport.
  52. PIWIL1 activates the R2TP-TELO2-mTORC1 axis independently of piRNA to promote TOP mRNA translation in gastric cancer.
  53. Prothrombinase processivity is conferred by substrate allostery.
  54. Photo-click Proteolysis-Targeting Chimeras Enable Intracellular Generation of PROTACs for Precise Dual Protein Degradation.
  55. ZIP10 governs Zn influx into the cytoplasm from the endoplasmic reticulum and maintains Zn homeostasis in rice.
  56. Pharmacological inhibition of the PERK pathway modulates hepatocellular carcinoma growth and immune signaling.
  57. Tissue-selective COPII modulator SEC16B aggravates cardiovascular disease by promoting lipid export.
  58. Dual Role of 3' UTR Length in Modulating Translation Termination Efficiency.
  59. Pharmacological strategies targeting chaperone-mediated autophagy.
  60. Discovery of molecular glues that bind FKBP12 and structurally distinct targets using DNA-encoded libraries.
  61. Repertoire-scale antibody structural prediction informs therapeutic design.
  62. Unveiling the thioredoxin fold: a systematic review and bioinformatic analysis of protein disulfide isomerase and Dsb family proteins.
  63. Hepatic SEC16B regulates lipid homeostasis by coordinating VLDL secretion and lipid droplet expansion.
  64. Mathematical modeling of ribosome competition informs testable treatment strategies for drug-tolerant cancer persister cells.
  65. TRIM26-mediated NKRF degradation drives Osimertinib resistance through SNRPD2-dependent stress granule formation in lung adenocarcinoma.
  66. Organelle interactome disruption: The systemic pathological mechanisms and therapeutic prospects of mitochondria-lysosome-ER crosstalk in Alzheimer's disease.
  67. CryptoBank: A resource for the identification and prediction of cryptic sites in proteins.
  68. ISGylation is disrupted by UBA7 gene variants identified in individuals with neurodevelopmental disorder phenotypes.
  1. J Biol Chem. 2026 Apr 22. pii: S0021-9258(26)00353-4. [Epub ahead of print] 111481
    Identification of novel ubiquitin receptors on the 26S proteasome by photo-crosslinking mass spectrometry.
    Nicole S MacRae, Ken C Dong, Hiromitsu Harimoto, Andreas Martin.
      The 26S proteasome is the endpoint of the ubiquitin-proteasome system, an essential pathway for maintaining cellular homeostasis through targeted degradation of misfolded, damaged, and obsolete proteins. Substrates labeled with ubiquitin are directed to the 26S proteasome by binding to one or more ubiquitin receptors. However, ubiquitin-dependent degradation occurs even when the canonical receptor sites are mutated, suggesting the presence of additional, unidentified binding sites. Here we created photo-crosslinkable probes for ubiquitin interactions by incorporating the unnatural amino acid p-benzoyl-L-phenylalanine into ubiquitin. We show that these probes can be used to measure apparent affinities for known receptors and to reveal novel ubiquitin-binding sites on the yeast 26S proteasome. Through photo-crosslinking mass-spectrometry experiments we identified a groove on the top of the proteasome, formed by Rpn2, Rpn9, Rpn10, and Rpn12, that serves as an additional ubiquitin-binding interface. Our photo-crosslinkable probes thus serve as versatile tools for the characterization of ubiquitin-protein interactions and the identification of ubiquitin-binding domains.
    Keywords:  ATPases associated with diverse cellular activities (AAA); proteasome; protein degradation; proteostasis; ubiquitin
    DOI:  https://doi.org/10.1016/j.jbc.2026.111481
  2. ACS Sens. 2026 Apr 21.
    Proximity Binding Assay for PROTAC Ternary Complex Analysis.
    Irene Ponzo, Alice Soldà, Charlotte Crowe, Göran Dahl, Tereza Jahodová, Andreas Heerwig, Stefan Geschwindner, Alessio Ciulli, Ulrich Rant.
      The engineered formation of ternary complexes, in which two proteins are bridged by small molecules such as PROTACs or molecular glues, is a prerequisite for the targeted enzymatic degradation of pathogenic proteins; however, the combined analysis of these ternary interactions during the drug discovery process remains challenging. Here, we introduce a proximity binding assay for the simultaneous measurement of binary and ternary interaction kinetics on a biosensor surface. Target proteins and the substrate binding subunit of ubiquitin E3 ligase are tethered to mobile swivel arms of a Y-shaped DNA scaffold. The Y-structure induces spatial proximity between the proteins and presents them to PROTAC analytes flown across the sensor. PROTAC-induced ternary complex formation is measured by fluorescence energy transfer (FRET), while binary interactions are detected by fluorescence quenching. The assay is applied to cereblon (CRBN) and von Hippel-Lindau (VHL) as E3 ligase substrate receptors, a range of compounds including AT1, MZ1, dBETs, and ARV-825 as PROTACs, and the two bromodomains of BRD2, BRD3, BRD4, and BRDT proteins as targets. Automated workflows enable the measurement of 384 real-time sensorgrams in a single run using picomole sample quantities. The insights into proximity-mediated binding kinetics can enable the development of PROTACs and molecular glues with improved properties for targeted protein degradation.
    Keywords:  BET; BRD; CRBN; PROTAC; VHL; Y-structure; affinity; avidity; kinetics; molecular glue; switchSENSE; targeted protein degradation; ternary complex
    DOI:  https://doi.org/10.1021/acssensors.5c04944
  3. Nat Commun. 2026 Apr 20. pii: 3410. [Epub ahead of print]17(1):
    Disruption of the SAGA CORE triggers collateral degradation of KAT2A.
    Paul Batty, Hannah Beneder, Caroline Schätz, Gabriel Onea, Maciej Zaczek, Ana P Kutschat, Miriam Abele, Sophie Müller, Giulio Superti-Furga, Georg E Winter, Davide Seruggia.
      The Spt-Ada-Gcn5 acetyltransferase (SAGA) complex regulates gene expression through histone acetylation at promoters, mediated by its histone acetyl transferase (HAT), KAT2A. While SAGA structure and function are well characterised, mechanisms controlling the stability of individual subunits, including KAT2A, remain unclear. Here, using a fluorescence-based KAT2A stability reporter, we systematically dissect the molecular dependencies controlling KAT2A protein abundance, and identify the non-enzymatic SAGA CORE module subunits-TADA1, TAF5L, and TAF6L- as necessary for KAT2A stability. Loss of these subunits disrupts SAGA complex integrity, leading to non-chromatin-bound KAT2A that is degraded by the proteasome and consequent reduced H3K9 acetylation. Proteomic profiling reveals progressive loss of components from the CORE and HAT modules upon acute SAGA CORE disruption, indicating that an intact CORE is required for the stability of numerous SAGA components. Finally, a focused CRISPR screen of ubiquitin-proteasome system genes identifies the E3 ligase UBR5, a known regulator of orphan protein degradation, and the deubiquitinase OTUD5, as regulators of KAT2A degradation when the SAGA CORE is perturbed. Together, these findings reveal a dependency of KAT2A protein stability on SAGA CORE integrity and define an orphan quality control mechanism targeting unassembled KAT2A, revealing a potential vulnerability in SAGA-driven malignancies.
    DOI:  https://doi.org/10.1038/s41467-026-71613-7
  4. Nat Commun. 2026 Apr 23.
    Structural basis of NSD2 degradation via targeted recruitment of SCF-FBXO22.
    Kevin C Robertson, Sascha J Amann, Tongkun Liu, Adam V Funk, Xianxi Wang, Irina Grishkovskaya, Aamir Mehmood, John R Tabor, Jacqueline L Norris-Drouin, Cheryl H Arrowsmith, Jon L Collins, Yinglong Miao, Michael J Emanuele, David Haselbach, Lindsey I James, Nicholas G Brown.
      Targeted protein degradation (TPD) through the ubiquitin-proteasome system is driven by compound-mediated polyubiquitination of a protein-of-interest by an E3 ubiquitin (Ub) ligase. Relatively few E3s have been successfully utilized for TPD and the governing principles of functional ternary complex formation between the E3, degrader, and protein target remain elusive. FBXO22 has recently been harnessed for TPD applications by degraders that covalently modify its cysteine residues. Here, we reveal that the aldehyde derivative of UNC10088 promotes cooperative binding of FBXO22 to NSD2, a histone methyltransferase and oncogenic protein, leading to a cryo-EM structure of the SKP1-CUL1-F-box (SCF)-FBXO22 complex with NSD2. This structure revealed a conformational change in the FBXO22 loop surrounding C326, further exposing the cysteine for covalent recruitment. Additional medicinal chemistry efforts led to the discovery of benzaldehyde-based non-prodrug degraders that similarly engage C326 of FBXO22 and potently degrade NSD2. Unlike many degraders, our molecules recruit NSD2 to a different surface of FBXO22 than the known FBXO22 substrate BACH1, allowing for concurrent complex formation and structural determination of SCFFBXO22 bound to both the neosubstrate NSD2 and native substrate BACH1. Overall, we demonstrate the biochemical and structural basis for NSD2 degradation, revealing key principles for efficient and selective TPD by SCFFBXO22.
    DOI:  https://doi.org/10.1038/s41467-026-72235-9
  5. Infect Immun. 2026 Apr 21. e0003726
    Interplay between proteostasis pathways and innate immune responses in Caenorhabditis elegans.
    Annesha Ghosh, Jogender Singh.
      Microbial pathogens frequently manipulate host protein homeostasis to undermine immunity by targeting protein synthesis, folding, trafficking, and degradation. Conversely, effective immune responses themselves impose substantial proteostatic demands, as the rapid production of antimicrobial effectors increases the burden on cellular quality-control systems. This bidirectional pressure has likely driven the evolution of surveillance mechanisms that sense disruptions in protein homeostasis as indicators of infection. Using Caenorhabditis elegans as a genetically tractable model, recent studies have revealed that perturbations in proteostasis across multiple cellular compartments, including the cytosol, endoplasmic reticulum (ER), mitochondria, proteasome, and extracellular space, are actively integrated with innate immune signaling. Stress-response pathways such as the heat shock response, translational regulation, and the unfolded protein responses of the ER and mitochondria function not only to restore proteome integrity but also to directly shape immune gene expression and pathogen resistance in a context-dependent manner. This review highlights proteostasis as an evolutionarily conserved immune surveillance system, linking cellular stress sensing to host defense and offering broader insights into the coupling of stress adaptation, immunity, and organismal health.
    Keywords:  C. elegans; endoplasmic reticulum; mitochondria; proteasome; unfolded protein response
    DOI:  https://doi.org/10.1128/iai.00037-26
  6. FEBS J. 2026 Apr 21.
    Redirecting TRIM21 with TRIMTACs for the targeted degradation of multimeric proteins.
    Marc A Scemama de Gialluly, Drew J Adams.
      PROTACs (PROteolysis-Targeting Chimeras) are heterobifunctional small molecules that induce proximity between E3 ubiquitin ligases and target proteins to drive target protein ubiquitination and proteasomal degradation. TRIM21 is an intracellular Immunoglobulin G (IgG) receptor and E3 ubiquitin ligase that functions to degrade cytoplasmic antibody-coated viral particles. Genetic approaches have redirected TRIM21 towards a wide range of cellular proteins, and mechanistic studies have demonstrated TRIM21's preference for degrading multimeric substrates such as protein aggregates. Recently, the first small molecules targeting TRIM21 have been reported, including some that have been elaborated into PROTACs (TRIMTACs) that degrade multimeric proteins. In this State-of-the-Art review, we describe the unique biology of TRIM21, detail recently reported TRIMTACs, and suggest future opportunities for TRIMTACs to impact targeted protein degradation.
    Keywords:  TRIM21; chemical biology; drug discovery; targeted protein degradation; ubiquitin‐proteasome system
    DOI:  https://doi.org/10.1111/febs.70548
  7. Nat Commun. 2026 Apr 22.
    Zinc-redox crosstalk regulates proteostasis in the endoplasmic reticulum.
    Yuta Amagai, Chihiro Arai, Wakana Yamamoto, Satoshi Watanabe, Toshiyuki Kowada, Roberto Sitia, Jun Hoseki, Shin Mizukami, Masaki Matsumoto, Kenji Inaba.
      Zinc homeostasis is crucial for various biological processes, including gene regulation, signal transduction, and proteostasis. ZIP7 is a membrane transporter that exports zinc ions (Zn2+) from the lumen of the endoplasmic reticulum (ER) to the cytosol, and its dysfunction causes ER stress, although the underlying mechanism remains unclear. Here, we show that ZIP7 inhibition increases the labile Zn2+ concentration in the ER to micromolar levels, approximately 106 times higher than its steady-state level. Such abnormally high Zn2+ concentrations disrupt the function and trafficking of the Zn2+-dependent chaperone ERp44 at the ER-Golgi interface. In vitro assays using recombinant proteins demonstrated that Zn2+ inhibits the Ero1α-PDI oxidative system, and that ERp44 enhances this inhibitory effect. Consequently, the ER redox environment becomes more reducing, severely impairing the oxidative folding of key membrane receptors such as Notch1 and EGFR. These findings reveal the essential role of zinc homeostasis in redox-dependent proteostasis within the ER.
    DOI:  https://doi.org/10.1038/s41467-026-72250-w
  8. PLoS One. 2026 ;21(4): e0345890
    Differential regulation of p62-ubiquitin conjugates in neurons versus astrocytes during cellular stress.
    David K Sidibe, Erin M Smith, Maeve L Spivey, Maria C Vogel, Sandra Maday.
      Sequestosome 1/p62 (hereafter referred to as p62) is a multifunctional protein that orchestrates various cellular stress response pathways including autophagy, proteasome-mediated degradation, antioxidant defense, nutrient sensing, and inflammatory signaling. Mutations in distinct functional domains of p62 are linked with the neurodegenerative disease amyotrophic lateral sclerosis (ALS), underscoring its importance in neural cells. Neurons and astrocytes, two key cell types in the brain, perform distinct roles in brain physiology and thus encounter a unique landscape of cellular stress. However, how p62 is regulated in these cell types in response to various stress modalities remains largely unexplored. Several functions for p62 depend on its engagement with ubiquitinated substrates. Thus, we investigated how the regulation of p62-ubiquitin conjugates differs between neurons and astrocytes exposed to two stress modalities: lysosomal membrane damage and metabolic stress. Lysosomal damage triggered ubiquitin-dependent assembly of p62 puncta in both neurons and astrocytes. In contrast, nutrient deprivation elicited different responses between neurons and astrocytes. Neurons formed p62-ubiquitin structures more prominently and displayed a greater dependence on ubiquitin for p62 clustering. Together, these findings reveal cell-type-specific and stress-specific regulation of p62-ubiquitin conjugates, indicating that neurons and astrocytes can deploy distinct quality control strategies.
    DOI:  https://doi.org/10.1371/journal.pone.0345890
  9. Nat Rev Mol Cell Biol. 2026 Apr 21.
    The regulation, function and disease relevance of cytoplasmic tRNAs.
    Robin E Stanley, Todd M Lowe, Zoya Ignatova.
      Transfer RNAs (tRNAs) are core components of protein synthesis. Recent studies and technological advances have expanded our understanding of the complexities of tRNA biology. In this Review, we discuss the genomic organization and spatiotemporal expression of human cytoplasmic tRNAs, the quality control pathways that govern their maturation and functionality, and how dysregulation of tRNA biogenesis and function contributes to human pathologies. We also present emerging concepts regarding how tissue-specific tRNA abundance regulates translation velocity and how tRNAs are centrally involved in surveillance and stress signalling pathways, including ribosome-associated quality control and the integrated stress response. We further discuss the potential of tRNA-based therapeutics, highlighting new strategies to address tRNA-associated translation defects. By bridging between molecular tRNA biology and its clinical implications, we emphasize the crucial need to understand the intricacies of tRNA regulation in order to therapeutically target them in a variety of diseases.
    DOI:  https://doi.org/10.1038/s41580-026-00963-3
  10. Cell Stress Chaperones. 2026 Apr 16. pii: S1355-8145(26)00034-9. [Epub ahead of print] 100178
    The Human DBR1 Interactome Reveals Coupling Between Intron Lariat Turnover, Pre-mRNA Splicing and RNA Quality Control Pathways.
    Tiffany Barwell, Dipendra Gautam, Nitika, Bo Zheng, Andrew W Truman, Kausik Chakrabarti.
      Pre-mRNA splicing produces intron lariats that must be cleaved at their internal 2'-5' phosphodiester bond by the debranching endonuclease DBR1. While human DBR1 (hDBR1) is established as the lariat debranching enzyme, how it interfaces with broader RNA-metabolc pathways is less clear. Using chemical inhibition of splicing, we show that DBR1 expression correlates with splicing activity. We then mapped the hDBR1 interactome by immunopurification coupled to mass spectrometry using complementary gel-based and on-bead workflows. hDBR1 associates with spliceosome and intron-turnover factors, and with RNA quality-control proteins including UPF1, XRN2, and the RNA helicase DHX29. RNase A treatment identifies an RNA-dependent subnetwork enriched for stress-granule proteins and hnRNPs, linking hDBR1 to RNA surveillance during stress. Comparison with BioGRID indicates that most detected associations were not previously reported. Finally, phosphoproteomic profiling reveals multiple hDBR1 phosphorylation sites, including four residues preferentially detected after RNase treatment, suggesting regulatory modifications that may tune hDBR1 interactions or activity. Together, these data expand the functional landscape of hDBR1 across splicing, intron turnover, and RNA quality control.
    Keywords:  DBR1; Mass Spectrometry; Proteomics; RNA Lariat Debranching Enzyme; Splicing; Stress Granules; mRNA Decay
    DOI:  https://doi.org/10.1016/j.cstres.2026.100178
  11. J Biol Chem. 2026 Apr 22. pii: S0021-9258(26)00354-6. [Epub ahead of print] 111482
    An inhibitor of GCN2 and the integrated stress response directly targets ZAK protein kinase to limit cytotoxicity.
    Jagannath Misra, Dan F Spandau, Jonah Z Vilseck, Tracy G Anthony, Kirk A Staschke, Ronald C Wek.
      The integrated stress response (ISR) is a major mechanism protecting cells against environmental and physiological stresses. Central to the ISR is a collection of stress-sensing kinases, such as GCN2 (EIF2AK4). When nutrients are limiting or translating ribosomes stall or collide, activated GCN2 phosphorylates eIF2, lowering global protein synthesis, which conserves resources and confers targeted expression of stress-adaptive genes, such as the transcription factor ATF4. While beneficial during acute stress, chronic GCN2 activation can promote cancer progression and neurological disease, spurring the development of GCN2 inhibitors. However, achieving therapeutic specificity and understanding the pathological context of ISR modulation remains challenging and requires careful evaluation. One of the earliest and most widely used GCN2 inhibitors is GCN2iB. In this study, we report that GCN2iB is a direct inhibitor of the ZAK protein kinase, a critical upstream regulator of stress-activated MAPK signaling that functions in the ribotoxic stress response (RSR). Using biochemical measurements, cell-based assays, and structural modeling, we demonstrate that inhibition of ZAK by GCN2iB dampens stress-induced JNK and p38 activation, thereby masking the cytotoxic consequences normally associated with GCN2 inhibition. While suppression of GCN2 activity may be beneficial in specific disease models, concurrent inhibition of ZAK can negate these effects, obscure its therapeutic benefits, and lead to unanticipated phenotypes. These findings highlight the importance of assessing kinase selectivity in pharmacological studies of ISR modulation and emphasize that dual inhibition of GCN2 and ZAK can yield complex and context-dependent cellular responses.
    DOI:  https://doi.org/10.1016/j.jbc.2026.111482
  12. Curr Opin Cell Biol. 2026 Apr 17. pii: S0955-0674(26)00030-X. [Epub ahead of print]100 102642
    Selective autophagy receptors: Multifunctional regulators of organelle turnover.
    Akiko Kuma, Tamotsu Yoshimori.
      Organelle-selective autophagy (organellophagy) is essential for organelle quality control and cellular homeostasis. Selective degradation of most major organelles has been described and is mediated by specialized autophagy receptors. These receptors were initially defined by their ability to tether target substrates to the growing phagophore through interactions between their LC3-interacting region (LIR) motifs and ATG8 family proteins. Recent studies have expanded this view, revealing that autophagy receptors function as multifunctional regulators. Beyond substrate recognition, they have been shown to promote local concentration of substrates and autophagy factors via liquid-liquid phase separation, actively drive fragmentation of large organelles into autophagosome-compatible sizes, and recruit the autophagy initiation machinery. Together, these findings refine current models of organellophagy and highlight autophagy receptors as central coordinators of organelle turnover.
    DOI:  https://doi.org/10.1016/j.ceb.2026.102642
  13. Nucleic Acids Res. 2026 Apr 13. pii: gkag354. [Epub ahead of print]54(7):
    rRNA expansion segments mediate ribosome dimerization as a conserved stress response.
    Wenhong Jiang, Chen Chen, Xing Wang, Wei Huang, Dawid Krokowski, Ziyao Chen, Jiahao Xie, Zhaoming Su, Maria Hatzoglou, Derek J Taylor, Qiang Guo.
      Inhibition of messenger RNA translation is a common feature in proteostatic stress cellular responses. Puromycin, a widely used compound for studying translation, disrupts protein synthesis by mimicking the 3' end of aminoacyl-transfer RNAs. Despite its extensive use as a research tool to probe the connection between translation activity and various physiological and pathological states, the cellular response associated with puromycin-induced translation stress remains incompletely understood. Here, we used electron tomography and topology analysis to define the effects of puromycin on the translation machinery in situ. We show that puromycin-treated neuronal cells exhibit an accumulation of eIF5A-bound ribosomes in a translationally inactive "idle" state, and thereby defining a broader role of eIF5A in ribosome homeostasis. Additionally, the idle ribosomes formed dimeric complexes mediated by ribosomal RNA expansion segments, suggesting an evolved mechanism involving these regions in translational hibernating and protecting idle ribosomes. We further show that the hibernating disome formation is not unique to puromycin administration but represents a conserved mechanism as a response to different cellular stressors including endoplasmic reticulum stress and amino acid depletion. Collectively, our findings illuminate distinct states of mammalian ribosome hibernation and dimerization, providing new insights into the relationship of cellular stress and the dynamic regulation of ribosomal activity.
    DOI:  https://doi.org/10.1093/nar/gkag354
  14. Cancer Res. 2026 Apr 21.
    Stress Tested: Aging Rewires Tumors for Metastatic Spread Through Activation of the Integrated Stress Response.
    Mitchell E Fane, Daniel J Zabransky.
      Aging is a major risk factor for cancer incidence and mortality, but its effect on tumor evolution and metastatic progression remains incompletely understood. A recent study by Patel and colleagues published in Nature reveals a paradoxical role for aging in cancer biology: while aging constrains primary tumor growth, it simultaneously enhances metastatic spread. Using genetically engineered mouse models and patient-derived data, the authors demonstrate that aging epigenetically reprograms mutant KRAS-driven lung adenocarcinoma through activation of the integrated stress response (ISR). Central to this process is the transcription factor ATF4, which promotes epithelial plasticity and metabolic adaptations, thereby enabling metastasis. This work provides a mechanistic framework linking host aging to tumor cell state transitions that favor distant spread of cancer cells. Importantly, it challenges a long-held assumption that tumor aggressiveness is primarily reflected by primary tumor growth kinetics and properties, and instead, it highlights metastasis as a distinct, age-influenced evolutionary trajectory. The identification of ATF4-driven ISR signaling as a mediator of metastasis highlights new therapeutic vulnerabilities, such as an acquired dependence on glutamine, particularly for older patients who comprise the majority of lung cancer cases. More broadly, this study underscores the need to incorporate aging biology into cancer models and therapeutic strategies, redefining how we conceptualize tumor progression across the lifespan.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-26-1612
  15. FEBS Lett. 2026 Apr 24.
    The ubiquitin ligase RNF115 is required for the clearance of damaged lysosomes.
    Sae Nakanaga, Toshiki Takahashi, Akiko Kuma, Hiroyuki Kawahara.
      Lysosomes play a critical role in the quality control of cellular organelles. However, lysosomal membranes can be damaged under a variety of conditions, leading to the onset of various diseases. Damaged lysosomes are selectively cleared via a ubiquitin-dependent mechanism, but the molecular mechanisms underlying this process have not been adequately elucidated. In this study, we found that RNF115 is a lysosomal damage-responsive ubiquitin ligase that undergoes massive translocation from the cytosol to the p62/SQSTM1-positive puncta around ruptured lysosomes. In accordance with the changes in its distribution, the depletion of RNF115 delayed the removal of Gal3 from damaged lysosomes during the restoration process following lysosomal damage. These observations suggest that RNF115 is responsible for the clearance of damaged lysosomes.
    Keywords:  BAG6; E3 ubiquitin ligase; RNF115; autophagy; lysophagy; lysosomal membrane damage; lysosome
    DOI:  https://doi.org/10.1002/1873-3468.70346
  16. J Radiat Res. 2026 Apr 22. pii: rrag025. [Epub ahead of print]
    Quantitative analysis of autophagic flux reveals radiation-induced activation of SQSTM1-mediated degradation of protein aggregates and ER-phagy.
    Takahito Moriwaki, Tsuyoshi Masuda.
      Autophagy is an evolutionarily conserved process that degrades and recycles intracellular components through lysosomes, thereby maintaining cellular homeostasis under stress conditions. Although radiation is known to influence autophagy, most previous studies have relied on static marker expression rather than quantitative evaluation of autophagic flux. In the present study, we quantitatively analyzed autophagic flux in hTERT/RPE-1 cells exposed to γ-rays (0.5-4 Gy) using both bafilomycin A1-based assays and HaloTag reporter systems that visualize lysosomal degradation. LC3-based total autophagic flux remained unchanged even at 4 Gy, indicating that lysosomal function is preserved after irradiation. In contrast, SQSTM1-dependent selective autophagy increased significantly at doses of 2 Gy or higher, suggesting enhanced clearance of radiation-induced protein aggregates. HaloTag-based analyses further revealed that γ-irradiation induced mitophagy and ER-phagy in a dose-dependent manner, consistent with activation of oxidative stress and unfolded protein response pathways. These findings demonstrate that ionizing radiation does not globally suppress autophagy but selectively activates organelle-specific autophagy, particularly SQSTM1-mediated ER-phagy. The selective activation of these quality-control pathways likely contributes to maintaining cellular integrity and stress adaptation following irradiation. Quantitative flux analysis thus provides new insight into the hierarchical regulation of autophagy and its role in cellular survival and repair mechanisms after radiation exposure.
    Keywords:  ER-phagy; aggrephagy; autophagy; mitophagy; oxidative stress
    DOI:  https://doi.org/10.1093/jrr/rrag025
  17. Nature. 2026 Apr 22.
    Ubiquitination of glycogen and metabolites in cells and tissues.
    Marco Jochem, Simon A Cobbold, Craig A Goodman, Catharina Kueng, Anthony Cerra, Laura F Fielden, Man Lyang Kim, Philipp Schenk, Ria Agarwal, Xiangyi S Wang, Simon R Scutts, Michael Pandos, Lin Tang, Thomas Hermanns, Shane M Devine, Martin Brzozowski, Yuri Shibata, Niall D Geoghegan, Catriona A McLean, Bernhard C Lechtenberg, Kay Hofmann, Paul Gregorevic, David Komander.
      Ubiquitin signalling covers a vast realm of protein modifications, yet may still be underestimated due to non-proteinaceous substrates, such as sugars, lipids, and nucleotides1 . The breadth of ubiquitinated non-protein substrates, their abundance, and cellular roles are currently unclear, since current ubiquitinomic and proteomic techniques are blind to non-proteinaceous modifications. We report Non-Protein Ub-clipping (NoPro-clipping) as a mass-spectrometry-based technique that combines ubiquitin clippases with sortase labelling. Targeted and untargeted workflows unveil a vast new canvas of ubiquitin modifications in mammalian cells, and in mouse and human tissues. We find ubiquitinated glycogen in any glycogen-containing tissue in mice, with highest abundance in liver and skeletal muscle. Ubiquitination can deliver glycogen to lysosomes, and leads to reduced glycogen levels. Glycogen ubiquitination is modulated in glycogen storage diseases and regulated by the Met1-polyubiquitin machinery. Strikingly, glycogen depletion in the liver during fasting coincides with elevated glycogen ubiquitination, suggesting that ubiquitin is a previously unknown component of physiological glycogen catabolism. We also reveal ubiquitination of endogenous glycerol and spermine in cells and tissues. NoPro-clipping hence unveils unexpected endogenous non-proteinaceous targets of ubiquitination, broadening the role of ubiquitin from a protein modifier to a general modifier of biomolecules.
    DOI:  https://doi.org/10.1038/s41586-026-10548-x
  18. ChemMedChem. 2026 Apr 28. 21(8): e202501032
    DNA-Encoded Libraries for the Discovery of E3 Ligase Ligands.
    Lulu Wen, Qingqing Zhang, Zhiqiang Duan, Rui Jin, Xiaojie Lu.
      DNA-encoded library (DEL) technology has emerged as a powerful tool to accelerate drug discovery, and its application has expanded to challenging targets such as E3 ubiquitin ligases, whose ligands are essential for the development of targeted therapies, including proteolysis-targeting chimeras (PROTACs). In this review, we summarize recent advances in the use of DELs for the discovery of small-molecule non-covalent E3 ligase ligands and discuss their advantages in hit-to-lead optimization and the design of targeted protein degradation systems. Furthermore, we highlight the potential and application basis of covalent DELs and DNA-encoded cyclic peptide libraries, which together outline promising future directions for DEL-based discovery of E3 ligase ligands. Emerging DEL-based strategies for the direct discovery and optimization of TPD molecules are also discussed.
    Keywords:  DNA‐encoded cyclic peptide library; DNA‐encoded library; E3 ubiquitin ligases; covalent DEL; targeted protein degradation
    DOI:  https://doi.org/10.1002/cmdc.202501032
  19. Autophagy. 2026 Apr 23. 1-15
    Depletion of TECPR2 leads to mitochondrial failure associated with neurodegeneration.
    Madhuri Chaurasia, Milana Fraiberg, Nemanja Subic, Oren Shatz, Kamilya Kokabi, Olee Gogoi, Olena Trofimyuk, Bat Chen Tamim-Yecheskel, Saskia Freud, Alik Demishtein, Ekaterina Kopitman, Inna Goliand, Sabita Chourasia, Yoav Peleg, Elena Ainbinder, Nili Dezorella, Zvulun Elazar.
      HSAN9 is a rare progressive neurodegenerative disease in children linked to bi-allelic loss-of-function mutations in the TECPR2 gene. TECPR2 is a multi-domain protein harboring N-terminal WD repeats and C-terminal TECPR repeats, followed by a functional LIR motif that serves in phagophore targeting. Here, we demonstrate that the absence of TECPR2 results in impaired mitophagy, which can be restored by expressing its C-terminal domain. Accordingly, we uncover severe mitochondrial dysfunction and accumulation of mitochondrial content in primary fibroblasts derived from an HSAN9 patient, as well as in embryonic fibroblasts and dorsal root ganglia derived from an HSAN9 mouse model. Notably, these mitochondrial defects are mediated by mitochondrial stress through the activation of the integrated stress response (ISR), whereas mitochondrial function is restored by pharmaceutical or genetic suppression of ISR. Our findings establish a new connection between mitophagy and ISR in maintaining mitochondrial homeostasis during neurodegeneration.Abbreviations: Baf. A1: bafilomycin A1; CYCS: cytochrome c, somatic; HSAN9: hereditary sensory and autonomic neuropathy IX; ISR: integrated stress response; OA: oligomycin + antimycin A; ROS: reactive oxygen species; TECPR2: tectonin beta-propeller repeat containing 2.
    Keywords:  HSAN9; TECPR2; integrated stress response; mitophagy; neurodegeneration; unfolded protein response
    DOI:  https://doi.org/10.1080/15548627.2026.2660850
  20. Sci Adv. 2026 Apr 24. 12(17): eaec4477
    Bacteria use P-body condensates to attenuate host translation during infection.
    Manuel González-Fuente, Nico Schulz, Alibek Abdrakhmanov, Thorben Krüger, Gaiea Izzati, Shanshuo Zhu, Gautier Langin, Paul Gouguet, Mirita Franz-Wachtel, Boris Macek, Anders Hafrén, Yasin Dagdas, Suayib Üstün.
      Pathogens use sophisticated strategies to modulate host protein homeostasis by targeting proteolytic pathways, but their impact on protein synthesis remains elusive. We report that pathogenic bacteria Pseudomonas syringae (Pst) targets ribonucleoprotein condensates, known as processing bodies (P-bodies), to attenuate host translation through two effectors with liquid-like properties. We uncovered a previously unknown link that Pst-mediated repression of the endoplasmic reticulum stress response is required for P-body assembly. Furthermore, we identify a functional link between P-bodies and autophagy, demonstrating that autophagic clearance of P-bodies is crucial for maintaining the balance between translationally active and inactive messenger RNAs. Together, our findings provide insights on how host translation is attenuated by bacteria to dampen plant immunity and uncover unknown connections between ER stress responses and autophagy with P-body dynamics.
    DOI:  https://doi.org/10.1126/sciadv.aec4477
  21. Commun Biol. 2026 Apr 21.
    The transcription factor Rlm1 couples the MAPK Slt2/ERK1 pathway to the IRE1-driven unfolded protein response.
    Anish Chakraborty, Saswata Chakrabarty, Jagadeesh Kumar Uppala, Kimberly Ann Mayer, Anna J Evans, Jasmine George, Chandrima Ghosh, Ritisha Dey, Franca Ohikhuare, Shama Mirza, An Phu Tran Nguyen, Nadège Gouignard, Pradeep Chaluvally-Raghavan, Madhusudan Dey.
      Unfolded protein response (UPR) is a conserved cellular strategy that enhances the protein folding capacity of cells under stress conditions. In Saccharomyces cerevisiae, the dual kinase RNase IRE1 initiates the UPR by catalyzing the cytosolic splicing of HAC1 mRNA, a process conserved in humans where IRE1 splices XBP1 mRNA. The spliced HAC1/XBP1 mRNA yields a transcription factor that upregulates the expression of protein-folding enzymes and chaperones, thereby boosting the cell's ability to cope with unfolded proteins. Our study demonstrates that the UPR involves two distinct phases. The early phase operates predominantly through the canonical IRE1 signaling pathway, while the later phase involves additional regulation by the MAP kinase Slt2 or its human ortholog ERK1/ERK2/ERK5 and the downstream target the MADS-box transcription factor Rlm1 (an ortholog of human MEF2C). We further show that Slt2 promotes IRE1 expression through Rlm1. Together, these findings reveal a previously unrecognized crosstalk between the MAPK and IRE1-mediated arm of the UPR.
    DOI:  https://doi.org/10.1038/s42003-026-10090-6
  22. Curr Protein Pept Sci. 2026 Apr 14.
    Post-translational Modification that Shines in the Age of Viruses: ISGylation from a Structural Perspective.
    Oktay Gocenler, Nilufer Cakir, Cansu Deniz Tozkoparan Ceylan, Çağdaş Dağ.
      Post-translational modifications (PTMs) orchestrate the dynamic functional landscape of proteins, governing cellular immunity, signaling, and stress responses. Among these modifications, ISGylation, a ubiquitin-like conjugation process driven by interferon signaling, has emerged as a pivotal regulator of antiviral defense. ISG15 (Interferon-stimulated gene 15) functions through covalent attachment of its protein product to target proteins or as a secreted immunomodulator. ISG15 plays a pivotal role in antiviral immunity and cellular stress responses via ISGylation. In this review, we present an integrative structural and evolutionary analysis of ISG15 and its conjugation/deconjugation machinery, highlighting key steps of the molecular basis of ISG15 and its function. Comparative analysis of Ubiquitin and Ubiquitin-like proteins reveals the evolutionary emergence of ISG15 as a distinct modifier. Structural modeling and visualization of ISG15 elucidates its enzymatic activation via the E1 enzyme UBA7 and its conjugation through the E2 enzyme UBCH8 and E3 ligase HERC5. Cryo-EM and modeled complexes provide detailed views of domain interactions and catalytic interfaces essential for ISG15 transfer. Furthermore, we identify flexible regions in the Ubiquitin-Fold Domains (UFD) of various E1 enzymes that may underlie substrate specificity. The interaction between ISG15 and its specific protease USP18, revealing conformational changes upon substrate binding that are likely critical for de-ISGylation. Together, our findings offer a comprehensive structural framework for understanding ISGylation, paving the way for targeted therapeutic strategies in immune modulation.
    Keywords:  E1-E2-E3 cascade; ISG15; ISGylation; USP18; Ubiquitin-like modifiers; innate immunity; structural modeling.; viral PTMs
    DOI:  https://doi.org/10.2174/0113892037454020260318203401
  23. Nat Commun. 2026 Apr 21. pii: 3653. [Epub ahead of print]17(1):
    Oxidative stress causes a reversible decrease of deubiquitylases activity in old vertebrate brains.
    Amit Kumar Sahu, Alberto Minetti, Domenico Di Fraia, Antonio Marino, Patrick Rainer Winterhalter, Daniela Giustarini, Ranieri Rossi, Andreas Simm, Francesco Neri, Federico Galvagni, Christoph Gerhardt, Thorsten Pfirrmann, Alessandro Ori.
      The ubiquitin-proteasome system is essential for neuronal proteostasis, yet its function declines with age. How aging affects deubiquitylating enzymes (DUBs) in the vertebrate brain remains unclear. Here we used activity-based proteomics to profile cysteine protease DUBs in aging mouse and killifish brains. We identified a subset of DUBs that progressively lose catalytic activity with age despite stable protein abundance. Mechanistically, oxidative stress impaired DUB function through thiol oxidation, whereas antioxidant treatment with N-acetylcysteine ethyl ester (NACET) restored activity in aging brains. In human iPSC-derived neurons, global DUB inhibition and targeted inhibition of USP7, one of the most strongly age-affected DUBs, partially recapitulated ubiquitylation changes observed in aged brains. Temporal analysis in mice further revealed that DUB inhibition precedes proteasome decline during brain aging. Together, these findings identify redox-sensitive DUBs that lose activity with age and suggest impaired deubiquitylation as an early, potentially reversible driver of proteostasis decline in the aging brain.
    DOI:  https://doi.org/10.1038/s41467-026-71921-y
  24. Essays Biochem. 2025 Dec 22. pii: EBC20253031. [Epub ahead of print]69(5):
    The Ubiquitin Script: writing protein fates in chains.
    Devanshi Gupta, Subbareddy Maddika.
      Ubiquitination is a fundamental post-translational modification that orchestrates a wide range of cellular processes. This modification is executed through a cascade of enzymatic steps involving E1 activating enzymes, E2 conjugating enzymes, and E3 ligases. Among these, E2 enzymes and specific E3 ligases primarily dictate the type of ubiquitin linkage formed. Ubiquitination system can form chains of ubiquitin on any of its seven lysine residues or its N-terminal methionine, each generating a distinct three-dimensional topology. These structurally diverse polyubiquitin chains are selectively recognized by ubiquitin receptors, influencing substrate stability, localization, and interactions. These topologically diverse polyubiquitin chains function as discrete molecular signals, each with distinct physiological outcomes. This review focuses on key developments in our understanding of how specific ubiquitin linkage types participate in various cellular pathways and their implications on the fate and function of the protein.
    Keywords:  protein degradation; ubiquitin; ubiquitin chain; ubiquitin linkage
    DOI:  https://doi.org/10.1042/EBC20253031
  25. Angew Chem Int Ed Engl. 2026 Apr 23. e23960
    GRP78 Selective Inhibitors From a Direct-to-Biology Strategy.
    Xiaoyi Zhu, Carlee A Trindl, Qiu Li, Haofeng Ye, Lewis Alexander, Dichun Huang, Yongyi Wei, Vyana Trieu, Ben N Stansfield, Aikseng Ooi, Yang Yang-Hartwich, Donna D Zhang, Eli Chapman.
      Because cancer cells have heightened protein homeostasis (proteostasis) requirements, there is interest in targeting proteostasis machinery, including the 70 kDa heat shock proteins (HSP70s), as potential cancer therapeutics. However, studies have shown that the HSP70 family is differentially regulated across cancers, and global targeting may produce unwanted toxicities. For this reason, our lab has focused on isoform-selective targeting of HSP70s, including the endoplasmic reticulum-resident HSP70, GRP78 (HSPA5 or BiP). GRP78 is a central component of protein homeostasis in the secretory system and is the principal regulator of the unfolded protein response (UPR). Here, we report the use of a direct-to-biology (D2B) strategy to optimize a dipeptide-based scaffold that binds selectively to GRP78, relative to the other canonical HSP70s. We show that our lead compound, 12, potently and selectively inhibits GRP78, binds to the substrate binding pocket, kills A549 lung cancer cells in 2D (grown as a monolayer) and 3D (grown as spheroids) cultures, engages GRP78 in cells, and that GRP78 inhibition is responsible for the mode of action. This work represents the first GRP78-selective inhibitor that inhibits substrate binding.
    Keywords:  BiP; ER stress; GRP78; HSP70; HSPA5; lung cancer; proteostasis
    DOI:  https://doi.org/10.1002/anie.202523960
  26. Cell Rep. 2026 Apr 22. pii: S2211-1247(26)00368-2. [Epub ahead of print]45(5): 117290
    PKR condensation at viral replication complexes initiates its activation.
    Ebba K Blomqvist, Nicole Bracci, Helena Winstone, J Monty Watkins, Susan R Weiss, James M Burke.
      Protein kinase R (PKR) is a critical component of mammalian intracellular antiviral immunity. Here, we examine the process of PKR activation in response to Middle East respiratory syndrome coronavirus (MERS-CoV) and Zika virus (ZIKV) using super-resolution confocal microscopy, proximity ligation assay, immunogold transmission electron microscopy, and live-cell imaging. Our data support that PKR activates upon condensation on double-stranded RNA (dsRNA) exposed at membrane-associated viral replication complexes. Subsequently, p-PKR condensates disassociate from dsRNA and dissolve, releasing activated PKR molecules into the cytosol, where they phosphorylate eIF2α to initiate the integrated stress response (ISR). Importantly, the disassociation of p-PKR from dsRNA allows for the exchange of inactive PKR monomers, thus promoting robust PKR activation from limited exposed viral dsRNA substrates. MERS-CoV NS4a prevents PKR activation via competitive condensation on viral dsRNA. These findings establish a comprehensive model for PKR activation in response to positive-strand RNA viruses that replicate within membrane-associated complexes.
    Keywords:  CP: microbiology; CP: molecular biology; DRIF; MERS-CoV; NS4a; PKR; Zika virus; condensation; dsRNA; innate immunity; nsp15; viral antagonist proteins
    DOI:  https://doi.org/10.1016/j.celrep.2026.117290
  27. Nat Commun. 2026 Apr 22. pii: 3619. [Epub ahead of print]17(1):
    An in vitro approach for simulating divergent Golgi O-glycosylation of tumor-associated MUC1 from normal MUC1.
    Abdullateef Nashed, Kyllen Dilsook, Tharindu Senapathi, Kevin J Naidoo.
      Peptide O-glycosylation relies on the coordinated action of glycosyltransferases across the endoplasmic reticulum (ER) and Golgi apparatus. However, the molecular mechanisms driving aberrant glycosylation in cancer remain poorly understood. Here we show an in vitro one-pot synthetic biology approach that simulates divergent glycosylation pathways to map the synthesis of mucin 1 (MUC1) tumor-associated antigens. By modeling the cancer-associated relocation of initiation enzymes (GALNTs) to the ER, we demonstrate that this spatial shift leads to complete GalNAc (Tn antigen) occupancy. This occurs because ER localization extends reaction times and prevents inhibition by downstream Golgi enzymes. Furthermore, combined kinetic and computer reaction dynamic simulations reveal that ST6GALNAC1 exclusively drives α-2-6 sialylation, with a strict preference for the T13 site on fully glycosylated MUC1. This suggests that cancer-associated sTn upregulation is directly linked to T13 occupancy. Ultimately, this systems modeling approach decodes the enzyme localization and substrate specificities fundamental to tumourigenesis.
    DOI:  https://doi.org/10.1038/s41467-026-72151-y
  28. Asian J Pharm Sci. 2026 Apr;21(2): 101149
    Targeted delivery of glucocerebrosidase to lysosomes: The LYSOTAC (LYSOsome-TArgeting Chimera) technology.
    Hee-Yeon Kim, Eun Nam Choi, Gee Eun Lee, Sanghwa Yoon, Su Ran Mun, Eui Jung Jung, Minji Kim, Hyomin Lim, Yang Jae Kang, Woo-Jae Park, Yong Tae Kwon, Joo-Won Park.
      Lysosomal storage diseases (LSDs) are a group of inherited metabolic disorders caused by misfolding of lysosomal proteins and their degradation via endoplasmic reticulum-associated degradation (ERAD). Deficiency in LSD-associated enzymes leads to the accumulation of toxic materials within the lysosome. In macroautophagy (hereafter autophagy), autophagic receptors as represented by p62/SQSTM1/Sequestosome-1 collect and deliver their cargoes to the lysosome. Here, we developed the LYSOTAC (LYSOsome-TArgeting Chimera) technology, which enables lysosomal targeting of LSD-associated enzymes while preserving their enzymatic activities. LYSOTAC employs a bifunctional chimera that simultaneously binds an LSD-associated enzyme via the enzyme-binding ligand (EBL) and p62 via the autophagy-targeting ligand (ATL). Upon binding, p62 undergoes self-polymerization to form cargo-p62 complexes, which are sequestered into autophagosomes and delivered to lysosomes, where the enzymes exhibit maximal activity. Here, LYSOTAC compounds targeting β-glucocerebrosidase (GCase) were designed to restore GCase activity in lysosomes and promote glucosylceramide degradation in Gaucher disease fibroblasts. We suggest that LYSOTAC provides a potential therapeutic strategy for LSDs.
    Keywords:  Autophagy; Gaucher disease; Lysosomal storage diseases; Lysosomal targeting; N-degron pathway; p62/SQSTM1/Sequestosome-1
    DOI:  https://doi.org/10.1016/j.ajps.2026.101149
  29. Aging Cell. 2026 May;25(5): e70513
    Long-Term Stress Adaptation as a Highly-Conserved Key Factor in Yeast Aging.
    Yanzhuo Kong, Damola Adejoro, Christopher Winefield, Stephen L W On, Philip A Wescombe, Arvind Subbaraj, Andrew Saunders, Venkata Chelikani.
      Aging is commonly viewed as a passive consequence of accumulated damage; however, emerging evidence suggests that it may also represent an adaptive response to environmental stress. Here, we combined transcriptomic and metabolomic profiling of Saccharomyces cerevisiae to investigate how short-term, long-term, and recovery phases of stress exposure shape cellular physiology and lifespan. Short-term stress-induced protective pathways and longevity-associated metabolites, including trehalose and 5'-methylthioadenosine, consistent with enhanced stress resilience and proteostasis. In contrast, prolonged stress activated heat shock proteins and epigenetic regulators, coupled with metabolic signatures associated with loss of proteostasis, reduced energy homeostasis, and shortened chronological lifespan. Upon recovery, beneficial metabolites such as S-adenosylhomocysteine were restored, highlighting the reversibility of stress-induced aging trajectories. Phylogenetic analysis demonstrated conservation of these stress- and aging-related genes across eukaryotes and prokaryotes, suggesting an evolutionary basis for aging as a long-term stress adaptation. Together, these findings suggest that aging-associated molecular changes are closely linked to conserved stress response pathways, with implications for understanding the hallmarks of aging.
    Keywords:  cell aging and yeast biology; cell survival; stress adaptation; stress response
    DOI:  https://doi.org/10.1111/acel.70513
  30. Nat Commun. 2026 Apr 21. pii: 3697. [Epub ahead of print]17(1):
    Conserved and divergent features of human mRNA decapping revealed by biochemical reconstitution.
    Eric A J Simko, Sowndarya Muthukumar, Tanner M Myers, Anna L Valkov, Eugene Valkov.
      Decapping is a critical step in mRNA decay, but the mechanisms regulating human decapping enzyme DCP2 remain poorly understood. Here, we reconstitute the human decapping network using full-length recombinant proteins and compare it to the yeast system. Unlike in yeast, we find that the C-terminal region of human DCP2 is not autoinhibitory. RNA-binding residues of yeast Dcp2 are not conserved in the human homolog, and we find instead that a charged C-terminal region mediates substrate recognition. Human DCP1 does not stably interact with or directly stimulate DCP2, but mediates activation by the enhancer PNRC2. We also demonstrate that decapping enhancer EDC4 forms tetramers through an extended coiled-coil region, and that both DCP1 and EDC4 homomeric species can further assemble into higher-order oligomers. Furthermore, structural predictions incorporating these findings suggest a model for DCP2 recruitment by EDC4 tetramers. These findings reveal key mechanistic differences between human and yeast decapping regulation and provide insight into the molecular architecture underlying mRNA decay.
    DOI:  https://doi.org/10.1038/s41467-026-72177-2
  31. Clin Sci (Lond). 2026 Apr 22. pii: CS20250639. [Epub ahead of print]
    The unfolded protein response and its activation by insulin in muscle are not altered by obesity or type 2 diabetes.
    Rikke Kruse, Jonas Møller Kristensen, Birgitte Falbe Vind, Stine Juhl, Jacob Volmer Stidsen, Rugivan Sabaratnam, Kurt Højlund.
      Insulin resistance in obesity and type 2 diabetes (T2D) is characterized by reduced insulin-stimulated glucose uptake, accumulation of triacylglycerol, mitochondrial dysfunction, and altered protein metabolism in skeletal muscle. This may involve disturbed endoplasmic reticulum (ER) homeostasis, leading to alterations in the unfolded protein response (UPR), and hence the protein folding capacity. Here, we investigated if markers of UPR activity are elevated in skeletal muscle in obesity and T2D, and to what extent insulin regulates these UPR markers. In a case-control design, we determined mRNA expression, protein abundance, and phosphorylation of key UPR markers in skeletal muscle biopsies obtained from patients with T2D, matched to glucose-tolerant individuals with obesity and lean individuals, before and after 4-h insulin infusion during a hyperinsulinemic-euglycemic clamp. The mRNA expression or protein abundance of GRP78, the canonical ER stress sensors (ATF6, PERK, and IRE-1α), several downstream UPR markers, and related markers of mitochondrial dynamics did not differ between groups. Insulin increased the mRNA expression of ATF6, ERN1 (encoding IRE-1α), XBP1, DDIT3 (encoding CHOP), and a marker of mitochondrial fission DNM1l (encoding DRP1), as well as eIF2α Ser51 phosphorylation in skeletal muscle in all groups (all p<0.05), with no between-group differences. Our results demonstrate that markers of UPR activity are not elevated in skeletal muscle in obesity or T2D. Interestingly, insulin increases the expression of UPR markers and activates eIF2α, which is necessary for increasing the protein folding capacity of ER in muscle, and these responses are intact in obesity and T2D.
    Keywords:  ER stress; Insulin; Obesity; Skeletal muscle; Unfolded protein response; type 2 diabetes
    DOI:  https://doi.org/10.1042/CS20250639
  32. Cell Syst. 2026 Apr 22. pii: S2405-4712(26)00070-0. [Epub ahead of print] 101588
    Comprehensive RNA-binding protein analyses and deep learning uncover genetic constraints and disease associations in protein-RNA interfaces.
    Hsuan-Lin Her, Brian A Yee, Shuhao Xu, Evan A Boyle, Katherine L Rothamel, Zia Z Zhao, Steven M Blue, Jasmine R Mueller, Samuel S Park, Grady G Nguyen, Jack T Naritomi, Adam Klie, Xintao Wei, Sara Olson, Lijun Zhan, Stefan Aigner, Brenton R Graveley, Gene W Yeo.
      RNA-binding proteins (RBPs) orchestrate post-transcriptional processes, including splicing, cleavage and polyadenylation, and translation. Our updated RBP resource integrates data from 92 additional RBPs (286 in total) profiled by enhanced CLIP (eCLIP), enabling comprehensive characterization of RNA elements within human K562 and HepG2 cells. To interrogate RBP-binding syntax, we trained deep-learning models on eCLIP profiles, allowing us to score genetic variants and quantify constraints on RBP-binding sites. We observed opposing selective-constraint profiles at splicing enhancers versus silencers, including an unexpected enrichment of strengthening mutations in ELAVL1- and HNRNPC-binding sites. Finally, our model prioritizes disease variants, exposing unexpected RBP-related mechanisms of pathogenesis, exemplified by the enrichment of weakening mutations in spliceosomal protein-binding sites among retinal disease variants. The complete eCLIP resource offers an integrated platform for exploring RBP-RNA interactomes.
    Keywords:  RNA-binding protein; deep learning; eCLIP; negative selection; splicing; variant interpretation
    DOI:  https://doi.org/10.1016/j.cels.2026.101588
  33. PLoS Comput Biol. 2026 Apr 22. 22(4): e1014215
    Using experimental results of protein design to guide biomolecular energy-function development.
    Hugh K Haddox, Gabriel J Rocklin, Francis C Motta, Devin Strickland, Samer F Halabiya, Cameron Cordray, Hahnbeom Park, Eric Klavins, David Baker, Frank DiMaio.
      Computational models of macromolecules have many applications in biochemistry, but physical inaccuracies limit their utility. One class of models uses energy functions rooted in classical mechanics. The standard datasets used to train these models are limited in diversity, pointing to a need for new training data. Here, we sought to explore a new paradigm for training an energy function, where the Rosetta energy function was used to design de novo proteins. Experimental results on these designs were then used to identify failure modes of design, which were subsequently used as a "guiding principle" to retrain the energy function. Specifically, we examined a diverse set of de novo protein designs experimentally tested for their ability to stably fold, identifying unstable designs that were predicted to be stable by the Rosetta energy function. Using deep mutational scanning, we identified single amino-acid mutations that rescued the stability of these designs, providing insight into common failure modes of the energy function. We identified one key failure mode, involving steric clashing in protein cores. We identified similar overpacking when using Rosetta to refine high-resolution protein crystal structures, quantified the degree of overpacking, and refit a small set of energy-function parameters to better recapitulate native-like packing. Following fitting, we largely eliminated the failure mode in the refinement task, while retaining performance on other benchmarks, resulting in an updated version of the Rosetta energy function. This work shows how learning from protein designs can guide energy-function development.
    DOI:  https://doi.org/10.1371/journal.pcbi.1014215
  34. Exp Neurol. 2026 Apr 16. pii: S0014-4886(26)00151-2. [Epub ahead of print]402 115787
    mtHsp70 overexpression enhances neuroprotection through ATF5-dependent UPRmt signaling after traumatic brain injury.
    Yuanqing Zhang, Yi Jin, Runze Han, Yucheng Shen, Zongqi Wang, Xiaoou Sun, Jiangang Liu.
      Traumatic brain injury (TBI) induces secondary neuronal damage, in which mitochondrial dysfunction plays a central role. Mitochondrial heat shock protein 70 (mtHsp70) is a key mitochondrial chaperone involved in protein folding and proteostasis, yet its role in TBI pathology remains unclear. In the present study, we investigated the neuroprotective function of mtHsp70 and its underlying mechanisms using a controlled cortical impact (CCI) mouse model. We found that CCI selectively reduced mtHsp70 levels within mitochondria, accompanied by its cytoplasmic accumulation, while total cellular mtHsp70 expression remained unchanged. Stereotactic AAV-mediated overexpression of mtHsp70 in the cortex significantly reduced neuronal apoptosis, improved motor and cognitive behavioral outcomes, and increased neuronal survival following CCI. In vitro, mtHsp70 overexpression in HT22 cells attenuated H₂O₂-induced neuronal injury, improved mitochondrial respiration (OCR), and reduced mitochondrial protein aggregation. Mechanistically, mtHsp70 overexpression increased the expression of mitochondrial unfolded protein response (UPRmt)-related proteins, including HSP60 and Lonp1, and restored mitochondrial membrane potential. Importantly, ATF5 knockdown attenuated mtHsp70-induced upregulation of UPRmt-associated proteins and diminished mitochondrial respiratory improvement, suggesting that mtHsp70-mediated protection is dependent on ATF5-associated UPRmt signaling. Together, these findings indicate that mitochondrial mtHsp70 deficiency contributes to neuronal injury after CCI, whereas restoration of mtHsp70 improves mitochondrial proteostasis and neuronal survival. Targeting the mtHsp70-UPRmt pathway may represent a potential therapeutic strategy for TBI.
    Keywords:  DNAJA3; Mitochondrial proteostasis; Mitochondrial unfolded protein response; Neuroprotection; Traumatic brain injury; mtHsp70
    DOI:  https://doi.org/10.1016/j.expneurol.2026.115787
  35. J Biol Chem. 2026 Apr 16. pii: S0021-9258(26)00333-9. [Epub ahead of print] 111461
    The E3 ligase β-TRCP1 earmarks OTUD3 for destruction to fine-tune cGAS activation.
    Jianfeng Chen, Smaran Sivashankar, Ying Wang, Pengda Liu.
      Activation of cytosolic DNA sensing through cGAS induces the production of type I interferons and pro-inflammatory cytokines, which are essential for antiviral and antibacterial responses, inflammation, and immune modulation. While hyperactivation of cGAS leads to autoimmune diseases, its inactivation contributes to immune evasion and resistance to immunotherapies. Therefore, cGAS activity must be tightly regulated. One mechanism involves the deubiquitination and stabilization of cGAS by the deubiquitinase OTUD3; however, the upstream signals and pathophysiological cues governing OTUD3 regulation remain poorly understood. Here, we report that the E3 ubiquitin ligase β-TRCP1 targets OTUD3 for ubiquitination and proteasomal degradation. This recognition is dependent on RSK3-mediated phosphorylation of a conserved "ESG" degron motif in OTUD3, which serves as a phospho-degron for β-TRCP1 binding. Intriguingly, cytosolic DNA challenge inactivates the β-TRCP1/RSK3 pathway, resulting in OTUD3 stabilization and enhanced cGAS activation, representing a fine-tuning mechanism of innate immune signaling. Notably, this DNA-induced inactivation of RSK3 is independent of canonical Ras/MEK/ERK signaling and DNA damage-responsive kinases, but dependent on mTORC2 signaling. Collectively, our studies identify β-TRCP1/RSK3 as a previously unrecognized upstream signaling axis that regulates OTUD3 protein stability in response to DNA stress, thereby modulating cGAS-driven innate immune responses. This pathway presents a potential therapeutic target for modulating innate immunity in autoimmune diseases and cancer.
    Keywords:  OTUD3; RSK3; cGAS; innate immunity; protein stability; β-TRCP1
    DOI:  https://doi.org/10.1016/j.jbc.2026.111461
  36. Proc Natl Acad Sci U S A. 2026 Apr 28. 123(17): e2530496123
    A conserved E3 ubiquitin ligase rewires carotenoid, sterol, and lipid metabolism in Xanthophyllomyces dendrorhous.
    Ruilin Huang, Jiurong Wang, Ruirui Ding, Yu Liu, Juanjuan Su, Zhihang Chen, Yong Fan, Fuli Li, Linqi Wang, Xiao Liu, Shi'an Wang.
      Sterols, lipids, and carotenoids are major metabolites that share common biosynthetic precursors and underpin key physiological processes in eukaryotes. Yet, how cells coordinate metabolic flux through these competing pathways to maintain homeostasis remains unclear. Here, we identify a conserved RING-type E3 ubiquitin ligase, PTR1, as a central regulatory hub that orchestrates the interplay among these pathways in the yeast Xanthophyllomyces dendrorhous. Disruption of PTR1 triggers a concerted metabolic rewiring that enhances astaxanthin and sterol biosynthesis while shifting fatty acid composition toward polyunsaturation. Integrated multiomics and protein interaction analyses suggest that PTR1 targets White Collar 1 (WC1) for ubiquitination, establishing a reciprocal regulatory loop that maintains carotenoid homeostasis. Beyond WC1, PTR1 interfaces with a broader metabolic network to fine-tune central metabolism through discrete regulatory nodes. Notably, PTR1 homologs are found across evolutionarily distant eukaryotic lineages, including fungi, algae, plants, and animals, highlighting deep evolutionary conservation of the underlying protein architecture. These findings uncover a mechanism by which protein ubiquitination contributes to the coordination of distinct yet interconnected biosynthetic pathways in X. dendrorhous and point to the potential broader relevance of ubiquitin-mediated metabolic coordination beyond this species.
    Keywords:  E3 ubiquitin ligase; carotenoid; lipid; metabolic regulation; sterol
    DOI:  https://doi.org/10.1073/pnas.2530496123
  37. iScience. 2026 May 15. 29(5): 115543
    Localized phosphoinositide metabolism regulates STIM1/ORAI1 fast inactivation.
    Ning Dai, Shawn M Lamothe, Jody Groenendyk, Nicolas Touret, Harley T Kurata, Marek Michalak.
      Store-operated Ca2+ entry (SOCE) is central for maintaining cellular Ca2+ homeostasis, and it is initiated by the depletion of Ca2+ in the endoplasmic reticulum (ER) and activation of stromal interaction molecule 1 (STIM1). STIM1 acts as an ER Ca2+ sensor and engages with plasma membrane ORAI1 channels to facilitate ORAI1 activation and Ca2+ influx. Here, we found that STIM1 forms a complex with myotubularin-related protein 7 (MTMR7) to regulate ORAI1 inactivation during prolonged Ca2+ entry. MTMR7 alters plasma membrane PI(3,5)P2 and PI(4,5)P2 levels, increasing ORAI1 inactivation and decreasing SOCE. Loss of catalytic phosphatase function of MTMR7 weakens ORAI1 inactivation and enhances SOCE activity, while the disruption of MTMR7 and STIM1 association retains ORAI1 inactivation. The MTMR7/STIM1 complex positions MTMR7 at ER-plasma membrane contact sites to fine-tune lipid signaling, prevent premature STIM1 activation, and modify ORAI1 inactivation. These findings provide insight into novel modes of regulation of ORAI1 inactivation by phosphoinositides (PIPs).
    Keywords:  Biochemistry; Molecular biology; Pharmacology
    DOI:  https://doi.org/10.1016/j.isci.2026.115543
  38. Nucleic Acids Res. 2026 Apr 13. pii: gkag353. [Epub ahead of print]54(7):
    Multimodal profiling reveals cell type-specific pseudouridine modification and density-dependent translational regulation.
    Caroline A McCormick, Michele Meseonznik, Yuchen Qiu, Oleksandra Fanari, Priyanka Goyal, Mitchell Thomas, Mina Shokoufandeh, Yifang Liu, Dylan Bloch, Cole Greenfield, Isabel N Klink, Miten Jain, Meni Wanunu, Sara H Rouhanifard.
      Pseudouridine (psi) is one of the most abundant mRNA modifications, yet its impact on translation is unclear, in part because existing modification maps are inconsistent, curated comparisons across cell types are lacking, and paired analyses with translation are limited. Using direct RNA nanopore sequencing coupled with our Mod-p ID analytical framework, we mapped psi at single-nucleotide resolution across six immortalized human cell lines. Nanopore sequencing provided single-molecule resolution, enabling quantification of relative modification occupancy and detection of co-occurring modifications. Integrating these psi maps with matched proteomic and ribosome profiling datasets revealed that conserved psi sites installed by the psi synthase TRUB1 are associated with increased protein production. TRUB1 knockout experiments demonstrated a motif-specific reduction in protein abundance, providing direct causal evidence that pseudouridylation enhances protein output. In contrast, transcripts bearing clustered psi sites exhibited reduced protein abundance despite elevated translation efficiency. Controlled in vitro translation experiments confirmed that increasing pseudouridine density within a physiologically relevant range directly reduces protein output, demonstrating a density-dependent effect of pseudouridylation on translation. Together, these findings establish a mechanistic framework in which single-site pseudouridylation enhances protein production, whereas hypermodification impairs translational throughput, revealing pseudouridine density and enzyme specificity as key determinants of proteome output across human cell types.
    DOI:  https://doi.org/10.1093/nar/gkag353
  39. Nat Commun. 2026 Apr 20.
    Subcellular mRNA localization patterns across tissues resolved with spatial transcriptomics.
    Roy Novoselsky, Ofra Golani, Tal Barkai, Merav Kedmi, Inna Goliand, Michal Fine, Ilan Kent, Ido Nachmany, Shalev Itzkovitz.
      Subcellular RNA localization, including nuclear retention and apical-basal compartmentalization in polarized epithelia plays a central role in post-transcriptional regulation. However, methods for high-throughput mapping of mRNA localization within intact tissue sections remain limited. Here, we apply high-resolution spatial transcriptomics to systematically resolve intracellular mRNA localization across diverse mammalian tissues. We introduce a computational approach that leverages image-derived features to extract subcellular information from spatial data and quantifies transcript localization patterns. Using this framework, we map apical-basal mRNA localization and nuclear retention in gastrointestinal epithelia and in liver hepatocytes. Our analyses reveal conserved and tissue-specific localization signatures. This approach broadens the scope of spatial transcriptomics by enabling routine investigation of intracellular RNA distributions in both healthy and diseased tissues.
    DOI:  https://doi.org/10.1038/s41467-026-72156-7
  40. ACS Bio Med Chem Au. 2026 Apr 15. 6(2): 118-129
    Pyrazolylpyrimidinamines Decorated via Petasis Reaction as Small-Molecule Activators of the RNA-Degrading Ribonuclease IRE1α.
    Amrutha K Avathan Veettil, Yang Liu, Leon Wagner, Oguz Hastürk, Nguyen Song Thu Huynh, Giorgia Mancino, Maria Beerbaum, Peng Wu.
      The multicomponent Petasis boron-Mannich reaction (PR) enables the generation of functionalized amines that are of biological interest. Here, we demonstrated that a series of pyrazolylpyrimidinamines decorated via PR are new small-molecule activators of the dual kinase and ribonuclease RNA-degrading protein inositol-requiring enzyme 1α (IRE1α), which is an essential effector in the unfolded protein response associated with many human diseases. Compound SH4 was identified via a FRET assay and showed potent activity in activating the IRE1α ribonuclease (RNase) activity, inducing increased XBP1 mRNA splicing, and inducing Bloc1s1 mRNA degradation. Based on a binding mode analysis, the following series of PR-decorated functionalized amines was further probed as IRE1α RNase activators. One PR-derived compound, AK177, showed nanomolar activating potency in biochemical assays but minimal activities in cellular evaluations. Overall, we present here a series of pyrazolylpyrimidinamines as new small-molecule activators of the IRE1α RNase activity, which served as the first examples of applying PR in accessing bioactive compounds targeting the kinase domain of a ribonuclease involved in mRNA cleavage and splicing.
    Keywords:  Petasis reaction; RNA degradation; pyrimidinamine; ribonuclease; small-molecule activator
    DOI:  https://doi.org/10.1021/acsbiomedchemau.5c00161
  41. Nat Commun. 2026 Apr 21. pii: 3659. [Epub ahead of print]17(1):
    The vault associates with membranes in situ.
    Katharina Geißler, Jan Philipp Kreysing, Yuning Wang, Desislava Glushkova, Agnieszka Obarska-Kosinska, Patrick C Hoffmann, Stefanie Böhm, Alexander Schmidt, Jakob Meier-Credo, Julian D Langer, Gerhard Hummer, Martin Beck.
      The eukaryotic vault particle is a giant ribonucleoprotein complex that assembles into an iconic barrel-like cage. Its cellular function has remained elusive despite extensive characterization. Using cryo-electron tomography of Dictyostelium discoideum cells, we define the distribution, structural states, and interaction landscape of vault particles in situ. Surprisingly, we detect a subpopulation of vault particles associated with the endoplasmic reticulum (ER) and nuclear envelope membranes. This association occurs at a defined barrel height of the vault particle. Membrane-associated particles appear to localize to patches of reduced membrane bilayer thickness and altered curvature. We further find that a fraction of vaults encloses 80S ribosomes in highly ordered orientations. These structural findings are further corroborated by proximity labeling experiments, which identify ER-resident proteins and numerous ribosomal components as vault particle interactors. The membrane-bound and ribosome-encapsulating vault populations that we uncover will direct future studies towards revealing vault function.
    DOI:  https://doi.org/10.1038/s41467-026-71837-7
  42. Proc Natl Acad Sci U S A. 2026 Apr 28. 123(17): e2523032123
    Simple biological controllers drive the evolution of soft modes.
    Christopher Joel Russo, Kabir Husain, Rama Ranganathan, David Pincus, Arvind Murugan.
      Biological systems, with many interacting components, face high-dimensional environmental fluctuations, ranging from diverse nutrient deprivations to toxins, drugs, and physical stresses. Yet, many biological control mechanisms are "simple," i.e., restoring homeostasis through low-dimensional representations of the system's high-dimensional state. How do low-dimensional controllers maintain homeostasis in high-dimensional systems? We develop an analytically tractable model of integral feedback for complex systems in fluctuating environments. We find that selection for homeostasis leads to the emergence of a soft mode that provides the dimensionality reduction required for the functioning of simple controllers. Our theory predicts that simple controllers that buffer environmental perturbations (e.g., stress response pathways) will also buffer mutational perturbation, an equivalence we test using experimental data across 5,000 strains in the yeast knockout collection. We also predict, counterintuitively, that knocking out a simple controller will decrease the dimensionality of the response to environmental change; we outline transcriptomics tests to validate this. Our work suggests an evolutionary origin of soft modes, with implications ranging from cryptic genetic variation to global epistasis.
    Keywords:  dimensionality reduction; soft modes; stress response
    DOI:  https://doi.org/10.1073/pnas.2523032123
  43. Nat Commun. 2026 Apr 21.
    SMG7 and eIF4A constitute a homeostatic module controlling P-body condensation and function of meiotic bodies.
    Albert Cairo, Neha Shukla, Sofia Kanavorova, Jan Skalak, Pavlina Mikulkova, Anna Vargova, David Potesil, Zbynek Zdrahal, Jan Hejatko, Karel Riha.
      Processing bodies (P-bodies) are ribonucleoprotein condensates that regulate RNA processing and storage. Although constitutively present in most cells, their size and composition change dynamically in response to developmental and environmental cues. However, mechanisms governing P-body assembly and remodeling remain poorly understood. Here we show that in Arabidopsis, SMG7 interacts with the eIF4A helicases and recruits them to P-bodies. eIF4As limit P-body condensation and also restrict stress granule (SG) formation under heat stress. We further identify meiotic bodies (M-bodies) as composite RNP granules with a P-body core surrounded by a SG-like shell. The SMG7-eIF4A module regulates the recruitment of the meiosis-specific protein TDM1 into M-bodies, thereby influencing meiotic exit and plant reproduction. Our findings suggest that SMG7 functions as an adaptor protein that recruits client proteins into P-bodies and, together with eIF4A, forms a regulatory module that controls P-body composition and maintains their size homeostasis.
    DOI:  https://doi.org/10.1038/s41467-026-72218-w
  44. Adv Mater. 2026 Apr 21. e17261
    Reprogramming Disulfide Reduction in Endoplasmic Reticulum Uncouples Immune Evasion of Pancreatic Cancer.
    Zhongqiu Guo, Yuting Lu, Li Zhang, Yang Chen, Huiyan Li, Tao Wang, Wenjun Gu, Fan Wu, Yelin Wu, Peiran Zhao, Changjing Zuo, Wenbo Bu.
      The modulation of immune checkpoint activity exerts profound impacts on tumor immunotherapy. However, the interfere of mature immune checkpoints encounter efficacy challenges in solid tumors, which underlies a critical barrier in clinical translation of multiple potential targets. Herein, we propose a biochemical immune modulation strategy for immunosuppression reversal by blocking the mature of CD47 within the endoplasmic reticulum (ER). Clinically used radionuclides iodine-131 (131I) is reengineered to encapsulate within microporous barium titanate nanoparticles, forming an immunoactive nanomodulator. Leveraging polarized and collisional relaxation, the electrons emitted from 131I mediate continuous disulfide bond reduction, blocking CD47 folding and surface translocation, resulting in a 93.6% reduction in CD47 expression. Together with the remarkable increase of tumor antigen presentation induced by ER reductive stress in pancreatic tumor-bearing mice, we realize a 93% tumor inhibition and a 3-fold prolongation of survival. This work underscores the role of organellar biochemistry in reshaping immunosuppression for tumor immunotherapy.
    Keywords:  CD47; biochemical immune modulation; disulfide bond reduction; immunosuppression reversal; pancreatic cancer
    DOI:  https://doi.org/10.1002/adma.202517261
  45. Sci Adv. 2026 Apr 24. 12(17): eaeb1729
    Cell-internal autocrine receptor inactivation supports maintenance of mating-type identity in yeast.
    Alexander Anders, Gabriele Malengo, Laura Kley, Victor Sourjik.
      Efficient and exclusive recognition of nonself requires quality control mechanisms to eliminate self-signaling in various types of organisms and cells. Here, we discovered a previously unknown mechanism, which inactivates self-reactive G protein-coupled receptor (GPCR) used in premating communication between the two mating types of budding yeast. Our results suggest that this mechanism of cell-internal autocrine inactivation involves receptor interaction with its cosecreted peptide ligand within the secretory pathway. We demonstrate that ligand binding elicits inactivation of the self-reactive receptor already before it reaches the cell surface. This inactivation is apparently initiated through the same pathway that is involved in the endocytic internalization and subsequent vacuolar degradation of the activated cell-surface localized receptors. We hypothesize that, beyond contributing to mating-type identity in yeast, this mechanism of proofreading may be used more generally in eukaryotic cells to suppress autocrine signaling by self-secreted peptide ligands.
    DOI:  https://doi.org/10.1126/sciadv.aeb1729
  46. Mol Cell Proteomics. 2026 Apr 20. pii: S1535-9476(26)00067-8. [Epub ahead of print] 101571
    A landscape analysis of human SUMOylation.
    Shireen S Al-Momani, Kerry Rambsbottom, Andrew Collins, Ellen Boswell, Ivo Alexander Hendriks, Michael L Nielsen, Alfred C O Vertegaal, Ronald T Hay, Zhi Sun, Yasset Perez Riverol, Emily H Bowler-Barnett, Maria J Martin, Jun Fan, Ari Sadanandom, Eric W Deutsch, Juan Antonio Vizcaíno, Andrew R Jones.
      SUMOylation is an understudied post-translational modification (PTM) linked to diverse physiological and pathological processes. Advances in enrichment strategies, combined with mass spectrometry (MS), have enabled large-scale mapping of SUMOylation sites. Here, we reanalyzed publicly available MS-based datasets to construct a comprehensive and high-confidence reference set of human SUMOylation sites. Our workflow integrated database searching and scoring through the Trans-Proteomic Pipeline (TPP) with a statistical approach to independently estimate global false localization rate (FLR) of modification sites. SUMOylated lysine sites identified at <5% FLR were classified into three confidence tiers and compared with a high-quality set of non-SUMOylated lysines. The Human SUMO Build comprises 35,721 SUMOylation sites across 6,146 proteins. SUMOylated lysines were enriched within intrinsically disordered regions and underrepresented in tightly packed structural elements. These sites exhibited a higher frequency of nearby phosphosites at -2, +1, and +5, and were enriched for disease-linked variants at the modified lysine and the -2 position. Motif analysis revealed canonical, inverted, and novel SUMOylation motifs with flanking amino acid enrichment, including aspartic acid at -2, isoleucine and valine at -1, proline at +1, and glutamic acid at +2. Comparative analysis of SUMOylation and ubiquitination sites revealed that the two modifications frequently target the same lysine residue. Sites exclusively SUMOylated are preferentially located within intrinsically disordered regions, whereas sites exclusively ubiquitinated are enriched in secondary structural elements. Sites modified by both PTMs are enriched more strongly for disease-associated variants at the modified lysine and the -1 position than sites unique to SUMOylation or ubiquitination. Gene Ontology enrichment analysis linked motifs to biological processes, with most motifs contributing to chromatin remodeling, histone modification, and mRNA processing. The Human SUMO Build is publicly available through the PTMeXchange initiative, with data deposited in PRIDE and integrated into UniProtKB and PeptideAtlas to facilitate downstream analyses and predictive modeling.
    Keywords:  SUMOylation; computational proteomics; false localization rate; human SUMO proteome; mass spectrometry
    DOI:  https://doi.org/10.1016/j.mcpro.2026.101571
  47. Mol Ther. 2026 Apr 22. pii: S1525-0016(26)00302-3. [Epub ahead of print]
    SEC62-mediated ER-Phagy activation alleviates Alzheimer's disease pathology and restores cognitive function in 5×FAD mice.
    Jing Huang, Yu-Bin Wang, Jian Wu, Pin-Jue Qian, Jue Shao, Dong-Dong Cao, Yanfen Liu, Zhen-Ge Luo.
      Alzheimer's disease (AD) is a common age-related neurodegenerative disorder. Previous studies have shown that patients with AD exhibit dysregulation of endoplasmic reticulum (ER) homeostasis in the brain, such as ER stress and ER damage. As a type of selective autophagy that specifically clears damaged ER, ER-phagy (endoplasmic reticulum-phagy) plays a key role in ER quality control, but the role in AD progression remains elusive. In this study, we found that ER homeostasis is severely disrupted in the pathological state of AD, characterized by enhanced ER stress response, the presence of ER damage, and concurrent defects in ER-phagy function. Notably, some receptors mediating ER-phagy were decreased in neurons differentiated from induced pluripotent stem cells (iPSCs) derived from AD patients and in 5×FAD mouse samples. Interestingly, overexpression of the ER-phagy receptor SEC62 in the brain of 5×FAD mice via intrathecal AAV injection markedly alleviated disease phenotypes, including β-amyloid (Aβ) plaque deposition, neuroinflammation, and cognitive impairment. These results indicate that restoring ER-phagy activity provides a potential strategy for the treatment of AD.
    DOI:  https://doi.org/10.1016/j.ymthe.2026.04.037
  48. Autophagy. 2026 Apr 22.
    A CRISPR-Cas9 screen identifies LAPTM4A (lysosomal protein transmembrane 4 alpha) as a key host barrier against PRRSV infection.
    Zhan He, Min Liu, Nianqi Zhang, Jiecong Yan, Fangfang Li, Pengwei Zhao, Chunhe Guo.
      Porcine reproductive and respiratory syndrome virus (PRRSV) manipulates host intracellular processes, particularly macroautophagy/autophagy and lysosomal function, to facilitate its replication and spread. However, the precise host factors and molecular mechanisms by which PRRSV remodels the autophagy-lysosome axis remain poorly defined. Here, we performed a CRISPR-Cas9 knockout screen targeting 1,332 genes involved in protein degradation, metabolism, and vesicular trafficking, and identified LAPTM4A (lysosomal protein transmembrane 4 alpha) as a critical antiviral factor involved in the lysosomal pathway. A yeast two-hybrid screen identified LAPTM4A as an interactor of PRRSV GP5 (glycoprotein 5). Mechanistically, GP5 recruits the E3 ubiquitin ligase NEDD4 and the autophagy receptor SQSTM1/p62 to promote K63-linked polyubiquitination of LAPTM4A, leading to its autophagic degradation. This selective degradation activates the AMPK-ULK1-MAP1LC3/LC3 signaling cascade, initiating autophagy while facilitating MTOR-lysosome colocalization, thereby suppressing TFEB nuclear translocation and transcription of lysosome-related genes. The resulting incomplete autophagic flux enhances viral replication. Additionally, in terms of host defense, LAPTM4A maintains lysosomal homeostasis by restraining excessive autophagy through AMPK-ULK1-LC3 signaling and promoting TFEB-dependent lysosomal gene expression by impairing the binding of RPTOR/raptor to MTOR, thus providing broad antiviral protection against multiple RNA viruses. Collectively, our findings identify LAPTM4A as a central regulator of lysosome-autophagy homeostasis and reveal a viral strategy that dismantles this defense axis to facilitate infection.
    Keywords:  Autophagy; CRISPR-Cas9 library; PRRSV GP5; host-virus interaction; lysosomal homeostasis
    DOI:  https://doi.org/10.1080/15548627.2026.2664607
  49. STAR Protoc. 2026 Apr 18. pii: S2666-1667(26)00163-2. [Epub ahead of print]7(2): 104510
    Protocol for SUMOylome analysis using a SUMO-T86K mutant combined with Lys-C digestion.
    Yaning Wu, Rin Imai, Hidetaka Kosako, Haruhiko Siomi, Kensaku Murano.
      Small ubiquitin-like modifier (SUMO) modification, also known as SUMOylation, is a critical post-translational modification. Here, we present a protocol using the SUMO-T86K (Thr86→Lys) mutant and Lys-C digestion, followed by enrichment of modified peptides and mass spectrometry, to identify SUMOylated proteins and modification sites. This strategy overcomes a major limitation of the commonly used SUMO-T86R (Thr86→Arg) approach with trypsin digestion, in which the resulting diglycine (GG) remnant is indistinguishable from ubiquitin modifications. For complete details on the use and execution of this protocol, please refer to Wu et al.1.
    Keywords:  Cell-based Assays; Gene Expression; Mass Spectrometry; Molecular Biology; Protein Biochemistry; Proteomics
    DOI:  https://doi.org/10.1016/j.xpro.2026.104510
  50. Eur J Pharmacol. 2026 Apr 18. pii: S0014-2999(26)00354-7. [Epub ahead of print] 178872
    Lysosomal accumulation of Masitinib alters autophagy via pH-dependent trapping.
    Abdulrahman El Sayed, Monika Kluzek, Remigiusz Serwa, Abdelhalim Azzi.
      Small-molecule kinase inhibitors often exhibit complex cellular behaviors that cannot be explained solely by target inhibition. Masitinib is a clinically investigated tyrosine kinase inhibitor with reported anti-inflammatory and neuroprotective effects, yet its intracellular mechanism of action remains poorly defined. Here, we show that masitinib undergoes pH-dependent lysosomal sequestration that dominates its cellular activity. Across multiple cell lines, masitinib suppresses mTORC1 signaling while paradoxically inducing AKT phosphorylation through a VPS34 and rapamycin-sensitive pathway independent of class I PI3K. Thermal proteome profiling identifies lysosomal proteins as the primary off-target signature of masitinib. Using defined membrane model systems that recapitulate lysosomal lipid composition and acidity, we demonstrate that masitinib preferentially accumulates and intercalates into acidic, negatively charged membranes. This lysosomal accumulation impairs lysosomal acidification and disrupts autophagic flux, providing a mechanistic link between the physicochemical properties of masitinib and its downstream signaling effects. Together, our findings highlight lysosomal sequestration as a key determinant of kinase inhibitor behavior and underlie the importance of subcellular drug distribution in modulating cellular responses.
    Keywords:  GUVs; LUVs; Masitinib; autophagy; lysosome trapping
    DOI:  https://doi.org/10.1016/j.ejphar.2026.178872
  51. Protein Sci. 2026 May;35(5): e70587
    Proteostasis at the mitochondrial outer membrane: Quality control of mitochondrial protein transport.
    Shunsuke Matsumoto, Suzuka Ono, Toshiya Endo.
      Mitochondria are enclosed by a double-membrane structure composed of the outer and inner membranes, and this architectural organization underlies their diverse cellular functions. In particular, the mitochondrial outer membrane serves as an essential interface between the cytosol and the mitochondrial interior, regulating the flux of proteins, lipids, small molecules, and ions through the coordinated activities of its resident proteome. Consequently, structural and functional defects of outer membrane proteins are subject to continuous surveillance, and aberrant proteins are rapidly recognized and degraded. Defects in precursor translocation or translation can lead to the stalling of precursor proteins at the primary protein import gate, the TOM complex. Such situations are resolved by multiple quality control systems operating across both the mitochondria and the cytosol. In addition, proteins normally destined for the endoplasmic reticulum or peroxisomes may be mistargeted to mitochondria, and these mislocalized proteins are likewise managed through dedicated mechanisms that promote their degradation or re-targeting. In this review, we summarize current insights into the molecular factors and mechanisms that maintain proteostasis at the mitochondrial outer membrane.
    Keywords:  mitochondria; outer membrane; protein degradation; quality control; re‐targeting
    DOI:  https://doi.org/10.1002/pro.70587
  52. Oncogene. 2026 Apr 22.
    PIWIL1 activates the R2TP-TELO2-mTORC1 axis independently of piRNA to promote TOP mRNA translation in gastric cancer.
    Tianqu Fan, Jiangsha Zhao, Ling Li, Meihua Cui, Jiawei Zhang, Tian Chi, Shuo Shi.
      PIWI proteins, a subfamily of the PAZ-PIWI domain (PPD) protein family, are traditionally regarded as germline factors that partner with PIWI-interacting RNAs (piRNAs) to silence transposons and regulate gene expression. However, growing evidence implicates PIWI proteins as oncogenic drivers in diverse somatic cancers, often acting through piRNA-independent mechanisms that remain incompletely understood. Here, we integrate transcriptomic, translatomic, and proteomic profiling of wild-type versus PIWIL1-knockout gastric cancer cells to uncover a non-canonical, translational role for PIWIL1, one of the four human PIWI proteins. We find that PIWIL1 selectively enhances the translation of 5'-terminal oligopyrimidine (TOP) mRNAs by activating mTOR complex 1 (mTORC1). Mechanistically, PIWIL1 interacts with the R2TP chaperone complex (RUVBL1-RUVBL2-RPAP3-PIH1D1) and promotes its association with TELO2, facilitating mTOR-RAPTOR assembly and mTORC1 activation. Functionally, PIWIL1 deficiency sensitizes gastric cancer cells to mTOR inhibition, and in clinical samples, PIWIL1 expression positively correlates with mTORC1 pathway activity. Together, these findings define a novel piRNA-independent mechanism through which PIWIL1 contributes to tumor progression, extend PIWI-mediated translational control from the germline to human cancers, and establish PIWIL1 as a potential therapeutic target for gastric cancer in synergy with mTOR inhibition.
    DOI:  https://doi.org/10.1038/s41388-026-03791-z
  53. EMBO J. 2026 Apr 22.
    Prothrombinase processivity is conferred by substrate allostery.
    Fatma Işık Üstok, Alexandre Faille, Alan J Warren, James A Huntington.
      The prothrombinase complex, comprised of factor (f) Xa and fVa, converts prothrombin to thrombin through sequential cleavage at two sites in a rapid and processive manner. The molecular basis of prothrombin processing is an enzymatical mystery that to solve requires structural insight into how the substrate and intermediate bind to prothrombinase. Here we present two 3.1 Å cryo-EM structures of prothrombinase bound to prothrombin and to meizothrombin. The prothrombin complex revealed a surprising interaction between the end of the heavy chain of fVa with exosite I of prothrombin, accounting for 70% of the contact interface. Triggering of the zymogen-to-protease conformational change following cleavage at Arg320 alters all domain-domain and fVa interactions observed for prothrombin, and results in a large-scale rearrangement of meizothrombin that presents the second cleavage site (Arg271) for processing. Together, these structures reveal a remarkable enzymatic mechanism that requires the active participation of the substrate itself, and introduces a new paradigm of 'substrate allostery'.
    DOI:  https://doi.org/10.1038/s44318-026-00782-4
  54. Angew Chem Int Ed Engl. 2026 Apr 23. e18897
    Photo-click Proteolysis-Targeting Chimeras Enable Intracellular Generation of PROTACs for Precise Dual Protein Degradation.
    Jing Pang, Shihong Li, Yuhui Zhang, Qingyu Jia, Ya-Qiu Long.
      Proteolysis-targeting chimeras (PROTACs) are an emerging therapeutic modality via targeted protein degradation, but plagued by concerns about systemic toxicity and a poor pharmacokinetic profile. To tackle the issues, we have devised a photo-click proteolysis targeting chimera (PCPTAC) that enables spatiotemporally controllable intracellular synthesis of PROTACs by photo-triggered bioorthogonal ligation. A photocaged dibenzosilacycloheptyne (photo-DBSH) and the complementary azide were deployed to tag the oncoprotein ligands (i.e., (+)-JQ1 for BRD4 and Olaparib for PARP1) and the E3 ligase ligand (i.e., Pomalidomide for CRBN), respectively, for a proof-of-concept study and potential treatment for triple-negative breast cancer (TNBC). Upon light irradiation, photo-DBSH-JQ1/-Olap was rapidly uncaged to give the reactive cycloalkyne-JQ1/-Olap, which immediately underwent a strain-promoted azide-alkyne cycloaddition with azide-Pomalidomide, in situ generating dual PROTACs for simultaneous degradation of BRD4 and PARP1 in TNBC MDA-MB-231 cells, with 25- and 2.4-fold more potent antiproliferative activity than the un-irradiated inhibitors and the corresponding PROTAC combination, respectively (IC50 = 0.032 µM vs. 0.846 µM and 0.075 µM). Further in zebrafish models, PCPTAC promoted BRD4 degradation leading to thinner yolk sac extension and achieved 94% tumor inhibition in HeLa xenografts. This split-and-photoclick strategy paves a new avenue for developing safer and more efficacious PROTACs with synergistic antitumor effects.
    Keywords:  in‐cell synthesis; photo‐click reactions; protein degradation; proteolysis targeting chimeras; spatiotemporal control
    DOI:  https://doi.org/10.1002/anie.202518897
  55. Plant Physiol. 2026 Apr 22. pii: kiag239. [Epub ahead of print]
    ZIP10 governs Zn influx into the cytoplasm from the endoplasmic reticulum and maintains Zn homeostasis in rice.
    Longtao Tan, Mengmeng Qu, Xinxin Zhang, Yu Peng, Yuxing Zhu, Can Peng, Chunyong Li, Jiurong Wang, Guanghui Liu, Yonglong Chen, Donghai Mao, Caiyan Chen.
      Zn is an essential micronutrient for all organisms. Understanding how Zn homeostasis is controlled in plants is crucial for agriculture and human health. In the present study, we characterized a transporter in rice (Oryza sativa), ZRT/IRT-LIKE PROTEIN10 (OsZIP10), which is primarily expressed in the roots and localized in the endoplasmic reticulum (ER) membrane. OsZIP10 transports Zn from the ER lumen into the cytoplasm and facilitates the radial delivery of Zn via the symplastic pathway in rice roots. Notably, both OsZIP10 knockout mutants and overexpression lines enhanced Zn accumulation by upregulating Zn uptake in roots and the root-to-shoot transfer of Zn, albeit through different mechanisms. Overexpression of OsZIP10 triggered an unfolded protein response and induced the expression of the ER stress-responsive transcription factor BASIC LEUCINE ZIPPER TRANSCRIPTION FACTOR74 (bZIP74), producing an unconventional alternatively spliced isoform. This isoform of OsbZIP74 then activated the expression of ZRT/IRT-LIKE PROTEIN7 (OsZIP7) and ZRT/IRT-LIKE PROTEIN9 (OsZIP9), enhancing Zn uptake and translocation. Through a distinctive mechanism, the knockout of OsZIP10 promotes the translocation of BASIC LEUCINE ZIPPER TRANSCRIPTION FACTOR50 (bZIP50) from the cytosol to the nucleus, where it activates the expression of OsZIP7 and OsZIP9. Our findings fill a gap in the understanding of Zn transfer in rice roots and establish two distinct signaling pathways linking Zn homeostasis control in the ER with the regulation of Zn uptake, transport, and accumulation.
    Keywords:  ER stress; OsZIP10; rice; zinc homeostasis
    DOI:  https://doi.org/10.1093/plphys/kiag239
  56. FEBS Open Bio. 2026 Apr 21.
    Pharmacological inhibition of the PERK pathway modulates hepatocellular carcinoma growth and immune signaling.
    Ada Lerma-Clavero, Maria Kopsida, Nathalie Arendt, Hans Lennernäs, Markus Sjöblom, Femke Heindryckx.
      The unfolded protein response (UPR) plays an important role in tumor progression and cellular stress adaptation. In hepatocellular carcinoma (HCC), pharmacological inhibition of the protein kinase R-like endoplasmic reticulum kinase (PERK) is a potential therapeutic strategy, yet its effects on tumor growth and the microenvironment remain unclear. We investigated the selective PERK inhibitor AMG PERK 44 in a diethylnitrosamine (DEN)-induced mouse model of advanced HCC. Tumor burden, proliferation, fibrosis, immune-related gene expression, and ER stress signaling were assessed alongside analyses of single-cell RNA-sequencing data from HCC mouse models and liver-specific PERK knockout mice. Our results show that AMG PERK 44 did not alter tumor number nor cause a decrease in tumor area and proliferation. Furthermore, fibrotic burden was unchanged, although fibrosis architecture and stromal gene expression (TGF-β, CTGF, F4/80) were modified. Despite PERK inhibition, the expression of ER stress associated genes (CHOP, EIF2AK3, ERdj4) increased. Single-cell analysis revealed context-dependent PERK activity, highest in dendritic cells and macrophages under inflammatory and tumor conditions, while PERK knockout livers showed impaired UPR responses after tunicamycin treatment. Finally, AMG PERK 44 did not enhance idarubicin efficacy and caused no major off-target effects. These findings highlight the context-dependent role of PERK in the HCC microenvironment and its implications for targeting UPR pathways in liver cancer. Impact statement This study provides an evaluation of PERK as a therapeutic target in hepatocellular carcinoma by demonstrating that its inhibition does not produce the anticipated anti-tumor effects in advanced disease, but instead exerts nuanced, context-dependent influences on the tumor microenvironment.
    Keywords:  AMG PERK44; ER stress; PERK; carcinogenesis; fibrosis; hepatocellular carcinoma; idarubicin; inflammation
    DOI:  https://doi.org/10.1002/2211-5463.70252
  57. EMBO J. 2026 Apr 24.
    Tissue-selective COPII modulator SEC16B aggravates cardiovascular disease by promoting lipid export.
    Xiao Wang, Yating Hu, Lu Liu, Runze Huang, Yawei Wang, Bing Liu, Yifei Zhao, Yuangang Zhu, Jia Lv, Liang Liu, Huimin Wang, Lingzhi Wu, Xinxuan Xu, Yaxin Li, Guanlin Wang, Xiao-Wei Chen.
      The biogenesis and transport of lipoproteins are essential for systemic homeostasis and cardiometabolic health, yet how the secretory pathway acquires specialization to support high-capacity lipoprotein export remains unclear. Here, we report SEC16B as a tissue-selective modulator of the COPII machinery, critical for the efficient secretion of APOB-containing lipoproteins. Integrative bioinformatic analyses identify that SEC16B co-emerges with core genes involved in lipoprotein biogenesis. Functional studies, coupled with AI-driven prediction, reveal that SEC16B acts as a molecular brake to fine-tune COPII condensation for lipoprotein export. Mining of UK biobank data links SEC16B to metabolic traits in humans and suggests HNF4A-dependent regulation of SEC16B expression. Hepatic deletion of SEC16B in mice markedly reduces circulating APOB, triglycerides and cholesterol, while conferring robust protection against atherosclerosis and cardiac dysfunction and maintaining liver health. Collectively, these findings position SEC16B as a specialized modulator of lipoprotein export via the general secretory (SEC) pathway in the liver, suggesting potential therapeutic avenues for combating cardiometabolic diseases.
    Keywords:   SEC16B ; COPII; Cardio-metabolic Health; Lipid Metabolism; Lipoprotein Secretion
    DOI:  https://doi.org/10.1038/s44318-026-00754-8
  58. RNA. 2026 Apr 21. pii: rna.080776.125. [Epub ahead of print]
    Dual Role of 3' UTR Length in Modulating Translation Termination Efficiency.
    Ali Salman, Mikhail Loev, Tatiana Egorova, Alexey V Shuvalov, Anastasia Zharikova, Sergey Dmitriev, Ekaterina Shuvalova, Nikita Biziaev, Elena Alkalaeva.
      The 3' untranslated region of mRNAs are involved in post-transcriptional control, influencing mRNA stability, localization, and translation efficiency through its interaction with various proteins and RNAs. While eukaryotic 3' UTRs are typically several hundred nucleotides long, certain protozoan species possess remarkably short 3' UTRs and have evolved alternative genetic codes where canonical stop codons are reassigned to sense codons. This suggests a potential link between 3' UTR architecture and the efficiency of translation termination. In this study, we investigate how the length and secondary structure of the 3' UTR modulate translation termination efficiency across different species. We demonstrate that shortening of structured 3' UTRs confer a translational advantage for mRNAs bearing UAA stop codons. Using purified pre-termination complexes, we show that 3' UTR secondary structures enhance the termination rate by facilitating the spatial proximity of PABP (bound to the poly(A) tail) to eRF3a on the ribosome. Furthermore, we found that the termination rate at UGA stop codons is highly sensitive to 3' UTR length when assayed with both human and ciliate release factors. Our investigation of stop codon reassignment underscores the primary role of release factor recognition efficiency in this process. Collectively, our findings reveal a dual regulatory mechanism: while long, structured 3' UTRs can sterically hinder stop codon recognition, they simultaneously promote eRF3a-PABP interactions that facilitate the recruitment of release factors to the ribosome. This work establishes 3' UTR length as a key cis-regulatory factor fine-tuning the fundamental process of translation termination.
    Keywords:  3&#8242; UTR; PABP; eRF1; eRF3; ribosome
    DOI:  https://doi.org/10.1261/rna.080776.125
  59. Trends Pharmacol Sci. 2026 Apr 20. pii: S0165-6147(26)00084-2. [Epub ahead of print]
    Pharmacological strategies targeting chaperone-mediated autophagy.
    Eva Berenger, Alice Maestri, Daniel R Vaz, Elena Kochetkova, Erik Norberg, Vitaliy O Kaminskyy, S Joseph Endicott, Helin Vakifahmetoglu-Norberg.
      Chaperone-mediated autophagy (CMA) is a selective lysosomal protein degradation pathway that regulates proteostasis, metabolism, and stress adaptation. Genetic- and disease-model studies show that altered CMA activity contributes to diverse human disorders, including neurodegenerative, metabolic, inflammatory, and malignant diseases. However, pharmacological targeting has remained challenging due to a limited understanding of its regulatory architecture and a lack of criteria to distinguish pathway-selective from indirect modulation. Recent advances in mapping CMA regulatory checkpoints and the in vivo validation of CMA-biased compounds have revealed discrete, mechanistically defined control nodes that render CMA pharmacologically tractable. In this review, we synthesize these advances and introduce a mechanistic classification of CMA-modulating compounds by level of action, distinguishing physiological inducers, permissive potentiators, and proximal activators to clarify pathway selectivity and guide translational drug discovery.
    Keywords:  LAMP-2A; chaperone-mediated autophagy; pharmacological modulation; proteostasis; therapeutic targeting
    DOI:  https://doi.org/10.1016/j.tips.2026.03.008
  60. Nat Commun. 2026 Apr 22.
    Discovery of molecular glues that bind FKBP12 and structurally distinct targets using DNA-encoded libraries.
    Trevor A Zandi, Michael J Romanowski, Jessica S Viscomi, Karl Gunderson, Zher Yin Tan, Bingqi Tong, Simone Bonazzi, Frédéric J Zécri, Stuart L Schreiber, Gregory A Michaud.
      Molecular glues are small molecules that engage their target and presenter proteins cooperatively. FKBP12 molecular glues (FK506 and rapamycin) were discovered several decades ago and have been used clinically, but our understanding of the breadth of FKBP12 molecular glues and targets has yet to be fully revealed. To expand the target classes of FKBP12 molecular glues, we construct and screen a multi-million-member non-macrocyclic FKBP12-ligand DNA-encoded library using 25 structurally distinct proteins. Synthesis and validation of select hits in biophysical and cell-based assays confirm FKBP12-dependent molecular-glue recruitment to bromodomain-containing protein 9 (BRD9) and quinoid dihydropteridine reductase (QDPR). One glue shows no measurable binding to QDPR alone but has appreciable binding in the presence of FKBP12 using either purified proteins or intact cells. The sites of recruitment are characterized with mutational analysis, competition-based methods and X-ray crystallography. The results of this study confirm that FKBP12-binding DELs can yield molecular glues generating highly selective FKBP12-target protein interactions.
    DOI:  https://doi.org/10.1038/s41467-026-71512-x
  61. Sci Adv. 2026 Apr 24. 12(17): eaef7163
    Repertoire-scale antibody structural prediction informs therapeutic design.
    Zhe Sang, Yufei Xiang, Wei Huang, Paul R Sargunas, Yong Joon Jeffery Kim, Zirui Feng, Derek J Taylor, Yi Shi.
      We present AF3-TurboAb, a scalable framework that makes a repertoire-scale antibody-antigen complex structural decoding routine for antibody engineering. By eliminating preprocessing bottlenecks, AF3-TurboAb enables end-to-end complex modeling in 0.5 minutes per seed on a single GPU while preserving near-experimental interface fidelity, as validated on ~1000 posttraining Protein Data Bank (PDB) benchmarks and 12 experimentally determined cryo-electron microscopy nanobody-antigen structures. Applying this capability to 275,371 immunization-derived antigen-specific nanobodies produced 28,013 high-confidence complex predictions, substantially expanding the structural landscape of antibody recognition. The resulting atlas reveals hundreds of previously unmapped epitopes, extensive coverage of solvent-exposed surfaces, and recurrent affinity hotspots enriched in aromatic and charged residues. Despite wide sequence diversity, we observe structural convergence at shared epitopes and consistent physicochemical and geometric features that complement and extend existing PDB entries. We demonstrate translational utility by (i) designing durable (escape-proof), multiepitope neutralizers against highly evolved viruses, (ii) identifying cross-species and glycoform-specific binders to a cancer checkpoint, and (iii) enabling near-real-time in silico binder triage. The models and metadata will be shared for community use, establishing repertoire-scale structural decoding as a practical design modality that transforms the scale and speed of structure-guided antibody engineering.
    DOI:  https://doi.org/10.1126/sciadv.aef7163
  62. Front Bioinform. 2026 ;6 1776111
    Unveiling the thioredoxin fold: a systematic review and bioinformatic analysis of protein disulfide isomerase and Dsb family proteins.
    Daniel Cuevas Ortiz, Karen Werner, Maria Fernanda Frias Mayo, Pablo A Cárdenas Arredondo, Gabriela F García Manzano, Cristina Revilla-Monsalve, Héctor Retana, Nelly F Altamirano-Bustamante, Myriam M Altamirano-Bustamante.
       Introduction: Protein Disulfide Isomerases (PDIs) and bacterial Dsb proteins are key members of the thioredoxin-fold superfamily, essential for oxidative protein folding in eukaryotic and prokaryotic systems, respectively. Despite their differences in cellular context, these proteins share a conserved thioredoxin domain architecture that enables catalysis of disulfide bond formation, isomerization, and reduction. This systematic review integrates biochemical, structural, and bioinformatic data to identify conserved features within the PDI and Dsb families that underline their catalytic functions.
    Methods: Using a PRISMA-based methodology, we screened and analyzed 96 relevant articles and conducted a comparative structural analysis of 11 representative PDI proteins, most of which lack experimentally resolved structures. We leveraged AlphaFold models alongside crystal structures of canonical PDI (PDIA1), DsbC, and DsbG.
    Results: We reveal conserved tertiary folds, catalytic motifs, and domain arrangements across species. These findings highlight the evolutionary conservation and structural versatility of thioredoxin-fold enzymes and underscore their biomedical relevance in diseases linked to protein misfolding, such as neurodegeneration, cancer, and infection.
    Discussion: The results offer a foundation for future experimental studies and therapeutic exploration targeting redox-regulating thioredoxin-fold proteins.
    Keywords:  Dsb proteins; chaperone activity; isomerase activity; protein design; protein disulfide isomerase; protein evolution; redox reactions; thioredoxin
    DOI:  https://doi.org/10.3389/fbinf.2026.1776111
  63. J Clin Invest. 2026 Apr 24. pii: e204602. [Epub ahead of print]
    Hepatic SEC16B regulates lipid homeostasis by coordinating VLDL secretion and lipid droplet expansion.
    Wei Lu, Zhiming Zhao, Donald Molina, Huaxun Fan, Ruicheng Shi, Ye Tian, Raja Gopoju, Tiantian Yang, Xinyuan Zhang, Yanqiao Zhang, Kai Zhang, Jaume Amengual, Bo Wang.
      The liver plays a critical role in lipid homeostasis, where lipids are either secreted as very-low-density lipoproteins (VLDL) or stored in lipid droplets (LDs). However, the regulatory mechanisms governing these two interconnected processes remain poorly understood. Here, we demonstrate that SEC16B functions as a lipid-responsive regulator in the liver, promoting VLDL secretion and LD expansion to handle lipid flux and maintain lipid homeostasis. Genome-wide association studies have identified single-nucleotide polymorphisms in SEC16B to be highly associated with serum lipid levels in humans. Hepatic Sec16b deficiency decreases serum lipid levels by impairing VLDL secretion through mechanisms that are at least partially independent of microsomal triglyceride transfer protein (MTP)-mediated ApoB lipidation and COPII-mediated intracellular trafficking. SEC16B partially localizes at ER-LD contact sites and promotes LD expansion by facilitating the targeting of ER proteins to LDs. More importantly, suppression of Sec16b dramatically lowers serum lipid levels and reduces atherosclerotic lesion size in Ldlr null mice. These data reveal a mechanism that coordinates VLDL and LD metabolism and suggest SEC16B as a potential therapeutic target for atherosclerosis treatment.
    Keywords:  Atherosclerosis; Cardiovascular disease; Hepatology; Lipoproteins; Metabolism
    DOI:  https://doi.org/10.1172/JCI204602
  64. iScience. 2026 Apr 17. 29(4): 115493
    Mathematical modeling of ribosome competition informs testable treatment strategies for drug-tolerant cancer persister cells.
    Xinpu Tang, Yuqing Wang, Yi Pu, Kaixiu Li, Zheyu Ding, Mengyao Wang, Luis Almeida, Michael Cerezo, Yarong Cao, Caroline Robert, Diane Peurichard, Shensi Shen.
      Systemic therapies for advanced cancers often induce initial responses but rarely achieve durable cures due to acquired resistance. Drug-tolerant persister (DTP) cells survive treatment without additional genetic mutations. We previously showed that melanoma DTP cells globally suppress mRNA translation while selectively maintaining translation of specific mRNAs, but the basis of this selectivity remained unclear. Here, we integrate stochastic modeling with experimental analyses to define the principles governing selective translation in DTP cells. We identify translational reprogramming as a conserved feature of DTP cells across cancer types and treatments. Reduced MYC-dependent ribosome biogenesis limits ribosome availability, creating a translational bottleneck. Modeling reveals that ribosome scarcity drives competition among mRNAs, thereby shaping selective translation. This framework uncovers a ribosome-dependent survival checkpoint in DTP cells and highlights ribosome thresholds as a potential vulnerability for overcoming therapy resistance.
    Keywords:  cancer; mathematical biosciences; therapy
    DOI:  https://doi.org/10.1016/j.isci.2026.115493
  65. Cell Death Dis. 2026 Apr 24.
    TRIM26-mediated NKRF degradation drives Osimertinib resistance through SNRPD2-dependent stress granule formation in lung adenocarcinoma.
    Tao Wang, Hai-Yan Yang, Xing Wang, Xin-Hao Han, Zhen Zhang, Yu Zhang, Xiao-Jian Han, Zhuo Lu.
      Osimertinib is the standard first-line therapy for EGFR-mutant lung adenocarcinoma; however, the inevitable development of acquired resistance leads to disease progression and treatment failure. While established resistance mechanisms primarily involve genetic alterations, stress-adaptive pathways, particularly stress granule-mediated therapeutic tolerance, remain poorly understood. This study aims to elucidate the transcriptional and post-translational mechanisms governing stress granule-mediated survival and their contribution to Osimertinib resistance in lung adenocarcinoma. We identify NF-κB repressing factor (NKRF) as a critical suppressor of Osimertinib resistance, whose expression is markedly reduced in resistant lung adenocarcinoma cells. Restoration of NKRF significantly sensitized resistant cells to Osimertinib in vitro and inhibited tumor growth in xenograft models. Mechanistically, NKRF directly repressed transcription of the ribonucleoprotein component Small nuclear ribonucleoprotein D2 (SNRPD2), thereby constraining stress granule formation and attenuating drug tolerance. We further demonstrate that the E3 ubiquitin ligase TRIM26 interacts with NKRF and promotes its K48-linked ubiquitination at Lys411, leading to proteasomal degradation. This process sustains SNRPD2 expression and enhances stress granule assembly. Genetic depletion of TRIM26 restored NKRF stability, suppressed stress granule formation, and re-sensitized resistant tumors to Osimertinib, effects that were abrogated by concomitant NKRF silencing. Collectively, this study defines a previously unrecognized TRIM26/NKRF/SNRPD2 regulatory axis that integrates ubiquitin-mediated proteostasis with transcriptional control of stress granule dynamics. This work provides mechanistic insight into stress-adaptive Osimertinib resistance and identifies potential therapeutic targets for overcoming resistance in EGFR-mutant lung adenocarcinoma.
    DOI:  https://doi.org/10.1038/s41419-026-08787-x
  66. Ageing Res Rev. 2026 Apr 21. pii: S1568-1637(26)00137-6. [Epub ahead of print]118 103145
    Organelle interactome disruption: The systemic pathological mechanisms and therapeutic prospects of mitochondria-lysosome-ER crosstalk in Alzheimer's disease.
    Liping Xing, Annan Liu, Wei Gao, Jianhui Li, Mingyuan Yao, Jing Song, Peihan Duan, Honglin Li.
      The traditional pathological framework of Alzheimer's disease (AD) primarily focuses on the accumulation of β-amyloid (Aβ) and tau proteins. However, therapeutic strategies targeting these molecules have repeatedly encountered setbacks in clinical translation. Recent studies have progressively revealed that the dynamic interaction network among intracellular organelles plays a central role in the pathogenesis of AD. This systematic review examines the independent dysfunctions of three key organelles-mitochondria, lysosomes, and the endoplasmic reticulum (ER)-in AD, along with their physical and functional connectivity mechanisms. It emphasizes how their interaction network, formed through membrane contact sites, synergistically drives core AD pathological processes, including calcium signaling dysregulation, Aβ metabolism imbalance, mitochondrial quality control failure, lipid metabolism disorders, and neuroinflammation with apoptosis. This paper innovatively proposes that AD can be regarded as a "mitochondrial network disorder," the pathological essence of which lies in the systemic breakdown of communication between mitochondria. Building on this premise, we further discuss a therapeutic strategy centered on mitophagy enhancers to reshape the mitochondrial network and explore the translational medical prospects of achieving multi-target synergistic intervention by restoring the homeostasis of the mitochondrial network.
    Keywords:  Alzheimer's disease; Endoplasmic reticulum stress; Lysosomal dysfunction; Membrane contact sites; Mitochondrial-endoplasmic reticulum connections; Organelle interaction networks
    DOI:  https://doi.org/10.1016/j.arr.2026.103145
  67. Sci Adv. 2026 Apr 24. 12(17): eady6364
    CryptoBank: A resource for the identification and prediction of cryptic sites in proteins.
    Pedro Febrer Martinez, Thorben Fröhlking, Alberto Borsatto, Francesco L Gervasio.
      Cryptic binding sites offer opportunities to modulate targets previously considered "undruggable." However, the scarcity of validated examples limits the development of predictive tools. Here, we introduce CryptoBank, a large-scale database of cryptic sites identified by applying a machine learning model to detect ligand-induced conformational changes in more than 6 million structural alignments of unbound (apo) and bound (holo) protein pairs from the Protein Data Bank (PDB). Our analysis reveals that cryptic pockets are widespread, occurring in ~18% of protein clusters. Leveraging this resource, we fine-tuned a protein language model (PLM) to predict cryptic sites directly from protein sequences. Crucially, we show the broad applicability of our strategy by predicting cryptic sites in four proteins with low sequence identity to any CryptoBank entry and then validating these predictions using molecular dynamics simulations. CryptoBank and the predictive PLM are publicly accessible via a web server, providing valuable resources for cryptic site discovery.
    DOI:  https://doi.org/10.1126/sciadv.ady6364
  68. iScience. 2026 May 15. 29(5): 115454
    ISGylation is disrupted by UBA7 gene variants identified in individuals with neurodevelopmental disorder phenotypes.
    Venkateshwarlu Bandi, Myrrhe Venema, Iona Wallace, Merel O Mol, Anita Nikoncuk, Rachel Schot, Marjon van Slegtenhorst, Emilia K Bijlsma, Amjad Khan, Susan M White, Rocio Rius, Martin B Delatycki, Vinodh Narayanan, Kirby N Swatek, Tahsin Stefan Barakat, Francisco Bustos.
      ISGylation is a ubiquitin-like enzymatic cascade that transfers the small modifier ISG15 to lysine residues of protein substrates. ISGylation occurs in a three-step enzymatic cascade involving UBA7 (E1), UBE2L6 (E2), and HERC5, TRIM25, or human homolog of ariadne (HHARI) (E3) enzymes. This mechanism regulates core cellular processes, but its role in neurodevelopmental disorders remains unclear. Here, we identified individuals with neurodevelopmental disorder phenotypes harboring biallelic UBA7 gene variants and assessed their functional effects. Truncating UBA7 variants result in loss of catalytic activity, protein stability, and localization. In contrast, a missense variant drives no functional defects. Fibroblasts harboring the variant p.Lys709Serfs∗45 had reduced UBA7 transcript and produced a truncated and unstable UBA7 protein. These fibroblasts were unable to induce ISGylation upon interferon beta treatment, indicating a dysfunctional ISGylation system. Together, our findings identify cellular mechanisms disrupted by UBA7 variants and lay the foundation for uncovering the role of the ISGylation system and UBA7 in neurodevelopment.
    Keywords:  Genetics; Molecular biology; Neuroscience
    DOI:  https://doi.org/10.1016/j.isci.2026.115454
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