bims-proteo Biomed News
on Proteostasis
Issue of 2026–09–27
fifty-five papers selected by
Eric Chevet, INSERM
  1. Subtlety is underrated: Physiological UPR activation in meiosis.
  2. Protein entanglement misfolding influences whether proteins undergo proteasomal degradation or persist in near-native misfolded states.
  3. A luminal proteome of the endoplasmic reticulum and Golgi apparatus reveals a novel modulator of ER stress tolerance in African trypanosomes.
  4. CDKL5 deficiency impairs TBK1-mediated autophagy and clearance of neuronal protein aggregates.
  5. Discovery of PROTACs recruiting the E3 ligase CHIP.
  6. An Evolutionarily Conserved Ypk1/SGK1 Kinase Pathway Regulates the Unfolded Protein Response by Modulating the Ire1 Protein Abundance.
  7. Adaptability of the GroEL/GroES chaperonin to proteostatic challenge revealed by directed evolution.
  8. Adenovirus early proteins E1A and E3-19K reveal separable regulatory states of the ER stress sensor IRE1a.
  9. Components of an ESCRT-independent nuclear envelope assembly pathway.
  10. Fitness criteria for PROTACs as chemical probes: principles and applications.
  11. Beyond ER-Golgi trafficking: unconventional protein secretion as a new design frontier for synthetic secretion switches in mammalian cells.
  12. TOR-NOT4 signalling couples translation to co-translational quality control in plants.
  13. Role of Nuclear SUMO-Targeted Ubiquitin Ligase Uls2 (Slx5-Slx8) in Quality Control of Cytosolic Proteins.
  14. A human cell-free translation screen identifies the NT-2 mycotoxin as a ribosomal inhibitor that binds the peptidyl transferase center.
  15. Mitochondrial Calcium Sensor Tusc2 Protects the Aging Hippocampus from Proteostasis Collapse in a Sex-Specific Manner.
  16. Local translation couples synaptic activity to mitochondrial adaptation in dendrites.
  17. The anion channel GPR89 is a tumor-specific dependency in breast cancer.
  18. PhSAN induces PANoptosis via targeting RNF25-mediated endoplasmic reticulum stress.
  19. Mapping the membrane-enriched proteome of recombinant Chinese hamster ovary cells following induction of endoplasmic reticulum stress.
  20. Defective ATP13A2-ITCH-ALIX signaling impairs intraluminal vesicle biogenesis and increases neuronal vulnerability.
  21. TPC2-mediated lysosomal Ca2+ release puts the brakes on store-operated Ca2+ entry.
  22. Affinity selection mass spectrometry screening discovers new COP1 peptide binders.
  23. Fluorophore Placement and Size Impact E2 Ubiquitination Efficiency.
  24. PRMT1-mediated methylation controls OFIP ubiquitination and centrosome duplication to maintain epidermal homeostasis.
  25. Ethylene receptors at the ER: Potential hubs integrating hormone, redox, and Ca2+ signaling.
  26. E3 ubiquitin ligase SYVN1 mediates K63-linked ubiquitination of DDX3X to activate Macrophage NLRP3 Inflammasome.
  27. Targeted Control of Protein O-GlcNAcylation in Living Cells.
  28. HSP90 shields ROC1/RBX1 from proteasomal degradation by CHIP E3 ubiquitin ligase to promote lung adenocarcinoma.
  29. RAF1 scaffold integrity shapes chemogenetic degradation outcomes in KRAS-driven lung cancer models.
  30. The predicted interactome of the human mitochondrial proteome.
  31. DesignMaster: A Multi-Conditional Diffusion Framework for Rational PROTAC Design.
  32. Lysosomal function and homeostasis: From cellular adaptation to disease pathogenesis.
  33. The E3 ubiquitin ligase HECTD3 controls immune colonic inflammation by restricting Myd88 activation and signaling.
  34. Lsp2 links mTORC1 to TOP mRNA translation and lifespan in Drosophila.
  35. TRPML1 loss disrupts lysosome-mitochondria homeostasis and sensitizes MDA-MB-231 triple-negative breast cancer cells to chemotherapy.
  36. dubTAGs enable on-demand stabilization for tunable and reversible control of endogenous protein levels.
  37. COMMD3 coordinates mannose-6-phosphate receptor trafficking to sustain lysosomal protease maturation.
  38. HCMV US30 induces TMED10-DRP1-mediated mitochondrial fission and apoptosis to promote viral multiplication.
  39. Specific host translation perturbations promote Tn Smu 1 loss independently of the canonical ImmA regulator.
  40. USP19 protects against cigarette smoke-induced lung injury and epithelial stress.
  41. Coordinated regulation of the metaboproteome by Hsp90 chaperones controls metabolic plasticity.
  42. VMP1 restricts STING trafficking and activation through controlling CDIPT recruitment to ER membrane curvature.
  43. Modular Lysosome-Targeting Platform Based on a Multivalent DNA Framework for Programmable Protein Degradation.
  44. Exosomal export of activated CASPASE-8 is linked to the prevention of TNF-induced cytotoxicity.
  45. Programmed inhibition of an innate immune receptor via de novo designed transmembrane proteins.
  46. Proteolytic remodeling by Yme1 enables mitochondrial-derived compartment formation.
  47. Src inhibition attenuates neuroinflammation via promoting p62 UFMylation-dependent microglial mitophagy.
  48. Single-cell visual proteomics of a minimal bacterium reveals structural coordination of gene expression machineries.
  49. Aberrant PCM1 accumulation in Trisomy 21 mislocalizes E3 ligases, delaying primary ciliogenesis.
  50. RpS19a depletion alters the hematopoietic translatome to drive tissue overgrowth.
  51. Unbiased, systematic surfaceome profiling of Acute Leukemia to identify novel immunotherapy targets.
  52. Latent generative search unlocks de novo design of untapped biomolecular interactions at scale.
  53. Synaptic proteomics identifies cathepsin B as a regulator of synapse remodelling during learning.
  54. Characterization of disease-initiating hematopoietic stem cells in calreticulin-mutated myeloproliferative neoplasms.
  55. Ubiquitination-mediated degradation of NLRX1 drives metabolic vulnerability and accelerates intervertebral disc degeneration.
  1. J Cell Biol. 2026 Oct 05. pii: e202608015. [Epub ahead of print]225(10):
    Subtlety is underrated: Physiological UPR activation in meiosis.
    David Pincus, Vladimir Denic.
      In this issue, Bartolutti et al. (https://doi.org/10.1083/jcb.202509100) identify a physiological function for the unfolded protein response (UPR). The UPR has long been viewed as a coping mechanism for protein misfolding in the endoplasmic reticulum (ER). The authors here show that budding yeast naturally use this response to reorganize their ER during meiosis and sporulation, suggesting an ancient origin for the UPR as an adaptive developmental program.
    DOI:  https://doi.org/10.1083/jcb.202608015
  2. Nat Commun. 2026 Aug 25. pii: 10135. [Epub ahead of print]17(1):
    Protein entanglement misfolding influences whether proteins undergo proteasomal degradation or persist in near-native misfolded states.
    Yang Jiang, Anushka Jain, Sina Ghaemmaghami, Edward P O'Brien.
      A novel class of protein misfolding involving changes in entanglement status occurs across the bacterial cytosolic proteome and likely exists in many other organisms. Here, we test whether this class of misfolding has measurable consequences for protein homeostasis by examining its relationship with ubiquitin-mediated proteasomal degradation immediately after protein synthesis. Integrating protein structural information with ubiquitin mass spectrometry (Ubq-MS) data from human fibroblasts, we find that proteins containing native non-covalent lasso entanglements (NCLEs), which are known to be more prone to misfolding, are 93% (95% Confidence Interval: 44-160%) more likely to be ubiquitinated and targeted for proteasomal degradation than proteins lacking native entanglements. Coarse-grained folding simulations further show that ubiquitinated proteins with native entanglements are four-fold more likely to misfold than non-ubiquitinated proteins without entanglements. These results suggest that entanglement misfolding, primarily through failure to form native entanglements, increases susceptibility to proteasomal degradation. We further estimate that approximately one-third of the globular proteome populates near-native entanglement-misfolded states that evade proteasomal degradation because they remain structurally similar to the native ensemble. Given that entanglement misfolding is inherent to the polymeric nature of proteins, these findings are likely applicable across diverse organisms.
    DOI:  https://doi.org/10.1038/s41467-026-76875-9
  3. Open Biol. 2026 Sep 23. pii: 260178. [Epub ahead of print]16(9):
    A luminal proteome of the endoplasmic reticulum and Golgi apparatus reveals a novel modulator of ER stress tolerance in African trypanosomes.
    Siqi Shen, Farnaz Zahedifard, Emmanuel A Agbebi, Anna Zavrelova, Johanna Krenzer, Carla G Carbajo, Silke Braune, Susanne Kramer, Calvin Tiengwe, Martin Zoltner.
      African trypanosomes employ specialized mechanisms of membrane trafficking as a strategy to persist in both the mammalian host and insect vector. Their survival relies on continuous synthesis and surface delivery of extremely abundant surface coat proteins, imposing an extraordinary biosynthetic burden on the secretory pathway. Despite this, their ER and Golgi luminal proteomes remain incompletely characterized. Here, we exploit proximity biotinylation, using the abundant ER chaperone BiP as bait to map the ER proteome in bloodstream and procyclic lifecycle stages. Comparison with BiPN, a truncated secretory form of BiP that escapes the ER and transits the Golgi, provides differential compartmental labelling. Quantitative ranking of BiP labelling intensity identifies a candidate BiP interactor cohort including a divergent homologue to the mammalian BiP nucleotide exchange inhibitor MANF. Reciprocal manipulation of TbMANF abundance produces opposing shifts in cellular sensitivity to ER stress. These data are consistent with a role in regulating BiP ATPase cycling in an organism that, unlike opisthokonts, lacks a canonical unfolded protein response, making TbMANF the first regulator of BiP activity identified in kinetoplastids. Finally, proximity labelling anchored at the inner face of the nuclear pore via NUP65 extends our endomembrane map to the inner nuclear membrane, identifying candidate proteins of this specialized ER-continuous domain.
    Keywords:   Trypanosoma brucei ; ERAD; ERQC; Golgi; endoplasmic reticulum; secretory pathway; vesicle trafficking
    DOI:  https://doi.org/10.1098/rsob.260178
  4. bioRxiv. 2026 Sep 18. pii: 2026.09.13.751248. [Epub ahead of print]
    CDKL5 deficiency impairs TBK1-mediated autophagy and clearance of neuronal protein aggregates.
    Zhongju Zou, Bilal Kahn, Salwa Sebti, Jason Lucavs, Giomar Rivera-Cancel, Josephine Thinwa.
      The clearance of unwanted protein aggregates is essential for maintaining proteostasis and cellular function, particularly in long-lived cells such as neurons, yet the signaling pathways that activate selective autophagy of protein aggregates remain incompletely understood. Here, we identify the neurodevelopmental kinase CDKL5 as an upstream regulator of a signaling pathway involving the TBK1 adaptor SINTBAD and the selective autophagy receptors p62 and TAX1BP1. CDKL5-deficient mice show age-dependent accumulation of detergent-insoluble protein aggregates in the brain, accompanied by impaired TAX1BP1 recruitment and reduced p62 Ser405 phosphorylation. In cultured cells and primary cortical neurons, loss of CDKL5 delays clearance of puromycin- and proteasome-inhibitor-induced aggregates in a manner dependent on CDKL5 kinase activity. Mechanistically, CDKL5 kinase activity is required for SINTBAD Ser504 phosphorylation, a SINTBAD modification that promotes TBK1 activation, resulting in p62 Ser403/405 phosphorylation and TAX1BP1-dependent aggregate clearance. Phosphomimetic SINTBAD rescues these responses in CDKL5-deficient cells. These findings define a CDKL5/SINTBAD/TBK1 signaling axis that couples proteotoxic stress to activation of selective autophagy receptors and identify impaired proteostasis as a previously unrecognized consequence of CDKL5 deficiency.
    DOI:  https://doi.org/10.64898/2026.09.13.751248
  5. RSC Chem Biol. 2026 Sep 21.
    Discovery of PROTACs recruiting the E3 ligase CHIP.
    Tokiha Masuda-Ozawa, Shusuke Tomoshige, Eisuke Hayakawa, Shinichi Sato, Kenji Ohgane, Fumiaki Ohtake, Minoru Ishikawa.
      Proteolysis-targeting chimeras (PROTACs) are promising degraders in targeted protein degradation (TPD) systems. Although more than 600 E3 ubiquitin (Ub) ligases exist in the human genome, only a few E3 ligases have been engaged in PROTACs. It is essential to expand the range of available E3 ligase resources to combat drug resistance caused by their mutations and to find suitable candidates for the degradation of certain target proteins. In this study, we aimed to develop novel PROTACs utilizing the carboxyl terminus of the Hsc70-interacting protein (CHIP) E3 ligase, which was previously unutilized. We designed and synthesized PROTACs conjugated with CHIP ligands and target protein ligands via linkers. These PROTACs form a ternary complex with CHIP and a target protein and ubiquitylate the target protein in vitro. Furthermore, taking advantage of the fact that CHIP is not an intricate multi-subunit E3 ligase, unlike other E3 ligases utilized for PROTACs, an in vitro ubiquitylation assay revealed that CHIP induced not only the lysine (K) 48-linked polyubiquitin (poly-Ub) chain, which is a typical proteasome degradation signal, but also the K63 linkage. Furthermore, it induces the proteasome-dependent degradation of HaloTag protein and endogenous bromodomain-containing protein 4 (BRD4). Thus, we successfully expanded the E3 ligase toolbox for PROTACs. These new PROTACs using CHIP, which induce non-canonical proteasome degradation signals containing a mixed linkage of poly-Ub chains on the target protein, can be applied to the degradation of other proteins, especially disease-related proteins.
    DOI:  https://doi.org/10.1039/d6cb00124f
  6. bioRxiv. 2026 Sep 18. pii: 2026.09.11.751087. [Epub ahead of print]
    An Evolutionarily Conserved Ypk1/SGK1 Kinase Pathway Regulates the Unfolded Protein Response by Modulating the Ire1 Protein Abundance.
    Saswata Chakrabarty, Anish Chakraborty, Jagadeesh Kumar Uppala, Noelle Marie Bryan, Nadege Gouignard, Nicholas J Reiter, An-Phu Tran, Madhusudan Dey.
      The unfolded protein response (UPR) is a cellular mechanism that maintains protein homeostasis (proteostasis) under conditions of endoplasmic reticulum (ER) stress. The dual kinase/RNase Ire1 is a conserved regulator of the UPR, mediating the unconventional cytosolic splicing of HAC1 mRNA in yeast and XBP1 mRNA in human cells. The resulting spliced HAC1/XBP1 transcript encodes a transcription factor that induces the expression of protein-folding chaperones and stress-responsive genes, thereby restoring proteostasis. In our previous work, we showed that the MAP kinase Slt2 (homolog of human ERKs) contributes to UPR signaling by promoting IRE1 expression through the transcription factor Rlm1 (homolog of human MEF2C). Here, we demonstrate that Hac1 expression is reduced in yeast strains deficient in essential protein kinase Cdc28, Pkc1, Rio2, Tor2, Pkh1, or Ypk1, suggesting that these kinases also serve as UPR regulators. We focused on the kinase Ypk1, the yeast ortholog of human SGK1 (serum/glucocorticoid-regulated kinase 1). We provide genetic and biochemical evidence that Ypk1/SGK1 acts upstream of the Pkc1/PKCδ signaling pathway and is required for maintaining IRE1 protein abundance in both yeast and human cells. Collectively, our results identify an evolutionarily conserved Ypk1/SGK1 signaling pathway that regulates the HAC1 and XBP1 mRNA splicing by modulating the Ire1 protein abundance.
    DOI:  https://doi.org/10.64898/2026.09.11.751087
  7. Proc Natl Acad Sci U S A. 2026 Sep 29. 123(39): e2608599123
    Adaptability of the GroEL/GroES chaperonin to proteostatic challenge revealed by directed evolution.
    Marie-Pierre Castanié-Cornet, Tatsuya Niwa, Émile Dupuy, Anne-Marie Cirinesi, Manajit Hayer-Hartl, Hideki Taguchi, F Ulrich Hartl, Pierre Genevaux.
      The folding of newly synthesized proteins is assisted by an essential network of proteins known as molecular chaperones. In bacteria, the chaperones Trigger Factor (TF), DnaK/DnaJ (Hsp70 system), and GroEL/GroES (chaperonin system) are key players in proteostasis maintenance. Here, we further explore the cooperation and substrate preference within the bacterial chaperone network by performing directed evolution of GroEL/GroES in Escherichia coli lacking both TF and DnaK chaperone pathways. We found that single amino acid substitutions in GroEL were sufficient to significantly improve its chaperone activity in vivo at high temperature in the absence of TF and DnaKJ, with a combination of selected mutations further enhancing functionality. In vitro analysis showed that high-performing GroEL variants have a higher rate of ATP hydrolysis and an increased folding rate for certain substrates at low ATP concentration, thereby compensating for the significant drop in ATP level observed in vivo in cells lacking TF and DnaKJ. Analysis of substrates bound to GroEL in vivo showed that experimentally evolved chaperones likely adapted toward obligate GroEL substrates with low solubility, thus bypassing cooperation with upstream chaperones like TF and DnaKJ.
    Keywords:  GroESL; directed evolution; molecular chaperones; proteostasis network
    DOI:  https://doi.org/10.1073/pnas.2608599123
  8. Mol Biol Cell. 2026 Sep 24. mbcE26060273
    Adenovirus early proteins E1A and E3-19K reveal separable regulatory states of the ER stress sensor IRE1a.
    Debkanya Sengupta, Shikha Srivastava, Fedor Bezrukov, Silvio Hemmi, Urs F Greber, Vibhu Prasad.
      The unfolded protein response (UPR) controls cellular homeostasis and virus infections. It is canonically initiated by dissociation of ER chaperone BiP/GRP78 from lumenal domains of transmembrane sensor proteins, including the central UPR sensor inositol-requiring enzyme 1 alpha (IRE1a). This results in IRE1a activation and splicing of X-box binding protein 1 (XBP1) mRNA, leading to transcriptional activation of XBP1 for cellular adaptation and sustained infection. Human adenovirus (AdV) preferentially activates the IRE1a-XBP1 pathway through the viral membrane protein E3-19K, yet the mechanisms underlying this selective activation remain unclear. Here, we show that AdV uses two distinct early proteins to dissociate BiP from IRE1a and activate IRE1a-mediated XBP1 splicing. The immediate early protein E1A forms a complex with the cytoplasmic domain of IRE1a, sufficient to dissociate BiP from IRE1a without inducing XBP1 splicing or UPR activation. In contrast, E3-19K is expressed downstream of E1A, associates with the lumenal domain of IRE1a, and induces XBP1 splicing without promoting BiP dissociation from IRE1a. Both proteins were detected in IRE1a-containing complexes, consistent with stepwise viral regulation. Together, our findings show that canonical IRE1a activation hallmarks can be mechanistically separated during viral infection, revealing distinct AdV-regulated IRE1a activation states with discrete upstream and downstream signaling outputs.
    DOI:  https://doi.org/10.1091/mbc.E26-06-0273
  9. J Cell Biol. 2026 Nov 02. pii: e202601189. [Epub ahead of print]225(11):
    Components of an ESCRT-independent nuclear envelope assembly pathway.
    Emma M Sydir, M Humam Farra, Abigail L Whitford, Shea Hinojosa, Pei-Yi Kao, Joao A Paulo, Sharan Swarup, C Patrick Lusk, J Wade Harper, I-Ju Lee, David Pellman.
      In many cells, the nuclear envelope (NE) must be reassembled after mitosis, and holes in the nuclear membrane must be sealed. During NE assembly, the NE-specific adaptor, Cmp7, recruits/activates endosomal sorting complex required for transport (ESCRT)-III proteins to mediate NE sealing. However, recent evidence suggests the presence of additional mechanisms. In a screen using the fission yeast, Schizosaccharomycesjaponicus, we recently implicated the ESCRT adaptor, Alx1, and a conserved but little-studied protein, Vid27, in Cmp7-independent NE assembly. Here, we provide direct evidence that Alx1 functions in a Cmp7- and ESCRT-independent NE assembly pathway via positive regulation of Vid27. Consistent with a role in membrane remodeling, Vid27 localizes to sites of postmitotic NE sealing and is essential in S. japonicus. Alx1 and Vid27 interact, and mutations disrupting the predicted interaction interface abolish Alx1's enhancement of Vid27 function at the NE. These findings define components of a new Cmp7- and ESCRT-independent NE assembly pathway, advancing our understanding of mechanisms that maintain the integrity of the nucleus.
    DOI:  https://doi.org/10.1083/jcb.202601189
  10. Essays Biochem. 2026 Sep 24. pii: EBC20260006. [Epub ahead of print]
    Fitness criteria for PROTACs as chemical probes: principles and applications.
    Manon Sturbaut, Alessio Ciulli.
      Proteolysis-targeting chimeras (PROTACs) have emerged as a powerful class of chemical probes that degrade rather than inhibit target proteins, thus expanding the tools for studying protein function in cells. PROTACs trigger catalytic and sub-stoichiometric degradation of the target protein in contrast with stoichiometric, occupancy-based inhibition. Because of this distinct mode of action, PROTACs overcome key limitations of inhibitors, including incomplete functional suppression, the requirement for sustained target occupancy, and poor selectivity within conserved protein families. PROTAC activity depends on multiple factors, including cell permeability, binary target engagement, ternary complex formation, stability and cooperativity, and efficiency of ubiquitination and degradation. Robust evaluation of PROTAC chemical probes therefore requires systematic assessment of potency, degradation kinetics, mechanistic validation, and selectivity profiling. Advances in mechanistic understanding have positioned PROTACs as versatile chemical probes that enable precise and temporally controlled protein depletion, offering unique opportunities for target validation, pathway dissection, and drug discovery. Recent case studies demonstrate clinical and preclinical PROTACs targeting previously undruggable proteins, highlighting the potential of degradation strategies, while emerging modalities such as molecular glues and proximity-inducing molecules further broaden the landscape of protein regulation.
    Keywords:  PROTAC; chemical tools; probe validation; probes; selectivity; target protein degradation
    DOI:  https://doi.org/10.1042/EBC20260006
  11. Commun Biol. 2026 09 19. pii: 1221. [Epub ahead of print]9(1):
    Beyond ER-Golgi trafficking: unconventional protein secretion as a new design frontier for synthetic secretion switches in mammalian cells.
    Bingshun Shi, Xinyuan Qiu, Yongheng Jiang, Jiabo Cai, Lingyun Zhu.
      Mammalian gene switches enable programmable cell behavior. However, current switches on transcriptional and translational layers require de novo RNA and protein synthesis, and secreted outputs must additionally undergo folding, post-translational processing, and intracellular trafficking, imposing delays that limit rapid extracellular responses. Rapid secretion-control switches instead act on pre-synthesized proteins by controlling retention, trafficking, storage, or release. Most current platforms exploit the classical endoplasmic reticulum (ER)-Golgi pathway, including engineered stimulus-secretion coupling in specialized secretory cells and ER retention, retrieval-signal cleavage, or synchronized trafficking in general mammalian hosts. Although these strategies improve response kinetics, they remain limited by ER dependence, host-cell specificity, cargo compatibility, basal leakage, and post-release transport delays. Here, we review current secretion-control architectures and highlight unconventional protein secretion as an underexplored source of design principles for positioning regulatory control closer to terminal protein export and expanding the architectures available for mammalian secretion control.
    DOI:  https://doi.org/10.1038/s42003-026-10984-5
  12. Nat Commun. 2026 Aug 24. pii: 10101. [Epub ahead of print]17(1):
    TOR-NOT4 signalling couples translation to co-translational quality control in plants.
    Maximillian A Schwarze, Rory Osborne, Margot Raffeiner, Manuel González-Fuente, Anastasia Kanali, Mark Bailey, Ross D Etherington, Lina Zhou, Suayib Üstün, Daniel J Gibbs.
      Protein synthesis must be tightly coordinated with quality control to prevent proteotoxic stress, yet the mechanisms underlying co-translational surveillance in plants, and how these are aligned with translational output, remain poorly understood. Here, we identify three NOT4-like E3 ubiquitin ligases in Arabidopsis thaliana as regulators of co-translational protein quality control and uncover a functional link between NOT4 and TARGET OF RAPAMYCIN (TOR) signalling that coordinates quality-control capacity with translational output. Loss of NOT4 function increases basal TOR activity and global translation rates, resulting in the accumulation of polyubiquitylated proteins and heightened sensitivity to proteasome inhibition, TOR inhibition, and protein misfolding stress. Consistent with prior evidence that NOT4 proteins are TOR-regulated phosphotargets, not4 mutants also phenocopy TOR-inhibited wild-type plants for a subset of transcriptional and growth-related processes. Furthermore, elevated translation in NOT4-deficient plants enhances resistance to Pseudomonas syringae pv. tomato. Collectively, our findings reveal a functional coupling between TOR signalling and NOT4 activity that may scale quality control with translational demand to safeguard proteome homoeostasis across eukaryotes.
    DOI:  https://doi.org/10.1038/s41467-026-77200-0
  13. Biomolecules. 2026 Sep 11. pii: 1322. [Epub ahead of print]16(9):
    Role of Nuclear SUMO-Targeted Ubiquitin Ligase Uls2 (Slx5-Slx8) in Quality Control of Cytosolic Proteins.
    Friederike Profe-Austermann, Lennard-Maximilian Döring, Luisa Schmidt, Lena Avci, Maximilian Haka, Ganapathi Kandasamy, Judith Müller, Nils Johnsson, Marcus Krüger, R Jürgen Dohmen.
      The interplay between the posttranslational modifiers SUMO and ubiquitin mediates the degradation of proteins. This crosstalk is conveyed by SUMO-targeted ubiquitin ligases (STUbLs). The best-studied STUbL in Saccharomyces cerevisiae is the heterodimer Slx5-Slx8 (Uls2). Uls2 mainly resides in the nucleus and is involved in stress tolerance, DNA repair and genome stability maintenance. So far, the majority of known Uls2 targets are nuclear proteins. The role of Uls2 in the targeting of cytosolic proteins remains to be elucidated. In this study, we identify Nis1 and Fir1 as two cytosolic proteins that become substrates of Uls2 in the absence of their partner polypeptides, which results in their SUMO-dependent aggregate formation in the nucleus. To uncover further Uls2 targets, we performed whole-cell proteomics of slx5Δ cells with and without oxidative stress. Comparison to wild-type cells revealed a large pool of potential Uls2 substrates, a subset of which is targeted upon oxidative stress, suggesting a quality control (QC) mechanism. Based on our results, we propose a role for Uls2 in a QC system targeting cytosolic proteins lacking their partners or that are damaged, for example, by oxidation.
    Keywords:  Fir1; Nis1; STUbL; SUMO; Slx5; Slx8; quality control
    DOI:  https://doi.org/10.3390/biom16091322
  14. Commun Biol. 2026 Sep 23. pii: 1237. [Epub ahead of print]9(1):
    A human cell-free translation screen identifies the NT-2 mycotoxin as a ribosomal inhibitor that binds the peptidyl transferase center.
    Nino Schwaller, Dominic Andenmatten, Jonas Luginbühl, Julius Rabl, Helena Baur, Marc Chambon, Jonathan Vesin, Gerardo Turcatti, Evangelos D Karousis.
      Translation inhibitors are invaluable for probing ribosome function and therapeutic applications, but systematic discovery in human systems is limited by the lack of scalable, screening-compatible cell-free platforms. Here, we establish a robust high-throughput screening using human lysates that bypasses cellular cytotoxic effects. After screening ~28,000 small molecules, we identified known and a novel translation inhibitor, including NT-2, a trichothecene mycotoxin produced by the pathogenic Fusarium sporotrichioides. NT-2 suppressed protein synthesis in human cells and yeast lysates, while sparing translation in bacteria and intact yeast cells. Cryo-EM at 1.76 Å revealed NT-2 bound at the peptidyl transferase center of the human 60S ribosome. In addition, cryoEM classification of NT-2 treated cells shows ribosomes in an inactive eEF2/SERBP1-bound dormant state. Together, these results expose NT-2 as a previously unrecognized environmental inhibitor of mammalian protein synthesis and demonstrate the power of cell-free translation screening to reveal new inhibitors with unexpected ribosome fates.
    DOI:  https://doi.org/10.1038/s42003-026-10743-6
  15. Mech Ageing Dev. 2026 Sep 19. pii: S0047-6374(26)00105-3. [Epub ahead of print] 112253
    Mitochondrial Calcium Sensor Tusc2 Protects the Aging Hippocampus from Proteostasis Collapse in a Sex-Specific Manner.
    Sergey V Ivanov, Victor Paromov, Metin Aksu, Harshana Rajakaruna, Jane Tonello, Salvador González-Ochoa, Muna Mohammed, Tonie Farris, George Babineaux, Sanika S Chirwa, Anil Shanker, Alla V Ivanova.
      Progressive mitochondrial dysfunction coupled with calcium dyshomeostasis is a hallmark of aging and neurodegenerative conditions, yet the molecular links to cognitive decline remain unclear. Moreover, although sex differences in susceptibility to neurodegeneration are well recognized, their molecular basis remains poorly defined. In our previously engineered mouse model, systemic depletion of Tusc2 (Fus1), a mitochondrial calcium-regulatory protein, accelerates aging and recapitulates key features of human aging, including sex-specific cognitive decline. Here, we identify Tusc2 as a key modulator of hippocampal (HP) resilience to aging. To define the impact of Tusc2 loss on molecular determinants of cognition, we profiled HP transcriptomes in both sexes and proteomes in males at 4 months of age, when sex-specific differences in cognitive behavior first emerge. Male knockout HP exhibited broad mitochondrial dysfunction, including suppression of oxidative phosphorylation (OxPhos) proteins, activation of the ATF4 branch of the integrated stress response (ISR), and coordinated downregulation of translational, proteasomal, and synaptic pathways. These molecular alterations were accompanied by increased protein aggregate size, consistent with impaired proteostatic capacity, and reduced PSD-95 neuropil intensity, indicative of compromised synaptic integrity in the HP. In contrast, female knockout HP exhibited comparatively modest transcriptional alterations and preferential activation of adaptive ATF6-associated unfolded protein response (UPR) pathways, consistent with a protective response that may be influenced by estrogen signaling, sex chromosome complement, epigenetic regulation, and other sex-dependent mechanisms. Comparative analysis with aging human HP datasets revealed significant and broad overlaps, suggesting that Tusc2 deficiency recapitulates key molecular features of human brain aging. Together, these findings identify TUSC2 as a principal regulator of mitochondrial calcium homeostasis that contributes to maintenance of proteostatic and synaptic integrity of the HP during aging, and reveal marked sex differences in mitochondrial stress resilience. These results establish Tusc2 deficiency as a mechanistically defined model for investigating early, potentially reversible stages of mitochondrial and proteostatic decline in brain aging.
    Keywords:  Aging; Dementia; Mitochondrial calcium signaling; Proteostasis; TUSC2 (FUS1)
    DOI:  https://doi.org/10.1016/j.mad.2026.112253
  16. bioRxiv. 2026 Sep 20. pii: 2026.09.17.752159. [Epub ahead of print]
    Local translation couples synaptic activity to mitochondrial adaptation in dendrites.
    Madison T Jones, Natalie Noble, Robert B Darnell, Ezgi Hacisuleyman.
      Neurons rely on localized protein synthesis to rapidly adapt synaptic function to activity, yet how dendritic translation regulates mitochondrial remodeling during synaptic plasticity remains poorly understood. Here, we show that neuronal activity engages a spatially restricted translational program that couples local protein synthesis to mitochondrial function through the non-canonical translation initiation factor eIF4G2. Using proximity labeling to profile the dendritic RNA interactome, translatome, and proteome, we identify a cohort of nuclear-encoded mitochondrial mRNAs that are selectively recruited for translation following depolarization and mGluR activation. This program drives activity-dependent increases in mitochondrial membrane potential, mitochondrial abundance, and oxygen consumption. Loss of eIF4G2 abolishes these responses, whereas dendrite-specific, but not soma-restricted, rescue restores mitochondrial remodeling, demonstrating that eIF4G2 functions locally at postsynaptic sites. Mechanistically, eIF4G2 binds the 5 prime or minute untranslated regions of activity-responsive mitochondrial transcripts and promotes translation of both upstream open reading frames (uORFs) and downstream coding sequences. Using a dendritically targeted split-GFP reporter, we further show that neuronal activity induces local uORF translation to generate previously unannotated micropeptides. Together, our findings identify eIF4G2-dependent local translation as a mechanism that establishes mitochondrial competence during synaptic activity by coordinating the production of mitochondrial proteins and uORF-encoded micropeptides.
    DOI:  https://doi.org/10.64898/2026.09.17.752159
  17. Nat Commun. 2026 Aug 24. pii: 10091. [Epub ahead of print]17(1):
    The anion channel GPR89 is a tumor-specific dependency in breast cancer.
    Riccardo Ferro, Alexandra Carroll, Ana M Mendes-Pereira, Virinder Reen, George Vlachogiannis, Rebeca Uceda-Castro, Dragomir Krastev, Valeria Amodeo, Stephen Pettitt, Nadja D'Uonno, Ioanna Mavrommati, Blanca Navarro, Luke Hitchen, Jennifer Trendell, Ana Stojiljkovic, Cynthia Prince, Narinder Janghra, Ioannis Roxanis, Patrycja Gazinska, Daniel Larcombe-Young, Rebecca Marlow, Stefano Annunziato, Jos Jonkers, Tejashree Rajaram Kanitkar, Amadeus Xu, Nirmesh Patel, Nalan Liv, John Alexander, Jelmar Quist, Mercedes Pardo, Theodoros I Roumeliotis, Jyoti S Choudhary, Daniel Weekes, Pierfrancesco Marra, Joanna I Loizou, Rachael Natrajan, Anita Grigoriadis, Mallur Srivatsan Madhusudhan, Syed Haider, Christopher J Lord, Andrew Tutt.
      How cancers regulate endoplasmic reticulum (ER) pH and minimize ER stress remains unclear. Here we show that in breast cancer, these processes are governed by the anion channel GPR89. While normally localized to the Golgi, we find GPR89 is also present in the ER of tumor cells, where it collaborates with vacuolar H⁺ ATPase to regulate pH, and reduces ER stress via IRE1α-HSP47-XBP1s, ATF6 and ATP2A2 pathways. This ER localization of GPR89 drives a tumor-specific dependency, rendering breast cancer cells, but not normal tissues, dependent on this anion channel. Structural modeling and mutagenesis identify five key amino acids essential for GPR89's ER pH regulatory function and tumor cell survival. Consistent with its cancer-specific functions, GPR89 cooperates with Myc to accelerate mammary tumorigenesis. These findings uncover how breast cancers adapt to oncogenic stress by co-opting Golgi mechanisms of pH regulation to support ER homeostasis and survival.
    DOI:  https://doi.org/10.1038/s41467-026-76250-8
  18. Cell Insight. 2026 Oct;5(5): 100353
    PhSAN induces PANoptosis via targeting RNF25-mediated endoplasmic reticulum stress.
    Jialu Kang, Yanlin Jian, Yong Zhang, Lei Li, Zixi Wang, Tianjie Liu, Yuzeshi Lei, Mingming Lu, Leihong Ye, Haohan Xiang, Buyun Li, Shan Xu, Ke Wang, Wenyue Huang, Bohan Ma, Jian Ma, Lei Li.
      PANoptosis is an inflammatory programmed cell death (PCD) pathway integrating pyroptosis, apoptosis, and necroptosis, typically triggered by extrinsic stressors such as pathogen-associated signals. However, whether tumor-intrinsic stress can activate PANoptosis and the underlying regulatory mechanisms remain unclear. Here, we show that sustained and unresolved endoplasmic reticulum (ER) stress induces PANoptosis in renal cell carcinoma (RCC). Mechanistically, inhibition of the E3 ubiquitin ligase RNF25 disrupts eEF1A ubiquitination and degradation, leading to its aberrant accumulation. This accumulation impairs proteostasis and provokes ER stress. When combined with thapsigargin (Tg), which further exacerbates ER stress beyond the adaptive threshold, this sustained and unresolved tumor-intrinsic stress signal triggers PANoptosis. We further identify 3-(phenylsulfonyl)acrylonitrile (PhSAN) as a selective inhibitor of RNF25 that suppresses its ubiquitin ligase activity and induces ER stress. Notably, the combination of PhSAN and bortezomib (BTZ) drives ER stress, synergistically activating PANoptosis and significantly inhibiting tumor growth in RCC. Our findings establish sustained and unresolved ER stress as a key upstream signal for PANoptosis induction and propose a novel therapeutic strategy for overcoming treatment resistance in RCC through pharmacological inhibition of RNF25 with PhSAN in combination with BTZ.
    Keywords:  ER stress; PANoptosis; PhSAN; RNF25
    DOI:  https://doi.org/10.1016/j.cellin.2026.100353
  19. Biotechnol Lett. 2026 Sep 19. pii: 116. [Epub ahead of print]48(5):
    Mapping the membrane-enriched proteome of recombinant Chinese hamster ovary cells following induction of endoplasmic reticulum stress.
    Christiana-Kondylo Sideri, Michael Henry, David Ryan, Paula Meleady.
       OBJECTIVE: Chinese hamster ovary (CHO) cells are the dominant platform for monoclonal antibody (mAb) production. Despite their widespread use, an understanding of endoplasmic reticulum (ER) stress during recombinant protein production remains limited, often creating bottlenecks that hinder improvements in production titres and product quality. Because many critical regulators of protein folding, processing and quality control are membrane-embedded or membrane-associated, they are frequently underrepresented in whole-cell lysate proteomic analyses. In this study, we applied a membrane proteome enrichment strategy to selectively enhance detection of ER-resident and secretory pathway proteins and thereby improve the resolution of ER stress responses in recombinant CHO cell lines.
    METHODS: Sustained ER stress was induced using tunicamycin for 72 h in two IgG producing CHO cell lines, CHO DP-12 and NISTCHO. Membrane-enriched proteomes were analysed using label-free quantitative LC-MS/MS, followed by orthogonal validation using targeted LC-MS.
    RESULTS: Membrane enrichment expanded coverage of ER-resident and secretory pathway proteins, revealing minimal overlap with whole-cell lysate analyses. ER stress induced distinct, pathway-level changes in the two cell lines that were more clearly resolved in the membrane fraction. In CHO DP‑12 cells, ER stress resulted in decreased abundance of proteins involved in protein folding, oxidative folding, and glycosylation, together with altered abundance of proteins involved in ER-associated degradation (ERAD) suggesting remodelling of the ER quality-control network and a potential shift towards enhanced clearance of misfolded proteins. In contrast, NISTCHO cells showed more moderate changes, including increased abundance of several ER chaperones and oxidative folding proteins, alongside comparatively limited changes in degradation-related pathways. Targeted LC-MS using parallel reaction monitoring (PRM) confirmed the direction of regulation of a panel of these proteins, providing additional confidence in the observed trends.
    CONCLUSIONS: This study highlights membrane proteomics as an important approach for studying ER-associated processes relevant to CHO cell function under ER stress conditions.
    Keywords:  Chinese hamster ovary cells; ER stress; Membrane proteomics; Parallel reaction monitoring (PRM); Recombinant protein production; Unfolded protein response (UPR)
    DOI:  https://doi.org/10.1007/s10529-026-03784-8
  20. Cell Signal. 2026 Sep 19. pii: S0898-6568(26)00556-5. [Epub ahead of print]149 112897
    Defective ATP13A2-ITCH-ALIX signaling impairs intraluminal vesicle biogenesis and increases neuronal vulnerability.
    Lin Luo, Wen Chen, Shishi Luo, Suzhen Ma, Kaiyue Liu, Qian Gong, Birong Huang, Zhiming Chen, Yaohui He, Danling Wang.
      ATP13A2 is a lysosomal P5B-type ATPase whose loss-of-function mutations are associated with a spectrum of neurodegenerative disorders, including early-onset Parkinson's disease, Kufor-Rakeb syndrome, neuronal ceroid lipofuscinosis, hereditary spastic paraplegia, and amyotrophic lateral sclerosis. Although ATP13A2 is known to contribute to lysosomal homeostasis and, thereby, to neuronal degeneration, emerging evidence suggests that it may also influence exosome biology. However, the mechanisms by which endogenous ATP13A2 regulates exosome biogenesis and the relevance of this process to neuronal vulnerability remain unclear. In the present study, using multiple ATP13A2-deficient human cell models, we demonstrated that ATP13A2 deficiency impairs intraluminal vesicle (ILV) biogenesis and reduces exosome secretion across diverse cellular contexts. Loss of ATP13A2 did not markedly affect endocytosis, early endosome abundance, or multivesicular body formation, but it consistently reduced ILV density within multivesicular bodies. Mechanistically, ATP13A2 deficiency promoted lysosome-associated accumulation of the E3 ubiquitin ligase ITCH, which enhanced ubiquitin-proteasome-dependent degradation of ALG-2-interacting protein X (ALIX), a critical adaptor of the endosomal sorting complex required for transport machinery that mediates ILV membrane remodeling. Restoration of ALIX expression or reduction of Itchy E3 ubiquitin-protein ligase (ITCH) activity rescued the ILV biogenesis defects in ATP13A2-deficient neuronal cells. Furthermore, dysregulation of the ATP13A2-ITCH-ALIX pathway increased neuronal susceptibility to mitochondrial stress, whereas restoration of ALIX or reduction of ITCH activity markedly improved neuronal survival. Together, these results identify an ATP13A2-ITCH-ALIX signaling axis linking lysosomal dysfunction to impaired ILV biogenesis and exosome regulation. Our study suggests that defective ILV biogenesis contributes to neuronal vulnerability and that modulation of the ATP13A2-ITCH-ALIX pathway may represent a therapeutic strategy for ATP13A2-associated neurodegeneration.
    Keywords:  ALIX; ATP13A2; Exosome; ITCH; Intraluminal vesicle; Multivesicular body; Neuronal death
    DOI:  https://doi.org/10.1016/j.cellsig.2026.112897
  21. Cell Calcium. 2026 Sep 22. pii: S0143-4160(26)00090-4. [Epub ahead of print]138 103197
    TPC2-mediated lysosomal Ca2+ release puts the brakes on store-operated Ca2+ entry.
    Qianru Mu, Sandip Patel, David Yule, Siddhi Shetty.
      Lysosomal Ca2+ release can trigger endoplasmic reticulum (ER) Ca2+ mobilisation, which would be expected to activate store-operated Ca2+ entry (SOCE). Recent work by Lee et al. reveals that activation of the lysosomal two-pore channel TPC2 instead suppresses SOCE despite ER Ca2+ depletion. TPC2-derived Ca2+ signals recruit calmodulin to promote STIM1 inactivation, imparing STIM oligomerisation and coupling to Orai1. These findings identify a lysosomal feedback pathway that restrains Ca2+ influx and expand the role of TPC2 from an initiator of intracellular Ca2+ release to a brake on SOCE.
    Keywords:  Calcium signalling; Lysosome; STIM1; Store-operated Ca(2+) entry; TPC2
    DOI:  https://doi.org/10.1016/j.ceca.2026.103197
  22. RSC Chem Biol. 2026 Sep 10.
    Affinity selection mass spectrometry screening discovers new COP1 peptide binders.
    Harsha Negi, Noor Radhi, Nicolas Schiff, Sam A Jamieson, Deanna Shea, Martin Middleditch, Robert Mullin, Renata Kowalczyk, Paul W Harris, Peter D Mace, Daniel Conole.
      Targeting E3 ubiquitin ligases with chemical probes remains a major challenge, despite their central roles in cellular regulation and disease. Constitutive photomorphogenic 1 (COP1) is an E3 ligase whose complex, adaptor-dependent biology has made its selective targeting difficult. Here, we develop a peptide-based affinity selection mass spectrometry (Pep-AS-MS) platform to discover new peptide based COP1 binders. Leveraging a mass spectrometry compatible library design, fluorescence-guided selection optimisation, and an open-source software driven target-decoy database strategy for peptide identification and quantification, we enable hit ranking from highly complex combinatorial libraries. Using this approach, we identify and validate six previously unreported COP1-binding peptides, including ligands with binding potencies comparable to the native TRIB1 motif. This work establishes a quantitative and accessible Pep-AS-MS framework for ligand discovery against challenging protein-protein interaction targets and provides new chemical tools to interrogate COP1 biology.
    DOI:  https://doi.org/10.1039/d6cb00250a
  23. Biochem J. 2026 Aug 22. pii: BCJ20260496. [Epub ahead of print]
    Fluorophore Placement and Size Impact E2 Ubiquitination Efficiency.
    Jashanjot Kaur Gill, Rachel E Lacoursiere, Gary S Shaw.
      E2 conjugating enzymes function in the ubiquitin-mediated proteolysis pathway by accepting ubiquitin (Ub) from an E1 enzyme (Uba1), forming an E2~Ub thioester conjugate, and transferring Ub to a substrate or to an E3 ligase enzyme. Fluorescent or affinity tags are often used as sensitive readouts for catalytic variability and specificity of E2 enzymes and their variants. Here we examined how the size or placement of fluorescent tags compromise Ub conjugation for the E2 enzymes UbcH7, UbcH5a and Ubc13. Large green fluorescent protein (GFP) based fluorophores were placed at the N- or C-terminus of the E2 enzyme UbcH7 and the N-terminus of Ub, and compared to Alexa-based dyes, approximately 30 times smaller, at the same positions. While all modified proteins formed E2~Ub conjugates, placing a smaller Alexa dye at the C-terminus of the E2 enzyme improves the initial rate of E2~Ub conjugate formation by up to 10-fold compared to a larger GFP-based tag (YPet) at the N-terminus. In the case of UbcH5a, YPet labelling at its N-terminus significantly slowed formation of an E2~Ub conjugate and Ub unloading to the HECT domain of HUWE1 when compared to UbcH7. Overall, we find that small Alexa dye-based tags, especially when placed at the C-terminus of E2 enzymes, are an optimal choice for monitoring E2 ubiquitination using fluorescence-based experiments.
    Keywords:  enzyme activity; fluorescence resonance energy transfer; ubiquitins
    DOI:  https://doi.org/10.1042/BCJ20260496
  24. Proc Natl Acad Sci U S A. 2026 Sep 29. 123(39): e2532363123
    PRMT1-mediated methylation controls OFIP ubiquitination and centrosome duplication to maintain epidermal homeostasis.
    Kai Liu, Ting Song, Junkui Zhao, Shaodong Yan, Weiwen Bu, Shenying Zhang, Die Hu, Dengwen Li, Huijie Zhao, Jun Zhou.
      Epidermal homeostasis relies on the precise balance between the self-renewal and differentiation of basal keratinocytes, a process highly dependent on the fidelity of cell division and centrosome function. However, the molecular mechanism regulating this process remains poorly understood. Here, we identify protein arginine methyltransferase 1 (PRMT1) as a crucial orchestrator of epidermal homeostasis. Genetic ablation of Prmt1 in mice causes severe epidermal hyperplasia characterized by aberrant expansion of the stratum basale and disruption of the mitotic fidelity of basal cells. Mechanistically, PRMT1 directly interacts with and catalyzes the asymmetric arginine dimethylation of the centrosomal OFD1/FOR20-interacting protein (OFIP) at arginine 50. This methylation is required for the subsequent recognition and ubiquitination of OFIP by the E3 ubiquitin ligase STUB1. Consequently, PRMT1 deficiency prevents OFIP methylation and degradation, resulting in its dramatic accumulation at the centrosome. This buildup drives aberrant centrosome overduplication and the formation of multipolar spindles, ultimately compromising the integrity of epidermal renewal. Our findings delineate the PRMT1-OFIP-STUB1 axis as a mechanistic framework governing centrosome numerosity and epidermal homeostasis, advancing understanding of cutaneous barrier integrity and providing a potential therapeutic target for dermatopathological conditions.
    Keywords:  OFIP; PRMT1; arginine methylation; centrosome; epidermal homeostasis
    DOI:  https://doi.org/10.1073/pnas.2532363123
  25. J Integr Plant Biol. 2026 Sep 20.
    Ethylene receptors at the ER: Potential hubs integrating hormone, redox, and Ca2+ signaling.
    Qianshen Zhang, Yiping Wang, Ruiqi Wang, Jiale Zhang, Savithramma P Dinesh-Kumar, Xiaofeng Wang, Yongliang Zhang.
      Arabidopsis thaliana Ethylene Response 1 (ETR1) has long been viewed as a canonical hormone receptor initiating ethylene signaling at the endoplasmic reticulum (ER). Recent studies demonstrate that ETR1 also acts as an ER redox sensor, with disulfide-dependent dimerization controlling receptor conformation and activity. In parallel, subfamily I ethylene receptors, including ETR1, function as Ca2+-permeable channels, directly linking ethylene perception to rapid cytosolic Ca2+ elevation. Here, we summarize emerging evidence that redefines ETR1 as a multifunctional signaling hub connecting ethylene perception, redox regulation, and Ca2+ signaling. We present this integration as a working model and highlight unresolved questions concerning the mechanistic relationships among these functions. This framework provides a new perspective on how plants integrate ER homeostasis with hormone signaling to coordinate development and stress adaptation.
    Keywords:  Ca2+ channel; ethylene receptor; ethylene response 1 (ETR1); evolution; multifunctional signaling hub; plant stress response; redox sensor
    DOI:  https://doi.org/10.1111/jipb.70398
  26. bioRxiv. 2026 Sep 20. pii: 2026.09.15.751797. [Epub ahead of print]
    E3 ubiquitin ligase SYVN1 mediates K63-linked ubiquitination of DDX3X to activate Macrophage NLRP3 Inflammasome.
    Mohammad Anas, Abhalaxmi Singh, Nithish Raj Prasad, Joshua W Thompson, Chinnaswamy Tiruppathi, Asrar B Malik.
      DDX3X (DEAD box helicase 3, X linked) is a common and essential component for both stress granules and NLRP3 inflammasome assembly and their activation; however, the upstream cellular stress signals driving DDX3X to activate the contrasting cellular pathway remain unclear. We identified the pivotal role of the E3 ubiquitin ligase SYVN1(Synoviolin) as the upstream regulator of DDX3X and thereby controlling NLRP3 activation and stress granule assembly. We observed SYVN1 silencing in macrophages prevented both NLRP3 driven inflammation and stress granule formation. SYVN1 deficiency prevented LPS induced inflammatory lung injury and increased the survival rate of the mice. SYVN1 sustains DDX3X gene expression and promotes stimulus-dependent ubiquitination of DDX3X. Under inflammatory conditions, SYVN1 mediated 63 linked ubiquitination of DDX3X, a requirement for NLRP3 inflammasome activation. Conversely, stress conditions reduced K63 linked DDX3X ubiquitination in coordination with activity of the deubiquitinase OTUB1 (OTU domain-containing ubiquitin aldehyde-binding protein 1). Thus, the balance between SYVN1 and OTUB1 functioned to optimize DDX3X activity and activation of NLRP3 or stress granule. These findings show the upstream role of SYVN1 OTUB1 axis in integrating cellular stress signals to decide the cell fate and suggest that ubiquitination of DDX3X is a potential target for inflammasome driven inflammation.
    DOI:  https://doi.org/10.64898/2026.09.15.751797
  27. Glycobiology. 2026 Sep 24. pii: cwag081. [Epub ahead of print]
    Targeted Control of Protein O-GlcNAcylation in Living Cells.
    Tongyang Xu, Billy Wai-Lung Ng.
      O-linked N-acetylglucosamine glycosylation (O-GlcNAcylation) regulates many intracellular proteins, but linking a cellular phenotype to O-GlcNAcylation of a specific substrate remains difficult. Global perturbation of O-GlcNAc transferase (OGT) or O-GlcNAcase (OGA) changes many proteins at once and therefore provides limited information about individual substrates. Protein-selective approaches address this problem by directing OGT or OGA activity toward chosen proteins in living cells. Here, we review small-molecule recruiters, nanobody-based systems, inducible recruitment strategies, RNA aptamers, and complementary site-level approaches. We compare what each method can establish and the controls needed for interpretation, with particular attention to target engagement, target-protein O-GlcNAcylation, site assignment, selectivity, and functional validation. Together, these approaches provide increasingly direct ways to define how O-GlcNAcylation of individual proteins contributes to cellular function.
    Keywords:  O-GlcNAcylation; OGA; OGT; induced proximity; post-translational modification
    DOI:  https://doi.org/10.1093/glycob/cwag081
  28. Signal Transduct Target Ther. 2026 Sep 21. pii: 394. [Epub ahead of print]11(1):
    HSP90 shields ROC1/RBX1 from proteasomal degradation by CHIP E3 ubiquitin ligase to promote lung adenocarcinoma.
    Lihui Li, Ying Zhang, Meng Li, Xuhui Yang, Gaili Chang, Wenjuan Zhang, Yueren Yan, Yunjian Pan, Yupei Liang, Shiwen Wang, Mingsong Wang, Robert M Hoffman, Wenyi Wei, Lijun Jia.
      The Regulator of Cullins 1 (ROC1) or RING box protein-1 (RBX1) is an essential component of the largest multiunit Cullin-RING ubiquitin ligase (CRL). Previous studies demonstrated that ROC1 is frequently overexpressed in multiple malignancies, which predicts advanced cancer stages and poor prognosis. However, the molecular mechanisms driving ROC1 overexpression in cancers remain largely unknown. Herein, we reveal that HSP90 binds to ROC1 with its N-Terminus, thus promoting ROC1 stabilization. HSP90 inhibition with the N-Terminal, but not the C-Terminal inhibitors accelerate ROC1 destabilization by facilitating its ubiquitination and subsequent degradation by CHIP E3 ligase. CHIP specifically interacts with ROC1 at its CC domain, thus promoting the K48-linked-ubiquitin-mediated degradation of ROC1 at the K26 residue. Indeed, deletion of CHIP markedly blocks HSP90-inactivation-induced ROC1 reduction. Function exploration reveals that HSP90 inhibition suppresses lung adenocarcinoma (LUAD) cell growth substantially by decreasing ROC1 abundance. In clinic, HSP90β and ROC1 are overexpressed in LUAD samples, which have positive correlation and predict poor prognosis of LUAD patients. LUAD organoids analysis reveals that HSP90 blockage promotes ROC1 destabilization and inhibits the growth of organoid cells. Taken together, the present results demonstrate the regulatory mechanism of ROC1 in malignancies and suggest a novel mechanism of the oncogenic role of HSP90 to promote lung tumorigenesis.
    DOI:  https://doi.org/10.1038/s41392-026-02958-0
  29. Life Sci Alliance. 2026 Dec;pii: e202603839. [Epub ahead of print]9(12):
    RAF1 scaffold integrity shapes chemogenetic degradation outcomes in KRAS-driven lung cancer models.
    Laura de-la-Puente-Ovejero, Ana Domostegui, Inés María García-Pérez, Gonzalo Aizpurua, Lucía Lomba-Riego, Pilar Ximenez-Embún, Cristina Mayor-Ruiz, Mariano Barbacid, Sara García-Alonso.
      Scaffold integrity is essential for the activity of proteins that function through protein-protein interactions rather than catalytic output. RAF1 exemplifies this duality: although it is a bona fide kinase and a core component of the MAPK cascade, its tumor-promoting role is largely kinase-independent, relying instead on scaffold-mediated suppression of apoptosis. Genetic Raf1 ablation in KRAS-driven lung adenocarcinoma mouse models induces tumor regression without systemic toxicity, making it an attractive candidate for targeted protein degradation. Chemogenetic systems like the dTAG platform are widely used for preclinical target validation. Here, we generated a dTAG-RAF1 mouse model and showed that pharmacological degradation is efficient and systemically well tolerated but fails to reproduce the tumor regression observed upon genetic Raf1 ablation. Mechanistically, the N-terminal FKBP12F36V tag (dTAG) perturbs the RAF1 interactome, including scaffold associations with apoptotic regulators, thereby blunting the phenotypic consequences of its degradation. These results establish scaffold integrity as a determinant of chemogenetic system fidelity and argue that degradation tools must be validated at the functional level, not only for target elimination, before assessing their therapeutic relevance.
    DOI:  https://doi.org/10.26508/lsa.202603839
  30. Nat Commun. 2026 Aug 25. pii: 10162. [Epub ahead of print]17(1):
    The predicted interactome of the human mitochondrial proteome.
    Abhinav B Swaminathan, Mohammad Zulkifli, Rachel M Guerra, Sofia M Calabrese, Dimitris T Kalafatis, David J Pagliarini, Vishal M Gohil.
      Despite the fundamental importance of mitochondria in cellular metabolism, the molecular function(s) of many mitochondrial proteins remain unknown. Since protein function can be inferred from their interacting partners, we repurpose the protein structure prediction algorithm AlphaFold Multimer (AFM) as a classification model to predict protein-protein interactions of the entire human mitochondrial proteome. By screening 630,003 protein pairs, we create a compendium of 2,895 previously known and newly observed interactions, which include the interacting partner(s) of 85 uncharacterized mitochondrial proteins, thereby linking them to a known biochemical pathway. Extending the AFM-based analysis to 11 diverse eukaryotes identifies evolutionarily conserved interactions among human hits, including regulators of core bioenergetic pathways. Our experiments, guided by these predictions, nominate protein interactions that form the coenzyme Q metabolon and define the mitochondrial copper delivery pathway to cytochrome c oxidase. Our compendium represents a powerful resource for the systematic, structure-based functionalization of the human mitochondrial proteome.
    DOI:  https://doi.org/10.1038/s41467-026-77112-z
  31. Bioinformatics. 2026 Sep 24. pii: btag714. [Epub ahead of print]
    DesignMaster: A Multi-Conditional Diffusion Framework for Rational PROTAC Design.
    Binze Shi, Yi Hao, Jie Liu, Tong Pan, Luke Isbel, Michael Roy, Ashley P Ng, Xuequn Shang, Fuyi Li.
       MOTIVATION: Proteolysis-targeting chimeras (PROTACs) enable targeted protein degradation through ternary complex formation with E3 ubiquitin ligase. However, the rational design of PROTACs remains highly challenging due to limited structure-activity relationship data and the vast conformational diversity of linkers. Existing computational approaches can be broadly divided into structure-based ternary modelling methods and fragment-based linker generation models. Although these approaches have advanced PROTAC design, they typically neglect key physicochemical constraints and linker-length control during the generation process, causing the generated PROTACs to lack balanced structural properties required for effective ternary complex formation with drug-like characteristics.
    RESULTS: To address these limitations, we propose DesignMaster, a diffusion-based generative framework that explicitly incorporates linker length and physicochemical properties as controllable conditioning signals. DesignMaster employs an E(3)-equivariant graph Transformer with a gated multi-condition fusion module to inject linker length and physicochemical constraints throughout the diffusion process, enabling fine-grained and constraint-aware molecular generation. Experiments on PROTAC-DB 2.0 and 3.0 demonstrate that DesignMaster achieves the best or highly competitive performance across Validity, Uniqueness, and Recovery. The Case study further shows that DesignMaster consistently achieves improved geometric agreement with the reference PROTAC conformations across both the 6W7O and 6HAY complexes, highlighting its potential for practical structure-guided and property-aware PROTAC design.
    AVAILABILITY: The source code and datasets are available at https://github.com/ABILiLab/DesignMaster.
    DOI:  https://doi.org/10.1093/bioinformatics/btag714
  32. Int Rev Cell Mol Biol. 2026 ;pii: S1937-6448(26)00034-1. [Epub ahead of print]406 1-42
    Lysosomal function and homeostasis: From cellular adaptation to disease pathogenesis.
    Satoshi Minami, Maho Hamasaki.
      Lysosomes were once considered terminal degradative organelles responsible for disposing of cellular waste. However, recent studies have revealed that lysosomes serve as dynamic signalling and metabolic hubs at the center of diverse biological processes, including nutrient sensing, metabolic regulation, membrane trafficking, autophagy, inflammation, and cell death. To support this broad functional repertoire, lysosomes must possess robust mechanisms to maintain their integrity in the face of damage or stress. In response to lysosomal membrane damage, cells engage multilayered adaptive mechanisms that act in coordination-membrane repair (Repair), selective removal of damaged organelles (Removal), and de novo biogenesis of lysosomes (Regeneration). These processes are mediated by a range of molecular pathways, including the ESCRT complex, the PITT pathway, lysophagy, and TFEB-dependent lysosomal regeneration. Notably, recent findings highlight the noncanonical autophagy-like pathway known as ATG8ylation (conjugation of ATG8s on single membranes), which is activated via the STING-V-ATPase-ATG16L1 axis and functions as a critical hub connecting multiple arms of the lysosomal damage response. In this review, we systematically outline the molecular basis of lysosomal damage responses, including ATG8ylation, and explore how these networks are implicated in a broad spectrum of pathological conditions such as aging, neurodegeneration, cancer, obesity-related disorders, and immune dysfunction. Understanding these lysosomal quality control mechanisms not only sheds light on the fundamental principles of organelle homeostasis but also opens new avenues for therapeutic innovation.
    Keywords:  Lysophagy; Lysosome; Organelle damage; Selective autophagy
    DOI:  https://doi.org/10.1016/bs.ircmb.2026.04.002
  33. JCI Insight. 2026 Sep 24. pii: e185437. [Epub ahead of print]
    The E3 ubiquitin ligase HECTD3 controls immune colonic inflammation by restricting Myd88 activation and signaling.
    Shamima Islam, Shahnewaj Mannan, Ashley Zuniga, Upasana Parthasarathy, Valeriu B Cismasiu, Leonardo Silvane, Sayan Chakraborty, Divya Priyanka Talada, Raghwendra Pratap Singh, Tomas Zelenka, Amreen Naveen, Sephra Chyanne Vickers, Michael Gm Grant, Jonathan J Cho, Theodore Drashansky, Alexander J Kwiatkowski, Xintong Liu, Ross Tomaino, Olga A Guryanova, Mariola J Ferraro, Sang Yong Kim, Christian Jobin, Benjamin G Keselowsky, Hongmin Li, Paulo C Rodriguez, Martina Molgora, Amer A Beg, Timothy I Shaw, Zheng Ruan, Lixin Wan, Dorina Avram.
      Ubiquitination is an important post-translational modification associated with essential cellular processes and implicated in regulation of immunity. Here we show that deletion of the E3 ubiquitin ligase Hectd3, germline or in hematopoietic compartment, including in CD11c+ cells, causes a more severe DSS-induced colitis and increased production of proinflammatory cytokines. Hectd3 mRNA levels were found reduced in colonic tissues of patients with ulcerative colitis (UC), which highlights a potential role for Hectd3 in regulating inflammatory responses in UC. We identified Myd88, a central adaptor in the TLR/IL1R signaling and inflammatory response, as a target for Hectd3 ubiquitination. We demonstrate that Hectd3 directly ubiquitinates Myd88 through K27-linked Poly-Ub chains in a nondegradative manner. Hectd3 KO GM-CSF-bone marrow derived cells treated with the TLR4 ligand lipopolysaccharide (LPS) produced more proinflammatory cytokines, show elevated phosphorylation of NF-κB and IRAK4, as well as elevated association of Myd88 with IRAK4, demonstrating that Hectd3 controls Myd88-IRAK4-NF-κB axis. Inhibition of Myd88 activity rescued colitis severity in the Hectd3 KO mice, including the elevated proinflammatory cytokine production. Thus, our results establish Myd88 as a new target for Hectd3 non-degradative polyubiquitination and restriction of immune colonic inflammation.
    Keywords:  Immunology; Inflammation; Inflammatory bowel disease; Ubiquitin-proteosome system
    DOI:  https://doi.org/10.1172/jci.insight.185437
  34. Nature. 2026 Sep 23.
    Lsp2 links mTORC1 to TOP mRNA translation and lifespan in Drosophila.
    Jun Wang, Zixin Cai, Jiaojiao Gu, Shiqi Xiong, Jianhan Yi, Meng Yang, Kexin Chang, Xinrui Ning, Yilin Wen, Yan Yan, Jiongming Lu, Yirong Wang, Zongzhao Zhai.
      Mechanistic target of rapamycin complex 1 (mTORC1) senses nutrient availability to orchestrate metabolic processes that are crucial for physiological homeostasis and ageing1. mTORC1 preferentially regulates the translation of 5'-terminal oligopyrimidine (TOP) motif-containing mRNAs (which encode mainly ribosomal proteins) through the 4E-BP translational repressor2; however, this function of mTORC1 is resistant to rapamycin inhibition3. TOP mRNAs are exceptionally abundant, and thus impose a major translational burden on cells, but how their translation is physiologically tuned and linked with lifespan remains unclear. Here we show that Lsp2, which was previously known to be a storage protein4, is also an adipose effector and feedback activator of mTORC1 that modulates lifespan in Drosophila. Expression of Lsp2 is induced by essential amino acids through mTORC1 and is gated by additional signals of nutrient sufficiency. Genetic ablation of Lsp2 robustly extends lifespan without impairing key life history traits such as reproduction. Translatomic profiling shows that loss of Lsp2 selectively reduces global TOP mRNA translation in a 4E-BP-dependent manner, thereby extending lifespan through a mechanism distinct from the effects of rapamycin. Evolutionarily, TOP motifs co-emerged with 4E-BP and are present in nearly all Drosophila ribosomal protein mRNAs. Moreover, we show that the role of TOP motifs in translational control extends to Drosophila. Collectively, our findings reveal a nutrient-induced physiological factor that amplifies mTORC1 output in TOP mRNA translation and regulates organismal longevity.
    DOI:  https://doi.org/10.1038/s41586-026-11029-x
  35. J Biol Chem. 2026 Sep 22. pii: S0021-9258(26)02468-3. [Epub ahead of print] 113596
    TRPML1 loss disrupts lysosome-mitochondria homeostasis and sensitizes MDA-MB-231 triple-negative breast cancer cells to chemotherapy.
    Alia K Syeda, Shekoufeh Almasi, Cory J Benson, Barry E Kennedy, Ryan M Yoast, Scott M Emrich, Amari Delima-Baril, Logan Slade, Shanmugasundaram Pakkiriswami, Vishnu V Vijayan, Unnikrishnan B Sheela, Shashi Gujar, Thomas Pulinilkunnil, Mohamed Trebak, Yassine El Hiani.
      Signaling mechanisms at the lysosome-mitochondria interface form a critical network that enables cancer cells to maintain mitochondrial quality control, adapt to metabolic stress, and survive therapy. However, the incomplete understanding of the mechanisms coordinating this network has limited the development of effective therapies, especially for triple-negative breast cancers (TNBC). Here, we identify TRPML1 as an important regulator of lysosome-mitochondrial communication in MDA-MB-231 TNBC cells. We find that TRPML1 knockdown (ML1-KD) impaired mitochondrial respiration, oxidative substrate utilization, ATP production and redox balance in MDA-MB-231 cells, whereas comparable changes were not observed in non-cancerous MCF10A cells. ML1-KD reduced lysosomal acidification and impaired autophagic flux and was accompanied by reduced TFEB nuclear localization, impaired mitophagy, and alterations in mitochondrial maintenance proteins. These changes were accompanied by organellar proximity remodelling, with increased mitochondria-ER proximity and reduced mitochondria-lysosome proximity, together with altered cytosolic/mitochondrial Ca2+ responses, broad metabolic remodelling, G0/G1 arrest, and caspase-3/7-independent cell death. Importantly, ML1-KD cells showed enhanced responses to otherwise subeffective concentrations of doxorubicin and paclitaxel. Together, our findings support TRPML1-dependent lysosomal signaling as an important contributor to mitochondrial-metabolic resilience and chemotherapy responsiveness in MDA-MB-231 TNBC cells.
    DOI:  https://doi.org/10.1016/j.jbc.2026.113596
  36. bioRxiv. 2026 Sep 18. pii: 2026.09.11.751045. [Epub ahead of print]
    dubTAGs enable on-demand stabilization for tunable and reversible control of endogenous protein levels.
    Sunil Guharajan, Xiangyang Song, Qiong Wu, Sachi Sengupta, Wenyi Wei, Yan Xiong, Jian Jin, Sahin Naqvi.
      Precise and rapid control over cellular protein levels is essential to dissect complex biological systems. Chemical genetic approaches such as dTAG, in which a target is fused to a degron tag (FKBP12F36V) and degraded upon small molecule-mediated recruitment of E3 ligases, have enabled rapid and tunable control over protein abundance. However, no analogous tool exists to precisely increase protein levels and actively reverse dTAG-mediated degradation. Here, we developed heterobifunctional small molecules (dubTAGs) that stabilize FKBP12F36V-tagged proteins by recruiting endogenous deubiquitinases. Utilizing stem cell-derived cranial neural crest cells (CNCCs) in which the transcription factors SOX9 or TWIST1 are endogenously tagged with FKBP12F36V, we identified OTUB1- or USP7-recruiting heterobifunctional molecules that demonstrated effective target stabilization and ternary complex formation. We demonstrate that dubTAG-mediated protein stabilization is dependent on deubiquitinase recruitment, target-specific, and can tunably and rapidly reverse dTAG-mediated degradation. We applied dubTAGs to assess how stabilizing endogenous SOX9 impacts chromatin accessibility in CNCCs, finding both monotonic and non-monotonic regulatory element responses that are driven by distinct sequence features. dubTAGs are readily applicable tools for investigating the effects of elevated protein levels and tunably reversing targeted degradation, enabling new approaches to study protein dosage effects in development, disease, and therapeutic discovery.
    DOI:  https://doi.org/10.64898/2026.09.11.751045
  37. Res Sq. 2026 Sep 15. pii: rs.3.rs-10821157. [Epub ahead of print]
    COMMD3 coordinates mannose-6-phosphate receptor trafficking to sustain lysosomal protease maturation.
    Yong-Hui Zheng, Yixiang Hu.
      Lysosomal function depends on the cation-independent and cation-dependent mannose-6-phosphate receptors (CI-MPR and CD-MPR), which deliver newly synthesized acid hydrolases from the trans-Golgi network (TGN) to the endolysosomal system. However, how the trafficking of these receptors is coordinately regulated remains incompletely understood. Here we identify COMMD3 as a regulator of both MPRs that promotes their exit from early endosomes and sustains lysosomal hydrolase maturation. Loss of COMMD3 causes accumulation of CI-MPR and CD-MPR in early endosomal compartments and profoundly impairs the maturation and activity of Cathepsin L (CTSL). Combined deletion of both MPRs phenocopies COMMD3 deficiency, functionally linking COMMD3-dependent MPR trafficking to CTSL maturation. Unexpectedly, this trafficking activity is mediated primarily by the N-terminal domain of COMMD3 rather than its canonical C-terminal COMM domain involved in Commander complex assembly. Disruption of COMMD3 or both MPRs also selectively restricts CTSL-dependent entry of SARS-CoV-2 and Ebola virus. Together, our findings uncover a COMMD3-MPR trafficking axis that couples endosomal sorting to lysosomal protease maturation and supports endosome-dependent viral entry.
    DOI:  https://doi.org/10.21203/rs.3.rs-10821157/v1
  38. mBio. 2026 Sep 22. e0174026
    HCMV US30 induces TMED10-DRP1-mediated mitochondrial fission and apoptosis to promote viral multiplication.
    Ya-Li Lei, Yu-Ting Cai, Ruo-Tong Chen, Peng Ren, Xue-Mei Yi, Yu-Zhi Fu, Yan-Yi Wang, Shu Li, Hong-Bing Shu.
      Human cytomegalovirus (HCMV) hijacks host components to modulate cell death for its optimized replication and dissemination. We identified HCMV US30 as a viral factor that induces caspase-dependent apoptosis. US30 induces both DRP1-dependent mitochondrial fission and subsequent apoptosis, as well as IRE1α-mediated unfolded protein responses (UPR). Mechanistically, US30 interacts with NPL4 to impair ER-associated protein degradation and subsequently induce UPR. In parallel, US30 associates with the Endoplasmic reticulum-Golgi intermediate compartment (ERGIC) protein TMED10 and promotes its translocation to the cytoplasm, where it activates DRP1 to initiate mitochondrial fission and subsequent caspase-dependent apoptosis. US30 induces UPR and mitochondrial fission/apoptosis via distinct domains, and the two distinct effects are uncoupled. We also show that US30-induced mitochondrial fission and apoptosis, but not UPR, contribute to the multiplication and dissemination of HCMV. These findings reveal that HCMV US30 induces mitochondrial fission and apoptosis to promote viral replication and dissemination and provide potential targets for intervention of HCMV-induced diseases.IMPORTANCEHuman cytomegalovirus (HCMV) is a human pathogenic herpesvirus that causes global epidemics. HCMV hijacks cellular compartments to maintain its replication and dissemination, which is associated with host cell fate. Here, we identified HCMV US30 as a viral factor to induce caspase-dependent apoptosis. Proteomics analysis revealed that US30 disrupts both ER and mitochondrial homeostasis. We further found that US30-induced mitochondrial fission, but not UPR, mediates apoptosis. Mechanistically, our results indicate that US30 interacts with NPL4 to activate UPR and associates with TMED10 to trigger mitochondrial fission, which are dependent on distinct domains of US30. Most importantly, we found that US30 alters the localization of TMED10 from ERGIC to the cytosol to activate DRP1. Finally, our results showed that US30-induced mitochondrial fission and apoptosis, but not UPR, contribute to the multiplication and dissemination of HCMV. These findings enhance our understanding of HCMV-host interplay and provide potential targets for intervention of HCMV-induced diseases.
    Keywords:  HCMV; UPR; US30; apoptosis; mitochondrial fission; viral replication
    DOI:  https://doi.org/10.1128/mbio.01740-26
  39. bioRxiv. 2026 Sep 22. pii: 2026.09.15.751695. [Epub ahead of print]
    Specific host translation perturbations promote Tn Smu 1 loss independently of the canonical ImmA regulator.
    Liang Bao, Todd Kitten, Ping Xu.
      Integrative and conjugative elements (ICEs) are major drivers of horizontal gene transfer and bacterial genome evolution. Although ICE-encoded regulatory circuits have been extensively characterized, the impact of host physiology on the stability of integrated ICEs remains poorly understood. Here, we identify a host-dependent pathway that links specific host translation perturbations to loss of the ICE Tn Smu1 in Streptococcus mutans . Analysis of host-gene deletion mutants revealed that disruption of fmt , rnjA , or rnjB -three translation-associated host genes-reproducibly promoted Tn Smu1 loss through a mechanism that bypasses the canonical ICE-encoded metalloprotease ImmA but remains dependent on the native attachment site attR . This phenotype was selective, as mutations affecting other essential cellular functions, including protein folding, tRNA modification, cell division, and fatty acid biosynthesis, failed to destabilize Tn Smu1 despite undergoing the same experimental evolution and accumulating adaptive genomic changes. Preventing Tn Smu1 loss in these translation-associated mutants markedly reduced bacterial growth, whereas loss of the element improved fitness, indicating that ICE elimination alleviates the cost associated with Tn Smu1 retention under these conditions. Finally, we show that the relationship between host translation and Tn Smu1 stability extends to a genetically distinct S. mutans clinical isolate, although with strain-dependent penetrance. Together, these findings identify host translational state as an important physiological determinant of Tn Smu1 stability and reveal that bacterial hosts can influence the maintenance of integrated mobile genetic elements through mechanisms that extend beyond element-encoded regulatory circuits.
    DOI:  https://doi.org/10.64898/2026.09.15.751695
  40. Biochem Biophys Res Commun. 2026 Sep 17. pii: S0006-291X(26)01355-0. [Epub ahead of print]837 154589
    USP19 protects against cigarette smoke-induced lung injury and epithelial stress.
    Atsushi Miyamoto, Kiyoshi Uemasu, Xiuying Li, Kazuya Tanimura, Simon S Wing, Toru Nyunoya.
      Cigarette smoke (CS) imposes substantial proteostatic stress on lung epithelial cells, yet the protein quality control mechanisms that determine susceptibility to injury remain incompletely understood. We investigated the role of the ubiquitin-specific protease 19 (USP19) in CS-related lung injury across human lung tissue, a chronic CS-exposure mouse model, and cigarette smoke extract (CSE)-treated bronchial epithelial BEAS-2B cells. USP19 protein abundance was reduced in lung tissue from patients with severe COPD. Usp19-deficient mice developed greater CS-induced airspace enlargement compared to wild-type mice. In BEAS-2B cells, CSE reduced USP19 abundance, and USP19 knockout increased CSE-induced apoptosis. In addition, re-expression of USP19 partially restored viability. USP19 deficiency altered the temporal profile of integrated stress response signaling, culminating in enhanced CHOP induction, and CHOP (DDIT3) knockdown partially rescued CSE-induced loss of viability. USP19-deficient cells also showed a decrease in p62 abundance, puncta number, and area during CSE exposure, suggesting altered p62-associated protein handling. Together, these findings identify USP19 as a protective modifier of CS-related lung injury and epithelial stress, consistent with a role in supporting the capacity of lung epithelial cells to accommodate CS-induced proteostatic stress.
    Keywords:  CHOP; Chronic obstructive pulmonary disease; Cigarette smoke; Integrated stress response; Proteostasis; USP19
    DOI:  https://doi.org/10.1016/j.bbrc.2026.154589
  41. iScience. 2026 Oct 16. 29(10): 116105
    Coordinated regulation of the metaboproteome by Hsp90 chaperones controls metabolic plasticity.
    R Felipe Perez, Gianna L Mochi, Julia K Burkacki, Victoria Zoccoli-Rodriguez, Landon D Arcadi, Sarah J Backe, Joel R Wilmore, Mark R Woodford.
      Heat shock protein 90 (Hsp90) chaperones participate in the stabilization and activation of hundreds of proteins, thereby acting as signaling hubs. A mitochondrial subpopulation of Hsp90 has been previously described; however, little is known about its role in metabolism. Here, we showed that loss of individual Hsp90 isoforms differentially affects oxygen consumption and metabolic flexibility. Proteomic and metabolomic evaluation demonstrated that Hsp90 regulates the mitochondrial metabolic network, including respiration, fatty acid oxidation, and redox homeostasis. Loss of the mitochondrial chaperone tumor necrosis factor receptor-associated protein 1 (TRAP1) induced compensatory binding of Hsp90s to TRAP1-dependent proteins, indicating a mechanism for the role of Hsp90 chaperones in metabolic reprogramming. When considered with previous findings, a temporal pattern of regulation emerges whereby Hsp90s control the transcription, translation, import, and assembly of mitochondrial protein complexes. Our findings expand the scope of Hsp90-regulated processes and potentially inform the effects of isoform-specific Hsp90 inhibitors on metabolic reprogramming in cancer and other diseases.
    Keywords:  Hsp90; TRAP1; metabolism; metaboproteome; mitochondria; molecular chaperone
    DOI:  https://doi.org/10.1016/j.isci.2026.116105
  42. Cell Death Differ. 2026 Sep 22.
    VMP1 restricts STING trafficking and activation through controlling CDIPT recruitment to ER membrane curvature.
    Chen Zhou, Dongsheng Bai, Jiawei Zhao, HongJie Yin, Jiaying Du, Chunyang Gu, Yuxiang Wang, Binyan Lin, Na Lu, Yue Zhao.
      The cGAS-STING signaling serves as a central hub for innate immunity by orchestrating type I interferon production and inflammatory cascades in response to cytosolic DNA. A critical rate-limiting step in this pathway involves STING exit from the endoplasmic reticulum (ER), a process initiated by COPII-mediated trafficking that requires ER membrane curvature formation. However, the molecular mechanism that drives this process is poorly understood. In this study, we identify VMP1, an ER-resident transmembrane protein, as a negative regulator that constrains STING ER exit and downstream signaling activation. VMP1 controlled ER PtdIns(3)P accumulation, which was essential for ER membrane curvature formation. Depletion of Vmp1 triggered CDIPT-dependent PtdIns(3)P synthesis through a non-canonical pathway independent of VPS34 stability and MTMR3 expression. Furthermore, VMP1-mediated macroautophagy degraded Rab10 GTPase, thereby suppressing CDIPT recruitment to the ER membrane. Myeloid-specific Vmp1 knockout mice exhibited augmented antiviral defense against DNA virus infection but displayed unaltered susceptibility to RNA virus infection. These results suggest that VMP1 controls STING trafficking by modulating the Rab10-CDIPT axis to restrict ER PtdIns(3)P accumulation and limit ER membrane curvature formation required for COPII vesicle biogenesis.
    DOI:  https://doi.org/10.1038/s41418-026-01861-z
  43. ACS Appl Mater Interfaces. 2026 Sep 22.
    Modular Lysosome-Targeting Platform Based on a Multivalent DNA Framework for Programmable Protein Degradation.
    Xin Wan, Quanhao Dou, Jialin Zeng, Xi Chen, Miao Mao, Yuanqing Zhang.
      Targeted degradation of extracellular and membrane-bound proteins holds immense therapeutic potential but remains technically challenging. Lysosome-targeting chimeras (LYTACs) have emerged to bridge this gap, yet platforms built on monomeric aptamers suffer from inadequate stability, inefficient cellular uptake, and a lack of modularity. Here, we developed a tetrahedral DNA nanostructure-based multivalent lysosome-targeting antibody platform (TDN-MLYTAB) to overcome these limitations. Our platform employs two key engineered components: a rigid TDN scaffold enables the precise multivalent display of aptamers to enhance binding stability and lysosomal targeting while preventing steric hindrance, and an engineered secondary antibody serves as a universal adaptor, conferring plug-and-play modularity. By simply exchanging the primary antibody, we achieved efficient degradation of multiple distinct cell-surface proteins in different cellular models without platform re-engineering. Compared to conventional flexible and monovalent systems, TDN-MLYTAB uniquely avoids structural collapse, exhibiting substantially improved internalization and a remarkable degradation efficiency of ∼71% at 100 nM after 24 h. This work not only presents a versatile degradation platform but also demonstrates how programmable DNA nanostructures can overcome persistent bioconjugation challenges, advancing modular therapeutics toward application.
    Keywords:  DNA nanostructure; cell membrane rewiring; lysosome-targeting chimeras; multivalent aptamers; protein degradation
    DOI:  https://doi.org/10.1021/acsami.6c15457
  44. Nat Commun. 2026 Aug 25. pii: 10178. [Epub ahead of print]17(1):
    Exosomal export of activated CASPASE-8 is linked to the prevention of TNF-induced cytotoxicity.
    Jon Huyghe, Dario Priem, Annelore Haems, Lien Lippens, Margaux De Meyer, Tom Delanghe, Yves Dondelinger, Inge Bruggeman, Peter Vandenabeele, Sven Eyckerman, An Hendrix, Mathieu Jm Bertrand.
      Tumor Necrosis Factor (TNF) is a key pro-inflammatory cytokine whose sensing by TNFR1 triggers gene activation or cell death induction. While TNF cytotoxicity can be beneficial during infections by supporting effective immune responses, its chronic or excessive induction is harmful and promotes inflammatory pathologies. Protective brakes, known as cell death checkpoints, normally repress TNF cytotoxicity and therefore constitute crucial safeguards against these diseases. Death by TNF mainly proceeds upon inactivation of a checkpoint by microbial effector proteins or pathological mutations. We previously identified lysosomal turnover of TNFR1 Complex II by TAX1BP1-mediated selective macro-autophagy as a brake on TNF cytotoxicity. Here, we propose an alternative mechanism that prevents TNF-induced RIPK1 kinase-independent apoptosis. We found that inhibiting the ESCRT machinery, HSC70 or TAX1BP1 interferes with the TNF-dependent targeting of activated CASPASE-8 into endosomal intralumenal vesicles (ILVs) and is associated with apoptosis induction. Furthermore, we identified TAX1BP1 and TNFR1 Complex II components as TNF-induced cargoes of extracellular vesicles, suggesting that exosomal release of TNFR1 Complex II serves as a parallel detoxification pathway to lysosomal turnover. Finally, we show that Salmonella Typhimurium and Mycobacterium tuberculosis effector proteins activate TNF cytotoxicity by inhibiting components of the ESCRT machinery involved in this detoxification process.
    DOI:  https://doi.org/10.1038/s41467-026-75544-1
  45. Proc Natl Acad Sci U S A. 2026 Sep 29. 123(39): e2536559123
    Programmed inhibition of an innate immune receptor via de novo designed transmembrane proteins.
    Colleen A Maillie, Minghao Zhang, Nadia Gosiet, George Goldenfeld, Gerard J Kroon, Andrew B Ward, Marco Mravic.
      Transmembrane domains of immune complexes transmit precise signals across lipid bilayers. Probing their interactions has the potential to yield mechanistic insights relevant to therapeutic design. However, our capability to generate molecules that bind lipid-embedded sites is limited. Here, we created synthetic polypeptides targeting a prominent mediator of inflammatory signaling directly within membranes, Toll-like receptor 4 (TLR4), and clarify structural principles of its cross-membrane signaling mechanism. Doing so, we test emerging design principles for computationally encoding protein interactions within lipid and validate a protein-protein interaction screening platform for rapid discovery of de novo transmembrane (TM) protein antagonist of inflammatory signaling via this innate immune receptor. Binding the TM domain of TLR4 poses a formidable de novo molecular recognition challenge not yet achieved, given the membrane-spanning region is predominantly apolar and lacks any recognizable interaction motifs (e.g., sticky small residue repeats). Likewise, TLR4's structure-function relationship and key residues for oligomerization and cross-membrane signaling are underdetermined. Our engineering strategy identifies lead synthetic TM proteins that specifically bind TLR4's transmembrane domain and antagonizes NFκB signaling in human cells. These transmembrane-directed chemical probes prove that receptor TM domain interaction geometries are essential for TLR4's cross-membrane conformational coupling, informing a revised structural mechanism to leverage in future drug design of this protein family. This work refines principles for encoding stable interactions in cellular membranes and expands the range of lipid-embedded mechanisms accessible to probe with computationally derived molecules.
    Keywords:  Toll-like receptor; innate immune signaling; membrane protein; peptide therapeutics; protein design
    DOI:  https://doi.org/10.1073/pnas.2536559123
  46. bioRxiv. 2026 Apr 05. pii: 2026.04.03.716366. [Epub ahead of print]
    Proteolytic remodeling by Yme1 enables mitochondrial-derived compartment formation.
    Sai Sangeetha Balasubramaniam, Amy E Curtis, Jonathan R Friedman, Adam L Hughes.
      Mitochondrial-derived compartments (MDCs) are remodeling domains that form from the outer mitochondrial membrane during metabolic and proteotoxic stress and selectively sequester hydrophobic membrane proteins. Although MDC formation depends on mitochondrial lipid composition and occurs at organelle contact sites, the molecular mechanisms that permit their biogenesis remain poorly defined. Here we identify the conserved inner mitochondrial membrane i-AAA protease Yme1 as a critical regulator of MDC formation. Loss of Yme1 blocks MDC biogenesis in response to multiple stressors, and this requirement depends on its proteolytic activity rather than secondary defects in mitochondrial morphology. Quantitative mitochondrial proteomics under MDC-inducing conditions revealed Yme1-dependent remodeling of lipid transfer proteins of the Ups family and components of the MICOS complex. Disruption of either pathway partially restores MDC formation in yme1Δ cells, while combined perturbation substantially bypasses the requirement for Yme1. Finally, Yme1 overexpression drives MDC formation in the absence of stress, although this activity remains constrained by metabolic conditions. Together, these findings support a model in which Yme1-dependent proteolysis relieves lipid- and MICOS-dependent constraints to permit MDC formation.
    DOI:  https://doi.org/10.64898/2026.04.03.716366
  47. Biochem Pharmacol. 2026 Sep 25. pii: S0006-2952(26)00845-2. [Epub ahead of print] 118503
    Src inhibition attenuates neuroinflammation via promoting p62 UFMylation-dependent microglial mitophagy.
    Yi-Rong Dong, Jin-Rong Wang, Yang Yang, Shou-Peng Cao, Mei-Chuan Zhou, Sen-Xiang Zeng, Hui-Qing Mi, Jia-Hui Wang, Cai-Xia Zang, Fang-Fang Li, Xiu-Qi Bao, Dan Zhang.
      Src tyrosine kinase, a prototypical oncogene, has recently emerged as a critical modulator of neuroinflammation. However, the precise molecular mechanisms underlying its regulatory role remain poorly characterized. Herein, pharmacological inhibition of Src attenuated lipopolysaccharide-induced neuroinflammatory responses in both in vivo and in vitro experiments. Proteomic analysis identified that microglial mitophagy and p62 UFMylation were involved in Src-mediated neuroinflammation. Further studies demonstrated that Src inhibition reduced the phosphorylation of UFL1, the E3 ligase of UFM1 conjugation, which correlated with decreased UFMylation of p62. Notably, the function of p62 was regulated by a dynamic interplay between UFMylation and ubiquitination. Consequently, diminished p62 UFMylation competitively facilitated ubiquitination of p62 at the same residue. This led to p62 degradation and induced microglial mitophagy, ultimately alleviating neuroinflammation. Moreover, Src inhibition significantly ameliorated neuroinflammatory pathology and cognitive deficits in LPS-challenged mice, an effect attributed to p62 UFMylation-mediated microglial mitophagy. Collectively, our findings revealed that the Src-UFL1-p62 signaling axis governing microglial mitophagy and neuroimmune homeostasis, positioning Src kinase as a promising therapeutic target for Alzheimer's disease and related neuroinflammatory disorders.
    Keywords:  Alzheimer’s disease; Microglial mitophagy; Neuroinflammation; Src tyrosine kinase; UFMylation
    DOI:  https://doi.org/10.1016/j.bcp.2026.118503
  48. Cell. 2026 Sep 25. pii: S0092-8674(26)01065-2. [Epub ahead of print]
    Single-cell visual proteomics of a minimal bacterium reveals structural coordination of gene expression machineries.
    Joseph M Dobbs, Rasmus K Jensen, Julia Mahamid.
      Translation is a central process in gene expression. Its regulation is complex, depends on factors that include cell state and the subcellular environment, and is subject to modulation via crosstalk to processes such as transcription or translocation. Here, we used cryo-electron tomography of native and antibiotic-perturbed Mycoplasma pneumoniae cells to resolve 140 maps that recapitulate bacterial translation during the initiation, elongation, and recycling phases. We visualized multiple transcription-translation complexes, allowing us to propose a threading-based translation reinitiation mechanism and to provide structural evidence for a long-hypothesized supercomplex that coordinates transcription, translation, and membrane attachment. We resolved abundant membrane-associated large ribosomal subunits and suggest that dissociation from membranes depends on the conditional initiation of new translation, consistent with a potentially conserved mechanism in mammalian cells. This work visualizes the multilayered control of bacterial translation and demonstrates the power of in-cell structural biology to investigate regulatory circuits in gene expression.
    Keywords:  Mycoplasma pneumoniae; RNA polymerase; SecDF; cryo-electron tomography; expressome; ribosome; subtomogram analysis; transcription-translation coupling; transertion
    DOI:  https://doi.org/10.1016/j.cell.2026.08.054
  49. bioRxiv. 2026 Sep 17. pii: 2026.09.14.751618. [Epub ahead of print]
    Aberrant PCM1 accumulation in Trisomy 21 mislocalizes E3 ligases, delaying primary ciliogenesis.
    Bailey L McCurdy, Chad G Pearson.
      Primary cilia are microtubule-based extracellular signaling structures essential for development and tissue homeostasis, and their defects can cause ciliopathies. Trisomy 21, the cause of Down syndrome, also disrupts cilia formation and function. Here we show that Pericentrin (PCNT), a chromosome 21 resident gene whose protein is elevated in Trisomy 21, impairs primary ciliogenesis by delaying mother centriole uncapping. Elevated PCNT forms pericentrosomal assemblies that promote the accumulation of PCM1 in the pericentrosomal compartment. PCM1 binds and localizes the CP110 E3 ubiquitin ligases HERC2 and MIB1 to the centrosome, so mislocalizing PCM1 depletes these ligases from the centrosome, lowering CP110 ubiquitination and delaying uncapping. Reducing PCNT rescues these defects, whereas elevating PCM1 phenocopies them, establishing PCM1 accumulation as a critical mediator of uncapping. These findings reveal how a dosage-sensitive chromosome 21 gene disrupts ciliogenesis and show that centrosome function depends not only on PCM protein composition but on the spatial partitioning of proteins between the centrosome and pericentrosomal compartments.
    SUMMARY: Elevated Pericentrin in Trisomy 21 remodels the pericentrosomal space, causing PCM1-dependent sequestration of CP110 ubiquitin ligases away from the centrosome. This delays CP110 degradation, centriolar uncapping, and primary ciliogenesis revealing a mechanism linking centrosome architecture to cilium assembly.
    DOI:  https://doi.org/10.64898/2026.09.14.751618
  50. iScience. 2026 Oct 16. 29(10): 117515
    RpS19a depletion alters the hematopoietic translatome to drive tissue overgrowth.
    Naomi C Mitchell, Arjun Chahal, Tanya Javaid, Katrina Woodward, Ralf B Schittenhelm, Cheng Huang, Julie Lorent, Jiwon Lee, Melanie Rug, Amee J George, Ross D Hannan, Ola Larsson, Anthony W Purcell, Eduardo Eyras, Nikolay Shirokikh, Teresa T Bonello, Leonie M Quinn, Olga Zaytseva.
      Despite ribosomal protein loss correlating with increased tumor predisposition, direct mechanisms for the counterintuitive oncogenic effect of ribosomal protein depletion have not been reported. We used genetic models to investigate ribosomal protein S19a (RpS19a) depletion in the Drosophila blood organ, the lymph gland. Intriguingly, we demonstrate that RpS19a depletion directly drives excess proliferation and tissue overgrowth. Proteomic and differential translation analysis of RpS19a-depleted cells revealed altered stoichiometry of translation initiation factors and increased association of ribosomes with mRNAs encoding growth-promoting proteins. Furthermore, ribosomes in RpS19a-depleted cells are associated with mRNA encoding dNep1, a putative ribosomal RNA methyltransferase. Although uncharacterized in Drosophila, NEP1 is implicated in ribosomal RNA methylation and ribosome stability in yeast and humans, and its mutations underpin the ribosomopathy Bowen-Conradi syndrome. The RpS19a knockdown phenotype is suppressed by dNep1 co-depletion, altogether suggesting that dNep1 enables assembly of pro-proliferative ribosomes essential for blood lineage overgrowth driven by ribosomal protein loss.
    Keywords:  Drosophila; NEP1; RpS19a; blood; growth control; lymph gland; protein translation; ribosomal protein; ribosomopathy
    DOI:  https://doi.org/10.1016/j.isci.2026.117515
  51. bioRxiv. 2026 Sep 18. pii: 2026.09.16.752145. [Epub ahead of print]
    Unbiased, systematic surfaceome profiling of Acute Leukemia to identify novel immunotherapy targets.
    Benson M George, Anna Rodriguez-Pöhnlein, Donavelle J DeCastro, Jennifer Porat, Benyu Zhou, Dinah M Abeja, Ryan J Lumpkin, Rebecca J Metivier, Anna Schmoker, Wencke Walter, Torsten Haferlach, Yana Pikman, Katherine A Donovan, Kimberly Stegmaier, Eric S Fischer, Franziska Wachter, Ryan A Flynn.
      Cell surface proteomics provides a direct topological assessment of the outer membrane of cells and enables the capture of low abundance proteins that may be missed by whole cell proteomics. Here we present an unbiased atlas of the whole cell and surface proteomes of 25 commonly used leukemic cell lines, encompassing both lymphoid and myeloid lineages, and a variety of driver mutations. Paired-wise analysis highlights recurrent surface proteins that are not detected by whole cell proteomics. Coupling this dataset to RNA-sequencing, we also discovered genes where protein and RNA abundances are discordant. In KMT2A -rearranged AML, CD70 expression was increased across cell lines and validated in primary patient samples, supporting CD70 as a candidate therapeutic target in this disease. Several proteins are enriched in the surface proteomes but lack surface annotation, adding to the growing list of potential non-canonical cell surface proteins. These findings reveal a substantial pool of proteins absent from conventional surface annotations, including RNA-binding proteins, an emerging class of candidate immunotherapeutic targets.
    Key Points: Direct surface proteomics identifies leukemia cell-surface proteins not reliably predicted by transcriptomic or whole-proteome profilingSurface profiling reveals genotype-specific therapeutic targets, including CD70 in KMT2A-rearranged AML.
    DOI:  https://doi.org/10.64898/2026.09.16.752145
  52. bioRxiv. 2026 Sep 18. pii: 2026.09.12.751118. [Epub ahead of print]
    Latent generative search unlocks de novo design of untapped biomolecular interactions at scale.
    Kieran Didi, Danny Reidenbach, Matthew Penner, Supriya Ravichandran, Marshall Case, Mike Nichols, Erik Swanson, Alex Reis, Maggie Prescott, Yue Qian, Dongming Qian, Jingjing Yang, Weiji Li, Le Li, Daichi Shonai, Sean Gay, Bhoomika Basu Mallik, Ho Yeung Chim, Liurong Chen, Miguel Atienza Juanatey, Hubert Klein, Dominic Rieger, Phillip Schlegel, Anna U Macintyre, Maxim Secor, Daniele Granata, Sooyoung Cha, Zhonglin Cao, Guoqing Zhou, Tomas Geffner, Xi Chen, Micha Livne, Zuobai Zhang, Tianjing Zhang, Kyle Gion, Michael M Bronstein, Martin Steinegger, Kristine Deibler, Scott Soderling, Clara T Schoeder, Alena Khmelinskaia, Florian Hollfelder, Christian Dallago, Emine Kucukbenli, Arash Vahdat, Pierce Ogden, Karsten Kreis.
      De novo protein design has advanced rapidly, yet designing binders to polar, solvent-exposed epitopes and small, flexible ligands remains challenging. Such hydrated surfaces and flexible molecules, including carbohydrates, provide few of the hydrophobic contacts favoured by current methods and have largely resisted de novo binders. To address this challenge, here we introduce latent generative search for binder design, a novel framework that uses reward-guided search at inference time to steer the Proteina-Complexa generative model. The model codesigns sequence and structure - generating them together in a continuous latent space - and thereby removes the inverse-folding step on which current methods rely. In a screen of more than one million designs by multiplexed phage display, latent generative search produced more validated binders than every other method tested, its codesigned sequences surpassing post hoc redesign. It delivered high-affinity binders across therapeutic receptors, a viral attachment protein and intracellular signalling targets. Our approach also accessed previously untapped biology, generating the first de novo proteins that bind a free carbohydrate, including one that discriminates between blood-group antigens - a polar, flexible target class beyond the reach of current design methods.
    DOI:  https://doi.org/10.64898/2026.09.12.751118
  53. bioRxiv. 2026 Sep 16. pii: 2026.09.13.751219. [Epub ahead of print]
    Synaptic proteomics identifies cathepsin B as a regulator of synapse remodelling during learning.
    Aelon Rahmani, Michaela E Johnson, Rosemary A Coleman, Nina Hartman, Anne Poljak, Yee Lian Chew.
      Learning requires dynamic changes in synaptic protein composition. Most synaptic proteomic studies capture endpoint snapshots following training, overlooking molecular changes occurring during learning itself. We previously established TurboID proximity proteomics as an approach to capture protein-level changes during learning in the nervous system of Caenorhabditis elegans . Here, we apply this strategy to synapses. Trained synapses exhibited a distinct proteome compared with mock-trained controls, with pathways enriched for neurotransmission, synaptic reorganisation, protein trafficking, and autophagy. Enrichment of autophagy proteins led us to investigate the cathepsin B orthologue CPR-4, a previously uncharacterised candidate for learning identified exclusively in trained synapses. Functional validation identified CPR-4 as a novel regulator of memory: CPR-4 is required for learning, and the absence of CPR-4 results in trained synaptic proteomes that are more like those of mock-trained synapses. Our findings support a model through which CPR-4 promotes synaptic remodelling required for learning through targeted protein clearance.
    DOI:  https://doi.org/10.64898/2026.09.13.751219
  54. Blood. 2025 Sep 25. pii: blood.2026033236. [Epub ahead of print]
    Characterization of disease-initiating hematopoietic stem cells in calreticulin-mutated myeloproliferative neoplasms.
    Camélia Benlabiod, Laetitia Borderon, Gurvan Hermange, Quentin Blampey, Maxime Evrard, Antonio Rodriguez-Romera, Stephanie G Moreno, Nathalie Gault, Philippe Rameau, Cyril Catelain, Elodie Rosa, Guillemette Fouquet, Lionel Faivre, Florence Pasquier, Bethan Psaila, Claus Nerlov, Sten Eirik W Jacobsen, William Vainchenker, Hana Raslova, Paul-Henry Cournède, Isabelle Plo, Caroline Marty.
      Myeloproliferative neoplasms (MPNs) arise following the acquisition of a mutation in a hematopoietic stem cell (HSC) that causes oncogenic cytokine receptor signaling. Mutations in the calreticulin (CALR) gene are the second most common key driver mutations in MPNs, yet the identity of the disease-initiating HSCs and the mechanisms underlying their clonal expansion remain elusive. Knock-in mice bearing CALRdel52 and CALRins5 mutations recapitulate disease phenotypes, with a greater HSC amplification in CALRdel52 mice. Here, we crossed these strains with transgenic reporter mice expressing GFP under the control of the Von willebrand factor (Vwf) promoter, enabling discrimination between different HSC subsets. We show that CALR-mutated MPNs are mainly initiated from the expansion of platelet-biased, Vwf-positive HSCs, without substantially altering their lineage bias. Notably, the selective amplification of Vwf-positive CALRdel52 compared to CALRins5 HSCs is associated with increased signaling of the thrombopoietin receptor MPL and activation of the integrated stress response as evidenced by eIF2a phosphorylation downstream of PERK kinase triggered by endoplasmic reticulum stress. This pathway is also transcriptionally upregulated in CALRdel52-like compared with CALRins5-like patient hematopoietic stem and progenitor cells (HSPCs), as supported by reanalysis of a previous dataset, and is associated with increased phosphorylation of eIF2a. Pharmacological inhibition of PERK markedly reduces the proliferation of mouse CALRdel52 HSCs and impairs the megakaryocytic differentiation of CALRdel52-like HSPCs from patients while sparing cells from healthy donors. These findings identify the PERK/eIF2a pathway as a mechanistic vulnerability in the MPN cell-of-origin and offer a rationale for exploring new treatment approaches.
    DOI:  https://doi.org/10.1182/blood.2026033236
  55. Cell Death Differ. 2026 Sep 23.
    Ubiquitination-mediated degradation of NLRX1 drives metabolic vulnerability and accelerates intervertebral disc degeneration.
    Zhi Du, Di Wu, Hanpeng Xu, Huaizhen Liang, Dingchao Zhu, Shuchang Peng, Bide Tong, Jie Lei, Xingyu Zhou, Hongchuan Wang, Yifan Du, Zixuan Ou, Junyu Wei, Xinyu Li, Rui Shi, Zhengdong Zhang, Bingjin Wang, Kun Wang, Xiaobo Feng, Cao Yang, Yu Song.
      Intervertebral disc degeneration (IVDD) is driven in part by senescence of nucleus pulposus (NP) cells, yet the metabolic defects underlying this process remain incompletely defined. Although NLRX1 has been implicated in mitochondrial quality control, the mechanisms governing its stability and its role in OXPHOS regulation during IVDD remain unclear. Here, we show that oxidative phosphorylation (OXPHOS) progressively declines with increasing IVDD severity and that loss of NLRX1 contributes to this defect by disrupting mitochondrial respiration and redox homeostasis in NP cells. Nlrx1-/- mice exhibited accelerated age-related IVDD, accompanied by reduced abundance of OXPHOS markers and increased senescence markers. Mechanistically, RNF126 promotes K48-linked polyubiquitination of NLRX1 at K520, leading to its degradation and consequent impairment of OXPHOS and redox balance in NP cells. A degradation-resistant NLRX1K520R mutant restored OXPHOS function, reduced mitochondrial fragmentation, and attenuated oxidative stress under senescence-inducing conditions. Engineered exosomes delivering NLRX1K520R alleviated IVDD-related phenotypes in vivo. These findings identify the RNF126-NLRX1 axis as a critical checkpoint of metabolic vulnerability that couples mitochondrial stress to senescence in NP cells during IVDD and highlight NLRX1 stabilization as a proof-of-concept therapeutic strategy.
    DOI:  https://doi.org/10.1038/s41418-026-01864-w
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