bims-proteo Biomed News
on Proteostasis
Issue of 2026–02–01
48 papers selected by
Eric Chevet, INSERM
  1. Phenylhydrazone-based endoplasmic reticulum proteostasis regulator compounds with enhanced biological activity.
  2. Structural basis and pathological implications of the dimeric OS9-SEL1L-HRD1 ERAD Core Complex.
  3. Sec61β maintains cytoplasmic proteostasis via ARIH1-mediated translational repression upon ER stress.
  4. Ribosome-NAC collaboration: A regulatory platform for cotranslational chaperones, enzymes, and targeting factors.
  5. Indirect ubiquitination independent of endogenous ubiquitination machinery for targeted protein degradation.
  6. Cultured cells activate IRE1 during attachment and flattening after routine passaging.
  7. Chronic stress antagonizes formation of stress granules.
  8. Deubiquitinase USP15 restricts LC3-dependent targeting of Mycobacterium tuberculosis.
  9. ER proteostasis meets mitochondrial function: contact sites as hubs of communication and therapeutic targets.
  10. CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis.
  11. Coordination of cell organelles to promote metabolon formation.
  12. A disease-causing Isoleucyl-tRNA synthetase variant leads to altered protein complex formation and cellular stress response.
  13. Reversible ubiquitination regulates HSF1 phase separation in response to proteotoxic stress.
  14. Aptamer-Mediated Covalent Dual Lysosome-Targeting Chimeras Enhance Targeted Degradation of Cell Surface Proteins.
  15. Cryo-EM structures of human ClpXP reveal mechanisms of assembly and proteolytic activation.
  16. Lysosomes as hubs of metabolic sensing and cellular homeostasis.
  17. Landscape expansion microscopy reveals interactions between membrane and phase-separated organelles.
  18. Engineering an orthogonal ubiquitin transfer cascade with Ring E3 RNF38 by phage display to reveal its regulation of nuclear transport.
  19. The Liver-Enriched Long Non-Coding RNA FAM99A Suppresses Tumorigenesis through Negative Regulation of Protein Synthesis.
  20. Ether lipids influence cancer cell fate by modulating iron uptake.
  21. Association-induced folding governs surrogate light chain and pre-B cell receptor core assembly.
  22. Mechanistic insights into RNA chaperoning by Ro60 and La autoantigens.
  23. Building a functional endoplasmic reticulum for proper cell growth and stress responses: a plant perspective.
  24. Chloroplast Stress Signals Orchestrate Epidermis-Specific Remodeling of Mitochondria and ER Under High Light.
  25. The dual face of reprogrammed proteostasis in cancer and its epigenetic regulation: A survival option and a therapeutic opportunity.
  26. TRIM9 and TRIM26 Interact with UBQLN2P497H to Modulate Its Proteasomal Degradation.
  27. Mito-nuclear communication: From cellular responses to organismal health.
  28. Biomolecular condensates sustain pH gradients at equilibrium through charge neutralization.
  29. Context-specific Angiogenin-mediated tRNA fragments (tDRs) biogenesis shapes the mitochondrial stress response.
  30. Meta-analysis fails to show any correlation between protein abundance and ubiquitination changes.
  31. Signaling to make human ribosomes: Connections between the cytoplasm and the nucleolus.
  32. Sec62 restricts ER-replicating positive-strand RNA virus infections via UPR-dependent ER-phagy.
  33. GlycoRNA complexed with heparan sulfate regulates VEGF-A signalling.
  34. Directional Modulation of the Integrated Stress Response in Neurodegeneration: A Systematic Review of eIF2B Activators, PERK-Pathway Agents, and ISR Prolongers.
  35. Metabolically regulated proteasome supramolecular organization in situ.
  36. Why m⁶A? An RNA surveillance model.
  37. Non-coding small RNAs Buffer protein interactions to prevent oncogenic aggregation: structural dampening of aberrant PPIs by RNA.
  38. Zinc accumulation-induced integrated stress response triggers β-cell identity loss.
  39. LncRNA P4HA2-AS1 drives renal interstitial fibrosis via trim32-mediated k63 ubiquitination of ULK1 and autophagic dysregulation.
  40. SAG/RBX2/ROC2/RNF7 dual E3 ligase: From target identification, validation to drug discovery.
  41. In vitro reconstitution in membrane environment reveals critical lipid dependence of substrate S-acylation by protein palmitoyltransferase enzymes.
  42. Mapping targetable sites on the human surfaceome for the design of novel binders.
  43. Reduced Proteasome Degradation of HSF-1 Shifts Protein Stress Management With Age in Caenorhabditis elegans.
  44. Phosphorylation-dependent STAMBP drives the progression of pancreatic ductal adenocarcinoma by deubiquitinating and stabilizing BAG3.
  45. Axonal distribution of mitochondria maintains neuronal autophagy during aging via eIF2β.
  46. Vectorized ULK1/2 and VPS34 Inhibitors for Tissue-Selective Autophagy Inhibition in Oncology.
  47. Concentration-dependent cytoplasmic phase separation of TDP-43 drives aggregation and proteinopathy.
  48. In situ NMR and integrative proteomics reveal the interaction signature of serum α-synuclein.
  1. Elife. 2026 Jan 26. pii: RP107000. [Epub ahead of print]14
    Phenylhydrazone-based endoplasmic reticulum proteostasis regulator compounds with enhanced biological activity.
    Gabriel M Kline, Lisa Boinon, Adrian Guerrero, Sergei Kutseikin, Gabrielle Cruz, Marnie P Williams, Ryan J Paxman, William E Balch, Jeffery W Kelly, Tingwei Mu, R Luke Wiseman.
      Pharmacological enhancement of endoplasmic reticulum (ER) proteostasis is an attractive strategy to mitigate pathology linked to etiologically diverse protein misfolding diseases. However, despite this promise, few compounds have been identified that enhance ER proteostasis through defined mechanisms of action. We previously identified the phenylhydrazone-based compound AA263 as a molecule that promotes adaptive ER proteostasis remodeling through mechanisms including preferential activation of the ATF6 signaling arm of the unfolded protein response (Plate et al., 2016). However, the protein target(s) of AA263 and the potential for further development of this class of ER proteostasis regulators had not been previously explored. Here, we employ chemical proteomics to demonstrate that AA263 covalently targets a subset of ER protein disulfide isomerases, revealing a potential molecular mechanism for the activation of ATF6 afforded by this compound. We then use medicinal chemistry to establish next-generation AA263 analogs showing improved potency and efficacy for ATF6 activation, as compared to the parent compound. Finally, we show that treatment with these AA263 analogs enhances secretory pathway proteostasis to correct the pathologic protein misfolding and trafficking of both a destabilized, disease-associated α1-antitrypsin (A1AT) variant and an epilepsy-associated GABAA receptor variant. These results establish AA263 analogs with enhanced potential for correcting imbalanced ER proteostasis associated with etiologically diverse protein misfolding disorders.
    Keywords:  ATF6; biochemistry; chemical biology; endoplasmic reticulum; human; mouse; protein homeostasis; small molecule; unfolded protein response
    DOI:  https://doi.org/10.7554/eLife.107000
  2. Nat Commun. 2026 Jan 27.
    Structural basis and pathological implications of the dimeric OS9-SEL1L-HRD1 ERAD Core Complex.
    Liangguang Leo Lin, Emir Maldosevic, Linyao Elina Zhou, Ahmad Jomaa, Ling Qi.
      The SEL1L-HRD1 complex represents the most conserved branch of endoplasmic reticulum (ER)-associated degradation (ERAD), a critical quality-control pathway that clears misfolded ER proteins. However, the molecular organization and pathogenic mechanisms of mammalian ERAD have remained elusive. Here, we report the cryo-EM structure of the core mammalian ERAD complex, comprising the ER lectin OS9, SEL1L, and the E3 ubiquitin ligase HRD1. The structure, validated by mutagenesis and crosslinking assays, reveals a dimeric assembly of the core complex in which SEL1L and OS9 form a claw-like configuration in the ER lumen that mediates substrate engagement, while HRD1 dimerizes within the membrane that may facilitate substrate translocation. Furthermore, pathogenic SEL1L mutations at the SEL1L-OS9 (Gly585Asp) and SEL1L-HRD1 (Ser658Pro) interfaces disrupt complex formation and impair ERAD activity. A newly identified disease-associated HRD1 variant (Ala91Asp), located in transmembrane helix 3, impairs HRD1 dimerization and substrate processing. These findings provide structural and functional insights for mammalian SEL1L-HRD1 ERAD and elucidate how mutations destabilizing this machinery contribute to human disease.
    DOI:  https://doi.org/10.1038/s41467-026-68777-7
  3. EMBO Rep. 2026 Jan 27.
    Sec61β maintains cytoplasmic proteostasis via ARIH1-mediated translational repression upon ER stress.
    Hisae Kadowaki, Tomohisa Hatta, Kazuma Sugiyama, Tomohiro Fukaya, Takao Fujisawa, Takashi Hamano, Naoya Murao, Yasunari Takami, Shuya Mitoma, Tohru Natsume, Katsuaki Sato, Hiromi Hirata, Tamayo Uechi, Hideki Nishitoh.
      Disrupted proteostasis causes various degenerative diseases, and organelle homeostasis is therefore maintained by elaborate mechanisms. Endoplasmic reticulum (ER) stress-induced preemptive quality control (ERpQC) counteracts stress by reducing ER load through inhibiting the translocation of newly synthesized proteins into the ER for their rapid degradation in the cytoplasm. Here, we show that Sec61β, a translocon component, prevents the overproduction of ERpQC substrates, allowing for their efficient degradation by the proteasome. Sec61β inhibits the binding of translation initiation factor eIF4E to the mRNA 5' cap structure by recruiting E3 ligase ARIH1 and eIF4E-homologous protein 4EHP, resulting in selective translational repression of ERpQC substrates. Sec61β deficiency causes overproduction of ERpQC substrates and reduces proteasome activity, leading to cytoplasmic aggresome formation. We also show that Sec61β deficiency causes motor dysfunction in zebrafish, which is restored by exogenous ARIH1 expression. Collectively, translational repression of ERpQC substrates by the Sec61β-ARIH1 complex contributes to maintain ER and cytoplasmic proteostasis.
    Keywords:  ER Stress; ERpQC; Proteostasis; Translational Regulation
    DOI:  https://doi.org/10.1038/s44319-026-00690-y
  4. Mol Cell. 2026 Jan 27. pii: S1097-2765(25)01030-5. [Epub ahead of print]
    Ribosome-NAC collaboration: A regulatory platform for cotranslational chaperones, enzymes, and targeting factors.
    Martin Gamerdinger, Nicolas Burg, Elke Deuerling.
      Protein biogenesis requires the ribosome to collaborate with a diverse set of cotranslational factors that shape the fate of nascent chains. These interactions must be precisely choreographed: while cytonuclear proteins require immediate N-terminal maturation and folding, endoplasmic reticulum (ER) and mitochondrial proteins must be maintained in an unfolded state for targeting to their organelles. Reconciling these opposing demands requires a highly selective sorting mechanism operating at the ribosomal exit tunnel. Recent studies identify the conserved nascent polypeptide-associated complex (NAC) as a central coordinator of this process. By sensing nascent signals and dynamically modulating factor access to the ribosome, NAC directs substrates toward the appropriate maturation or targeting pathway. This emerging framework positions NAC as a molecular hub that organizes cotranslational interactions into efficient and orderly protein-biogenesis pathways. In this review, we discuss the mechanistic principles underlying NAC function and consider broader implications for how ribosome-associated networks enforce fidelity in protein biogenesis.
    Keywords:  ER; METAP; MTS; N-acetylation; N-myristoylation; N-myristoyltransferase; N-terminal acetyltransferase; N-terminal modification; NAC; NAT; NMT; NatA; NatD; NatE; SRP; SS; UBA; endoplasmic reticulum targeting; methionine aminopeptidase; methionine excision; mitochondrial targeting sequence; nascent polypeptide-associated complex; ribosome; signal recognition particle; signal sequence; ubiquitin-associated domain
    DOI:  https://doi.org/10.1016/j.molcel.2025.12.031
  5. Commun Chem. 2026 Jan 29. 9(1): 52
    Indirect ubiquitination independent of endogenous ubiquitination machinery for targeted protein degradation.
    Takafumi Furuhata, Kazuki Yoshida, Ryoka Fujita, Jotaro Miyamoto, Chiharu Moriyama, Tokiha Masuda-Ozawa, Hikaru Tsuchiya, Yasushi Saeki, Akimitsu Okamoto.
      Heterobifunctional small degrader molecules that hijack endogenous E3 ubiquitin ligases have attracted attention for the rapid and irreversible knock-down of target proteins via ubiquitination. However, the formation of appropriately oriented E3 ligase-target complexes is required for efficient ubiquitination of the target, which complicates the molecular optimization and leads to acquired drug resistance caused by the loss of E3 ligase activity and mutations at the E3-target interfaces. Here, we report on indirect ubiquitination as a chemical strategy for E3-indepedent ubiquitin-tethering to the target substrate. Comprising a ligand molecule and a ubiquitin moiety, the designed chimeric molecule enables the ubiquitination of the target proteins via non-covalent interactions, which lead to the proteasomal degradation of recombinant Bcl-2 and NF-κB p50, and intracellular endogenous Bcl-2. Indirect ubiquitination offers a design platform for non-covalent tethering of a ubiquitin-based proteolytic modifier to be added in the molecular toolbox for the targeted protein degradation.
    DOI:  https://doi.org/10.1038/s42004-026-01895-x
  6. MicroPubl Biol. 2026 ;2026
    Cultured cells activate IRE1 during attachment and flattening after routine passaging.
    Paige Dillon, Lincoln Hollingshead, Julie Hollien.
      During endoplasmic reticulum (ER) stress, the ER membrane protein IRE1 initiates the regulated splicing of Xbp1 mRNA, leading to the production of a potent transcription factor that helps cells restore proteostasis. We report that Xbp1 is also spliced following the routine passaging of mouse MC3T3-E1 cells, without the addition of canonical ER stressors. This splicing was independent of the type of dissociation buffer used to release cells from the surface, but was reduced when cells were plated on non-adherent culture dishes. These findings suggest that certain cultured mammalian cells induce an unfolded protein response during reattachment and spreading after passaging.
    DOI:  https://doi.org/10.17912/micropub.biology.001968
  7. iScience. 2026 Jan 16. 29(1): 114556
    Chronic stress antagonizes formation of stress granules.
    Yuichiro Adachi, Allison M Williams, Masashi Masuda, Yutaka Taketani, Paul J Anderson, Pavel Ivanov.
      Stress granules (SGs) are cytoplasmic ribonucleoprotein condensates formed in response to stress-induced inhibition of mRNA translation and polysome disassembly. Despite the broad interest in SG assembly and disassembly in response to acute stress, SG dynamics under chronic stress has not been extensively investigated. We show that cells pre-conditioned with low-dose chronic (24 h exposure) stresses of various natures fail to assemble SGs in response to acute stress. While protein synthesis is drastically decreased by acute stress in pre-conditioned cells, polysome profiling analysis reveals the partial preservation of polysomes. Mechanistically, chronic stress slows down the rate of mRNA translation at the elongation phase, and triggers phosphorylation of translation elongation factor eEF2. These events further promote ribosome stalling, which is distinct from ribosome collisions known to trigger ribosome-associated quality-control pathways. In summary, chronic stress triggers ribosome stalling, which prevents efficient polysome disassembly and SG formation by subsequent acute stress.
    Keywords:  biochemistry; cell biology
    DOI:  https://doi.org/10.1016/j.isci.2025.114556
  8. Autophagy. 2026 Jan 28. 1-15
    Deubiquitinase USP15 restricts LC3-dependent targeting of Mycobacterium tuberculosis.
    Kathryn C Rahlwes, Priscila C Campos, Beatriz R S Dias, Paola K Párraga Solórzano, Michael U Shiloh.
      Macroautophagy/autophagy enables macrophages to degrade intracellular Mycobacterium tuberculosis (Mtb), and this defense depends on E3 ubiquitin ligases such as PRKN/PARKIN/PARK2 and SMURF1, which tag Mtb-associated structures for lysosomal clearance. Deubiquitinases (DUBs) counter ubiquitin ligases by removing ubiquitin from molecular targets. We hypothesized that DUBs might offset ubiquitin ligase activity and negatively regulate host immunity to Mtb. Here, we identify USP15 (ubiquitin specific peptidase 15) as a negative regulator of MAP1LC3/LC3-dependent targeting pathways (consistent with xenophagy or CASM/LAP-related ATG8ylation) that mediate macrophage immunity to Mtb. Using a targeted knockdown screen in mouse macrophages, we found that Usp15 loss increased K63-linked ubiquitination and LC3 recruitment to Mtb-associated structures, leading to reduced bacterial replication. These effects required USP15's catalytic activity and were reversed by knockdown of PRKN or inhibition of autophagy initiation. In primary human macrophages, USP15 knockdown similarly enhanced LC3 targeting and restricted Mtb growth. Importantly, pharmacological inhibition of USP15 with a selective small molecule decreased Mtb burden in human macrophages. Our findings identify USP15 as a suppressor of macrophage immunity and suggest that targeting deubiquitinases may represent a promising host-directed therapeutic strategy against tuberculosis.Abbreviations: CFU: colony-forming unit; DUBs: deubiquitinases; K48-Ub: K48-linked ubiquitin; K63-Ub: K63-linked ubiquitin; Mtb-pLux: luminescent Mtb strain Mtb; Mycobacterium tuberculosis; MOI: multiplicity of infection; NTC: non-targeting control; TB: tuberculosis.
    Keywords:  Deubiquitinase; host-directed therapy; innate immunity; tuberculosis; ubiquitin; xenophagy
    DOI:  https://doi.org/10.1080/15548627.2026.2618632
  9. FEBS J. 2026 Jan 29.
    ER proteostasis meets mitochondrial function: contact sites as hubs of communication and therapeutic targets.
    Giorgia Maria Renna, Alessandro Cherubini, Ersilia Varone, Serena Germani, Alice Marrazza, Ester Zito.
      Proteostasis maintains the balance between protein synthesis, folding, and degradation within the endoplasmic reticulum (ER). This quality-control system ensures that proteins undergo proper post-translational modifications-such as PDI-ERO1-mediated oxidative folding and STT3-dependent N-glycosylation-so that only correctly folded proteins proceed through the secretory pathway. Impairment of protein load, folding capacity, or degradation via the ER-associated degradation (ERAD) pathway leads to the accumulation of unfolded proteins, triggering ER stress and activating the unfolded protein response (UPR), which, in the first instance, is an adaptive signaling network designed to restore homeostasis by adjusting protein synthesis, enhancing folding capacity, and promoting the clearance of misfolded proteins. During ER stress, the ER undergoes morphological and functional remodeling to manage the increased folding burden, including an increase of ER-mitochondria contact sites (ERMCs). These nanometric junctions (~10-100 nm) facilitate lipid and metabolite exchange and mediate calcium and reactive oxygen species signaling to support cellular metabolism. However, chronic ER stress can further tighten ERMCs, leading to calcium overload, mitochondrial dysfunction, and apoptosis. This review examines the core mechanisms underlying ER proteostasis in the context of ER stress and explores how ER stress first boosts mitochondrial activity and later impairs it through ERMCs, contributing to cell death and disease. Finally, emerging therapeutic strategies aimed at restoring proteostasis and modulating the dynamics of ERMCs are highlighted as promising interventions for conditions, such as cancer and congenital myopathies, where ER and mitochondrial dysfunction play central roles in pathogenesis.
    Keywords:  ERMC; cancer; mitochondria metabolism; neuromuscular diseases; proteostasis
    DOI:  https://doi.org/10.1111/febs.70431
  10. Cell. 2026 Jan 28. pii: S0092-8674(25)01487-4. [Epub ahead of print]
    CRISPR screens in iPSC-derived neurons reveal principles of tau proteostasis.
    Avi J Samelson, Nabeela Ariqat, Justin McKetney, Gita Rohanitazangi, Celeste Parra Bravo, Rudra S Bose, Kyle J Travaglini, Victor L Lam, Darrin Goodness, Thomas Ta, Gary Dixon, Emily Marzette, Julianne Jin, Ruilin Tian, Eric Tse, Romany Abskharon, Henry S Pan, Emma C Carroll, Rosalie E Lawrence, Jason E Gestwicki, Jessica E Rexach, David S Eisenberg, Nicholas M Kanaan, Daniel R Southworth, John D Gross, Li Gan, Danielle L Swaney, Martin Kampmann.
      Aggregation of the protein tau defines tauopathies, the most common age-related neurodegenerative diseases, which include Alzheimer's disease and frontotemporal dementia. Specific neuronal subtypes are selectively vulnerable to tau aggregation, dysfunction, and death. However, molecular mechanisms underlying cell-type-selective vulnerability are unknown. To systematically uncover the cellular factors controlling the accumulation of tau aggregates in human neurons, we conducted a genome-wide CRISPRi screen in induced pluripotent stem cell (iPSC)-derived neurons. The screen uncovered both known and unexpected pathways, including UFMylation and GPI anchor biosynthesis, which control tau oligomer levels. We discovered that the E3 ubiquitin ligase CRL5SOCS4 controls tau levels in human neurons, ubiquitinates tau, and is correlated with resilience to tauopathies in human disease. Disruption of mitochondrial function promotes proteasomal misprocessing of tau, generating disease-relevant tau proteolytic fragments and changing tau aggregation in vitro. These results systematically reveal principles of tau proteostasis in human neurons and suggest potential therapeutic targets for tauopathies.
    Keywords:  CRISPR screen; CUL5; SOCS4; neurodegeneration; protein aggregation; proteostasis; tau
    DOI:  https://doi.org/10.1016/j.cell.2025.12.038
  11. Proc Natl Acad Sci U S A. 2026 Feb 03. 123(5): e2532504123
    Coordination of cell organelles to promote metabolon formation.
    Zhou Sha, Anthony M Pedley, Timothy D Iles, Shaoqing Zhang, Jack R Staub, Ruobo Zhou, Stephen J Benkovic.
      The spatial coordination between cellular organelles and metabolic enzyme assemblies represents a fundamental mechanism for maintaining metabolic efficiency under stress. While previous work has shown that membrane-bound organelles regulate metabolic activities and that membrane-less condensates conduct metabolic reactions, the coordination between these two organizations remains unaddressed. By using a combination of proximity labeling, superresolution fluorescence microscopy, and metabolite analyses using isotopic tracing, we investigated the relationships between these metabolic hotspots. Here, we show that nutrient deficiency elongates mitochondria and transforms the ER from a tubular to sheet-like morphology, coinciding with increased mitochondrial respiration and inosine 5'-monophosphate levels. These structural changes promote the colocalization of purinosomes with these organelles, enhancing metabolic channeling. Disruption of ER sheet formation via MTM1 knockout destabilizes purinosomes, impairs substrate channeling, and reduces intracellular purine nucleotide pools without altering enzyme expression. Our findings reveal that organelle morphology and interorganelle contacts dynamically regulate the assembly and function of metabolic condensates, providing a structural basis for coordinated metabolic control in response to nutrient availability.
    Keywords:  biomolecular condensates; cell metabolism; de novo purine biosynthesis; metabolon; purine
    DOI:  https://doi.org/10.1073/pnas.2532504123
  12. J Biol Chem. 2026 Jan 23. pii: S0021-9258(26)00066-9. [Epub ahead of print] 111196
    A disease-causing Isoleucyl-tRNA synthetase variant leads to altered protein complex formation and cellular stress response.
    Han Gao, Rasangi Tennakoon, Felicia Pais Araújo, Jolie M Miller, Samuel Protais Nyandwi, Qingyu Shi, Juan Pablo Padilla-Martínez, Hui Peng, Haissi Cui.
      Aminoacyl-tRNA synthetases are key enzymes in protein synthesis, as they catalyze the attachment of amino acids to their designated, cognate tRNAs. As such, mutations in aminoacyl-tRNA synthetases are associated with severe diseases, such as neurodevelopmental disorders. Many of these mutations occur in the catalytically active site or tRNA binding domains, however, others can affect domains associated with multisynthetase complex formation. Here, we investigate a disease-causing mutation in the UNE-I domain of Isoleucyl-tRNA synthetase (IARS1, IleRS), which mediates IleRS interactions within the multisynthetase complex. Interestingly, levels of the resulting protein were severely reduced in comparison to wildtype IleRS. While bulk protein synthesis and cell proliferation were not affected, the integrated stress response signaling pathway was altered. This change was exacerbated in low glucose medium, suggesting that mutant cells could respond differently to cellular stress. Our study hints at a possible underlying disease mechanism, where catalytic activity might not be affected but instead complex formation and protein stability.
    Keywords:  aminoacyl-tRNA synthetase; integrated stress response; mulitsynthetase complex; neurodevelopmental disorder; tRNA
    DOI:  https://doi.org/10.1016/j.jbc.2026.111196
  13. Life Sci. 2026 Jan 22. pii: S0024-3205(26)00032-9. [Epub ahead of print] 124224
    Reversible ubiquitination regulates HSF1 phase separation in response to proteotoxic stress.
    Yue Zhu, Jianhua Wang, Shuhong Tang, Zhiqiang Li, Ruilin Wang, Peng Wang, Jiayu Li, Shaoxuan Cheng, Han Liu, Yingqiu Zhang, Zhaoxia Dai, Qitao Yan, Shuyan Liu.
       AIMS: Heat shock factor 1 (HSF1) undergoes phase separation to form nuclear condensates in response to proteotoxic stress, which governs cell fate. Protein ubiquitination is a widely existed post-translational modification and closely participated in liquid-liquid phase separation. However, the exact roles of ubiquitination in HSF1 condensation remain obscure. Here, we aimed to investigate the regulation of HSF1 phase separation by ubiquitination in cells under proteotoxic conditions.
    MATERIALS AND METHODS: Endogenous and exogenous HSF1 condensate formation was detected by immunofluorescence assays. HSF1 phase separation properties were analyzed by fluorescence recovery after photobleaching (FRAP) analysis. Western blotting, immunofluorescence, immunoprecipitation and co-transfection assays were performed to identify E3 ubiquitin ligases and deubiquitinating enzymes (DUBs) regulating HSF1 phase separation. The influence of ubiquitination sites on HSF1 phase separation was investigated by site-directed mutagenesis.
    KEY FINDINGS: Proteasome inhibitor PS341 induced HSF1 to form nuclear phase-separated condensates in a time-dependent manner. E3 ubiquitin ligase STUB1 promoted the phase separation of HSF1 by enhancing HSF1 ubiquitination, while DUBs USP13 and ATXN3 negatively regulated HSF1 condensation. Mutations of all nine ubiquitination sites within HSF1 dramatically inhibited condensate formation, with single-site mutations also showing significantly attenuated phase separation.
    SIGNIFICANCE: Ubiquitination at multiple lysine residues jointly drives HSF1 phase separation in cells exposed to proteotoxic stress, which is coordinately regulated by E3 ubiquitin ligase STUB1 and DUBs including USP13 and ATXN3.
    Keywords:  Deubiquitinating enzyme; E3 ligase; HSF1; Phase separation; Proteotoxic stress; Ubiquitination
    DOI:  https://doi.org/10.1016/j.lfs.2026.124224
  14. JACS Au. 2026 Jan 26. 6(1): 144-153
    Aptamer-Mediated Covalent Dual Lysosome-Targeting Chimeras Enhance Targeted Degradation of Cell Surface Proteins.
    Tao Peng, Min Su, Zuying Zhang, Ya Wang, Yingdi Zhu, Juan Li.
      Aptamer-based lysosome-targeting chimeras (Apt-LYTACs) have emerged as a promising strategy for the selective degradation of cell surface proteins by linking a target-specific aptamer to a lysosome-trafficking receptor ligand. However, their degradation efficiency is often limited by weak noncovalent interactions, heterogeneous receptor distribution, and the constraints of a 1:1 complex stoichiometry. To address these challenges, we developed aptamer-mediated covalent dual lysosome-targeting chimeras (Apt-cdLYTACs), which enable specific covalent anchoring to the protein of interest with spatiotemporal control by combining the specificity of aptamer recognition with proximity-induced photoreactive cross-linking. These chimeras incorporate two lysosomal receptor ligands to enhance the local avidity and promote multivalent complex formation. Compared to conventional noncovalent or single-ligand covalent Apt-LYTAC, Apt-cdLYTAC forms more stable degradation complexes, exhibits prolonged intracellular retention, and reduces efflux, thereby significantly improving degradation efficiency. Apt-cdLYTAC provides a modular, efficient, and user-friendly platform for the selective degradation of membrane proteins, with broad potential for applications in biochemical research and therapeutic development.
    Keywords:  LYTAC; aptamer; covalent; dual lysosome-targeting ligand; targeted protein degradation
    DOI:  https://doi.org/10.1021/jacsau.5c00978
  15. Nat Commun. 2026 Jan 27. 17(1): 1064
    Cryo-EM structures of human ClpXP reveal mechanisms of assembly and proteolytic activation.
    Wenqian Chen, Gabriel C Lander, Jie Yang.
      The human ClpXP complex (hClpXP) orchestrates mitochondrial protein quality control through targeted degradation of misfolded and unnecessary proteins. While bacterial ClpXP systems are well characterized, the assembly and regulation of human ClpXP remain poorly understood. In this study, we elucidate the complete assembly pathway of hClpXP through high-resolution cryo-electron microscopy (cryo-EM) structures. Our findings confirm that hClpP exists as a single-ring heptamer in isolation and reveal a previously undocumented initial assembly complex in which hexameric hClpX first engages with heptameric hClpP. We further demonstrate how this interaction drives substantial conformational rearrangements that facilitate the formation of tetradecameric hClpP within the fully assembled complex. Notably, we characterize a unique eukaryotic sequence in hClpX, termed the E-loop, which plays a critical role in stabilizing hexamer assembly and maintaining ATPase activity. Additionally, we show that peptide binding at the hClpP active site triggers further structural changes essential for achieving full proteolytic competence. Together, these structures provide unprecedented mechanistic insights into the stepwise assembly and activation of hClpXP, significantly advancing our understanding of this essential mitochondrial protein degradation machinery.
    DOI:  https://doi.org/10.1038/s41467-025-67010-1
  16. Mol Cell. 2026 Jan 28. pii: S1097-2765(26)00031-6. [Epub ahead of print]
    Lysosomes as hubs of metabolic sensing and cellular homeostasis.
    Aakriti Jain, Roberto Zoncu.
      Lysosomes are hubs that couple macromolecular breakdown to cell-wide signaling by sensing metabolic, damage-associated, and environmental cues. Nutrients liberated in the lysosomal lumen as end-products of macromolecular degradation, including amino acids, lipids, and iron, are exported by dedicated transporters for utilization in the cytoplasm. Nutrient transport across the lysosomal membrane is coupled to its sensing by specialized signaling complexes on the cytoplasmic face, which, in response, mediate communication with other organelles and control cell-wide programs for growth, catabolism, and stress response. Lysosomes acquire specialized sensing-signaling features in immune cells, where they shape antigen processing, innate immune signaling, and inflammatory cell death, and in neurons, where they act as sentinels of proteostatic and mitochondrial stress, supporting local translation, organelle quality control, and neuroimmune crosstalk. We highlight recently identified pathways and players that position lysosomes as integrators of nutrient status and organelle health to drive tissue-specific physiology.
    Keywords:  amyloid; autophagy; inflammation; lysosome; mTORC1; metabolites; neurodegeneration; organelle contacts; signaling
    DOI:  https://doi.org/10.1016/j.molcel.2026.01.011
  17. J Cell Biol. 2026 Apr 06. pii: e202502035. [Epub ahead of print]225(4):
    Landscape expansion microscopy reveals interactions between membrane and phase-separated organelles.
    Yinyin Zhuang, Zhao Zhang, Zhipeng Dai, Xiaoyu Shi.
      Landscape expansion microscopy (land-ExM) is a light microscopy technique that visualizes both the lipid and protein ultrastructural context of cells. Achieving this level of detail requires both superresolution and a high signal-to-noise ratio. Although expansion microscopy (ExM) provides superresolution, obtaining high signal-to-noise images of both proteins and lipids remains challenging. land-ExM overcomes this limitation by using self-retention trifunctional anchors to significantly enhance protein and lipid signals in expanded samples. This improvement enables the accurate visualization of diverse membrane organelles and phase separations, as well as the 3D visualization of their contact sites. As a demonstration, we revealed triple-organellar contact sites among the stress granule, the nuclear tunnel, and the nucleolus. Overall, land-ExM offers a high-contrast superresolution platform that advances our understanding of how cells spatially coordinate interactions between membrane organelles and phase separations.
    DOI:  https://doi.org/10.1083/jcb.202502035
  18. J Biol Chem. 2026 Jan 23. pii: S0021-9258(26)00069-4. [Epub ahead of print] 111199
    Engineering an orthogonal ubiquitin transfer cascade with Ring E3 RNF38 by phage display to reveal its regulation of nuclear transport.
    Li Zhou, In Ho Jeong, Hang Li, Nicolas Rios, Jing Zhang, Xiaoyu Wang, Shu Liu, Yayun Xie, Wei Wei, Geon H Jeong, Duc Duong, Nicholas T Seyfried, Bingzhong Xue, Hang Shi, Angela M Mabb, Yiyang Wang, Hiroaki Kiyokawa, Jun Yin.
      Ring E3 ubiquitin (UB) ligases rely on signature Ring domains for mediating UB transfer to substrate proteins. The large number of Ring E3s and their weak association with substrates pose a significant challenge in identifying the substrates of individual E3s, thereby hindering the elucidation of their biological functions. Here, we utilized phage display to engineer an "orthogonal UB transfer" (OUT) cascade with Ring E3 RNF38, enabling the exclusive transfer of an engineered UB (xUB) to its substrates in the cell. The OUT screen revealed RNF38 substrates regulating nucleocytoplasmic transport (Ran, RanGAP1, and KPNA2), protein translation (HuR and Rack1), and endosomal sorting (VPS35). Furthermore, RNF38-catalyzed ubiquitination was found to induce the degradation of the substrate proteins and negatively affect the translocation of transcription factors E2F1 and phosphorylated STAT3 (p-STAT3) into the nucleus. Phage selection of the RNF38 Ring library also revealed hotspot residues for E2 interaction, which may guide the engineering of orthogonal E2-E3 pairs with other Ring E3s. Overall, our work discovered new roles of RNF38 in regulating nuclear transport and established an anchoring point for expanding OUT cascades within the large family of Ring E3s for revealing their UB transfer targets and cellular functions.
    Keywords:  E3 ubiquitin ligase; Ring domain; Ubiquitin; phage display; protein engineering
    DOI:  https://doi.org/10.1016/j.jbc.2026.111199
  19. J Mol Biol. 2026 Jan 23. pii: S0022-2836(26)00026-4. [Epub ahead of print] 169653
    The Liver-Enriched Long Non-Coding RNA FAM99A Suppresses Tumorigenesis through Negative Regulation of Protein Synthesis.
    Nima Sarfaraz, Ranjit Kaur, Sky Harper, Lilly Oni, Srinivas Somarowthu, Michael J Bouchard.
      Primary liver cancer represents a significant global health burden, with limited therapeutic options for advanced disease. Long non-coding RNAs (lncRNAs) are increasingly found to play crucial roles in hepatic biology and disease progression. Here, we identify FAM99A as a highly liver-enriched lncRNA that is systematically downregulated across liver malignancies, with reduced expression correlating with poor clinical outcomes. FAM99A exhibits remarkable tissue specificity with minimal expression outside the liver, and its levels rapidly decline during primary hepatocyte dedifferentiation in culture. Through isoform analysis, we establish FAM99A-203 as the predominant transcript in normal liver tissue and observe altered isoform distribution in liver cancers. Functionally, FAM99A overexpression inhibits anchorage-independent growth in liver cancer cell lines. Transcriptomic analysis reveals that FAM99A negatively regulates translation-related pathways in both liver cancer cells and primary hepatocytes. This is corroborated by protein synthesis assays showing that FAM99A overexpression substantially reduces global translation rates. Targeted RNase H-mediated extraction coupled with mass spectrometry identifies multiple components of the translation machinery as direct FAM99A binding partners, including eukaryotic translation initiation factors and RNA helicases involved in ribosome biogenesis. Clinical data analysis demonstrates significant inverse correlations between FAM99A expression and ribosomal protein genes in liver cancer patients. Additionally, hepatitis B virus appears to downregulate FAM99A expression, potentially contributing to its oncogenic properties. Our findings establish FAM99A as a liver-enriched translational regulator that exerts tumor-suppressive effects by restraining protein synthesis rates, offering insights into hepatocarcinogenesis and the potential of FAM99A as both a biomarker and agent in new therapeutic avenues.
    Keywords:  FAM99A; Hepatocellular Carcinoma; Liver Cancer; LncRNA; Ribosome; Translation; Tumor Suppressor
    DOI:  https://doi.org/10.1016/j.jmb.2026.169653
  20. Nat Commun. 2026 Jan 27.
    Ether lipids influence cancer cell fate by modulating iron uptake.
    Ryan P Mansell, Sebastian Müller, Jia-Shu Yang, Sarah Innes-Gold, Sunny Das, Ferenc Reinhardt, Kim Janina Sigmund, Vaishnavi V Phadnis, Zhengpeng Wan, Jillian Stark, Daehee Hwang, Fabien Sindikubwabo, Laurène Syx, Nicolas Servant, Elinor Ng Eaton, Julio L Sampaio, George W Bell, Prathapan Thiru, Amartya Viravalli, Amy Deik, Clary B Clish, Paula T Hammond, Roger D Kamm, Adam E Cohen, Ilya Levental, Natalie Boehnke, Victor W Hsu, Kandice R Levental, Raphaël Rodriguez, Robert A Weinberg, Whitney S Henry.
      Cancer cell fate has been widely ascribed to mutational changes within protein-coding genes associated with tumor suppressors and oncogenes. In contrast, the mechanisms through which the biophysical properties of membrane lipids influence cancer cell survival, dedifferentiation and metastasis have received little scrutiny. Here, we report that cancer cells endowed with high metastatic ability and cancer stem cell-like traits employ ether lipids to maintain low membrane tension and high membrane fluidity. Using genetic approaches and lipid reconstitution assays, we show that these ether lipid-regulated biophysical properties permit non-clathrin-mediated iron endocytosis via CD44, resulting in significant increases in intracellular redox-active iron and enhanced ferroptosis susceptibility. Using a combination of in vitro three-dimensional microvascular network systems and in vivo animal models, we show that loss of ether lipids from plasma membranes also strongly attenuates extravasation, metastatic burden and cancer stemness. These findings illuminate a mechanism whereby ether lipids in carcinoma cells serve as key regulators of malignant progression while conferring a unique vulnerability that can be exploited for therapeutic intervention.
    DOI:  https://doi.org/10.1038/s41467-026-68547-5
  21. Nat Commun. 2026 Jan 30.
    Association-induced folding governs surrogate light chain and pre-B cell receptor core assembly.
    Jasmin König, Natalia Catalina Sarmiento Alam, Ruiming He, Nicolas Blömeke, Olga Sieluzycka, Florian Rührnößl, Maximilian Riedl, Bernd Reif, Matthias J Feige, Johannes Buchner.
      Binding of the surrogate light chain (SLC) to the heavy chain (HC) of the pre-B cell receptor (preBCR) is an important quality control checkpoint during B cell development as roughly 50% of the rearranged HCs are defective. Unlike the regular light chain (LC), the SLC is a hetero-dimer of VpreB and λ5, both containing unstructured extensions, the unique regions. The molecular mechanisms that underlie the complex assembly processes which give rise to the final pre-BCR is not fully understood. Here we show, via reconstitution of the pre-BCR in vitro and in cells that λ5 plays a key role in the pre-BCR assembly. During SLC assembly, a β-strand, located between the λ5 domain and the unique region, induces structure in the largely unfolded VpreB, creating a high affinity complex. In addition, association of λ5 with the unstructured HC CH1 domain is required for its folding. This is essential for pre-BCR assembly and its release from the endoplasmic reticulum (ER). Finally, the unique region of λ5 plays a pivotal role in the antigen interaction of the SLC-HC complex. Together, our results reveal a multi-step mechanism for SLC and pre-BCR assembly, governed by association-induced folding reactions required for structural integrity and function.
    DOI:  https://doi.org/10.1038/s41467-026-68965-5
  22. Cell. 2026 Jan 28. pii: S0092-8674(25)01479-5. [Epub ahead of print]
    Mechanistic insights into RNA chaperoning by Ro60 and La autoantigens.
    Hyeyeon Nam, Justin C Deme, Soyeong Sim, Marco Boccitto, Susan M Lea, Sandra L Wolin.
      Although ATP-independent chaperones assist RNA folding, the mechanisms by which they function remain elusive. Here, we demonstrate how two RNA chaperones collaborate to unfold misfolded noncoding RNAs (ncRNAs). The ring-shaped Ro60 protein binds the ends of misfolded ncRNAs in its cavity, whereas La stabilizes nascent ncRNAs and assists their folding. Using cryo-electron microscopy to resolve the structure of a misfolded RNA complexed with Ro60 and La, we show that La cradles the Ro60 ribonucleoprotein (RNP), with its N-terminal domain binding the RNA 3' end after it passes through the Ro60 cavity, while its C-terminal domain destabilizes structures in the misfolded RNA body. Using selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP), we show that La and Ro60 function synergistically to unfold non-native structures. As the RNAs bound by Ro60 and La include both ncRNA precursors and ncRNAs with oligouridine tails, this RNA chaperone machine may function widely to recognize misfolded and otherwise aberrant ncRNAs and assist their unfolding.
    Keywords:  La autoantigen; RNA chaperones; RNA folding; Ro60 autoantigen; conformational flexibility
    DOI:  https://doi.org/10.1016/j.cell.2025.12.030
  23. Open Biol. 2026 Jan 28. pii: 250331. [Epub ahead of print]16(1):
    Building a functional endoplasmic reticulum for proper cell growth and stress responses: a plant perspective.
    Weina Wang, Huanquan Zheng.
      The endoplasmic reticulum (ER) is an interconnected network of membrane-bound tubules and sheets stretching throughout the cytoplasm of all eukaryotic cells including plant cells. The ER is highly dynamic and undergoes constant remodelling. A properly formed ER is essential for cell growth, development and cellular responses to stresses. It is known that the dynamics of the cytoskeleton is linked to the formation and/or remodelling of a functional ER. Over the past 20 years, research has revealed that a set of ER localized ER-shaping proteins play crucial roles in building a functional ER. Recent research also indicates that maintaining a functional ER, in particular under stressful conditions, requires a proper turnover of the ER mediated by selective autophagy of the ER. In this review, we discuss the current understanding of functions of reticulons and atlastins, two classes of ER-shaping proteins in the formation of the ER in both animal and plant cells, with an emphasis on the plant system. We also discuss how the two classes of proteins may interplay to maintain a proper ER and how their actions may be regulated. Finally, we briefly mention how autophagy of the ER may be regulated during cell development and stress responses.
    Keywords:  ER-phagy; ER-phagy receptors; Lunapark; RHD3; atlastins; endoplasmic reticulum; polarized cell growth; reticulons; stress responses
    DOI:  https://doi.org/10.1098/rsob.250331
  24. Adv Sci (Weinh). 2026 Jan 27. e14970
    Chloroplast Stress Signals Orchestrate Epidermis-Specific Remodeling of Mitochondria and ER Under High Light.
    Evan R Angelos, Hee-Seung Choi, Jingzhe Guo, Andrea A Zanini, Tessa M Burch-Smith, Emily Snyder, Matthew Part, Wilhelmina van de Ven, Manhoi Hur, Gerd Ulrich Balcke, Alain Tissier, Quanqing Zhang, Katayoon Dehesh.
      Environmental stress demands precise coordination among organelles to maintain cellular homeostasis. In Arabidopsis, high light (HL) exposure triggers chloroplast-dependent remodeling of mitochondrial and endoplasmic reticulum (ER) morphology specifically in adaxial and abaxial epidermal cells, but not in mesophyll cells. Live-cell imaging reveals that HL rapidly suppresses mitochondrial motility, followed by fusion-driven elongation and ER cisternal expansion. Inhibition of photosynthetic, but not mitochondrial, electron transport abolishes these changes, confirming chloroplast activity as the upstream trigger. Pharmacological analyses show that exogenous H2O2 induces mitochondrial elongation, whereas calcium chelation blocks both H2O2- and HL-induced responses, demonstrating that chloroplast-derived H2O2 activates a Ca2 + flux essential for remodeling. Proteomic and functional studies identify the Ca2 +-binding GTPase MIRO1 as a central integrator of this pathway. MIRO1 overexpression mimics HL-induced morphodynamics, while mutations disrupting its Ca2 +-binding or acetylation motifs abolish the response, establishing Ca2 +-dependent MIRO1 activity as a prerequisite for remodeling. Together, these findings reveal an epidermis-specific, light-responsive network in which chloroplast-derived H2O2 initiates Ca2 + signaling through MIRO1 to coordinate mitochondrial and ER remodeling-a spatially restricted mechanism of organellar communication and stress adaptation at the plant-environment interface.
    Keywords:  Miro1; chloroplast signaling; epidermal organelle dynamics; high light stress; mitochondrial‐ER remodeling; organelle plasticity
    DOI:  https://doi.org/10.1002/advs.202514970
  25. Biochim Biophys Acta Mol Cell Res. 2026 Jan 23. pii: S0167-4889(26)00012-1. [Epub ahead of print]1873(3): 120116
    The dual face of reprogrammed proteostasis in cancer and its epigenetic regulation: A survival option and a therapeutic opportunity.
    Mara Cirone.
      Proteostasis is essential for cellular homeostasis and is maintained through an integrated network encompassing the unfolded protein response (UPR), molecular chaperones such as heat shock proteins (HSPs), and degradative systems including the ubiquitin-proteasome and autophagy-lysosomal pathways. In cancer, microenvironmental stresses such as hypoxia, nutrient deprivation, and oxidative imbalance impose a persistent proteotoxic burden, driving a context-dependent rewiring of these pathways that supports tumor survival, plasticity, and progression. Increasing evidence indicates that the functional outcomes of proteostasis responses, whether adaptive or cytotoxic, are determined by specific molecular cues, including the intensity and duration of stress, pathway crosstalk, and cell-intrinsic oncogenic alterations. Epigenetic mechanisms, comprising DNA methylation, histone modifications, and non-coding RNAs, further fine-tune these proteostatic programs by modulating the expression and activity of key regulators, thereby contributing to drug resistance but also generating cancer-selective vulnerabilities. This review provides a structured and mechanistic overview of how UPR, chaperone networks, and protein degradation pathways are remodeled in cancer and examines the epigenetic determinants that shape their adaptive behavior. Finally, we discuss emerging translational opportunities arising from the dual role of proteostasis in cancer, highlighting therapeutic strategies that exploit the dynamic interplay between proteostatic and epigenetic regulation.
    Keywords:  Autophagy; Cancer; Epigenetics; HSPs; UPR; UPS
    DOI:  https://doi.org/10.1016/j.bbamcr.2026.120116
  26. ACS Chem Biol. 2026 Jan 25.
    TRIM9 and TRIM26 Interact with UBQLN2P497H to Modulate Its Proteasomal Degradation.
    Xingyuan Chen, Zhongwen Cao, Xiaochen Liang, Ting Zhao, Yinsheng Wang.
      Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder characterized by progressive motor neuron loss. ALS-linked mutations in UBQLN2 promote protein aggregation and disrupt proteostasis, yet the mutation-specific protein interactomes and their functional relevance remain poorly defined. We employed APEX2 proximity labeling, together with affinity enrichment of biotinylated peptides and LC-MS/MS analysis, to profile the interactomes of wild-type UBQLN2 and two ALS-linked variants, UBQLN2P497H and UBQLN2P497S. We identified 785 unique biotinylated proteins, many of which exhibit augmented enrichment in the proximity proteomes of the two mutants over wild-type UBQLN2. Notably, the E3 ubiquitin ligases TRIM9 and TRIM26 were selectively enriched in the proximity proteome of UBQLN2P497H, which we validated by coimmunoprecipitation followed by Western blot analysis. Fractionation analysis revealed coaccumulation of TRIM9 and TRIM26 with UBQLN2P497H in the insoluble fraction, consistent with its heightened aggregation propensity. Treatment of UBQLN2P497H-expressing cells with a proteasomal inhibitor led to elevated accumulation of a C-terminal UBQLN2 fragment that is absent in cells expressing wild-type UBQLN2 or its P497S mutant. Individual knockdown of TRIM9 and TRIM26 significantly increased the abundance of the fragment, establishing UBQLN2P497H as a substrate for TRIM9- and TRIM26-mediated ubiquitinylation and subsequent proteasomal degradation. These findings nominate TRIM9 and TRIM26 as specific interactors of UBQLN2P497H and as regulators of a previously underexplored C-terminal UBQLN2 fragment, suggesting that impaired clearance of this species may contribute to ALS pathogenesis.
    DOI:  https://doi.org/10.1021/acschembio.5c00911
  27. Mol Cell. 2026 Jan 28. pii: S1097-2765(26)00021-3. [Epub ahead of print]
    Mito-nuclear communication: From cellular responses to organismal health.
    Guanyu Chen, Hangyu Dong, Ye Tian.
      The co-evolution of mitochondria and the nucleus established constant mito-nuclear communication that is essential for both cellular and organismal homeostasis. At the cell-autonomous level, mitochondrial perturbations activate retrograde pathways such as the mitochondrial unfolded protein response (UPRmt) and the mitochondrial integrated stress response (ISRmt), which couple organelle dysfunction to nuclear transcriptional programs, thereby promoting mitochondrial function and preserving cellular integrity. Importantly, this communication is not confined to individual cells but extends across tissues to coordinate systemic adaptations. Stress signals can be sensed, broadcasted through secreted mitokines and neural circuits, and then interpreted by distal organs to coordinate systemic adaptations. These systemic responses integrate metabolism, immunity, and behavior, conferring resilience to stress and shaping the trajectory of aging. Understanding this multi-layered communication, from the organelle to the organism and its microbial ecosystem, promises new therapeutic strategies to enhance mitochondrial function, promote resilience, and extend healthspan.
    Keywords:  ISRmt; UPRmt; aging; mito-nuclear communication; mitokine; proteostasis
    DOI:  https://doi.org/10.1016/j.molcel.2026.01.001
  28. Nat Chem. 2026 Jan 29.
    Biomolecular condensates sustain pH gradients at equilibrium through charge neutralization.
    Hannes Ausserwöger, Rob Scrutton, Charlotte M Fischer, Tomas Sneideris, Daoyuan Qian, Ella de Csilléry, Ieva Baronaite, Kadi L Saar, Alan Z Białek, Marc Oeller, Georg Krainer, Titus M Franzmann, Sina Wittmann, Juan M Iglesias-Artola, Gaetano Invernizzi, Anthony A Hyman, Simon Alberti, Nikolai Lorenzen, Tuomas P J Knowles.
      Electrochemical gradients are essential to the functioning of cells and form across membranes using active transporters. Here we show in contrast that condensed biomolecular systems-often termed condensates-sustain pH gradients without any external energy input. By studying individual condensates on the micrometre scale using a microdroplet platform, we reveal dense-phase pH shifts towards conditions of minimal electrostatic repulsion. We demonstrate that protein condensates can drive substantial alkaline and acidic gradients, which are compositionally tunable and can extend to complex architectures sustaining multiple unique pH conditions simultaneously. Through in silico characterization of human proteomic condensate networks, we further highlight potential wide-ranging electrochemical properties emerging from condensation in nature, while correlating intracellular condensate pH gradients with complex biomolecular composition. Together, the emergent nature of condensation shapes distinct pH microenvironments, thereby creating a regulatory mechanism to modulate biochemical activity in living and artificial systems.
    DOI:  https://doi.org/10.1038/s41557-025-02039-9
  29. Redox Biol. 2026 Jan 16. pii: S2213-2317(26)00036-4. [Epub ahead of print]90 104038
    Context-specific Angiogenin-mediated tRNA fragments (tDRs) biogenesis shapes the mitochondrial stress response.
    Shadi Al-Mesitef, Daisuke Ando, Tomoya Saigasaki, Yuki Sakaguchi, Shunya Akagi, Abdulrahman Mousa, Sherif Rashad, Kuniyasu Niizuma.
      Transfer RNA-derived small RNAs (tDRs) are emerging regulators of cellular stress response, yet their biogenesis and activities during mitochondrial dysfunction remain poorly understood. Here we profiled tDRs generated in HEK293T cells exposed to inhibitors of respiratory complexes I-V (rotenone, TTFA, antimycin A, KCN, oligomycin) or to arsenite and assessed the impact of CRISPR-mediated angiogenin (ANG) knockout, ANG over-expression and recombinant ANG supplementation on the stress response and tDRs production. tDR-seq revealed stress-specific, highly ordered tDR repertoires: rotenone and antimycin predominantly induced internal (i-tRF) and 3' tRNA (tRF3) fragments, whereas arsenite induced anticodon-cleaved tRNA halves (tiRNAs). mito-tDRs were mostly internal fragments and antimycin induced the strongest mitochondrial tDRs expression. ANG deletion markedly impaired stress-induced tDR biogenesis and sensitized cells to antimycin and oligomycin stress, whereas its overexpression selectively enhanced tDR biogenesis and conferred protection against these mitochondrial stressor. Synthetic tDR mimics failed to rescue viability, implying that native modification patterns or cooperative tDR pools are required. tDR motif enrichment analysis identified YBX1-binding sites among antimycin-induced tDRs, and genetic perturbation of YBX1 phenocopied aspects of enhanced mitochondrial bioenergetics and stress resistance. Together, these findings demonstrate that context-specific, ANG-directed tDR biogenesis forms a crucial arm of the mitochondrial stress response.
    Keywords:  Angiogenin; Mitochondrial stress; RNA binding proteins; YBX1; tRNA; tRNA derived fragments
    DOI:  https://doi.org/10.1016/j.redox.2026.104038
  30. FEBS Open Bio. 2026 Jan 24.
    Meta-analysis fails to show any correlation between protein abundance and ubiquitination changes.
    Nerea Osinalde, Unai Alduntzin, Gorka Prieto, Ugo Mayor.
      Ubiquitination serves as a key regulatory mechanism in nearly all cellular processes, though it was originally identified as a post-translational modification that targets proteins for degradation. Accordingly, these two molecular events have since been tightly linked, and changes in protein abundance are frequently interpreted as indirect indicators of ubiquitination dynamics. Nevertheless, the relationship between protein abundance and ubiquitination has not been systematically examined across distinct biological systems. Here, we conducted a comprehensive meta-analysis to assess the correlation between protein abundance and ubiquitination levels determined by mass spectrometry in mammals, plants, and yeast. Quantitative proteomics and diGly-ubiquitin peptides data from 19 independent studies encompassing over 50 experimental conditions were analyzed. The findings indicate that alterations in protein abundance cannot reliably be used to infer ubiquitination events - and vice versa - highlighting the need for caution when interpreting proteomic data as a proxy for ubiquitin-mediated regulation.
    Keywords:  correlation; mass spectrometry; proteome; ubiquitome
    DOI:  https://doi.org/10.1002/2211-5463.70197
  31. Mol Cell. 2026 Jan 28. pii: S1097-2765(26)00027-4. [Epub ahead of print]
    Signaling to make human ribosomes: Connections between the cytoplasm and the nucleolus.
    Isabella R Lawrence, Emily C Sutton, Shivang Bhaskar, Susan J Baserga.
      Ribosome biogenesis is a complex, multi-step cellular process that begins in the nucleolus and produces ribosomes that translate mRNA into proteins in the cytoplasm. This process is essential for cellular growth yet is resource intensive. It is therefore tightly coordinated with cytoplasmic requirements, energy availability, and the cell cycle through several kinase signaling pathways. Increasing evidence indicates that proteins shared between the cytoplasm and nucleolus may enhance this coordination. Here, we evaluate the interplay between the cytoplasm and nucleolus in human cells, presenting an intricate bidirectional regulatory network with emerging clinical relevance. We describe the phosphorylation events that promote ribosome biogenesis during interphase, focusing on mammalian target of rapamycin complex 1 (mTORC1), extracellular signal-regulated kinase (ERK), and casein kinase II (CK2). By contrast, protein phosphorylation inactivates ribosome biogenesis during mitosis. We further summarize several factors shared among the mitotic machinery, cytoplasmic organelles, and the nucleolus. Moreover, we highlight the mounting evidence that dysregulated cytoplasmic-nucleolar feedback contributes to the progression of several diseases.
    Keywords:  cancer; endoplasmic reticulum; lysosome; mTOR; mitochondria; mitosis; muscle atrophy; rRNA; ribosome biogenesis; ribosomopathies
    DOI:  https://doi.org/10.1016/j.molcel.2026.01.007
  32. Plant Cell. 2026 Jan 27. pii: koag014. [Epub ahead of print]
    Sec62 restricts ER-replicating positive-strand RNA virus infections via UPR-dependent ER-phagy.
    Ruiqi Wang, Qianshen Zhang, Lifan Zhou, Dingliang Zhang, Yiping Wang, Xinyu Zhang, Xiuling Cao, Chenchen Zhong, Xiaofei Zhao, Meng Yang, Dawei Li, Xiaofeng Wang, Yongliang Zhang.
      Positive-strand RNA [(+)RNA] viruses induce endomembrane remodeling to form viral replication organelles (VROs), which disrupt organelle homeostasis. How hosts restore organelle homeostasis and how these responses influence viral replication remain elusive. Using beet black scorch virus (BBSV), a (+)RNA virus that replicates on the endoplasmic reticulum (ER) and induces severe deformation of ER membranes, as a model in Nicotiana benthamiana, we demonstrated that BBSV induces ER-phagy, primarily mediated by its auxiliary replication protein p23. p23 interacts with the ER-phagy receptor NbSec62, with phenylalanine at position 48 being critical for this interaction and ER-phagy induction. Upon BBSV infection, the unfolded protein response (UPR) is triggered to promote viral replication. However, the activation of the UPR also induces NbSec62-mediated ER-phagy to suppress BBSV replication. Furthermore, NbSec62 restricts other ER-replicating (+)RNA viruses, including tobacco mosaic virus and turnip mosaic virus. Our findings reveal NbSec62 as a restriction factor that interacts with BBSV VROs to regulate the balance of viral replication and ER homeostasis, providing insights into the UPR-ER-phagy signaling network in virus-host interactions.
    Keywords:  ER-phagy; Positive-strand RNA [(+)RNA] viruses; Sec62; beet black scorch virus (BBSV); endoplasmic reticulum (ER); replication; restriction factor; unfolded protein response (UPR)
    DOI:  https://doi.org/10.1093/plcell/koag014
  33. Nature. 2026 Jan 28.
    GlycoRNA complexed with heparan sulfate regulates VEGF-A signalling.
    Peiyuan Chai, Sina Kheiri, Andrew Kuo, Jessica Shah, Lauren Kageler, Ruiqi Ge, Jonathan Perr, Jennifer Porat, Charlotta G Lebedenko, Joao M L Dias, Eliza Yankova, Sandeep K Rai, Christopher P Watkins, Petar Hristov, Konstantinos Tzelepis, Timothy Hla, Ritu Raman, Eliezer Calo, Jeffrey D Esko, Ryan A Flynn.
      Heparan sulfate proteoglycans (HSPGs) have been recognized as key plasma membrane-tethered co-receptors for a broad range of growth factors and cytokines containing cationic heparan-binding domains1,2. However, how HSPGs mechanistically mediate signalling at the cell surface-particularly in the context of cell surface RNA-remain poorly understood. During developmental and disease processes, vascular endothelial growth factor (VEGF-A), a heparan sulfate-binding factor, regulates endothelial cell growth and angiogenesis3. The regulatory paradigm for endothelial cell-mediated selectively of VEGF-A binding and activity has largely been focused on understanding the selective sulfation of the anionic heparan sulfate chains4-8. Here we examine the organizational rules of a new class of anionic cell surface conjugates, glycoRNAs9,10, and cell surface RNA-binding proteins (csRBPs11,12). Leveraging genome-scale knockout screens, we discovered that heparan sulfate biosynthesis and specifically the 6-O-sulfated forms of heparan sulfate chains are critical for the assembly of clusters of glycoRNAs and csRBPs (cell surface ribonucleoproteins (csRNPs)). Mechanistically, we show that these clusters antagonize heparan sulfate-mediated activation of ERK signalling downstream of VEGF-A. We demonstrate that the heparan sulfate-binding domain of VEGF-A165 is responsible for binding RNA, and that disrupting this interaction enhances ERK signalling and impairs vascular development both in vitro and in vivo and is conserved across species. Our study thus uncovers a previously unrecognized regulatory axis by which csRNPs negatively modulate heparan sulfate-mediated signalling in the context of angiogenesis driven by VEGF-A.
    DOI:  https://doi.org/10.1038/s41586-025-10052-8
  34. Biomedicines. 2026 Jan 08. pii: 126. [Epub ahead of print]14(1):
    Directional Modulation of the Integrated Stress Response in Neurodegeneration: A Systematic Review of eIF2B Activators, PERK-Pathway Agents, and ISR Prolongers.
    Isabella Ionela Stoian, Daciana Nistor, Mihaela Codrina Levai, Daian Ionel Popa, Roxana Popescu.
      Background and Objectives: The integrated stress response (ISR) is a convergent node in neurodegeneration. We systematically mapped open-access mammalian in vivo evidence for synthetic ISR modulators, comparing efficacy signals, biomarker engagement, and safety across mechanisms and disease classes. Methods: Following PRISMA 2020, we searched PubMed (MEDLINE), Embase, and Scopus from inception to 22 September 2025. Inclusion required mammalian neurodegeneration models; synthetic ISR modulators (eIF2B activators, PERK inhibitors or activators, GADD34-PP1 ISR prolongers); prespecified outcomes; and full open access. Extracted data included model, dose and route, outcomes, translational biomarkers (ATF4, phosphorylated eIF2α), and safety. Results: Twelve studies met the criteria across tauopathies and Alzheimer's disease (n = 5), prion disease (n = 1), amyotrophic lateral sclerosis and Huntington's disease (n = 3), hereditary neuropathies (n = 2), demyelination (n = 1), and aging (n = 1). Among interpretable in vivo entries, 10 of 11 reported benefit in at least one domain. By class, eIF2B activation with ISRIB was positive in three of four studies, with one null Alzheimer's hAPP-J20 study; PERK inhibition was positive in all three studies; ISR prolongation with Sephin1 or IFB-088 was positive in both studies; and PERK activation was positive in both studies. Typical regimens included ISRIB 0.1-2.5 mg per kg given intraperitoneally (often two to three doses) with reduced ATF4 and phosphorylated eIF2α; oral GSK2606414 50 mg per kg twice daily for six to seven weeks, achieving brain-level exposures; continuous MK-28 delivery at approximately 1 mg per kg; and oral IFB-088 or Sephin1 given over several weeks. Safety was mechanism-linked: systemic PERK inhibition produced pancreatic and other exocrine toxicities at higher exposures, whereas ISRIB and ISR-prolonging agents were generally well-tolerated in the included reports. Conclusions: Directional ISR control yields consistent, context-dependent improvements in behavior, structure, or survival, with biomarker evidence of target engagement. Mechanism matching (down-tuning versus prolonging the ISR) and exposure-driven safety management are central for translation.
    Keywords:  drug effects; drug therapy; endoplasmic reticulum; eukaryotic metabolism; neurodegenerative diseases; protein kinase; protein response physiology
    DOI:  https://doi.org/10.3390/biomedicines14010126
  35. Cell. 2026 Jan 27. pii: S0092-8674(25)01485-0. [Epub ahead of print]
    Metabolically regulated proteasome supramolecular organization in situ.
    Xiaomeng Tang, Lu Qu, Florian Wilfling, Florian Beck, Oliver P Ernst, Brenda A Schulman, Wolfgang Baumeister, Cordula Enenkel.
      Many proteins localize in membraneless organelles. However, understanding the steps along membraneless organelle formation-and the structural impact on granule constituents-has been hindered by limited resolution of intracellular data. We address these challenges through in situ cryo-electron tomography (cryo-ET) along with formation of yeast proteasome storage granules (PSGs). During the transition from proliferation to quiescence, doubly capped 26S proteasomes arrested in an inactive state arrange into ∼7.5 MDa trimeric units, dispersed in the nucleoplasm and congregated along the nuclear envelope near the nuclear pore. 9-Å-resolution cryo-ET structures reveal that cytoplasmic PSGs formed in various energy-limiting conditions are paracrystalline arrays of bundled fibers, assembled from stacking of proteasome trimers. The paracrystalline arrangement maintains a pool of fully assembled inactive 26S proteasomes that are released in energy-rich conditions. Overall, our data reveal structural steps along the assembly of an intracellular membraneless organelle in situ and quinary structure formation controlling a major eukaryotic regulatory machine.
    Keywords:  biomolecular condensate; membraneless organelle; metabolism; oligomerization; paracrystalline array; phase separation; proteasome; proteasome storage granule; ubiquitin; yeast
    DOI:  https://doi.org/10.1016/j.cell.2025.12.035
  36. Mol Cell. 2026 Jan 27. pii: S1097-2765(26)00022-5. [Epub ahead of print]
    Why m⁶A? An RNA surveillance model.
    D Dierks, S Schwartz.
      N6-methyladenosine (m⁶A) is the most abundant internal modification of mRNA and is most strongly linked to promoting mRNA decay. Why transcripts are born with a death-promoting mark has remained unclear. A previously proposed "fast-track" model posited regulated, gene-specific modulation of m⁶A to coordinate translation and turnover. However, emerging evidence reveals that m⁶A is broadly and mostly constitutively installed at all DRACH motifs except in the vicinity of splice sites, all of which challenge a fast-track model. We propose an "m⁶A surveillance model": properly spliced transcripts mostly evade methylation, while unspliced, transposon-derived, viral, or aberrant RNAs are hypermethylated and selectively degraded. This model reframes m⁶A as a default quality-control mark that flags undesirable unspliced RNAs for removal. We discuss literature supporting and challenging this model as well as experimental priorities that could allow for a more thorough investigation of this model.
    Keywords:  DRACH motifs; N6-methyladenosine; RNA surveillance; YTH readers; aberrant RNAs; exon-junction complex; gene expression regulation; m6A; mRNA stability and decay; methyltransferase complex; splicing-dependent methylation
    DOI:  https://doi.org/10.1016/j.molcel.2026.01.002
  37. RNA Biol. 2026 Jan 28.
    Non-coding small RNAs Buffer protein interactions to prevent oncogenic aggregation: structural dampening of aberrant PPIs by RNA.
    Masanobu Chinami.
      Non-coding RNAs (ncRNAs) modulate protein - protein interactions (PPIs) by shaping the structural context in which binding occurs, rather than acting as direct inhibitors or enhancers. Using an integrative framework combining catRAPID RNA - protein interaction prediction and AlphaFold3-based structural modelling, we analysed RNA-dependent modulation of interaction states across physiological and oncogenic protein complexes. At the network level, physiological PPIs exhibit high shared ncRNA buffering capacity, whereas oncogenic interactions are characterized by reduced or absent RNA overlap. AlphaFold3 modelling of mutant IDH1/2 complexes illustrates how loss of RNA buffering permits excessive stabilization of enzyme-associated interfaces, reflected by directional changes in buried surface area (ΔBSA) and contact heterogeneity.
    Keywords:  AlphaFold3; Non-coding RNA; Rb1–HPV16-E7 and kras–Raf1; aggregation; catRAPID; p53-MDM2; protein–protein interactions; structural buffering
    DOI:  https://doi.org/10.1080/15476286.2026.2623239
  38. Cell Res. 2026 Jan 28.
    Zinc accumulation-induced integrated stress response triggers β-cell identity loss.
    Qing Ma, Wenjun Xu, Xuan Wang, Haoyu Nie, Yukun Gao, Rui Hu, Zhihao Yang, Xushu Wang, Ta Na, Xiangyi Chen, Zhaoyue Wang, Minglu Xu, Li Shao, Meng Guo, Yanfang Liu, Rongrong Le, Shaorong Gao, Weida Li.
      Pancreatic β-cell identity loss is increasingly recognized as a critical pathogenic contributor to β-cell failure in type 2 diabetes (T2D), but the specific mechanism remains to be characterized. In this study, we demonstrate that zinc accumulation contributes to β-cell identity loss during diabetes progression in both human and mouse islets. Using a model of human embryonic stem cell-derived islets (SC-islets), we reveal that accumulated zinc triggers the integrated stress response (ISR), with elevated ATF4 expression in SC-β cells. This, in turn, initiates expression of the α cell-specific transcription factor ARX, resulting in the conversion of β cells to α cells, thus forming a zinc-ATF4-ARX regulatory axis. Like primary β cells, SC-β cells also undergo identity loss after transplantation into diabetic animals, which can be prevented by an ISR inhibitor, resulting in improved glycemic control. Furthermore, both genetic depletion and chemical inhibition of zinc accumulation effectively safeguard SC-β cells from identity loss and enhance their efficacy in diabetic animals. Our study thus reveals a pathogenic mechanism in which zinc accumulation induces β-cell identity loss through lineage-tracing approaches and proposes a protective strategy to counteract this process.
    DOI:  https://doi.org/10.1038/s41422-026-01222-y
  39. Commun Biol. 2026 Jan 29.
    LncRNA P4HA2-AS1 drives renal interstitial fibrosis via trim32-mediated k63 ubiquitination of ULK1 and autophagic dysregulation.
    Zhou Pan, Fei Xiao, Wei Hu, Ting Liu, Wenjing Shu, Yan Leng, Qingqing Yi, Yan Zeng, Fan Cheng, Hengcheng Zhu, Kang Yang.
      Renal interstitial fibrosis (RIF), the central pathological driver of chronic kidney disease (CKD) progression, remains mechanistically incompletely defined. While long non-coding RNAs (lncRNAs) are emerging as critical regulators of CKD, their roles in RIF pathogenesis are poorly understood. Here, we identify the fibrosis-associated lncRNA P4HA2-AS1 as a key modulator of RIF through integrated analyses of unilateral ureteral obstruction (UUO) mice and TGF-β-stimulated human renal tubular epithelial cells (HK-2), combined with RNA sequencing, RNA pull-down, ubiquitination profiling, and autophagic flux assays. P4HA2-AS1 was markedly upregulated in fibrotic kidneys, and its suppression attenuated fibrotic phenotypes in vivo and in vitro while restoring autophagic flux. Mechanistically, P4HA2-AS1 directly binds the E3 ubiquitin ligase TRIM32, impeding its proteasomal degradation. This stabilization enhances TRIM32-mediated K63-linked ubiquitination of ULK1, a master autophagy initiator, leading to aberrant autophagic activation and fibrotic progression. Our study uncovers a previously unrecognized P4HA2-AS1/TRIM32/ULK1 axis that couples dysregulated autophagy to RIF, proposing lncRNA-protein interaction targeting as a therapeutic strategy against renal fibrosis.
    DOI:  https://doi.org/10.1038/s42003-026-09618-7
  40. Biochim Biophys Acta Rev Cancer. 2026 Jan 27. pii: S0304-419X(26)00018-1. [Epub ahead of print] 189546
    SAG/RBX2/ROC2/RNF7 dual E3 ligase: From target identification, validation to drug discovery.
    Qing Yu, Shizhen Zhang, Zhijian Li, Ting Liang, Yi Sun.
      SAG (Sensitive to Apoptosis Gene), also known as RBX2/ROC2/RNF7, was originally cloned as a redox-inducible gene encoding a cysteine-enriched antioxidant protein. SAG was subsequently characterized as the second family member of the RBX with RING domain, essential for E3 ligase activity in both ubiquitylation and neddylation. Data accumulated over the past 26 years have shown that SAG is overexpressed in many types of human cancer tissues with positive correlation of poor patient survival. Functional studies have revealed that SAG is essential for cancer cell growth, and for tumorigenesis induced by oncogene activation and tumor suppressor inactivation in several genetically modified mouse models. Mechanistically, SAG acts as a catalytic subunit of CRL5 as well as CRL1 to ubiquitylate and degrade mainly tumor suppressor substrates, whereas SAG knockdown or knockout causes their accumulation to inhibit the growth and survival of cancer cells, and tumor progression. Thus, SAG E3 is emerging as an attractive anti-cancer target with drug discovery of small molecule inhibitors and PROTAC degraders being currently pursued. Here, we provide a comprehensive literature review on SAG, from its molecular cloning, biochemical activities, and biological function, to SAG validation as an anti-cancer target, and finally to the drug discovery efforts of SAG targeting agents. The perspectives are also proposed for current challenges and future directions on the study of SAG-associated neddylation-CRLs.
    Keywords:  Antioxidant; E3 ligase; Neddylation; Small molecule inhibitors; Tumorigenesis; Ubiquitylation
    DOI:  https://doi.org/10.1016/j.bbcan.2026.189546
  41. J Biol Chem. 2026 Jan 23. pii: S0021-9258(26)00064-5. [Epub ahead of print] 111194
    In vitro reconstitution in membrane environment reveals critical lipid dependence of substrate S-acylation by protein palmitoyltransferase enzymes.
    Tanmay Mondal, Anirban Banerjee.
      Protein S-acylation, also known as protein palmitoylation, is a common form of post-translational modification and the most abundant form of lipid modification of proteins with several thousands of substrates. Protein S-acylation is critically important in a host of physiological processes including protein trafficking, stability and synaptic organization. 23 transmembrane enzymes belonging to the zDHHC family catalyze this modification in humans. Yet, dissection of how the membrane environment modulates zDHHC activity and their interactions with substrates are poorly understood. Here, we report a direct fluorescence polarization-based assay in completely reconstituted membrane environments using zDHHC15 and -20 and their substrates, PSD-95 and EGF receptor respectively. Our assay enables investigation of the role of lipid composition on the activity of zDHHC enzymes. We show, using this assay that cholesterol modulates activity of zDHHC enzymes. We use the assay reconstituted in giant unilamellar vesicles to directly visualize localization of S-acylated proteins to cholesterol-rich membranes, a phenomenon known for many decades through cell-based experiments. Our work demonstrates the role of lipid composition in zDHHC activity and opens up avenues to dissect the role of different lipids in the activity of 23 zDHHC enzymes. Our nanodisc assay will facilitate high throughput screening of small molecule probes and discovery of novel small therapeutic leads for human diseases by targeting protein S-acylation.
    Keywords:  S-acyltransferase; cholesterol; fluorescence polarization; giant unilamellar vesicles (GUVs); lipid nanodisc; membrane; palmitoyltransferase; protein S-acylation; protein palmitoylation; zDHHC enzyme
    DOI:  https://doi.org/10.1016/j.jbc.2026.111194
  42. Proc Natl Acad Sci U S A. 2026 Feb 03. 123(5): e2506269123
    Mapping targetable sites on the human surfaceome for the design of novel binders.
    Petra E M Balbi, Ahmed Sadek, Anthony Marchand, Ta-Yi Yu, Jovan Damjanovic, Sandrine Georgeon, Joseph Schmidt, Simone Fulle, Che Yang, Hamed Khakzad, Bruno E Correia.
      The human cell surfaceome, integral to cell communication and disease mechanisms, presents a prime target for therapeutic intervention. De novo protein binder design against these cell surface proteins offers a promising yet underexplored strategy for drug development. However, the vast search space and limited data on natural or competitive binders have historically limited experimental success. In this study, we systematically analyzed the entire human surfaceome, identifying approximately 4,500 targetable sites and introducing potential binding seeds for initiating protein design applications. To validate these seeds, we implemented two experimental approaches (protein scaffolding and peptide cyclization) on three representative targets (FGFR2, IFNAR2, and HER3). Our results revealed a high success rate, showing that seeds provide valuable starting points for binder design against our identified targetable sites, as well as the need for constant improvements of computational protein design pipelines utilizing machine learning and physics-based methods. Additionally, we present SURFACE-Bind, an interactive database offering open access to all generated data. The high-throughput computational design methods and target-specific binder seeds established here pave the way for a new generation of targeted therapeutics for the human surfaceome.
    Keywords:  de novo protein design; geometric deep learning; human surfaceome; mapping of targetable binding sites; protein–protein and protein-peptide interactions
    DOI:  https://doi.org/10.1073/pnas.2506269123
  43. Aging Cell. 2026 Feb;25(2): e70399
    Reduced Proteasome Degradation of HSF-1 Shifts Protein Stress Management With Age in Caenorhabditis elegans.
    Hongwei Wang, Fengzhen Sun, Zhidong He, Xiaojie Wang, Hao Liu, Mengjiao Song, Qingxia Chen, Zhixue Li, Ligang Wu, Xiumin Yan, Xueliang Zhu, Yidong Shen.
      To maintain protein homeostasis, which is essential for health, animals have developed complex protective mechanisms against various acute and chronic stresses. However, the coordination of responses to these protein stresses, especially their age-dependent changes, is not well understood. HSF-1 is a key regulator of protein homeostasis. Our study identifies PBS-7, a proteasome subunit, as its crucial regulator. In aged C. elegans, decreased PBS-7 binding reduces proteasome-mediated degradation of HSF-1. The increase in HSF-1 enhances responses to chronic stresses, like accumulating protein aggregates, by upregulating heat shock proteins (HSPs) and autophagy genes. Meanwhile, the upregulated HSPs suppress the activation of HSF-1 upon acute stress, such as heat shock. Our findings reveal a mechanism that coordinates responses to acute and chronic protein stresses and highlights an adaptation prioritising protection against increasing protein aggregates in ageing.
    Keywords:  HSF‐1; proteasome; stress resistance
    DOI:  https://doi.org/10.1111/acel.70399
  44. Cell Death Differ. 2026 Jan 29.
    Phosphorylation-dependent STAMBP drives the progression of pancreatic ductal adenocarcinoma by deubiquitinating and stabilizing BAG3.
    Yongkang Shi, Jun Gong, Lin Chen, Min Zhou, Shutao Pan, Taoyuan Yin, Chunle Zhao, Yuhui Liu, Zhenxiong Zhang, Yu Bai, Yangwei Liao, Qilong Xia, Min Wang, Renyi Qin.
      Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer that is usually diagnosed at a late stage and has a modest clinical response and poor prognosis. Therefore, identifying targets for the effective treatment of PDAC is particularly important. STAM-binding protein (STAMBP) is a JAMM metalloprotease of the deubiquitinase (DUB) family that typically regulates the stabilization and trafficking of substrates in a range of cell types by specifically removing ubiquitin chains. However, its roles in the initiation and progression of PDAC remain unclear. Here, we found that STAMBP is highly expressed in PDAC and is associated with a poor prognosis. STAMBP facilitates the proliferation and migration of PDAC cells and the growth of pancreatic cancer xenograft tumours in mice. We then identified the cochaperone BAG3, which plays a pivotal role in tumourigenesis, as a potential substrate of STAMBP using mass spectrometry (MS). Mechanistically, STAMBP interacts with BAG3 and promotes its stabilization by removing its K63-linked polyubiquitin chains. The Lys29 and Lys60 residues of BAG3 are essential for the K63-linked ubiquitination of BAG3. Moreover, a phosphorylation-dependent mechanism of STAMBP was identified as follows: STAMBP is phosphorylated by IKKα at Ser2 without affecting STAMBP protein abundance, and this phosphorylation enables it to deubiquitinate BAG3. In addition, we found that STAMBP deficiency effectively increases cisplatin/oxaliplatin sensitivity in PDAC. Overall, IKKα phosphorylates STAMBP at Ser 2, which activates STAMBP to deubiquitinase BAG3, thus resulting in an IKKα/STAMBP/BAG3 signaling axis that promotes PDAC progression. STAMBP might serve as a potential therapeutic target for PDAC therapy.
    DOI:  https://doi.org/10.1038/s41418-026-01665-1
  45. Elife. 2026 Jan 26. pii: RP95576. [Epub ahead of print]13
    Axonal distribution of mitochondria maintains neuronal autophagy during aging via eIF2β.
    Kanako Shinno, Yuri Miura, Koichi M Iijima, Emiko Suzuki, Kanae Ando.
      Neuronal aging and neurodegenerative diseases are accompanied by proteostasis collapse, while the cellular factors that trigger it have not been identified. Impaired mitochondrial transport in the axon is another feature of aging and neurodegenerative diseases. Using Drosophila, we found that genetic depletion of axonal mitochondria causes dysregulation of protein degradation. Axons with mitochondrial depletion showed abnormal protein accumulation and autophagic defects. Lowering neuronal ATP levels by blocking glycolysis did not reduce autophagy, suggesting that autophagic defects are associated with mitochondrial distribution. We found that eIF2β was increased by the depletion of axonal mitochondria via proteome analysis. Phosphorylation of eIF2α, another subunit of eIF2, was lowered, and global translation was suppressed. Neuronal overexpression of eIF2β phenocopied the autophagic defects and neuronal dysfunctions, and lowering eIF2β expression rescued those perturbations caused by depletion of axonal mitochondria. These results indicate the mitochondria-eIF2β axis maintains proteostasis in the axon, of which disruption may underlie the onset and progression of age-related neurodegenerative diseases.
    Keywords:  D. melanogaster; aging; autophagy; cell biology; mitochondria; neuronal proteostasis; protein aggregation; proteome
    DOI:  https://doi.org/10.7554/eLife.95576
  46. J Med Chem. 2026 Jan 26.
    Vectorized ULK1/2 and VPS34 Inhibitors for Tissue-Selective Autophagy Inhibition in Oncology.
    Lorenzo Cianni, Kathryn Jacobs, Sergei Grintsevich, Sophie Lyssens, Eline Roeyen, Koen Augustyns, Maya Berg, Hans De Winter, Guido R Y de Meyer, Wim Martinet, Patrizia Agostinis, Gabriele Bergers, Pieter Van der Veken.
      Autophagy, the primary lysosomal degradation pathway, plays a key role in cell survival and homeostasis. In tumors, it is upregulated to support cancer cell plasticity, adaptation to the microenvironment, and therapy resistance, making its inhibition an attractive therapeutic strategy. However, since autophagy is essential in healthy tissues, selective inhibition in tumors is critical. To address this, we designed inhibitors of two autophagy initiation factors (ULK1/2 and VPS34) equipped with tumor-targeting vectors. Our most promising candidates combine a low-nanomolar ULK1/2 inhibitory scaffold with an RGR-sequence targeting peptide. These compounds were validated across in vitro, in cellulo, and in vivo models, demonstrating selective activity and preserved efficacy. As the first examples of tumor-targeted autophagy inhibitors, they open new avenues for developing tissue-specific modulators of autophagy, with potential applications in oncology and beyond.
    DOI:  https://doi.org/10.1021/acs.jmedchem.5c00997
  47. FEBS J. 2026 Jan 30.
    Concentration-dependent cytoplasmic phase separation of TDP-43 drives aggregation and proteinopathy.
    Pauline Combe, Chloé Subecz, Gaïzka Le Goff, Marie Aude Plamont, Delphine Bohl, Zoher Gueroui.
      TDP-43 mislocalization and aggregation are common features of several neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). However, the mechanisms underlying the transition of nuclear TDP-43 to cytoplasmic aggregates, and their contribution to disease pathogenesis, remain poorly understood. To address this gap, we present a methodology to chemically control the assembly and disassembly of cytoplasmic TDP-43 condensates. By fusing TDP-43 to a phase separation-prone protein scaffold, we can induce the formation of cytoplasmic TDP-43 condensates or, conversely, promote nuclear localization upon addition of a disassembly molecule. TDP-43 accumulates into various assemblies, ranging from submicrometric puncta to larger aggregate-like structures that display hallmarks of proteinopathy in a concentration-dependent manner. Furthermore, oxidative stress drives the maturation of TDP-43 assemblies from puncta into aggregates through interactions with stress granule components. Finally, we show that cytoplasmic TDP-43 aggregates deplete nuclear endogenous TDP-43 and induce cytotoxicity. Collectively, these findings highlight the local cytoplasmic concentration of TDP-43 and stress exposure as key determinants in the onset of TDP-43 proteinopathy, providing a relevant model to study pathological TDP-43 aggregation.
    Keywords:  ALS; LLPS; TDP‐43; condensates; phase separation
    DOI:  https://doi.org/10.1111/febs.70429
  48. Proc Natl Acad Sci U S A. 2026 Feb 03. 123(5): e2521639123
    In situ NMR and integrative proteomics reveal the interaction signature of serum α-synuclein.
    Jinfeng Huang, Rashik Ahmed, Madoka Akimoto, José Carlos Bozelli, Richard M Epand, Giuseppe Melacini.
      Alpha-synuclein (αS) plays a central role in several neurodegenerative diseases. Although predominantly neuronal, αS is also present in peripheral fluids such as serum and cerebrospinal fluid (CSF), where it may contribute to disease propagation. However, its extracellular interactions remain poorly understood. By combining in situ NMR spectroscopy and bottom-up MS proteomics, we reveal that monomeric αS exhibits distinct interactomes in serum versus CSF. Both N- and C-terminal αS regions bind to serum components, while in CSF, αS remains largely unbound. The N- and C-terminal interactions are mechanistically diverse: C-terminal binding is electrostatic, whereas N-terminal interactions persist under high ionic strength, implicating hydrophobic interactions. Deletion of the first ten N-terminal residues, which include several hydrophobic side chains, abolishes these interactions, highlighting their functional importance. Proteomic profiling and NMR validation identify key αS serum partners, including albumin, γ-globulins, and lipoproteins, which, together, are sufficient to recapitulate the serum αS interactome and elicit redundant interactions with the αS N-terminal region. Despite such redundancy, αS methionine oxidation selectively disrupts N-terminal binding, suggesting a redox-sensitive mechanism regulating the αS extracellular interactome. Notably, C-terminal interactions are preserved when the N-terminal binding is detuned, indicating that the N- and C-termini elicit independent interactions with the extracellular matrix, a marked difference from the intracellular milieu. These findings uncover dynamic and fluid-specific αS interaction signatures, offering new molecular insights into its peripheral roles and identifying potential new epitopes as synucleinopathy biomarkers. These results are also relevant for other amyloidogenic intrinsically disordered proteins (IDPs), for which αS serves as a prototype.
    Keywords:  CSF; NMR; alpha synuclein; plasma
    DOI:  https://doi.org/10.1073/pnas.2521639123
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