bims-proteo Biomed News
on Proteostasis
Issue of 2026–02–15
53 papers selected by
Eric Chevet, INSERM
  1. Harnessing FBXO31 with terminal amide-functionalized molecules for targeted protein degradation.
  2. SLC33A1 exports oxidized glutathione to maintain endoplasmic reticulum redox homeostasis.
  3. Tuning tRNA synthetase inhibition reveals parabolic induction of stress granules limited in size and RNA content.
  4. Golgi fragmentation driven by the USP11-ITCH axis triggers autolysosomal failure in neurodegeneration.
  5. CSN5i-3 is an orthosteric molecular glue inhibitor of COP9 signalosome.
  6. Identification of clofibric acid as a SYVN1 ligand for PROTAC development.
  7. FidlTrack: high-fidelity structure-aware single particle tracking resolves intracellular molecular motion in organelles sensing APP processing.
  8. Triglycerides induce endoplasmic reticulum lipid bilayer stress to activate PERK and enhance antifungal immunity.
  9. Function within Disorder: Small heat shock proteins use different functional regions to chaperone tau aggregation.
  10. The nonsense-mediated mRNA decay factor Upf3 negatively regulates bulk autophagy progression in Saccharomyces cerevisiae.
  11. Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation.
  12. A dose-dependent switch in translation capacity controls the transcription factor response to H 2 O 2 stress.
  13. Translation elongation as a rate-limiting step of protein production.
  14. Cdc42 interacts with chaperone Ydj1 to enhance its stability and partitioning during asymmetric cell division and aging in yeast.
  15. Palmitoyl Acyltransferases Control the Membrane Localization of DNAJC5 to Regulate Unconventional Protein Secretion.
  16. STIM1-containing contact sites promote direct calcium flux from the endoplasmic reticulum to mitochondria.
  17. P-bodies act as dynamic control hubs for RNA processing and storage.
  18. OSTM1 is a ubiquitin E3 ligase that suppresses B-cell malignancy by activating the cAMP/PKA/CREB pathway.
  19. Negative regulation of the NF-κB pathway by the ubiquitin ligase Nedd4-1(NE).
  20. A peptide catalyst can replace an essential enzyme in a eukaryotic cell.
  21. A HaloTag-4R-Tau Pulse-Chase Sensor Reveals Neddylation Inhibition Promotes Degradation of Tau in iNeurons.
  22. M1-linked ubiquitination by LUBAC regulates AMPK signalling and the response to energetic stress.
  23. Discovery of KRAS-G12D degraders via exploration of various E3 ligases.
  24. Quasi-continuous cotranslational compaction and folding of a multidomain protein.
  25. Degraders of the dengue virus capsid protein exhibit differentiated pharmacology relative to capsid inhibitors.
  26. Active transport of tRNAs facilitates distributed protein synthesis.
  27. NCBP1 stress signaling drives alternative S6K1 splicing inhibiting translation.
  28. Targeted Protein Degrader from Ginkgo to Mitigate Amyloid β-Induced Neurotoxicity.
  29. Regorafenib enhances anti-PDCD1/PD-1 therapeutic efficacy in colorectal cancer by promoting SQSTM1/p62-mediated CD274/PD-L1 degradation.
  30. Control of Inositol 1,4,5-Trisphosphate Receptor Activity by Posttranslational Modifications.
  31. Negative feedback regulation of STING signaling by TAX1BP1-directed Golgiphagy.
  32. A selective Cullin 3 RING E3 ligase inhibitor attenuates hyperglycemia via dual insulin sensitizing and insulinotropic action.
  33. Heritable ER stress impairs mitochondrial metabolism and maintenance of hematopoietic stem cells after low-dose irradiation.
  34. MARCH6 Confers Protection Against Endoplasmic Reticulum Autophagy in Gliomas by Destabilizing FAM134B.
  35. Subcellular proteomic analyses reveal REEP5 knockdown in the mouse heart disrupts mitochondrial networks.
  36. Signal recognition particle-dependent secretome in humans.
  37. The active secretion of a subunit of IL-12 by tissue cells is regulated by Valosin-Containing Protein and intracellular calcium redistribution.
  38. HSPA1A and DNAJB1 regulate NELF condensate dynamics to safeguard transcriptional recovery under heat stress.
  39. An integrated framework identified potent inhibitors targeting IRE1α.
  40. Flexibility and modulation of translation initiation in enterovirus genomes.
  41. A Novel Paradigm for Targeting Challenging Targets: Advancing Technologies and Future Directions of Molecular Glue Degraders.
  42. Legionella employs the multimodal ubiquitination of Sec22b to modulate SNARE pairing.
  43. Domain-specific folding of the tandem β-propeller protein Coronin 7 (Coro7) by CCT/TRiC.
  44. Lack of MDA5 delays hematopoietic aging by modulating inflammaging and proteostasis in mice.
  45. The allosteric landscape of the Src kinase.
  46. Defining the reference proteomes for small extracellular vesicles and non-vesicular components.
  47. Increased FICD-mediated protein AMPylation triggers conserved ER stress signaling across species.
  48. Components of an ESCRT-independent nuclear envelope assembly pathway.
  49. Protein disulfide isomerase A6 (PDIA6) is essential for acrosome biogenesis and male fertility in mice.
  50. RBPscan: A quantitative in vivo tool for profiling RNA-binding protein interactions.
  51. Structural ontogeny of protein-protein interactions.
  52. Circadian rhythm heterogeneity modulates drug response variations in neuroblastoma models.
  53. Regulation of ER-Resident Transcription Factor NFE2L1 in HEK293 Cells.
  1. bioRxiv. 2026 Jan 29. pii: 2026.01.28.702440. [Epub ahead of print]
    Harnessing FBXO31 with terminal amide-functionalized molecules for targeted protein degradation.
    Chenlu Zhang, Xiaokang Jin, Chen Zhou, M Jamal Jenkins, Isabella A Riha, Xiaoyu Zhang.
      Targeted protein degradation (TPD) is a powerful strategy for controlling protein abundance. Here, we establish FBXO31 as a TPD-competent E3 ligase by exploiting its recognition of C-terminal amide-bearing degrons. Using an amidated Ala-Phe motif as a chemical recruiter, multiple small-molecule binders can be transformed into FBXO31-dependent degraders that induce rapid and potent target degradation. Mechanistic studies confirm FBXO31-mediated ternary complex formation and identify key residues in FBXO31 required for recruiter engagement and target degradation. We further show that an FBXO31-based multi-kinase degrader exhibits a distinct and broader degradation profile than a CRBN-based degrader, highlighting a potentially expanded degradable target space beyond CRBN.
    DOI:  https://doi.org/10.64898/2026.01.28.702440
  2. bioRxiv. 2026 Feb 03. pii: 2026.02.01.703113. [Epub ahead of print]
    SLC33A1 exports oxidized glutathione to maintain endoplasmic reticulum redox homeostasis.
    Shanshan Liu, Mark Gad, Caifan Li, Kevin Cho, Yuyang Liu, Khando Wangdu, Viktor Belay, Alon Millet, Hiroyuki Kojima, Henry Sanford, Michele Wölk, Linas Urnavicius, Maria Fedorova, Gary J Patti, Ekaterina V Vinogradova, Richard K Hite, Kıvanç Birsoy.
      The endoplasmic reticulum (ER) requires an oxidative environment to support the efficient maturation of secretory and membrane proteins. This is in part established by glutathione, a redox-active metabolite present in reduced (GSH) and oxidized (GSSG) forms. The ER maintains a higher GSSG:GSH ratio than the cytosol; however, the mechanisms controlling ER redox balance remain poorly understood. To address this, we developed a method for the rapid immunopurification of the ER, enabling comprehensive profiling of its proteome and metabolome. Combining this approach with CRISPR screening, we identified SLC33A1 as the major ER GSSG exporter in mammalian cells. Loss of SLC33A1 leads to GSSG accumulation in the ER and a liposome-based assay demonstrates that SLC33A1 directly transports GSSG. Cryo-EM structures and molecular dynamics simulations reveal how SLC33A1 binds GSSG and identify residues critical for its transport. Finally, an imbalance in GSSG:GSH ratio induces ER stress and dependency on the ER-associated degradation (ERAD) pathway, driven by a shift in protein disulfide isomerases (PDIs) toward their oxidized forms. Altogether, our work establishes SLC33A1-mediated GSSG export as a key mechanism for ER redox homeostasis and protein maturation.
    DOI:  https://doi.org/10.64898/2026.02.01.703113
  3. RNA. 2026 Feb 08. pii: rna.080883.125. [Epub ahead of print]
    Tuning tRNA synthetase inhibition reveals parabolic induction of stress granules limited in size and RNA content.
    Max Baymiller, Noah S Helton, Benjamin Dodd, Stephanie L Moon.
      Translation elongation defects cause ribosome stalling and activate the integrated stress response (ISR). During the ISR, translation initiation suppression and ribosome runoff drive mRNA condensation into stress granules. However, the effects of partial translation elongation inhibition on stress granules are poorly defined. We demonstrate that intermediate levels of tRNA synthetase inhibitors activate the ISR and cause assembly of stress granules in a parabolic dose-response pattern. These stress granules are limited in size and number due to ribosome association with mRNAs. Assembly of stress granules by intermediate levels of the prolyl-tRNA synthetase inhibitor halofuginone requires the canonical stress granule scaffolding proteins G3BP1/2 and GCN2-mediated ISR activation. We performed a candidate-based comparative analysis of the composition of stress granules induced by intermediate levels of halofuginone or canonical stressors arsenite or thapsigargin. The stress granules induced by halofuginone, arsenite, or thapsigargin harbor polyadenylated RNA and the canonical stress granule proteins PABPC1, G3BP1, and UBAP2L. We observe stress- and transcript- specific differences in the localization of candidate RNA molecules to stress granules. These results demonstrate that partial translation elongation inhibition permits stress granule assembly through the balance of ISR activation and mRNA association with ribosomes, with implications for the stress response associated with amino acid or tRNA deficiency, therapeutic tRNA synthetase inhibition, or diseases associated with tRNA synthetase mutations.
    Keywords:  integrated stress response; stress granules; tRNA synthetase; translation; translation elongation
    DOI:  https://doi.org/10.1261/rna.080883.125
  4. Autophagy. 2026 Feb 10. 1-2
    Golgi fragmentation driven by the USP11-ITCH axis triggers autolysosomal failure in neurodegeneration.
    Qiwang Xiang, Yang Liu, Jiou Wang.
      Golgi fragmentation is a prominent early hallmark of neurodegenerative diseases such as Alzheimer disease (AD) and amyotrophic lateral sclerosis (ALS), yet the shared molecular mechanisms underlying this phenomenon remain poorly understood. Here we identify the E3 ubiquitin ligase ITCH as a central regulator of Golgi integrity and proteostasis. Elevated ITCH disrupts both cis- and trans-Golgi networks, dislocates lysosomal hydrolase sorting factors, and impairs maturation of hydrolases. The ensuing lysosomal dysfunction leads to autophagosome accumulation and defective clearance of accumulated cytoplasmic toxic proteins like TARDBP/TDP-43. Genetic and pharmacological inhibition of ITCH restores autolysosomal degradation and protects neurons in both mammalian and Drosophila models. Aberrant buildup of the deubiquitinase USP11 drives ITCH accumulation, intensifying neuronal proteotoxic stress in individuals with AD and ALS. These findings reveal a mechanistic pathway connecting Golgi disorganization, autolysosomal impairment, and proteotoxic stress in neurodegeneration.
    Keywords:  Autophagy; Golgi fragmentation; ITCH; USP11; lysosome; neurodegenerative diseases
    DOI:  https://doi.org/10.1080/15548627.2026.2629295
  5. Nature. 2026 Feb 11.
    CSN5i-3 is an orthosteric molecular glue inhibitor of COP9 signalosome.
    Huigang Shi, Xiaorong Wang, Clinton Yu, Haibin Mao, Fenglong Jiao, Merav Braitbard, Ben Shor, Zhongsheng Zhang, Thomas R Hinds, Shiyun Cao, Erkang Fan, Dina Schneidman-Duhovny, Lan Huang, Ning Zheng.
      Orthosteric inhibitors block enzyme active sites and prevent substrates from binding1. Enhancing their specificity through substrate dependence seems inherently unlikely, as their mechanism hinges on direct competition rather than selective recognition. Here we show that a molecular glue mechanism unexpectedly imparts substrate-dependent potency to CSN5i-3, an orthosteric inhibitor of the COP9 signalosome (CSN). We first confirm that CSN5i-3 inhibits CSN, which catalyses NEDD8 (N8) deconjugation from the cullin-RING ubiquitin ligases, by occupying the active site of its catalytic subunit, CSN5, and directly competing with the iso-peptide bond substrate. Notably, the orthosteric inhibitor binds free CSN with only micromolar affinity, yet achieves nanomolar potency in blocking its deneddylase activity. Cryogenic electron microscopy structures of the enzyme-substrate-inhibitor complex reveal that active site-engaged CSN5i-3 occludes the substrate iso-peptide linkage while simultaneously extending an N8-binding exosite of CSN5, acting as a molecular glue to cement the N8-CSN5 interaction. The cooperativity of this trimolecular CSN5i-3-N8-CSN5 assembly, in turn, sequesters CSN5i-3 at its binding site, conferring high potency to the orthosteric inhibitor despite its low affinity for the free enzyme. Together, our findings highlight the modest affinity requirements of molecule glues for individual target proteins and establish orthosteric molecular glue inhibitors as a new class of substrate-dependent enzyme antagonists.
    DOI:  https://doi.org/10.1038/s41586-026-10129-y
  6. bioRxiv. 2026 Jan 28. pii: 2026.01.26.701774. [Epub ahead of print]
    Identification of clofibric acid as a SYVN1 ligand for PROTAC development.
    Julia Warren, Anandarao Munakala, Keith D Zientek, Kilsun Kim, Phil A Wilmarth, Ashok P Reddy, Bingbing X Li, Xiangshu Xiao.
      Targeted protein degradation (TPD) is an emerging therapeutic modality for numerous diseases. PROteolysis-TArgeting Chimeras (PROTACs) represent a potentially generalizable strategy to achieve TPD. A PROTAC is composed of a ligand for a protein of interest, a linker and a ligand for E3 ligase. As such, PROTACs can bring the E3 ligase into the close proximity of a protein target leading to polyubiquitination followed by target protein degradation. While the human genome encodes over 600 E3 ligases, only a handful of them have been harnessed for developing PROTACs. In order to expand the repertoire of E3 ligases for PROTAC development, we developed clickable photoaffinity probes based on clinically used drugs and metabolites to identify potential E3 ligases as the targets. In this paper, we report the discovery of clofibric acid with a molecular weight of only 214 Daltons as a ligand for synoviolin (SYVN1). We demonstrate its utility by developing clofibric acid-based BRD4 PROTACs. The linker length and architecture play a critical role in target degradation efficiency. The clofibric acid-derived BRD4 PROTACs achieve selective BRD4 degradation in a SYVN1-dependent manner. Our findings establish clofibric acid as a robust addition to the TPD toolbox, offering a novel E3 ligase recruitment strategy for the development of next-generation degraders.
    TOC Graphics:
    DOI:  https://doi.org/10.64898/2026.01.26.701774
  7. Nat Commun. 2026 Feb 11.
    FidlTrack: high-fidelity structure-aware single particle tracking resolves intracellular molecular motion in organelles sensing APP processing.
    Pierre Parutto, Yutong Yuan, Valentina Davì, Roger Pons-Lanau, Svenja Ebeling, Karnika Gupta, Francesca Bottanelli, Maria F Garcia-Parajo, Felix Campelo, Clemens F Kaminski, Joseph E Chambers, Jonathon Nixon-Abell, Edward Avezov.
      Single Particle Tracking (SPT) is a powerful technique for elucidating the dynamic behaviours of macromolecules within live cells. However, SPT's application to subcellular environments is hampered by the error-proneness of tracking at high particle velocities and densities and the lack of tools to assess trajectory reliability. Here, we introduce FidlTrack, a methodology that benchmarks and improves SPT fidelity. It contains three modules: a parameter optimiser that uses synthetic ground truth SPT data to determine the fidelity-maximising experimental and tracking settings; Structure-aware tracking, that exploits the information provided by organelle structures to constrain particle tracking algorithms; And a tracking quality evaluator that detects, quantifies and removes error-prone ambiguous track segments. Together these tools allow the rational design of SPT experiments, resolving the motion in tight and convoluted organelles, and provide up to 2-fold enrichment in accurate data. We showcase FidlTrack's utility for reliably tracking proteins in the cytosol, mitochondria and endoplasmic reticulum (ER). Further, we demonstrate its efficacy by analysing ER protein dynamics at exit sites, resolving BACE1 amyloidogenic cleavage of the amyloid precursor protein and characterising the spatiotemporal binding dynamics of an ER-targeted intrabody. FidlTrack is provided as a universal open-access platform that can be incorporated into any SPT pipeline.
    DOI:  https://doi.org/10.1038/s41467-026-69067-y
  8. Cell Rep. 2026 Feb 11. pii: S2211-1247(26)00054-9. [Epub ahead of print]45(2): 116976
    Triglycerides induce endoplasmic reticulum lipid bilayer stress to activate PERK and enhance antifungal immunity.
    Han Wu, Qing Shui, Xiaoxi Luan, Kexin Wang, Wei Zhao, Xiaopeng Qi, Bingyu Liu, Wanwei Sun, Chengjiang Gao.
      Invasive fungal infections remain a major clinical challenge due to limited antifungal drugs, drug toxicity, and resistance. Fungal infections trigger endoplasmic reticulum (ER) stress. However, the mechanism through which this stress response affects antifungal immunity remains unclear. Here, we showed that de novo triglyceride synthesis promotes antifungal innate immune signaling and proinflammatory gene expression in macrophages. Upon fungal stimulation, triglycerides induce ER lipid bilayer stress and activate the protein kinase R (PKR)-like ER kinase (PERK) branch of the unfolded protein response pathway. Furthermore, activated PERK mediates autophagic degradation of Src homology 2 domain-containing protein tyrosine phosphatase 1 (SHP-1) to amplify spleen tyrosine kinase-associated antifungal signaling. Mice with PERK deficiency in myeloid cells are more susceptible to the lethal sequelae of systemic infection with Candida albicans. Notably, administration of the PERK agonist CCT020312 improved host outcomes in disseminated fungal infections. Overall, our study identified a critical function of PERK in positively regulating antifungal immune responses and offers a potential therapeutic strategy for controlling C. albicans infections.
    Keywords:  CP: immunology; CP: metabolism; PERK; antifungal immunity; drug target; lipid bilayer stress; triglycerides
    DOI:  https://doi.org/10.1016/j.celrep.2026.116976
  9. bioRxiv. 2026 Jan 29. pii: 2026.01.28.702414. [Epub ahead of print]
    Function within Disorder: Small heat shock proteins use different functional regions to chaperone tau aggregation.
    Mia Cervantes, Maria K Janowska, Lisa M Tuttle, Abhinav Nath, Rachel E Klevit.
      In numerous neurodegenerative diseases known collectively as tauopathies, the microtubule-associated protein tau forms fibrillar aggregates that are hallmarks of disease pathology. Tauopathies represent a substantial fraction of diseases associated with protein misfolding. Cellular chaperones known as small heat shock proteins (sHSPs) play a critical role in maintaining protein homeostasis by delaying the onset of protein aggregation. Two sHSPs, HSPB1 (Hsp27) and HSPB5 ( α B-crystallin), are constitutively expressed in brain and neurons. Here, we show that HSPB1 and HSPB5 delay tau aggregation in vitro through distinct mechanisms dictated by their disordered N-terminal regions (NTRs). HSPB1 inhibits tau aggregation under normal cellular conditions, whereas HSPB5 displays activity towards tau when activated by stress conditions such as pH acidosis. Using chimeric HSPB1/HSPB5 constructs in which small NTR subregions are swapped, we identify functional regions within the NTRs that modulate chaperone function for tau. The functional regions contain known sites of phosphorylation, suggesting that they are also control points that respond to cellular stress conditions. Our findings support an emerging model in which specific functional motifs within disordered regions of sHSPs govern activity and client engagement under normal and stress conditions.
    Broader Audience: In many neurodegenerative diseases, the microtubule-associated protein tau forms fibrillar aggregates in the brain. Small heat shock proteins (sHSP) help prevent such aggregation, but their mechanisms of action remain enigmatic. We show HSPB1 and HSBP5, two sHSPs that are abundant and co-localize with tau, delay the onset of tau aggregation through distinct mechanisms. Each relies on specific small regions within their disordered N- terminal domains whose accessibility can be regulated by stress conditions and post- translational modifications.
    DOI:  https://doi.org/10.64898/2026.01.28.702414
  10. Autophagy Rep. 2026 ;5(1): 2623730
    The nonsense-mediated mRNA decay factor Upf3 negatively regulates bulk autophagy progression in Saccharomyces cerevisiae.
    Tabassum Ahmad Tasmi, Emily Solomon, Emmanuella Wesome Avogo, Swaroopa Badenahalli Narasimhaiah, Elizabeth Delorme-Axford.
      Macroautophagy/Autophagy is a highly conserved mechanism that targets cytoplasmic cargo for degradation and recycling. At present, 45 autophagy-related (ATG) genes have been identified in fungi. Due to this complexity, the autophagy pathway must be strictly regulated at multiple levels (transcriptional, post-transcriptional, translational, and post-translational). Dysregulation of autophagy can have detrimental effects on cell health and survival. Therefore, investigation into the mechanisms regulating autophagy is critical. The nonsense-mediated mRNA decay (NMD) pathway targets transcripts with premature translation termination codons (PTCs), although NMD also regulates normal transcripts. NMD requires conserved factors in yeast - Upf1, Upf2, and Upf3. Here, we demonstrate that autophagy activity increases in upf1∆ upf2∆ upf3∆ cells. We also show that autophagy is enhanced in upf3∆ cells through multiple assays. UPF3/Upf3 expression decreases during starvation and autophagy induction. Loss of UPF3 results in the upregulation of ATG16/Atg16, which is required for autophagosome formation. Furthermore, ATG16 is likely targeted by NMD. These findings provide insight into how yeast cells may modulate autophagy through the mRNA decay factor Upf3.
    Keywords:  Atg16; NMD; autophagosome; macroautophagy; stress; yeast
    DOI:  https://doi.org/10.1080/27694127.2026.2623730
  11. Science. 2026 Feb 12. 391(6786): eaea1272
    Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation.
    Mohamed A El-Brolosy, Atharv Oak, An T Hoang, Yassine Damergi, André Fischer, Reuben A Saunders, Jingchuan Luo, Amer Balabaki, Jeremy Guez, Troy W Whitfield, Seth R Goldman, Arash Latifkar, Yuancheng Ryan Lu, Didier Y R Stainier, Konrad J Karczewski, Olivia Corradin, Jonathan S Weissman.
      Transcriptional adaptation (TA) is a genetic robustness mechanism through which mutant messenger RNA (mRNA) decay induces sequence-dependent up-regulation of so-called adapting genes. How cytoplasmically generated mRNA fragments affect nuclear transcription remains poorly understood. Using genome-wide CRISPR screens, we uncover ILF3 as an RNA binding protein connecting cytoplasmic mRNA decay and transcription during TA and show that it is required for a range of TA substrates. ILF3 is enriched at adapting genes' RNAs, and its artificial recruitment through dCas13 promotes gene expression. Using tiling oligonucleotide screens, we identify trigger RNA fragments that activate adapting genes when introduced into cells. Further functional dissection reveals a critical role for homology between trigger and target sequences. These findings enhance our molecular understanding of TA and inform the design of programmable oligonucleotides for gene expression augmentation.
    DOI:  https://doi.org/10.1126/science.aea1272
  12. bioRxiv. 2026 Jan 31. pii: 2026.01.28.701883. [Epub ahead of print]
    A dose-dependent switch in translation capacity controls the transcription factor response to H 2 O 2 stress.
    Chance Parkinson, Woody March-Steinman, Elizabeth Jose, Lisa Shanks, Andrew L Paek.
      Hydrogen Peroxide (H 2 O 2 ) stress activates transcription factors (TFs) in a dose-dependent manner, with distinct TFs activated in response to low versus high H 2 O 2 . Here, we show that high H₂O₂ imposes a translational constraint that prevents accumulation of TFs requiring de novo protein synthesis. Under low H 2 O 2 conditions, TFs including p53, NRF2, and ATF4, accumulate and drive stress-responsive gene expression. In contrast, high H 2 O 2 induces coordinated inhibition of translation initiation and elongation through activation of the integrated stress response (ISR), suppression of mTORC1 signaling, and activation of eEF2K, thereby blocking accumulation of these TFs. Inhibition of translation and repression of p53, NRF2, and ATF4 coincides with nuclear shuttling of pre-existing TFs, including FOXO1, NFAT1, and NF-κB. We propose that shuttling TFs provide a backup mechanism to respond to severe oxidative stress while translation is inhibited. Together, these findings identify translational control as a central switch governing transcription factor response to H 2 O 2 stress.
    DOI:  https://doi.org/10.64898/2026.01.28.701883
  13. Cell Syst. 2026 Feb 11. pii: S2405-4712(25)00323-0. [Epub ahead of print] 101490
    Translation elongation as a rate-limiting step of protein production.
    Elijah F Lyons, Lou C Devanneaux, Ryan Y Muller, Anna V Freitas, Zuriah A Meacham, Maria V McSharry, Van N Trinh, Anna J Rogers, Joseph H Lobel, Nicholas T Ingolia, Liana F Lareau.
      Synonymous codons are decoded at different speeds, but simple models predict that this should not drive protein output: translation initiation, not elongation, should limit the rate of protein production. We showed previously that the output of a series of synonymous fluorescent reporters in yeast spanned a 7-fold range corresponding to translation elongation speed. Here, we show that this effect is not due primarily to the established impact of slow elongation on mRNA stability. Rather, slow elongation further decreases the number of proteins made per mRNA. Our simulations, experiments on fluorescent reporters, and analysis of endogenous protein synthesis in yeast show that translation is limited on non-optimally encoded transcripts. Using a genome-wide CRISPRi screen, we find that impairing initiation attenuates the impact of slow elongation, showing a dynamic balance between rate-limiting steps of protein production. Our results show that codon choice can directly limit protein production across the full range of endogenous codon usage.
    Keywords:  codon usage; mRNA translation; synonymous codons; translation elongation; translation regulation
    DOI:  https://doi.org/10.1016/j.cels.2025.101490
  14. PLoS Biol. 2026 Feb;24(2): e3003306
    Cdc42 interacts with chaperone Ydj1 to enhance its stability and partitioning during asymmetric cell division and aging in yeast.
    Pil Jung Kang, Hana Mazak, Sung Sik Lee, Hay-Oak Park.
      Cdc42, a small GTPase essential for cell polarity, often becomes hyperactive with age and promotes senescence in yeast and animal cells. Yet, the mechanisms driving its age-related upregulation remain unclear. Here, we show that in budding yeast, Cdc42 accumulates over successive cell divisions and that reducing its levels extends life span. Using microfluidics-assisted live-cell imaging and genetic analysis, we found that Cdc42 is distributed unevenly between mother and daughter cells during division. Daughter cells inherit lower Cdc42 levels, which likely help them remain young. This asymmetric distribution depends on Cdc42's association with and/or release from endomembranes and likely involves Ydj1, a farnesylated Hsp40/DnaJ chaperone anchored to the endoplasmic reticulum. Ydj1 interacts with Cdc42, promoting its stability and proper partitioning during cell division. We propose that ER-bound Ydj1 facilitates the asymmetric distribution of Cdc42, thereby restricting aging to mother cells.
    DOI:  https://doi.org/10.1371/journal.pbio.3003306
  15. Traffic. 2026 Mar;27(1): e70031
    Palmitoyl Acyltransferases Control the Membrane Localization of DNAJC5 to Regulate Unconventional Protein Secretion.
    Yue Xu, Robbins Puthenveetil, Juhyung Lee, Layla Saidi, Anirban Banerjee, Yihong Ye.
      Misfolded proteins lacking signal sequence can be secreted into the extracellular space via an unconventional protein secretion (UcPS) process termed misfolding-associated protein secretion (MAPS), which involves HSP70 and a membrane-associated HSP70 co-chaperone named DNAJC5. Here, we show that DNAJC5 can be palmitoylated by several DHHC palmitoyl acyltransferases in human cells. Among them, DHHC11 has a modest activity toward DNAJC5, but its overexpression enriches DNAJC5 in a Golgi-associated compartment, which correlates with increased secretion. Mutagenesis studies show that a minimum DNAJC5 module (DC95) consisting of the palmitoyl acceptor-enriched cysteine string (CS) domain plus the C-terminal 62 residues and a short upstream segment is sufficient to drive palmitoylation, Golgi translocation and secretion. In contrast, removal of 5 residues from DC95 abolishes its palmitoylation, Golgi association and secretion. These findings suggest that the palmitoylation sites of DNAJC5 act with flanking sequences to control its subcellular localization and UcPS function.
    DOI:  https://doi.org/10.1111/tra.70031
  16. EMBO J. 2026 Feb 11.
    STIM1-containing contact sites promote direct calcium flux from the endoplasmic reticulum to mitochondria.
    Yolanda Orantos-Aguilera, Irene Sanchez-Lopez, Carlos Pascual-Caro, Patricia Gómez-Suaga, Estela Area-Gomez, Eulalia Pozo-Guisado, Jorge Montesinos, Francisco Javier Martin-Romero.
      STIM1 is a transmembrane protein localized in the endoplasmic reticulum (ER), where it acts as a calcium ion sensor, activating store-operated Ca2+ entry upon ER Ca2+ depletion. Via cellular calcium influx, STIM1 is thought to indirectly affect mitochondrial calcium content. Here we show that STIM1 also interacts with mitochondrial proteins such as PTPIP51 and GRP75, suggesting its presence in mitochondria-associated ER membranes (MAMs), which are specialized ER regions that facilitate ER-mitochondria communication. Lowering STIM1 expression disrupts ER-to-mitochondria Ca2+ transfer, reduces basal mitochondrial Ca2+ levels, impairs maximal mitochondrial respiration, and reduces ATP production. The STIM1-GRP75 interaction depends on STIM1's Ca2+-sensing ability. ER Ca2+ depletion or the constitutive-open R429C mutation both reduce STIM1 binding to GRP75, suggesting that conformational changes in STIM1 play a role in this interaction. Deletion analysis revealed that the STIM1 (551-611) segment is crucial for GRP75 binding, as the peptide STIM1(551-611) binds GRP75, while STIM1(Δ551-611) shows reduced binding. These findings reveal a previously unrecognized role of STIM1 in direct inter-organelle communication.
    Keywords:  Calcium; GRP75; MAM; Mitochondria; STIM1
    DOI:  https://doi.org/10.1038/s44318-026-00700-8
  17. J Biol Chem. 2026 Feb 10. pii: S0021-9258(26)00143-2. [Epub ahead of print] 111273
    P-bodies act as dynamic control hubs for RNA processing and storage.
    Matthew Wenjie Feng, Amir Mossanen-Parsi, Viktoras Stonys, Simon J Hubbard, Mark P Ashe, Chris M Grant.
      Processing bodies (PBs) are cytoplasmic granules that function in the cellular response to stress conditions by regulating mRNA metabolism. Initially, they were thought to represent sites of mRNA turnover, whereas more recent work points to a role in the storage of useful mRNAs. However, their exact intracellular role remains unclear. We used SH-linked alkylation for the metabolic sequencing of RNA (SLAM-seq) to study PB-localisation and global mRNA fate during glucose depletion conditions that induce PB formation in yeast. This enabled us to differentiate newly synthesized and pre-existing RNAs and to separately track mRNA synthesis and degradation. We show that pre-existing mRNAs localise to PBs with differing kinetics with some transcripts localising over the time-course of glucose starvation and some transcripts localising in a more dynamic manner. We identified a small number of transcripts that are enriched only transiently in PBs, consistent with the traditional view of PBs acting as sites for RNA decay. However, most transiently localised transcripts are not destabilized following glucose starvation, with PBs appearing to act as temporary storage sites for transcripts that later undergo alternative fates. For other transcripts, both their pre-existing and newly made transcripts accumulate in PBs over the time-course of glucose depletion and we suggest that these transcripts are important for adaptation once the nutrient stress is relieved. Together, our data indicate a model where transcripts partition into different classes that behave differently following nutrient depletion with PBs acting as triage sites for mRNAs to direct their fate.
    Keywords:  RNA decay; RNA storage; glucose starvation; processing body (P‐body); translation; yeast
    DOI:  https://doi.org/10.1016/j.jbc.2026.111273
  18. bioRxiv. 2026 Jan 26. pii: 2026.01.23.701155. [Epub ahead of print]
    OSTM1 is a ubiquitin E3 ligase that suppresses B-cell malignancy by activating the cAMP/PKA/CREB pathway.
    Muhammad Usama Tariq, Namratha Sheshadri, Jianliang Shen, Jaeyong Jung, Rongrong Li, Kevin Lu, Junrong Yan, Mark C Koch, Giuseppe Caso, Hassan Sajjad, Brinda Vallat, Stephen K Burley, Yi Sun, Tong Liu, Hong Li, Christian Hinrichs, Francesco Bertoni, Richard Z Lin, Jun Wang, Y Lynn Wang, Jean Vacher, Ping Xie, Wei-Xing Zong.
      Osteoclastogenesis-associated transmembrane protein 1 (OSTM1) is a membrane-integral glycosylated protein known for regulating lysosomal homeostasis, with loss-of-function mutations causing autosomal recessive osteopetrosis. Through a whole-genome CRISPR/Cas9 screen, we identified OSTM1 as a critical tumor suppressor in B-cell malignancies. In humans, OSTM1 is frequently deleted or downregulated across a wide range of B-cell malignancies. In mice, B-cell-specific monoallelic or biallelic Ostm1 ablation cooperates with Cdkn2a loss to drive lymphomagenesis with near 100% penetrance. Mechanistically, we reveal that a cytosolic, non-glycosylated fraction of OSTM1 functions as an E3 ligase that targets phosphodiesterase 3B (PDE3B) for proteasomal degradation. Because PDE3B catalyzes the conversion of cAMP to AMP and thereby negatively regulating the cAMP-dependent PKA/CREB/CREBBP tumor suppressive pathway, the loss of OSTM1 leads to PDE3B stabilization and enhanced cell transformation. Our findings establish OSTM1 as a pivotal E3 ligase that prevents B-cell lymphomagenesis through the regulation of the cAMP/PKA/CREB pathway.
    DOI:  https://doi.org/10.64898/2026.01.23.701155
  19. Commun Biol. 2026 Feb 07.
    Negative regulation of the NF-κB pathway by the ubiquitin ligase Nedd4-1(NE).
    Avinash Persaud, George Kefalas, Alina Shteiman, Amulya Priya, Huazhu Liang, Roman A Melnyk, Audrey Astori, Brian Raught, Daniela Rotin.
      The NF-κB pathway plays a critical role in mediating the innate immune response downstream of activated immune receptors such as the TNFαR. Activation of this pathway is induced by several ubiquitin ligases (e.g., cIAP, TRAFs, NEMO, β-TrCP, KPC1), including Nedd4-1. Nedd4-1 comprises a C2-WW(4)-HECT domain architecture. We recently characterized a primate-specific splice isoform of Nedd4-1, Nedd4-1(NE), in which the C2 domain is replaced by a large N-terminally Extended (NE) region. Using miniTurbo BioID, we identified here several components of the NF-κB pathway in complex with Nedd4-1(NE) (but not with the canonical Nedd4-1), including IKKα/β and p105-NF-κB1. We further show that (i) Nedd4-1(NE) ubiquitinates and promotes degradation of IKKβ, therefore inhibiting phosphorylation and promoting stability of its substrate, the inhibitory IκBα; (ii) active Nedd4-1(NE) binds and destabilizes NF-κB1, an interaction that is dependent upon Nedd4-1(NE)-mediated KPC1 ubiquitination. Furthermore, KPC1 promotes translocation of NF-κB1 to late endosomal membranes, where Nedd4-1(NE) resides, to facilitate the Nedd4-1(NE): NF-κB1 interaction. Consequently, Nedd4-1(NE)-mediated regulation of both IKKβ and NF-κB1 suppresses NF-κB1 nuclear translocation and activation of its target genes; and (iii) Nedd4-1(NE) (but not canonical Nedd4-1) mRNA expression is increased upon prolonged TNFα treatment of cells. This work uncovered an E3 ubiquitin ligase that suppresses the NF-κB1 pathway to ensure termination of this pro-inflammatory signaling pathway in primates via a negative feedback mechanism; Such an additional layer of immune regulation has important implications for understanding inflammatory homeostasis and its dysregulation in human disease.
    DOI:  https://doi.org/10.1038/s42003-026-09634-7
  20. bioRxiv. 2026 Jan 29. pii: 2026.01.27.701630. [Epub ahead of print]
    A peptide catalyst can replace an essential enzyme in a eukaryotic cell.
    Kira A Podolsky, Oscar J Molina, Vivian Y Long, Ronald T Raines.
      Protein enzymes are central to modern biology, yet how catalysis emerged before the evolution of large, folded proteins remains unresolved. Here we show that a short, genetically encoded peptide can replace an essential enzyme in a living eukaryotic cell. We designed minimal peptides containing a Cys-Xaa-Cys catalytic motif and an endoplasmic reticulum retention signal, and identified variants that rescue the otherwise lethal deletion of protein disulfide isomerase (PDI) in Saccharomyces cerevisiae . Cells relying on these peptides remain viable, though they grow more slowly and adapt by activating stress-response pathways, consistent with PDI being replaced by catalysts of lower intrinsic efficiency. Biochemical analyses show that peptide activity depends on local chemical environment and secondary structure rather than a globular fold. These results demonstrate that short peptides can replace an essential cellular reaction in vivo at the system level, supporting the plausibility of peptide-based catalysis as a precursor to modern protein enzymes.
    DOI:  https://doi.org/10.64898/2026.01.27.701630
  21. bioRxiv. 2026 Jan 29. pii: 2026.01.28.702105. [Epub ahead of print]
    A HaloTag-4R-Tau Pulse-Chase Sensor Reveals Neddylation Inhibition Promotes Degradation of Tau in iNeurons.
    Qiang Xiao, Zi Gao, Seth Allen, Danny Garza, Richard I Morimoto, Jeffery W Kelly.
      Tau accumulation is a central driver of neurodegenerative diseases, yet strategies to promote its clearance remain limited. We developed a HaloTag-4R-Tau sensor in human iPSC-derived neurons (iNeurons) that enables sensitive monitoring the kinetics of both lysosomal partitioning and overall cellular turnover of tau. Using this sensor, we screened a small collection of small-molecule modulators of proteostasis network function and identified Neddylation inhibition by Pevonedistat as a robust promoter of soluble tau degradation. Mechanistic analysis including proteomic profiling revealed that Neddylation inhibition hastens HaloTag-Tau clearance via compensatory activation of a proteasome-dependent pathway(s) as well as the autophagy-lysosome pathway. Our findings establish a powerful tool for probing tau homeostasis and highlight Neddylation inhibition as a potential therapeutic approach for enhancing both proteasome and lysosome-mediated tau clearance in tauopathies.
    DOI:  https://doi.org/10.64898/2026.01.28.702105
  22. Cell Death Differ. 2026 Feb 13.
    M1-linked ubiquitination by LUBAC regulates AMPK signalling and the response to energetic stress.
    Camilla Reiter Elbæk, Sophie Gradinaru, Anna M Dahlström, Alexander Frueh, Akhee S Jahan, Joyceline Cuenco, Anna L Aalto, John Rizk, Simon A Hawley, Sarah N J Franks, Michael Stumpe, Srinivasa Prasad Kolapalli, Chris Kedong Wang, Cara J Ellison, Ximena Hildebrandt, Klara Nielsen, Dominik Priesmann, Julian Koch, Mathilde Deichmann, Josef Gullmets, Lien Verboom, Geert van Loo, Nieves Peltzer, Lisa B Frankel, Paul R Elliott, Mads Gyrd-Hansen, Jörn Dengjel, Brent J Ryan, D Grahame Hardie, Annika Meinander, Kei Sakamoto, Rune Busk Damgaard.
      Methionine-1 (M1)-linked ubiquitin chains, assembled by the linear ubiquitin chain assembly complex (LUBAC) and disassembled by the deubiquitinase OTULIN, are critical regulators of inflammation and immune homoeostasis. Genetic loss or mutation of the LUBAC subunits HOIP and HOIL-1 or of OTULIN causes autoinflammatory syndromes accompanied by metabolic defects, including amylopectinosis, lipodystrophy, and fatty liver disease. Yet, it remains unclear how LUBAC and OTULIN control metabolic signalling. Here, we demonstrate that LUBAC and OTULIN dynamically regulate the energy-sensing kinase AMPK, a central sensor and switch for cellular and organismal energy balance. LUBAC's activity through the catalytic subunit HOIP is required for full AMPK activation in response to energetic stress, whereas OTULIN antagonises this response. LUBAC and OTULIN form a complex with AMPK, and LUBAC can directly ubiquitinate AMPKα and β subunits in cells and in vitro, establishing AMPK as a bona fide M1-linked ubiquitin substrate. Loss of LUBAC blunts AMPK activation, reduces bioenergetic adaptability, impairs autophagy, and sensitises cells to starvation-induced death, while Drosophila lacking Lubel - the fly orthologue of LUBAC - exhibit defective AMPK activation and reduced survival during starvation. Our findings identify M1-linked ubiquitination as a previously unrecognised regulatory layer controlling AMPK activation, metabolic adaptability, and the cellular response to energetic stress.
    DOI:  https://doi.org/10.1038/s41418-026-01675-z
  23. Eur J Med Chem. 2026 Feb 03. pii: S0223-5234(26)00080-2. [Epub ahead of print]307 118635
    Discovery of KRAS-G12D degraders via exploration of various E3 ligases.
    Hyerin Yim, Xiangyang Song, Yue Zhong, Jacqueline Hu, Yan Xiong, Jian Jin.
      PROteolysis TArgeting Chimera (PROTAC) is a promising modality for targeted protein degradation. Although 600+ E3 ligases exist in the human genome, most PROTACs exploit a very limited set of E3 ligases, primarily CRBN and VHL. In this study, we designed, synthesized and evaluated a series of KRAS-G12D degraders that recruit one of four E3 ligases (CRBN, VHL, DCAF1, or KLHDC2) using a common KRAS-G12D binder derived from the KRAS-G12D inhibitor MRTX1133. Through this structure-activity relationship (SAR) study, we discovered two potent degraders: 30 (CRBN-based) and 41 (VHL-based), both of which effectively degraded KRAS-G12D and suppressed downstream signaling. By introducing a triazole-based VHL ligand, we subsequently discovered 43, which showed improved degradation and antiproliferative activity comparable to a previously reported KRAS-G12D degrader. In contrast, KLHDC2- and DCAF1-based degraders failed to induce KRAS-G12D degradation, potentially due to suboptimal ternary complex formation or insufficient E3 ligase compatibility. These findings highlight the importance of E3 ligase selection in the development of effective KRAS-G12D degraders.
    DOI:  https://doi.org/10.1016/j.ejmech.2026.118635
  24. bioRxiv. 2026 Feb 06. pii: 2026.02.04.703729. [Epub ahead of print]
    Quasi-continuous cotranslational compaction and folding of a multidomain protein.
    Spyridoula Mitsikosta, Justin M Westerfield, Fátima Pardo-Avila, Michael Levitt, Gunnar von Heijne, Ane Metola.
      Most proteins start to fold cotranslationally as they come off the ribosome. So far, studies of cotranslational folding have focused mainly on small, single-domain proteins. Here, we have used Force Profile Analysis to study the cotranslational folding of Firefly luciferase, a complex 550-residue protein composed of an N-terminal domain (NTD) encompassing two split Rossmann folds (RF-1, RF-2) and a β-roll, and a flexibly attached C-terminal domain (CTD). The folding process is characterized by a quasi-continuous series of compaction/folding steps that generate intermediate-size pulling forces on the nascent chain, punctuated by a prominent high-force event that represents the folding of the RF-2 domain, and a few low-force instances that likely indicate the formation of distinct folding intermediates. Trigger Factor interacts extensively with the nascent chain when the central part of RF-2 and the early parts of the CTD are synthesized. Our analysis uncovers a cotranslational compaction/folding process that is rich in detail and not just a simple succession of a few distinct, cooperative folding transitions.
    DOI:  https://doi.org/10.64898/2026.02.04.703729
  25. Nat Commun. 2026 Feb 10.
    Degraders of the dengue virus capsid protein exhibit differentiated pharmacology relative to capsid inhibitors.
    Antara Chakravarty, Lu-Ning Wang, Ryan P Golden, Zhengnian Li, Katherine A Donovan, Oshri Afanzar, Yupeng Zhang, Eric S Fischer, Nathanael S Gray, Priscilla L Yang.
      Due to the limited size of viral genomes, most viral proteins are multifunctional; yet most direct-acting antivirals are designed as single-function inhibitors. The dengue virus (DENV) capsid protein serves as a building block for new virions while also interacting with multiple host factors to remodel the cellular environment. Using established capsid inhibitor ST148 as a targeting ligand, we develop a DENV capsid degrader, RPG-01-132, that exhibits a broadened spectrum of activity against the four DENV serotypes and an ST148-resistant mutant virus. Using multiple approaches, we show that RPG-01-132's sub-micromolar antiviral activity is due to CRL4CRBN-dependent degradation of capsid and that this mechanism disrupts capsid-related pathways required for productive infection, including infectious virus output and capsid-mediated antagonism of the interferon response. This pharmacology is well-differentiated from ST148, which interferes with assembly of new virions, but has no demonstrated effect on the capsid's nonstructural functions. These findings demonstrate that targeted protein degradation can thus enable antiviral pharmacology not observed with conventional antiviral inhibitors and that is resilient to point mutations that reduce inhibitor potency.
    DOI:  https://doi.org/10.1038/s41467-026-69263-w
  26. bioRxiv. 2026 Jan 27. pii: 2026.01.26.698744. [Epub ahead of print]
    Active transport of tRNAs facilitates distributed protein synthesis.
    Jennifer Morgan Petrosino, Vasiliki Courelli, Keita Uchida, Charles Bond, Barry Cooperman, Alexey I Bogush, Melike Lakadamyali, Benjamin L Prosser.
      Terminally differentiated cells such as cardiomyocytes, skeletal myofibers, and neurons rely on localized protein synthesis to sustain size, remodel and adapt to stress. The subcellular architecture of these cells is also inherently unfavorable for long-range, diffusion-based transport, which may promote their heavy reliance on active transport mechanisms for the localization of RNA and proteins. Transfer RNAs (tRNAs) function as essential regulators of protein synthesis by linking transcription and translation. Since their discovery in the 1950s, tRNA subcellular distribution has been assumed to occur through passive diffusion. Here, we report that there are pools of tRNAs that depend on the microtubule network for distribution in cardiomyocytes, skeletal myofibers and neurons. Employing dual-color live and fixed-cell super-resolution imaging, we demonstrate that active transport of tRNAs involves hitchhiking on the exterior of endolysosomal vesicles (ELV). We establish that leucyl-tRNA synthetase (LeuRS), the tRNA-binding protein that charges leucine to its cognate tRNA and interacts with Rag GTP on the surface of ELVs, is essential for tRNA transport. Disruption of LeuRS-ELV interactions is sufficient to impair long-range, microtubule-dependent tRNA transport, without affecting mRNA or rRNA transport. We also show that preventing tRNA transport is sufficient to impair translation at sites distal from the nucleus as well as globally impair protein synthesis, ultimately reducing cell size. These findings redefine tRNAs as actively trafficked cargo and establish their directed transport as a fundamental layer of translation regulation required for myocyte homeostasis.
    DOI:  https://doi.org/10.64898/2026.01.26.698744
  27. Nat Chem Biol. 2026 Feb 10.
    NCBP1 stress signaling drives alternative S6K1 splicing inhibiting translation.
    Dalu Chang, Mahdi Assari, Chananya Suwathep, Khomkrit Sappakhaw, Chayasith Uttamapinant, Marcus J C Long, Yimon Aye.
      Subcellular stress profoundly influences protein synthesis. However, both the nature of spatiotemporally restricted chemical cues and local protein responders to these cues remain elusive. Unlocking these mechanisms requires the ability to functionally map in living systems locale-specific stress responder proteins and interrogate how chemical modification of each responder impacts proteome synthesis. We resolved this problem by integrating precision localized electrophile generation and genetic code expansion tools. Upon examination of four distinct subcellular locales, only nuclear-targeted electrophile stress stalled translation. We discovered that NCBP1-a nuclear-resident protein with multifaceted roles in eukaryotic mRNA biogenesis-propagated this nuclear stress signal through a single cysteine (C436) from among its 19 conserved cysteines. This NCBP1(C436)-specific modification elicited alternative splicing of more than 250 genes. Mechanistically, global protein synthesis stall was choreographed by impaired association between electrophile-modified NCBP1(C436) and SF3A1, an essential component of spliceosome, triggering the production of alternatively spliced S6 kinase, whose expression was sufficient to dominantly inhibit protein translation.
    DOI:  https://doi.org/10.1038/s41589-025-02135-4
  28. Biochemistry. 2026 Feb 12.
    Targeted Protein Degrader from Ginkgo to Mitigate Amyloid β-Induced Neurotoxicity.
    Bamaprasad Dutta, Shining Loo, Antony Kam, Chuan-Fa Liu, James P Tam.
      Protein degradation through the autophagy-lysosome process by eukaryotic cells is a major pathway to remove unwanted proteins, organelles, and invading pathogens. It is also an emerging intervention strategy to selectively eliminate inaccessible toxic amyloid proteins to prevent amyloid β (Aβ)-induced neurotoxicity. Currently, there is no natural product-derived peptide that targets amyloid proteins for degradation through the autophagy-lysosome pathway. We recently discovered a new peptide family from Ginkgo biloba nuts, which we termed β-ginkgotides. The prototype β-gB1 is 20-residue in length, cross-braced by three disulfides, and stable to proteolytic degradation. Importantly, it has an LC3-interacting region (LIR) motif, which promotes selective autophagy to degrade harmful proteins and to prevent cell death. Here, we show that β-gB1 is cell-penetrating, primarily entering cells through energy-dependent endocytosis, and protects Aβ-induced neurotoxicity using an SH-SY5Y neuronal cell-based model. Functional studies using synthetic β-gB1 revealed that it impedes Aβ accumulation and reverses the altered gene expression associated with Alzheimer's disease (AD) pathophysiology induced by Aβ. Importantly, β-gB1 maintains cellular homeostasis and enhances the clearance of Aβ aggregates through selective autophagy, thereby safeguarding neurons from Aβ toxicity. Collectively, these results support that β-ginkgotide is a first-in-class cysteine-rich peptide (CRP)-based targeted protein degrader and underscore its potential as a novel and promising neuroprotective therapeutic to manage Aβ-induced neurotoxicity in AD and other neurodegenerative disorders.
    DOI:  https://doi.org/10.1021/acs.biochem.5c00763
  29. Autophagy. 2026 Feb 08.
    Regorafenib enhances anti-PDCD1/PD-1 therapeutic efficacy in colorectal cancer by promoting SQSTM1/p62-mediated CD274/PD-L1 degradation.
    Ming Zhu, Yinjun He, Siqin Lei, Xuan Lai, Chaoyi Chen, Kehong Ye, Dianyang Li, Honghe Zhang, Maode Lai, Weiqin Jiang.
      Despite the clinical success of PDCD1/PD-1 and CD274/PD-L1 immune checkpoint blockade in multiple cancers, its efficacy in colorectal cancer (CRC) remains limited. Here, we report that the combination of the tyrosine kinase inhibitor regorafenib with PDCD1 blockade enhances anti-tumor immunity in CRC, both in clinical observations and preclinical models. Mechanistically, regorafenib acts as a molecular glue, directly promoting the interaction between CD274 and the selective autophagy receptor SQSTM1/p62, leading to SQSTM1-mediated autophagic degradation of CD274 and restoration of T cell-mediated cytotoxicity. In summary, these findings identify a previously unrecognized role of regorafenib in modulating tumor immune evasion and provide a mechanistic rationale for its combination with PDCD1 inhibitors in CRC treatment.
    Keywords:  Antitumor immunity; PD-L1; molecular glue; p62; protein degradation; regorafenib
    DOI:  https://doi.org/10.1080/15548627.2026.2629288
  30. Cold Spring Harb Perspect Biol. 2026 Feb 09. pii: a041769. [Epub ahead of print]
    Control of Inositol 1,4,5-Trisphosphate Receptor Activity by Posttranslational Modifications.
    Maarten Vanmunster, Ian de Ridder, Manon Callens, David Yule, Irina Serysheva, Jan B Parys, Geert Bultynck.
      Inositol 1,4,5-trisphosphate receptors (IP3Rs) are tetrameric calcium (Ca2+) release channels localized in the endoplasmic reticulum (ER), where they regulate cellular function by mediating local and global Ca2+ fluxes toward the cytosol, cell membrane, and organelles including mitochondria. Disruptions in these Ca2+ signals, whether excessive or diminished, due to alterations in IP3R function have been implicated in a wide range of diseases and pathophysiological conditions. Consequently, the Ca2+-flux properties, protein abundance, and localization of IP3Rs must be tightly regulated. Various mechanisms, including interactions with accessory proteins, ensure proper IP3R function across diverse physiological contexts. In this review, we highlight the role of posttranslational modifications (PTMs) in modulating IP3R activity, including phosphorylation/dephosphorylation, redox modifications, glycosylation, palmitoylation, ubiquitination, proteolysis, and transglutaminase-mediated cross-linking. We discuss not only the functional consequences of these PTMs but also provide structural insights when specific modified IP3R residues have been identified. Furthermore, whenever possible, we emphasize IP3R isoform-specific effects of PTMs, offering a nuanced perspective on their regulatory significance.
    DOI:  https://doi.org/10.1101/cshperspect.a041769
  31. Nat Commun. 2026 Feb 11.
    Negative feedback regulation of STING signaling by TAX1BP1-directed Golgiphagy.
    Sujit Suklabaidya, Suchitra Mohanty, Irene E Reider, Jesse White, Dominic Colter, Sarah M McCormick, Noula Shembade, Young Bong Choi, Christopher C Norbury, Edward W Harhaj.
      The cGAS-STING pathway is a critical regulator of type I Interferon (IFN) and inflammation upon cytosolic DNA-sensing. cGAS-STING signaling termination is regulated by lysosomal-mediated degradation of STING; however, the mechanisms controlling the inhibitory targeting of STING are incompletely understood. Here, we identify the selective autophagy receptor TAX1BP1 as a negative regulator of the cGAS-STING pathway. TAX1BP1-deficient macrophages activated by cGAS or STING agonists accumulate higher-order STING aggregates, exhibit heightened STING signaling, and increased production of type I IFN and proinflammatory cytokines. Mechanistically, TAX1BP1 promotes STING degradation through microautophagy by facilitating the interaction of STING with the ESCRT-0 protein HGS. Furthermore, STING activation is associated with the swelling and fragmentation of the Golgi apparatus, and TAX1BP1 and p62/SQSTM1 are essential for the autophagic degradation of fragmented Golgi (Golgiphagy). Our findings suggest that STING activation at the Golgi is coupled to its downregulation by Golgiphagy to restrict innate immune responses.
    DOI:  https://doi.org/10.1038/s41467-026-69422-z
  32. bioRxiv. 2026 Feb 01. pii: 2026.01.28.702366. [Epub ahead of print]
    A selective Cullin 3 RING E3 ligase inhibitor attenuates hyperglycemia via dual insulin sensitizing and insulinotropic action.
    Lijie Gu, Lei Xiong, Mohammad Nazmul Hasan, Yanhong Du, Timothy Wu, Tiangang Li.
      Hyperglycemia is a hallmark of type-2 diabetes and a key pathogenic driver of diabetic complications. Cullin RING E3 ligases (CRLs) are multi-subunit E3 ubiquitin ligases that mediate cellular protein turnover. The activity of CRLs requires cullin neddylation, a post-translational modification that can be pharmacologically targeted with therapeutic potentials. By using hyperinsulinemic-euglycemic clamp analysis, we discover that pan neddylation inhibitor exerts both insulin sensitization effect in liver and muscle and insulinotropic effect in pancreatic β cells. This dual action is mediated by Cullin 3 (Cul3), a member of the 7 canonical cullin family proteins. DI-1859, a selective Cul3 neddylation inhibitor, effectively protects against hyperglycemia in obese mice. DI-1859 enhances insulin signaling by preventing Cul3-mediated insulin receptor substrate degradation in liver and muscle cells. DI-1859 increases insulin secretion in a glucagon-like peptide-1-independent manner in mice and directly potentiates glucose-stimulated insulin secretion in INS-1 832/13 β cells and human islets. Mechanistic studies reveal that DI-1859 does not promote glycolytic flux or bioenergetics function but potentiates glucose-stimulated insulin secretion via mechanisms involving RhoA activation and cytoskeleton remodeling in β cells. This study shows that a single agent targeting Cul3 neddylation simultaneously promotes insulin sensitization and insulin secretion to attenuate hyperglycemia in mice.
    Article Highlights: a. Pan cullin neddylation inhibitors exhibit potent hypoglycemic effect.b. The target organs and mechanisms underlying the hypoglycemia effect of cullin pan neddylation inhibitors are incompletely understood.c. We found that inhibition of Cul3 leads to a dual insulin sensitization and insulinotropic effect.d. Selective inhibition of Cul3 neddylation is a feasible approach to lower hyperglycemia.
    DOI:  https://doi.org/10.64898/2026.01.28.702366
  33. iScience. 2026 Feb 20. 29(2): 114738
    Heritable ER stress impairs mitochondrial metabolism and maintenance of hematopoietic stem cells after low-dose irradiation.
    Stephanie G Moreno, Federica Ferri, Daniel Lewandowski, Vilma Barroca, Saiyiramii Devanand, Nathalie Dechamps, Paul-Henri Romeo, Nathalie Gault.
      How hematopoietic stem cells (HSCs) respond to low doses of radiation currently used in medicine is largely unknown. Here, we show that HSC exposed to a single 20 mGy dose of irradiation (20 mGy-HSC) exhibit, when proliferating, oxidative stress and altered metabolism associated with increased mitochondrial reactive oxygen species and mitochondrial Ca2+ overload. These mitochondrial defects arise from immediate and sustained endoplasmic reticulum (ER) stress, induced by proliferative 20 mGy-HSC through the activation of the eIF2α-ATF4 branch of the unfolded protein response (UPR). The ER stress is heritable and leads, in long-term quiescent 20 mGy-HSC, to the activation of the IRE1α-Xbp1 branch of UPR, which fails to restore ER homeostasis, resulting in a decreased long-term HSC pool. Finally, we show that this heritable ER stress leads to global DNA hypomethylation, partially reversed by the early inhibition of ER stress. Our studies illuminate how adaptive ER stress responses can lead to mitochondrial defects and HSC dysfunctions.
    Keywords:  Cell biology
    DOI:  https://doi.org/10.1016/j.isci.2026.114738
  34. Neurochem Res. 2026 Feb 09. 51(1): 71
    MARCH6 Confers Protection Against Endoplasmic Reticulum Autophagy in Gliomas by Destabilizing FAM134B.
    Yeming Zhou, Rui Chen, Guokun Liu, Lu Zhang, Hongyan Zheng, Jinyu Zheng, Xiaohua Zuo, Peng Xie.
      This study probed the mechanism of MARCH6 in endoplasmic reticulum autophagy (ER-phagy) during glioma development by regulating FAM134B stability. MARCH6 and FAM134B expression levels were measured in glioma tissues. A comparative analysis was conducted on the correlation between clinical parameters and FAM134B expression in 46 glioma patients. FAM134B and MARCH6 were knocked down in glioma cells, followed by detection of cell viability and apoptosis, typical ER stress (ERS) markers (PERK, IRE1α, eIF2α, and CHOP), autophagy-related proteins (P62 and LC3B), and autophagosome cytoplasmic accumulation. A mouse glioma model was established for in vivo validation. MARCH6-FAM134B interaction, FAM134B ubiquitination levels, and protein stability were examined. FAM134B expression was high and MARCH6 expression was low in glioma tissues. MARCH6 induced FAM134B protein ubiquitination and degradation, reducing its stability in glioma cells. Knockdown of FAM134B reduced glioma cell survival, inhibited PERK, IRE1α, eIF2α, and CHOP expression, decreased LC3I to LC3II conversion, lowered LC3B fluorescence expression, and reduced the accumulation of autophagosomes with continuous ER structures in the cytoplasm, while enhancing apoptosis and P62 expression. This effect can be reversed by knocking down MARCH6. In vivo, FAM134B knockdown suppressed tumorigenesis in mice. MARCH6 exerts a repressive effect on ERS responses and ER-phagy in glioma cells by destabilizing FAM134B.
    Keywords:  Endoplasmic reticulum autophagy; Endoplasmic reticulum stress response; FAM134B; Glioma; MARCH6; Ubiquitination
    DOI:  https://doi.org/10.1007/s11064-026-04684-z
  35. Mol Cell Proteomics. 2026 Feb 09. pii: S1535-9476(26)00022-8. [Epub ahead of print] 101527
    Subcellular proteomic analyses reveal REEP5 knockdown in the mouse heart disrupts mitochondrial networks.
    Michelle Di Paola, Cristine J Reitz, Uros Kuzmanov, Kateleen Jia, Anthony O Gramolini.
      Receptor Expression-Enhancing Protein 5 (REEP5) is a cardiac-enriched, membrane-shaping protein localized to the sarco(endo)plasmic reticulum (SR/ER), where it supports membrane network architecture and cardiomyocyte function. While REEP5 has been implicated in calcium handling and contractility, its role in regulating inter-organelle communication and mitochondrial homeostasis remains less well-understood. In this study, we used recombinant adeno-associated virus serotype 9(rAAV9)-mediated shRNA knockdown of Reep5 in mouse hearts, combined with subcellular fractionation and data-independent acquisition mass spectrometry (DIA-MS), to define proteomic remodeling across microsomal (SR/ER), mitochondrial, and cytosolic compartments. Loss of REEP5 altered the composition of SR/ER membrane-shaping proteins, including upregulation of RTN4, ATL3, and CKAP4, suggesting a partial compensatory response. Microsomal, mitochondrial and cytosolic proteomes exhibited broad reorganization, with enrichment of proteins involved in redox adaptation and proteostasis, alongside depletion of mitochondrial import machinery and antioxidant enzymes. Imaging of isolated cardiomyocytes confirmed fragmented mitochondrial networks and increased reactive oxygen species (ROS), consistent with proteomic signatures of disrupted mitochondrial dynamics and oxidative stress. Gene ontology enrichment across all fractions highlighted widespread dysregulation in organelle-specific processes, including translation, protein localization, and metabolic remodeling. Notably, several altered pathways converged on mitochondria-associated membranes (MAMs), suggesting that REEP5 may support SR/ER-mitochondria tethering and functional crosstalk. These findings position REEP5 as a key regulator of organelle homeostasis in the heart and underscore how its loss disrupts mitochondrial integrity and inter-organelle communication across cellular compartments.
    DOI:  https://doi.org/10.1016/j.mcpro.2026.101527
  36. Sci Rep. 2026 Feb 13.
    Signal recognition particle-dependent secretome in humans.
    Sarah C Miller, Elena B Tikhonova, Cristian Camilo Rodríguez-Almonacid, Christian Bustamante, Susan T Weintraub, Andrey L Karamyshev.
      About 30% of all cellular proteins are secreted and membrane proteins. They can be transported by signal recognition particle (SRP)-dependent or SRP-independent mechanisms. However, little is known about which proteins are SRP-dependent and SRP-independent in mammals. In this work, we address this fundamental question by mass spectrometry analysis of proteins in cells and conditioned medium when SRP is defective. The analysis demonstrates that the majority of secretory proteins in the medium and many in cells have lower abundance relative to controls, demonstrating the SRP dependence of the human secretome. We also described new SRP-independent proteins. Moreover, we found potential compensatory pathways activated when SRP is defective, and protein network that may play a role in quality control of the secretory and membrane proteins and their mRNAs in humans.
    Keywords:  Protein targeting; Protein transport; Secretome; Secretory pathway; Signal peptide; Signal recognition particle (SRP)
    DOI:  https://doi.org/10.1038/s41598-026-35427-3
  37. bioRxiv. 2026 Feb 01. pii: 2026.01.28.702376. [Epub ahead of print]
    The active secretion of a subunit of IL-12 by tissue cells is regulated by Valosin-Containing Protein and intracellular calcium redistribution.
    Elizabeth M Hill, Jaclyn Bredenkamp, Gabrielle C McBroom, Budhaditya Chatterjee, Kenneth M Rosenberg, Nevil J Singh.
      One molecular mechanism for collaboration between innate immune and tissue stromal cells in regulating effector responses is the formation of the innate cytokine IL-12 as a result of the two cell types contributing distinct subunits (p40 and p35) allowing for the localized assembly of the functional IL-12 heterodimer. Dendritic cell activation leads to p40 secretion, but the pathways in stromal cells allowing p35 secretion are unknown. We identify the inhibition of Valosin-Containing Protein (VCP) and increases in intracellular calcium signaling as the key regulators for the secretion of p35 from its homeostatic reservoirs in the endoplasmic reticulum. This p35 secretion, in the absence of co-expression of the p40 subunit, requires active gene expression, is independent of ER stress pathways, and is distinct from passive (cell-death dependent) release processes. Thus, an active sensory apparatus in non-hematopoietic cells contributes to the collaborative control of the trajectory of early immune differentiation.
    One Sentence Summary: VCP inhibition and calcium flux allows stromal cells to release the p35 subunit of the cytokine IL-12 and regulate localized cytokine activity.
    DOI:  https://doi.org/10.64898/2026.01.28.702376
  38. Mol Cell. 2026 Feb 06. pii: S1097-2765(26)00035-3. [Epub ahead of print]
    HSPA1A and DNAJB1 regulate NELF condensate dynamics to safeguard transcriptional recovery under heat stress.
    Shuyao Jiang, Zixuan Jia, Wenxuan Zhu, Yu Liu, Huanyi Fu, Feifeng Zhu, Zhuo Li, Jiaye Yang, Yiying Zhu, Zhongxing Sun, Tianyi Zhu, Xuebo Quan, Huipeng Jiao, Kai Huang, Zhibing Wu, Wei Zou, Bing Yang, Yi Lu, Long Zhang, Fangfang Zhou, Dong Fang, Huasong Lu.
      Promoter-proximal pausing by negative elongation factor (NELF) establishes a critical checkpoint for RNA polymerase II (RNA Pol II) transcription. Heat shock (HS) induces NELF to form nuclear condensates, yet how their dynamics are regulated and coupled to transcriptional adaptation remains unclear. Using a nanobody-based proximity labeling strategy (NbPro), we identify the molecular chaperones HSPA1A and DNAJB1 as key regulators of NELF condensate dynamics. Although dispensable for initial HS-induced transcriptional repression, chaperone-mediated regulation is required for efficient transcriptional reactivation during recovery. Mechanistically, DNAJB1 recognizes NELFA's tentacle domain and facilitates HSPA1A recruitment, thereby preventing aberrant aggregation and enabling timely condensate disassembly. Disruption of NELF condensate dynamics leads to persistent NELFA phosphorylation, impaired chromatin association, destabilized RNA Pol II pausing, and premature release of non-productive RNA Pol II complexes. Together, these findings reveal a chaperone-dependent mechanism that governs NELF condensate dynamics and highlight promoter-proximal pausing as a checkpoint to prevent immature RNA Pol II escape, rather than merely a means of transcriptional repression.
    Keywords:  NELF; RNA Pol II pausing; biomolecular condensate; heat shock
    DOI:  https://doi.org/10.1016/j.molcel.2026.01.015
  39. Bioorg Med Chem. 2026 Feb 07. pii: S0968-0896(26)00046-5. [Epub ahead of print]136 118590
    An integrated framework identified potent inhibitors targeting IRE1α.
    Subramaniyan Divya, Priti Talwar, Palaniyandi Ravanan.
      Inositol-requiring enzyme 1 (IRE1α) is one of the key sensors and signaling effectors of the unfolded protein response (UPR), which is essential for preserving endoplasmic reticulum (ER) homeostasis. Dysregulation of IRE1α signaling can lead to several illnesses. Initially, we employed the multidocking approach utilizing AutoDock Vina, AutoDock Wizard, and iGEMDOCK to predict the accurate binding affinities of the flavonoid library against IRE1α and rank them based on their affinities. Subsequently, post-docking approaches were used to refine the hit selection. Finally, the top-ranked flavonoids were selected based on their consistent high binding affinity and exhibited strong binding within the ATP-binding pocket of the kinase active site. In vitro kinase assays revealed that both amentoflavone and glycitein significantly inhibited IRE1α kinase activity, with IC50 values of 16.4 μM and 23.68 μM, respectively. Cell-based studies demonstrated that these flavonoids have anti-inflammatory properties and significantly promote robust activation of XBP1 splicing and IRE1α expression under normal conditions. In contrast, flavonoid pretreatment significantly attenuated LPS-induced IRE1α-XBP1 signaling and reduced inflammatory responses. Overall, our results indicate that both glycitein and amentoflavone exhibit promising modulatory effects on IRE1α. To the best of our knowledge, this is the first study to report the modulatory potential of flavonoids amentoflavone and glycitein to possess both IRE1α kinase inhibitory and RNase-activating properties. This work provides a valuable basis for the development of flavonoid-based IRE1α inhibitors to treat ER stress and associated inflammatory diseases.
    Keywords:  Flavonoids; IRE1α modulators; Post-docking approaches
    DOI:  https://doi.org/10.1016/j.bmc.2026.118590
  40. PLoS Pathog. 2026 Feb;22(2): e1013967
    Flexibility and modulation of translation initiation in enterovirus genomes.
    Rhian L O'Connor, Georgia M Cook, Jacqueline Hankinson, Ksenia Fominykh, Samantha H Cheng, Daniel A Nash, Aurélie Cenier, Komal M Nayak, Stephen C Graham, Janet E Deane, Matthias Zilbauer, Andrew E Firth, Valeria Lulla.
      Enteroviruses comprise a large group of mammalian pathogens that often utilize two open reading frames (ORFs) to encode their proteins: the upstream protein (UP) and the main polyprotein. In some enteroviruses, in addition to the canonical upstream AUG (uAUG), there is another AUG that may represent an alternative upstream initiation site. An analysis of enterovirus sequences containing additional upstream AUGs identified several clusters, including strains of pathogenic Enterovirus alphacoxsackie and E. coxsackiepol. Using ribosome profiling on coxsackievirus CVA13 (E. coxsackiepol), we demonstrate that both upstream AUG codons can be used for translation initiation in infected cells. Moreover, we confirm translation from both upstream AUGs using a reporter system. Mutating the additional upstream AUG in the context of CVA13 did not result in phenotypic changes in immortalized cell lines. However, the wild-type virus outcompeted this mutant in human intestinal organoids and differentiated neuronal systems, representing an advantage in physiologically relevant infection sites. Mutation of the stop codon of the shorter upstream ORF led to dysregulated translation of the other ORFs in the reporter system, suggesting a potential role for the additional uORF in modulating the expression level of the other ORFs. Additionally, we demonstrate regulation of uORF translation in response to stress. These findings reveal the remarkable plasticity of enterovirus IRES-mediated initiation and the competitive advantage of double-upstream-AUG-containing viruses in terminally differentiated intestinal organoids and neuronal systems.
    DOI:  https://doi.org/10.1371/journal.ppat.1013967
  41. Molecules. 2026 Jan 28. pii: 459. [Epub ahead of print]31(3):
    A Novel Paradigm for Targeting Challenging Targets: Advancing Technologies and Future Directions of Molecular Glue Degraders.
    Yifan Zhang, Linlin Li, Jiajia Xu, Chunchen Che, Jiaqing Jia, Haohao Lu, Qidong You, Xiaoli Xu.
      Molecular glue degraders (MGDs) constitute a class of innovative therapeutic agents within the field of targeted protein degradation (TPD). In contrast to proteolysis-targeting chimeras (PROTACs), MGDs induce protein degradation by stabilizing the interaction between an E3 ubiquitin ligase and a target protein. They typically exhibit favorable drug-like characteristics, including lower molecular weight and enhanced bioavailability. Although their discovery was historically serendipitous, recent advances in high-throughput screening, bioinformatics, and artificial intelligence are enabling more systematic identification and optimization. To date, three MGD-based drugs have been approved for clinical use, with numerous candidates under active investigation. This review comprehensively traces the technological progression of MGDs from serendipitous discovery to the current era of rational design. We systematically introduce and critically evaluate strategies for discovering MGDs, accompanied by illustrative examples. Concurrently, we discuss the major challenges hindering the broader application of MGDs and propose potential approaches to address these issues. Finally, we outline prospective research directions in the field. This review aims to provide a holistic framework for understanding the past, present, and future of molecular glue degraders, underscoring their significant potential to reshape the landscape of drug discovery.
    Keywords:  drug discovery methods; molecular glue degraders; targeted protein degradation
    DOI:  https://doi.org/10.3390/molecules31030459
  42. iScience. 2026 Jan 16. 29(1): 114341
    Legionella employs the multimodal ubiquitination of Sec22b to modulate SNARE pairing.
    Tomoe Kitao, Rina Iida, Hideki Kondo, Yoshiki Miura, Hikari Taka, Susan Kiiru, Toru Okamoto, Kohei Arasaki, Hideaki Higashi, Tomoko Kubori, Hiroki Nagai.
      Legionella pneumophila establishes its replicative niche through the deployment of multiple effector proteins. During this process, the host v-SNARE Sec22b is recruited from the endoplasmic reticulum to bacterial phagosomes and engages in non-canonical pairings with plasma membrane syntaxins. We previously reported that Sec22b undergoes polyubiquitination at early stages of infection and that the Legionella deubiquitinase LotB cleaves polyubiquitin chains from Sec22b, resulting in Sec22b dissociating from syntaxin 3. The current study investigates the molecular mechanisms underlying Sec22b ubiquitination and its physiological function during L. pneumophila infection. SdeA, a Legionella ubiquitin ligase, is identified as a crucial factor in promoting Sec22b polyubiquitination. SdeA catalyzes the conjugation of phosphoribosyl-linked ubiquitin to serine 137 of Sec22b; subsequently, the canonical ubiquitin system appears to polyubiquitinate Sec22b. Additionally, multimodal ubiquitination of Sec22b facilitates non-canonical SNARE pairing during early infection. This research outlines a bacterial strategy for modulating SNARE protein dynamics via reversible post-translational modifications.
    Keywords:  Biochemistry; Cell biology; Microbiology
    DOI:  https://doi.org/10.1016/j.isci.2025.114341
  43. J Biol Chem. 2026 Feb 05. pii: S0021-9258(26)00128-6. [Epub ahead of print] 111258
    Domain-specific folding of the tandem β-propeller protein Coronin 7 (Coro7) by CCT/TRiC.
    DeHaven J McCrary, Teri Naismith, Silvia Jansen.
      The Chaperonin containing tailless complex polypeptide 1 (CCT) or TCP-1 ring complex (TRiC) plays a central role in maintaining cellular homeostasis by supporting protein folding and damping protein aggregation. Besides the abundant cytoskeletal proteins, actin and tubulin, CCT/TRiC is emerging as an obligate chaperone for the β-propeller domain of WD40 proteins. To date, only WD40 proteins consisting of a single β-propeller domain have been described as CCT/TRiC substrates. Using a combination of biotin proximity ligation, co-immunoprecipitation, and knockdown studies, we here identify the tandem β-propeller protein, Coronin 7 (Coro7), as a novel substrate of CCT/TRiC. This raised the question how CCT/TRiC can fold a protein that is too large to fit into its folding chamber, but consists of two domains that require its folding. Surprisingly, co-immunoprecipitation of truncated Coro7 proteins or cleaved full length Coro7 demonstrated that CCT/TRiC only interacts with the first β-propeller domain (PropA) of Coro7. Further experiments showed that CCT/TRiC preferentially binds to PropA, independently of whether this domain is situated at the N- or C-terminus of Coro7. This strongly suggests that CCT/TRiC does not identify β-propeller substrates by their topology, but instead developed specific ways to recognize β-propeller sequences that require folding.
    Keywords:  CCT/TRiC; Coro7; chaperone-mediated folding; β-propeller
    DOI:  https://doi.org/10.1016/j.jbc.2026.111258
  44. Nat Commun. 2026 Feb 12. 17(1): 1645
    Lack of MDA5 delays hematopoietic aging by modulating inflammaging and proteostasis in mice.
    Veronica Bergo, Pavlos Bousounis, Giang To Vu, Mélodie Douté, Aikaterini Polyzou, Maria-Eleni Lalioti, Bogdan B Grigorash, Lyudmila Tsurkan, Nicholas Morchel, Ward Deboutte, Frédéric Brau, Thomas Manke, Sagar, Hind Medyouf, Dmitry V Bulavin, Nina Cabezas-Wallscheid, Marta Derecka, Eirini Trompouki.
      "Inflammaging", the chronic increase in inflammatory signaling with age, remains poorly understood in hematopoietic aging. Here, we identify the innate immune RNA sensor melanoma differentiation-associated protein 5 (MDA5) as an important factor of hematopoietic stem cell (HSC) aging. Aged Mda5-/- mice exhibit reduced HSC accumulation and myeloid bias. Importantly, aged Mda5-/- HSCs retain greater quiescence and superior repopulation capacity in noncompetitive transplants compared to wild-type counterparts. Multiomic analyses- including chromatin accessibility, transcriptomics, and metabolomics-reveal decreased inflammatory signaling, a youthful metabolic profile, and improved proteostasis in Mda5-/- HSCs, through regulation of HSF1 and phospho-EIF2A, key proteostasis regulators. Activation of HSF1 in aged wild-type HSCs partially restores youthful features, supporting a causal role for proteostasis maintenance. Collectively, our findings demonstrate that attenuating MDA5-dependent inflammation preserves HSC function during aging by maintaining metabolic fitness and proteostasis and provide insight into potential therapeutic strategies for mitigating hematopoietic aging.
    DOI:  https://doi.org/10.1038/s41467-026-69424-x
  45. Sci Adv. 2026 Feb 13. 12(7): eaea2726
    The allosteric landscape of the Src kinase.
    Antoni Beltran, Mohsin M Naqvi, Andre J Faure, Ben Lehner.
      Enzymes catalyze the reactions of life and are the targets of many drugs. Most inhibitors bind conserved active sites, frequently lacking specificity. Targeting allosteric sites can increase specificity, reduce toxicity, and allow fine-tuning of activity; however, most allosteric sites in enzymes are unmapped. Here, we present a comprehensive experimental allosteric map of the Src protein kinase. We quantify the effects of more than 50,000 single and double amino acid substitutions on activity and abundance and use thermodynamic modeling to disentangle changes in fold stability and catalysis. The comprehensive energy landscape reveals that allostery across the kinase domain is extensive, directionally biased, and modulated by its regulatory domains. Inhibitory-but not activating-allosteric mutations show a strong distance-dependent decay away from the active site. Using the map, we identify multiple potentially druggable allosteric sites not previously reported in Src or other kinases. Our results establish a framework for comprehensive mapping of allostery in kinases and other enzymes important for medicine and biotechnology.
    DOI:  https://doi.org/10.1126/sciadv.aea2726
  46. Nat Cell Biol. 2026 Feb 13.
    Defining the reference proteomes for small extracellular vesicles and non-vesicular components.
    Julia Morales-Sanfrutos, Joanes Etxeberria-Ugartemendia, Orhi Barroso-Gomila, Esperanza González, Maria Sendino, Pilar Ximénez-Embún, Fernando García, Eduardo Zarzuela, Juan M Falcón-Pérez, Héctor Peinado, Javier Muñoz.
      Extracellular vesicles (EVs) are key mediators of intercellular communication and promising biomarkers. However, their molecular characterization remains challenging due to the heterogeneity of EV subtypes and co-isolated non-vesicular components. Here we leverage protein correlation profiling along density gradients to systematically analyse over 9,000 proteins in human cancer cell lines and biofluids, providing a rigorous reassessment of virtually all protein constituents associated with small EVs (sEVs) and non-vesicular entities. We show that sEVs primarily incorporate plasma membrane proteins via selective cargo-loading mechanisms, with low inclusion of intraluminal soluble proteins. By contrast, the abundant cytosolic proteins frequently detected in sEV preparations are not encapsulated within vesicles but are externally associated, probably originating from copurifying cellular debris and aggregates. Our work provides a reference resource for understanding the biogenesis, molecular determinants of cargo selection and functional roles of sEVs.
    DOI:  https://doi.org/10.1038/s41556-026-01878-z
  47. Cell Stress Chaperones. 2026 Feb 06. pii: S1355-8145(26)00005-2. [Epub ahead of print] 100149
    Increased FICD-mediated protein AMPylation triggers conserved ER stress signaling across species.
    Mirella A Hernandez-Lima, Blaise L Mariner, William Giblin, Mark McCormick, Matthias C Truttmann.
      Post-translational protein modifications (PTMs) are fundamentally important in regulating protein function across species. One such PTM, referred to as protein AMPylation, is increasingly recognized to finetune ER stress signaling in metazoans. Protein AMPylation in the ER is catalyzed by conserved fic-domain containing enzymes (fic AMPylases), including FICD (Homo sapiens) and FIC-1 (Caenorhabditis elegans). However, it remains unclear whether enhanced fic AMPylase-mediated protein AMPylation promotes a conserved cellular response. In this study, we determined the transcriptomic consequences of increased fic AMPylase-mediated protein AMPylation in mouse fibroblasts and young adult nematodes. We find that in C. elegans, FIC-1(E274G) over-expression (OE) triggers a unique transcriptional signature, leading to the marked upregulation of pathways involved in cellular stress signaling. We further show that FIC-1(E274G) OE upregulates genes involved in antibacterial innate immune responses and identify a potentially co-regulated gene cluster sensitive to changes in AMPylation levels. Intriguingly, we observe a similar transcriptomic signature in mouse fibroblasts in response to FICD(E234G) OE. A cross-species comparison of the transcriptomes of nematodes, yeast, and mouse fibroblasts enduring increased fic AMPylase-mediated protein AMPylation revealed a conserved transcriptional core response to enhanced AMPylation. Collectively, this study defines a conserved cellular stress response to enhanced fic AMPylase-mediated protein AMPylation.
    Keywords:  AMPylation; BiP; ER stress; FICD; UPR
    DOI:  https://doi.org/10.1016/j.cstres.2026.100149
  48. bioRxiv. 2026 Feb 03. pii: 2026.02.01.703137. [Epub ahead of print]
    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.
      Following chromosome segregation, the nuclear envelope (NE) must be reassembled and holes in the nuclear membrane must be "sealed." During NE assembly, the NE-specific adaptor, Cmp7, recruits/activates ESCRT-III proteins to mediate NE sealing. However, recent evidence suggests the presence of alternative mechanisms. In a screen using the fission yeast, S. japonicus , 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 form a complex and mutations disrupting their interaction 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 the mechanisms crucial for maintaining the integrity of the nucleus.
    DOI:  https://doi.org/10.64898/2026.02.01.703137
  49. Cell Commun Signal. 2026 Feb 11.
    Protein disulfide isomerase A6 (PDIA6) is essential for acrosome biogenesis and male fertility in mice.
    Xiaofeng Yan, Yaqiong Zhang, Aizhen Yang, Yufeng Hou, Raymond B Birge, Jinxing Lv, Yi Wu.
       BACKGROUND: The family of protein disulfide isomerases (PDIs) are thiol oxidoreductases located predominantly in the endoplasmic reticulum that catalyze thiol-disulfide exchange for normal protein folding. Recent studies have shown that this family enzymes such as PDI contribute to the meiosis of spermatocytes and male fertility. However, the role of PDIA6 in the PDI family in spermatogenesis has not been characterized using genetically modified animal models.
    METHODS: A premeiotic PDIA6 conditional knockout (Stra8-Cre/Pdia6fl/fl) mouse model was generated for showing an essential role for PDIA6 in male fertility. To investigate the mechanism underlying the role of PDIA6 in this process, we performed a series of experiments including fertility assessment, scanning and transmission electron microscopy, TUNEL assay, spermatocyte spreading, immunofluorescence staining, intracellular calcium concentration measurement, 3-(N-maleimide-propionyl) biocytin (MPB) labeling and protein quantitative mass spectrometry.
    RESULTS: Abnormal round-headed shape resembling partial globozoospermia was observed in Stra8-Cre/Pdia6fl/fl mice. Ultrastructural analysis of PDIA6-deficient sperm demonstrated acrosome fragmentation and detachment from the nucleus, disrupted acroplaxome structure, disorganized flagellar axonemes, and cytoplasmic retention. PDIA6 deficiency also impaired the sperm acrosome reaction and calcium mobilization. Proteomic profiling revealed downregulation of acrosomal membrane and vesicle proteins, as well as calcium channel complexes in PDIA6-deficient testes. Moreover, PDIA6 deficiency down-regulated the synthesis of zona pellucida binding protein (ZPBP) in testes by impairing disulfide bond formation, and induced endoplasmic reticulum stress and apoptosis.
    CONCLUSIONS: PDIA6 is essential for redox regulation of protein synthesis and spermatogenesis causing male fertility in mice.
    Keywords:  Acrosome biogenesis; Male infertility; PDIA6; Redox; Sperm morphogenesis
    DOI:  https://doi.org/10.1186/s12964-026-02709-2
  50. Mol Cell. 2026 Feb 06. pii: S1097-2765(26)00023-7. [Epub ahead of print]
    RBPscan: A quantitative in vivo tool for profiling RNA-binding protein interactions.
    Dmitry A Kretov, Owen Sanborn, Thora McIsaac, Elaine Park, Imrat Imrat, Samuel Wu, Marianne Régis, Louis-Mathieu Harvey, Daniel Cifuentes.
      RNA-binding proteins (RBPs) are essential regulators of gene expression at the post-transcriptional level, yet obtaining quantitative insights into RBP-RNA interactions in vivo remains challenging. Here, we developed RBP specificity and contextual analysis via nucleotide editing (RBPscan), which integrates RNA editing with massively parallel reporter assays to profile RBP binding in vivo. In RBPscan, fusion of an RBP to the adenosine deaminase acting on RNA (ADAR) catalytic domain induces RNA editing of a recorder mRNA carrying the tested RBP-binding site, serving as a readout of the RBP-RNA interaction. We demonstrate the utility of RBPscan in zebrafish embryos, human cells, and yeast, showing that it quantifies binding strength, resolves dissociation constants, identifies binding motifs for various RBPs, and links binding affinities to their impact on mRNA stability. RBPscan also provides positional mapping of Pumilio-binding sites in the long non-coding RNA NORAD. With its simplicity, scalability, and cross-system compatibility, RBPscan is a versatile tool for investigating protein-RNA interactions and complements established methods for studying post-transcriptional regulatory networks.
    Keywords:  ADAR; RBP-binding specificity; RBPs; RNA editing; RNA motif discovery; RNA-binding proteins; adenosine deaminase acting on RNA; dose-response analysis; massively parallel reporter assays; microRNAs; protein-RNA interactions
    DOI:  https://doi.org/10.1016/j.molcel.2026.01.003
  51. Science. 2026 Feb 12. 391(6786): eadx6931
    Structural ontogeny of protein-protein interactions.
    Aerin Yang, Hanlun Jiang, Kevin M Jude, Deniz Akpinaroglu, Stephan Allenspach, Alex Jie Li, James Bowden, Carla Patricia Perez, Liu Liu, Po-Ssu Huang, Tanja Kortemme, Jennifer Listgarten, K Christopher Garcia.
      Understanding how protein binding sites evolve interactions with other proteins could hold clues to targeting "undruggable" surfaces. We used synthetic coevolution to engineer new interactions between naïve surfaces, simulating the de novo formation of protein complexes. We isolated seven distinct structural families of protein Z-domain complexes and found that synthetic complexes explore multiple shallow energy wells through ratchet-like docking modes, whereas complexes formed by natural binding sites converged in a deep energy well with a relatively fixed geometry. Epistasis analysis of a machine learning-estimated fitness landscape revealed "seed" contacts between binding partners that anchored the earliest stages of encounter complex formation. Our results suggest that "silent" surfaces have a shallower energy landscape than natural binding sites, disfavoring tight binding, likely owing to evolutionary counterselection.
    DOI:  https://doi.org/10.1126/science.adx6931
  52. Cell Rep. 2026 Feb 11. pii: S2211-1247(26)00053-7. [Epub ahead of print]45(2): 116975
    Circadian rhythm heterogeneity modulates drug response variations in neuroblastoma models.
    Carolin Ector, Christoph Schmal, Jeff Didier, Sébastien De Landtsheer, Johannes H Schulte, Ulrich Keilholz, Thomas Sauter, Achim Kramer, Hanspeter Herzel, Adrián E Granada.
      Circadian clocks regulate essential cellular functions and influence cancer development and treatment outcomes. Aligning therapy with circadian rhythms can improve efficacy and reduce toxicity, yet whether neuroblastoma, a heterogeneous pediatric tumor, maintains circadian function remains unclear. Here, we systematically profiled circadian dynamics across 12 neuroblastoma cell models using long-term bioluminescence assays and computational analysis. Our findings reveal heterogeneous circadian patterns ranging from robust to arrhythmic, which we linked to distinct neuroblastoma genetic features. By integrating drug sensitivity data, we identified candidate compounds whose effectiveness correlates with circadian expression profiles. Moreover, time-of-day treatment assays with the ALK inhibitor lorlatinib and frontline chemotherapeutics revealed distinct temporal drug responses that were more pronounced in circadian-competent than weakly rhythmic cell lines. Together, these findings establish circadian heterogeneity as a previously unrecognized dimension of neuroblastoma biology and highlight the therapeutic potential of chronotherapy approaches for improved treatment efficacy.
    Keywords:  CP: cancer; CP: metabolism; cancer; chronotherapy; circadian clock; circadian rhythms; neuroblastoma; systems biology; time-of-day sensitivity
    DOI:  https://doi.org/10.1016/j.celrep.2026.116975
  53. Biol Pharm Bull. 2026 ;49(2): 254-266
    Regulation of ER-Resident Transcription Factor NFE2L1 in HEK293 Cells.
    Maiko Yasui, Izumi Nagae, Ryoichi Murase, Kozue Uchio-Yamada, Mahmoud Kandeel, Tadayuki Tsujita, Kentaro Oh-Hashi.
      Nuclear factor erythroid-derived 2 like 1 (NFE2L1) is reported to be embedded in the endoplasmic reticulum (ER) membrane and subsequently undergo N-glycosylation at several asparagine residues as well as other ER-resident factors including cAMP response element binding protein 3 (CREB3)/ATF6 family members. In this study, we investigated the regulation of NFE2L1 protein expression by treating wild-type HEK293 cells and HEK293 cells deficient in selected ER-associated degradation (ERAD) factors with various reagents. NFE2L1 protein expression in wild-type HEK293 cells was negligible, but MG132/bortezomib treatment induced Endo H-resistant two bands. Suppressor/enhancer of lin-12-like (SEL1L)/hydroxymethylglutaryl-CoA (HMG-CoA) reductase degradation 1 (Hrd1) loss increased NFE2L1 protein expression without any stimuli. In these deficient cells, the band shift of NFE2L1 by MG132 was mostly suppressed. Treatment with the valosin containing protein (VCP) inhibitor CB-5083 increased NFE2L1 expression, but deficiencies in other ERAD-associated factors (ER degradation-enhancing α-mannosidase-like protein 2 (EDEM2), thioredoxin domain-containing protein 11 (TXNDC11), gp78, ring finger protein 5 (RNF5), ring finger protein 185 (RNF185), and USP19) did not affect its expression. Comparing the stability of the two intrinsic NFE2L1, which increases with proteasome inhibition, the higher molecular weight form corresponding to full-length form, was more unstable. Therefore, we constructed NFE2L1 genes with mutations in the site where NFE2L1 is cleaved by DDI2 and in the four asparagine residues where N-glycosylation occurs, and found that the high molecular weight form, especially a hypoglycosylated mutant, tended to be more unstable. Taken together, this study using several ERAD disordered models shows that the regulation of NFE2L1 is different in some ways from the regulation of CREB3/ATF6 family, and these findings implicate the diversity of N-glycosylated protein regulation in the ER.
    Keywords:  endoplasmic reticulum-associated degradation (ERAD); hydroxymethylglutaryl-CoA (HMG-CoA) reductase degradation 1 (Hrd1); nuclear factor erythroid-derived 2 like 1 (NFE2L1); suppressor/enhancer of lin-12-like (SEL1L); valosin containing protein (VCP)
    DOI:  https://doi.org/10.1248/bpb.b25-00607
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