bims-proteo Biomed News
on Proteostasis
Issue of 2026–09–06
fifty-four papers selected by
Eric Chevet, INSERM
  1. From Ternary Modeling to Predictive PROTAC Design: A Computational Perspective.
  2. Mass spectrometry-based mapping of the ubiquitin chaperone code.
  3. ER-associated sorting links proteostasis to photosynthesis.
  4. The moonlighting functions of SEC13 in nonsense-mediated mRNA decay and the regulation of ER stress.
  5. A Co-Chaperone Mimetic Perturbs Cellular Nitrogen Metabolism in Mycobacteria.
  6. Unbiased screen of human transcriptome reveals an unexpected role of 3'UTRs in translation initiation.
  7. RAB1 mediates OPTN-dependent mitophagy via ATG9A recruitment.
  8. An integrated landscape of mRNA and protein isoforms.
  9. Reconstitution of multistep recruitment of ULK1 to membranes in autophagy.
  10. A single-amino-acid cleavage controls global mitochondrial complex integrity.
  11. Ratiometric transcriptional activation by protein degradation.
  12. YTHDC1 functions as a molecular chaperone to suppress ALS-linked hnRNPA1 mutants from aggregation.
  13. Design and structural basis of selective nonsteroidal inhibitors of aster cholesterol trafficking.
  14. Flavokawain B inhibits ER-associated protein dislocation and reduces infectious Zika virus production.
  15. TEX264-mediated ER-phagy dysfunction contributes to Cadmium-induced ER stress: Implication of hippocampal neuronal apoptosis and cognitive deficits.
  16. Chaperone-assisted selective autophagy (CASA) in polyglutamine-related diseases: From mechanisms to therapeutic perspectives.
  17. Micro- and macro- heterogeneity of N-glycoproteome remodeling in endoplasmic reticulum stress.
  18. A GABARAP-PtdIns3K-C1 positive feedback loop at the heart of the phagophore nucleation.
  19. Induced degradation of Ufd1 reveals regulation of cohesin by the VCP/p97Ufd1-Npl4 complex.
  20. Proximity Proteomics Maps Candidate Cellular Uptake Pathways for Cell-Derived Nanovesicles.
  21. OsKish coordinates with Lunapark and RHD3 to maintain the structural stability of endoplasmic reticulum network in rice.
  22. General Strategy for Controlling Functional Lysine Acetylation via Induced Proximity.
  23. Integrative Proteomics and Ubiquitomics Reveal on-Targets and off-Targets of PROTAC dBET1.
  24. Democratizing LYTACs-A Modular Click Chemistry Platform for the Rapid Assembly of Lysosome-Targeting Chimeras.
  25. Targeted O-GlcNAcylation enables functional rewiring of c-Myc.
  26. A Molecular Mechanistic Deep Dive into 14-3-3 Molecular Glue Cooperativity.
  27. MGRN1 preserves transiently damaged mitochondria for antioxidant-mediated repair.
  28. Exploration of protein degradability enables fully endogenous MrTAC degraders.
  29. Crosstalk between UPR and mitochondria: The triad of ER-mitochondria contacts, Ca²⁺, and ROS.
  30. DNTTIP2 coordinates RNA exosome activities to ensure fidelity of human ribosome assembly.
  31. Autophagic degradation of RAB8A promotes ferroptosis through dysregulation of TFRC-mediated iron uptake.
  32. Pharmacological Inhibition of Small Extracellular Vesicle Secretion by ALK5i SD-208 via Lysosomal Rerouting of CD63+ Compartments.
  33. BioPROTACs: a promising approach for targeted protein degradation.
  34. Ribo-ITP enables identification of translons from limited input samples.
  35. An Epstein-Barr virus-encoded snoRNA directs 2'-O-methylation of human rRNAs to control translation and the viral lytic switch.
  36. Functional chimeric mRNAs encode proteins in mammalian immunity.
  37. Screening of amphipathic helices identifies features linked to inner nuclear membrane properties.
  38. Genetic dissection of human ABCE1 in yeast reveals separable requirements for ribosome recycling and suppression of aberrant reinitiation.
  39. Unfolded protein response signaling promotes myeloid cell production and cooperates with oncogenic mutation.
  40. Interactions Between E3 Ubiquitin Ligases and Deubiquitinases in AKT Regulation: Implications in Skeletal Muscle Homeostasis.
  41. Synergies and trade-offs in the heat shock response mechanism.
  42. Posttranslational Dynamics of the Subcellular Proteome by Mass Spectrometry-Based Proteomics.
  43. Long-read proteogenomic atlas of human neuronal differentiation reveals isoform diversity informing neurodevelopmental risk mechanisms.
  44. Macropinocytosis-mediated recyclable LYTACs (McR-TACs) for receptor-independent protein degradation.
  45. Mechanisms and therapeutic opportunities of the ribotoxic stress response in cancer.
  46. Glycoprotein-induced phase separation drives unconventional secretion of galectin-3.
  47. Translational control by RPL22L1-specific ribosomes enhances DNA repair and chemoresistance.
  48. Non-canonical activation of VEGFA through TIMM44-dependent mitochondrial remodelling.
  49. Mitochondrial Microautophagy: An Emerging Pathway in Maintaining Mitochondrial Homeostasis.
  50. Beyond random splits: A hierarchical benchmark of transferability and reliability in PROTAC activity prediction.
  51. Functional mapping and engineering of the Sec translocon unlocked by a cell-free system.
  52. Non-genetic remodeling drives leukemia propagation and reveals actionable vulnerabilities in acute myeloid leukemia.
  53. Selective Autophagy in Plant Immunity: Mechanisms, Regulation, and Emerging Concepts in Xenophagy.
  54. Rewiring the ribosome to translate proteins encoded in its own RNA.
  1. J Chem Inf Model. 2026 Aug 24. 66(16): 9743-9760
    From Ternary Modeling to Predictive PROTAC Design: A Computational Perspective.
    Joseph M Schulz, Robert C Reynolds, Stephan C Schürer.
      Proteolysis-targeting chimeras (PROTACs) are heterobifunctional small molecules that induce targeted protein degradation by recruiting an E3 ligase to a protein of interest. Since 2019, publication volume has accelerated, and computational methods have expanded from isolated demonstrations into practical tools for modeling PROTAC-induced ternary complexes, designing linkers, and forecasting degradation-related outcomes. Here, we present a Perspective on computational PROTAC methodologies published from 2019 to the present, organizing the field into two complementary streams: (i) constraint-driven, physics-based workflows that assemble and refine ternary complex models by enforcing geometric feasibility and evaluating pose stability using docking and molecular simulation; and (ii) data-driven workflows, including deep learning predictors and generative models that predict ternary complex structure, degradation end points, or linker chemistry from structural and assay data. We highlight representative approaches spanning restrained/tethered docking, MD-based refinement and dynamic stability scoring, coarse-grained free-energy modeling, SE(3)/E(3)-equivariant structure prediction, supervised degradation efficacy prediction, and generative linker design. We close by emphasizing persistent gaps, fragmented benchmarking, score robustness across targets and E3 ligases, and nonstandard molecular representations that currently limit generalization and reproducible, pipeline-ready deployment.
    DOI:  https://doi.org/10.1021/acs.jcim.6c01824
  2. Methods Enzymol. 2026 ;pii: S0076-6879(26)00175-8. [Epub ahead of print]734 199-216
    Mass spectrometry-based mapping of the ubiquitin chaperone code.
    Ayush Nigam, Prasun Kumar Bhunia, Trayambak Basak, Prasad Kasturi.
      Maintenance of proteome integrity is essential for cellular homeostasis and organismal health. This integrity depends on proteostasis, a coordinated network of protein quality control systems that regulate protein folding, stabilization, and degradation. Molecular chaperones, together with proteolytic pathways such as the ubiquitin-proteasome system (UPS) and the autophagy-lysosomal pathway, prevent the accumulation of misfolded and aggregation-prone proteins. Perturbations, including genetic mutations, environmental stress, and aging challenge protein folding fidelity, leading to proteotoxic stress and contributing to the pathogenesis of neurodegenerative disorders. Among the chaperone machinery, the HSP70 and HSP90 families play central roles in maintaining protein conformational homeostasis and directing damaged or misfolded substrates toward refolding or degradation pathways. Recent studies show that chaperone activity is dynamically regulated by diverse post-translational modifications (PTMs), including phosphorylation, acetylation, and ubiquitination, collectively termed the "chaperone code." These modifications modulate chaperone-client interactions, enzymatic activity, localization, and coordination with protein degradation systems. Mass spectrometry (MS)-based proteomics has emerged as a powerful approach for mapping ubiquitination sites and quantifying ubiquitin signaling dynamics. This chapter outlines experimental and computational strategies for MS-based analysis of the ubiquitin chaperone code, including di-glycine peptide enrichment, site identification, quantitative analysis, and validation.
    Keywords:  Chaperone code; Chaperones; PTMs; Proteomics; Proteostasis; Ubiquitination
    DOI:  https://doi.org/10.1016/bs.mie.2026.05.047
  3. Trends Cell Biol. 2026 Sep 04. pii: S0962-8924(26)00167-4. [Epub ahead of print]
    ER-associated sorting links proteostasis to photosynthesis.
    Elin Zatterman, Flavie Soubigou, Adrien Rousseau.
      Proteotoxic stress challenges multiple organelles, but how plants coordinate proteasome capacity with organellar function remains unclear. Langin et al. reveal that endoplasmic reticulum (ER)-associated sorting of NAC53/78 toggles these transcription factors between ER-associated degradation and nuclear activation, coupling proteasome induction to repression of photosynthesis-associated genes during stress.
    Keywords:  ER-associated sorting; NAC transcription factors; chloroplast retrograde signalling; proteasome; proteostasis
    DOI:  https://doi.org/10.1016/j.tcb.2026.08.011
  4. RNA. 2026 Sep 02. pii: rna.081099.126. [Epub ahead of print]
    The moonlighting functions of SEC13 in nonsense-mediated mRNA decay and the regulation of ER stress.
    Laura Monaghan, Chetan Srinath, Abigail R Mann, Nila Roy Choudhury, Graeme R Grimes, Dasa Longman, Javier F Caceres.
      The nonsense-mediated decay pathway (NMD) is an RNA quality control mechanism that regulates the stability of target RNAs. We previously identified the ER-localized SEC13 protein as a novel NMD factor in C. elegans and in HeLa cells; raising the possibility that it could be involved in regulating the stability of mRNAs translated at the ER. SEC13 is a component of several cellular complexes, including the COPII vesicle coat, the nuclear pore complex (NPC) and the nutrient sensing GATOR2 complex. Here, we show that SEC13 interacts with core NMD factors and using a newly developed dual-color fluorescent NMD sensor in U2OS cells, we assessed SEC13 NMD activity, at a single-cell level. Transcriptomic profiling revealed that unlike the previously described ER-NMD factor, NBAS, SEC13 co-regulates the stability of substrates translated both in the cytoplasm and at the ER. We also show that SEC13 function in NMD is largely independent of its function in other cellular complexes. Altogether, these results show that SEC13 is a bona fide NMD factor in mammalian cells. Finally, we utilized an ER stress-activated indicator (ERAI) in U2OS cells to demonstrate that SEC13, together with canonical NMD factors, has a role in the regulation of the unfolded protein response (UPR) at the ER. Thus, the moonlighting functions of SEC13 include a role in NMD pathway and the regulation of ER stress.
    Keywords:  Moonlighting; RNA-quality control; SEC13; Stress response; nonsense-mediated decay (NMD)
    DOI:  https://doi.org/10.1261/rna.081099.126
  5. Chembiochem. 2026 Sep 14. 27(17): e70504
    A Co-Chaperone Mimetic Perturbs Cellular Nitrogen Metabolism in Mycobacteria.
    Brock Nelson, Tania J Lupoli.
      Protein quality control in bacteria relies on dynamic chaperone networks that rapidly respond to environmental stresses. In mycobacteria, a central Hsp70 chaperone, DnaK, and its co-chaperones, J-domain proteins (JDPs), play essential roles in the cellular response to stress and antibiotics. Conserved "J-domain" sequences of JDPs are known to mediate transient interactions with Hsp70s and other protein partners. We have previously shown that a rationally designed proteomimetic of a J-domain is toxic to stressed mycobacterial cells. Here, we aimed to trap J-domain mimetic interaction partners to potentially reveal vulnerabilities in cellular stress-response pathways. To do so, we modified a J-domain proteomimetic of the mycobacterial JDP DnaJ1 (J1C) with a photoaffinity label moiety, resulting in J1C-PAL. In heat-shocked mycobacteria, J1C-PAL crosslinked to DnaK in cells, confirming retention of canonical Hsp70-binding activity under proteotoxic stress. Chemoproteomic profiling revealed additional cellular targets, namely a conditionally essential mycobacterial protein, glutamine synthetase (GS). Biochemical assays demonstrated that J1C-PAL bound GS and inhibited its enzymatic activity. Cellular studies validated that J1C perturbed nitrogen metabolism mediated by GS in mycobacteria. Together, these findings establish J1C-PAL as a cell-permeable chemoproteomic tool for mapping protein targets and uncover a surprising link between a co-chaperone mimetic and bacterial metabolism.
    Keywords:  J‐domain proteins; chemoproteomics; glutamine synthetase; molecular chaperones; mycobacteria; proteomimetics
    DOI:  https://doi.org/10.1002/cbic.70504
  6. Nat Commun. 2026 08 03. pii: 9320. [Epub ahead of print]17(1):
    Unbiased screen of human transcriptome reveals an unexpected role of 3'UTRs in translation initiation.
    Yun Yang, Xiaojuan Fan, Yanwen Ye, Zhenzhen Zhang, Chuyun Chen, Sebastian E J Ludwig, Sirui Zhang, Qianyun Lu, Cindy L Will, Henning Urlaub, Jing Sun, Reinhard Lührmann, Zefeng Wang.
      Although most eukaryotic mRNAs require a 5'-cap for translation initiation, some can also be translated through a poorly studied cap-independent pathway. Here we develop a circRNA-based system and unbiasedly identify more than 10,000 sequences in the human transcriptome that contain Cap-independent Translation Initiators (CiTIs). Surprisingly, most of the identified CiTIs are located in 3'UTRs, which mainly promote translation initiation in mRNAs bearing highly structured 5'UTR. Mechanistically, CiTI recruits several translation initiation factors including eIF3 and DHX29, which in turn unwind 5'UTR structures and facilitate ribosome scanning. Functionally, we show that the translation of HIF1A mRNA, an endogenous DHX29 target, is antagonistically regulated by its 5'UTR structure and a new 3'-CiTI in response to hypoxia. Consistently, deletion of 3'-CiTI suppresses cell growth in hypoxia and tumor progression in vivo. Collectively, our study uncovers a new regulatory mode for translation where the 3'UTR actively participate in the translation initiation.
    DOI:  https://doi.org/10.1038/s41467-026-75574-9
  7. Autophagy. 2026 Sep 01.
    RAB1 mediates OPTN-dependent mitophagy via ATG9A recruitment.
    Waka Kojima, Ryu Endo, Kei Okatsu, Hiroki Kinefuchi, Tomoko Tokita, Reika Kikuchi, Noriyuki Matsuda, Shuya Fukai, Koji Yamano.
      Damaged mitochondria are selectively eliminated through mitophagy, a critical quality control process. A kinase PINK1 and an E3 ubiquitin ligase PRKN/Parkin, both of which are mutated in familial Parkinson disease, amplify ubiquitin signals on the damaged mitochondria. The autophagy receptor OPTN plays a pivotal role in mitophagy by bridging ubiquitinated mitochondria with autophagy components. Although OPTN is known to recruit ATG9A-positive vesicles to facilitate mitophagy progression, the precise molecular mechanisms governing this recruitment remain poorly understood. In this study, we identify the small RAB GTPases RAB1A and RAB1B as direct binding partners of the OPTN leucine zipper (LZ) domain. We demonstrate that RAB1A/1B is required for the recruitment of ATG9A vesicles to mitochondria during the initial stages of mitophagy. Knockdown of RAB1A and RAB1B significantly impaired the assembly of OPTN at phagophore formation sites, leading to a profound inhibition of mitophagy progression. Mechanistically, we found that RAB1A/1B associate with ATG9A-positive vesicles via their C-terminal prenylation, thereby tethering these vesicles to the OPTN-bound mitochondria. Our findings establish a novel OPTN-RAB1-ATG9A axis that drives the de novo synthesis of phagophore membranes in close proximity to damaged mitochondria. This work clarifies how selective autophagy receptors spatially coordinate membrane trafficking to ensure the efficient clearance of dysfunctional organelles.
    Keywords:  Autophagy; Optineurin; PINK1; Parkin; RAB GTPase; mitochondria; ubiquitin
    DOI:  https://doi.org/10.1080/15548627.2026.2728346
  8. Cell Rep. 2026 Sep 01. pii: S2211-1247(26)00976-9. [Epub ahead of print]45(9): 117898
    An integrated landscape of mRNA and protein isoforms.
    Amir Kedan, Henrik Zauber, Meng-Ran Wang, Suyeon Kim, Qionghua Zhu, Liang Fang, Kathryn S Lilley, Wei Chen, Matthias Selbach.
      Alternative splicing and proteolytic processing expand proteome diversity by generating distinct protein isoforms from a single gene. However, the relationship between transcript isoforms and protein products remains poorly understood because of limitations in current proteomic workflows. Here, we combined full-length mRNA sequencing with protein fractionation and quantitative mass spectrometry to generate an integrated landscape of mRNA and protein isoforms in human RPE-1 cells. To overcome the ambiguity of bottom-up proteomics, we developed IsoFrac, a computational pipeline that resolves protein isoforms from molecular-weight-resolved peptide migration profiles. Using this approach, we identified ∼45,000 full-length transcripts, ∼32,000 open reading frames (ORFs), and ∼14,000 protein isoform candidates. Comparative analyses revealed widespread translation of alternative transcripts and identified shorter protein variants, likely arising from proteolytic processing and/or alternative translation, as a major and underappreciated source of proteome complexity. Our results establish a scalable framework for isoform-resolved proteogenomics and provide a resource for studying protein isoform diversity.
    Keywords:  CP: genomics; CP: molecular biology; alternative splicing; alternative translation; bottom-up proteomics; long-read sequencing; peptide correlation profiling; protein isoforms; proteogenomics; proteolytic processing; transcriptomics
    DOI:  https://doi.org/10.1016/j.celrep.2026.117898
  9. Sci Adv. 2026 Sep 04. 12(36): eaeg3201
    Reconstitution of multistep recruitment of ULK1 to membranes in autophagy.
    Yongjia Duan, Ye Lu, Sanjoy Paul, Johannes Betz, Léa P Wilhelm, Annan S I Cook, Xuefeng Ren, Elias Adriaenssens, Sascha Martens, Ian G Ganley, Gerhard Hummer, James H Hurley.
      The human Unc51-like kinase 1 (ULK1) autophagy-initiating complex consists of ULK1, FIP200, and the Hop/Rev7/Mad2 (HORMA) domain heterodimer ATG13:ATG101. Phosphatidylinositol 3-phosphate (PI3P) is essential to recruit ULK1 complex (ULK1C) to membranes for ULK1, but ULK1C subunits do not contain PI3P-binding domains. Here, we show that the ATG13:ATG101 dimer forms a complex with the PI3P-binding protein WD40 interacting with phosphoinositide protein 3 (WIPI3), as well as WIPI2. Bound to WIPI2 and WIPI3, ATG13:ATG101 inserts its Trp-Phe (WF) finger into the membrane. Molecular dynamics simulations show that WIPIs and the WF finger cooperatively stabilize the complex on membranes. Biochemical reconstitution and cell-based assays show that WIPI3:ATG13 engagement promotes ATG16L1 phosphorylation, autophagy, and mitophagy. A kinase domain (KD)-proximal Pro-Val-Pro (PVP) motif in the ULK1 intrinsically disordered region docks onto the ATG13:ATG101 HORMA dimer brings the ULK1 KD close to the membrane. The PVP motif is essential for in vitro ULK1 phosphorylation of ATG16L1 and important for autophagy and mitophagy. These data establish a stepwise pathway for recruitment of the ULK1 KD to the vicinity of the membrane surface.
    DOI:  https://doi.org/10.1126/sciadv.aeg3201
  10. Nat Struct Mol Biol. 2026 Aug 31.
    A single-amino-acid cleavage controls global mitochondrial complex integrity.
    Cansu Kücükköse, Marcin Luzarowski, Fabian Stockert, Annette Flotho, Miguel Cosenza-Contreras, Fatih Demir, Max Gilbert, Jörn Dengjel, Friedel Drepper, Mandy Jeske, Hans-Georg Koch, Pitter F Huesgen, F-Nora Vögtle.
      Mitochondrial proteostasis depends on precise N-terminal processing of imported precursor proteins. Defects in this maturation step are implicated in disease, yet the functional impact in humans remains unclear. Here we show that the intermediate cleaving peptidase ICP55, which removes a single amino acid, acts as a key stabilizer of multimeric mitochondrial protein complexes. Using proteomics and complexome profiling, we identify over 100 human ICP55 substrates and demonstrate that loss of ICP55 triggers widespread destabilization of protein assemblies, with a global shift toward smaller subcomplexes. Thus, we uncover a conserved, post-translational mechanism that safeguards mitochondrial proteostasis by regulating complex integrity through a single amino-acid cleavage, and we reveal N-terminal proteoform control as an unexpected layer of organellar homeostasis.
    DOI:  https://doi.org/10.1038/s41594-026-01876-7
  11. Cell. 2026 Sep 01. pii: S0092-8674(26)00936-0. [Epub ahead of print]
    Ratiometric transcriptional activation by protein degradation.
    Melissa A Gray, Katelyn L Randal, Jennifer A Co, Michelle T Tang, Athena Z Xue, Sophia W Chen, Hlib Razumkov, Qusay Q Omran, David E Solow-Cordero, Jeonghye Yu, Stephanie A Robinson, Cara A Starnbach, Nathanael S Gray, Steven M Corsello, Steven M Banik.
      Cells can respond to alterations in the abundances of specific proteins through transcriptional outputs. Synthetic approaches inspired by native post-transcriptional circuits that convert protein abundance changes into programmable gene expression would be transformative. Here, we discover and describe design principles that effectively convert protein degradation into transcriptional outputs in live cells. We define ratiometric transcriptional activation, where control over the ratio between a transcription factor and a protein of interest fused to its inhibitor enables detection of abundance changes with high sensitivity at scale. We show that ratiometric transcriptional activation can be implemented in single cells using triply orthogonal circuits or in multicellular pools, operating independently of the mechanism of protein downregulation and enabling simultaneous detection of multiple protein downregulation events through outputs such as cell survival, fluorescent protein expression, or barcode sequencing. These circuits can be applied to oncogenic targets and enable discovery of new molecular glue degraders.
    Keywords:  CRISPR; PROTAC; amplification; anti-CRISPR; gene circuits; high-throughput; molecular glue; multiplexed circuits; proteostasis detection; synthetic biology; synthetic circuits; targeted protein degradation
    DOI:  https://doi.org/10.1016/j.cell.2026.08.009
  12. Nat Commun. 2026 08 21. pii: 9357. [Epub ahead of print]17(1):
    YTHDC1 functions as a molecular chaperone to suppress ALS-linked hnRNPA1 mutants from aggregation.
    Kang Ren, Mingjie Cheng, Qiudan Luo, Boxin Zhang, Haosheng Zhang, Zhe Li, Yuxin Liu, Yujie Wang, Ting Kang, Xiaoming Dai, Jiong Chen, Yuanming Cheng, Liangqian Huang.
      Proteostasis failure drives multiple neurodegenerative disorders (NDs), and ATP-independent chaperone pathways that support neuronal proteostasis remain poorly defined. Here, we identify the N6-methyladenosine (m6A)-binding protein YTHDC1 as an ATP-independent molecular chaperone, whose activity is mediated by a highly acidic polyaspartate/glutamate (polyD/E) segment. YTHDC1 prevents protein misfolding and aggregation, unfolds kinetically trapped substrates, and resolubilizes pre-formed aggregates. Deletion of the polyD/E segment abolishes these activities, whereas aromatic-cage mutants retain chaperone activity, demonstrating independence from m6A recognition. We identify the amyotrophic lateral sclerosis (ALS)-associated RNA-binding protein hnRNPA1 as a YTHDC1 client. YTHDC1 maintains liquid-like hnRNPA1 condensates, delays fibrillization of disease-associated mutants, and limits stress-granule sequestration, while mitigating mutant hnRNPA1-induced neurite growth defects in primary neurons. These findings define a proteostatic function of YTHDC1 and highlight its chaperone activity as a potential target for mitigating protein aggregation in ALS-related NDs.
    DOI:  https://doi.org/10.1038/s41467-026-77016-y
  13. Proc Natl Acad Sci U S A. 2026 Sep 08. 123(36): e2617638123
    Design and structural basis of selective nonsteroidal inhibitors of aster cholesterol trafficking.
    Hyunsoo Kim, Beatriz Romartinez-Alonso, Xu Xiao, Yajing Gao, John Paul Kennelly, Alessandra Ferrari, Rui Li, Liujuan Cui, Emily Whang, John W R Schwabe, Michael E Jung, Peter Tontonoz.
      Aster proteins (Aster-A, -B, and -C) are crucial for transporting cholesterol from the plasma membrane (PM) to the endoplasmic reticulum (ER). Asters are expressed in a cell type-specific manner across tissues. Their global disruption leads to varied physiological outcomes given the diverse roles of cholesterol throughout the body. We previously identified sterol analogs, such AI-3d, that inhibit all three Aster proteins. However, their utility is limited by toxicity and off-target effects. Here, we report the development of nonsteroidal Aster inhibitors that are active in cells and in vivo, using binding-guided design to generate compounds with isoform-selective affinities. We found that YKJ-124 is a low-toxicity, Aster-A-preferring inhibitor that elevates PM-accessible cholesterol in primary T cells and potentiates store-operated Ca2+ entry in Th17 cells, phenocopying Aster-A deficiency. YKJ-300 and YKJ-305 selectively target Aster-C; cocrystal structures and point mutation studies reveal a Ser477-dependent hydrogen bond (Gly in Aster-A/B) that underlies this specificity. We also explored the in vivo consequences of pharmacologic Aster-C inhibition. YKJ-305 treatment of mice blunted fasting-induced hepatic cholesterol transport and cholesterol ester formation, accompanied by compensatory activation of the SREBP2 pathway. Last, we also identify broader-spectrum inhibitors (YKJ-86) and dual Aster-A/C inhibitors (YKJ-262) that drive PM cholesterol accumulation in fibroblasts and human intestinal enteroids. Together, these chemical probes enable isoform-resolved manipulation of Aster-dependent cholesterol trafficking and provide a foundation for developing Aster-targeted therapies for cholesterol dysregulation.
    Keywords:  cholesterol; lipid transport; small molecule inhibitors
    DOI:  https://doi.org/10.1073/pnas.2617638123
  14. Biochem Biophys Res Commun. 2026 Aug 31. pii: S0006-291X(26)01282-9. [Epub ahead of print]835 154518
    Flavokawain B inhibits ER-associated protein dislocation and reduces infectious Zika virus production.
    Wenjing Yan, Yongwang Zhong, Shengyun Fang.
      Flavokawain B (FB), a chalcone from kava, induces endoplasmic reticulum (ER) stress and inhibits protein neddylation, but its effect on ER protein quality control is unknown. Here we identify inhibition of ER-associated degradation (ERAD) substrate dislocation as a cellular activity of FB. In a live-cell dislocation-dependent reconstituted GFP (drGFP) assay, FB inhibited dislocation of the luminal ERAD substrate null Hong Kong α1-antitrypsin (NHK) and of the membrane substrate CD3δ, with apparent IC50 values of 4.26 and 9.79 μM. FB also reduced NHK ubiquitination and stabilized NHK in a concentration-dependent manner. Unlike bortezomib, FB did not stabilize the short-lived cytosolic ubiquitin-proteasome system reporter GFPu, measured by live-cell imaging and immunoblotting, arguing against generalized proteasome blockade as the primary cause of NHK stabilization. In a temperature-series cellular thermal shift assay (CETSA), FB increased the heat-resistant soluble fraction of both HRD1 and gp78, suggesting that FB perturbs an ERAD-associated protein environment involving these ligases. Because HRD1-mediated ERAD sustains flaviviral protein homeostasis, we asked whether this phenotype extends to virus production: FB reduced infectious Zika virus (ZIKV) output to approximately 40% of control at 5 μM and to below 20% at 7.5-10 μM, without a proportional loss of cell viability. FB is therefore a chemical probe of ERAD dislocation with an associated antiviral phenotype.
    Keywords:  ER-associated degradation; Flavokawain B; HRD1; Protein dislocation; Zika virus; gp78
    DOI:  https://doi.org/10.1016/j.bbrc.2026.154518
  15. Chem Biol Interact. 2026 Aug 29. pii: S0009-2797(26)00430-8. [Epub ahead of print]439 112322
    TEX264-mediated ER-phagy dysfunction contributes to Cadmium-induced ER stress: Implication of hippocampal neuronal apoptosis and cognitive deficits.
    Yufei Gao, Luyang Cao, Yibo Hong, Hao Ke, Quan Yuan, Jun Hu, Qiwen Xu, Zhanxu Liu, Dongmei Wang, Hua Fan.
      Cadmium (Cd), a well-recognized neurotoxicant, elicits neuronal death and cognitive impairment. Cd cytotoxicity disrupts endoplasmic reticulum (ER) proteostasis, leading to the accumulation of misfolded and unfolded proteins and subsequent ER stress-mediated apoptosis. Endoplasmic reticulum autophagy (ER-phagy) serves as a crucial quality-control mechanism that resolves excessive ER stress and maintains ER homeostasis. However, the precise roles of ER-phagy, ER stress-mediated apoptosis, and their crosstalk in Cd-induced neurotoxicity remain poorly defined. Here, we demonstrated that Cd exposure robustly induces ER stress and the subsequent apoptotic injury in the mouse hippocampus and HT-22 hippocampal neurons. Pharmacological inhibition of ER stress with 4-phenylbutyric acid (4-PBA) effectively rescued Cd-triggered neuronal damage, reduced cell death, and ameliorated Cd-associated cognitive deficits. Notably, Cd exposure leads to pronounced ER-phagy dysfunction, as evidenced by decreased LC3-II accumulation, elevated calnexin levels, and impaired ER-phagy autophagic flux in vivo and in vitro. Furthermore, the ER-phagy receptor TEX264 was downregulated under Cd stress. Importantly, restoration of ER-phagy via overexpressing TEX264 markedly mitigated Cd-elicited ER stress, thereby blocking the downstream apoptotic cascade. Collectively, our findings identify impaired ER-phagy as a previously unrecognized mechanism underlying Cd neurotoxicity, which synergizes with ER stress-mediated apoptosis to promote hippocampal neuronal injury. These results highlight ER quality control pathways as promising therapeutic targets for the intervention of Cd-induced cognitive and neuronal damage.
    Keywords:  Apoptosis; Cadmium; Cognitive deficits; ER stress; ER-Phagy; TEX264
    DOI:  https://doi.org/10.1016/j.cbi.2026.112322
  16. J Huntingtons Dis. 2026 Sep 03. 18796397261478173
    Chaperone-assisted selective autophagy (CASA) in polyglutamine-related diseases: From mechanisms to therapeutic perspectives.
    Barbara Tedesco, Marta Chierichetti, Riccardo Cristofani, Angelo Poletti.
      Chaperone-assisted selective autophagy (CASA) is a crucial process aimed at maintaining proteostasis in several neurodegenerative diseases associated with protein misfolding, including polyglutamine (polyQ) diseases. Autophagy is a critical lysosome-mediated degradation pathway, particularly essential in neurons, which are highly susceptible to proteotoxic stress due to their post-mitotic nature. Selective autophagy pathways, including CASA, ensure the targeted removal of misfolded proteins and damaged organelles, thereby preserving cellular homeostasis. CASA is based on the intersection of chaperones and autophagy, where HSPB8 and BAG3 interact with HSPA and STUB1 forming a complex that identifies, ubiquitinates, and directs aberrant proteins toward autophagosomes for subsequent lysosomal degradation. In polyQ diseases, such as spinal and bul muscular atrophy (SBMA) and Huntington's disease (HD), mutant proteins accumulate, overwhelming the protein quality control systems. The CASA components are upregulated as a compensatory response, promoting toxic aggregates clearance and cellular damage mitigation. However, chronic proteotoxic stress and progressive impairment of autophagic and lysosomal pathways eventually limit CASA efficiency, contributing to disease progression. The review highlights how CASA exerts its protective activities in polyQ diseases and reports therapeutic strategies aimed at enhancing CASA activity, including pharmacological inducers and combinatorial approaches targeting autophagy and the ubiquitin-proteasome system. Overall, CASA emerges as a crucial adaptive mechanism and a promising therapeutic target in polyQ-related neurodegeneration.
    Keywords:  CAG repeat expansions; Huntington disease; chaperone-assisted selective autophagy; polyglutamine diseases; protein misfolding; spinal and bul muscular atrophy
    DOI:  https://doi.org/10.1177/18796397261478173
  17. Mol Cell Proteomics. 2026 Sep 01. pii: S1535-9476(26)00149-0. [Epub ahead of print] 101653
    Micro- and macro- heterogeneity of N-glycoproteome remodeling in endoplasmic reticulum stress.
    Alexander Black, Tiffany Ngo, Boomathi Pandi, Andrew Mongin, Dominic C M Ng, Edward Lau, Maggie P Y Lam.
      N-glycosylation plays essential roles in the folding, trafficking, and maturation of proteins in the secretory pathways, but how individual protein- and site- specific glycosylation rewires under endoplasmic reticulum (ER) stress is unknown. Particularly, intact glycopeptide data that retain the connectivity between glycosylation sites and the attached glycans are needed to reveal the micro- and macro- heterogeneity of N-glycosylation sites and their permutations in stressed cells. Here, we developed and optimized a magnetic polyethyleneimine boronic acid-containing scaffold (mPBA) enrichment workflow to achieve sensitive and broad enrichment of intact glycopeptides for mass spectrometry analysis, requiring only 0.1 to 0.5 mg total peptide input. With this method, we performed a large intact glycopeptide comparative study, systematically analyzing 13,759 unique protein-, site-, and glycoform combinations, termed glycopeptidoforms, in normal and stressed human cells. The data reveals a dynamic rewiring of N-glycosylation involving hundreds of proteins with complex protein-, site-, and glycan- specific granularity. The magnitude of differential glycosylation far exceeds that of protein expression changes. Individual glycoform reconfigurations can be observed that indicate likely disruptions within specific steps in protein maturation and trafficking. Mannose trimming emerges as a shared disruption across multiple proteins, suggesting a processing bottleneck of the ER stress glycoproteome. Together, these results reveal molecular details into the remodeling of protein secretory pathways upon ER stress and highlight the utility of mPBA for sensitive N-glycoproteomics studies. The data can be visualized on https://glycoproteome.info.
    DOI:  https://doi.org/10.1016/j.mcpro.2026.101653
  18. Nat Commun. 2026 Jul 30. pii: 9473. [Epub ahead of print]17(1):
    A GABARAP-PtdIns3K-C1 positive feedback loop at the heart of the phagophore nucleation.
    Antoine N Dessus, Yohei Ohashi, Maxime Bourguet, Tomos E Morgan, Anastasia Nunez, Maria Manifava, Nicholas T Ktistakis, Roger L Williams.
      In mammalian cells, autophagosomes can reach diameters of over 1000 nm within 30 min after triggering starvation, but how such substantial amounts of membranes can be synthesized remains elusive. The phagophore initiation needs the lipid kinase PIK3C3-Complex 1 (PtdIns3K-C1), which produces phosphatidylinositol-3-phosphate (PtdIns3P). PtdIns3P recruits WIPI2 that facilitates lipidation of mammalian ATG8 (mATG8) family proteins on phagophores. Here we show that recombinant membrane-coupled GABARAP binds to and potently activates PtdIns3K-C1. By a combination of cryo-electron microscopy, structural mass spectrometry, activity assays and mutagenesis, we show that GABARAP activates PtdIns3K-C1 through two binding sites. We propose that once GABARAP is indirectly recruited by PtdIns3P generated by basal activity of PtdIns3K-C1, a positive feedback loop is formed where PtdIns3K-C1 interacts with GABARAP and becomes activated to produce more PtdIns3P, thereby further stimulating GABARAP lipidation. This mechanism would be central for autophagosome biogenesis, where enlarged membranes need to be rapidly synthesized.
    DOI:  https://doi.org/10.1038/s41467-026-76135-w
  19. Life Sci Alliance. 2026 Nov;pii: e202603698. [Epub ahead of print]9(11):
    Induced degradation of Ufd1 reveals regulation of cohesin by the VCP/p97Ufd1-Npl4 complex.
    Daniella Munro, Maike Reinders, Aikaterini Pravi, Johannes van den Boom, Pinki Gahlot, Ekaterina Isaakova, Caio Ab Oliveira, Dominik Boos, Petra Beli, Hemmo Meyer.
      The AAA ATPase VCP/p97 has emerged as a critical regulator of ubiquitin and chromatin-associated processes but progress in understanding has been hampered by the complexity of p97 functions and the various p97 cofactors involved. Here, we combined ubiquitin profiling with acutely induced degradation of the Ufd1 subunit of the p97 ubiquitin adapter, Ufd1-Npl4, in human cells. We identified a set of chromatin regulators, HUS1, XRCC1, MORF4L1, and the cohesin subunit RAD21 as targets of p97Ufd1-Npl4 We find that RAD21 is ubiquitylated and targeted by p97Ufd1-Npl4 specifically in S phase to remove a subpopulation of cohesin from chromatin. Acute degradation of Ufd1 in S phase, after replication licensing is completed, impedes replication and leads to replication-associated DNA damage. Our findings suggest that a fraction of cohesin rings need to be removed by p97Ufd1-Npl4 from DNA to allow unhindered replication and reveal a critical function of p97 that ensures genome stability.
    DOI:  https://doi.org/10.26508/lsa.202603698
  20. Small Methods. 2026 Sep 02. e71014
    Proximity Proteomics Maps Candidate Cellular Uptake Pathways for Cell-Derived Nanovesicles.
    Eisuke Kanao, Ryosuke Mizuta, Saki Tarao, Yukika Hara, Yuka Li, Kazunari Akiyoshi, Yasushi Ishihama, Koshi Imami, Yoshihiro Sasaki.
      Although extracellular vesicles (EVs) facilitate selective molecular exchange between cells, their low yields and inherent heterogeneity limit translational applications. Cell-derived nanovesicles (CDNs), produced by mechanical extrusion of donor cells, offer a scalable alternative while retaining key membrane features of EVs. Yet how fabrication reshapes vesicle-cell communication remains poorly understood. Here, vesicle-side proteomics is integrated with TurboID proximity labeling of recipient-cell proteins to construct quantitative, dual-sided maps of CDN and small extracellular vesicle (sEV) interactions. Despite similar size and surface charge, CDNs displayed a substantially more diverse proteome and a broader repertoire of predicted uptake-associated signatures. Recipient-cell proximity proteomics further resolved distinct molecular cohorts. The CDN-associated cohort contained recipient-derived CALR and NCL, which are literature-linked to LRP1/CD91-associated efferocytic recognition and NCL-associated macropinocytic processes, respectively, whereas the sEV-associated cohort contained signatures consistent with HSPG-assisted docking and clathrin-mediated or CLIC/GEEC-related uptake. Together, these complementary datasets reveal molecular interfaces for extrusion-generated CDNs that are distinct from those of naturally secreted sEVs. Receptor dependence and the contributions of surface association and internalization require direct testing; however, the identified associations define specific mechanistic targets for further investigation. This dual-sided proteomic strategy establishes a quantitative framework for dissecting vesicle-cell communication and engineering membrane-based nanocarriers.
    Keywords:  cellular uptake pathway; cell‐derived nanovesicle; extracellular vesicle; proximity labelling
    DOI:  https://doi.org/10.1002/smtd.71014
  21. Plant Cell. 2026 Sep 03. pii: koag260. [Epub ahead of print]
    OsKish coordinates with Lunapark and RHD3 to maintain the structural stability of endoplasmic reticulum network in rice.
    Pengcheng Zhang, Yihua Wang, Yun Zhu, Yu Zhang, Xiaohang Han, Yu Chen, Jianing Zhang, Bingke Luo, Xiuhao Bao, Hongming Wu, Fan Wang, Ao Zhang, Cailin Lei, Xin Wang, Zhijun Cheng, Chao Li, Yuqiang Liu, Haiyang Wang, Yulong Ren, Jianmin Wan.
      The endoplasmic reticulum (ER) is the largest intracellular membrane-bound organelle in eukaryotic cells, comprising an interconnected network of tubules and sheets. Lunapark (LNP) functions as an E3 ubiquitin ligase that targets RHD3, a dynamin-like GTPase essential for homotypic fusion of ER tubules, for proteasomal degradation, thereby modulating ER tubule stability. However, the regulatory mechanism governing LNP activity remains largely unknown. Here, we report the characterization of the rice oskish mutant, which exhibits aberrant aggregation of ER tubules and defective ER exit of seed storage proteins. OsKish is an ER-localized small protein that physically interacts with both OsLNPs and RHD3-like (RHD3L) protein. OsKish stabilizes OsLNPs by suppressing their auto-ubiquitination; concomitantly, OsKish attenuates the membrane fusion activity of RHD3L possibly by inhibiting its oligomerization. Altogether, our studies propose an OsKish-OsLNPs-RHD3L framework for fine-tuning homotypic ER tubule fusion in rice, providing mechanistic insights into the maintenance of ER architecture in plants.
    DOI:  https://doi.org/10.1093/plcell/koag260
  22. ACS Chem Biol. 2026 Aug 24.
    General Strategy for Controlling Functional Lysine Acetylation via Induced Proximity.
    Brianna Hill-Payne, Mohd Younis Bhat, George M Burslem.
      Assigning causal function to post-translational modifications (PTMs) remains a central challenge in molecular biology, as most modification events cannot be readily interrogated in their native cellular context. Here, we present a generalizable chemical biology strategy for investigating the functional consequences of lysine acetylation through programmable induced proximity. By combining modular effector recruitment with chemically controlled proximity, this approach enables systematic elucidation of how enzyme identity shapes acetylation outcomes on target proteins in living cells. Across multiple substrates, including histone H3 and p53, we find that distinct acetyltransferases generate reproducible and target-dependent site-selective acetylation patterns, indicating that effector identity encodes predictable features of modification outcomes. These observations establish a framework for linking enzyme recruitment to site-specific PTM deposition and provide a route to identify candidate functional modification events. Rather than providing a single mechanistic insight, this work introduces a broadly applicable strategy for interrogating causal relationships between proximity-driven enzyme recruitment and protein modification, as demonstrated by the impact of p53 acetylation on downstream transcripts. This platform is readily extensible to additional effectors and targets and enables systematic discovery of functional PTMs in cellular systems.
    DOI:  https://doi.org/10.1021/acschembio.6c00510
  23. Anal Chem. 2026 Sep 01. 98(34): 24746-24760
    Integrative Proteomics and Ubiquitomics Reveal on-Targets and off-Targets of PROTAC dBET1.
    Hongtao Wen, Hui Liu, Jinfang Liu, Bendong Yang, Jiaxing Dai, Lei Chang, Yanchang Li, Yao Zhang, Liyan Yu, Ping Xu.
      Proteolysis-targeting chimeras (PROTACs) are heterobifunctional molecules that induce selective degradation of target proteins by hijacking the ubiquitin-proteasome system (UPS). Despite their transformative potential in eliminating disease-associated proteins, comprehensively identifying off-target degradation events remains technically challenging. Here, we employed an integrated proteomic and ubiquitinomic strategy to systematically profile the degradation landscape of the PROTAC molecule dBET1 in Jurkat T cells. By capturing the upstream ubiquitination events─which serve as earlier and more sensitive indicators than total protein abundance─our approach enabled the identification of previously overlooked off-target candidates. While dBET1 efficiently degraded its canonical BET family targets, our data also revealed the mitochondrial outer membrane protein VDAC1 as a putative off-target, evidenced by its depletion and increased multisite ubiquitination. Notably, our analysis framework enabled site-specific resolution of degradation events within BRD3, revealing preferential ubiquitination at functionally essential bromodomains, suggesting that degron-enriched regions may underlie domain-selective degradation. Additionally, dBET1 treatment was associated with mitochondrial depolarization and calcium homeostasis disruption, defects that we hypothesize may be functionally linked to the observed VDAC1 depletion. Together, this study demonstrates that integrating ubiquitomics provides a superior sensitivity layer for PROTAC safety assessment, capable of uncovering mechanism-based liabilities that escape conventional global proteomic screening.
    DOI:  https://doi.org/10.1021/acs.analchem.6c00787
  24. ACS Chem Biol. 2026 Aug 24.
    Democratizing LYTACs-A Modular Click Chemistry Platform for the Rapid Assembly of Lysosome-Targeting Chimeras.
    Peter A Szijj, Sherry Li, Madeline K Gilbert, Chloë Wood Rollock, Mariko Morimoto, Carolyn R Bertozzi.
      Lysosome-targeting chimeras (LYTACs) are emerging therapeutics that mediate extracellular targeted protein degradation. Through simultaneous engagement of a target protein of interest and a lysosomal trafficking receptor, these bifunctional molecules can facilitate the degradation of both secreted and cell-surface proteins. The original LYTACs were designed to engage the cation-independent mannose-6-phosphate receptor (CI-M6PR) via complex glycopolymer or glycopolypeptide ligands conjugated to target-specific antibodies. However, the complexity of these ligands has limited the broader adoption of LYTACs as research tools. Here, we describe a simple, rapid, and modular click chemistry platform for the generation of CI-M6PR-binding LYTACs. The approach utilizes only commercially available reagents and standard laboratory equipment and allows for the conversion of virtually any antibody into a LYTAC. This method for "democratizing" LYTAC generation should facilitate the widespread adoption of these tools for biological discovery.
    DOI:  https://doi.org/10.1021/acschembio.6c00315
  25. Cell Chem Biol. 2026 Sep 02. pii: S2451-9456(26)00318-1. [Epub ahead of print]
    Targeted O-GlcNAcylation enables functional rewiring of c-Myc.
    Tongyang Xu, Zhihao Guo, Khadija S Khan, Yunpeng Huang, Bowen Ma, Shuhui Ji, Jialin Liu, Dean W Felsher, Billy Wai-Lung Ng.
      Chemically induced proximity has transformed targeted protein degradation but has been applied far less extensively to directly reprogram protein function through post-translational modification (PTM). Here, we develop an O-GlcNAcylation-targeting Chimera (OGTAC) that recruits O-GlcNAc transferase (OGT) to the oncogenic transcription factor c-Myc, enabling targeted O-GlcNAcylation in living cells without globally perturbing cellular O-GlcNAcylation. OGTAC suppresses HeLa cell proliferation, rewires c-Myc genomic occupancy, and reprograms expression of the downstream oncogene MALAT1 in an O-GlcNAcylation-dependent manner. By selectively modulating the regulatory state of c-Myc rather than its abundance, OGTAC establishes targeted O-GlcNAcylation as a chemically induced proximity strategy for functional rewiring of transcription factors. More broadly, this work expands proximity-induced protein regulation beyond degradation to programmable PTM.
    Keywords:  CIP; MALAT1; O-GlcNAcylation; O-GlcNAcylation-targeting Chimera; OGT; OGTAC; PTM; TF; bifunctional molecule; c-Myc; chemically induced proximity; post-translational modification; transcription factor
    DOI:  https://doi.org/10.1016/j.chembiol.2026.08.008
  26. Biochemistry. 2026 Sep 01. 65(17): 2769-2783
    A Molecular Mechanistic Deep Dive into 14-3-3 Molecular Glue Cooperativity.
    Marloes A M Pennings, Edmee M F Vandenboorn-Bönner, Lisa Nooren, Markella Konstantinidou, Chad Altobelli, Christian Ottmann, Albert J Markvoort, Galen P Miley, Michelle R Arkin, Luc Brunsveld.
      Molecular glues (MGs) stabilize protein-protein interactions (PPIs) through interactions at composite binding interfaces, thereby promoting cooperative ternary complex formation. For hub proteins that engage in multiple PPIs with widely varying intrinsic affinities, the interplay between binary PPI affinity and MG cooperativity is therefore a key determinant of selective stabilization. Here, we use the multiclient 14-3-3 scaffold protein as a model system to systematically dissect the relationship between binary 14-3-3/client affinity (KDI) and MG-induced cooperativity (α). Client peptide affinity was systematically tuned by modifying residues N-terminal to the phosphorylated 14-3-3 binding motif while preserving the C-terminal composite interface required for MG recognition. Using a combination of biophysical techniques and protein crystallography, we show that changes in KDI alter the thermodynamic and kinetic parameters of both binary and ternary complex formation, but do not affect MG cooperativity. This principle was observed for the noncovalent MG fusicoccin-A as well as covalent MGs targeting 14-3-3σ/client complexes. Competitive binding experiments and thermodynamic modeling further revealed that, although α is independent of KDI, the interplay between KDI, MG affinity (KDII), and cooperativity determines which PPIs are preferentially stabilized in a multiclient environment. Together, these findings establish cooperativity, intrinsic PPI affinity, and MG affinity as key parameters governing MG activity and selectivity, providing a framework for the rational design of MGs targeting hub protein interactomes.
    DOI:  https://doi.org/10.1021/acs.biochem.6c00427
  27. Cell Rep. 2026 Sep 01. pii: S2211-1247(26)01008-9. [Epub ahead of print]45(9): 117930
    MGRN1 preserves transiently damaged mitochondria for antioxidant-mediated repair.
    Nuo Chen, Zhirong Li, Xiyuan Wang, Hong Xu, Wei Wang, Weina Shang, Liquan Wang, Chao Tong.
      Mitochondria are continuously exposed to damage that contributes to aging and disease. While prolongedly damaged mitochondria are eliminated by mitophagy, how cells respond to transient damage remains unclear. Here, we establish a cell-based system to induce transient mitochondrial stress and resolve its recovery dynamics. We identify the E3 ubiquitin ligase mahogunin ring finger 1 (MGRN1) as a damage-threshold sensor that discriminates between transient and prolonged mitochondrial insults. Under transient stress, MGRN1 shows enhanced association with the outer mitochondrial membrane via MFN1, where it restrains mitophagy, potentially preserving mitochondria for repair. Loss of MGRN1 disrupts this checkpoint, leading to inappropriate mitophagy and impaired recovery. Mechanistically, mitochondrial repair is coordinated by the DELE1-eIF2α-ATF4 axis, Nrf2 signaling, and JUN/FOS activation, which collectively drive an antioxidant program, with TXNRD1 and SLC7A11 as downstream effectors. Together, our findings uncover a damage-sensing checkpoint that gates the decision between recovery and clearance, and reveal active and regulated pathways for mitochondrial repair.
    Keywords:  CP: cell biology; CP: metabolism; antioxidant defenses; mitochondrial integrated stress response; mitochondrial repair; mitophagy; transient mitochondrial damage
    DOI:  https://doi.org/10.1016/j.celrep.2026.117930
  28. Chem. 2026 Jul 09. pii: 102998. [Epub ahead of print]12(7):
    Exploration of protein degradability enables fully endogenous MrTAC degraders.
    Laurence J Seabrook, Endri Karaj, Shaimaa Sindi, Glen Brodie, Catherine R Livelo, Carolina N Franco, Melissa Campos, Jack T Leonard, Fangyuan Gao, Dorota Skowronska-Krawczyk, Matthew E Griffin, Stuart J Conway, Amit Choudhary, Lauren V Albrecht.
      Small molecules can induce protein degradation by hijacking natural degrons, but most degraders rely on the same proteasome-targeting degron. Motivated by the need for chemically exploitable degrons, this study leverages the lysosome-targeting methylarginine degron for the development of methylarginine-targeting chimeras (MrTACs). First, lysosomal-capture proteomics identify substrates naturally modified by methylarginine degrons. Next, a tag-based protein library is used for understanding the characteristics that affect degradation by MrTACs, which induces methylarginine degrons by recruiting protein arginine methyltransferases (PRMTs). MrTACs degrade proteins regardless of their native proteolytic route, including targets that have eluded classic degrader modalities, across multiple PRMTs. We leverage this for endogenous MrTACs that recruit PRMTs with repurposed inhibitors, which can be transformed into silent recruiters via group-transfer chemistry. MrTACs drive <95% target degradation across disease-linked proteins at nanomolar doses. Overall, this study integrates native and chemically induced degradation to establish a platform for fully endogenous, therapeutically viable degraders.
    DOI:  https://doi.org/10.1016/j.chempr.2026.102998
  29. Pharmacol Res. 2026 Aug 31. pii: S1043-6618(26)00343-9. [Epub ahead of print]232 108428
    Crosstalk between UPR and mitochondria: The triad of ER-mitochondria contacts, Ca²⁺, and ROS.
    Ester Zito, György Hajnóczky.
      Endoplasmic reticulum (ER) stress is triggered by several cellular perturbations causing protein misfolding, and activates the unfolded protein response (UPR), an initially adaptive signaling network that aims to restore ER and cellular homeostasis. Growing evidence indicates that UPR signaling extends beyond ER proteostasis, influencing mitochondrial function and bioenergetics through ER-mitochondria contact sites (ERMCs). The CHOP-ERO1A-IP3R axis has a primary role in recruiting mitochondria to adaptive UPR. However, its sustained activation renders UPR signaling maladaptive, leading to mitochondrial dysfunction through both outer mitochondrial membrane permeabilization (OMMP) and mitochondrial permeability transition pore (mPTP) opening, ultimately contributing to irreversible cell injury and disease pathogenesis. Here, we examine the molecular mechanisms that govern adaptive and maladaptive UPR signaling and discuss how these ER-centered responses impinge on mitochondrial and cellular physiology. We analyze three major drivers of coupling mitochondrial function to UPR signaling: (i) enhanced ERMCs, (ii) IP3R-mediated Ca²⁺ transfer from the ER to mitochondria, and (iii) bidirectional ROS/H₂O₂ exchange between the two organelles. We also discuss unresolved questions in the field and technological advances, including approaches to investigate ERO1-dependent redox nanodomains, ERO1 inhibitors and engineered ERMC linkers, that are advancing our understanding of ER-mitochondria crosstalk and revealing potential therapeutic opportunities. These insights may inform precision medicine strategies for diseases driven by chronic ER stress and mitochondrial dysfunction.
    Keywords:  CHOP; Ca²⁺ handling; ER stress; ERO1; ER–mitochondria contact sites (ERMCs); IP₃ receptor (IP₃R); Mitochondrial permeability transition pore (mPTP); Pharmacological therapy; Unfolded protein response (UPR)
    DOI:  https://doi.org/10.1016/j.phrs.2026.108428
  30. Nat Commun. 2026 Aug 07. pii: 9488. [Epub ahead of print]17(1):
    DNTTIP2 coordinates RNA exosome activities to ensure fidelity of human ribosome assembly.
    Agnese Pisano, Jessie Bourdeaux, Jarosław Mazur, Florine Roses, Yves Romeo, Elisabeth Petfalski, Tobias von Arx, Daniela Portugal-Calisto, Michaela Oborská-Oplová, Cohue Peña, Clément Chapat, David Tollervey, Anthony K Henras, Vikram Govind Panse.
      The RNA exosome-associated helicase Mtr4/MTR4 (yeast/human) is recruited by adaptor proteins bearing Arch-Interacting Motifs (AIMs) to selectively degrade RNA substrates. Although the exosome targets diverse RNAs, only a few adaptors have been identified. Here, we extend the inventory of human adaptors to include a pre-tRNA splicing-ligase complex component, a spliceosome-associated factor, and DNTTIP2, a constituent of the small ribosomal subunit (40S) precursor, the 90S pre-ribosome. Structure-guided studies reveal how the DNTTIP2AIM-docked processive exosome core and its associated distributive exonuclease EXOSC10, which contact distant sites on the 90S pre-ribosome, cooperate to degrade part of the 5'-external transcribed spacer (5'-ETS), a key RNA scaffold that coordinates early 40S assembly. By contrast, productive pre-ribosomal RNA trimming within the 90S pre-ribosome necessitates EXOSC10, which safeguards against uncontrolled processive degradation by the DNTTIP2AIM-docked exosome core. We propose that multivalent contacts provide a mechanistic framework by which the RNA exosome coordinates its distinct enzymatic activities, ensuring selective processing and surveillance during ribonucleoprotein particle maturation.
    DOI:  https://doi.org/10.1038/s41467-026-76536-x
  31. Autophagy. 2026 Aug 30.
    Autophagic degradation of RAB8A promotes ferroptosis through dysregulation of TFRC-mediated iron uptake.
    Jingbo Li, Qile Zhou, Jiao Liu, Xin Chen, Chunhua Yu, Rui Kang, Daolin Tang.
      Ferroptosis is an iron-dependent form of regulated cell death driven by lipid peroxidation; however, how selective autophagy regulates ferroptotic sensitivity remains incompletely understood. Here, we identify RAB8A as a selective autophagic substrate and negative regulator of ferroptosis. Quantitative proteomic analyses reveal that ferroptotic stress induces ATG5- and ATG7-dependent degradation of RAB8A. Mechanistically, ferroptotic stimuli induce RNF126-dependent polyubiquitination of RAB8A and subsequent SQSTM1-mediated autophagic degradation. Functionally, loss of RAB8A sensitizes cancer cells to ferroptosis, whereas expression of the degradation-resistant active mutant RAB8AQ67L suppresses ferroptotic cell death. RAB8A interacts with TFRC and facilitates stress-induced redistribution of TFRC from the plasma membrane toward endolysosomal compartments. RAB8A deficiency impairs TFRC clearance, enhances transferrin-dependent iron uptake, and increases intracellular Fe2+ accumulation and lipid peroxidation. In fibrosarcoma and pancreatic cancer xenograft models, RAB8A depletion enhances the antitumor efficacy of ferroptosis-inducing therapy. Clinically, RAB8A is upregulated and associated with poor prognosis and ferroptosis resistance in pancreatic cancer. Collectively, these findings establish an autophagy-RAB8A-TFRC axis that regulates ferroptotic sensitivity.
    Keywords:  Iron metabolism; SQSTM1; lysosomal degradation; membrane trafficking; selective autophagy
    DOI:  https://doi.org/10.1080/15548627.2026.2726089
  32. J Extracell Vesicles. 2026 Sep;15(9): e70362
    Pharmacological Inhibition of Small Extracellular Vesicle Secretion by ALK5i SD-208 via Lysosomal Rerouting of CD63+ Compartments.
    Rahul Sanwlani, Georgina H Thompson, Kyle Bramich, Ching-Seng Ang, Millie L Trowbridge, Chris E Duringer, Vlad Stolojan, Sean M Davidson, Konstantinos Savvatis, John H McVey, Suresh Mathivanan, Aled Clayton, Patrizia Camelliti.
      Pharmacological tools to selectively modulate extracellular vesicle (EV) secretion are scarce. Here, we identify the ALK5 (TGF-β receptor I) inhibitor SD-208 as a potent suppressor of small EV (sEV) secretion that acts independently of its canonical anti-fibrotic activity. SD-208 not only reversed myofibroblast activation but also markedly inhibited sEV secretion. Strikingly, this inhibitory effect persisted in non-activated cardiac fibroblasts and non-fibrotic HEK293 cells, demonstrating that SD-208 regulates EV secretion through mechanisms uncoupled from TGF-β/Smad signalling. Mechanistic analyses revealed that SD-208 disrupts vesicle trafficking rather than EV biogenesis. Reduced secretion of CD63+ EVs was accompanied by intracellular accumulation of CD63+ structures and their selective diversion into LAMP1+ lysosomes. Proteomic profiling of SD-208-treated and control HEK293 cells and cardiac fibroblasts revealed dysregulation of vesicle trafficking pathways, enrichment of ubiquitin ligase complexes, and enhanced endosome-to-lysosome transport. Together, these findings demonstrate that SD-208 diverts CD63+ multivesicular bodies (MVBs) from a secretory fate toward lysosomal degradation. This work identifies SD-208 as a small-molecule tool to interrogate the secretory-versus-degradative fate of MVBs and uncovers a new regulatory link between lysosomal pathways and EV trafficking. Beyond its established role as an anti-fibrotic agent, SD-208 provides mechanistic and therapeutic opportunities for the control of EV secretion in diseases such as fibrosis, cardiac remodelling, hypertrophic cardiomyopathy, and cancer.
    Keywords:  ALK5 inhibitor (SD‐208); TGF‐β signalling; cardiac fibroblasts; extracellular vesicles; fibrosis; hypertrophic cardiomyopathy; lysosome–autophagy pathway; myofibroblasts; vesicle trafficking
    DOI:  https://doi.org/10.1002/jev2.70362
  33. Acta Pharmacol Sin. 2026 Sep 02.
    BioPROTACs: a promising approach for targeted protein degradation.
    Yu-Yang Li, Fu-Ru Zhang, Ren-Shuai Zhang, Dong-Ling Shao, Li-Li Yang, Xin-Yu Wang, Xue-Wei Cao, Shu-Ang Sun, Rui-Xin Ge, Song-Bo Xie.
      Targeted protein degradation (TPD) has emerged as an important therapeutic strategy in recent years. Proteolysis-targeting chimeras (PROTACs) are among the most extensively studied TPD technologies that eliminate target proteins through a "degradation rather than inhibition" mechanism. This mechanism offers opportunities to target proteins that are difficult to modulate using conventional small-molecule inhibitors and may also help mitigate drug resistance. However, the development of small-molecule PROTACs remains constrained by challenges associated with druggability, target accessibility, E3 ubiquitin ligase availability, and clinical translation. BioPROTACs have subsequently emerged as an alternative degradation platform in which genetically encoded protein modules replace conventional small-molecule ligands while preserving the underlying degradation mechanism. Their molecular design enables broader target recognition, flexible E3 ligase recruitment, and improved molecular specificity. Their emerging applications span cancer, viral infections, and neurodegenerative diseases. This review summarizes the molecular mechanisms, recent advances, and emerging applications of bioPROTAC technology, evaluates the current technical challenges, discusses potential strategies to address these limitations, and highlights future directions that may facilitate its clinical translation.
    Keywords:  BioPROTAC; E3 ubiquitin ligase; anticancer therapeutics; targeted protein degradation; ubiquitin-proteasome system
    DOI:  https://doi.org/10.1038/s41401-026-01918-2
  34. Nat Commun. 2026 07 31. pii: 9264. [Epub ahead of print]17(1):
    Ribo-ITP enables identification of translons from limited input samples.
    Vighnesh Ghatpande, Uma Paul, Logan Persyn, Yifan Tian, MacKenzie A Howard, Can Cenik.
      In the last decade, an unexpectedly large number of translated regions (translons) have been discovered using ribosome profiling and proteomics. Translons can act as regulatory elements or encode functional micropeptides. However, identification of translons has been limited to cell lines or large organs due to high input requirements for conventional ribosome profiling and mass spectrometry. Here, we address this input limitation using Ribo-ITP on difficult-to-collect samples such as microdissected hippocampal tissues and single preimplantation embryos to identify thousands of translons. To test the translational capacity of the identified translons, we engineer a translon-dependent GFP reporter system and detect expression of translons initiating at ATG and near-cognate start codons in mouse embryonic stem cells (mESCs). We identify distinct expression patterns of translons using a comparative analysis of more than a thousand ribosome profiling datasets across a wide range of cell types. Further, using a machine learning model, we predict that specific upstream translons in synaptically enriched mRNAs regulate translation efficiency of the annotated coding region. Taken together, we present a proof-of-concept study to identify non-canonical translation events from low input samples which can be applied to cell and tissue types inaccessible to conventional methods.
    DOI:  https://doi.org/10.1038/s41467-026-75571-y
  35. Cell Rep. 2026 Aug 28. pii: S2211-1247(26)00892-2. [Epub ahead of print]45(9): 117814
    An Epstein-Barr virus-encoded snoRNA directs 2'-O-methylation of human rRNAs to control translation and the viral lytic switch.
    Yarden Dan, Beáta E Jády, Yudit Halperin, Yuval Nevo, Aliza Fedorenko, Anat Bashan, Maram Arafat, Pnina Glick, Ada Yonath, Tamás Kiss, Daphna Nachmani.
      Epstein-Barr virus (EBV) establishes life-long latency in human B cells yet the molecular strategies that balance its persistence with lytic replication remain incompletely understood. Here, we identify the EBV-encoded small nucleolar RNA, v-snoRNA1, as a bona fide 2'-O-methylation guide that directs methylation of host ribosomal RNAs at 18S-C621 and 28S-U1760, two conserved residues in the ribosomal A-site. V-snoRNA1-mediated hypermethylation impairs 18S rRNA maturation and compromises translational fidelity and output, resulting in slower cellular proliferation. Infection with a v-snoRNA1 deleted virus (Δv-snoRNA1) leads to enhanced protein synthesis and increased proliferation, together with extensive rewiring of host and viral gene expression. This rewiring includes suppression of immune and interferon pathways and alterations in transcription factor activities important for B cell differentiation. Importantly, we find that v-snoRNA1 is required to facilitate viral production. Our findings reveal a molecular strategy by which EBV directly controls translation to promote infection.
    Keywords:  2′-O-methylation; CP: immunology; CP: molecular biology; EBV; rRNA; ribosome; snoRNA; translation
    DOI:  https://doi.org/10.1016/j.celrep.2026.117814
  36. Nature. 2026 Sep 02.
    Functional chimeric mRNAs encode proteins in mammalian immunity.
    Olivia Venezia, Harry Kane, Gang Du, Hannah D Coughlan, Timothy M Johanson, Hongshen Wang, Pathricia Tilstam, Samuel W Kazer, Georgia Gunner, Daisy A Hoagland, Megha G Basavappa, Kanchana Ravichandran, Eren Ada, Ademi Zhakyp, Sandhya Kumar, Coco Duizer, Owen Searle, Chris Geo Provido, Leonel Joannas, Shilong Yang, Liam B Healy, Qiankun Wang, Joia Capocchi, Bahawar Sharif Dhillon, Sarah Slavoff, Liang Shan, Jorge Henao-Mejia, Ruth A Franklin, Isaac M Chiu, Jose Ordovas-Montanes, Kate L Jeffrey, Judy Lieberman, Rhys S Allan, Jonathan C Kagan, Hao Wu, Ruaidhrí Jackson.
      Individual mammalian mRNAs and proteins are typically believed to originate from single genomic loci, with isoform diversity arising through cis-splicing of pre-mRNA. Whether mRNA from distant genes can undergo trans-splicing to generate functionally relevant chimeric transcripts has remained unclear. Here we develop a pipeline combining long-read direct RNA sequencing with non-targeted and targeted validation to identify chimeric transcripts in macrophages. Chromatin conformation capture studies reveal that inflammation induces interchromosomal DNA interactions, positioning parent genes proximally to facilitate the formation of chimeric mRNA. Notably, we identify a protein-coding chimeric mRNA representing a fusion between the pore-forming protein gasdermin D (GSDMD)1,2 and a C-terminal domain translated out of frame from Tmem106a (Gsdmd-Tmem106a) in mice. We show that inflammasome priming upregulates Gsdmd-Tmem106a, with the protein localizing to the plasma membrane. After activation of the inflammasome, GSDMD-TMEM106A directly interacts with canonical GSDMD N termini to accelerate and enhance pore formation and IL-1β release. Finally, we show that GSDMD-TMEM106A balances host defence and immunopathology in vivo: its loss protects against lethal sepsis but compromises antibacterial defence, whereas overexpression enhances host protection while increasing sepsis lethality. We establish that protein-coding chimeric mRNAs formed by regulated transcript fusion events are operative during inflammation and immunity.
    DOI:  https://doi.org/10.1038/s41586-026-10982-x
  37. Nat Commun. 2026 07 30. pii: 9316. [Epub ahead of print]17(1):
    Screening of amphipathic helices identifies features linked to inner nuclear membrane properties.
    Shoken Lee, Anabel-Lise Le Roux, Marc Goudge, Mira Mors, Stefano Vanni, Pere Roca-Cusachs, Shirin Bahmanyar.
      Inner nuclear membrane (INM) proteins control numerous nuclear functions, yet properties governing peripheral INM-association remain poorly defined. Here, we perform an image-based screen to identify features in candidate and established amphipathic helices (AHs) that mediate INM association. AHs that localize to ER/Golgi membranes become INM-associated when directed to the nucleus, whereas mitochondrial-localized AHs become largely nucleoplasmic. Mutating a mitochondrial-localized AH to increase its preference for membranes with lipid packing defects enables INM-association upon nuclear targeting. Structural studies of an INM-associated AH in TMEM214 show folding upon binding to lipid packing defects, and full-length TMEM214 localizes to nuclear pores. Consistently across multiple AHs, INM binding depends primarily on sensitivity to lipid packing defects, with a minor electrostatic contribution. Highlighting distinct effects of different mechanical inputs, nuclear swelling, but not cell stretching, enhances INM association of select AHs. These findings define AH features that promote INM association, with implications for nucleo-mechanical responses.
    DOI:  https://doi.org/10.1038/s41467-026-75561-0
  38. FEBS Open Bio. 2026 Aug 31.
    Genetic dissection of human ABCE1 in yeast reveals separable requirements for ribosome recycling and suppression of aberrant reinitiation.
    Eriko Nakata, Yuxin Li, Kei Endo, Koichi Ito.
      The ATP-binding cassette E1 (ABCE1) protein is an essential factor for ribosome recycling, splitting post-termination ribosomes into subunits for subsequent rounds of translation. Despite high conservation, human ABCE1 (hABCE1) fails to functionally complement the depletion of its essential yeast homolog, Rli1. In this study, we leveraged this species-specificity to dissect the functional architecture of ABCE1. Through analysis of yeast-human chimeric proteins, we identified the N-terminal nucleotide-binding domain (NBD1) as the primary determinant of this incompatibility. To further investigate, we isolated multiple hABCE1 point mutants (revertants) that successfully restored yeast growth. We then developed a novel dual-luciferase reporter assay to quantify aberrant translation reinitiation in the 3'UTR, an event recognized as a direct consequence of ABCE1 deficiency. Notably, while the revertant mutants rescued yeast viability, they failed to suppress aberrant reinitiation, exhibiting levels equivalent to the nonfunctional hABCE1. This genetic uncoupling of viability from the suppression of reinitiation suggests that the canonical ribosome recycling function required for cell growth and the role in preventing aberrant reinitiation have distinct functional thresholds or are genetically separable aspects of ABCE1 activity.
    Keywords:  ABCE1; Rli1; Saccharomyces cerevisiae; ribosome recycling; species‐specificity; translational integrity
    DOI:  https://doi.org/10.1002/2211-5463.70337
  39. Blood Adv. 2026 Sep 04. pii: bloodadvances.2026019895. [Epub ahead of print]
    Unfolded protein response signaling promotes myeloid cell production and cooperates with oncogenic mutation.
    Hyunjoo Choi, Sang-Eun Jung, Yesenia Earth, Hyojung Paik, Shuyang Lin, Jiye Yi, Maggie J Cox, Stephen M Sykes, Stephen T Oh, Yoon-A Kang.
      Unfolded protein response (UPR) promotes protein homeostasis under endoplasmic reticulum stress. UPR signaling has numerous functions in metabolism, cancer, immunology, and neurodegenerative diseases. Recent studies also showed that UPR signaling has important roles in hematopoietic stem and progenitor cell biology. However, whether UPR signaling regulates hematopoietic lineage fate decision remains elusive. Here, we found that FcgR- MPP3 generates erythroid lineage and Jak2V617F mutation leads to overproduction of erythroid cells by expanding FcgR- MPP3. We showed that UPR signaling increases myeloid cell production through promoting FcgR- MPP3 transition to granulocyte/macrophage progenitor producing FcgR+ MPP3 at the expense of erythroid lineage via the XBP1 pathway. Under a disease condition, UPR signaling cooperates with Jak2V617F mutation and exacerbates disease phenotype in a mouse model of polycythemia vera (PV) through the ATF4 pathway. Activation of UPR signaling also increased myeloid output in healthy donor bone marrow MPP cells while skewing the output towards erythroid lineage in PV patient bone marrow MPP cells. Together, our results identify a novel function of UPR signaling in hematopoietic lineage specification and provide critical insights into targeting UPR signaling in hematological malignancies.
    DOI:  https://doi.org/10.1182/bloodadvances.2026019895
  40. Cell Biochem Funct. 2026 Sep;44(9): e70297
    Interactions Between E3 Ubiquitin Ligases and Deubiquitinases in AKT Regulation: Implications in Skeletal Muscle Homeostasis.
    Rajesh Dabur.
      AKT (protein kinase B, PKB) coordinates the balance between anabolic and catabolic signaling in skeletal muscle through distinct ubiquitin chain types. Some E3 ubiquitin ligases (E3s) and deubiquitinases (DUBs) form stable binary complexes via non-catalytic interfaces, adding a regulatory layer unavailable to either enzyme alone. This mechanistic synthesis review presents a systematic literature analysis (inception to May 2026; 26 eligible studies). It identified four E3-DUB pairs proposed to regulate AKT in skeletal muscle. These are TRAF6-CYLD (plasma-membrane K63-ubiquitination), MUL1-USP9X (mitochondrial K48-ubiquitination of AKT2), CHIP-UCH37 (proteasome-proximal quality control), and SCF-Skp2-USP37 (PHLPP1/2-dependent control of AKT Ser473 phosphorylation). All four interfaces are structurally separate from the catalytic sites and are regulated by upstream kinase phosphorylation. Evidence for the four pairs is markedly uneven. TRAF6-CYLD is supported by endogenous co-immunoprecipitation and functional data in muscle models. CHIP and UCH37 each act on AKT-related substrates independently and are individually well documented, but a direct CHIP-UCH37 interaction has not itself been demonstrated. SCF-Skp2-USP37 interaction data rest on a real but non-muscle direct interaction, whereas MUL1-USP9X has no reported direct interaction at all; CHIP-UCH37, SCF-Skp2-USP37, and MUL1-USP9X are therefore all presented as testable hypotheses of varying strength. In chronic atrophy, available data are consistent with disruption of these complexes contributing to AKT suppression through parallel, largely independent mechanisms. However, simultaneous disruption of all four has not been demonstrated in a single system. Available gene expression and protein datasets from sarcopenic muscle broadly support these predictions, though direct experimental validation in human tissue remains pending. This complex-centric framework recasts AKT ubiquitination as an integrated regulatory framework. Each structurally autonomous interface may represent a potentially distinct target for muscle-wasting conditions that currently lack approved therapies.
    Keywords:  AKT ubiquitination; E3 ubiquitin ligase; deubiquitinase; muscle atrophy; sarcopenia; skeletal muscle; ubiquitin chain topology
    DOI:  https://doi.org/10.1002/cbf.70297
  41. PLoS Comput Biol. 2026 Sep 02. 22(9): e1014729
    Synergies and trade-offs in the heat shock response mechanism.
    Rupal Chauhan, Biswajit Das, Ajeet K Sharma.
      E. coli relies on the heat shock response (HSR) to preserve protein homeostasis under stress, through three feedback modules: feedforward translational control, chaperone-mediated sequestration and targeted degradation. Although previous studies have highlighted how this layered architecture ensures rapid and robust protection compared to simpler designs, not much attention is paid to how these modules interact. Moreover, how do interactions among the three modules balance performance trade-offs, where gains in one module may come at the expense of another, yet together yield an optimal overall response? We address this using a mathematical model that integrates protein folding with σ32 regulation. We show that the feedback modules both cooperate and compete, giving rise to nonmonotonic dynamics that govern HSR performance. Specifically, increasing feedforward strength does accelerate response, but beyond a threshold, despite increasing chaperone levels, it paradoxically slows recovery. Similarly, while sequestration enhances relative chaperone production and per-chaperone efficiency, when excessive, it traps σ32 in inactive complexes, prolonging recovery and delaying shutdown. Mapping the parameter space reveals regimes of synergy as well as trade-offs between speed and efficiency, with wild-type parameters lying near the optimal region. These results reveal design principles that produces a robust and efficient heat shock response.
    DOI:  https://doi.org/10.1371/journal.pcbi.1014729
  42. Methods Mol Biol. 2026 ;3070 331-347
    Posttranslational Dynamics of the Subcellular Proteome by Mass Spectrometry-Based Proteomics.
    Ana Martínez-Val, Jose Manuel Rodríguez, Jesper V Olsen, Jesús Vázquez.
      Localization of proteins to different cell compartments is a major posttranslational regulatory mechanism that eukaryotic cells have evolved to coordinate protein homeostasis and responses to stimuli. Subcellular fractionation allows the separation of distinct protein populations from cellular compartments such as the cytosol, cytoskeleton, membrane, endoplasmic reticulum, or nucleolus. This fractionation can be followed by mass spectrometry-based proteomics to provide insights into spatiotemporal regulation or cellular protein networks. Here, we describe a high-throughput workflow based on sequential cell lysis, which enables the profiling of subcellular proteome architecture and the detection of changes in protein localization at global and posttranslational levels.
    Keywords:  Cell signalling; Mass spectrometry; Posttranslational regulation; Proteomics; Subcellular fractionation
    DOI:  https://doi.org/10.1007/978-1-0716-5515-3_19
  43. Nat Commun. 2026 08 19. pii: 9363. [Epub ahead of print]17(1):
    Long-read proteogenomic atlas of human neuronal differentiation reveals isoform diversity informing neurodevelopmental risk mechanisms.
    Nuo Xu, Katherine M Rynard, Elizabeth Radley, Ai Tian, Maahil Arshad, Chaoying Long, Jimmy Ly, Hua Luo, Ellie Hogan, Maria Eleni Fafouti, Melanie Davie, Fatima Naimi, Yun Li, John A Calarco, Brett Trost, Julien Muffat, Hyun O Lee, Howard D Lipshitz, Craig A Smibert, Shreejoy J Tripathy.
      RNA splicing shapes neuronal identity and disease risk, yet current maps lack the developmental resolution and depth to resolve this complexity. Here, we integrate deep long-read RNA sequencing and proteomics in induced pluripotent stem cell-derived cortical neurons to generate a high-resolution proteogenomic atlas of human neuron development. We identify 182,371 mRNA isoforms (over half previously unknown) and provide direct peptide evidence for the translation of hundreds of novel protein-coding sequences. Population genetics demonstrates that variants affecting novel exons and splice sites are under negative selection, underscoring the potential significance of these isoforms. During neuronal maturation, we observe that autism risk genes undergo dynamic isoform switching, including microexon inclusion and intron retention, that remodel key protein domains and regulatory regions. Furthermore, we uncover widespread, long-range coordination between alternative transcript processing events, including transcription start sites, exon splicing, and polyadenylation. Finally, our atlas enables variant reinterpretation in autism, highlighting the value of an isoform-centric view for interpreting pathogenic variation in neurodevelopment.
    DOI:  https://doi.org/10.1038/s41467-026-76675-1
  44. Nat Biotechnol. 2026 Aug 31.
    Macropinocytosis-mediated recyclable LYTACs (McR-TACs) for receptor-independent protein degradation.
    Peixin Liu, Yule Li, Tianyi Ma, Yawen You, Yu Chen, Michelle Y Cai, Quanyin Hu.
      The degradation of cell membrane and extracellular proteins with lysosome-targeting chimeras (LYTACs) is limited by nonrecyclable, receptor-dependent mechanisms that shuttle proteins to lysosomes, restricting the broad use of this emerging technology. Here we developed a recyclable chimera composed of a polyzwitterion and protein of interest (POI) ligand for protein degradation. This chimera could interact with the cell membrane to trigger macropinocytosis together with the POI in a receptor-independent manner. Furthermore, it can dissociate from the POI in the acidic endocytic compartments and subsequently be exocytosed through the endoplasmic reticulum-Golgi transcytosis pathway. Ultimately, the exocytotic chimera initiates the next round of targeted protein degradation. These macropinocytosis-mediated recyclable LYTACs (McR-TACs) durably degrade the cell membrane protein (programmed cell death ligand 1) or the extracellular protein (macrophage migration inhibitory factor) in a triple-negative breast cancer mouse model, thereby inhibiting the tumor growth. Collectively, McR-TACs show the potential of leveraging natural transport pathways to create recyclable protein degraders with wide-ranging applications.
    DOI:  https://doi.org/10.1038/s41587-026-03302-1
  45. Mol Oncol. 2026 Sep 02.
    Mechanisms and therapeutic opportunities of the ribotoxic stress response in cancer.
    Anastassiya Kim, Maryam Aslam, Elouise Torruella, Alphons Sony, Asif Rahman, Simira Smith, Columba de la Parra, Moira Sauane.
      Various environmental and endogenous stressors, including ultraviolet (UV) radiation, cytotoxins, and dysregulated translation, can induce ribosome stalling and collisions, disrupting protein homeostasis. The ribotoxic stress response (RSR) is a cellular surveillance mechanism that senses translational stress and activates stress signaling via the MAP3 kinase ZAKα and the stress-activated protein kinases (SAPKs) p38 and JNK. This review outlines the molecular mechanisms behind RSR, distinguishes RSR from other translational stress response pathways, such as the well-studied integrated stress response (ISR), discusses the role of RSR in key cellular processes, and presents new evidence linking RSR to cancer biology. We explore how ribotoxic stress is exploited by chemotherapeutic agents and other compounds to induce cancer cell death, and the potential limitations of such therapeutic strategy. Finally, we highlight future considerations for inducing the RSR pathway in cancer, highlighting both therapeutic potential and the challenges in this emerging field.
    Keywords:  ZAKα; cancer; ribosome collision; ribosome stalling; ribotoxic stress response; stress‐activated protein kinase
    DOI:  https://doi.org/10.1002/1878-0261.70323
  46. Nat Commun. 2026 Aug 06. pii: 9484. [Epub ahead of print]17(1):
    Glycoprotein-induced phase separation drives unconventional secretion of galectin-3.
    Zihan Zhao, Zhen He, Hongming Gu, Andong Zhou, Yibing Wang, Zhaoyi Liang, Jie Geng, Xuejiao Xu, Menghui Wang, Chunyao Li, Yuying Fan, Hairong Cheng, Lin Sun, Kevin H Mayo, Avraham Raz, Guihua Tai, Yifa Zhou.
      The mechanism of unconventional protein secretion remains an unresolved issue. Here, we describe an unconventional protein secretion pathway for galectin-3 that is mediated by phase separation and condensation. Using four lysosomal damage models, we observed a rapid, pronounced release of galectin-3 in large, non-exosomal particles. This secretion is driven by glycoprotein-induced galectin-3 phase separation and is independent of pyroptosis and secretory autophagy. During phase separation, the S-face of galectin-3 carbohydrate recognition domain binds glycoproteins that triggers galectin-3 N-terminal tail release and condensation. These condensates then recruit ALG-2 via the exposed N-terminal tail. ALG-2 directs the condensates to the endoplasmic reticulum-late endosome interface. After translocation into late endosomes, galectin-3 condensates are secreted into the extracellular milieu by SNARE-dependent vesicular transport. This mechanism of exporting phase-separated protein condensates may serve as a clean-up response to membrane damage.
    DOI:  https://doi.org/10.1038/s41467-026-76321-w
  47. Nat Commun. 2026 08 04. pii: 9367. [Epub ahead of print]17(1):
    Translational control by RPL22L1-specific ribosomes enhances DNA repair and chemoresistance.
    Saisai Wei, Wentao Yu, Yilin Shen, Yu Qian, Ye Wang, Tiezheng Li, Jiaqi Cao, Xiangwei Gao, Xiujun Cai.
      Ribosome heterogeneity has emerged as a regulatory layer in gene expression, yet its biological roles in cancers remain poorly characterized. Here, we identify RPL22L1, a paralog of the ribosomal protein RPL22, as a key modulator of DNA damage response (DDR) in colorectal cancer cells. DNA damage induces RPL22L1 upregulation and ribosomal incorporation, forming RPL22L1-specific ribosomes. Ribosome profiling reveals that RPL22L1-containing ribosomes preferentially translate mRNAs with highly structured 5' untranslated region (5'UTR). In particular, RPL22L1 enhances the translation of ATRX through a cap-independent mechanism. ATRX subsequently recruits DNA-PKcs to DNA damage sites, thereby enhancing the DNA repair capacity. RPL22L1 loss creates exploitable DDR vulnerabilities, sensitizing cancer cells to cisplatin and PARP inhibitors in vitro and in vivo. Collectively, these findings uncover a specialized ribosome-mediated translational program in DDR and highlight RPL22L1 as a potential therapeutic target in DDR-based cancer therapy.
    DOI:  https://doi.org/10.1038/s41467-026-76283-z
  48. Redox Biol. 2026 Sep 02. pii: S2213-2317(26)00380-0. [Epub ahead of print]97 104381
    Non-canonical activation of VEGFA through TIMM44-dependent mitochondrial remodelling.
    Tanvi Chaudhary, Sharath Mohan Bhat, Priyadarshika Pradhan, Manjunath B Joshi, Devanjan Sinha.
      Coordination of mitochondrial functional states with nuclear transcriptional programs remain critical for cellular adaptation. Here, we identify mitochondrial protein import capacity as a regulator of redox-dependent signalling in tumour cells. We show that the mitochondrial import motor component TIMM44, which is upregulated in angiogenesis-driven tumours, drives respiratory remodelling without increasing mitochondrial abundance. This mitochondrial reprogramming establishes a redox-competent state that activates ASK1-p38MAPK, resulting in SP1-dependent upregulation of VEGFA independently of HIF stabilization. Importantly, induction of mitochondrial biogenesis via PGC-1α fails to recapitulate this response despite increased active mitochondrial content, demonstrating that abundance of active mitochondria or generic metabolic activation is insufficient to drive this HIF-independent transcription. Collectively, our findings identify mitochondrial protein import process as an active signalling regulator rather than a passive housekeeping role, which links mitochondrial proteostasis to redox-sensitive kinase activation and transcriptional control. This work highlights a non-canonical mitochondrial signalling mechanism through which cells couple organelle remodelling to gene expression programs.
    DOI:  https://doi.org/10.1016/j.redox.2026.104381
  49. Antioxid Redox Signal. 2026 Sep 02. 15230864261481794
    Mitochondrial Microautophagy: An Emerging Pathway in Maintaining Mitochondrial Homeostasis.
    Huijia Zhang, Ying Chen, Junjie Jiang, Yarong Ding, Si Hu, Zhongzhi Zhou, Li Chen.
      Background:Mitochondrial quality control has traditionally been attributed to mitophagy. However, emerging evidence indicates that mitochondrial microautophagy represents a distinct quality control pathway. This pathway enables selective removal of damaged mitochondrial subdomains while preserving overall organelle integrity. Therefore, mitochondrial microautophagy can be viewed as a redox-adaptive, sub-organelle quality control system that responds to localized mitochondrial stress.Scope of Review: In this review, we integrate recent mechanistic, imaging, and molecular studies to establish an updated framework of mitochondrial microautophagy. We describe this process as a sequential pathway involving damage sensing, mitochondria-lysosome contact formation, lysosomal membrane remodeling, selective degradation, and metabolic recycling. Localized reactive oxygen species (ROS) serve as important signals during this process. ROS define specific damage microdomains and facilitate selective mitochondrial component recognition. Subsequent cargo delivery and degradation are regulated by multiple molecular modules. These modules include the ubiquitin-autophagy-related protein 8 system, vacuolar-type H+-ATPase-dependent membrane remodeling, Ras-related in brain-endosomal sorting complexes required for transport signaling, the spermatogenesis-associated 18/mitochondria-eating protein pathway, and the mechanistic target of rapamycin complex 1-transcription factor EB and nuclear factor erythroid 2-related factor 2 stress-response networks.Outstanding Questions: Despite substantial progress, several fundamental questions remain unresolved. The mechanisms underlying cargo recognition require further clarification. The existence of specific redox-sensitive receptors remains to be determined. In addition, future technological advances will provide deeper insights into this pathway.Conclusions: Understanding mitochondrial microautophagy may reveal new therapeutic opportunities for mitochondrial dysfunction-associated disorders, including neurodegeneration, ischemic injury, metabolic disorders, and aging. Antioxid. Redox Signal. 00, 000-000.
    Keywords:  ESCRT complex; Rab GTPase; SPATA18/Mieap; TFEB; V-ATPase; autophagy; lysosomal membrane remodeling; mitochondrial microautophagy; mitochondrial quality control
    DOI:  https://doi.org/10.1177/15230864261481794
  50. Comput Biol Chem. 2026 Aug 27. pii: S1476-9271(26)00485-8. [Epub ahead of print]126(Pt 1): 109358
    Beyond random splits: A hierarchical benchmark of transferability and reliability in PROTAC activity prediction.
    Renguang Zhu, Guanghao Guo, Lulu Li, Sihan Luo.
      Computational prediction of PROTAC degradation activity (DC50) has attracted growing interest, yet the reliability of reported model performance remains poorly understood because sufficiently stringent evaluation protocols are rarely applied. Here, we present a hierarchical benchmark designed to expose evaluation pitfalls and quantify the transferability and reliability limits of current PROTAC predictors. Using a curated dataset of 2405 DC50 measurements spanning 22 target proteins and two E3 ligases (CRBN and VHL), we benchmarked classical machine learning (Random Forest, ExtraTrees, Ridge, PLS), gradient-boosted trees (XGBoost), nearest-neighbor retrieval baselines, protein negative controls, and a representative multi-modal deep learning ensemble (HybridMoECrossAttn) across Random, Scaffold, Leave-One-Target-Out (LOTO), and Leave-One-Family-Out (LOFO) splits. Under Random evaluation, a simple Random Forest + ECFP4 baseline achieved pooled R² = 0.693 ± 0.025, indicating that conventional models already approach the apparent ceiling under interpolation-oriented settings. However, all methods collapsed under LOTO (best R² = -0.012), revealing that much of the apparent progress in the literature reflects chemical-neighbor memorization rather than robust target-level generalization. We further show that target-wise error is significantly associated with continuous protein semantic proximity in ProtBERT space (Spearman ρ = -0.461, p = 0.047), whereas coarse family-level descriptors are uninformative. A four-quadrant failure taxonomy reveals that protein shift is more damaging than chemical novelty (MAE 1.09-1.12 vs. 0.85-0.97), and conformal prediction becomes severely overconfident under target extrapolation, with empirical 90% coverage dropping to 63.9-66.7%. These results reposition PROTAC prediction as a problem of transferability and reliability rather than leaderboard optimization and provide practical guidelines for future benchmark design.
    Keywords:  Applicability domain; Benchmarking; Conformal prediction; Cross-target generalization; Distribution shift; Evaluation bias; PROTAC; Protein language models; Targeted protein degradation; Uncertainty quantification
    DOI:  https://doi.org/10.1016/j.compbiolchem.2026.109358
  51. Sci Adv. 2026 Sep 04. 12(36): eaej0987
    Functional mapping and engineering of the Sec translocon unlocked by a cell-free system.
    Markus Meier, Scott A Scholz, Leo von Bank, João E Levandoski, Mosche Lückhof, Maximilian Schaaf, Nataliya Safronova, Nathan F Greenwood, Shutian Si, Ingo Lieberwirth, Anna Lena Jung, Katharina Landfester, Arnold J M Driessen, Tobias J Erb.
      Almost all membrane proteins are inserted or translocated across membranes by the universally conserved Sec translocon. Despite its central role, experimental access to Sec function has remained limited. Here, we present ProSecCO (Protein Secretion in Cell-free via synthetic Operons), which is a cell-free protein synthesis platform that inserts SecYEG into synthetic vesicles, enabling direct testing of Sec in real-time and high-throughput, circumventing longstanding viability constraints. Screening 300 Sec variants in a single experiment, we consolidate three decades of Sec research, while vastly expanding mutant diversity for structure-function insights. Mapping over 30 functionally critical regions that modulate Sec activity across three orders of magnitude, we uncover dozens of super-active translocation variants and one variant of improved insertion activity. We further leverage ProSecCO to increase membrane protein quality and nanobody export, highlighting the potential of our system for advancing applications in synthetic biology and biotechnology.
    DOI:  https://doi.org/10.1126/sciadv.aej0987
  52. Cell Rep Med. 2026 Aug 31. pii: S2666-3791(26)00434-9. [Epub ahead of print] 103017
    Non-genetic remodeling drives leukemia propagation and reveals actionable vulnerabilities in acute myeloid leukemia.
    Clement Larrue, Paolo Angelino, Sarah Mouche, Alexa S Green, Emeline Boet, Ismael Boussaid, Claudia Perez-Carretero, Rudy Birsen, Maxime Sajot, Thomas A Mckee, Ambrine Sahal, Nicolas Chapuis, François Vergez, Christian Recher, Véronique Mansat-De Mas, Olivier Kosmider, Pierre Sujobert, Frederic Catez, Jean-Jacques Diaz, Jean-Emmanuel Sarry, Petros Tsantoulis, Jerome Tamburini.
      Acute myeloid leukemia (AML) persistence and relapse are sustained by leukemia-propagating cells, yet the molecular programs supporting their expansion during disease evolution remain incompletely understood. Using serial patient-derived xenotransplantation, we establish a longitudinal model in which leukemia-initiating capacity progressively increases. Integrated single-cell transcriptomics and multi-omics profiling reveal a predominantly non-genetic trajectory that follows a conserved pattern across models and is associated with coordinated changes across epigenetic, transcriptional, and proteomic layers. Ribosome profiling and rRNA 2'-O-methylation analyses further support a stage-specific increase in translational activity with ribosome remodeling in advanced xenografts. A pharmacological screen of 3,247 compounds uncovers a limited set of vulnerabilities that consistently emerge during disease progression, including CRBN-dependent degradation of GSPT1 (CC-885) and IAP antagonism (AZD5582). In vivo validation shows that both agents markedly reduce leukemic burden, impair leukemia propagation, and enhance cytarabine activity in patient-derived xenograft (PDX) models. Together, these findings show that leukemic propagation is driven by a non-genetic remodeling program, providing a framework to prioritize and test stage-specific therapeutic strategies in AML.
    Keywords:  DNA methylation; acute myeloid leukemia; drug screening; leukemic stem cells; patient-derived xenografts; ribosome profiling; serial xenotransplantation; translational regulation
    DOI:  https://doi.org/10.1016/j.xcrm.2026.103017
  53. Plant Cell Environ. 2026 Sep 01.
    Selective Autophagy in Plant Immunity: Mechanisms, Regulation, and Emerging Concepts in Xenophagy.
    Laha Supriya, Deepika Dake, Pooja Shukla, Namisha Sharma, Padmaja Gudipalli, Mehanathan Muthamilarasan.
      Selective autophagy has emerged as a critical component of plant immunity, yet its role as a dedicated antimicrobial mechanism, xenophagy, remains conceptually underdeveloped. In plants, xenophagy extends beyond bulk degradation to function as a highly regulated, cargo-specific pathway that targets invading pathogens and their effector molecules for autophagic clearance. Recent evidence demonstrates that selective autophagy receptors, particularly NBR1, integrate ubiquitin-mediated recognition with ATG8-dependent sequestration, enabling the elimination of bacterial, fungal, and viral components. However, this process is not merely degradative but operates at the intersection of immune signaling, proteostasis, and cellular decision-making. Here, we synthesize current advances in plant xenophagy and propose a unifying framework in which xenophagy appears to function as a cell-autonomous immune hub comprising three interconnected modules: cargo recognition, selective sequestration, and autophagic execution, dynamically modulated by pathogen-derived countermeasures. We further examine how pathogens subvert or exploit host autophagic machinery, revealing xenophagy as a contested interface in plant-pathogen interactions. By integrating molecular, cellular, and cross-kingdom perspectives, we highlight key conceptual gaps, including the specificity of cargo selection, the regulatory logic of receptor engagement, and the coordination between autophagy and canonical immune pathways. Resolving these gaps will be essential for repositioning xenophagy as a central determinant of plant immune competence, with significant implications for engineering disease-resistant crops.
    Keywords:  NBR1‐signalling; autophagy; effector protein; plant‐microbe interaction; xenophagy
    DOI:  https://doi.org/10.1111/pce.70830
  54. Nature. 2026 Sep 02.
    Rewiring the ribosome to translate proteins encoded in its own RNA.
    Kasra Alizadeh, Dorota Klepacki, Nora Vázquez-Laslop, Alexander S Mankin.
      Cellular protein synthesis relies on random encounters between ribosomes and mRNAs, limiting optimization of the translation machinery for production of a single protein-a key need in biotechnology. One potential solution is integrating the protein-coding sequence into the ribosome itself, thereby committing the ribosome to synthesis of a single polypeptide. The feasibility of such integration could also address a long-standing challenge in RNA world models: explaining how early protein synthesis could function reliably despite the scarcity and poor organization of its components1. Whether a ribosome can translate its own ribosomal RNA (rRNA) has remained unclear. Here we show that bacterial ribosomes can synthesize proteins encoded within their own RNA. We engineered a chimeric messenger-ribosomal RNA (mrRNA) by appending a protein-coding sequence to 16S rRNA. The hybrid mrRNA assembles into a small ribosomal subunit that binds to the large subunit to form Ribo-M, a ribosome capable of translating mrRNA-encoded proteins. Translation is abolished by mutations or antibiotics that impair the function of the small subunit, demonstrating that mrRNA translation is carried out in cis by ribosomes assembled on the chimeric mrRNA. Incorporating mrRNA into a ribosome with tethered subunits yielded Ribo-TM, in which encoding, decoding and peptide synthesis are united within a single RNA scaffold. These findings establish the mechanistic feasibility of a ribosome translating its own rRNA in vivo and in vitro, offering a versatile platform for orthogonal protein production and insights into the origin of translation.
    DOI:  https://doi.org/10.1038/s41586-026-10962-1
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