bims-proteo Biomed News
on Proteostasis
Issue of 2026–07–26
53 papers selected by
Eric Chevet, INSERM
  1. Dual regulation of the unfolded protein response by IGF2BP3 during ER stress.
  2. Nascent chain folding status modulates ribosome dynamics and mRNA stability through the ribosome-associated chaperone Zuo1.
  3. Proteome analyses reveal endoplasmic reticulum stress-induced changes in protein abundance associated with Ube2j2 deficiency in human cell culture.
  4. Structural dynamics of IRE1 and its interaction with unfolded peptides.
  5. Dynamic O-GlcNAcylation of Sec23-interacting protein regulates COPII function.
  6. USP28 Deficiency is Linked to Impaired Ubiquitin-dependent Proteostasis in Huntington's Disease.
  7. Atg23 prevents aberrant fusion of Atg9 vesicles during delivery to autophagosome formation sites.
  8. Blm10 and PI31 comprise a failsafe mechanism for proteasome inhibition.
  9. Pan-cancer proteogenomic interrogation of the ubiquitin-proteasome system.
  10. An optimized RNF126-targeting covalent handle for molecular glue degraders.
  11. Dual-targeting pharmacological UFMylation inhibition reprograms tumor and immune microenvironments to achieve long-term glioblastoma regression.
  12. Impaired mitochondrial quality control and stress signalling machinery modulate senescence induction by genotoxic challenge.
  13. Mitochondrial-derived vesicles drive budding-type fission of damaged lysosomes.
  14. Oxidative protein folding and Ca2+ homeostasis under redox control.
  15. Activity-dependent ribosome profiling reveals the landscape of canonical and non-canonical translation in brain tissue.
  16. The protein kinase GCN2 senses the integrity of the multi-tRNA synthetase complex.
  17. Mitochondrial translation termination, recycling, reinitiation, and rescue for in-frame and out-of-frame contexts.
  18. Expanding the scope of protein language modeling to protein-protein interactions with MSA Pairformer.
  19. UTR-ly unexpected: RNA chaperones tame intrinsically disordered proteins.
  20. TBC1D9 and TBC1D9B are ARL8 effectors that modulate exosome secretion through a RAB11A-exocyst pathway.
  21. Structural and mechanistic insights into protein glycosylation and glycosylphosphatidylinositol anchoring in the endoplasmic reticulum membrane.
  22. Structures of dynamic interactors at native proteasomes by PhIX-MS and cryo-electron microscopy.
  23. The role of E3 ubiquitin ligases in selective types of macroautophagy.
  24. PLA2G2F suppresses ferroptosis through phospholipid remodeling.
  25. Complex assembly and activity states as multifaceted protein attributes explaining phenotypic variability.
  26. HIT-MAP: A scalable approach to multimodal mapping of subcellular organization.
  27. Structural basis of the RNA-editing cascade in trypanosome mitochondria.
  28. Dual-function PROTAC suppresses ferroptosis and restores neuronal function via brain-targeted delivery.
  29. Self-Splicing RNA Platform Encodes Twin PROTACs for Dual-E3 Ligase Recruitment and Programmable Protein Degradation.
  30. DNAJC12 Stabilizes Phenylalanine Hydroxylase and Facilitates Its Substrate-Dependent Activation.
  31. NDRG1 expression in cancers confers dependence on DNA damage repair and sensitivity to quinacrine.
  32. A bivalent molecular glue linking lysine acetyltransferases to oncogene-induced cell death.
  33. Upstream non-AUG initiation and ribosomal -1 frameshifting in ATXN8OS CTA/CTG repeat-associated translation.
  34. Repurposing an E3 ligase to chaperone for the sake of thermotolerance.
  35. Global cellular responses to lysosomal damage.
  36. AlphaFold-driven structural proteomics reveals extensive cellulosome machinery in human ruminococcal symbionts.
  37. The emerging role of ERphagy/reticulophagy in pathogen invasion.
  38. Assessing the Stability of Molecular Glues with Weighted Ensemble Simulations.
  39. Structural and mechanistic basis for membrane recognition and activation of the vacuolar lipase Atg15.
  40. Zebrafish RNF128a positively regulates innate immunity by promoting the K63-linked ubiquitination of TBK1.
  41. Epitope-guided detection of a molecular glue-induced ternary complex using engineered synthetic antibody fragments.
  42. A Blood-Derived Factor Rescues ALS: Platelet Factor 4 Activates OPTN-Dependent Autophagy to Clear SOD1 Aggregates Independently of PINK1.
  43. ETTAS: a modular aptamer-recruited platform for programmable translational activation.
  44. RNA-based ATTEC: an RNA-guided autophagy-lysosome platform for targeted protein degradation.
  45. Tripartite ER-mitochondria-lipid droplets contact sites control adipocyte metabolic flexibility.
  46. Mapping Non-Homologous Pocket Compatibilities to Identify Hidden Drug-Target Relationships: A Pocket Hopping Framework.
  47. The PERK paradox in aging: how ER stress shapes senescence and neurodegeneration.
  48. Differential assembly of RNP granules via activation of distinct dsRNA sensors by adenovirus mutants.
  49. Vps1 drives membrane constriction and fission necessary for endosomal protein sorting.
  50. Deciphering the mechanism of protein aggregation and effects of inhibitors using single-molecule mass photometry.
  51. The RNA-binding protein RALY promotes ATM activation by stabilizing Tip60.
  52. HUWE1 targets mitochondria via RMC1 to promote neurodevelopment.
  53. The N-terminal domain of the endoplasmic reticulum-resident chaperone Grp94 functions in aggregation prevention.
  1. Genes Dev. 2026 Jul 23.
    Dual regulation of the unfolded protein response by IGF2BP3 during ER stress.
    Aleksandra S Anisimova, Sabina Omerbegovic, Milica Mihailovic, Sascha Gratzl, Harald Hornegger, Irmgard Fischer, Gijs A Versteeg, Stefan L Ameres, G Elif Karagöz.
      Misfolded protein accumulation in the endoplasmic reticulum (ER) perturbs cellular homeostasis, causing pathological ER stress. While a transcriptional response is paramount for the unfolded protein response (UPR), which counters ER protein stress, multiple UPR-linked mRNAs are posttranscriptionally regulated. However, the mechanisms mediating this regulation remain unclear. Here, we reveal specific interactions between the conserved RNA-binding protein IGF2BP3 and transcripts encoding UPR effectors. During ER stress, IGF2BP3 destabilizes many of its target transcripts, including UPR effectors. Mechanistically, ER stress enhances IGF2BP3's association with the mRNA decapping complex and the ER stress sensor RNase IRE1, which correlates with a shift toward mRNA destabilization. Unexpectedly, prolonged depletion of IGF2BP3 inhibits the UPR via decreased transcription of UPR target genes. Together, our findings suggest that IGF2BP3 contributes to proteostasis during ER stress through a dual mechanism: directly promoting mRNA degradation to reduce translation and folding burden and indirectly supporting transcriptional activation of the UPR.
    Keywords:  IGF2BP3; IRE1; RNA-binding proteins; endoplasmic reticulum; mRNA decapping complex; posttranscriptional regulation; unfolded protein response
    DOI:  https://doi.org/10.1101/gad.353291.125
  2. Mol Cell. 2026 Jul 22. pii: S1097-2765(26)00457-0. [Epub ahead of print]
    Nascent chain folding status modulates ribosome dynamics and mRNA stability through the ribosome-associated chaperone Zuo1.
    Suhee Chang, Ryan Kawalerski, Mehmet Tardu, Sophie Martin, Kristin S Koutmou, Jeff Coller.
      Ribosome dynamics during mRNA translation elongation regulate mRNA stability. Yet, known regulators of ribosome transit, such as codon usage, cannot fully explain transcriptome-wide decay rates. Here, we demonstrate that nascent polypeptide folding modulates elongation rates, with Zuotin (Zuo1) serving as an essential mediator. Using reporter constructs encoding co-translationally unstructured proteins and RNA sequencing under proteotoxic stress, we show that Zuo1 is required for selective destabilization of transcripts whose nascent peptides fail to fold properly. This process relies on the co-translational mRNA decay factor Not5, which detects slowed ribosomes. 35S labeling indicates that nascent peptide folding defects correlate with reduced elongation rates in a Zuo1-dependent manner, and ribosome profiling reveals that global protein misfolding induces Zuo1-dependent ribosome pausing. These findings position Zuo1 as a key mediator linking nascent peptide folding status to ribosome dynamics and mRNA stability. Furthermore, this work suggests an expanded role for Not5 beyond codon optimality sensing.
    Keywords:  Not5; Zuo1; elongation rate; mRNA degradation; mRNA stability; post-transcriptional regulation; protein chaperones; protein folding; ribosome speed
    DOI:  https://doi.org/10.1016/j.molcel.2026.06.041
  3. G3 (Bethesda). 2026 Jul 21. pii: jkag172. [Epub ahead of print]
    Proteome analyses reveal endoplasmic reticulum stress-induced changes in protein abundance associated with Ube2j2 deficiency in human cell culture.
    Caroline L Dahlberg, Matthew Zinkgraf, Sophie Heiden Laugesen, Cecile Lützen Søltoft, Queralt Ginebra, Eric Paul Bennett, Rasmus Hartmann-Petersen, Lars Ellgaard.
      The unfolded protein response (UPR) helps reinstate cellular proteostasis upon an accumulation of misfolded proteins in the endoplasmic reticulum (ER), in part through ER-associated degradation (ERAD). Ube2j2 is an ER-localized E2 ubiquitin-conjugating enzyme that participates in ERAD. We used mass spectrometry analysis of cultured U2OS cells to investigate how the loss of Ube2j2 affects the cellular proteome in response to tunicamycin-induced ER stress. We constructed a network of twelve statistically distinct modules of protein abundance profiles across conditions. We describe the gene ontology annotations for each module along with the "hub gene" proteins whose abundance levels most closely adhere to each module's protein abundance profile. Our analysis identifies known Ube2j2-associated pathways (eg the UPR and ERAD) and cellular functions that were previously unassociated with Ube2j2 (eg RNA metabolism, ER-Golgi transport, and cell-cycle progression). These data are available via ProteomeXchange with identifier PXD076153 and provide avenues for further investigation into the cellular functions of Ube2j2 under basal and ER-stressed conditions.
    Keywords:  E2 ubiquitin-conjugating enzyme; ER-associated degradation; Ube2j2; protein degradation; proteomics; ubiquitin proteasome system; unfolded protein response
    DOI:  https://doi.org/10.1093/g3journal/jkag172
  4. Elife. 2026 Jul 23. pii: RP106716. [Epub ahead of print]14
    Structural dynamics of IRE1 and its interaction with unfolded peptides.
    Elena Spinetti, Grzegorz Ścibisz, Gülsün Elif Karagöz, Roberto Covino.
      The unfolded protein response (UPR) is a crucial signaling network that preserves endoplasmic reticulum (ER) homeostasis, impacting both health and disease. When ER stress occurs, often due to an accumulation of unfolded proteins in the ER lumen, the UPR initiates a broad cellular program to counteract cytotoxic effects. Inositol-requiring enzyme 1 (IRE1), a conserved ER-bound protein, is a key sensor of ER stress and activator of the UPR. While biochemical studies confirm IRE1's role in recognizing unfolded polypeptides, high-resolution structures showing direct interactions remain elusive. Consequently, the precise structural mechanism by which IRE1 senses unfolded proteins is debated. In this study, we employed advanced molecular modeling and 137 µs of atomistic molecular dynamics simulations to clarify how IRE1 detects unfolded proteins. Our results demonstrate that IRE1's luminal domain directly interacts with unfolded peptides and reveal how these interactions can stabilize higher-order oligomers. We provide a detailed molecular characterization of unfolded peptide binding, identifying two distinct binding pockets at the dimer's center, separate from its central groove. Furthermore, we present high-resolution structures illustrating how BiP associates with IRE1's oligomerization interface, thus preventing the formation of larger complexes. Our structural model reconciles seemingly contradictory experimental findings, offering a unified perspective on the diverse sensing models proposed. We elucidate the structural dynamics of unfolded protein sensing by IRE1, providing key insights into the initial activation of the UPR.
    Keywords:  IRE1; S. cerevisiae; UPR; endoplasmic reticulum; human; molecular biophysics; structural biology
    DOI:  https://doi.org/10.7554/eLife.106716
  5. J Biol Chem. 2026 Jul 22. pii: S0021-9258(26)02228-3. [Epub ahead of print] 113356
    Dynamic O-GlcNAcylation of Sec23-interacting protein regulates COPII function.
    Tetsuya Hirata, Quyen Nguyen, Coco Liu, Michael Boyce.
      About one-third of the eukaryotic proteome transits the secretory pathway to reach its correct cellular or extracellular destination. At the earliest stage, transport from the endoplasmic reticulum (ER) to the ER-Golgi intermediate compartment (ERGIC) or Golgi apparatus is mediated by coat protein complex II (COPII). COPII coats consist of inner and outer layers formed by Sec23-Sec24 heterodimers and Sec13-Sec31 heterotetramers, respectively, which initially assemble at ER exit sites (ERES) to form transport carriers. Sec23-interacting protein (Sec23IP) links the inner and outer coats through its interactions with both Sec23A and Sec31A, positioning it as a key potential regulator of COPII function. However, the mechanisms controlling Sec23IP activity remain poorly understood. Here, we investigate how physiological stimuli regulate COPII function through the dynamic modification of Sec23IP by O-linked β-N-acetylglucosamine (O-GlcNAc), a reversible, intracellular form of glycosylation. We first validated Sec23IP as a bona fide O-GlcNAcylated protein. Rescue experiments in Sec23IP knockout cells with a nearly unglycosylatable mutant protein demonstrated the essential role of O-GlcNAcylation in the intrinsically disordered domain in protein transport and in recruiting Sec31A to ERES. Moreover, O-GlcNAcylation of Sec23IP increased during protein transport, coinciding with a reduction in its interaction with Sec31A. These results indicate that distinct site-specific O-GlcNAcylation of Sec23IP spatiotemporally modulates its association with Sec31A to fine-tune ERES recruitment and COPII assembly/disassembly. Our work provides new insight into Sec23IP regulation and suggests that O-GlcNAc on other COPII proteins may govern carrier formation, uncoating, and transport.
    Keywords:  COPII; ER exit site; O-GlcNAcylation; Sec23IP; Sec31A; glycosylation; protein transport
    DOI:  https://doi.org/10.1016/j.jbc.2026.113356
  6. Mol Neurobiol. 2026 Jul 20. pii: 780. [Epub ahead of print]63(1):
    USP28 Deficiency is Linked to Impaired Ubiquitin-dependent Proteostasis in Huntington's Disease.
    Kyoungjoo Cho, Eun Jin Park.
      Huntington's disease (HD) is characterized by mutant huntingtin (mHTT) aggregation and impaired proteostasis; however, upstream regulators of ubiquitin system imbalance remain incompletely understood. This study identified the deubiquitinase USP28 as a potential modulator of ubiquitin-dependent proteostasis in HD. Bulk RNA sequencing of R6/2 mouse brain tissues showed reduced USP28 expression compared with wild-type controls. Consistently, USP28 expression decreased in STHdh striatal cells expressing expanded polyQ huntingtin (Q111). HD cells (STHdh-Q111) exhibited increased accumulation of ubiquitinated proteins and altered ubiquitin turnover, consistent with impaired proteostasis. USP28 overexpression attenuated ubiquitinated protein accumulation and reduced mHTT aggregation, whereas a catalytically inactive USP28 mutant showed limited rescue effects. In addition, USP28 depletion was associated with reduced UBR5 levels, while USP28 restoration partially recovered UBR5 expression in a catalytic activity-dependent manner. Modulation of HECT E3 ligase activity further altered ubiquitination dynamics and mHTT aggregation, suggesting that HECT E3 ligase-related pathways may contribute to proteostasis regulation in HD cells. Collectively, these findings identify USP28 as a proteostasis-associated deubiquitinase reduced in HD models and suggest that USP28 deficiency contributes to ubiquitin burden and mHTT aggregation. Changes in UBR5 expression further point to a potential involvement of HECT E3 ligase-linked ubiquitin regulation, although the direct mechanistic relationship between USP28 and UBR5 remains.
    Keywords:  Huntington’s disease; Protein aggregation; Proteostasis; UBR5; USP28; Ubiquitin–proteasome system
    DOI:  https://doi.org/10.1007/s12035-026-06073-7
  7. EMBO J. 2026 Jul 20.
    Atg23 prevents aberrant fusion of Atg9 vesicles during delivery to autophagosome formation sites.
    Takumi Kimura, Takayuki Shima, Tetsuya Kotani, Hitoshi Nakatogawa.
      Autophagosome biogenesis depends on the accurate delivery of membrane lipids to the pre-autophagosomal structure. Golgi/endosome-derived Atg9 vesicles provide the membrane seed for this process, but how they are trafficked through the cytoplasm while avoiding inappropriate fusion remains unclear. Here we show that in Saccharomyces cerevisiae, the soluble Atg9-interacting protein Atg23 remains associated with Atg9 vesicles after their biogenesis. This association shields Atg9 vesicles from aberrant SNARE-dependent fusion as they diffuse through the cytoplasm en route to the autophagosome formation site. We further show that upon vesicle arrival at the site, Atg9 phosphorylation by the autophagy initiation kinase Atg1 releases Atg23, facilitating recruitment of the downstream factor Atg2, a lipid transfer protein for membrane expansion. Together, these findings reveal an Atg1-dependent phosphorylation switch that regulates Atg9 vesicle dynamics during autophagosome biogenesis.
    DOI:  https://doi.org/10.1038/s44318-026-00867-0
  8. Proc Natl Acad Sci U S A. 2026 Jul 28. 123(30): e2611708123
    Blm10 and PI31 comprise a failsafe mechanism for proteasome inhibition.
    Darlene Fung, Shaun Rawson, Richard M Walsh, Erignacio Fermin Perez, Urte Venclovaite, Tamayanthi Rajakumar, Benjamin Velez, John Hanna.
      Blm10 (PA200 in mammals) is an evolutionarily conserved regulator of the proteasome's core particle (CP), a barrel-shaped complex that houses six individual protease subunits. Despite decades of study, Blm10's function has remained unresolved. Here, we provide structural, biochemical, and genetic evidence that yeast Blm10 inhibits the proteasome and that it does so in cooperation with a second proteasome inhibitor, PI31 (also known as Fub1). Both proteins are highly enriched in CPs with abnormal subunit composition, suggesting that Blm10 and PI31 may function to neutralize aberrant proteasomes. We report an unexpected proteasome configuration in which Blm10's dome-like structure completely encases PI31's N-terminal domain, which sits outside and atop the CP, while PI31's C-terminal domain is present inside the CP, simultaneously inhibiting all six active sites. These Blm10/PI31-bound CP are strongly deficient in degradation of both proteins and small peptides, and loss of both proteins results in strongly synergistic genetic phenotypes in vivo. These data suggest that Blm10 and PI31 constitute a partially redundant failsafe system for proteasome inhibition.
    Keywords:  Blm10; PA200; PI31; proteasome; protein degradation
    DOI:  https://doi.org/10.1073/pnas.2611708123
  9. Cell Death Differ. 2026 Jul 19.
    Pan-cancer proteogenomic interrogation of the ubiquitin-proteasome system.
    Tania J González-Robles, Maha Khan, Paul Sastourné, Marisa Triola, Hua Zhou, Yuki Kito, Sharon Kaisari, David Fenyö, Gergely Rona, Yadira M Soto-Feliciano, Benjamin G Neel, Kelly V Ruggles, Michele Pagano.
      Somatic mutations rewire the ubiquitin-proteasome system (UPS) to support tumor growth, but the proteome-wide consequences of cancer-driver alterations on UPS composition remain incompletely understood. Using harmonized proteogenomic data from up to 11 CPTAC cohorts, we performed an integrated pan-cancer analysis of UPS protein dysregulation, prognostic associations, and mutation-driven remodeling. We show that mRNA poorly predicts UPS protein abundance, that a defined set of E3 ligases is recurrently dysregulated across cancers, and that somatic mutations (most strikingly TP53 loss) produce coherent UPS protein-quantitative trait locus (pQTL) signatures. Two case studies (UBR5 and TRIM28) illustrate orthogonal modes of UPS rewiring: a mutation-driven axis in which TP53-mutant tumors elevate UBR5 to support replication stress tolerance, and a lineage-driven axis in which TRIM28 engages tissue-restricted regulatory networks with opposing prognostic effects in glioblastoma versus head and neck cancer. Each axis exposes context-specific therapeutic vulnerabilities, including sensitivity to DNA damage response inhibitors (UBR5-high) and lineage-specific drug responses (TRIM28-high). Together, these analyses define a mechanistic framework for how cancer-driver mutations reshape proteostasis through the UPS and nominate mutation- and lineage-defined dependencies for precision degrader therapy. The harmonized pan-tissue atlas and the UbiDash interactive resource that underpin parts of this analysis are reported in our companion paper [1].
    DOI:  https://doi.org/10.1038/s41418-026-01787-6
  10. Bioorg Med Chem Lett. 2026 Jul 23. pii: S0960-894X(26)00210-6. [Epub ahead of print] 130743
    An optimized RNF126-targeting covalent handle for molecular glue degraders.
    Aman Modi, Ethan S Toriki, Christian E Stieger, Emily A Lau, Claire Song, Alyssa Chew, Amy Tsao, Kaila Nishikawa, Jeffrey McKenna, Daniel K Nomura.
      Molecular glue degraders represent a powerful modality for targeting proteins that are refractory to traditional inhibition. However, rational design principles for molecular glue degraders remain poorly defined. Previously, we reported a chemistry-centric strategy to identify covalent degradative handles that, when appended to established ligands, convert non-degradative inhibitors into molecular glue degraders by engaging permissive E3 ligases. This effort identified a fumarate-based electrophilic handle that covalently modified the E3 ligase RNF126, enabling degradation of multiple protein targets when transplanted across diverse ligands. Despite its conceptual impact, the high intrinsic reactivity and cytotoxicity of the fumarate handle limited its translational utility. Here, we report the development of an optimized and metabolically stabilized RNF126-targeting covalent handle incorporating a trans-cyclobutane linker that exhibits reduced glutathione reactivity and diminished cytotoxicity while retaining robust degradative activity. When appended to the BET bromodomain inhibitor JQ1, this optimized handle yielded a potent and selective BRD4 degrader whose activity was dependent on RNF126. Importantly, transplantation of this handle onto a previously non-inhibitory ligand targeting the androgen receptor (AR) and its truncation variant, AR-V7, enabled selective degradation of both AR and AR-V7 in androgen-independent prostate cancer cells, thereby robustly inhibiting AR transcriptional activity beyond the established AR antagonist enzalutamide. Collectively, these findings demonstrate an optimized RNF126-based covalent handle for the rational development of molecular glue degraders against transcriptional regulators, including undruggable variants such as AR-V7.
    Keywords:  AR-V7; Activity-based protein profiling; Androgen receptor; BRD4; Covalent; E3 ligase; RNF126; Targeted protein degradation
    DOI:  https://doi.org/10.1016/j.bmcl.2026.130743
  11. Signal Transduct Target Ther. 2026 Jul 20. pii: 281. [Epub ahead of print]11(1):
    Dual-targeting pharmacological UFMylation inhibition reprograms tumor and immune microenvironments to achieve long-term glioblastoma regression.
    Pengcheng Tan, Zhimin Liu, Xiaodan Hu, Yuxia Zhang, Hedi Chen, Baoliang Lan, Tianhua Ma, Sheng Ding.
      UFMylation, a recently identified ubiquitin-like modification, is essential for cellular stress homeostasis, particularly endoplasmic reticulum (ER) stress regulation. However, its biological and therapeutic exploration has been hindered by the absence of potent small-molecule inhibitors. Here, we report the first discovery of two compounds targeting the UFMylation E3 ligase complex core protein DDRGK1: Osimertinib, originally designed as an EGFR T790M selective inhibitor, acting through a previously unrecognized covalent mechanism, and CP-24, a novel non-covalent inhibitor. Both compounds disrupt the DDRGK1-UFL1 interaction, globally suppress UFMylation, inhibit ER-phagy, and induce ER stress. In glioblastoma (GBM), pharmacological UFMylation inhibition markedly reduces tumor cell viability and sensitizes cells to Temozolomide and radiotherapy. Both compounds also exert strong immunomodulatory activity, promoting macrophage polarization toward an anti-tumor M1 state. In vivo, Osimertinib, benefiting from superior pharmacokinetics, significantly suppresses tumor growth in immunodeficient models and achieves tumor-free outcomes in 65% of immunocompetent mice. These tumor-free mice develop durable anti-GBM immune memory, rapidly clearing tumors upon rechallenge, an outcome unattainable by previous GBM treatments. Mechanistically, Osimertinib enhances anti-tumor immunity by promoting macrophage M1 polarization, T cell expansion, and reducing PD-1 protein levels. Collectively, our study introduces Osimertinib and CP-24 as valuable chemical probes for dissecting UFMylation biology and highlights Osimertinib's potential for off-label use in EGFR-wildtype GBM. More broadly, we establish UFMylation inhibition as a dual-targeting therapeutic strategy that disrupts tumor survival pathways and reprograms the immune microenvironment, offering a promising avenue for durable GBM control.
    DOI:  https://doi.org/10.1038/s41392-026-02819-w
  12. Cell Signal. 2026 Jul 24. pii: S0898-6568(26)00420-1. [Epub ahead of print] 112763
    Impaired mitochondrial quality control and stress signalling machinery modulate senescence induction by genotoxic challenge.
    Mia Simons Weston, Marta Dominguez Prieto, Nicoleta Moisoi.
      Cellular senescence is a hallmark of ageing and age-related disease and is closely associated with mitochondrial dysfunction and the accumulation of DNA damage. However, the contribution of mitochondria-nucleus communication, mitochondrial quality control (mtQC) and stress signalling to senescence remains incompletely understood. Here, we investigated the interplay between mtQC pathways and cellular stress responses in DNA damage-induced senescence using mouse embryonic fibroblasts (MEFs). MEFs deficient in the mitochondrial protease HtrA2 (proteostasis), the transcription factor Chop (integrated stress response; ISR) or the mitophagy regulator Pink1 were exposed to three mechanistically distinct DNA-damaging agents: bleomycin, etoposide and doxorubicin. Senescence was characterised using multiple complementary markers, including the proportion of high senescence-associated β-galactosidase-positive cells, nuclear size, total and nuclear p21 abundance, and transcriptional analysis of p16, p21 and genes associated with cell-cycle regulation and stress signalling. Mitochondrial dysfunction through mtQC impairment enhanced sensitivity to senescence with HtrA2 and Pink1 loss promoting increased senescence under DNA damage. Although DNA damage response (DDR) was activated as seen by changes in p21 homeostasis, this did not always correlate with senescence levels, which indicates that DDR alone cannot account for all senescence characteristics. The ISR played a modulatory role in the senescence induction, with Chop loss of function reducing senescence induction following DNA damage despite DDR activation. The different DNA damaging drugs produced different senescence outcomes, thus highlighting the importance of the stressor context in addition to the cellular homeostasis mechanisms in the overall senescence profile. This approach allowed, for the first time, to identify senescence subtypes dependent of mtQC and ISR integrity in the context of genotoxic stress.
    Keywords:  Genotoxic stress; Integrated stress response; Mitochondria quality control; Senescence subtypes
    DOI:  https://doi.org/10.1016/j.cellsig.2026.112763
  13. Nat Cell Biol. 2026 Jul 20.
    Mitochondrial-derived vesicles drive budding-type fission of damaged lysosomes.
    Yuanchun Luo, Jianglong Yu, Zhuofan Li, Wanning Li, Le Jiang, Chen Huang, Zhouyi Rong, Long Lin, Yueguang Rong, Chaojun Yan, Zhishui Chen, Jingfeng Tang, He He, Anbing Shi, Zhiyin Song.
      Lysosomes are central degradative organelles essential for cellular homeostasis, yet the mechanisms that maintain their integrity and function under stress remain incompletely understood. Here we identify a previously unrecognized lysosomal renewal process, termed budding-type fission (B-fission), which restores lysosomal function during hypoxia-reoxygenation stress. During B-fission, damaged lysosomes generate membrane buds that undergo scission to form small, fully functional lysosomes, independently of autophagic lysosome reformation. Mechanistically, mitochondrial-derived vesicles (MDVs) deliver the fission adaptor MFF to lysosomes, where MFF recruits the dynamin-related GTPase DRP1 to drive membrane scission. MIRO2 promotes the formation of MFF+ MDVs through direct interaction with MFF, while the lysosomal membrane protein ITM2C binds MIRO2 to tether and guide MFF+ MDVs to lysosomes, enabling efficient MFF delivery and subsequent B-fission. Notably, AMPK activation by 991 or metformin promotes MFF-dependent lysosomal B-fission under normoxic conditions, whereas AMPK inhibition by dorsomorphin suppresses B-fission during hypoxia-reoxygenation. This stress-responsive ITM2C-MIRO2-MFF-DRP1 axis co-opts the mitochondrial division machinery to drive lysosomal fission from damaged lysosomes, thereby enabling the undamaged components to reorganize into daughter lysosomes and promote lysosomal renewal. Thus, our findings uncover a fundamental mode of lysosomal renewal and reveal an unexpected role for MDV-mediated mitochondria-lysosome communication in mediating lysosomal quality control during ischaemia-reperfusion and related stresses.
    DOI:  https://doi.org/10.1038/s41556-026-02010-x
  14. Cell Mol Life Sci. 2026 Jul 22.
    Oxidative protein folding and Ca2+ homeostasis under redox control.
    Jiro Ogura, Junichi Fujii, Hiroaki Yamaguchi.
      Secretory and membrane proteins undergo oxidative folding, the process of forming disulfide bonds between cysteine side chains to construct a stable higher-order structure, primarily in the endoplasmic reticulum (ER) followed by further post-translational modification in the Golgi apparatus, after which proteins proceed to pathways for secretion and membrane localization. Proteins involved in transferring oxidizing power to target proteins possess a pair of highly reactive forms of cysteine residue that mediate reduction-oxidation (redox) reactions. Oxidizing power, which is generally provided in the form of reactive oxygen/reactive nitrogen oxide species. Endoplasmic reticulum oxidoreductin 1 (ERO1) is the ancient ER oxidase that utilizes molecular oxygen to produce hydrogen peroxide, which is then utilized for thiol oxidation to form a disulfide bridge in target proteins. Excessive elevation of these species could promote aberrant oxidation of susceptible molecules, which could lead to an accumulation of misfolded proteins and consequent ER stress. The ER is also involved in cellular Ca2+ signaling in which Ca2+-pump ATPase and Ca2+ release channels coordinate to play essential roles. Ca2+ regulates the activity of some redox-reactive proteins, which are largely in the family of protein disulfide isomerase. Thus, the Ca2+ status indirectly associates with the oxidative folding of nascent proteins. Upon extensive oxidation, inactivation of the Ca2+-pump ATPase and inappropriate Ca2+ leak via the Ca2+ channels causes a depletion of Ca2+ in the ER lumen. When intracellular calcium is depleted, stromal interaction molecules (STIM) in the ER membrane sense the Ca2+ status within the ER lumen. STIM differentially regulates two types of Ca2+ channels in the plasma membrane: Ca2+-release-activated Ca2+ channel (ORAI), and voltage-operated Ca2+ channel (CaV1.2). This regulation coordinately maintains Ca2+ homeostasis within cells. Moreover, Zn2+ and H+ indirectly affect the potential of redox responses through controlling ER chaperone molecules. The redox capacity of the ER is maintained by resident proteins and small compounds, which include cations Ca2+, Zn2+ and H+, and hence the comprehensive care of them is necessary in order to maintain normal ER function.
    Keywords:  Calcium transport; Electron transfer; Glycosylation; Peroxiredoxin 4; Unfolded protein response (UPR)
    DOI:  https://doi.org/10.1007/s00018-026-06263-5
  15. Nat Commun. 2026 Jul 23. pii: 6179. [Epub ahead of print]17(1):
    Activity-dependent ribosome profiling reveals the landscape of canonical and non-canonical translation in brain tissue.
    Nayan Suryawanshi, Hitoshi Uchida, Ryo Endo, Kai Sato, Daisuke Satoh, Kazuya Tsumagari, Koshi Imami, Takayasu Mikuni, Motomasa Tanaka.
      Neural activity-dependent translation is essential for synaptic plasticity and diverse brain functions. Translation involves not only canonical main open reading frames (mORFs) but also upstream ORFs (uORFs), which may regulate mORF expression. However, due to technical limitations, systematic investigation of activity-dependent uORFs and mORFs in brain tissues remains challenging. Here, we developed a ribosome tagging and purification strategy that bypasses the prolonged turnover of ribosomal proteins, enabling ribosome profiling with one-hour temporal resolution after neural stimulation. Applying this strategy to mouse hippocampal slices undergoing long-term potentiation, we identify hundreds of activity-induced mORFs and uORFs, including a previously unknown uORF from Egr1. We demonstrate that this Egr1-uORF translation is tightly regulated by neuronal activity, and its encoded peptide interacts with peroxisomal machinery, suggesting a potential link between synaptic stimulus and peroxisome biology. This study provides a useful technique and resources for deciphering molecular mechanisms underlying activity- and translation-dependent brain functions in health and disease.
    DOI:  https://doi.org/10.1038/s41467-026-74968-z
  16. Biochem Biophys Res Commun. 2026 Jul 16. pii: S0006-291X(26)01037-5. [Epub ahead of print]831 154273
    The protein kinase GCN2 senses the integrity of the multi-tRNA synthetase complex.
    Richard Cardoso da Silva, Beatriz A Castilho.
      Aminoacyl-tRNA synthetases (ARSs) assemble with ARS-interacting multifunctional proteins (AIMPs) to form the multi-tRNA synthetase complex (MSC), a supramolecular complex proposed to enhance efficiency of tRNA aminoacylation. Here, we show that disassembly of MSC via siRNA-mediated depletion of the scaffold protein AIMP2 promotes a transient activation of the eIF2α kinase GCN2 in mouse embryonic fibroblasts (MEFs). Activation of GCN2 was accompanied by increased eIF2α phosphorylation, induction of ATF4, and attenuation of global protein synthesis. Importantly, these effects were abolished in Gcn2-/- MEFs, indicating that translational repression following MSC disassembly is largely dependent on GCN2. Notably, GCN2 activation and eIF2α phosphorylation were induced at early time points and resolved by 24h following AIMP2 depletion and progressively resolved despite sustained suppression of AIMP2 expression, suggesting adaptive restoration of translational homeostasis. Together, our findings link disruption of MSC integrity to the GCN2-dependent integrated stress response and support a functional link between higher-order organization of the translational machinery and cellular stress sensing.
    Keywords:  AIMP2; GCN2; Multi-tRNA synthetase complex; Translation initiation; eIF2α
    DOI:  https://doi.org/10.1016/j.bbrc.2026.154273
  17. Nat Commun. 2026 Jul 21. pii: 6128. [Epub ahead of print]17(1):
    Mitochondrial translation termination, recycling, reinitiation, and rescue for in-frame and out-of-frame contexts.
    Taisei Wakigawa, Mari Mito, Qi Fang, Yuzuru Itoh, Yoichi Shinkai, Shintaro Iwasaki.
      Because mitochondria diverged from a bacterial ancestor during evolution, the mitochondrial protein synthesis system includes both mRNAs and translation factors with unique characteristics. However, the molecular mechanisms underlying translation termination, recycling, and quality control remain unclear. Here, via high-resolution mitochondrial Ribo-Seq and Disome-Seq, we reveal: the specificity of release factors for different kinds of stop codons; the role of mtRF1 in vertebrates, which do not have noncanonical stop codons in their main translons; the recycling-coupled translation of internal translons; and the rescue of mitoribosomes in the early elongation stage. mtRF1L recognizes all stop codons, whereas mtRF1 recognizes only AGA/AGG noncanonical stop codons. Additionally, mtRF1 terminates the translation of out-of-frame translons that end with AGA/AGG. We also found that mtRRF and mtIF3 are required for mitoribosome recycling on stop codons and for the reinitiation of internal translon translation. Mitoribosomes that stall at the start codons and/or at the early elongation phase are major substrates of the rescue factors ICT1, mtRF-R, and mtRES1. Moreover, HEMK1-mediated methylation of release factors enhances the termination reaction on stop codons. Our results provide insights into the mitoribosome dynamics that are associated with the completion of protein synthesis.
    DOI:  https://doi.org/10.1038/s41467-026-75248-6
  18. Cell. 2026 Jul 21. pii: S0092-8674(26)00749-X. [Epub ahead of print]
    Expanding the scope of protein language modeling to protein-protein interactions with MSA Pairformer.
    Yo Akiyama, Zhidian Zhang, Olivia Tang, Rachel Seongeun Kim, Milot Mirdita, Martin Steinegger, Sergey Ovchinnikov.
      Protein-protein interactions underlie biological complexity, and modeling their coevolution is essential for characterizing and engineering molecular assemblies. While protein and genomic language models have excelled at modeling individual proteins, extending these capabilities to protein complexes remains challenging. We present multiple sequence alignment (MSA) Pairformer, a protein language model that builds on AlphaFold2/3's bidirectional refinement between sequence and pairwise residue representations to accurately model the evolution of protein-protein interactions, despite training exclusively on individual chains. MSA Pairformer achieves nearly 3-fold improvement over existing methods in predicting protein-protein interface contacts and better distinguishes binding from non-binding sequences. A learned attention mechanism selectively weights sequences by their inferred evolutionary relevance, enabling discovery of subfamily-specific contacts. On single-protein benchmarks, it achieves state-of-the-art contact prediction and strong variant effect prediction using only 111 million parameters, over two orders of magnitude smaller than frontier models. These results offer an evolutionarily grounded, computationally efficient alternative to the scaling paradigm.
    Keywords:  artificial intelligence; deep learning; evolutionary biology; machine learning; neural networks; protein engineering; protein evolution; protein language modeling; protein-protein interactions; structural biology
    DOI:  https://doi.org/10.1016/j.cell.2026.06.029
  19. Cell. 2026 Jul 23. pii: S0092-8674(26)00710-5. [Epub ahead of print]189(15): 4519-4521
    UTR-ly unexpected: RNA chaperones tame intrinsically disordered proteins.
    Miriam Linsenmeier, James Shorter.
      How do cells ensure that complex, multidomain proteins fold correctly? Luo et al. reveal a self-contained solution. The 3' UTR of an mRNA co-translationally chaperones the protein it encodes, preventing intrinsically disordered regions from making inappropriate contacts. This functionality, localized to mesh-like condensates, challenges Anfinsen's dogma and opens therapeutic possibilities.
    DOI:  https://doi.org/10.1016/j.cell.2026.06.023
  20. Proc Natl Acad Sci U S A. 2026 Jul 28. 123(30): e2527864123
    TBC1D9 and TBC1D9B are ARL8 effectors that modulate exosome secretion through a RAB11A-exocyst pathway.
    Ganesh Vilas Shelke, Chad D Williamson, Tal Keren-Kaplan, Juan S Bonifacino.
      Multivesicular endosomes (MVEs) are endolysosomal compartments containing intraluminal vesicles (ILVs) that follow two alternative pathways: fusion with lysosomes, leading to ILV degradation, or fusion with the plasma membrane, resulting in ILV secretion as exosomes. The mechanisms governing this fate decision have only recently begun to be elucidated. Previous work showed that the Biogenesis of lysosome related organelles complex-one-related complex (BORC) and the small guanosine triphosphatase (GTPase) ARL8 promote MVE-lysosome fusion through the ARL8 effector homotypic fusion and protein sorting complex (HOPS), thereby diverting MVEs from exosome secretion. Here, we identify TBC1D9 and TBC1D9B as ARL8 effectors that further suppress exosome release. Acting as GTPase-activating proteins, these proteins drive RAB11A inactivation and dissociation from endolysosomes. This reduces recruitment of the RAB11A effector exocyst complex, preventing MVE fusion with the plasma membrane. These findings thus define a BORC-ARL8-TBC1D9/TBC1D9B axis that further attenuates exosome secretion by blocking MVE-plasma membrane fusion.
    Keywords:  endosomes; exosomes; lysosomes; membrane fusion; small GTPases
    DOI:  https://doi.org/10.1073/pnas.2527864123
  21. Biochem J. 2026 Aug 05. 483(8): 1591-1609
    Structural and mechanistic insights into protein glycosylation and glycosylphosphatidylinositol anchoring in the endoplasmic reticulum membrane.
    David O Harris, Ana S Ramírez.
      The endoplasmic reticulum (ER) hosts several integral membrane enzymes responsible for post-translational modifications of proteins entering the secretory pathway. These include protein glycosylation and the attachment of glycosylphosphatidylinositol (GPI) anchors. At the ER membrane, protein glycosylation is catalyzed by glycosyltransferases from the C-superfamily (GT-C), which use lipid donor substrates to attach a complex oligosaccharide to asparagine residues (N-glycosylation), or a single mannose unit to threonine, serine (O-mannosylation), or tryptophan (C-mannosylation) residues. In contrast, the attachment of GPI anchors to acceptor proteins is catalyzed by the multimeric enzyme transamidase, which cleaves a C-terminal GPI signal peptide of the acceptor protein and replaces it with a GPI anchor. In the present review, we will discuss recent mechanistic studies that shed light on the architecture of these membrane protein machineries and on how they recognize their substrates and catalyze protein glycan modifications at the ER membrane.
    Keywords:  GPI anchors; cryo-electron microscopy; enzymology; glycosylation; membrane proteins
    DOI:  https://doi.org/10.1042/BCJ20250144
  22. Mol Cell. 2026 Jul 20. pii: S1097-2765(26)00421-1. [Epub ahead of print]
    Structures of dynamic interactors at native proteasomes by PhIX-MS and cryo-electron microscopy.
    Kitaik Lee, Hitendra Negi, Xiang Chen, Katerina Atallah-Yunes, Sophia Truslow, Rithik E Castelino, Mary R Guest, Anthony M Ciancone, Xiuxiu Lu, Sergey G Tarasov, Raj Chari, Kylie J Walters, Francis J O'Reilly.
      Molecular machines rely on dynamic, low-affinity interactions to perform their functional roles. We developed PhIX-MS (photo-induced in situ crosslinking-mass spectrometry), a structural proteomics workflow to capture topological information for such transient interactions in cells by UV-activated crosslinking. Applying PhIX-MS with cryo-electron microscopy (cryo-EM) to proteasomes, we mapped the redox sensor TXNL1 at the proteasome regulatory particle (RP), including its dynamic thioredoxin-like domain near RPN2/PSMD1 and RPN13/ADRM1, where it is ideal for reducing substrates prior to proteolysis. RPs without the proteolytic core particle (CP) were structurally resolved while bound to TXNL1 and/or the chaperone PSMD5/S5b, which inserts its C terminus into the ATPase pore, causing extensive structural rearrangements. Additionally, PhIX-MS and AlphaFold identified the ubiquitin ligase UBE3C/Hul5 at RPN2, RPN3, and a dynamic RPN10 region, tethering UBE3C above the substrate entry channel. Our integrative approach enables the localization of native, low-affinity protein interactions and is broadly applicable to dynamic macromolecular assemblies.
    Keywords:  ADRM1; AlphaFold; PSMD5; PhIX-MS; TXNL1; UBE3C; cryoelectron microscopy; in situ crosslinking mass spectrometry; integrative structural biology; proteasome
    DOI:  https://doi.org/10.1016/j.molcel.2026.06.032
  23. EMBO Rep. 2026 Jul 23.
    The role of E3 ubiquitin ligases in selective types of macroautophagy.
    Monja Müller, Konstanze F Winklhofer, Fulvio Reggiori.
      In contrast to the ubiquitin (Ub)-proteasome-system, which only degrades individual proteins, macroautophagy can eliminate protein complexes or aggregates, organelles and even pathogens. Terms such as mitophagy, aggrephagy, lysophagy and xenophagy have been coined based on the targeted substrate. In Ub-dependent selective macroautophagy, cargo selectivity is specified by E3 Ub ligases that append Ub chains that in turn are recognized by selective autophagy receptors (SARs), driving sequestration into autophagosomes. While several Ub-dependent SARs have been identified and characterized, the E3 Ub ligases that ultimately decide target fate remain poorly studied. In this review, we summarize what is known about the E3 Ub ligases involved in selective macroautophagy, with a particular emphasis on the degradation of mitochondria, protein aggregates, lysosomes and pathogens. A better characterization of these enzymes could improve therapeutic strategies for targeted degradation in acute and chronic diseases.
    DOI:  https://doi.org/10.1038/s44319-026-00887-1
  24. Nat Struct Mol Biol. 2026 Jul 22.
    PLA2G2F suppresses ferroptosis through phospholipid remodeling.
    Yingying Hu, Joleen Csuka, Presha Rajbhandari, Penghsuan Huang, Nicholas Carbone, Deguang Liang, Wei Gu, Alban Ordureau, Brent R Stockwell, Xuejun Jiang.
      Ferroptosis is an iron-dependent form of regulated cell death driven by phospholipid peroxidation, and it has emerged as a potential therapeutic vulnerability of cancer. Here we identify the secretory phospholipase PLA2G2F (phospholipase A2 group IIF) as a ferroptosis suppressor in bladder cancer and elucidate its regulation and mechanism of action. PLA2G2F functions through an intracellular mechanism by localizing to the endoplasmic reticulum to inhibit ferroptosis. Our genetic and pharmacological analyses reveal that peroxisome proliferator-activated receptor γ (PPARG), a nuclear hormone receptor and transcription factor previously implicated in ferroptosis regulation, upregulates PLA2G2F and that PPARG-mediated ferroptosis resistance is largely dependent on PLA2G2F in bladder cancer. Further, lipidomic profiling suggests that PLA2G2F preferentially acts on ether-linked phospholipids containing polyunsaturated fatty acids, thereby reducing the pool of peroxidation-prone polyunsaturated fatty acid-containing phospholipids. Together, our findings establish PLA2G2F as an endoplasmic reticulum-resident ferroptosis suppressor regulated by PPARG and show that inhibiting PPARG signaling or PLA2G2F activity can sensitize bladder cancer cells to ferroptosis induction.
    DOI:  https://doi.org/10.1038/s41594-026-01830-7
  25. Mol Syst Biol. 2026 Jul 22.
    Complex assembly and activity states as multifaceted protein attributes explaining phenotypic variability.
    George Rosenberger, Peng Xue, Isabell Bludau, Claudia Martelli, Evan Williams, Ben C Collins, Andrea Califano, Yansheng Liu, Ruedi Aebersold.
      The state of a cell depends not only on protein abundance, but also on the biochemical and cellular activities of proteins, which are largely invisible to abundance profiling alone. Here, we introduce a multi-omics framework that infers context-specific protein activities from transcriptomic, phosphoproteomic, and protein correlation-based protein-protein interaction data, integrating modality-specific algorithms via network diffusion. Applying it to a panel of phenotypically diverse HeLa cell lines, whose genetic drift provides a natural perturbation system, we make three findings. First, physical separation of monomeric and assembled protein fractions by protein correlation profiling provides direct evidence that complex assembly buffers variation in gene copy number and transcription, a mechanism previously only inferred from bulk measurements. Second, using Let7 perturbation data, CRISPR gene dependency scores, and subcellular localization, we orthogonally validate that inferred protein activities capture functional regulation linked to cellular phenotypes inaccessible from abundance data alone. Third, differential analysis of context-specific activity profiles identifies molecular mechanisms underlying phenotypic divergence, including a WIPF1/WIPF2--Arp2/3 axis governing invadopodium formation and infection susceptibility, and an immunoproteasome switch linked to immune adaptation.
    DOI:  https://doi.org/10.1038/s44320-026-00228-3
  26. Cell Rep Methods. 2026 Jul 22. pii: S2667-2375(26)00235-3. [Epub ahead of print] 101534
    HIT-MAP: A scalable approach to multimodal mapping of subcellular organization.
    Gege Qian, Joonwon Kim, Richa Tiwari, Benjamin J Polacco, Antoine Forget, Leah V Schaffer, Hark Kyun Kim, Jiahao Gao, Yuan Zhou, Gwendolyn M Jang, Marcus R Kelly, Xiaoyu Zhao, Helene Foussard, Liudeng Zhang, Nevan Krogan, Trey Ideker, Alejandro Chavez.
      Multimodal mapping of subcellular protein organization through imaging and interaction proteomics has been mostly confined to large consortia, owing to high per-target costs, reliance on target-specific antibodies or libraries of epitope-tagged cDNAs, and the lack of unified pipelines for coordinated data acquisition. Here, we present HIT-MAP (high-throughput integrated tagging for cell mapping), an end-to-end framework that couples endogenous epitope tagging with optimized wide-field immunofluorescence imaging and affinity purification-mass spectrometry (AP-MS). Applied to a pilot set of 16 representative proteins in HEK293T cells, HIT-MAP recovers 576 high-confidence protein-protein interactions, identifies canonical complexes, and resolves cross-modality protein communities. Integrative analysis identifies CCDC12 as a previously uncharacterized component of the Bact spliceosomal complex, supported by AP-MS interaction data, tag-free size-exclusion chromatography-mass spectrometry (SEC-MS) co-fractionation, and Perturb-seq transcriptional signatures. HIT-MAP lowers technical and economic barriers to generating coordinated multimodal protein maps.
    Keywords:  CP: cell biology; CP: systems biology; affinity purification-mass spectrometry; cell map; endogenous tagging; immunofluorescence; multimodal data integration; multiscale protein organization; spatial proteomics; spliceosome; virtual cell; wide-field microscopy
    DOI:  https://doi.org/10.1016/j.crmeth.2026.101534
  27. Nature. 2026 Jul 22.
    Structural basis of the RNA-editing cascade in trypanosome mitochondria.
    Yun-Tao Liu, Andres F Vacas, Jonathan Jih, Xiaojing Zhao, Clinton Yu, Jane K J Lee, Takuma Suematsu, Md Solayman, Hong Wang, Xiaorong Wang, Lan Huang, Liye Zhang, Inna Aphasizheva, Z Hong Zhou, Ruslan Aphasizhev.
      The molecular mechanism of uridine insertion-and-deletion mRNA editing in trypanosome mitochondria1-4 has remained unclear because of the highly dynamic nature of the underlying multi-enzyme machinery5. Here, we define editosomes as supramolecular assemblies formed by the RNA-editing substrate-binding complex (RESC) and either RNA-editing catalytic complex 1 or 2 (RECC1 or RECC2)6, and present cryo-electron microscopy structures of the approximately 1-MDa RECC1 and RECC2. Resembling dragonflies, with a head, thorax-like core, tail and wings, these ribonucleoproteins mediate the uridine deletion and uridine insertion cascades, respectively. In each RECC, a tetrameric core containing one active and three inactive RNase III domains captures the guide RNA (gRNA)-mRNA duplex, while auxiliary zinc fingers distinguish deletion sites from insertion sites and position the substrate for mRNA cleavage (step I). Three peripheral oligonucleotide-binding-fold heterotetramers are flexibly attached to the core, forming a spatially adaptable reaction chamber. The tail recruits the exonuclease and uridylyltransferase that remove or add uridines (step II), whereas the wings, coordinated by an architectural tRNA, position RNA ligases to seal the edited mRNA (step III). Together, these structures reveal how gRNA-directed substrate recognition, mRNA cleavage, uridine deletion and insertion and ligation are integrated in a single macromolecular machine. This architecture defines the mechanism of information transfer in RNA editing.
    DOI:  https://doi.org/10.1038/s41586-026-10831-x
  28. Cell Chem Biol. 2026 Jul 21. pii: S2451-9456(26)00234-5. [Epub ahead of print]
    Dual-function PROTAC suppresses ferroptosis and restores neuronal function via brain-targeted delivery.
    Tianyu Ma, Tianli Luo, Ming Wang.
      Targeted protein degradation (TPD) via proteolysis-targeting chimeras (PROTACs) offers a promising strategy for modulating disease-associated proteins, yet effective brain-preferred protein degradation remains challenging. Herein, we report a dual-function PROTAC, dACSL4, and its nose-to-brain delivery for brain-preferred protein degradation and therapeutic suppression of ferroptosis in neurodegeneration. dACSL4 selectively degrades acyl-CoA synthetase long-chain family member 4 (ACSL4) while concurrently activating peroxisome proliferator-activated receptor γ (PPARγ), thereby coordinating lipid metabolism and oxidative stress to suppress neuronal ferroptosis. dACSL4 achieved up to 30-fold greater protection against neuronal ferroptosis compared to conventional ferroptosis inhibitors. Intranasal delivery of dACSL4 using biodegradable lipid nanoparticles (BAmP-TK12) enabled brain-preferred ACSL4 degradation and PPARγ activation, reducing lipid peroxidation and preserving dopaminergic neurons in a Parkinson's disease model, ultimately improving motor function. Our findings establish a modular strategy for brain-preferred protein degradation and highlight the therapeutic potential of dual-function degraders for ferroptosis suppression in neurodegenerative diseases.
    Keywords:  Delivery; PROTAC; dual-function PROTAC; ferroptosis; lipid nanoparticles; neurodegeneration; targeted protein degradation
    DOI:  https://doi.org/10.1016/j.chembiol.2026.06.010
  29. J Am Chem Soc. 2026 Jul 22.
    Self-Splicing RNA Platform Encodes Twin PROTACs for Dual-E3 Ligase Recruitment and Programmable Protein Degradation.
    Jiani Ding, Shumin Wang, Zijie Tang, Yao Li, Peisen Zhang, Zhi-Ling Song, Xiliang Luo, Xiao-Bing Zhang.
      Proteolysis-targeting chimeras (PROTACs) offer a powerful strategy for targeted protein degradation but are frequently constrained by synthetic complexity and overreliance on a single-E3 ligase, leading to diminished efficacy in tumors with low or heterogeneous ligase expression. Here, we report a genetically encoded artificial self-splicing RNA (asRNA) platform that autonomously generates twin PROTAC effectors from a single transcript, enabling the coordinated recruitment of two distinct E3 ligases. Following transcription, the asRNA undergoes precise ribozyme-mediated self-cleavage to produce a peptide-based PROTAC that recruits the VHL ligase and an RNA aptamer-based PROTAC that engages the Dzip3 ligase, thereby activating complementary ubiquitination pathways. This dual-ligase architecture markedly enhances degradation of otherwise refractory oncogenic targets, including c-MYC and EGFR, resulting in pronounced antitumor efficacy in cancer models. The modular and programmable genetic design enables rapid reconfiguration of target-recognition elements without complex chemical synthesis. As the first single-transcript system to achieve coordinated dual-E3 ligase recruitment, this work establishes a new genetically encoded strategy for multivalent protein degradation and expands the scope of targets accessible to PROTAC-based strategies.
    DOI:  https://doi.org/10.1021/jacs.6c11759
  30. FASEB J. 2026 Jul 31. 40(14): e72151
    DNAJC12 Stabilizes Phenylalanine Hydroxylase and Facilitates Its Substrate-Dependent Activation.
    Mary Dayne S Tai, Trond-André Kråkenes, Gloria Gamiz-Arco, Christer F Didriksen, Juha P Kallio, Marte I Flydal, Fernando Moro, Aurora Martinez.
      Phenylalanine hydroxylase (PAH) is a tetrahydrobiopterin (BH4)-dependent enzyme that converts L-phenylalanine (L-Phe) to L-tyrosine. PAH dysfunction leads to the accumulation of L-Phe in the blood (hyperphenylalaninemia; HPA), which may reach neurotoxic levels, resulting in phenylketonuria (PKU). PKU is associated with pathogenic variants in PAH, mostly causing misfolding and instability, leading to decreased levels of PAH protein and activity. Recently, variants in the J-domain protein DNAJC12 have also been associated with HPA in patients, demonstrating the importance of protein homeostasis regulation for proper PAH function. DNAJC12 and PAH have previously been reported to interact, but the molecular and structural mechanisms behind complex formation have remained unclear. In this work, we show that DNAJC12 binds to PAH but presents higher affinity for its L-Phe activated form, which resembles the conformation of unliganded tyrosine hydroxylase, a structurally and functionally related enzyme that also binds to DNAJC12. At saturation, four DNAJC12 monomers bind and stabilize the PAH tetramer, protecting it from aggregation and lowering the L-Phe concentration necessary for substrate-induced activation, without affecting the interaction of the enzyme with its cofactor BH4. Importantly, DNAJC12 also stabilizes and delays the aggregation of the PKU-associated variant PAH-p.R261Q. This study provides the first detailed characterization of the molecular determinants driving PAH:DNAJC12 complex formation and reveals how this interaction modulates enzyme stability and activity, and stimulates Hsc70 ATPase activity. These findings provide mechanistic insight into the pathogenic basis of DNAJC12 deficiency and identify the PAH:DNAJC12 complex as a promising therapeutic target for HPA.
    Keywords:  DNAJC12; J‐domain protein; phenylalanine hydroxylase; phenylketonuria; proteostasis
    DOI:  https://doi.org/10.1096/fj.202504522RR
  31. Sci Signal. 2026 Jul 21. 19(947): eadv4272
    NDRG1 expression in cancers confers dependence on DNA damage repair and sensitivity to quinacrine.
    Garik V Mkrtchyan, Alexander Veviorskiy, Zarah G Meisen, Michael A Petr, Tobias Clausen Mercurio, Daniela Bakula, Peter Sykora, Li-Wei Kuo, Dean S Rosenthal, Cynthia M Simbulan-Rosenthal, Peiran Zhang, Qiuqiong Tang, Andreyan N Osipov, Ivan V Ozerov, Alex Aliper, Alex Zhavoronkov, Morten Scheibye-Knudsen.
      Cancer cells exploit DNA repair to overcome damage and errors induced by rapid proliferation and repressed checkpoints. Thus, the loss of one DNA repair protein can make tumors more susceptible to inhibition of other repair pathways. Here, using in silico methodologies and high-content genetic and cell survival screens, we found that the antimalarial drug quinacrine impaired the DNA damage response (DDR) in multiple cancer cell lines. Quinacrine disrupted the interaction of the stress-response protein NDRG1 with the major segregase VCP, which in turn promoted the degradation of the E3 ubiquitin ligase RNF8 and other proteins that mediate the recruitment of the critical DDR protein 53BP1 to sites of DNA damage. This impaired recruitment of 53BP1 caused increases in the DNA damage marker γH2AX. High NDRG1 expression in tumors correlated with poor survival in patients, and high expression in various cancer cell lines correlated with quinacrine sensitivity. Colorectal carcinoma cells were particularly vulnerable to pharmacological or genetic inhibition of NDRG1, and high NDRG1 expression and mutations in MLH1 and PARP3 resulted in synthetic lethality. Our findings identify combination genetic markers that might be therapeutically exploited in colon cancer, as well as provide a platform for such discovery in distinct cancer types.
    DOI:  https://doi.org/10.1126/scisignal.adv4272
  32. Cell. 2026 Jul 20. pii: S0092-8674(26)00757-9. [Epub ahead of print]
    A bivalent molecular glue linking lysine acetyltransferases to oncogene-induced cell death.
    Meredith N Nix, Sai Gourisankar, Kevin J Bowman, Sabin A Nettles, Haopeng Yang, Brendan G Dwyer, Roman C Sarott, Hind Abuzaid, Michael M Martinez, Nick Phillips, Vincent Cabaud, Artur Hakobyan, Vahram Arakelov, Garik Petrosyan, Aram Davtyan, Yanlan Wang, Juste M Simanauskaite, Bryan A Romero, Hannah M Jones, Andrey Krokhotin, Tara N Lowensohn, Lei Chen, Cara Low, Hannes Vogel, Mark M Davis, Daniel Fernandez, Tinghu Zhang, Michael R Green, Stephen M Hinshaw, Nathanael S Gray, Gerald R Crabtree.
      Developing cancer therapies that induce specific death of malignant cells is critical for preventing relapse. Highly effective strategies, such as immunotherapy, exemplify this principle. Here, we provide the mechanistic basis for a small-molecule approach that leverages chemically induced proximity (CIP) to kill diffuse large B cell lymphoma, the most common non-Hodgkin lymphoma. We developed lysine acetyltransferase (KAT)-based TCIPs (transcriptional/epigenetic chemical inducers of proximity), or KAT-TCIPs, which redirect p300/CREB-binding protein (CBP) to activate cell-death networks repressed by the oncogenic driver BCL6. Our lead KAT-TCIP reprograms the epigenome to initiate apoptosis. The crystal structure of the chemically induced p300-BCL6 complex reveals how chance protein-protein interactions may be exploited to confer the potency and selectivity of KAT-TCIPs. Thus, oncogenic drivers can be co-opted to activate robust cell death. Consistent with their gain-of-function mechanism, TCIPs recruiting different transcriptional activators-p300, BRD4, or CDK9-produce distinct genomic responses, suggesting specialized therapeutic uses.
    Keywords:  BCL6; CIP; DLBCL; chemically induced proximity; lymphoma; lysine acetyltransferases; transcription
    DOI:  https://doi.org/10.1016/j.cell.2026.06.037
  33. Nucleic Acids Res. 2026 Jul 17. pii: gkag730. [Epub ahead of print]54(14):
    Upstream non-AUG initiation and ribosomal -1 frameshifting in ATXN8OS CTA/CTG repeat-associated translation.
    Soyoka Sakamoto, Hayato Ito, Mayuka Hasumi, Tatsuya Morisaki, Makito Hirano, Tatsuya Niwa, Yoshitaka Nagai, Timothy J Stasevich, Hideki Taguchi.
      Microsatellite repeat expansions contribute to the pathogenesis of many neurodegenerative disorders. In spinocerebellar ataxia type 8 (SCA8), abnormal expansion of CTA/CTG repeats in the 3' untranslated region of the ATXN8OS (ATXN8 Opposite Strand) gene has been implicated in disease pathology. Although the occurrence of repeat-associated non-AUG (RAN) translation from the ATXN8 transcript has been reported, whether and how RAN translation occurs from the ATXN8OS transcript has remained unexplored. Here, using a cell-free translation system and cultured cells, we showed that ATXN8OS undergoes robust AUG-independent translation in a repeat length-dependent manner. Mechanistic analyses revealed that translation of the poly L (0) frame initiates at a non-AUG codon located upstream of the repeats. Moreover, using live-cell imaging at a single messenger RNA level, we directly visualized ribosomal -1 frameshifting from the poly L (0) frame to the poly T-poly A (+2) frame during translation elongation. We further showed that ATXN8OS translation was enhanced upon activation of the integrated stress response. Together, these findings establish both the occurrence and the molecular mechanisms of ATXN8OS translation from expanded CTA/CTG repeats and provide insights into the pathogenic processes underlying SCA8.
    DOI:  https://doi.org/10.1093/nar/gkag730
  34. Mol Plant. 2026 Jul 20. pii: S1674-2052(26)00232-7. [Epub ahead of print]
    Repurposing an E3 ligase to chaperone for the sake of thermotolerance.
    Sotirios Fragkostefanakis, Ayat Bakery.
      
    DOI:  https://doi.org/10.1016/j.molp.2026.07.013
  35. Curr Biol. 2026 Jul 20. pii: S0960-9822(26)00655-X. [Epub ahead of print]36(14): R807-R820
    Global cellular responses to lysosomal damage.
    Jingyue Jia.
      Lysosomes are membrane-bound organelles that orchestrate a wide range of cellular processes, including degradation, metabolism, signaling, gene regulation and quality control, while interacting with other organelles, thereby profoundly shaping cellular homeostasis and fate. Lysosomal membrane integrity is highly vulnerable to a broad spectrum of physiological and pathological insults, acting as both a cause and a consequence of diverse human conditions, including neurodegeneration, cancer, infectious disease and aging. Understanding the mechanisms by which cells respond to lysosomal damage is therefore of critical importance. Recent studies have revealed that cells deploy sophisticated damage response mechanisms locally to repair, remove, and replace damaged lysosomes. In contrast, how local lysosomal damage triggers global cellular responses is only beginning to be understood. This review summarizes recent conceptual advances in global cellular responses to lysosomal damage, encompassing translational, metabolic and transcriptional adaptations, and highlights their crucial roles in restoring cellular homeostasis and shaping outcomes in health and disease.
    DOI:  https://doi.org/10.1016/j.cub.2026.05.050
  36. mBio. 2026 Jul 23. e0129526
    AlphaFold-driven structural proteomics reveals extensive cellulosome machinery in human ruminococcal symbionts.
    Christine Minor, Allen Takayesu, Mark A Arbing, Sung Min Ha, Robert P Gunsalus, Matteo Pellegrini, Michael R Sawaya, Robert T Clubb.
      Cellulosomes are large, surface-displayed enzyme complexes that enable anaerobic bacteria to degrade recalcitrant plant polysaccharides, yet cellulosome-expressing bacteria are thought to be rare in the human gut. Here, we show that extensive sequence divergence obscures the detection of many ruminococcal cellulosomes by conventional sequence homology-based methods. Using proteome-scale AlphaFold2 structural predictions, we uncovered a substantially expanded set of putative cellulosome-producing Ruminococcus species, including six previously unrecognized human symbionts. Structure-based clustering identifies several novel cohesin families that retain conserved folds despite extreme sequence divergence and define distinct, phylogenetically conserved cellulosome architectures. The analysis reveals R. callidus and related human symbionts encode elaborate cellulosomes that are invisible to sequence-based annotation. Similarly, R. difficilis, a human gut symbiont, has been found to possess genes for an atypical cohesin-based assembly enriched in amylases and related starch-binding proteins, which may enable this microbe to degrade resistant starches that evade digestion in the upper gastrointestinal tract. Together, these findings reveal that ruminococcal cellulosomes are far more prevalent and diverse than previously appreciated and demonstrate the power of structural proteomics to uncover deeply divergent functional systems in the gut microbiome.IMPORTANCEPlant cell wall polysaccharides are a major dietary carbon source, yet their degradation relies on rare, highly specialized microbial enzyme assemblies known as cellulosomes, which have long been considered uncommon in the human gut. Using proteome-scale structure prediction combined with experimental validation, we show that cellulosomes are far more widespread and structurally diverse in human-associated Ruminococcus species than previously appreciated. We identify multiple new cohesin families and reveal distinct cellulosome architectures likely adapted to degrade different dietary substrates. Together, these findings redefine the distribution and evolution of cellulosomes in gut microbes and demonstrate the power of structural proteomics to uncover deeply diverged biological systems.
    Keywords:  AlphaFold; Ruminococcus; cellulosome; human gut; structural proteomics
    DOI:  https://doi.org/10.1128/mbio.01295-26
  37. Autophagy. 2026 Aug;22(8): 1743-1744
    The emerging role of ERphagy/reticulophagy in pathogen invasion.
    Damian Gatica, Daniel J Klionsky.
      In recent years ERphagy, the selective autophagic degradation of the endoplasmic reticulum (ER), has emerged as a key selective autophagic pathway involved not only in the recycling of the ER, but also in preventing the replication of viruses and bacteria. The mechanisms by which ERphagy achieves this do not seem immediately related to canonical xenophagy pathways and could provide a new avenue for therapeutic targets to combat pathogenic infections. In this editor's corner we briefly summarize the ways ERphagy is involved in pathogen infection, highlighting the potential ERphagy has as an understudied innate immune response pathway.Abbreviation: IFN-I: type I interferon; LPS: lipopolysaccharide; STING1: stimulator of interferon response cGAMP interactor 1.
    Keywords:  Bacteria; FAM134B; endoplasmic reticulum; virus; xenophagy
    DOI:  https://doi.org/10.1080/15548627.2026.2661121
  38. J Chem Theory Comput. 2026 Jul 21.
    Assessing the Stability of Molecular Glues with Weighted Ensemble Simulations.
    Seref Berk Atik, Alex Dickson.
      Targeted protein degradation is an emerging approach that utilizes cellular degradation pathways to inhibit a target protein. Small molecules such as molecular glues or PROTACs can be used to mediate the formation of a ternary complex with an E3 ligase and the target protein, which can dramatically enhance the degradation process. This approach is promising for cancer therapy, where degradation of oncogenic proteins can lead to cancer cell toxicity. To design new molecular glues, it is important to develop methods that predict how well a given molecule stabilizes a protein-protein interaction. However, conventional molecular dynamics simulations face challenges in capturing the long-time scale binding and unbinding events that would be used to evaluate this stabilization. In this study, we developed a strategy that allows us to evaluate the stability of protein-protein interactions in the presence of a glue molecule using weighted ensemble simulations in combination with weakened protein-protein interactions. Using this strategy, we generated unbinding trajectories of the DCAF15-RBM39 system with small molecules E7820, Indisulam, and several other Indisulam analogs. We were able to observe distinctly different behaviors between systems with different glues, which was in agreement with their reported EC50 values. We believe this approach could aid drug discovery efforts by expanding the set of druggable targets and improving the success rate of molecular glue development.
    DOI:  https://doi.org/10.1021/acs.jctc.6c00319
  39. Proc Natl Acad Sci U S A. 2026 Jul 28. 123(30): e2601290123
    Structural and mechanistic basis for membrane recognition and activation of the vacuolar lipase Atg15.
    Tomoko Kawamata, Nobuo N Noda, Michiko Sasaki, Yoshinori Ohsumi, Yuji Sakai.
      Atg15 is a vacuolar phospholipase B essential for the degradation of intravacuolar vesicles such as autophagic bodies. Despite its central role in cellular membrane turnover, the molecular basis of how Atg15 is activated and acts on internal membranes has remained elusive. Here, by combining all-atom and coarse-grained molecular dynamics (MD) simulations with in vitro and in vivo analyses, we elucidate the structural and mechanistic principles underlying Atg15 activation and substrate recognition. Our simulations revealed that disulfide bonds are critical for maintaining the structural integrity of the catalytic core, while the C-terminal region locks the catalytic center in a closed state that prevents activation. Membrane binding induces a transition to an open state, enabling catalysis. Through MD-guided mutational analysis, we identified three regions crucial for catalytic locking, membrane binding, and substrate recognition, and experimentally confirmed that mutations in these regions inhibit activity. Furthermore, Atg15 preferentially associates with positively curved membranes, providing a potential basis for its preferential action on internal vesicular membranes. These findings suggest that Atg15's activity is controlled through multiple regulatory layers to ensure safe and preferential membrane degradation.
    Keywords:  autophagic body; autophagy; membrane degradation; molecular dynamics simulation; phospholipase
    DOI:  https://doi.org/10.1073/pnas.2601290123
  40. Fish Shellfish Immunol. 2026 Jul 22. pii: S1050-4648(26)00512-7. [Epub ahead of print] 111608
    Zebrafish RNF128a positively regulates innate immunity by promoting the K63-linked ubiquitination of TBK1.
    Zeyin Jiang, Jihuan Hu, Hongying Zhang, Feng Cai, Xuefeng Liu, Xiaowen Xu, Chengyu Hu.
      RNF128, also known as GRAIL, is a well-studied E3 ubiquitin ligase involved in the induction and maintenance of T cell anergy. It contains PA_GRAIL_like domain, HRD1 domain and RING-H2_like domain. Recent studies have shown that RNF128 is involved in the regulation of innate immunity in mammals. It should be noted that zebrafish, possess two RNF128 paralogs, RNF128a and RNF128b. We focused on RNF128a, which shares the closest sequence homology with mammalian RNF128; however, its role in fish has not yet been elucidated. In this paper, we demonstrated that RNF128a acts as a positive regulator of innate immunity in Zebrafish. Zebrafish RNF128a responds to multiple stimuli including SVCV (Spring Viremia of Carp Virus), poly(I:C), B-DNA, LPS, and is characterized by the heightened sensitivity to SVCV. Notably, Zebrafish RNF128a up-regulates the expression of IFN1, ISG15, MX, as well as the inflammatory cytokines such as IL-6 and TNFα in response to SVCV. Mechanistically, Zebrafish RNF128a interacts with TBK1 through its protease-associated (PA) domain. However, the subcellular localization of RNF128a is associated with its HRD1 domain. In addition, Zebrafish RNF128a is localized to both early endosome RAB5 and late endosome RAB7 but rarely in Golgi apparatus and endoplasmic reticulum. Structurally, only full-length RNF128a promotes the K63-linked ubiquitination of TBK1, while none of the truncation mutants retains this activity. Our study identified Zebrafish RNF128a as an E3 ligase that catalyzes K63-linked ubiquitination and activates TBK1, and delineated its essential role in the antiviral innate immune response in zebrafish.
    Keywords:  Innate immunity; RNF128a; TBK1; Ubiquitination; Zebrafish
    DOI:  https://doi.org/10.1016/j.fsi.2026.111608
  41. J Mol Biol. 2026 Jul 20. pii: S0022-2836(26)00326-8. [Epub ahead of print] 169953
    Epitope-guided detection of a molecular glue-induced ternary complex using engineered synthetic antibody fragments.
    Kelly M O'Leary, Tomasz Slezak, Duc Anh Le, Anthony A Kossiakoff.
      Molecular glues represent a class of small molecules that enable the modulation of proteins lacking traditional ligand-binding pockets. A defining feature of molecular glues is their ability to bind cooperatively at weak or neomorphic protein-protein interfaces. Despite growing interest in these compounds, tools for selectively isolating native molecular glue-induced protein assemblies from heterogeneous populations in cells remain limited. Here, synthetic antibody fragment (Fab) reporters were generated by phage display to enable selective detection of the rapamycin-induced FKBP12-mTOR ternary complex as a model molecular glue-induced protein assembly. Crystallographic studies revealed the structural basis for three distinctive epitope recognition mechanisms to monitor the molecular glue activity of rapamycin using synthetic binders. Fab-1A and Fab-2C reported ternary complex formation with low to moderate precision by exploiting rapamycin-induced allosteric and interaction-gated epitopes, respectively. Fab-4R exhibited superior accuracy as a molecular glue reporter by sensing a rapamycin-gated junctional epitope that bridges the FKBP12-rapamycin-mTOR architecture. Structure-guided mutagenesis showed that the paratope of Fab-4R confers specificity for the ternary complex through hot spot interactions positioned directly across the conditional interface formed between FKBP12 and mTOR. Cell-based immunoprecipitation assays demonstrated that both Fab-4R and scFv-4R function as versatile molecular probes to report FKBP12-dependent mTOR inhibition by rapamycin with high fidelity and picomolar sensitivity. Taken together, these findings delineate the recognition properties for multiple antibody-based molecular glue reporters and highlight the versatility of synthetic binders for sensing conditionally formed epitopes within the proteome.
    Keywords:  molecular glue; phage display; rapamycin; synthetic antibody; ternary complex
    DOI:  https://doi.org/10.1016/j.jmb.2026.169953
  42. Adv Sci (Weinh). 2026 Jul 23. e76778
    A Blood-Derived Factor Rescues ALS: Platelet Factor 4 Activates OPTN-Dependent Autophagy to Clear SOD1 Aggregates Independently of PINK1.
    Qingjian Xie, Yanbo Zhu, Wenhua Jiang, Haobo Xie, Yaojia Li, Mengjie Hu, Kezheng Li, Huan Yu, Yixuan Pan, Chaoyi Jiang, Xueqin Song, Dongsheng Fan, Binbin Deng.
      Peripheral factors that systemically regulate amyotrophic lateral sclerosis (ALS) have remained elusive-until now. Here, by integrating population-scale epidemiology with mechanistic dissection, we identify platelet factor 4 (PF4) as the central driver of a circulating neuroprotective axis that restores proteostasis and rescues ALS. In a prospective cohort of >500 000 UK Biobank participants, platelet indices were strongly associated with ALS risk, and serum PF4 levels were significantly reduced in ALS patients. Systemic administration of recombinant PF4 in hSOD1G93A mice produced dramatic therapeutic effects: extended survival, preserved motor function, attenuated neuroinflammation, and reduced neuromuscular junction denervation. Remarkably, this efficacy appears pathology-selective-robust in SOD1-driven models but shows no observable effect in TDP-43 or C9orf72 ALS models. Mechanistically, PF4 achieves what few molecules can: it engages the cell surface receptor LRP1 to activate the TBK1-OPTN signaling axis, restoring impaired autophagic flux through a PINK1/Parkin-independent pathway requiring ATG7, establishing a previously unrecognized peripheral platelet-autophagy-neuron axis that facilitates the co-clearance of pathological SOD1 aggregates and damaged mitochondria. This study unveils PF4 as a first-in-class circulating autophagy regulator with therapeutic potential in ALS. Beyond identifying a candidate biomarker and drug lead, it reveals that systemic factors can directly engage central proteostatic machinery-opening a new frontier for ALS therapy.
    Keywords:  OPTN; PF4; SOD1; amyotrophic lateral sclerosis; mitophagy; proteostasis
    DOI:  https://doi.org/10.1002/advs.76778
  43. Nucleic Acids Res. 2026 Jul 17. pii: gkag692. [Epub ahead of print]54(14):
    ETTAS: a modular aptamer-recruited platform for programmable translational activation.
    Aolin Li, Xiaoting Zhang, Senmao Li, Yifan Wang, Chaojie Xu, Changning Lv, Min Zhao, Yuchen Liu, Mingxia Ding, Congcong Cao.
      Precise enhancement of endogenous protein synthesis offers a reversible therapeutic strategy without permanent genomic modification. However, existing Cas13-mediated translational activation systems are limited by modest potency and restricted modular expandability. Here, we developed the Enhanced Targeted Translational Activation System (ETTAS), a modular RNA-guided platform that combines dCas13a, the SINEB2 translational activation element, and an independently recruitable aptamer-mediated auxiliary module. Systematic ortholog screening identified dCas13a as the most effective scaffold for SINEB2-mediated translational activation, whereas direct tandem duplication of SINEB2 elements impaired rather than enhanced activity. To overcome this architectural limitation, we used aptamer-mediated recruitment to spatially separate target recognition from auxiliary activation. A binding-validated, non-interfering dCas13a-binding aptamer enabled construction of a dual-module system in which an aptamer-recruited SINEB2 element enhanced translation without altering target mRNA abundance or stability. Compared with the previously reported dCasRx-SINEB2 system, ETTAS produced stronger reporter activation, stronger endogenous induction of P53 and PTEN, and greater antiproliferative and pro-apoptotic effects in bladder cancer cells. Proteomic analyses showed selective target protein upregulation with limited global perturbation. In vivo, dual-AAV delivery of ETTAS activated endogenous P53 and suppressed tumor growth. ETTAS establishes a programmable framework for modular post-transcriptional upregulation of endogenous proteins.
    DOI:  https://doi.org/10.1093/nar/gkag692
  44. Bioorg Med Chem. 2026 Jul 18. pii: S0968-0896(26)00211-7. [Epub ahead of print]141 118755
    RNA-based ATTEC: an RNA-guided autophagy-lysosome platform for targeted protein degradation.
    Yunqiu Zhang, Wanting Yang, Yan Xu, Dingqiang Fu, Xiaokang Nie, Feng Du, Juan Dong, Fei Wang, Xin Cui, Zhuo Tang.
      Targeted protein degradation (TPD) has emerged as a breakthrough in drug discovery and a global biomedical research hotspot. However, its reliance on traditional small-molecule ligands inherently restricts the scope of targetable proteins. Herein, we report a novel autophagosome-tethering compound (ATTEC) strategy based on RNA aptamers to expand the target applicability of this technology. We designed and constructed a heterobifunctional molecule (GWD) that specifically recruits the autophagy protein LC3 to a genetically encoded tandem aptamer RNA scaffold. This scaffold recognizes target proteins via RNA aptamers, delivering them into the autophagy-lysosome degradation pathway. Through modular replacement of aptamer units on the RNA scaffold, we achieved efficient degradation of multiple transcription factors (E2F1, p50, p65). Furthermore, using this strategy, we demonstrated targeted degradation of the RNA-binding protein RBFOX1 and the oncoprotein EGFR in cervical cancer cells (HeLa). Collectively, this aptamer-based ATTEC platform provides a modular, programmable, and versatile strategy for targeted protein degradation, holding great promise for innovative drug discovery and fundamental biological research.
    Keywords:  Aptamer-based degrader; Autophagy-lysosome pathway; RNA-guided ATTEC; Targeted protein degradation
    DOI:  https://doi.org/10.1016/j.bmc.2026.118755
  45. EMBO J. 2026 Jul 22.
    Tripartite ER-mitochondria-lipid droplets contact sites control adipocyte metabolic flexibility.
    Marie Palard, Gilliane Chadeuf, Maxime Carpentier, Clotilde C N Renaud, Samuel Frey, Mikael Croyal, Rola Shaaban, Samy Hadjadj, Chloe Cloteau, Naima El Khallouki, Perrine Bomme, Soazig Le Lay, Manuel Majrouh, Perrine Paul-Gilloteaux, Alexandre Humbert, Christine Durand, Nicolas Bertocchini, Laurence Dubreil, Yoann Combot, Antria Antreou, Cedric Le May, Simon Ducheix, Bertrand Cariou, Francesca Giordano, Jennifer Rieusset, Abdou Rachid Thiam, Xavier Prieur.
      Adipocyte dysfunction is a major driver of obesity-associated cardiometabolic disease, underscoring the need to understand how lipid storage and mobilization are regulated and disrupted. The ER-anchored protein Seipin governs lipid droplet (LD) biogenesis and ER-LD and ER-mitochondria (MAM) contacts, and its loss impairs calcium transfer and causes lipodystrophy. Here, we investigated whether Seipin coordinates MAM and ER-LD remodeling during adipocyte lipid handling. In subcutaneous adipose tissue from inducible Seipin-knockout mice, electron microscopy and proximity ligation assays revealed that feeding reduces MAMs while increasing ER-LD and mitochondria-LD contacts, a remodeling abolished by Seipin deficiency. Lipid loading elevated tripartite MAM-LD contacts in controls but not knockouts. Fluorescence recovery after photobleaching showed that impaired triglyceride transfer to LDs in Seipin-deficient cells was rescued by the MAM-LD-stabilizing peptide 'Linker-ER-Mi', in a calcium-dependent manner. During adipogenesis and lipid loading, MAM-LD contacts increased, whereas MAM-cytosolic mitochondria contacts declined; however, obesity blunted this remodeling. Furthermore, disrupting membrane contact sites impaired lipid flux, lipolysis, and insulin signaling. Taken together, these findings identify MAM-LD as regulators of adipocyte metabolic flexibility.
    DOI:  https://doi.org/10.1038/s44318-026-00876-z
  46. J Med Chem. 2026 Jul 18.
    Mapping Non-Homologous Pocket Compatibilities to Identify Hidden Drug-Target Relationships: A Pocket Hopping Framework.
    Yingying Zhang, Tianbiao Yang, Buying Niu, Ruirui Yang, Keke Zhang, Ying Song, Chuanlong Zeng, Xiaochu Tong, Jiusheng Lin, Mingyue Zheng, Sulin Zhang, Xutong Li.
      Predicting small molecule-protein interactions across nonhomologous proteins remains challenging because shared ligand recognition is often not evident from sequence, fold, or pocket similarity. Here, we introduce pocket hopping, a machine-learning framework that learns residue-level interaction patterns from coligand binding pockets and infers compatibility between nonhomologous pockets for similar chemotypes. Using shared ligands as supervision rather than explicit geometric alignment, pocket hopping identifies pocket relationships that are not readily captured by conventional chemical-, sequence-, or structure-based comparisons. In two case studies, pocket hopping demonstrates broad utility in drug discovery by enabling de novo hit identification and mechanistic interpretation, identifying fedratinib and its analogues as helicase WRN inhibitors. The model also identified the clinical-stage HDAC inhibitor abexinostat as a direct ENPP1 binder and inhibitor, and cellular assays showed enhanced cGAMP-STING signaling under cGAMP stimulation. Together, these results indicate that pocket-level compatibility can complement existing approaches for target identification, hit discovery, and polypharmacology analysis.
    DOI:  https://doi.org/10.1021/acs.jmedchem.6c01050
  47. Geroscience. 2026 Jul 22.
    The PERK paradox in aging: how ER stress shapes senescence and neurodegeneration.
    Vivek Pandey, Rahul Sachdeva, Sanda Despa.
      Endoplasmic reticulum (ER) stress and activation of the unfolded protein response (UPR) are now recognized as integral components of the proteostasis network that preserves cellular and tissue function across the lifespan. With aging, increasing oxidative load, metabolic imbalance, and Ca2⁺ dysregulation elevate the burden of misfolded proteins in the ER, leading to progressive UPR engagement. When ER stress is mild or transient, UPR signaling restores folding capacity, restrains translation, and enhances redox and degradative programs, thereby promoting cellular resilience. In contrast, persistent or repeatedly unresolved ER stress narrows this adaptive window and biases UPR outputs toward chronic inflammation, stable growth arrest, and cell loss processes that collectively drive inflammaging, stem/progenitor exhaustion, tissue degeneration, and vulnerability to neurodegenerative disease. This review synthesizes evidence that ER stress is not merely a correlation of aging but a mechanistic contributor to age-related decline, with senescence emerging as a major downstream fate in multiple tissues. It also highlights how context- and duration-dependent PERK signaling can be protective early, yet maladaptive when chronically engaged, shaping senescence programs and influencing neuronal survival and neurodegenerative disease progressions. Finally, this review discusses therapeutic opportunities and open questions centered on restoring adaptive PERK/ISR dynamics to support healthy aging.
    Keywords:  Aging; ER stress; Neurodegeneration; Senescence; Unfolded protein response
    DOI:  https://doi.org/10.1007/s11357-026-02430-5
  48. PLoS Pathog. 2026 Jul 24. 22(7): e1014452
    Differential assembly of RNP granules via activation of distinct dsRNA sensors by adenovirus mutants.
    Robert T Steinbock, Orlando B Scudero, Joseph M Dybas, Amber R N Abbott, Katarzyna Kulej, Richard Lauman, Holly Chan, Eva L Agostino, Namrata Kumar, Cameron Stone, Skyler Briggs, Nicholas A Parenti, Yize Li, James M Burke, Susan R Weiss, Alexander M Price, Matthew D Weitzman.
      Recognition of double-stranded RNA (dsRNA) triggers antiviral defense mediated by PKR and OAS3/RNase L pathways through translational arrest and RNA decay. This is accompanied by assembly of distinct cytoplasmic ribonucleoprotein (RNP) condensates termed stress granules (SGs) and RNase L-dependent bodies (RLBs). Here we show that adenovirus mutants engage distinct RNA-sensing pathways and promote differential assembly of cytoplasmic RNP granules. Infection with splicing-defective ∆E4 mutant leads to dsRNA accumulation and activation of both PKR and OAS3/RNase L, promoting formation of RLB-like granules. In contrast, mutants lacking virus-associated (VA) RNAs trigger PKR activation and assembly of SGs despite absence of detectable dsRNA. Proximity labeling proteomic analysis revealed distinct protein compositions of canonical SGs and RLBs, which were reflected in virus-induced granules. While ∆VA-induced granules were PKR-dependent, ∆E4 mutants induced RLB-like granules independently of PKR and RNase L. In cells lacking these sensors, granule assembly during ∆E4 infection coincided with translational arrest independent of eIF2α phosphorylation, indicating additional pathways linking nuclear dsRNA sensing to translational control and RNP granule assembly during viral infection. These findings provide novel insights into how distinct dsRNA sensors modulate translation and RNP condensates in response to stress.
    DOI:  https://doi.org/10.1371/journal.ppat.1014452
  49. EMBO J. 2026 Jul 20.
    Vps1 drives membrane constriction and fission necessary for endosomal protein sorting.
    Shilpa Gopan, Uma Swaminathan, Gurmail Singh, Thomas J Pucadyil.
      The trafficking of cargo between endosomes and the Golgi apparatus uses both retromer-dependent and retromer-independent routes. Disruptions to these routes lead to the mis-sorting of lysosomal cargo, and associated metabolic and neurological disorders. The yeast dynamin Vps1 is essential for these trafficking pathways; however, it is not clear whether it directly causes membrane fission. Using cell-free reconstitution and live-cell assays, here we demonstrate that Vps1 assembles into scaffolds on membrane tubules, and uses GTP hydrolysis to force tubule constriction and fission. Vps1 mutants that are unable to assemble or to hydrolyze GTP fail to achieve fission in vitro and cause cargo mis-sorting in vivo. Furthermore, we identify two essential motifs, a lysine-rich phosphoinositide-binding motif and a phenylalanine-rich self-assembly motif, which, when mutated, render Vps1 dysfunctional. Finally, quantitative proteomics revealed a broad range of Golgi and plasma membrane proteins that mis-sort to the vacuole without Vps1. These findings define the Vps1-dependent retrograde pathway's cargo repertoire and confirm Vps1's mechanochemical role in membrane fission.
    DOI:  https://doi.org/10.1038/s44318-026-00855-4
  50. Proc Natl Acad Sci U S A. 2026 Jul 28. 123(30): e2536600123
    Deciphering the mechanism of protein aggregation and effects of inhibitors using single-molecule mass photometry.
    Aaron Lyons, Simanta Sarani Paul, Jack E MacArthur, Grace N Hoffman, Allan Yarahmady, Sue-Ann Mok, Michael T Woodside.
      Aggregation of misfolded proteins is a prominent feature of many diseases and hence an attractive drug target. However, the small oligomers that are critical early species in the aggregation cascade are difficult to monitor directly owing to their heterogeneity and transience, complicating efforts to define aggregation mechanisms and target oligomers therapeutically. Here, we observe changes in oligomer populations directly using single-molecule mass photometry (MP). Studying the pathogenic P301L mutant of tau protein linked to frontotemporal dementia, we globally fit the growth/decay kinetics for every oligomer population observed by MP to microscopic models of aggregation. A simple extension to the best-fit model also accounts for amyloid fibril kinetics, as monitored by Thioflavin T fluorescence, providing a quantitative model of aggregation kinetics across all stages of the cascade based on direct observation. Crucially, we find that models fitting amyloid kinetics alone fail to capture oligomer behavior, implying that-contrary to standard practice-amyloid kinetics cannot be relied on to deduce aggregation mechanisms. Furthermore, there is no single rate-limiting nucleation step preceding rapid growth, as generally assumed, suggesting that standard models of aggregation are overly simplistic. Repeating the analysis in the presence of aggregation inhibitors allows identification of the discrete steps in the cascade affected by the inhibitors. This work presents a powerful approach for defining protein aggregation mechanisms and the mechanism of action of inhibitors, with applications to understanding many diseases and developing novel therapeutics.
    Keywords:  aggregation inhibitors; kinetic mechanisms; mass photometry; protein aggregation; tau protein
    DOI:  https://doi.org/10.1073/pnas.2536600123
  51. Oncogene. 2026 Jul 21.
    The RNA-binding protein RALY promotes ATM activation by stabilizing Tip60.
    Bo Yao, Kailiang Zhao, Ning Yu, Ning Wang, Yinian Chang, Linzhu Luo, Fang Wang, Yide Mei.
      A rapid DNA damage response (DDR) and efficient DNA repair are essential for maintaining genome integrity. As a central apical kinase, ATM phosphorylates multiple downstream substrates to initiate DDR signaling and coordinate DNA repair following double-strand breaks (DSBs). However, the precise molecular mechanisms underlying ATM activation remain incompletely understood. Here, we identify the RNA-binding protein RALY as a critical regulator of ATM activation. We show that RALY directly interacts with and stabilizes the acetyltransferase Tip60, a key activator of ATM. Mechanistically, RALY competes with Tip60 for binding to the E3 ubiquitin ligase Mdm2, thereby inhibiting Mdm2-mediated ubiquitination and degradation of Tip60. Functionally, inhibition of RALY impairs ATM activation, compromises DNA repair capacity, and enhances radiosensitivity of cancer cells in a Tip60-dependent manner. Our findings uncover a previously unrecognized role of RALY in regulating ATM activation and indicate RALY as a potential therapeutic target for enhancing radiosensitivity in cancer.
    DOI:  https://doi.org/10.1038/s41388-026-03904-8
  52. Proc Natl Acad Sci U S A. 2026 Jul 28. 123(30): e2619864123
    HUWE1 targets mitochondria via RMC1 to promote neurodevelopment.
    Jiamin Yi, Qin Yang, Chunzhuang Zhou, Yunfei Zhu, Yingfeng Tu, Lin Zhao, Min Tang, Junhong Qin, Tao Long, Tianxing Li, Ping Li, Zikang Gong, Qilin Wang, Xin Yong, Da Jia.
      The HECT-type E3 ubiquitin ligase HUWE1 is a critical regulator of protein homeostasis, genome stability, and neurodevelopment. Variants in HUWE1 are linked to X-linked intellectual disability (XLID), yet a significant number of HUWE1 variants are noncatalytic, leaving their disease mechanisms unresolved. Here, we identify an AMBRA1-RMC1-HUWE1 signaling axis that directs HUWE1-mediated ubiquitination to mitochondria to regulate neural development. In zebrafish, noncatalytic HUWE1 variants found in XLID patients (M375I, G660R, and H669Q) recapitulate key neurodevelopmental deficits, including impaired brain growth and motor neuron defects. Global ubiquitin profiling reveals that these variants selectively disrupt the ubiquitination of mitochondrial proteins without affecting nuclear substrates. Mechanistically, AMBRA1 acts as a mitochondrial scaffold that recruits RMC1, enabling HUWE1 localization to mitochondria through direct interaction with RMC1. Disruption of this recruitment by disease-associated HUWE1 variants prevents mitochondrial targeting and impairs mitochondrial substrate ubiquitination. Notably, Urolithin A treatment ameliorates neurodevelopmental phenotypes in HUWE1-deficient zebrafish. Together, our findings define an AMBRA1-organized mitochondrial recruitment pathway in which RMC1 links HUWE1 to mitochondria, explain noncatalytic HUWE1-associated XLID, and suggest mitochondrial quality-control enhancement as a potential therapeutic strategy.
    DOI:  https://doi.org/10.1073/pnas.2619864123
  53. J Biol Chem. 2026 Jul 22. pii: S0021-9258(26)02230-1. [Epub ahead of print] 113358
    The N-terminal domain of the endoplasmic reticulum-resident chaperone Grp94 functions in aggregation prevention.
    Ayodeji Adedeji, Erin Unruh, Alyssa Derr, Chioma Ndolo, Melina Balch, Kylie Paul, A J Morton, Andrea N Kravats.
      Grp94, an Hsp90 molecular chaperone localized in the endoplasmic reticulum, plays a central role in maintaining cellular proteostasis by facilitating protein folding and refolding in a nucleotide-dependent manner. Beyond its folding functions, Grp94 also prevents the aggregation of client proteins under stress conditions; however, the mechanistic basis of this aggregation-prevention activity is not fully understood. In this study, we investigated the requirements of Grp94's prevention of aggregation activity and identified the functional domain responsible using in vitro light scattering and functional assays with two model client proteins, citrate synthase and luciferase. The results show that Grp94 suppresses the thermal aggregation of both clients independently of ATP-binding, ATP-hydrolysis and calcium binding. Notably, the aggregation prevention activity for both clients is localized to the N-terminal domain (NTD) of Grp94, where a peptide-binding deficient mutant (H146D) shows enhanced aggregation suppression at limiting chaperone concentrations. This enhanced prevention of aggregation activity is attributed to increased affinity for misfolded clients, which is likely due to decreased client dissociation rates. Consequently, client release by the Grp94 peptide-binding mutant is inhibited, thereby impairing downstream remodeling by the BiP chaperone system. While the NTD of Grp94 appears to be a general requirement in the prevention of aggregation, the involvement of Grp94's pre-N domain is likely client specific. Collectively, these findings provide new insights into the aggregation-prevention function of Grp94 and implicate a previously identified peptide-binding site in aggregation prevention activity.
    Keywords:  BiP; Grp94; aggregation prevention; chaperone
    DOI:  https://doi.org/10.1016/j.jbc.2026.113358
This page is being maintained by Thomas Krichel. It was last updated on 2026‒07‒26 at 5:11.