bims-proteo Biomed News
on Proteostasis
Issue of 2026–05–17
fifty papers selected by
Eric Chevet, INSERM
  1. Targeted degradation of USP7 in solid cancer cells reveals distinct effects of deubiquitinase degraders and inhibitors.
  2. Site-specific glycosylation of Sec24D and myoferlin recruit ERGIC to ER exit sites for collagen trafficking.
  3. Dual E3 ligase recruitment by monovalent degraders for tunable SMARCA 2/4 degradation.
  4. A role for CASM in the repair of damaged Golgi architecture.
  5. Stub1 promotes chaperone-mediated autophagy to suppress antiviral immunity.
  6. Biomolecular Condensates as Protein Degradation Tools for Intracellular Targets.
  7. Intracellular lipopolysaccharide binds RETREG1/FAM134B to regulate ER remodeling upon bacterial infection.
  8. Loss of macroautophagy results in abnormality of the endoplasmic reticulum in insulin-secreting MIN6 cells.
  9. ER-driven Contact Sites in Autophagosome Biogenesis Sequence.
  10. Proteasome inhibition enhances lysosome-mediated targeted protein degradation.
  11. TBK1 restricts IRGQ-mediated autophagy.
  12. SE(3)-PROTACs: Geometric deep learning for PROTAC degradation prediction.
  13. Photocrosslinking Activity-Based Probes to Capture the Dynamics of Ubiquitin RING E3 Ligase Interactions.
  14. Robust and interpretable machine learning for affinity prioritization of designed protein interactors.
  15. Protocol for the biochemical isolation of endosomal membranes associated with endoplasmic reticulum in HeLa cells.
  16. Exercise-induced modulation of the unfolded protein response: a therapeutic avenue for muscle wasting disorders.
  17. Methods to Study the Molecular Mechanism and Drive the Design of Protein Degraders.
  18. Evolutionarily conserved spliceosome-exosome pathway in nuclear mRNA surveillance.
  19. ClpP Activation in High-Risk Medulloblastoma: ONC206 as a Potent Inducer of the Integrated Stress Response and Mitochondrial Damage for a Broader Therapeutic Window.
  20. Atg7-Atg12 conjugation and autophagy are negatively regulated by the disordered region of Atg12.
  21. The Spatiotemporal Proteome Landscape of Aging: Structural determinants of age-sensitive proteome remodeling.
  22. Quantitative FRET FLIM imaging reveals multiple interactions between proteins of the ESYT, ORP and VAP families at the endoplasmic reticulum membrane.
  23. Dysregulation of the ubiquitin-proteasome system in aging skeletal muscle.
  24. Mitochondrial Signaling and Stress Responses, Key Regulators of Aging and Longevity.
  25. Beyond Free Virions: Interconnected Secretory Pathways and Reticulon 3 (RTN3) Coordinate Extracellular Vesicle Diversity for Infectious Exosome Generation.
  26. SNOR promotes translation restart after dormancy.
  27. NEXT-FRET maps nonequilibrium rerouting of Escherichia coli maltose-binding protein folding by its signal peptide and chaperones.
  28. Nanoplatform-Based Delivery Systems for PROTACs.
  29. D-SPIN constructs regulatory network models from scRNA-seq that reveal organizing principles of perturbation response.
  30. Properties of Stereopure Phosphorothioate Groups in RNA-PROTACs.
  31. Distinct mitochondrial-derived vesicle pathways connect mitochondria with peroxisomes and lysosomes.
  32. l-NBDNJ allosteric chaperone for multiple defective enzymes involved in lysosomal storage disorders (LSDs).
  33. Impact of Two Small-Molecule Proteasome Stimulators on Cellular Growth and Metabolism.
  34. S-acylation of TDP43 regulates its condensation in amyotrophic lateral sclerosis.
  35. mTOR-NAA10-C7orf50 axis senses nutritional status to coordinate ribosome biogenesis and autophagy.
  36. Large-scale discovery, analysis and design of protein energy landscapes.
  37. Atf4a Regulates Mitochondrial Homeostasis Through Parkin-Mediated Mitophagy to Enhance Hypoxia Tolerance in Zebrafish (Danio rerio).
  38. Making ends meet: Specialized translation of viral mRNAs lacking canonical features.
  39. High-throughput screening approach identifies substrate-selective Hsp104 variants that counter amyloid seeding with diminished off-target effects.
  40. A Plug-and-Play Platform for Customizing Multivalent Degraders and Degrader-Drug Conjugates.
  41. Approval of First PROTAC Opens New Era for Targeted Protein Degradation.
  42. LAMP2A-dependent chaperone-mediated autophagy enhances oxidative stress resistance in gastric cancer cells through selective degradation of accumulated oxidized DJ-1.
  43. Coronavirus protein interaction mapping in bat and human cells reveals network rewiring governing immune evasion and zoonotic potential.
  44. Chaperone-mediated autophagy protects against retinal photoreceptor degeneration by modulating proteostasis of glucose metabolism enzymes.
  45. Structural basis for prohibitin-mediated regulation of mitochondrial m-AAA protease.
  46. TIM-3-dependent lysosome biogenesis is required for myelin debris clearance in macrophages.
  47. α-Synuclein aggregates induce mitochondrial damage and trigger innate immunity to drive neuron-microglia communication.
  48. CRISPR screening identifies TRIM27 as a destabilizer of the Smith-Magenis syndrome protein RAI1.
  49. TP53-mutant AML with ribosomal gene loss exhibits impaired protein translation and sensitivity to HSP90 inhibition.
  50. A dual phospholipase system instructs membrane hydrolysis during the final stages of plant autophagy.
  1. Nat Commun. 2026 May 13. pii: 4331. [Epub ahead of print]17(1):
    Targeted degradation of USP7 in solid cancer cells reveals distinct effects of deubiquitinase degraders and inhibitors.
    Nikolas Klink, Sebastian Urban, Johanna A Seier, Bikash Adhikari, Martin P Schwalm, Juliane Müller, Madeleine Dorsch, Philine Steinbach, Jennifer Jung, Markus Vogt, Farnusch Kaschani, Johannes Koch, Siska Führer, Markus Kaiser, Nina Schulze, Stefan Knapp, Elmar Wolf, Annette Paschen, Barbara M Grüner, Malte Gersch.
      Proteolysis-targeting chimeras (PROTACs) co-op the ubiquitin system for targeted protein degradation, creating opportunities to interrogate cellular functions of proteins through "chemical knockdown". However, matched pairs of protein degraders and inhibitors, that possess high specificity and chemical complementarity, for individual components of the ubiquitin system have remained scarce. This includes reagents to modulate activity and abundance of deubiquitinases (DUBs). Here, using an integrated chemical biology approach, we explore cellular functions of the DUB USP7 as a case study by comparing inhibition and degradation in melanoma and pancreatic cancer cells. Through the synthesis of a degrader library, we identify and characterize potent USP7 PROTACs for each cancer type. Proteomic and cellular analyses reveal that selective USP7 degradation modulates both shared and distinct protein sets across both cancers without affecting cell growth. In contrast, prolonged inhibitor treatment induces USP7-independent proteomic and metabolic dysregulation, highlighting important caveats for the cellular use of hydroxypiperidine-based USP7 inhibitors. Collectively, our work provides a comprehensively characterized chemical toolbox to distinguish on-target phenotypes which will aid the understanding of USP7 in malignant diseases. More broadly, our data emphasize the importance of increased specificity via PROTAC-mediated degradation and the potential of this modality to elucidate cell-line specific functions of DUBs.
    DOI:  https://doi.org/10.1038/s41467-026-72295-x
  2. Nat Commun. 2026 May 13.
    Site-specific glycosylation of Sec24D and myoferlin recruit ERGIC to ER exit sites for collagen trafficking.
    Tetsuya Hirata, Dharmendra Choudhary, Quyen Nguyen, Brittany J Bisnett, Erik J Soderblom, Ela W Knapik, Michael Boyce.
      Coat protein complex II (COPII) mediates anterograde trafficking from the endoplasmic reticulum (ER). While the core COPII machinery is well-characterized, how cells regulate COPII to accommodate large cargoes, including collagens, remains incompletely understood. Here, we show that the cargo-selecting COPII subunit Sec24D is modified by site-specific O-linked β-N-acetylglucosamine (O-GlcNAc) in its N-terminal intrinsically disordered region upon induction of collagen transport. These glycosylations are required for collagen trafficking in human cells and developing zebrafish. Crosslinking proteomics demonstrated that each O-GlcNAcylation influences the Sec24D interactome in a distinct way, regulating nearly all steps of COPII-mediated transport through protein-protein interactions. In particular, myoferlin interacts with glycosylated Sec24D and unexpectedly facilitates fusion of ER exit sites (ERES) and the ER-Golgi intermediate compartment (ERGIC) to enable collagen transport. Our results establish Sec24D O-GlcNAcylation as a dynamic regulator of COPII protein-protein interactions and collagen trafficking and identify myoferlin as a mediator of this process.
    DOI:  https://doi.org/10.1038/s41467-026-73027-x
  3. Nat Chem Biol. 2026 May 12.
    Dual E3 ligase recruitment by monovalent degraders for tunable SMARCA 2/4 degradation.
    Valentina A Spiteri, Dmitri Segal, Alejandro Correa-Sáez, Kentaro Iso, Ryan Casement, Miquel Muñoz I Ordoño, Mark A Nakasone, Gajanan Sathe, Caroline Schätz, Hannah E Peters, Mark Doward, Lisa Kainacher, Angus D Cowan, Alessio Ciulli, Georg E Winter.
      Proteolysis-targeting chimeras (PROTACs) and molecular glue degraders (MGDs) target proteins for degradation by co-opting an E3 ligase. While heterotrivalent PROTACs that can recruit multiple E3 ligases have been described, all MGDs reported to date depend on a single E3. Using orthogonal genetic screening, biophysical and structural analyses, we show that a monovalent MGD can recruit CUL4DCAF16 and CRL1FBXO22 in parallel to degrade SMARCA2/4. Deep mutational scanning identifies C173 in DCAF16 as essential for degrader activity and intact protein mass spectrometry confirms covalent modification at this site. Elucidating the ternary complex structure reveals a unique binding mode and a distinct interface of neointeractions that underlie degrader specificity. We demonstrate that ligase dependency is chemically and genetically tunable. Minimal compound modifications shift preference from DCAF16 to FBXO22, while a single substitution boosts degrader dependency on DCAF16. These results establish a framework for designing tunable dual E3 ligase degraders to mitigate potential resistance mechanisms.
    DOI:  https://doi.org/10.1038/s41589-026-02224-y
  4. Autophagy. 2026 May 11.
    A role for CASM in the repair of damaged Golgi architecture.
    Seeun Oh, Saif Ullah, Bhaskar Saha, Michael A Mandell.
      The term CASM describes a process in which MAP1LC3B/LC3B and other Atg8-family proteins are covalently ligated to lipids in damaged endomembranes. While CASM is commonly described as a cytoprotective response to multiple types of membrane damage, how CASM helps cells maintain homeostasis is still unclear. Here, we show that CASM maintains Golgi apparatus architecture following the loss of TRIM46, a ubiquitin ligase with roles in microtubule organization. TRIM46 deficient cells were notable for enhanced TFEB-driven lysosomal biogenesis and Golgi ribbon fragmentation, with colocalization of the trans-Golgi marker TGOLN2 and the Atg8-family proteins LC3B and GABARAP. Further studies revealed that the Golgi Atg8ylation seen in TRIM46 knockout cells was not degradative and mechanistically resembled CASM. Genetic inhibition of CASM in TRIM46 deficient cells reduced TFEB activation and exacerbated the Golgi morphology defects, suggesting that CASM contributes to Golgi repair. Accordingly, Golgi reformation after drug-induced fragmentation was impaired upon knockdown of CASM genes. Together, these studies identify lysosomal biogenesis and CASM as coordinated features of a Golgi damage response, with CASM acting to preserve Golgi integrity.
    Keywords:  Atg8ylation; CASM; TFEB; TRIM46; VAIL; autophagy; golgi damage/golgi fragmentation; lysosomal biogenesis; microtubule; tripartite motif
    DOI:  https://doi.org/10.1080/15548627.2026.2673560
  5. Autophagy. 2026 May 11. 1-2
    Stub1 promotes chaperone-mediated autophagy to suppress antiviral immunity.
    Hongyang Liu, Li Huang, Changjiang Weng.
      The E3 ubiquitin ligase Stub1 (CHIP) is a core regulator of protein homeostasis and antiviral innate immunity, with established roles in targeting RIG‑I and MAVS for proteasomal or autophagic degradation. Here, we summarize our recent work revealing that Stub1 negatively regulates type I interferon (IFN‑I) production by driving chaperone‑mediated autophagy (CMA)-dependent degradation of TBK1. Stub1 directly interacts with TBK1 and catalyzes K27‑linked polyubiquitination at lysine 344 (K344) of TBK1, which enables recognition by the CMA chaperone HSC70 via a conserved KFDKQ CMA recognition motif. Subsequently, ubiquitinated TBK1 is delivered to lysosomes via HSC70 and the lysosomal membrane protein LAMP2A for degradation. This process is independent of macroautophagy and the ubiquitin - proteasome system. Myeloid‑specific Stub1 knockout mice show enhanced IFN‑I responses, lower viral loads, and improved survival rates upon viral infection. This study defines a Stub1-CMA signaling axis that fine‑tunes antiviral immunity and expands the regulatory scope of ubiquitin codes in selective protein degradation pathways.
    Keywords:  Chaperone‑mediated autophagy; HSC70; K27‑linked ubiquitination; LAMP2A; Stub1; TBK1
    DOI:  https://doi.org/10.1080/15548627.2026.2667376
  6. Nat Commun. 2026 May 13.
    Biomolecular Condensates as Protein Degradation Tools for Intracellular Targets.
    Yi Li, Zhicheng Jin, Sharif U Ahmed, Jagotamoy Das, Reiner Bleher, Dingran Chang, Xiaozhou Yu, Connor D Flynn, Jiajing Zhou, Xiaobing Hu, Kangfu Chen, Kimberly T Riordan, Ranjit Atwal, Julia M Mayes, Zongjie Wang, Shana O Kelley.
      Targeted protein degradation harnesses endogenous cellular machinery to eliminate disease-causing proteins, yet achieving phenotype-specific degradation across diverse cell types remains challenging. Here we show that antibody-enriched biomolecular condensates formed by liquid-liquid phase separation function as intracellular protein degradation tools, combining cytosolic trafficking with direct proteasome recruitment for targeted substrate clearance. These nanoscale condensates incorporate a short proteasome-targeting motif into phase-separation precursors, preserve antibody activity, enable direct proteasome recruitment, and improve delivery uniformity. When loaded with a mutation-specific antibody, these condensates selectively degrade oncogenic KRAS G12V without affecting wild-type KRAS in heterozygous cells, and suppress tumor growth in a KRAS G12V xenograft model. This strategy provides a modular platform for intracellular protein degradation that can be readily adapted by exchanging antibodies, without requiring genetic modification of cellular system.
    DOI:  https://doi.org/10.1038/s41467-026-72967-8
  7. Autophagy. 2026 May 12. 1-18
    Intracellular lipopolysaccharide binds RETREG1/FAM134B to regulate ER remodeling upon bacterial infection.
    Yi-Lin Cheng, João Mello-Vieira, Adriana Covarrubias-Pinto, Alexis Gonzalez, Santosh Kumar Kuncha, Chun Kew, Kaiyi Zhang, Muhammad Awais Afzal, Nour Diab, Sophia Borchert, Siou-Ying Hong, Timothy Chun Huang, Wenbo Chen, Uxía Gestal Mato, Mathias Walter Hornef, Christian A Hübner, Michael Hensel, Ivan Dikic.
      Selective autophagy of the endoplasmic reticulum (ER), termed ERphagy or reticulophagy, plays a key role in organelle remodeling and cellular homeostasis. However, whether and how ERphagy is regulated during Gram-negative bacteria infection to influence host responses remains unclear. Here, we show that Salmonella enterica serovar Typhimurium releases lipopolysaccharide (LPS) that colocalizes with RETREG1/FAM134B, a reticulon-like ER-resident receptor for ERphagy. Cytosolic delivery of LPS, either during infection or via transfection, markedly increases RETREG1- and LC3B-decorated ER fragments. Mechanistically, affinity-isolation assays demonstrate that LPS directly binds RETREG1 through interactions between lipid A and positively charged residues within its amphipathic helices and C-terminal region. This interaction promotes RETREG1 oligomerization and drives ER membrane fragmentation, a process further amplified by the O-antigen moiety of LPS. The resulting ER fragments accumulate around LC3-positive Salmonella-containing vacuoles, facilitating bacterial clearance. Importantly, both intracellular and extracellular Salmonella exploit outer membrane vesicles (OMVs) to deliver LPS into the host cytosol, triggering RETREG1 activation and ER remodeling. Collectively, our findings reveal a previously unrecognized host response by which LPS of Gram-negative bacteria are sensed by the host ERphagy machinery to promote xenophagy and enhance antibacterial defense.Abbreviations: AH: amphipathic helix; BMDMs: bone-marrow-derived macrophages; Co-IP: co-immunoprecipitation; BafA1: bafilomycin A1; Cterm: C-terminal region (Cterm); CFU: colony-forming units; DAPI: 4',6-diamidino-2-phenylindole; ER: endoplasmic reticulum; EPEC: enteropathogenic Escherichia coli; GBP: guanylate binding protein; Gm12250/IRGB10: predicted gene 12250; KDO: keto-3-deoxy-octonate; LPR: lipid-to-protein ratio; LPS: lipopolysaccharide; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; mtLIR: LC3B-interacting region mutant; MDP: muramyl dipeptide; OMVs: outer membrane vesicles; O-Ag: O-antigen; OmpA: outer membrane protein A; RHD: reticulum homology domain; R-LPS: rough-LPS; S-LPS: smooth-LPS; SCVs: Salmonella-containing vacuoles; SFB: S-protein-FLAG-streptavidin binding peptide; TM: transmembrane domain; TEM: transmission electron microscopy; WT: wild-type.
    Keywords:  ER remodeling; RETREG1; Salmonella; lipopolysaccharide; outer membrane vesicles; xenophagy
    DOI:  https://doi.org/10.1080/15548627.2026.2669978
  8. Cell Struct Funct. 2026 May 09.
    Loss of macroautophagy results in abnormality of the endoplasmic reticulum in insulin-secreting MIN6 cells.
    Asako Kishimoto, Shunsuke Saito, Byungseok Jin, Shigeomi Shimizu, Satoko Arakawa, Kazutoshi Mori.
      Macroautophagy is a highly conserved system that degrades various materials inside the cell ranging from proteins to organelles. Atg5 is a protein essential for the formation of autophagosomes, which sequester materials by double membrane and degrade them after fusion with lysosomes. MIN6 cells derived from mouse pancreatic β cells retain the ability to secrete insulin in response to a change in glucose concentration from low to high. We knocked out the Atg5 gene in MIN6 cells and identified an abnormality in the endoplasmic reticulum (ER) under normal culture conditions using electron microscopy. The ER was slightly enlarged and the ER membrane was ruptured at some places adjacent to inclusion body-like structures. Numerous granule-like structures were accumulated in the lumen of the ER, some of which appeared to have leaked into the cytoplasm. These abnormalities caused ER stress, resulting in activation of all three pathways (IRE1, PERK, and ATF6) of the unfolded protein response but no induction of apoptosis. We also observed the activation of alternative autophagy/Golgi membrane-associated degradation in Atg5-KO MIN6 cells, but this was insufficient for the removal of a majority of these granule-like structures from the ER. Thus, macroautophagy but not activation of the unfolded protein response or Golgi membrane-associated degradation is essential for the homeostasis of the ER in MIN6 cells.Key words: autophagy, endoplasmic reticulum, unfolded protein response, proinsulin, Golgi membrane-associated degradation.
    Keywords:  Golgi membrane-associated degradation; autophagy; endoplasmic reticulum; proinsulin; unfolded protein response
    DOI:  https://doi.org/10.1247/csf.26016
  9. Contact (Thousand Oaks). 2026 Jan-Dec;9:9 25152564261451671
    ER-driven Contact Sites in Autophagosome Biogenesis Sequence.
    Juliane Da Graça, Dobrawa Amiri Czajkowski, Etienne Morel.
      Autophagosome biogenesis is a highly coordinated membrane remodeling process that relies on the de novo formation and expansion of the phagophore, yet the cellular principles governing its spatial and temporal organization remain incompletely understood. Accumulating evidence now places the endoplasmic reticulum (ER) at the center of this process, not merely as a membrane source, but as a dynamic scaffold that organizes phagophore assembly through extensive membrane contact sites with multiple organelles. ER-mediated contacts with endosomes, mitochondria, the plasma membrane, and ER-Golgi intermediates create specialized microenvironments that integrate signaling, lipid transfer, vesicle formation and trafficking, and biophysical constraints to drive phagophore nucleation and growth. These contact sites enable the coordinated mobilization of diverse membrane carriers and autophagy regulators in a stress- and context-dependent manner. In this review, we discuss how ER-driven membrane contact sites orchestrate autophagosome biogenesis, highlight emerging mechanistic and biophysical concepts, and consider their broader implications for cellular stress adaptation and disease.
    Keywords:  ER-contact sites; autophagosome biogenesis; lipid transfer proteins
    DOI:  https://doi.org/10.1177/25152564261451671
  10. Cell Death Dis. 2026 May 11.
    Proteasome inhibition enhances lysosome-mediated targeted protein degradation.
    Ahmed M Elshazly, Nayyerehalsadat Hosseini, Janakiram Vangala, Shanwei Shen, Victoria Neely, Xiaoyan Hu, Piyusha P Pagare, Hisashi Harada, Steven Grant, Senthil K Radhakrishnan.
      Proteasome inhibitor drugs are currently used in the clinic to treat multiple myeloma and mantle cell lymphoma. These inhibitors cause accumulation of undegraded proteins, thus inducing proteotoxic stress and consequent cell death. However, cancer cells counteract this effect by activating an adaptive response through the transcription factor nuclear factor erythroid 2-related factor 1 (NRF1, also known as NFE2L1). NRF1 induces transcriptional upregulation of proteasome and autophagy/lysosomal genes, thereby reducing proteotoxic stress and diminishing the effectiveness of proteasome inhibition. While suppressing this protective autophagy response is one potential strategy, here we investigated whether this heightened autophagy could instead be leveraged therapeutically. To this end, we designed an autophagy-targeting chimera (AUTAC) compound to selectively degrade the anti-apoptotic protein Mcl1 via the lysosome. Our results show that this lysosome-mediated targeted degradation is significantly amplified in the presence of proteasome inhibition, in a NRF1-dependent manner. Mechanistically, AUTAC-driven Mcl1 clearance requires K63-linked ubiquitination by UBC13 and TRAF6 and recognition by the cargo receptor p62/SQSTM1. The combination of the proteasome inhibitor carfilzomib and Mcl1 AUTAC synergistically promoted cell death in both in vitro models, including wild-type and proteasome inhibitor-resistant multiple myeloma and lung cancer cells, and in mouse tumor xenografts. Thus, our work offers a novel strategy for enhancing proteasome inhibitor efficacy by exploiting the adaptive autophagy response. More broadly, our study establishes a framework for amplifying lysosome-mediated targeted protein degradation, with potential applications in cancer therapeutics and beyond.
    DOI:  https://doi.org/10.1038/s41419-026-08835-6
  11. Nat Commun. 2026 May 13. pii: 4335. [Epub ahead of print]17(1):
    TBK1 restricts IRGQ-mediated autophagy.
    Uxia Gestal-Mato, Pauline Lascaux, Sergio Alejandro Poveda-Cuevas, Alberto Cristiani, Belinda Camp, Mahyar Aghapour, Aparna Viswanathan Ammanath, Ramachandra M Bhaskara, Ivan Dikic, Lina Herhaus.
      The autophagy-lysosome system directs the degradation of a wide variety of cytoplasmic cargo such as damaged organelles, protein aggregates, and invading pathogens. The autophagy receptor IRGQ harbors two distinct LIR domains, with LIR1 exhibiting high selectivity for GABARAPL2. Proteomic, biochemical, and high-throughput microscopy studies reveal that the IRGQ-GABARAPL2 complex functions as a hub for the interaction between hATG8s and the autophagy initiation machinery, promoting their lipidation and overall autophagic flux. The interaction of IRGQ with GABARAPL2 is regulated via TBK1. Upon TBK1 activation, GABARAPL2 is phosphorylated on S10, which disrupts IRGQ-GABARAPL2 complexation and therefore its interaction with the autophagy initiation machinery, resulting in a reduction of the autophagic flux of GABARAPL2 and IRGQ-cargo, without affecting bulk autophagy. These findings broaden IRGQ's role in autophagy, identifying it as an interaction hub for autophagy initiation that is negatively regulated by TBK1.
    DOI:  https://doi.org/10.1038/s41467-026-73005-3
  12. Brief Bioinform. 2026 May 04. pii: bbag228. [Epub ahead of print]27(3):
    SE(3)-PROTACs: Geometric deep learning for PROTAC degradation prediction.
    Akash Reddy Kothakapu, Sharanya Madugula, Saketh Bharadwaj Sharma Gandeed, Kavya Sri Sai Yadlapati, Sharanya Sury, Vani Kondaparthi.
      Proteolysis-targeting chimeras (PROTACs) are a valuable therapeutic method for degrading target proteins of interest. Their success depends on forming a stable ternary complex composed of PROTAC, the target protein, and the E3 ligase-a relationship that is inherently difficult to predict. Existing deep learning methods often fail to accurately model the 3D arrangement of this ternary structure or overlook the critical background information provided by sequences, which is essential for accurate degradation predictions. Herein, we introduce SE(3)-PROTACs, a PROTAC degradation prediction model designed specifically using a geometric deep learning architecture. An SE(3)-equivariant transformer encodes PROTAC substructures-the warhead, linker, and E3 ligand-as molecular graphs invariant to translation and rotation while retaining geometrical features relevant to chemistry. Pretrained evolutionary scale modeling (ESM) embeddings provide functional and structural context to target proteins and E3 ligases directly from sequences, thus bypassing the limitations inherent in incomplete structural data. A Pairwise Interaction Mechanism computes all-pairs compatibility scores between target and E3 ligase residue positions conditioned on the PROTAC scaffold, using mean-pooled sigmoid weighting to reweight each protein representation before classification. A benchmark dataset of 1979 curated PROTAC samples sourced from PROTAC-DB was used for model development and evaluation. SE(3)-PROTACs achieved a test accuracy of 80.81% on a held-out random-split test set, with consistent performance across the cluster-split (65.62%) and temporal-split (64.08%) evaluations. SE(3)-PROTACs outperform baseline models across random, cluster-based, and temporal evaluations, demonstrating strong generalization to new targets and compounds, and serving as a reliable computational pre-filter for prioritizing candidate degraders before experimental validation.
    Keywords:  evolutionary scale modeling; geometric deep learning; pairwise interaction mechanism; protein language model; proteolysis-targeting chimera; special Euclidean group 3 transformer; targeted protein degradation
    DOI:  https://doi.org/10.1093/bib/bbag228
  13. Biochem J. 2026 May 11. pii: BCJ20260213. [Epub ahead of print]
    Photocrosslinking Activity-Based Probes to Capture the Dynamics of Ubiquitin RING E3 Ligase Interactions.
    Sarah F Chandler, Michael H Tatham, Emma Branigan, Mark A Nakasone, Nikolai Makukhin, Alessio Ciulli, Ronald T Hay.
      Almost all cellular processes are influenced by ubiquitination. A large family of enzymes known as E3 ligases provide the specificity for ubiquitination, with the largest class among them, the RING E3s, comprising over 600 members in humans. RING E3s facilitate transfer of ubiquitin (Ub) to substrates by constraining the highly dynamic E2-Ub thioester linkage to be primed for attack from the substrate nucleophile. We have established a workflow that uses an N-Maleimido Diazirine (NMD) photoactivatable crosslinker attached to ubiquitin, that once stably linked to the active site of an E2, creates an activity-based probe (ABP) to monitor interactions with E3 ligases. Crosslinking mass spectrometry using the NMD-Ub-E2 ABP identified regions of interaction between ubiquitin and a selection of different RING E3s, which not only agreed with existing crystal structures, but was also used to evaluate in silico structural models of complexes yet to be resolved by conventional means. The crosslinking data also provided insight into domains of conformational flexibility which likely adopt multiple configurations in solution and which are challenging to monitor by other methods. NMD-Ub-E2 ABPs offer great potential to explore the ensemble conformations of E2-E3 complexes in solution and have scope for applications beyond the ubiquitin system.
    Keywords:  Activity-based Probes; Structural Proteomics; Ubiquitin; cross-linking mass spectrometry; ubiquitin ligases
    DOI:  https://doi.org/10.1042/BCJ20260213
  14. Protein Sci. 2026 Jun;35(6): e70617
    Robust and interpretable machine learning for affinity prioritization of designed protein interactors.
    Yu-Chen Lo, Keng-Fu Chang, I-Hsuan Chu, Lu-Yi Chen, Kuen-Phon Wu.
      Recent advances in computational protein design have resulted in a large pool of de novo interactors that necessitate efficient and robust tools for candidate prioritization. Here, we introduce Proffinity, a one-stop computational workflow employing explainable machine learning (ML) for prioritizing high-affinity binders for protein design. Proffinity integrates knowledge-based contact potential and ML to extrapolate detailed residue-level interactions from protein structures. Trained on the structural mutants and de novo protein interactors, our model achieves robust performance for binding affinity estimation compared to the experimental ground truth. Application of the Proffinity workflow in the design of the ubiquitin variant raised for Rsp5 E3 ligase successfully identified tight binders with potent binding affinity. Our tool offers a timely, cost-effective approach to rapidly identifying high-affinity binders from large candidate pools, thus facilitating state-of-the-art protein design (https://github.com/yuchen-lo/Proffinity).
    Keywords:  E3 ubiquitin ligase; machine learning; protein design
    DOI:  https://doi.org/10.1002/pro.70617
  15. STAR Protoc. 2026 May 11. pii: S2666-1667(26)00216-9. [Epub ahead of print]7(2): 104563
    Protocol for the biochemical isolation of endosomal membranes associated with endoplasmic reticulum in HeLa cells.
    Juliane Da Graça, Etienne Morel.
      Endosome-endoplasmic reticulum contact sites (EERCS) are highly dynamic membrane interfaces that regulate trafficking and signaling, yet biochemical approaches to isolate them remain nonexistent, unlike established protocols for other types of contacts. Here, we present a protocol to isolate and purify endosomal membranes associated with endoplasmic reticulum membranes from cultured mammalian cells using subcellular fractionation and a two-step density-gradient centrifugation. We describe steps for cell expansion, post-nuclear supernatant collection, and the isolation of light membranes and EERCS. For complete details on the use and execution of this protocol, please refer to Da Graça et al.1.
    Keywords:  Cell Biology; Cell Membrane; Cell separation/fractionation
    DOI:  https://doi.org/10.1016/j.xpro.2026.104563
  16. J Physiol Biochem. 2026 May 11. pii: 50. [Epub ahead of print]82(1):
    Exercise-induced modulation of the unfolded protein response: a therapeutic avenue for muscle wasting disorders.
    Ao Ke, Zhuo Jinyuan, Lijuan Xiang, Zhanguo Su.
      Muscle wasting, prevalent in various pathological conditions including cancer, cardiac dysfunction, and neurodegeneration, is typified by sustained protein depletion in muscle and a compromised ability of the tissue to repair and regenerate effectively. Triggered by disruptions in protein folding in the endoplasmic reticulum (ER), the unfolded protein response (UPR) represents a key regulatory system that sustains intracellular proteostasis under conditions of stress. While the UPR is crucial for cellular survival, prolonged activation or dysfunction of the pathway can contribute to muscle atrophy and the progression of muscle wasting diseases. Recent evidence suggests that exercise, through its impact on cellular stress responses, can modulate the UPR in muscle cells, promoting a protective response that enhances protein folding capacity, reduces ER stress, and stimulates muscle regeneration. This review explores how exercise influences the UPR in muscle cells, focusing on the activation of key UPR sensors, including IRE1, PERK, and ATF6, and their downstream effects on protein quality control, autophagy, and muscle fiber maintenance. We also examine the role of exercise in promoting adaptive responses in muscle cells, including increased mitochondrial function, autophagy, and the activation of stress resistance pathways, all of which can counteract muscle wasting. The review also emphasizes exercise as an effective strategy to influence ER stress pathways and attenuate muscle atrophy associated with pathological conditions, offering critical insights into the molecular benefits of physical activity for muscle preservation.
    Keywords:  Autophagy; Endoplasmic reticulum stress; Exercise; Muscle wasting; Unfolded protein response
    DOI:  https://doi.org/10.1007/s13105-026-01190-2
  17. Chem Rev. 2026 May 14.
    Methods to Study the Molecular Mechanism and Drive the Design of Protein Degraders.
    Charlotte Crowe, Alessio Ciulli.
      Small-molecule degraders eliminate disease-driving proteins by hijacking the ubiquitin-proteasome system. To achieve cellular activity, protein degraders must perform a series of consecutive steps involving cell permeability, binary target engagement, and formation of a ternary complex with the target protein and a ubiquitin E3 ligase, followed by protein ubiquitination, culminating with protein degradation. Monitoring each mechanistic step of a degraders' mode of action is important to confirm its bona fide cellular activity and guide rational design and optimization. In this review, we offer an overview of how degraders work and outline the key parameters and associated methods to study each step of the mechanism. We compare and contrast biophysical and cellular in vitro assays and provide a concise framework for prioritizing and mapping them to decision stages. We also discuss the main factors affecting degrader's cellular performance and principles that have emerged to guide drug design.
    DOI:  https://doi.org/10.1021/acs.chemrev.5c00800
  18. Genes Dev. 2026 May 15.
    Evolutionarily conserved spliceosome-exosome pathway in nuclear mRNA surveillance.
    Daniel K Abbas, Fabien Bonneau, Max E Wilkinson, Steffen Schüssler, Jérôme Basquin, Elena Conti.
      Intron-containing mRNAs are cotranscriptionally spliced and assembled into messenger ribonucleoprotein (mRNP) particles, a process monitored by surveillance pathways. Here, we combined biochemical and structural approaches to elucidate the mechanisms by which mRNPs are sorted between two opposing fates: nuclear degradation and cytoplasmic export. While the human GANP-PCID2 complex is known to connect mRNPs to nuclear export, our data indicate that the LENG8-PCID2 complex operates as an mRNP decay connector, coupling nuclear mRNPs to the RNA-degrading exosome via the PAXT adaptor complex. Both recognize the mRNP component UAP56, but LENG8-PCID2 uniquely associates with early splicing factors through a direct interaction with U1A and RRP1B. Similarly, the Thp3-Csn12 ortholog in budding yeast couples the early splicing factors Mud2-Bbp with the nuclear exosome. The spliceosome-exosome mRNP decay pathway we uncovered reveals molecular principles that remain strikingly conserved across evolution, despite the fundamental differences in splicing and decay between humans and budding yeast.
    Keywords:  BioID; RRP1B; TREX-2; UAP56; cryo-EM; exosome-mediated decay; mRNA export; missplicing; quality control
    DOI:  https://doi.org/10.1101/gad.353594.125
  19. Neuro Oncol. 2026 May 09. pii: noag105. [Epub ahead of print]
    ClpP Activation in High-Risk Medulloblastoma: ONC206 as a Potent Inducer of the Integrated Stress Response and Mitochondrial Damage for a Broader Therapeutic Window.
    Peter Hau.
      
    DOI:  https://doi.org/10.1093/neuonc/noag105
  20. Commun Biol. 2026 May 15.
    Atg7-Atg12 conjugation and autophagy are negatively regulated by the disordered region of Atg12.
    Hana Popelka, Daniel J Klionsky.
      The macroautophagy/autophagy machinery has two ubiquitin-like (UBL) conjugation systems. The Atg8/MAP1LC3/GABARAP (yeast/human) and Atg12/ATG12 proteins are UBL substrates for Atg7/ATG7, a non-canonical E1 enzyme, that thioesterifies its substrates; however, autophagy requires a much greater amount of conjugated Atg8 (Atg8-PE) than Atg12 (Atg12-Atg5). Exactly how Atg7/ATG7 distinguishes between its two substrates to facilitate this differential biogenesis remains elusive. Here, analyses of recombinant complexes of yeast proteins reveal that the N termini of Atg8 and Atg12 are structural determinants for conjugation to Atg7, but play no role in conjugation to Atg3 or Atg10, non-canonical E2 enzymes. The disordered N terminus of Atg12 is a protector of the Atg12 C terminus and a negative regulator of Atg7-Atg12 conjugation and autophagy, whereas the N-terminal helical domain in Atg8 promotes autophagy and has a high avidity to Atg7. We show that balanced autophagy requires different specific N termini attached to the UBL domains, which are structural determinants for selective transfer to the native E2s. These findings deepen our understanding of the two autophagy UBL conjugation systems that is far from complete.
    DOI:  https://doi.org/10.1038/s42003-026-10269-x
  21. bioRxiv. 2026 Mar 01. pii: 2026.02.26.708310. [Epub ahead of print]
    The Spatiotemporal Proteome Landscape of Aging: Structural determinants of age-sensitive proteome remodeling.
    Seungmin Yoo, Lingraj Vannur, Liying Li, Christopher Young, Qingqing Liu, Zhihui T Wen, Ying Zhang, Laurence Florens, Kausik Si, Junming Zhuang, Fan Zheng, Chuankai Zhou.
      Aging is marked by a decline in cellular functions accompanied by widespread changes in mRNA and protein abundance, yet whether aging broadly remodels subcellular protein localization and concentration-and why some proteins change while others remain stable-remains unclear. This gap matters because cellular function depends not only on expression levels but also on correct spatial organization. Using yeast replicative aging as a model, we built a robotic pipeline to enrich old cells from 5,661 strains, acquired 90 million single-cell 3D images, and applied machine learning to map proteome-wide changes in localization, concentration, and aggregation throughout aging. This age-resolved single-cell atlas uncovers widespread proteome remodeling and rewiring of protein interaction networks. Moreover, structural analysis reveals biophysical determinants of age-sensitive proteome remodeling across ages and species. Together, these results reveal a structure-encoded intrinsic principle underlying spatial proteome breakdown during aging and provide a resource to dissect mechanistic links among aging hallmarks.
    DOI:  https://doi.org/10.64898/2026.02.26.708310
  22. J Biol Chem. 2026 May 13. pii: S0021-9258(26)02016-8. [Epub ahead of print] 113144
    Quantitative FRET FLIM imaging reveals multiple interactions between proteins of the ESYT, ORP and VAP families at the endoplasmic reticulum membrane.
    Dounia Zamiati, Mouna Abdesselem, Oliver Nüsse, Marie Erard.
      The endoplasmic reticulum (ER) is a highly dynamic intracellular organelle that forms close contact sites with other organelles and the plasma membrane. These membrane contact sites play essential roles in lipid exchange and calcium homeostasis. ER membrane proteins from the VAP, ORP, and ESYT families are key players in the formation and function of these contacts. Numerous interactions between these proteins are likely critical for their activity. We investigate the interactome between these protein families in live cells by analyzing two members from each family, using Förster Resonance Energy Transfer (FRET) between pairs of proteins labeled with fluorescent proteins (FP). FRET is detected by Fluorescence Lifetime Imaging Microscopy (FLIM). Our quantitative approach shows that all tested proteins clusterize and sometimes interact within their respective families, and that their organization at the nanometer scale can be disrupted by specific mutations or domain deletions. In particular, we show that the coiled-coil domains of ORP5 and ORP8 are required for the formation of both homomeric and heteromeric complexes. Moreover, we demonstrate that FRET-FLIM can detect intra-molecular conformational changes in response to alterations in the cellular environment, such as variations in Ca2+ concentration, as observed for ESYT1. We also identify novel inter-family organization, including clustering between VAPB and ORP8, and between ESYT2 and ORP5/8. Finally, our approach highlights the broad interaction network (interactome) of VAPA/B, and shows how various potential binding partners can influence FRET efficiency.
    Keywords:  Endoplasmic Reticulum; Extended Synaptotagmin; FRET FLIM microscopy; Membrane Contact Sites; Oxysterol-binding protein-Related Proteins; Vesicle-Associated membrane protein-associated Proteins; live-cell imaging; protein interactions
    DOI:  https://doi.org/10.1016/j.jbc.2026.113144
  23. Biomed Pharmacother. 2026 May 12. pii: S0753-3322(26)00540-8. [Epub ahead of print]199 119504
    Dysregulation of the ubiquitin-proteasome system in aging skeletal muscle.
    Gunju Song, Boo-Yong Lee, Kwang-Hyun Baek.
      Protein homeostasis (proteostasis) is essential for maintaining skeletal muscle integrity, and its disruption is a central feature of aging related sarcopenia. The ubiquitin-proteasome system (UPS) is the primary pathway responsible for selective protein degradation in muscle. However, its regulation during physiological aging remains incompletely understood. Most studies have focused on muscle-specific E3 ubiquitin ligases, particularly MuRF1 and MAFbx/atrogin-1, which are widely used as molecular markers of muscle atrophy. However, changes in E3 ligase expression do not consistently correspond to proteasome activity, suggesting a disconnect between ubiquitination signals and proteolytic capacity in aging muscle. In this review, we synthesize current evidence on age-related alterations in key components of the UPS, including proteasome activity, E3 ubiquitin ligases, and deubiquitinating enzymes (DUBs). We highlight that these components are differentially regulated across muscles and conditions. We further discuss DUBs as an additional regulatory layer that remains poorly understood in skeletal muscle aging. These findings emphasize the need to move beyond single-marker interpretations of UPS activity. Overall, current evidence indicates that aging skeletal muscle is characterized not by a simple increase in protein degradation, but by multi-layered dysregulation of proteostasis networks. A more integrated evaluation of UPS components will be required to better understand protein turnover in aging muscle.
    Keywords:  Deubiquitinating enzymes; E3 ubiquitin ligases; Muscle atrophy; Protein degradation; Proteostasis; Sarcopenia
    DOI:  https://doi.org/10.1016/j.biopha.2026.119504
  24. Bioessays. 2026 May;48(5): e70146
    Mitochondrial Signaling and Stress Responses, Key Regulators of Aging and Longevity.
    Yi Sheng, Zachary Markovich, Sung Min Han, Rui Xiao.
      Mitochondria are vital not only for energy production but also for regulating signaling pathways that influence aging. While mitochondrial dysfunction contributes to age-related decline, emerging evidence shows that mild, regulated mitochondrial stress can paradoxically promote longevity. This review highlights recent advances in mitochondrial biology and aging across species. We explore the dual role of reactive oxygen species (ROS) as both damaging agents and signaling molecules that activate adaptive stress responses. Key pathways such as the mitochondrial unfolded protein response (UPRMT) and integrated stress response (ISR) are discussed, including their tissue-specific as well as non-cell-autonomous effects on aging. Additionally, we examine the impact of mitochondrial protein import/export, dynamics (fission, fusion, mitophagy, biogenesis), and quality control in aging. Finally, we address challenges in understanding context-dependent mitochondrial responses and mitonuclear communication. Together, these insights position mitochondria as central regulators of aging and highlight their potential as therapeutic targets to enhance health span and longevity.
    Keywords:  aging; integrated stress response; mitochondria ROS; mitochondrial dynamics; mitochondrial unfolded protein response
    DOI:  https://doi.org/10.1002/bies.70146
  25. Biology (Basel). 2026 Apr 29. pii: 701. [Epub ahead of print]15(9):
    Beyond Free Virions: Interconnected Secretory Pathways and Reticulon 3 (RTN3) Coordinate Extracellular Vesicle Diversity for Infectious Exosome Generation.
    Razieh Bitazar, Clinton Njinju Asaba, Arnaldo Nakamura, Tatiana Noumi, Patrick Labonté, Terence Ndonyi Bukong.
      Extracellular vesicles (EVs) can disseminate replication-competent viral genomes complexed with selected host proteins, enabling stealth cell-to-cell transfer within lipid membrane-enclosed bubbles. In addition to complementing free-virion spread, EV-associated genomes can be protected from neutralizing antibodies and persist under conditions in which classical virion production decreases. Here, we propose a route-resolved framework in which interconnected cellular secretory pathways, including endoplasmic reticulum (ER) remodeling, multivesicular body (MVB) biogenesis, secretory autophagy, and plasma-membrane budding, jointly generate EV heterogeneity and create discrete opportunities for the capture, protection, and export of infectious cargo. We highlight reticulon-3 (RTN3), an ER-shaping protein, as an upstream regulator that can couple infection-induced ER microdomains to endosomal docking and to autophagy-linked trafficking decisions that bias intermediates toward secretion rather than degradation. Supporting this view, transmission electron microscopy of dengue virus-infected cells reveals extensive vesicular remodeling, including irregular MVBs adjacent to the plasma membrane and autophagosome-like double-membrane structures, consistent with altered vesicular routing following RTN3 perturbation. Collectively, these route-resolved, spatially organized spatio-organelle changes support a pathomechanistic model in which RTN3-mediated ER remodeling reshapes ER-endosome-autophagy trafficking interfaces, creating regulated decision points that can be leveraged to stratify infectious EV subsets (with infectivity-linked single-vesicle and quantitative proteomics approaches) and to inform host-directed strategies that curb non-lytic viral dissemination.
    Keywords:  dengue virus; endoplasmic reticulum contact sites; extracellular vesicles; host–pathogen interactions; infectious exosomes; multivesicular bodies; reticulon 3 (RTN3); secretory autophagy
    DOI:  https://doi.org/10.3390/biology15090701
  26. Nature. 2026 May 13.
    SNOR promotes translation restart after dormancy.
    Maciej Gluc, Higor Rosa, Maria Bozko, Lesley A Turner, Cassidy R Prince, Yelena Peskova, Heather A Feaga, Kathleen L Gould, Simone Mattei, Ahmad Jomaa.
      Cellular dormancy enables survival during prolonged nutrient limitation by reversibly suppressing protein synthesis1-4. How inactive eukaryotic ribosomes are reactivated when nutrients return remains unclear. Here, using high-resolution in situ cryo-electron tomography in Schizosaccharomyces pombe, we identify SNOR, an SBDS domain-containing ribosome-associated factor that binds at the peptidyl transferase centre and contacts the hypusinated loop of eIF5A during glucose depletion-induced dormancy. Rather than acting as a canonical hibernation factor, SNOR licenses dormant ribosomes for rapid translational restart. Upon glucose repletion, SNOR and eIF5A act together to promote efficient recovery of polysomes and exit from dormancy. These findings define a stress-responsive ribosome restart module that couples carbon-source limitation to surveillance of the ribosomal active site and reactivation of protein synthesis.
    DOI:  https://doi.org/10.1038/s41586-026-10530-7
  27. Proc Natl Acad Sci U S A. 2026 May 19. 123(20): e2529979123
    NEXT-FRET maps nonequilibrium rerouting of Escherichia coli maltose-binding protein folding by its signal peptide and chaperones.
    Chara Sarafoglou, Andreas Kofidis, Marijn de Boer, Mikis Mylonakis, Kostas Mavrakis, Giannis Zacharakis, Yannis Pantazis, Giorgos Gouridis.
      Proteins fold through dynamic intermediates that dictate their routes to functional structures, with ensembles predominantly displaying heterogeneity across nanosecond-to-microsecond timescales. Directly observing these states in solution remains challenging as single-molecule methods often require technically demanding microfluidics, surface attachment that alters behavior, or denaturants that distort natural energy landscapes. Here we introduce NEXT-FRET, a solution-based single-molecule platform combining single-molecule FRET (smFRET) with time-varying Gaussian mixture modeling to resolve how diffusing proteins populate and interconvert between conformations under near-native conditions. By incorporating prior equilibrium information into time-dependent analysis, NEXT-FRET requires a few molecules per condition and accessible instrumentation, enabling application in the presence of chaperones and aggregation-prone precursors. We apply NEXT-FRET to the Escherichia coli Maltose-Binding Protein (MBP) and pre-MBP to reveal a long-sought closed on-pathway intermediate that exchanges with both native and unfolded states. The signal peptide raises the barrier selectively for the intermediate-to-native transition. Profiling interactions with chaperones shows that each stabilizes nonnative conformations distinctively, generating kinetic traps. These findings demonstrate that sequence features and proteostasis factors actively reshape the folding landscape. By following molecules out of equilibrium, NEXT-FRET reveals intermediates invisible at equilibrium. This reflects the inherent nonequilibrium character of cells, which maintain order through ongoing energy exchange and dissipation, with fluctuations governing the kinetics and connectivity of biomolecular states. By exposing transient intermediates and quantifying kinetic flows, NEXT-FRET offers a scalable strategy to interrogate nonequilibrium dynamics, providing mechanistic insights into protein (mis)folding, enzyme catalysis, ligand binding and broader biomolecular reactions with implications for biotechnology and therapeutics.
    Keywords:  chaperones; molecular biophysics; protein folding; single-molecule FRET; statistical analysis
    DOI:  https://doi.org/10.1073/pnas.2529979123
  28. Drug Dev Res. 2026 May;87(3): e70301
    Nanoplatform-Based Delivery Systems for PROTACs.
    Wenbo Che, Xinlin Wang, Sijin Chen, Mao Du, Wenyu Wang, Dan Liu, Shuai Fan, Zundao Wu, Yi Wu, Yanbo Dong, Qin Xia.
      Proteolysis Targeting Chimera (PROTAC) is a bifunctional small molecule composed of a ligand for the target protein, a ligand for an E3 ubiquitin ligase, and a chemical linker. It induces the formation of a ternary complex between the target protein and the E3 ligase, thereby promoting ubiquitination and subsequent proteasomal degradation of the target. As an emerging targeted protein degradation (TPD) strategy, PROTACs offer notable advantages such as rapid action, sustained efficacy, and high selectivity. However, PROTACs encounter significant challenges in in vivo delivery due to their unfavorable physicochemical properties, including high molecular weight, limited membrane permeability, and poor plasma stability. In recent years, the development of nanodelivery platforms has emerged as a promising strategy to overcome these limitations, significantly enhancing the bioavailability and therapeutic efficiency of PROTACs while accelerating their clinical translation and application.
    Keywords:  E3 ubiquitin ligase; PROTACs; TPD; nanodelivery systems; stimuli‐responsive nanoplatforms
    DOI:  https://doi.org/10.1002/ddr.70301
  29. Cell. 2026 May 12. pii: S0092-8674(26)00463-0. [Epub ahead of print]
    D-SPIN constructs regulatory network models from scRNA-seq that reveal organizing principles of perturbation response.
    Jialong Jiang, Sisi Chen, Tiffany Tsou, Christopher S McGinnis, Tahmineh Khazaei, Qin Zhu, Jong H Park, Inna-Marie Strazhnik, Jost Vielmetter, Yingying Gong, John Hanna, Eric D Chow, David A Sivak, Zev J Gartner, Matt Thomson.
      Gene regulatory networks modulate the expression of the genome in response to signals and environmental conditions. Reconstructions of such networks can reveal the control principles cells use to maintain homeostasis and execute cell-state transitions. Here, we introduce a computational framework, dimension-scalable single-cell perturbation integration network (D-SPIN), that infers mechanistically interpretable and generative models of gene regulatory networks from single-cell mRNA-seq datasets collected across thousands of perturbation conditions. The models explain how perturbations modulate cell-state proportions by reconfiguring underlying regulatory interactions. Using large Perturb-seq and drug response datasets, D-SPIN models reveal key regulators of cell fate decisions and the coordination of distant cellular pathways in response to gene knockdowns and drug treatments, elucidate how combinations of immunomodulatory drugs induce combinatorial cell states through additive recruitment of gene expression programs, and simulate shifts in immune cell population structures across unobserved drug dosage combinations. D-SPIN provides a computational framework for revealing principles of cellular information processing and physiological control.
    Keywords:  D-SPIN; Perturb-seq; cell-state transition; drug combination; gene regulatory network; immunomodulatory drug; perturbation response; probabilistic graphical model; regulatory network inference; single-cell RNA sequencing
    DOI:  https://doi.org/10.1016/j.cell.2026.04.028
  30. Chimia (Aarau). 2026 Apr 29. 80(4): 222-225
    Properties of Stereopure Phosphorothioate Groups in RNA-PROTACs.
    Mathilde Vincent, Jonathan Hall.
      Proteolysis-targeting chimeras (PROTACs) are an emerging therapeutic modality that enable the degradation of target proteins via the endogenous ubiquitin-proteasome pathway. We are applying this concept to the degradation of RNA-binding proteins (RBPs), which often lack drug-like binding pockets for small molecules. When targeting RBPs with RNA-PROTACs, the targeting ligand consists of short, chemically modified oligoribonucleotides that are iso-sequential with endogenous RNA consensus sequences. Specifically, we are investigating the phosphorothioate (PS) backbone, in which a sulfur atom replaces a non-bridging oxygen in the RNA phosphodiester linkage. PS modifications enhance stability against nucleases, but introduce chirality at the phosphorus atom, when introduced using conventional synthesis reagents, generating diastereoisomers whose stereochemistry can significantly enhance RNA-protein interactions.
    Keywords:  Oligonucleotides; PROTACs; Phosphorothioate; RNA-binding proteins; Stereochemistry
    DOI:  https://doi.org/10.2533/chimia.2026.222
  31. Mitochondrion. 2026 May 12. pii: S1567-7249(26)00057-7. [Epub ahead of print]90 102167
    Distinct mitochondrial-derived vesicle pathways connect mitochondria with peroxisomes and lysosomes.
    Ayumu Sugiura, Kohta Nakamura, Heidi M McBride, Yasushi Okazaki.
      Mitochondrial-derived vesicles (MDVs) mediate selective trafficking of mitochondrial proteins and lipids to other organelles and contribute to organelle communication and mitochondrial quality control. While MDVs that deliver mitochondrial cargo to lysosomes have been extensively studied, the diversity of MDV pathways linking mitochondria to peroxisomes remains poorly understood. In particular, it is unclear how MDV pathways targeting peroxisomes relate to those delivering cargo to lysosomes, and whether cargos targeted to pre-existing peroxisomes utilize the same vesicular intermediates that participate in de novo peroxisome biogenesis. Here we examined MAPL trafficking using a peroxisome reconstitution system in PEX3-deficient fibroblasts. We found that MAPL is excluded from PEX3-positive pre-peroxisomal vesicles and instead is delivered to pre-existing peroxisomes, indicating that MAPL trafficking occurs through a pathway distinct from vesicles that initiate peroxisome formation. Structure-function analysis further revealed that a C-terminal amphipathic helix within MAPL is required for efficient targeting to peroxisomes. SNX9 depletion impaired both MAPL delivery to pre-existing peroxisomes and stress-induced lysosomal MDV pathways, whereas VPS35 depletion selectively reduced MAPL delivery without affecting lysosomal MDV pathways. In contrast, Parkin depletion impaired lysosomal MDV pathways but did not influence MAPL trafficking. Together, these findings demonstrate that mitochondria generate multiple classes of MDVs that are sorted into mechanistically distinct trafficking routes linking mitochondria with peroxisomes and lysosomes.
    Keywords:  Lysosomes; Mitochondria; Mitochondrial-derived vesicles; Peroxisomes
    DOI:  https://doi.org/10.1016/j.mito.2026.102167
  32. Bioorg Chem. 2026 May 06. pii: S0045-2068(26)00489-X. [Epub ahead of print]178 109953
    l-NBDNJ allosteric chaperone for multiple defective enzymes involved in lysosomal storage disorders (LSDs).
    Anna Esposito, Maria Stabile, Eliana De Gregorio, Alejandro Montesa, Uta Kanekiyo, Kosuke Yoshimura, Pedro Merino, Atsushi Kato, Annalisa Guaragna.
      Protein misfolding underlies a wide range of conformational diseases, including lysosomal storage disorders (LSDs) such as Gaucher, Pompe, and Fabry diseases. Pharmacological chaperones (PCs) have emerged as promising small molecules capable of rescuing mutant enzymes from endoplasmic reticulum (ER)-associated degradation by stabilizing their correct folding. While first-generation PCs act as competitive inhibitors at the active site, their therapeutic window is narrow due to concomitant enzyme inhibition. Second-generation PCs, or allosteric chaperones, aim to stabilize mutant enzymes without interfering with catalysis. In this study, the unnatural iminosugar l-NBDNJ (l-N-butyldeoxynojirimycin), enantiomer of the drug Miglustat, was synthesized and assessed for its ability to act as a non-inhibitory chaperone. Enzyme inhibition assays demonstrated no activity against a broad glycosidase panel, supporting its potential as an allosteric ligand. In vitro assays on patient-derived fibroblasts showed that l-NBDNJ alone failed to restore activity of GCase, GAA, or α-Gal A mutants. However, co-administration with active-site chaperones (Isofagomine, DNJ, or DGJ) yielded synergistic improvements, increasing residual enzyme activities by 16-30%. In silico docking and molecular dynamics confirmed stable binding at predicted allosteric sites, forming tertiary complexes with active-site chaperones and enhancing binding energies. Collectively, these findings identify l-NBDNJ as a second-generation allosteric enhancer of active-site chaperones, able to potentiate their efficacy across multiple LSDs.
    Keywords:  Allosteric chaperones; Iminosugars; Miglustat; Rare diseases; l-N-butyldeoxynojirimycin
    DOI:  https://doi.org/10.1016/j.bioorg.2026.109953
  33. Chembiochem. 2026 May 14. 27(9): e70362
    Impact of Two Small-Molecule Proteasome Stimulators on Cellular Growth and Metabolism.
    Kate A Kragness, Darci J Trader.
      The proteasome degrades ubiquitinated proteins as well as intrinsically disordered proteins that can be processed independently of ubiquitin signaling. The 20S core particle (CP) plays a key role in the degradation of unstructured proteins. Small molecules have been developed to enhance the degradation activity of the 20S CP; however, concerns remain that increasing 20S CP activity may promote cellular dysfunction or toxicity by altering cell proliferation or metabolic regulation. Here, we investigated the effects of two 20S CP stimulators on cell proliferation and on the expression of genes associated with growth and metabolism. Neither stimulator altered proliferation rates in any cell line examined nor did they significantly change growth-associated gene expression in younger cell passages. In contrast, in older cell passages where overall proteasome activity is known to be altered, 20S CP stimulation resulted in measurable changes in gene expression without affecting proliferation. Together, these findings demonstrate that 20S CP stimulation does not inherently drive increased cell proliferation and challenge the prevailing assumption that enhanced 20S CP activity promotes uncontrolled cellular growth.
    Keywords:  growth; proteasome; small molecule; stimulator
    DOI:  https://doi.org/10.1002/cbic.70362
  34. Mol Cell. 2026 May 12. pii: S1097-2765(26)00270-4. [Epub ahead of print]
    S-acylation of TDP43 regulates its condensation in amyotrophic lateral sclerosis.
    Wentao Xu, Huina Li, Wei Zhang, Ge Bai, Chengyong Shen, Kejing Zhang.
      TDP43 inclusion bodies are widely present in the majority of patients with familial and sporadic amyotrophic lateral sclerosis (ALS). The mechanisms regulating TDP43 solubility remain incompletely understood. Here, we report that TDP43 undergoes S-acylation primarily at the Cys244 residue by the S-acyltransferase zDHHC23. This S-acylation maintains the liquid-like properties of TDP43 by reducing the aberrant interaction with poly(ADP-ribose) polymerase 1 (PARP1) and PARylated proteins, thereby countering the pathological condensation of TDP43. S-acylation-deficient TDP43 inclusions sequester the translational machinery and inhibit cytoplasmic protein translation, ultimately resulting in neurotoxicity. Importantly, TDP43 S-acylation is decreased in the familial ALS-associated TDP43 mutants as well as in SOD1-G93A mice and C9orf72-ALS induced pluripotent stem cell (iPSC)-derived neurons, suggesting the widespread involvement of TDP43 S-acylation in ALS pathogenesis. Our findings reveal an undescribed modification of TDP43 and provide deeper insight into the regulation of TDP43 pathological condensation in ALS.
    Keywords:  S-acylation; TDP43; aggregation; amyotrophic lateral sclerosis; condensation
    DOI:  https://doi.org/10.1016/j.molcel.2026.04.016
  35. Sci Adv. 2026 May 15. 12(20): eadz3835
    mTOR-NAA10-C7orf50 axis senses nutritional status to coordinate ribosome biogenesis and autophagy.
    Jingyu Sun, Mei Yang, Qian Li, Jiawei Liang, Haiping Feng, Lijie Gao, Yun Wang, Hongmei Liu, Caixia Guo, Tie-Shan Tang.
      Cellular metabolism is precisely regulated in response to nutrient availability. As an extremely energy-consuming anabolic process, ribosome biogenesis should be tightly controlled in response to nutrient supply. However, how the nucleolus responds to different nutrient statuses remains poorly understood. Here, we show that C7orf50 is a nucleolus-localized protein and functions as a coordinator between ribosome biogenesis and autophagy, acting as what we term a "nutrient-responding nucleolar factor." C7orf50 undergoes reversible nucleolus-nucleoplasm translocation in response to nutrient deprivation and supply, with its nucleolus and nucleoplasm location dictating ribosome biogenesis and autophagic augmentation, respectively. The location-dependent function of C7orf50 is determined by acetylation at the lysine-71/lysine-72/lysine-76 residues by N-alpha-acetyltransferase 10, a substrate of mammalian target of rapamycin and a nutritional status-responsive acetyltransferase. In vivo and in vitro assays show that C7orf50 acts as an oncoprotein that promotes tumor growth. Our findings reveal a nucleolus-localized coordinating mechanism for the regulation of anabolism and catabolism transition by nutrient status.
    DOI:  https://doi.org/10.1126/sciadv.adz3835
  36. Nature. 2026 May 13.
    Large-scale discovery, analysis and design of protein energy landscapes.
    Állan J R Ferrari, Sugyan M Dixit, Jane Thibeault, Mario Garcia, Scott Houliston, Robert W Ludwig, Pascal Notin, Claire M Phoumyvong, Cydney M Martell, Michelle D Jung, Kotaro Tsuboyama, Lauren Carter, Cheryl H Arrowsmith, Miklos Guttman, Gabriel J Rocklin.
      All folded proteins continuously fluctuate between their low-energy native structures and higher-energy conformations that can be partially or fully unfolded. These rare states influence protein function1,2, interactions3, aggregation4-7 and immunogenicity8,9, yet they remain far less understood than protein native states. Although native protein structures are now often predictable with impressive accuracy, conformational fluctuations and their energies remain largely invisible10 and unpredictable11-14, and experimental challenges have prevented large-scale measurements that could improve machine learning and physics-based modelling. Here we introduce a multiplexed experimental approach to analyse the energies of conformational fluctuations for hundreds of protein domains in parallel using intact protein hydrogen-deuterium exchange mass spectrometry. We analysed 5,778 domains 28-64 amino acids in length, revealing hidden variation in conformational fluctuations, even between sequences sharing the same fold and global folding stability. Site-resolved hydrogen exchange nuclear magnetic resonance analysis of 13 domains showed that these fluctuations often involve entire secondary structural elements with lower stability than the overall fold. Computational modelling of our domains identified structural features that correlated with the experimentally observed fluctuations, enabling us to design mutations that stabilized low-stability structural segments. Our dataset enables new machine-learning-based analysis of protein energy landscapes, and our experimental approach promises to profile these landscapes at considerable scale.
    DOI:  https://doi.org/10.1038/s41586-026-10465-z
  37. FASEB J. 2026 May 31. 40(10): e71812
    Atf4a Regulates Mitochondrial Homeostasis Through Parkin-Mediated Mitophagy to Enhance Hypoxia Tolerance in Zebrafish (Danio rerio).
    Ranran Zhao, Jican Zhao, Weiyi Xia, Wanjuan Yu, Huihui Zhou, Xuan Wang, Kansen Mai, Gen He, Chengdong Liu.
      The Integrated Stress Response (ISR) is a vital cellular mechanism that regulates cell survival during various stress conditions, including hypoxia. Activating transcription factor 4 (ATF4) is recognized as a key regulator of ISR, however, its role in hypoxic stress responses remain underexplored. In the present study, we generated an Atf4a-deficient zebrafish model to investigate the role of Atf4a in hypoxia tolerance, mitochondrial homeostasis, and cellular stress adaptation. The results showed that atf4a knockout led to significant growth impairment, endoplasmic reticulum and mitochondrial dysfunction, and disrupted energy metabolism, particularly under hypoxic conditions. We observed an increase in mitochondrial DNA and impaired mitochondrial morphology in Atf4a-deficient zebrafish. Metabolomic analysis revealed significant alterations in the pentose phosphate pathway and TCA cycle following atf4a knockout. Additionally, we observed increased mitochondrial oxidative stress and reduced antioxidant capacity in atf4a mutants. Atf4a-deficiency also led to decreased expression of the mitophagy-related gene p62 and parkin. Atf4a transcriptionally regulates the expression of parkin, suggesting that Atf4a regulates mitochondrial homeostasis through parkin-mediated mitophagy in zebrafish. These results underscore the critical role of Atf4a in maintaining cellular homeostasis, mitochondrial integrity, and metabolic adaptation during hypoxic stress, highlighting its potential as a therapeutic target for stress-related diseases.
    Keywords:  ATF4; ISR; hypoxia; mitophagy; parkin
    DOI:  https://doi.org/10.1096/fj.202502855R
  38. Virology. 2026 May 08. pii: S0042-6822(26)00162-5. [Epub ahead of print]621 110947
    Making ends meet: Specialized translation of viral mRNAs lacking canonical features.
    Xayathed Somoulay, Gwen M Taylor, Terence S Dermody.
      Translation initiation in eukaryotic cells is usually driven by recognition of a 5' cap and a 3' poly(A) tail, which cooperate through interactions with eukaryotic initiation factors (eIFs) and poly(A)-binding protein (PABP) to promote mRNA circularization and efficient ribosome recruitment. However, many viral RNAs lack one or both of these canonical features and must use alternative strategies to access the host translational machinery. Diverse mechanisms are used to bypass cap dependence, including internal ribosome entry sites that recruit ribosomal subunits with variable requirements for canonical initiation factors as well as viral protein genome-linked strategies that functionally substitute for the cap by engaging components of the eIF4F complex. For viral mRNAs lacking poly(A) tails, translation can be supported by long-range RNA-RNA interactions that mediate 5'-3' communication and viral or host proteins that replace PABP to facilitate closed-loop formation. Emerging examples, including host protein ATXN2L during reovirus infection, illustrate how viruses use or mimic cellular factors to promote selective translation. Collectively, these strategies reveal fundamental principles of mRNA circularization and translational control, highlighting the dynamic interplay between viral and host machinery in regulating protein synthesis.
    Keywords:  ATXN2L; Cap-independent translation; Internal ribosome entry site (IRES); Nonpolyadenylated mRNA; Translation initiation; Viral protein genome-linked (VPg); mRNA circularization
    DOI:  https://doi.org/10.1016/j.virol.2026.110947
  39. Mol Cell. 2026 May 12. pii: S1097-2765(26)00269-8. [Epub ahead of print]
    High-throughput screening approach identifies substrate-selective Hsp104 variants that counter amyloid seeding with diminished off-target effects.
    Jeremy J Ryan, Karlie R Miller, Anuradhika Puri, Macy L Sprunger, Madalyn M Bochantine, April Lopez, Sheng Chen, Aaron Bao, Cendi Ling, Andy Xu, Braxton Bell, Brian S Sohn, Leo Li, Cynthia Chang, Kalid Mohammed, Max V Staller, Meredith E Jackrel.
      Hsp104, a yeast protein-remodeling factor, can disaggregate misfolded proteins implicated in neurodegeneration. Although many potentiated Hsp104 variants have been generated, suboptimal properties have limited their application in mammalian systems. Here, we present the development of a high-throughput screening approach for identifying enhanced Hsp104 variants. To screen a large library of variants in parallel and with a quantitative output, we coupled a live-or-die yeast-based selection with next-generation sequencing. The identified Hsp104 variants solubilize preformed α-synuclein and TDP-43 aggregates, inhibit seeding of preformed α-synuclein fibrils in mammalian biosensor cells, restore TDP-43 splicing of native targets, and have diminished off-target toxicity in mammalian cells. Certain variants show distinct changes in ATP hydrolysis, which we suggest is the key driver of these improved properties. We anticipate that our approach is broadly applicable to a range of protein engineering targets to allow coupling of a phenotypic readout to high-throughput quantitative analysis of variants in parallel.
    Keywords:  Hsp104; TDP-43; aggregate; amyloid; chaperone; deep-mutational scanning; disaggregase; protein engineering; ∝-synuclein
    DOI:  https://doi.org/10.1016/j.molcel.2026.04.015
  40. Adv Sci (Weinh). 2026 May 15. e75658
    A Plug-and-Play Platform for Customizing Multivalent Degraders and Degrader-Drug Conjugates.
    Mengqing Zhao, Yan Deng, Jianjian Han, Yong Xie, Kai Bao, Lixin Ma, Lilong Liu, Wuxiang Mao.
      Traditional targeted protein degradation (TPD) strategies are largely ineffective against membrane proteins, which constitute over 60% of drug targets. To address this, we develop a modular "plug-and-play" UPTAB (Ultrahigh-affinity Protein pairs fused to Targeting Binders) platform for TPD. The platform leverages orthogonal ultrahigh-affinity Im/CL protein pairs to assemble complexes between lysosomal trafficking receptor (LTR)-binding modules and protein of interest (POI)-binding modules. Three UPTAB configurations were engineered: Type-I (mono-targeted), Type-II (dual-targeted), and Type-III (tri-targeted). In vitro, Type-I UPTAB achieved near-complete degradation of EGFR and PD-L1 across multiple cancer cell lines, with optimal linker length critical for maximal activity. Type-II and Type-III UPTAB enabled simultaneous degradation of EGFR/c-MET, EGFR/PD-L1, and EGFR/c-MET/HER2. In a breast cancer xenograft model, Type-I UPTAB demonstrated approximately 80% tumor growth inhibition, reduced EGFR levels in tumors, and significantly extended survival. Furthermore, we developed degrader-drug conjugates (DDCs) by site-specific conjugation of the cytotoxic payload MMAE to UPTAB modules, which retained degradation capacity while exhibiting substantially enhanced anti-proliferative activity across diverse cancer cell lines. The UPTAB platform combines modular multivalent design, high degradation efficiency, and excellent bioconjugation capability, offering a versatile tool for membrane protein-targeted degradation and a potential strategy for developing next-generation cancer therapeutics.
    Keywords:  LYTAC; degrader‐drug conjugates; multivalency; plug‐and‐play; protein pairs
    DOI:  https://doi.org/10.1002/advs.75658
  41. Cancer Discov. 2026 May 15. OF1
    Approval of First PROTAC Opens New Era for Targeted Protein Degradation.
      The May 1 approval of vepdegestrant, the first PROTAC drug to earn regulatory clearance, establishes targeted protein degradation as a clinically validated therapeutic modality. For patients with ESR1-mutant advanced breast cancer, it offers a new therapeutic option after standard hormone-based regimens have failed. And for the broader field, it is proof of concept for a pipeline of protein-destroying drugs that now numbers in the dozens.
    DOI:  https://doi.org/10.1158/2159-8290.CD-NW2026-0054
  42. PLoS One. 2026 ;21(5): e0331823
    LAMP2A-dependent chaperone-mediated autophagy enhances oxidative stress resistance in gastric cancer cells through selective degradation of accumulated oxidized DJ-1.
    Shuangshuang Le, Tongtong Guo, Meng Yang, Tianjuan Tang, Zhijie Liu, Yang Zheng, Maogui Pang.
      Chaperone-mediated autophagy (CMA) promotes cancer cell survival by selectively removing oxidatively damaged proteins, yet its precise molecular mechanisms and role in redox adaptation remain incompletely understood. This study aimed to elucidate the function of CMA in regulating oxidative stress resistance in gastric cancer (GC) cells, focusing on the LAMP2A-DJ-1 regulatory axis. LAMP2A expression was assessed in GC tissues and cell lines via immunohistochemistry, qPCR, and western blot. Oxidative stress models were established using hydrogen peroxide (H₂O₂). Genetic manipulation of LAMP2A was performed to evaluate its impact on cell proliferation, apoptosis, and CMA substrate recognition. Protein interactions were examined by co-immunoprecipitation and immunofluorescence. We found that LAMP2A was upregulated in GC and further induced by oxidative stress. Knockdown of LAMP2A impaired CMA activity, sensitizing GC cells to H₂O₂-induced apoptosis. DJ-1, an antioxidant protein, was identified as a CMA substrate containing a conserved KFERQ-like motif. Oxidative stress enhanced DJ-1-LAMP2A interaction and promoted their lysosomal colocalization. LAMP2A deficiency led to accumulation of hyperoxidized DJ-1, concomitant with upregulation of pro-apoptotic BAX and downregulation of anti-apoptotic Bcl-2. We identify hyperoxidized DJ-1 as a novel CMA substrate and demonstrate that LAMP2A-dependent clearance of oxidized DJ-1 constitutes a key adaptive mechanism that maintains redox homeostasis and promotes survival in gastric cancer cells under oxidative stress.
    DOI:  https://doi.org/10.1371/journal.pone.0331823
  43. Cell Host Microbe. 2026 May 13. pii: S1931-3128(26)00171-X. [Epub ahead of print]
    Coronavirus protein interaction mapping in bat and human cells reveals network rewiring governing immune evasion and zoonotic potential.
    Jyoti Batra, Magdalena Rutkowska, Yuan Zhou, Chengjin Ye, Rithika Adavikolanu, Janet M Young, Durga Anand, Sooraj Verma, Haripriya Parthasarathy, Martin Gordon, Shivali Malpotra, Anastasija Cupic, Thomas Kehrer, Melanie Dos Santos, Ronald Benjamin, Jack M Moen, Declan M Winters, Vincent Caval, Ajda Rojc, Ignacio Mena, Sadaf Aslam, Carles Martinez-Romero, Isabela Conde Viñas, Zain Khalil, Keith Farrugia, Fernando Villalón-Letelier, Atoshi Banerjee, Dafna Tussia-Cohen, Amy Diallo, Sourobh Maji, Monita Muralidharan, Helene Foussard, Irene P Chen, Rotem Fuchs, C J San Felipe, Lorena Zuliani-Alvarez, Promisree Choudhury, Kirsten Obernier, Ségolène Gracias, Rahul K Suryawanshi, Boris Bonaventure, Carlos Ibáñez, Jeffrey R Johnson, Javier Juste, Lars Pache, Robert M Stroud, Kliment A Verba, James S Fraser, Harm van Bakel, Taha Y Taha, Melanie Ott, Tzachi Hagai, Nolwenn Jouvenet, Caroline Demeret, Benjamin J Polacco, Danielle L Swaney, Ignacia Echeverria, Mehdi Bouhaddou, Manon Eckhardt, Harmit S Malik, Luis Martinez-Sobrido, Lisa Miorin, Adolfo García-Sastre, Nevan J Krogan.
      Coronaviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), can cause severe disease in humans, whereas reservoir hosts such as horseshoe bats remain asymptomatic. To investigate how host-specific protein-protein interactions (PPIs) influence infection, we generated comparative PPI maps for SARS-CoV-2 and its bat progenitor RaTG13, using affinity purification mass spectrometry (AP-MS) in human and greater horseshoe bat cells. We identify both conserved and virus- and host-specific interactions that regulate infection dynamics. Notably, SARS-CoV-2 requires a nonsynonymous mutation in the nucleocapsid to replicate in bat cells expressing human ACE2 and TMPRSS2. Strikingly, a single amino acid difference in Orf9b between viruses acts as a molecular switch that reprograms mitochondrial targeting: in human cells, enhanced translocase of outer mitochondrial membrane 70 (Tom70) binding promotes immune evasion, whereas in bat cells, strengthened interaction with the bat-enriched restriction factor mitochondrial amidoxime reducing component 2 (MTARC2) limits infection. These findings establish a general principle by which minimal sequence variation can reshape virus-host interactions and contribute to immune antagonism, host adaptation, and species barriers.
    Keywords:  MTARC2; RaTG13; SARS-CoV-2; Tom70; bats; coronaviruses; host-pathogen interaction; proteomics; viral reservoirs; virus-host tropism
    DOI:  https://doi.org/10.1016/j.chom.2026.04.015
  44. Proc Natl Acad Sci U S A. 2026 May 19. 123(20): e2527503123
    Chaperone-mediated autophagy protects against retinal photoreceptor degeneration by modulating proteostasis of glucose metabolism enzymes.
    Raquel Gómez-Sintes, Inmaculada Tasset, Ignacio Ramírez-Pardo, Adrián Martín-Segura, Sandra Alonso-Gil, Antonio Díaz, Kristen Lindenau, Concepción Lillo, Pedro de la Villa, Simone Sidoli, Evripidis Gavathiotis, Ana María Cuervo, Patricia Boya.
      Defective proteostasis is a hallmark of aging cells and tissues. Among the different components of the proteostasis network, in this study, we focus on a selective form of autophagy known as chaperone-mediated autophagy (CMA), and we set out to understand its physiological role in the retina. Using mice deficient for CMA [knockout for lysosome-associated membrane protein type 2A (Lamp2A)], we have found that CMA blockade leads to impaired visual function, altered retinal proteostasis, and photoreceptor cell death. Conversely, mice that overexpress human LAMP2A show higher resistance to chemically induced photoreceptor degeneration and slower visual function decline. We found a similar protective effect against retinal degeneration upon pharmacological activation of CMA. To start elucidating the mechanisms behind CMA's protective role in the retina, we used comparative proteomics and found elevated levels of enzymes related with glucose metabolism in CMA-deficient retinas that phenocopy those observed in old mice retinas. Overall, our results highlight a cytoprotective role for CMA in retina, in part through proteostatic regulation of enzymes involved in glucose metabolism, and support the feasibility of pharmacologically upregulating CMA against retinal degeneration.
    Keywords:  aging; autophagy; metabolism; retina; small-molecules
    DOI:  https://doi.org/10.1073/pnas.2527503123
  45. Nat Commun. 2026 May 13.
    Structural basis for prohibitin-mediated regulation of mitochondrial m-AAA protease.
    Dingyi Luo, Lvqin Zheng, Ming-Ao Lu, Ziyao Chen, Panpan Wang, Qiang Guo, Ning Gao.
      Mitochondrial function critically depends on protein quality control systems, with the m-AAA protease playing a key role at the inner mitochondrial membrane (IMM). The evolutionarily conserved prohibitins (PHBs) are essential modulators of this protease across species, yet the molecular mechanisms remain unclear. Here, we present the cryo-EM structure of the Chaetomium thermophilum PHB (CtPHB) complex, revealing a cage-like assembly composed of 11 copies of PHB1/PHB2 heterodimers. Electron microscopic and biochemical analyses suggest that m-AAA proteases are enclosed within the PHB complex through interactions mediated by their SPFH-interacting motif (SIM) exposed in the intermembrane space. Further in situ cryo-ET directly visualizes these cage-protease assemblies in native mitochondria. Disruption of their interface leads to elevated m-AAA protease activity and diminished mitochondrial stress resistance. These data establish PHB complexes as spatial organizers that compartmentalize m-AAA proteases in membrane microdomains to fine-tune proteolytic homeostasis. Our findings reveal the critical role of the PHB complex in maintaining mitochondrial proteostasis, providing a unified mechanistic model to explain and reconcile the pleiotropic and often contradictory phenotypes of PHB and m-AAA protease in mitochondrial physiology and various disease conditions.
    DOI:  https://doi.org/10.1038/s41467-026-73040-0
  46. Brain. 2026 May 12. pii: awag170. [Epub ahead of print]
    TIM-3-dependent lysosome biogenesis is required for myelin debris clearance in macrophages.
    Xiaodi Zhang, Ziqing Xu, Yingxue Zhang, Zheng Tong, Xiaolei Ren, Ying Xiao, Hao Chen, Na Han, Chunyang Li, Xuetian Yue, Zhuanchang Wu, Xiaohong Liang, Chunhong Ma, Pin Wang, Lifen Gao.
      Multiple sclerosis (MS) is a chronic autoimmune disorder characterized by the immune-mediated demyelination and neurodegeneration of the central nervous system. Phagocyte mediated myelin debris clearance is required for remyelination. TIM-3 is highly expressed on mononuclear macrophages and promotes the phagocytosis of apoptotic cells. Here, we report that TIM-3 enhances the clearance of myelin debris in experimental autoimmune encephalomyelitis (EAE), a model of MS. Tim-3 knockout (KO) exacerbated EAE severity, neuroinflammation, and demyelination by regulating mononuclear macrophages. TIM-3 promoted the phagocytosis and degradation of myelin debris by macrophages. Mechanistically, Tim-3 deficiency impaired lysosomal biogenesis and function, leading to lysosomal membrane permeabilization and disrupted lysosomal acidification, which further exacerbated neuroinflammation and demyelination. Notably, TIM-3 blocked the interaction of mTOR-TFEB to inhibit TFEB phosphorylation and facilitate its nuclear translocation, followed by increased expression of lysosomal genes critical for myelin degradation. Importantly, the IgV domain is necessary in TIM-3-mediated lysosomal regulation and myelin degradation. These findings highlight TIM-3 as a key regulator of lysosomal homeostasis and the clearance of myelin debris, suggesting that the IgV domain has promise as a therapeutic agent for treating demyelinating diseases such as MS.
    Keywords:  TFEB; TIM-3; lysosomal biogenesis; macrophage; multiple sclerosis; myelin debris clearance
    DOI:  https://doi.org/10.1093/brain/awag170
  47. Nat Commun. 2026 May 15.
    α-Synuclein aggregates induce mitochondrial damage and trigger innate immunity to drive neuron-microglia communication.
    Ranabir Chakraborty, Stephanie Maya, Veronica Testa, Jara Montero-Muñoz, Takashi Nonaka, Masato Hasegawa, Antonella Consiglio, Chiara Zurzolo.
      Tunneling nanotubes (TNTs) enable direct intercellular transfer of macromolecules, organelles, and pathogenic protein aggregates. While α-synuclein (α-Syn) aggregates are known to promote TNT formation, the underlying mechanisms remain poorly defined. Here, using human neuronal and microglial cell lines, as well as iPSC-derived dopaminergic neurons and microglia, we show that α-Syn aggregates induce severe mitochondrial damage, leading to cytosolic release of mitochondrial DNA (mtDNA) and activation of the cGAS-STING-NF-κB-IRF3 pathway. This innate immune response drives actin cytoskeleton remodeling and the formation of TNT-like structures, promoting intercellular transfer of α-Syn from neurons to microglia. Additionally, neuronal cells transfer damaged mitochondria to microglia, where they undergo lysosome-mediated degradation. Neuron-to-microglia communication under α-Syn-induced stress also triggers a bystander inflammatory response in microglia, suggesting a neuroimmune activation. Our findings identify mitochondrial damage and STING-mediated inflammation as key drivers of TNT formation and α-Syn propagation, highlighting potential targets to modulate disease progression in Synucleinopathies.
    DOI:  https://doi.org/10.1038/s41467-026-73136-7
  48. Genetics. 2026 May 16. pii: iyag121. [Epub ahead of print]
    CRISPR screening identifies TRIM27 as a destabilizer of the Smith-Magenis syndrome protein RAI1.
    Yu Cheng Lin, Yu-Ju Lee, Catherine Xinrui Li, Hao-Cheng Chang, Max Kowalczyk, Minza Haque, Adrian Dragoiescu, Truc T Losier, James A Taylor, Maxime W C Rousseaux, Wei-Hsiang Huang.
      The nervous system is highly sensitive to alterations in the dosage of genes crucial for neurodevelopment, as exemplified by retinoic acid-induced 1 (RAI1). A 50% change in RAI1 gene copy number, resulting in either reduced or increased protein levels, leads to distinct neurodevelopmental disorders. RAI1 haploinsufficiency causes Smith-Magenis syndrome (SMS), whereas RAI1 duplication underlies Potocki-Lupski syndrome (PTLS). We recently demonstrated that restoring Rai1 levels can improve SMS-related disease phenotypes in mice. However, despite protein stability being a major determinant of protein abundance, there are currently no therapeutic approaches to modulate RAI1 protein stability. Here, we performed a forward CRISPR screen in human cells to identify post-translational regulators of RAI1 steady-state levels and identified tripartite motif containing 27 (TRIM27) as a destabilizer of RAI1. We show that RAI1 degradation occurs primarily through the ubiquitin proteasome system, with TRIM27 interacting with RAI1 and enabling TRIM27-dependent lysine(K)48- and K63-linked RAI1 ubiquitination. Finally, in SMS mouse primary neurons, we demonstrate that knocking down TRIM27 partially rescues SMS-associated morphological phenotypes. Our findings provide the first mechanistic insight into RAI1 proteostasis and highlight TRIM27 as a potential therapeutic target for SMS, highlighting the potential of manipulating ubiquitin-mediated proteostasis to restore gene dosage altered by copy number variations.
    Keywords:  CRISPR; Dendrite; Neurodevelopmental Disorder; Post-translational modification; RAI1; SMS; Synapse; TRIM27; Ubiquitination
    DOI:  https://doi.org/10.1093/genetics/iyag121
  49. Sci Adv. 2026 May 15. 12(20): eaed7122
    TP53-mutant AML with ribosomal gene loss exhibits impaired protein translation and sensitivity to HSP90 inhibition.
    Jean-François Spinella, Jalila Chagraoui, Céline Moison, Isabel Boivin, Guillaume Richard Carpentier, Nadine Mayotte, François Béliveau, Vincent P Lavallée, Josée Hébert, Guy Sauvageau.
      TP53-mutated acute myeloid leukemia (AML) represents a particularly aggressive and therapeutically refractory subtype of the disease. While recurrent chromosomal abnormalities such as -5/del(5q), -7/del(7q), and del(17p) are well studied in this context, additional co-occurring events remain less well defined. Using the multidimensional Leucegene dataset (~700 primary AML specimens), we identified and comprehensively characterized a distinct subset of TP53-altered AML marked by recurrent deletions on the short arm of chromosome 3 [del(3p), >20% TP53-mutated cases]. These deletions frequently co-occur with del(5q) and encompass several ribosomal protein genes (RPGs), leading to a global down-regulation of the ribosomal network and reduced protein synthesis. We show that this ribosomopathy-like phenotype is most pronounced in TP53-mutated cases with combined RPG deletions on chromosomes 3p and 5q, suggesting a cooperative oncogenic mechanism. Chemical screening identified HSP90 inhibition as a selective vulnerability in AML with low RPG expression. These findings highlight a previously unappreciated TP53-altered AML subset characterized by converging genomic and translational defects and suggest that ribosomal stress may serve as a therapeutic entry point for targeted intervention of this patient subgroup.
    DOI:  https://doi.org/10.1126/sciadv.aed7122
  50. Nat Commun. 2026 May 14.
    A dual phospholipase system instructs membrane hydrolysis during the final stages of plant autophagy.
    Julie Castets, Matthieu Buridan, Inés Toboso Moreno, Valérie Wattelet-Boyer, Víctor Sánchez de Medina Hernández, Rodrigo Enrique Gomez, Franziska Dittrich-Domergue, Josselin Lupette, Clément Chambaud, Stéphanie Pascal, Tarhan Ibrahim, Tolga O Bozkurt, Yasin Dagdas, Frédéric Domergue, Jérôme Joubès, Elena A Minina, Amélie Bernard.
      Autophagy is a conserved intracellular catabolic process, critical for plant stress tolerance. Upon their delivery in the vacuole, how autophagic bodies containing cargo are hydrolyzed to warrant autophagy degradation remains unclear in multicellular organisms. Here, we found that two Arabidopsis phospholipases, LCAT4 and LCAT3, traffic to the vacuolar lumen and converge on autophagic bodies through fundamentally different routes. While LCAT4 directly binds ATG8 and uses autophagy as a transport system to reach the vacuole prepackaged within autophagosomes, LCAT3 traffics to the lytic compartment independently of autophagosome formation. Knocking out both genes causes an accumulation of autophagic bodies accompanied with a reduction in autophagy degradation. In vivo reconstitution demonstrated that LCAT3 can hydrolyse the membrane of autophagic bodies, enabling the activity of LCAT4 to enhance this process. Together, this work sheds light on the vacuolar stages of autophagy, showing that plants have evolved a multi-component pathway for the efficient disruption of autophagosomal membranes as a critical step for the completion of the autophagy pathway.
    DOI:  https://doi.org/10.1038/s41467-026-73116-x
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