bims-proteo Biomed News
on Proteostasis
Issue of 2026–05–10
forty-nine papers selected by
Eric Chevet, INSERM
  1. Endoplasmic reticulum (ER) ubiquitin ligases: substrate recognition and emerging cellular functions.
  2. Cysteine availability tunes ubiquitin signaling via inverse stability of LRRC58 E3 ligase and its substrate CDO1.
  3. BAG2 Condensates Couple Proteostasis to CD8 + T Cell Surveillance.
  4. Endoplasmic reticulum and Golgi stress signaling-mediated regulation of protein secretion.
  5. Coronavirus M protein disperses the trans-Golgi network and inhibits anterograde protein trafficking in the secretory pathway.
  6. Turning adaptive resistance into vulnerability: AUTAC-Mediated degradation of Mcl1.
  7. Proteasome-dependent degradation and nucleus-vacuole junctions sustain proteostasis during acute glucose starvation.
  8. A molecular stabiliser of an inhibitory eIF2B-eIF2(αP) complex activates the Integrated Stress Response.
  9. CDS-localized m6A drives co-translational RNA decay to relieve biotic and abiotic endoplasmic reticulum stresses.
  10. When tau stalls the lysosome: decoupling trafficking and degradation in autophagy.
  11. The UFSP2-C1orf27 complex positions nascent GPCRs to the ufmylation system for ER export control.
  12. RYR:ATP6V0A1 complexes couple ER-lysosome contact sites to dynamic autophagy control.
  13. Posttranslational modifications remodel proteome-wide ligandability.
  14. Expanding the human proteome with microproteins and peptideins.
  15. First PROTAC gains FDA approval, bolstering targeted protein degradation and induced proximity ambitions.
  16. Direct observation of ATP-driven ubiquitin chain handling by Cdc48.
  17. N-terminal formylmethionine as a degron and a specific signal in proteostasis and stress adaptation.
  18. Phosphorylation tunes p62 condensates to drive autophagic degradation of ubiquitinated proteins.
  19. SEL1L3 suppresses colorectal cancer cell growth and metastasis by preventing endoplasmic reticulum-associated degradation of STING.
  20. Peroxisome-derived ether lipids regulate lysosomal exocytosis.
  21. Mitochondria serve as a holdout compartment for aggregation-prone proteins hindering efficient degradation.
  22. SPRY domains encode ubiquitin ligase specificity for ZAP and RIG-I.
  23. Paired CRISPR screens identify mitochondrial metabolism and UBE2H as aneuploid-specific dependencies in human cancer cell lines.
  24. Increased Protein Synthesis With Reduced Endoplasmic Reticulum Stress Defines a Specific Adaptation in Pancreatic Acinar Metaplasia.
  25. Targeting the integrated stress response or Ataxin-2 alleviates neurodegeneration in PolyGR models of C9orf72 associated frontotemporal dementia and amyotrophic lateral sclerosis.
  26. STREMI: a dual-function upstream ORF-encoded regulator of mitochondrial cristae architecture.
  27. Emerging mechanisms of COPII adaptation for large cargo ER export.
  28. MGRN1 in development and disease: a unifying view of a versatile membrane-tethered E3 ubiquitin ligase.
  29. Targeting the IRE1α-XBP1 signaling axis impairs tumor growth and promotes myogenic differentiation in rhabdomyosarcoma.
  30. Discovery of a pyrazolopyridine alkaloid that mitigates neuronal ER stress and age-related decline.
  31. Ubiquitylation by the GID/CTLH complex regulates the metabolic and innate immune response of macrophages to infection by Mycobacterium tuberculosis.
  32. The backside β-turn is a key structural element of Rad6-family E2 ubiquitin-conjugating enzymes.
  33. Global mitochondrial connectivity map reveals the landscape of yeast functional assemblies and conserved protein communities.
  34. Stress Granule Sequestration of CCR4-NOT Promotes Poly(A) Lengthening of Stress-Survival Transcripts.
  35. Adaptive Regulation of mTOR Activity by AMPK, Akt, and ATF6 Pathways in Pi*Z Alpha-1 Antitrypsin Deficient Hepatocytes.
  36. Phosphorylated ubiquitin is a secondary messenger and an epigenetic mark mediating mitochondria to nucleus signaling.
  37. Impaired collagen deposition in the absence of ERp44.
  38. A conserved ER protein prevents lipotoxicity by stimulating the key enzyme in glycerolipid synthesis.
  39. Mitochondrially tethered Mmm1 can function as a sole lipid transporter at ER-mitochondria contacts.
  40. Ribosome biogenesis bottlenecks reveal vulnerabilities in cancer.
  41. HSF1-mediated Proteostasis Decline Links Aging and Sleep Disruption.
  42. Interface Architecture of a VHL-PROTAC Complex with and without Cullin-2.
  43. Membrane insertion of mitochondrial-encoded proteins regulates ribosome decoding speed.
  44. A unified mechanism for tubulin cofactors catalyzing α/β-tubulin biogenesis and degradation.
  45. Mechanism of nucleolytic degradation of human ribosomes.
  46. Signal peptide peptidase-like proteases OsSPPL1 and OsSPPL2 facilitate ER-associated protein degradation in rice.
  47. An integrated RNA-centric imaging and omics approach reveals distinct properties and composition of neuronal RNA granules.
  48. Evaluating generalization in protein-ligand cofolding methods.
  49. A sterol-binding pocket in iRhom1 underlies paralog-specific regulation of the sheddase ADAM17.
  1. Trends Cell Biol. 2026 May 07. pii: S0962-8924(26)00062-0. [Epub ahead of print]
    Endoplasmic reticulum (ER) ubiquitin ligases: substrate recognition and emerging cellular functions.
    Qing Zhao, Zai-Rong Zhang, Yihong Ye, Yanfen Liu.
      Endoplasmic reticulum (ER)-resident ubiquitin ligases are essential to cellular homeostasis and diverse signaling pathways, functioning in protein quality control, lipid metabolism, innate immunity, and interorganelle communication. While best known for their roles in ER-associated degradation (ERAD) of misfolded proteins, accumulating evidence shows that they also mediate the regulated turnover of functional ER proteins and contribute to ER-phagy, thereby expanding their roles in ER homeostasis. This review summarizes recent advances in understanding substrate recognition mechanisms employed by ER ubiquitin ligases and how these enzymes coordinate ERAD and ER-phagy, with a primary focus on mammalian systems. We further discuss their roles in ER homeostasis and immune responses, and how their dysregulation contributes to diseases such as neurodegeneration and immune disorders.
    Keywords:  ER homeostasis; ER-associated degradation; ER-phagy; substrate recognition; ubiquitin ligase
    DOI:  https://doi.org/10.1016/j.tcb.2026.04.004
  2. Nat Commun. 2026 May 07. pii: 4196. [Epub ahead of print]17(1):
    Cysteine availability tunes ubiquitin signaling via inverse stability of LRRC58 E3 ligase and its substrate CDO1.
    Gisele A Andree, Luca J Stier, Kerstin Schmiederer, Alina S Thielen, Luis Schmid, Samuel A Maiwald, Karthik V Gottemukkala, Jiale Du, Susanne von Gronau, Claudia Strasser, Judith Müller, Lukas T Henneberg, Camille Guyot, Gary Kleiger, Matthias Mann, Peter J Murray, Brenda A Schulman.
      Cellular responses to amino acid fluctuations often hinge on ubiquitin-mediated control of metabolic enzymes, yet the underlying E3 ligase pathways remain poorly defined. Using quantitative proteomics and active cullin-RING ligase (CRL) profiling, we identify LRRC58 as a cysteine-responsive substrate receptor whose stability increases sharply under cysteine starvation. Proteomics reveals an inverse relationship between LRRC58 and the metabolic enzyme cysteine dioxygenase 1 (CDO1), suggesting a cysteine-linked regulatory axis. Biochemical reconstitution and cryo-EM structures show that LRRC58 forms an active CUL2- or CUL5-based CRL that selectively positions CDO1 for ubiquitylation at Lys8. Disease mutant versions of CDO1 mapping to the LRRC58 interface and impaired for the endogenous ubiquitylation pathway were degraded through orthogonal targeting by a VHL-based degrader. Together, our proteomics-guided discovery pipeline, cellular stability studies, and structural analyses uncover a metabolically-tuned LRRC58-CDO1 pathway that links cysteine availability to selective proteasomal turnover, reveals principles of metabolite-regulated CRL activity, and showcases mechanisms distinguishing endogenous and targeted protein degradation.
    DOI:  https://doi.org/10.1038/s41467-026-72524-3
  3. bioRxiv. 2026 Apr 27. pii: 2026.04.24.719751. [Epub ahead of print]
    BAG2 Condensates Couple Proteostasis to CD8 + T Cell Surveillance.
    Maria C Almeida, Tian Wang, Andrew P Longhini, Samuel Lobo, Carolina M Camargo, Eric D Tinkle, Mookwang Kwon, Guilherme Z Duarte, Isabel O Hirsch, Cesar A J Ribeiro, Fernando A Oliveira, M Scott Shell, Joan-Emma Shea, Judith A Steen, Kenneth S Kosik, Daniel C Carrettiero.
      Protein aggregation, impaired degradation, and immune activation are central hallmarks of neurodegenerative diseases, yet how these processes are coordinated remains unclear. Here, we identify Immune-Protein Degradation Bodies (I-PDBs), a previously unrecognized class of BAG2-driven, phase-separated organelles that integrate protein quality control with adaptive immunity. IFNγ induce I-PDB formation at the endoplasmic reticulum (ER), where they concentrate immunoproteasome components, MHC-I peptide-loading machinery, and ER-associated chaperones. I-PDBs redirect proteostatic cargo from centrosomal aggregation pathways to spatially restricted degradation sites optimized for antigenic peptide generation, coupling selective substrate clearance to CD8⁺ T cell engagement. Using a cellular model of aggregation-prone tau, we show that I-PDBs capture pathological tau fibrils at ER-microtubule interfaces and process them into potentially antigenic peptides, thus reducing the load of aggregation-prone tau peptides. We term this mechanism the Proteostasis-Associated Immune Relay (PAIR), establishing I-PDBs as critical hubs linking proteostasis to immune surveillance with broad implications for disease.
    Highlights: IFNγ drives BAG2-dependent Immune-Protein Degradation Bodies (I-PDBs)I-PDBs assemble at the endoplasmic reticulum and are enriched in immunoproteasome and MHC-I machineryI-PDBs shunt misfolded proteins, including pathological tau, away from aggresomesI-PDBs couple proteostasis to antigen presentation, enhancing CD8⁺ T cell recognitionThe Proteostasis-Associated Immune Relay (PAIR) defines a pathway linking proteostasis to adaptive immunity.
    DOI:  https://doi.org/10.64898/2026.04.24.719751
  4. Cell Mol Biol Lett. 2026 May 07.
    Endoplasmic reticulum and Golgi stress signaling-mediated regulation of protein secretion.
    Ketsia Bakambamba, Manon Nivet, Sophie Martin, Elodie Lafont, Eric Chevet, Tony Avril.
      The eukaryotic secretory pathway (SP) is essential to ensure cellular functions and multicellular communication. The early SP is constituted mostly of the endoplasmic reticulum (ER), the ER-Golgi intermediate compartment (ERGIC), and the Golgi apparatus. These intracellular organelles achieve proper folding and modification of newly synthesized transmembrane and secretory proteins, en route to their final destination, e.g., plasma membrane, endosomes, lysosomes, and the extracellular space. They also integrate quality control systems to ensure export of productively folded proteins and to trigger dysfunctional proteins to degradation. The ER as the first SP compartment is subjected to a precise control of its own homeostasis through signaling of the unfolded protein response. In this review, we provide an overview of the early SP and its regulatory mechanisms, focusing on the ER and Golgi stress-dependent signaling. We contextualize this information within physiological and pathological processes, and discuss how ER and Golgi stress responses might coordinate their regulatory effects across the entire SP.
    Keywords:  Endoplasmic reticulum stress response; Golgi stress response; Protein secretion machinery; Secretory pathway
    DOI:  https://doi.org/10.1186/s11658-026-00932-w
  5. PLoS Pathog. 2026 May 05. 22(5): e1014117
    Coronavirus M protein disperses the trans-Golgi network and inhibits anterograde protein trafficking in the secretory pathway.
    Taylor M Caddell, Rory P Mulloy, Jennifer A Corcoran, Eric S Pringle, Craig McCormick.
      Coronaviruses (CoVs) encode a variety of transmembrane proteins that are translated and processed at the endoplasmic reticulum (ER). Three host ER resident transmembrane proteins, activating transcription factor 6 (ATF6), inositol-requiring enzyme 1 (IRE1), and PKR-like endoplasmic reticulum kinase (PERK), sense the accumulation of unfolded proteins in the ER and initiate the unfolded protein response (UPR) to maintain ER proteostasis. We observed that SARS-CoV-2 Spike broadly activated all three arms of the UPR, whereas the Membrane (M) protein selectively inhibited ATF6. ATF6 has a unique activation mechanism whereby ER stress triggers translocation to the Golgi where ATF6 is processed by resident proteases to release the ATF6-N transcription factor. We observed that M inhibited the stress-induced production of ATF6-N, suggesting that ATF6 failed to engage with Golgi proteases for processing. M also inhibited sterol regulatory element binding protein-2 (SREBP2)-mediated activation of sterol responses and stimulator of interferon response cGAMP interactor 1 (STING)-mediated activation of interferon responses, both of which are activated in the ER and require translocation to the Golgi for interactions that yield transcriptional responses. We observed that M accumulated in the cis-Golgi, and triggered dispersal of the trans-Golgi network (TGN). Using a cargo sorting assay, we determined that ER-to-Golgi cargo trafficking was intact in the presence of M, but cargo accumulated with M in the cis-Golgi and did not proceed further in the secretory pathway. We also observed aberrant cholesterol accumulation at the cis-Golgi with M, consistent with our observation of M association with detergent resistant membranes. Together, these data suggest that CoV M proteins interfere with Golgi architecture and trafficking. Because CoV egress does not require the canonical secretory pathway, this mechanism could allow the virus to selectively interfere with host responses to infection without impeding egress of nascent virions.
    DOI:  https://doi.org/10.1371/journal.ppat.1014117
  6. Autophagy. 2026 May 04.
    Turning adaptive resistance into vulnerability: AUTAC-Mediated degradation of Mcl1.
    Ahmed M Elshazly, Senthil K Radhakrishnan.
      Proteasome inhibition remains the frontline therapy in multiple myeloma, yet its efficacy is attenuated by adaptive stress responses. Central to these is the transcription factor NRF1, which transcriptionally upregulates proteasome subunits and components of the autophagy-lysosomal machinery, restoring proteostasis and sustaining tumor cell survival. The anti-apoptotic protein Mcl1 has independently emerged as a dominant mediator of resistance to proteasome inhibitors. In our recent work, we report a first-in-class Mcl1-targeting autophagy-targeting chimera (AUTAC) that selectively degrades Mcl1 via the lysosomal pathway through K63-linked ubiquitination by TRAF6 and UBC13, and recognition by the cargo receptor p62/SQSTM1. Proteasome inhibition with carfilzomib markedly potentiates AUTAC activity, and this potentiation is abolished in NRF1-deficient cells, establishing NRF1 as the licensing factor that couples proteotoxic stress to enhanced lysosomal targeted protein degradation. The combination produces synergistic tumor cell death across proteasome inhibitor-sensitive and resistant multiple myeloma and lung cancer models in vitro and significantly suppresses tumor growth in a U266B1 multiple myeloma xenograft model. These findings reframe cytoprotective autophagy not as a resistance liability to be inhibited, but as an inducible degradation capacity that can be redirected to eliminate oncogenic survival factors, suggesting a generalizable strategy for amplifying lysosomal targeted protein degradation through controlled proteostasis stress.
    Keywords:  AUTAC; Mcl1; NRF1; autophagy; proteotoxic stress; resistance
    DOI:  https://doi.org/10.1080/15548627.2026.2669686
  7. bioRxiv. 2026 Apr 25. pii: 2026.04.22.720209. [Epub ahead of print]
    Proteasome-dependent degradation and nucleus-vacuole junctions sustain proteostasis during acute glucose starvation.
    Mihaela Pravica, Dina Franić, Matko Bazdan, Dominik Guzalić, Antonio Bedalov, Mirta Boban.
      How protein quality control is maintained during acute metabolic stress remains poorly understood. In budding yeast, abrupt glucose depletion rapidly lowers ATP levels and leads to the formation of chaperone-containing inclusions, suggesting that ATP-dependent degradation of misfolded proteins may be compromised when energy becomes limiting. Here we find that selective degradation of misfolded proteins remains active during acute glucose starvation despite reduced cellular ATP levels. Using model misfolded substrates in yeast Saccharomyces cerevisiae , we show that misfolded proteins continue to be efficiently degraded throughout both early and late phases of acute glucose depletion. This degradation requires the proteasome and depends on its functional 19S regulatory particle, indicating that ATP-dependent proteasomal activity persists during metabolic stress. We further find that nucleus-vacuole junctions (NVJs) promote efficient degradation during prolonged glucose starvation, revealing a role for organelle contact sites in supporting proteostasis under energy limitation. Together, these findings indicate that cells preserve proteasome-mediated proteostasis during acute glucose starvation, while NVJ membrane contact sites help sustain degradation capacity when metabolic resources are scarce.
    DOI:  https://doi.org/10.64898/2026.04.22.720209
  8. Nat Commun. 2026 May 06.
    A molecular stabiliser of an inhibitory eIF2B-eIF2(αP) complex activates the Integrated Stress Response.
    Fiona Shilliday, Miguel Gancedo-Rodrigo, Ginto George, Shintaro Aibara, Santosh Adhikari, Syedah Neha Ashraf, Evelyne J Barrey, Paolo A Centrella, Damian Crowther, Paige Dickson, Diana Gikunju, Marie-Aude Guié, John P Guilinger, Anders Gunnarsson, Heather P Harding, Christopher D Hupp, Rachael Jetson, Anthony D Keefe, JeeSoo Monica Kim, Richard J Lewis, Taiana Maia de Oliveira, Jennifer Le-Marshall, Usha Narayanan, Katherine A Nugai, Dušan Petrović, Emma Rivers, David Ron, Daisy Stringfellow, Karl Syson, Lewis Ward, John T S Yeoman, Yan Yu, Ying Zhang, Alisa Zyryanova, David J Baker, Perla Breccia, John E Linley.
      Eukaryotic initiation factor 2B (eIF2B), a guanine nucleotide exchange factor (GEF), promotes protein synthesis by charging translation initiation factor 2 (eIF2) with GTP. Stress-induced phosphorylation of eIF2 on its α-subunit [eIF2(αP)] inhibits this reaction triggering a protective Integrated Stress Response (ISR). A DNA-encoded chemical library (DEL) screen for modulators of eIF2B, led to the identification of a chemical series that stabilises the inactive state of eIF2B, stimulating the ISR. Cryo-EM of compound-bound eIF2B reveals a conformational switch to the inactive state engaged by eIF2(αP). In cells, compound activity is sensitive to eIF2's phosphorylation state and to a competing eIF2B ligand (ISRIB) that activates the GEF allosterically. These findings establish the feasibility of targeting eIF2B with a drug-like allosteric inhibitor, that serves as an ISR activator (ISRAC), paving the way to explore the therapeutic potential of eIF2B-directed ISR activation.
    DOI:  https://doi.org/10.1038/s41467-026-72688-y
  9. Nat Plants. 2026 May 08.
    CDS-localized m6A drives co-translational RNA decay to relieve biotic and abiotic endoplasmic reticulum stresses.
    Songxiao Zhong, Tae Rin Oh, Xindi Li, Jinming Zhang, Suk Won Choi, Chuyun Gao, Xu Peng, Juan Dong, Chuan He, Xiuren Zhang.
      The endoplasmic reticulum (ER) mitigates stress typically through unfolded protein response (UPR) and ER-associated degradation (ERAD) pathways, yet post-transcriptional regulation of ER stress remains poorly defined. N6-methyladenosine (m6A) modification, predominantly enriched near stop codons, can govern mRNA fates via P-bodies or stress granules in stress conditions. m6A also occurs within coding sequences (CDS-m6A), but its role remains unappreciated in plants. Here we demonstrate that m6A ablation sensitizes Arabidopsis ER stress despite normal UPR and ERAD activities. Mechanistically, CDS-m6A co-localizes with ribosome stalling sites and directs co-translational RNA decay (CTRD). Under stress, activation of m6A-triggered CTRD accelerates clearance of ER-engaged transcripts, thereby alleviating translational overload. During geminivirus infection, which increases translational demand on ER, m6A-triggered CTRD also targets viral RNAs, restricting their accumulation, translation and disease progression. Thus, CDS-m6A functions as a pivotal regulator of ER-linked RNA surveillance, establishing an organelle-specific mechanism that integrates RNA stability, protein homeostasis and antiviral defence.
    DOI:  https://doi.org/10.1038/s41477-026-02299-4
  10. Autophagy. 2026 May 06. 1-3
    When tau stalls the lysosome: decoupling trafficking and degradation in autophagy.
    Celeste M Karch, Farzaneh S Mirfakhar.
      Tauopathies are characterized by the accumulation of misfolded tau and lysosomal dysfunction, yet whether defects in the autophagy-lysosome pathway are causal or secondary remains unclear. Recent work using human iPSC-derived neurons harboring the MAPT p.R406W mutation demonstrates that pathogenic tau is sufficient to disrupt lysosomal function upstream of tau accumulation. Tau species are differentially processed within lysosomes, with phosphorylated tau retained at the lysosomal membrane, consistent with a barrier to efficient cargo processing. Importantly, pharmacologic activation of autophagy restores degradative capacity and reduces tau burden without rescuing lysosomal motility, suggesting that trafficking and degradation represent separable axes of lysosomal biology. These findings position tau as an active disruptor of proteostasis and define a degradative bottleneck that shares features with lysosomal storage disorders. Together, this work reframes autophagy dysfunction in tauopathy as a modular defect with distinct therapeutic entry points.
    Keywords:  Induced pluripotent stem cells; MAPT; lysosomal trafficking; neurons; tauopathy
    DOI:  https://doi.org/10.1080/15548627.2026.2669685
  11. iScience. 2026 May 15. 29(5): 115707
    The UFSP2-C1orf27 complex positions nascent GPCRs to the ufmylation system for ER export control.
    Xin Xu, Yinquan Fang, Lifen Qiu, Wei Huang, Honglin Li, Guangyu Wu.
      The ufmylation system is implicated in multiple cellular processes and human diseases; our recent study has identified its function in protein trafficking, but detailed mechanisms remain elusive. Here, we reveal cooperative actions of ufmylation protease UFSP2 and endoplasmic reticulum (ER)-anchored protein C1orf27 on ER-to-Golgi transport of some G protein-coupled receptors (GPCRs). UFSP2 interacts with C1orf27 for ER recruitment, and its activation is dispensable for recruitment but essential for ER export of GPCRs. Structural analysis suggests that UFSP2 and C1orf27 are diverged from a C. elegans ODR8-like protein. Similar to their C. elegans homologs, UFSP2, C1orf27, and cargo GPCRs form a multi-protein complex, and GPCR interaction with C1orf27 is required for their ER export and forward delivery. Collectively, these data demonstrate that the C1orf27-UFSP2 complex interacts with its cargo GPCRs, directs them to ufmylation regulation, and controls their ER export, providing important insights into the trafficking function of the ufmylation system and GPCR maturation processing.
    Keywords:  Biochemistry; Cell biology; Molecular biology
    DOI:  https://doi.org/10.1016/j.isci.2026.115707
  12. Autophagy. 2026 May 05.
    RYR:ATP6V0A1 complexes couple ER-lysosome contact sites to dynamic autophagy control.
    Jens Loncke, Manon Callens, Geert Bultynck, Tim Vervliet.
      Ryanodine receptors (RYRs) are ER-resident Ca2 + -release channels enriched in excitable cells, including neurons. RYR hyperactivity is implicated in early pathogenesis of disorders such as Alzheimer's disease (AD), which is associated with impaired autophagy. We recently uncovered a mechanism linking RYR activity to lysosome availability for autophagy. RYRs localize to ER - lysosome contact sites via direct binding to ATP6V0A1, a V-ATPase subunit that also suppresses RYR-mediated Ca2 + release. In human iPSC-derived cortical neurons, spontaneous RYR activity promotes lysosomal secretion, depleting the intracellular lysosomal pool and inhibiting autophagic flux. RYR inhibition promotes ER - lysosome contacts, limits lysosomal secretion, and restores lysosome availability for autophagosome fusion and cargo degradation (including APP). Conversely, disrupting the RYR:ATP6V0A1 interaction using a RYR-derived protein fragment serving as a "decoy" for ATP6V0A1 evokes RYR hyperactivity and stimulates lysosomal secretion. In this Punctum, we discuss how this RYR2:ATP6V0A1 "contact-site hub" may be perturbed in disease and highlight open questions on how lysosomes decode RYR-derived Ca2 + signals.
    Keywords:  Calcium signaling; V-type ATPase; endoplasmic reticulum; lysosome; membrane contact site; ryanodine receptor
    DOI:  https://doi.org/10.1080/15548627.2026.2669981
  13. Nat Chem Biol. 2026 May 05.
    Posttranslational modifications remodel proteome-wide ligandability.
    Weichao Li, Qijia Wei, Manuel Llanos, Clara Gathmann, Paolo Governa, Tzu-Yuan Chiu, Jacob M Wozniak, Appaso M Jadhav, Matthew Holcomb, Jacob Cravatt, Ashok Dongre, Mia L Huang, Stefano Forli, Christopher G Parker.
      Posttranslational modifications (PTMs) vastly expand the diversity of the human proteome, dynamically reshaping protein activity, interactions and localization in response to environmental, pharmacologic and disease-associated cues. However, their proteome-wide impact on small-molecule recognition-and, thus, druggability-remains largely unexplored. Here we present a chemical proteomic strategy to delineate how PTM states remodel protein ligandability in human cells. Using broad-spectrum photoaffinity probes, we identified more than 400 functionally diverse proteins whose ability to engage small molecules is impacted by phosphorylation or N-linked glycosylation status. Integrating binding site mapping with structural analyses reveals a diverse array of PTM-dependent pockets. Among these, we discovered that the phosphorylation status of common oncogenic KRAS mutants impacts the action of small molecules, including clinically approved inhibitors. These findings illuminate a previously underappreciated layer of proteome plasticity governed by PTMs and highlight opportunities to develop chemical probes that selectively target proteins in defined modification states.
    DOI:  https://doi.org/10.1038/s41589-026-02216-y
  14. Nature. 2026 May 06.
    Expanding the human proteome with microproteins and peptideins.
    Eric W Deutsch, Leron W Kok, Jonathan M Mudge, Cristian F Valls, Irwin Jungreis, Jorge Ruiz-Orera, Zhi Sun, Ulrike Kusebauch, Ivo Fierro-Monti, Jennifer G Abelin, M Mar Alba, Julie L Aspden, Sreejan Bandyopadhyay, Kaushik Banerjee, Pavel V Baranov, Ariel A Bazzini, Francis Bourassa, Elspeth A Bruford, Lorenzo Calviello, Steven A Carr, Anne-Ruxandra Carvunis, Sonia Chothani, Jim Clauwaert, Kellie Dean, Pouya Faridi, Adam Frankish, Amy Goodale, Thomas Green, Norbert Hubner, Nicholas T Ingolia, Manolis Kellis, Michele Magrane, Maria Jesus Martin, Thomas F Martinez, Gerben Menschaert, Uwe Ohler, Sandra Orchard, Alisa Potter, Owen J L Rackham, Matthew G Rees, David E Root, Jennifer A Roth, Xavier Roucou, Fernando J Sialana, Sarah A Slavoff, Michał I Świrski, Jack A S Tierney, Félix-Antoine Trifiro, Eivind Valen, Valeriia Vasylieva, Aaron Wacholder, Shengbo Wang, Li Wang, Jonathan S Weissman, Wei Wu, Zhi Xie, Jyoti S Choudhary, Michal Bassani-Sternberg, Juan Antonio Vizcaíno, Nicola Ternette, Marie A Brunet, Robert L Moritz, John R Prensner, Sebastiaan van Heesch.
      A major scientific drive is to characterize the protein-coding genome, which is a primary basis for studying human health. But the fundamental question remains of what has been missed in previous analyses. Over the past decade, the translation of non-canonical open reading frames (ncORFs) has been observed across human cell types and disease states1-3, with major implications for biomedical science. However, a key gap in knowledge has been which ncORFs produce small microproteins or alternative protein molecules that contribute to the human proteome. Here we report the collaborative efforts of the TransCODE Consortium4 to produce a consensus landscape of protein-level evidence for ncORFs. We show that about 25% of a set of 7,264 ncORFs gives rise to detectable peptides in a large-scale analysis of 95,520 proteomics experiments. We develop an annotation framework for ncORF-encoded microproteins as human proteins and codify the new conceptual model of 'peptideins' as microproteins that have indeterminate potential as functional proteins. To probe the biological implications of peptideins, we create an evolutionary analysis approach, termed ORF relative branch length (ORBL), and determine that evolutionary constraint is common and associates with observation of ncORF-derived peptides. We then characterize a pan-essential cellular phenotype for one peptidein from the OLMALINC long non-coding RNA. Overall, we generate public research tools supported by GENCODE and PeptideAtlas and advance biomedical discovery for understudied components of the human proteome.
    DOI:  https://doi.org/10.1038/s41586-026-10459-x
  15. Nat Rev Drug Discov. 2026 May 08.
    First PROTAC gains FDA approval, bolstering targeted protein degradation and induced proximity ambitions.
    Asher Mullard.
      
    DOI:  https://doi.org/10.1038/d41573-026-00078-6
  16. Nat Commun. 2026 May 04.
    Direct observation of ATP-driven ubiquitin chain handling by Cdc48.
    D Choudhary, J R Tait, M Kracht, A Roland, J van den Boom, V Sunderlíková, H Meyer, S J Tans.
      Cdc48 (p97 or VCP in metazoans) targets polyubiquitin to selectively disassemble and degrade proteins. Cdc48 is believed to move along the ubiquitin chain towards linked proteins, but this has not been directly observed. By following single molecules in time, we find that the polypeptide branch points of ubiquitin chains are repeatedly inserted and rejected from the Cdc48 pore in ATP-driven manner, in bursts lasting up to seconds. This non-processive mode either ends by terminal substrate rejection, or advances to processive action, which drives ubiquitin unfolding in two steps, branch point translocation, and the extrusion of ubiquitin and linked protein as polypeptide loops in trans. Final retrograde movement can bring polypeptide segments back to cis. Our results establish the dynamics of ubiquitin chain handling by Cdc48, and reveal key hallmarks of kinetic proofreading. We speculate that Cdc48 translocation may play a role in ubiquitin chain selection.
    DOI:  https://doi.org/10.1038/s41467-026-72290-2
  17. Exp Mol Med. 2026 May 08.
    N-terminal formylmethionine as a degron and a specific signal in proteostasis and stress adaptation.
    Chang-Seok Lee, Dasom Kim, Cheol-Sang Hwang.
      N-terminal (Nt) methionine formylation, once thought restricted to bacteria and organelles, is now recognized as a stress-inducible initiator modification in the eukaryotic cytosol. Under metabolic or environmental stress, mitochondrial methionyl-transfer RNA (tRNA) formyltransferase mislocalizes to the cytosol, generating formylated initiator tRNA (fMet-tRNAi) that initiates translation with N-formylmethionine (fMet). Nascent chains bearing Nt-fMet activate an fMet-directed ribosome-associated quality control checkpoint early in elongation, recruiting ribosome-splitting and disaggregation factors. Stalled complexes are routed to stress granules, conserving mRNA, translation machinery, and energy, while limiting aggregation. During prolonged stress, newly synthesized fMet proteins undergo maturation or selective degradation via the fMet/N-degron pathway. In mammals, E3 ligase TRIM52 acts as an Nt-fMet recognin, modulating apoptosis. Proteolytic clearance of cytosolic fMet substrates releases formylated peptides and free fMet, which are elevated in critical illness and activate formyl peptide receptors - linking translation surveillance to innate immune and inflammatory signaling in sepsis and age-related disease. Advances in N-terminomics and anti-fMet reagents now allow direct detection and quantification of cytosolic fMet proteoforms. This Review integrates bacterial and organellar paradigms with emerging cytosolic mechanisms, examines regulatory gating of Nt-formylation, and highlights therapeutic strategies to restore proteostasis and counter fMet-associated pathology.
    DOI:  https://doi.org/10.1038/s12276-026-01723-1
  18. EMBO J. 2026 May 05.
    Phosphorylation tunes p62 condensates to drive autophagic degradation of ubiquitinated proteins.
    Satoko Komatsu-Hirota, Keisuke Tabata, Yu-Shin Sou, Soichiro Kakuta, Jun-Ichi Sakamaki, Hikaru Tsuchiya, Jiachen Li, Hiroyuki Kumeta, Yuji Sakai, Yuko Fujioka, Daisuke Noshiro, Shunsuke F Shimobayashi, Tomo Kurimura, Takashi Taniguchi, Manabu Abe, Masato Koike, Hideaki Morishita, Nobuo N Noda, Masaaki Komatsu.
      p62/SQSTM1 self-assembles with polyubiquitin into liquid-like condensates ("p62 bodies") that function as stress-signaling hubs and selective autophagy cargo. We show that TBK1-dependent phosphorylation at Ser403 acts as a threshold-dependent modulator of a condensate's physical properties and promotes their rapid autophagic clearance. Phosphorylation within p62 bodies drives a transition from large, fluid droplets to compact, gel-like condensates that efficiently capture LC3-positive isolation membranes and accelerate the autophagic removal of ubiquitinated proteins. PP2A holoenzymes containing PPP2R5A/B/E, recruited via a KEAP1 bridge, counteract TBK1 by dephosphorylating Ser403. Homozygous p62S403E/S403E knock-in embryonic stem cells differentiate into post-mitotic neurons enriched in miniaturized, gel-like p62 bodies. Consistently, phosphorylation-mimetic knock-in mice show similar remodeling of p62 condensates in vivo, demonstrating that this phosphorylation-driven mechanism maintains proteostasis across scales. We propose that Ser403 phosphorylation functions as a molecular switch that couples the material state of p62 condensates to their stability and serves as a central control point for p62-mediated protein degradation.
    DOI:  https://doi.org/10.1038/s44318-026-00785-1
  19. Cell Death Dis. 2026 May 03.
    SEL1L3 suppresses colorectal cancer cell growth and metastasis by preventing endoplasmic reticulum-associated degradation of STING.
    Hui Zhang, Wenli Qian, Mengying Li, Xiuqun Zou, Xiaolin Chen, Keyan Miao, Mai Zhao, Mengjiang Xu, Jiali Dong, Jiamin Wang, Haixia Peng, Hao Jia, Zhaoyuan Hou.
      Endoplasmic reticulum associated degradation (ERAD) plays pivotal role in protein homeostasis and quality control in normal and cancer cells, yet the regulatory mechanism of ERAD remains elusive, especially regarding its ubiquitination function mediated by hydroxymethylglutaryl reductase degradation protein 1 (HRD1). Here, we report that Sel-1 Suppressor of Lin-12-Like 3 (SEL1L3) protein resided on the ER membrane can effectively prevent HRD1-mediated ERAD process via dual mechanisms: SEL1L3 disrupts SEL1L-HRD1 complex by mutually exclusively interacting with SEL1L and HRD1 respectively, resulting in concomitant prevention of substrate degradation; on the other hand, SEL1L3 can accelerate HRD1 protein degradation. Biologically, SEL1L3 inhibits colorectal cancer (CRC) cell growth and migration, which counteracts the oncogenic activity of HRD1; moreover, we identify STING as a HRD1 substrate and a critical downstream effector mediating tumor suppression activity of SEL1L3. Collectively, these data demonstrate that SEL1L3 is a critical regulator of ERAD and exerts a potent tumor-suppressing function, and that the SEL1L3/HRD1/STING axis plays a crucial role in CRC growth and migration.
    DOI:  https://doi.org/10.1038/s41419-026-08770-6
  20. EMBO J. 2026 May 02.
    Peroxisome-derived ether lipids regulate lysosomal exocytosis.
    Liang Chen, Danielle Henn, Zhongzheng Dong, Jiaxuan Liang, Aleksander Wielenga, Goncalo Vale, Bala Burugula, Junyi Zou, Yamuna Krishnan, Jeffrey G McDonald, Jacob Kitzman, Ming Li.
      Lysosomes and peroxisomes are essential for cellular homeostasis, yet how their activities are coordinated remains poorly understood. Here, we identify peroxisome-derived ether lipids as key regulators of lysosomal function. A genome-wide CRISPR/Cas9 screen in LYSET-deficient mucolipidosis V cells revealed that disruption of ether lipid synthesis genes or peroxins markedly reduces lysosome accumulation and restores degradative capacity. Genetic or pharmacological inhibition of ether lipid synthesis enhanced lysosomal exocytosis and promoted the clearance of undigested material independently of mannose-6-phosphate trafficking. Conversely, supplementation with the ether lipid precursor hexadecylglycerol increased lysosome abundance, while reducing their degradative capacity. These findings uncover a peroxisome-lysosome metabolic axis, in which ether lipids act as bidirectional regulators of lysosomal number and function independently of the lysosomal master regulator TFEB. Our findings reveal how peroxisome-localized lipid metabolism modulates lysosomal homeostasis, and suggest potential new strategies to combat lysosomal and peroxisomal disorders.
    DOI:  https://doi.org/10.1038/s44318-026-00791-3
  21. Nat Commun. 2026 05 07. pii: 4195. [Epub ahead of print]17(1):
    Mitochondria serve as a holdout compartment for aggregation-prone proteins hindering efficient degradation.
    Maria E Gierisch, Enrica Barchi, Mirco Marogna, Moritz H Wallnöfer, Maria Ankarcrona, Luana Naia, Florian A Salomons, Nico P Dantuma.
      The accumulation of protein aggregates has been causatively linked to the pathogenesis of neurodegenerative diseases. Here, we conduct a genome-wide CRISPR-Cas9 screen to identify cellular factors that regulate the degradation of an aggregation-prone reporter. Genes encoding proteins involved in mitochondrial homeostasis, including the translation factor eIF5A, are enriched among suppressors of the degradation of the reporter. Genetic or chemical inhibition of eIF5A leads to dissociation of the aggregation-prone substrate from mitochondria, which is accompanied by enhanced ubiquitin-dependent proteasomal degradation. The presence of an aggregation-prone, amphipathic helix that localizes the reporter to mitochondria is crucial for the stimulatory effect of eIF5A inhibition on proteasomal degradation. Additionally, inhibition of eIF5A also enhances degradation of mutant huntingtin and α-synuclein, two disease-associated proteins that contain amphipathic helices and mislocalize to mitochondria. We propose that mitochondria serve as a holdout compartment for aggregation-prone proteins. Therefore, preventing mitochondrial localization of aggregation-prone proteins may offer a viable therapeutic strategy for reducing disease-associated proteins in neurodegenerative disorders.
    DOI:  https://doi.org/10.1038/s41467-026-72783-0
  22. PLoS Pathog. 2026 May 08. 22(5): e1014195
    SPRY domains encode ubiquitin ligase specificity for ZAP and RIG-I.
    Ibrahim Syed, Sheng Chen, David J Peeler, Paul F McKay, Marco A Briones-Orta, Jennifer A Bohn, Robin J Shattock, Daniel Gonçalves-Carneiro.
      Innate immune sensors rely on ubiquitin ligases to calibrate antiviral responses, yet the rules governing substrate recognition by SPRY-containing ligases remain poorly defined. Here, we establish a large-scale structure-based screening pipeline using AlphaFold to systematically predict interactions between human nucleic acid sensors and SPRY-containing proteins. Our approach uncovered novel transient or degradation-sensitive interactions that are typically missed by proteomic methods, including a labile TRIM58-OAS1 complex. We show that SPRY domains dictate substrate specificity: TRIM25 preferentially engages ZAP, whereas Riplet favors RIG-I. Domain-swapping experiments demonstrated that SPRY domains are sufficient to reprogram ligase specificity and antiviral activity. Phylogenetic and structural analyses revealed that TRIM25 and Riplet evolved from a common ancestor but diverged in coiled-coil architecture and oligomeric state, while retaining conserved substrate preferences. Residue-level modeling identified hypervariable SPRY loops as critical determinants of recognition, a prediction validated by targeted mutagenesis of the TRIM25-ZAP interface. Finally, we show that distinct SPRY-containing ligases surveil self-amplifying RNA (saRNA) vaccines: Riplet-RIG-I primarily responds when RNA is delivered by lipofection, whereas TRIM25-ZAP is engaged upon lipid nanoparticle delivery, with functional consequences for vaccine expression. Together, these findings demonstrate that SPRY domains encode recognition logic for ubiquitin ligases, that AlphaFold enables discovery of otherwise hidden interactions and that these principles have direct implications for RNA-based therapeutics.
    DOI:  https://doi.org/10.1371/journal.ppat.1014195
  23. bioRxiv. 2026 Apr 28. pii: 2026.04.26.720636. [Epub ahead of print]
    Paired CRISPR screens identify mitochondrial metabolism and UBE2H as aneuploid-specific dependencies in human cancer cell lines.
    Klaske M Schukken, Saron M Akalu, Charles Zou, Pranav K Kandikuppa, Ryan A Hagenson, Jessica L Keane, Mason P Lynch, Toyoki Yoshimoto, Olaf Klingbeil, Erin L Sausville, Sanat Mishra, Christopher R Vakoc, Zuzana Storchova, Sarah J Aitken, Jason M Sheltzer.
      Aneuploidy is a hallmark of cancer and imposes widespread cellular stress, including proteotoxicity, transcriptional dysregulation, and increased metabolic demand. Although these stresses are predicted to create therapeutic vulnerabilities, the genetic dependencies of aneuploid cells remain incompletely characterized. Here, we performed paired CRISPR loss-of-function screens in isogenic aneuploid and near-euploid cancer cell line models to systematically identify aneuploidy-specific dependencies. Seven genome-wide paired screens identified ribosomes, rRNA processing, spliceosome-mediated RNA processing, proteasome subunits, and mitochondrial metabolism as top aneuploid-specific dependency gene groups. To identify therapeutically targetable aneuploid dependencies, we performed 18 additional paired CRISPR screens using a focused druggable genome library. This analysis identified the ubiquitin-conjugating enzyme UBE2H as a top aneuploid-selective dependency. Functional validation confirmed aneuploid cell dependency on UBE2H, and mechanistic analyses linked UBE2H to mitochondrial protein abundance, suggesting a role in maintaining mitochondrial proteostasis under aneuploid stress. Together, these findings define core cellular systems that support the viability of aneuploid cells and identify UBE2H as a potential therapeutic vulnerability connecting ubiquitin signaling to mitochondrial homeostasis.
    DOI:  https://doi.org/10.64898/2026.04.26.720636
  24. Gastro Hep Adv. 2026 ;5(6): 100931
    Increased Protein Synthesis With Reduced Endoplasmic Reticulum Stress Defines a Specific Adaptation in Pancreatic Acinar Metaplasia.
    Maxime Libert, Sophie Quiquempoix, Leyre López-Muneta, Ludivine Wacheul, Sabine Cordi, Christiane Zorbas, Patrick Jacquemin.
       Background and Aims: Tumorigenesis is usually associated with increased protein synthesis rates coupled with increased endoplasmic reticulum (ER) stress. In the pancreas, acinar cells already exhibit a very high protein synthesis rate in normal physiological conditions, which raises the question of how this cell type adapts during pancreatic tumor formation. Here, we characterize how acinar cells modulate their protein synthesis rate in metaplastic lesions, which are precursor lesions of pancreatic ductal adenocarcinoma.
    Methods: We evaluated protein synthesis by puromycin incorporation assays and investigated the control of translation and ER stress by transcriptomic analyses and phenotyping of a mouse model of pancreatic ductal adenocarcinoma. We also assessed the level of ribosomal RNA methylation systematically using a deep sequencing-based technique, RiboMethSeq.
    Results: During pancreatic tumorigenesis, protein synthesis rates were significantly increased in acinar-to-ductal metaplasia compared with normal acinar cells. This was associated with enhanced expression and activity of translation initiation factors, and with increased production of ribosomal components and ribosome assembly factors. We detected differential ribosomal RNA methylation at conserved ribosomal positions near the peptidyl transferase center and the exit tunnel, suggesting a potential role in modulating translation and/or cotranslational protein folding. Despite increased protein synthesis, ER stress was reduced, which was associated with an overall reduction in N-linked glycosylation and increased expression of proteasome components.
    Conclusion: Our findings reveal a pancreas-specific adaptation of the translational machinery during tumorigenesis, characterized by the production of differentially modified ribosomes and a combination of increased protein synthesis rate and decreased ER stress. This highlights the diversity of adaptive protein synthesis in transforming tissues.
    Keywords:  ER Stress; Pancreatic Tumorigenesis; Ribosome; Translation Initiation
    DOI:  https://doi.org/10.1016/j.gastha.2026.100931
  25. Acta Neuropathol Commun. 2026 May 05.
    Targeting the integrated stress response or Ataxin-2 alleviates neurodegeneration in PolyGR models of C9orf72 associated frontotemporal dementia and amyotrophic lateral sclerosis.
    Nikki S Harper, Joanne L Sharpe, Jasmine Speranza, Ravinder Gulia, Jeffrey X Chen, Scott P Allen, Manpreet S Atwal, Stuart Pickering-Brown, Matthew R Livesey, Craig L Bennett, Andreas Prokop, Albert R La Spada, Ryan J H West.
      Frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS) are fatal, early-onset neurodegenerative diseases. The most common genetic cause of FTD and ALS is a G4C2 hexanucleotide repeat expansion in the C9orf72 gene. This mutation leads to the production of toxic dipeptide repeat proteins (DPRs), via repeat-associated non-AUG (RAN) translation. These DPRs disrupt stress granule (SG) dynamics, with SG regulators such as Ataxin-2 (ATXN2) implicated in disease risk. The integrated stress response (ISR), a key driver of SG formation via eIF2α phosphorylation, has been linked to C9orf72 expansions, but the role of individual DPRs in ISR activation remains unclear. Here, using Drosophila models expressing physiologically relevant repeat length DPRs, we identify poly(GR) as a novel activator of the ISR, inducing early and sustained eIF2α phosphorylation and SG accumulation prior to motor decline. Genetic inhibition of the ISR or knockdown of ATX2, the Drosophila orthologue of ATXN2, rescues motor deficits in these models. ATXN2 knockdown also reduces poly(GR) toxicity in mouse primary neurons. These findings position poly(GR) as a key driver of ISR activation and highlight ATXN2 and the ISR as promising therapeutic targets in C9orf72-associated FTD/ALS.
    Keywords:   Drosophila ; Amyotrophic lateral sclerosis; Ataxin-2; C9orf72; Frontotemporal dementia; Integrated stress response; Motor neurone disease; Stress granules
    DOI:  https://doi.org/10.1186/s40478-026-02301-2
  26. EMBO Rep. 2026 May 02.
    STREMI: a dual-function upstream ORF-encoded regulator of mitochondrial cristae architecture.
    Ruiyang Guo, Yabo Guo, Runguo Shu, Jiajia Qian, Jiawei Wang, Ruobing Li, Ti Qin, Ziyi Wang, Hongtao Tian, Mengchen Wu, Long Zhou, Xiaogang Guo, Shan Zhang.
      Eukaryotic mRNAs typically encode a single functional polypeptide, a principle challenged by the discovery of widespread non-canonical peptide-coding ORFs within 5'UTRs. However, their functional significance at the protein level remains underexplored. Using a four-layered pipeline, we identify 14 human transcripts predominantly transcribed in polycistronic forms, each encoding two conserved proteins. Focusing on the SLC35A4 transcript, we show that its 5'UTR encodes a mitochondrial inner membrane-localized microprotein that we name STREMI (SLC35A4 stress response regulating MICOS interactor). Sharing topology and motifs with the MICOS core subunit MIC10, STREMI regulates mitochondrial cristae morphogenesis in mice and human cells. Additionally, the STREMI-encoding uORF mediates stress-responsive translation of SLC35A4-a Golgi nucleotide sugar transporter-upregulating its translation during the integrated stress response. Evolutionary analyses indicate that these bicistronic transcripts likely arose through transcriptional readthrough following retroposition. We propose a mechanism of "gene symbiosis" that enables functional partitioning and coordinated translation of protein pairs from bicistronic transcripts.
    DOI:  https://doi.org/10.1038/s44319-026-00783-8
  27. Curr Opin Cell Biol. 2026 May 06. pii: S0955-0674(26)00033-5. [Epub ahead of print]100 102645
    Emerging mechanisms of COPII adaptation for large cargo ER export.
    Patrick Morley Phillips, Giulia Zanetti.
      Export of secretory proteins from the endoplasmic reticulum is mediated by the COPII coat which must accommodate diverse cargoes. While small COPII vesicles are well characterised, they do not explain ER exit of exceptionally large and abundant cargoes such as procollagens. Recent work has expanded the classic vesicular model of COPII-mediated secretion toward a more flexible view of the COPII coat architecture, in which cell- and cargo-specific regulators of coat turnover and membrane tethers can remodel ER exit sites (ERES) to meet cargo-specific demands. Multicellular organisms have evolved an expanded network of COPII paralogues and interacting proteins such as SURF4, TMEM proteins, and TANGO1 that may generate enlarged carriers, membrane tubules, or transient intercompartmental continuities for large cargo exit from the ER. This review highlights recent progress and remaining gaps in understanding how COPII is regulated to mediate ER export of large cargo and identifies priorities for future investigation.
    DOI:  https://doi.org/10.1016/j.ceb.2026.102645
  28. Biochem Soc Trans. 2026 05 27. 54(5): 449-460
    MGRN1 in development and disease: a unifying view of a versatile membrane-tethered E3 ubiquitin ligase.
    Alyssa Riglos, Teresa M Gunn, Jennifer H Kong.
      Mahogunin Ring Finger 1 (MGRN1) is a multifunctional E3 ubiquitin ligase with broad biological significance and belongs to a small group of membrane-tethered E3s capable of regulating signaling receptors at the plasma membrane. Studies in mice first revealed its physiological importance, as loss of Mgrn1 leads to a wide range of phenotypes, including abnormal pigmentation, congenital malformations, and neurodegeneration. Remarkably, MGRN1 localizes to multiple cellular compartments, including the plasma membrane, mitochondria, nucleus, and endo-lysosomal pathway. MGRN1 is also involved in several cellular processes, including receptor regulation, protein homeostasis, and mitochondrial maintenance. While studies have emphasized the importance of MGRN1, it has been difficult to define unifying principles governing its function. In the present review, we summarize and integrate published findings to develop a clearer picture of MGRN1's roles, focusing on phenotypes observed in mouse models and the signaling pathways MGRN1 regulates. We propose shared mechanistic themes that reconcile the functional diversity of this unique E3 ligase, highlight gaps in the current literature, and identify areas for further investigation to better understand MGRN1's role in disease and evaluate its potential relevance for targeted protein degradation strategies.
    Keywords:  E3 ubiquitin ligase; GPCR trafficking; MGRN1; receptor regulation; substrate specificity; ubiquitination
    DOI:  https://doi.org/10.1042/BST20250109
  29. Commun Biol. 2026 May 06.
    Targeting the IRE1α-XBP1 signaling axis impairs tumor growth and promotes myogenic differentiation in rhabdomyosarcoma.
    Anh Tuan Vuong, Aniket S Joshi, Phuong T Ho, Meiricris Tomaz da Silva, Bin Guo, Meghana V Trivedi, Ashok Kumar.
      Rhabdomyosarcoma (RMS) is a pediatric soft-tissue sarcoma arising from mesenchymal progenitors with skeletal muscle features. The unfolded protein response (UPR) maintains proteostasis during endoplasmic reticulum stress, with the IRE1α-XBP1 axis representing a key signaling branch. Here, we demonstrate that components of this pathway are significantly upregulated in RMS cell lines and primary tumors. Genetic or pharmacological inhibition of IRE1α or spliced XBP1 (sXBP1) suppresses cell proliferation, promotes terminal myogenic differentiation, and enhances vincristine-induced cytotoxicity in RMS cells. Silencing of sXBP1 further reduces the cancer stem-like cell population and impairs migration and invasion. Mechanistically, IRE1α-XBP1 signaling promotes RMS progression through sXBP1-dependent upregulation of BMPR1A and subsequent activation of BMP-SMAD1 signaling. Consistently, inducible knockdown of sXBP1 or pharmacological inhibition of IRE1α endonuclease activity significantly attenuates xenograft RMS growth. Collectively, these findings identify the IRE1α-XBP1 axis as a critical regulator of RMS growth, differentiation, and chemosensitivity, and support its therapeutic targeting in RMS.
    DOI:  https://doi.org/10.1038/s42003-026-10184-1
  30. Commun Biol. 2026 May 08.
    Discovery of a pyrazolopyridine alkaloid that mitigates neuronal ER stress and age-related decline.
    Salinee Jantrapirom, Apiwat Sangphukieo, Natsinee U-On, Pattaporn Poonsawas, Wasinee Wongkumool, Ranchana Yeewa, Chansunee Panto, Puttachat Poound, Ester Zito, Alice Marrazza, Luca Lo Piccolo.
      Endoplasmic reticulum (ER) stress contributes to the pathogenesis of neurodegenerative and age-associated diseases, motivating the search for compounds that enhance ER-stress resilience. Modulation of ER-redox pathways, including those associated with the oxidase ERO1A, can attenuate maladaptive unfolded protein response (UPR) signaling and improve cellular stress tolerance. Here we develop an integrative discovery strategy to identify natural compounds that mitigate ER-stress-associated phenotypes across cellular and organismal models. Structure-informed virtual screening guided by ERO1A biology prioritized the pyrazolopyridine alkaloid S88. In human SH-SY5Y-derived neurons, S88 improves survival and reduces tunicamycin-induced ER-stress markers. In Drosophila, S88 ameliorates neuromuscular and locomotor phenotypes in a UBQLN2-associated ALS model and improves aging-related outcomes. Biochemical assays did not detect inhibition of ERO1A or radical scavenging activity by S88, indicating that its molecular target remains to be identified. Together, these findings identify S88 as a natural-product scaffold that enhances ER-stress resilience across neuronal and in vivo models.
    DOI:  https://doi.org/10.1038/s42003-026-10226-8
  31. bioRxiv. 2026 Apr 27. pii: 2026.04.24.720540. [Epub ahead of print]
    Ubiquitylation by the GID/CTLH complex regulates the metabolic and innate immune response of macrophages to infection by Mycobacterium tuberculosis.
    Nelson V Simwela, Luana Johnston, Christopher M Sassetti, David G Russell.
      The GID/CTLH E3 ligase complex is implicated in several biological processes, yet its full substrate repertoire remains poorly defined. We recently identified the complex as a broad modulator of macrophage responses to Mycobacterium tuberculosis (Mtb) infection. Here, we use label-free proteomics and diGly capture analysis of Mtb-infected macrophages to define the GID/CTLH-dependent ubiquitylome. We identify thousands of dynamically altered ubiquitylation sites, with strong enrichment among proteins involved in cellular metabolism and innate immune signaling. Concurrent proteome analysis revealed extensive rewiring in GID/CTLH-deficient macrophages, with >90% of enriched pathways among increased proteins consisting of metabolic targets. Notably, inhibitory phosphatases (PTEN, INPP5D) also emerged as candidate substrates. Functional studies revealed proteasome-dependent stabilization of PTEN and INPP5D in GID/CTLH-deficient macrophages with each phosphatase individually exerting an influence on Mtb intracellular survival. Together, our study defines a GID/CTLH-dependent ubiquitylome in macrophages and identifies the complex as a central regulator of metabolism and antimicrobial immunity.
    Author summary: Mycobacterium tuberculosis (Mtb), the bacterium that causes tuberculosis (TB), survives and replicates within macrophages, key immune cells that normally eliminate pathogens. How macrophages control their internal cellular environment in response to infection remains incompletely understood. One such important cellular control system is ubiquitylation, in which proteins are tagged with ubiquitin to determine their functional fate or target them for degradation. We recently identified the GID/CTLH E3 ligase ubiquitylation complex as a critical modulator of macrophage antimicrobial responses to Mtb. Here, we used proteomics approaches to define the proteins controlled by the GID/CTLH complex in Mtb-infected macrophages. We found that this complex ubiquitylates a broad network of proteins involved in cellular metabolism and immune signaling. When the complex is disrupted, macrophages undergo extensive metabolic reprogramming, particularly increased mitochondrial energy production, while showing reduced inflammatory signaling. Despite this dampened immune response, these cells are better able to restrict Mtb growth. We also identified the phosphatases PTEN and INPP5D as targets controlled by the GID/CTLH complex that independently influence intracellular bacterial survival. Our findings demonstrate that the GID/CTLH complex is a critical regulator of metabolism and immune function, shaping the outcomes of Mtb infection.
    DOI:  https://doi.org/10.64898/2026.04.24.720540
  32. Biochem J. 2026 May 07. pii: BCJ20260108. [Epub ahead of print]
    The backside β-turn is a key structural element of Rad6-family E2 ubiquitin-conjugating enzymes.
    Mahesh B Chandrasekharan, Prakash K Shukla, Andrew M Leng, Hui-Hsuan Chen, Rajarshi Ganguly, Nicholas Newell.
      Protein ubiquitination regulates diverse cellular processes, and its dysregulation contributes to human disease, including cancer. E2 ubiquitin‑conjugating enzymes share a conserved UBC fold in which surface loops fine‑tune catalysis and partner interactions, yet the roles of individual loops remain incompletely defined. Here, we identify loop 3-a component of the "backside" β2-β3 hairpin-as a conserved structural and allosteric element in Rad6‑family E2s. Structural and bioinformatic analyses of yeast Rad6 and its human homologs (UBE2A/UBE2B) reveal that loop 3 forms an overlapping triple β‑turns, with variable first turn and a highly conserved second/third turn that links catalytic regulation to E3 ligase engagement. Systematic mutagenesis of the yeast Rad6 backside β‑turn (residues 42-51) shows that this element is required in vivo for Bre1‑dependent histone H2B Lys123 monoubiquitination, Rad18‑dependent PCNA monoubiquitination, and Ubr1/Ubr2‑dependent polyubiquitination and degradation of Sml1 and N‑end rule substrates, and related biological processes. Charge‑reversal mutations at backside β‑turn Glu49 and Asp50 disrupt E3 binding, whereas cancer‑relevant substitutions in kink‑inducing prolines (Pro43/Pro47) impair mono‑ and polyubiquitination without abolishing E3 interactions. Certain backside β‑turn mutations, including cancer-relevant variants, compromise steady-state levels following DNA damage, revealing them as conditional null or loss-of-function alleles. NMR spectroscopy demonstrates that Pro43/Pro47 mutations induce long‑range structural perturbations from backside β‑turn into the front‑face catalytic pocket, correlating with reduced in vitro ubiquitination activity. Deletion or alanine replacement of the β‑turn destabilizes yeast Rad6 and human UBE2A/UBE2B. Together, these findings establish the loop 3/backside β‑turn as a critical structural element of Rad6‑family enzymes.
    Keywords:  E2 enzyme; genome integrity; histones; protein turnover; proteostasis; ubiquitin
    DOI:  https://doi.org/10.1042/BCJ20260108
  33. Nat Commun. 2026 May 05.
    Global mitochondrial connectivity map reveals the landscape of yeast functional assemblies and conserved protein communities.
    Matthew Jessulat, Sadhna Phanse, Hiroyuki Aoki, Kirsten Broderick, Qingzhou Zhang, Inês Gomes Castro, Noelle Alexa Novales, Sakib Abrar Hossain, Tatiana Saccon, Mohamed Taha Moutaoufik, Thomson Patrick Joseph, Shahreen Amin, Larrisa Hoell, Zoran Minic, Yury Bykov, Noga Preminger, Sahily Gonzalez Crespo, Jamie Snider, Ashkan Golshani, Igor Stagljar, Jose R Rodriguez-Medina, Catherine F Clarke, Maya Schuldiner, Mohan Babu.
      Mitochondria are essential organelles whose functions depend on coordinated multiprotein complexes, yet their composition and organization remain incomplete. Here, we present a large-scale map of mitochondrial protein complexes by integrating affinity purification of 740 endogenously GFP-tagged mitochondrial proteins with biochemical co-fractionation of mitochondrial extracts from yeast (Saccharomyces cerevisiae) grown under respiratory conditions. Mass spectrometry identifies 13,716 high-confidence protein associations and defines 556 heteromeric complexes, many previously unknown. These assemblies reveal factors involved in coenzyme Q6 biosynthesis, membrane contact sites, phospholipid transport, and coordination with the MICOS complex during respiration. We further link 538 assemblies to 294 candidate human disease genes and construct a conservation map of 852,146 predicted mitochondrial interactions across 271 genomes, and validate key predictions in human cell lines and mouse brain tissue. Together, this work provides a comprehensive mitochondrial interactome, assigning functions to poorly characterized proteins, and offering insights into mitochondrial biology and disease-associated assemblies.
    DOI:  https://doi.org/10.1038/s41467-026-72525-2
  34. bioRxiv. 2026 Apr 27. pii: 2025.02.04.636058. [Epub ahead of print]
    Stress Granule Sequestration of CCR4-NOT Promotes Poly(A) Lengthening of Stress-Survival Transcripts.
    Yi-Cheng Tsai, Hiroyuki Uechi, Sean R Millar, Eileigh Kadijk, Alon Minkovich, John Paul Tsu Ouyang, Karl J Schreiber, Jie Qi Huang, Carina A Lyons, Vesal Kasmaeifar, Zhixin Zhang, Rico Barsacchi, Claudia Möbius, Antje Janosch, Jonathan C Savage, Olivia S Rissland, Hannes Röst, Anthony A Hyman, Ji-Young Youn.
      Cells adapt to stress by rewiring their post-transcriptional gene regulation. Stress granules-biomolecular condensates composed of polyadenylated RNAs and RNA-binding proteins-are implicated in this process, yet their precise functional roles remain debated. To address this, we mapped the dynamic proteomic landscapes of stress granules formed under oxidative and hyperosmotic stress using multi-bait BioID proximity profiling coupled with quantitative mass spectrometry. This analysis revealed context-specific remodeling of proximal interaction networks and identified a conserved, stress-dependent shift in association with the CCR4-NOT deadenylase complex. A complementary genome-wide chemical genetic screen further implicated CCR4-NOT in stress granule biology, showing that reduced CCR4-NOT activity bypassed lipoamide-mediated inhibition of stress granule assembly. Microscopy showed sequestration of the CCR4-NOT complex into stress granules, and global transcriptomic analyses revealed that this relocalization promotes poly(A) tail lengthening and increased abundance of stress-induced survival transcripts. Together, integration of proteomics, chemical genetics, and transcriptomics uncovers a spatial mechanism by which stress granule assembly promotes cellular adaptation to stress through sequestration of CCR4-NOT from the cytosol and consequent remodeling of post-transcriptional regulation.
    DOI:  https://doi.org/10.1101/2025.02.04.636058
  35. Biomolecules. 2026 Mar 27. pii: 506. [Epub ahead of print]16(4):
    Adaptive Regulation of mTOR Activity by AMPK, Akt, and ATF6 Pathways in Pi*Z Alpha-1 Antitrypsin Deficient Hepatocytes.
    Yuanqing Lu, Jungnam Lee, Naweed Mohammad, Mark L Brantly.
      Alpha-1 antitrypsin deficiency (AATD) is an inherited disorder characterized by intracellular retention of mutant Z (Pi*Z) alpha-1 antitrypsin (AAT) within hepatocytes, resulting in progressive liver disease. Currently, no approved pharmacological therapies exist for AATD-associated hepatic injury. Emerging preclinical evidence indicates that inhibition of mammalian target of rapamycin (mTOR) ameliorates liver pathology in AATD; however, the status of mTOR activity and its regulatory mechanisms under Pi*Z AAT-induced cellular stress remains incompletely understood. In this study, we investigated alterations in mTOR signaling and its upstream regulatory pathways using a gene-edited human hepatocyte model harboring the Pi*Z mutation (Huh7.5Z cells) and a Pi*Z AAT transgenic mouse model. Attenuation of mTORC1 activity was observed in both cellular and murine Pi*Z models. In vitro analyses demonstrated activation of AMP-activated protein kinase (AMPKα), a key inhibitory regulator of mTORC1, accompanied by paradoxical activation of Akt and the unfolded protein response (UPR) branch ATF6α. Pharmacological inhibition of mTOR significantly reduced intracellular Pi*Z AAT accumulation, alleviated ER stress, and suppressed apoptotic signaling through enhancement of autophagy. These findings reveal that hepatocytes adapt to Pi*Z AAT-induced stress through coordinated regulation of mTOR by AMPK, Akt, and ATF6α pathways. This study provides mechanistic insight into metabolic and stress-response signaling in AATD and identifies mTOR modulation as a promising therapeutic strategy for AATD-associated liver disease.
    Keywords:  AMPK; ATF6; Akt; ER stress; alpha-1 antitrypsin deficiency; autophagy; hepatocytes; mTOR
    DOI:  https://doi.org/10.3390/biom16040506
  36. bioRxiv. 2026 Apr 25. pii: 2026.04.24.719390. [Epub ahead of print]
    Phosphorylated ubiquitin is a secondary messenger and an epigenetic mark mediating mitochondria to nucleus signaling.
    Thomas J Mercer, Bence Daniel, Craig Fredrickson, Daniel Le, Serena Lee, Vineet Vinay Kulkarni, Xu Hou, Fabienne C Fiesel, Hai Ngu, Min Jung, Brent J Ryan, Rachel Heon-Roberts, Amelia J Smith, Vasumathi Kameswaran, Tommy K Cheung, Denise Gastaldo, Dennis W Dickson, Wolfdieter Springer, Claire Jeong, Oded Foreman, Christopher M Rose, Baris Bingol.
      Parkinson's disease (PD) is commonly associated with dysfunctional mitochondrial homeostasis. PINK1, a S/T kinase mutated in early-onset PD, generates phosphoserine 65 ubiquitin (pS65Ub) on damaged mitochondria facilitating their removal. Here, we show that pS65Ub translocates into the nucleus after generation at damaged mitochondria and is directly attached to substrates by resident E3 ligases. Histone H2A is a major substrate and is modified at lysine 119 (H2AK119) by the polycomb silencer, E3 ligase RING1B. At nucleosomes, pS65Ub simultaneously suppresses RING1B and potentiates H2A deubiquitinases USP16 and USP21. Epigenetic profiling and RNA sequencing reveal that pS65Ub is enriched at the promoters of poorly expressed yet dynamically regulated genes and is associated with H2AK119ub depletion. Functionally, we show that pS65Ub enrichment drives polycomb target gene expression, which accelerates the maturation of dopaminergic neurons. Importantly, post-mortem PD brains exhibit elevated nuclear pS65Ub, potentially linking nuclear pS65Ub accumulation with disease pathogenesis. Together, these data indicate that pS65Ub generated at damaged mitochondria regulates fundamental cellular processes at distant sites.
    DOI:  https://doi.org/10.64898/2026.04.24.719390
  37. iScience. 2026 May 15. 29(5): 115736
    Impaired collagen deposition in the absence of ERp44.
    Maria Pannese, Barbara Canciani, Marta Carnovali, Marco Dalla Torre, Gianpiero Gallucci, Laura Mangiavini, Massimo Mariotti, Paola Panina-Bordignon, Rob Van't Hof, Roberto Sitia, Tiziana Anelli.
      The biogenesis of secretory proteins proceeds under sequential quality control checkpoints operating along the exocytic pathway. Unlike other chaperones that reside primarily in the endoplasmic reticulum, ERp44 cycles through the Golgi to control the assembly of polymeric proteins and the localization of a few endoplasmic reticulum resident enzymes (ERAP1, Prx4, Ero1α, and SUMF1). To gain information about its pathophysiological role, we generated ERp44-deficient models. ERp44 KO mice are smaller than control siblings, and show skeletal malformations and delayed bone development, with reduced collagen deposition. Similar skeletal defects were also observed in ERp44 knocked down zebrafish embryos, supporting a conserved role for ERp44 in skeletal development. In cellular models, ERp44 downregulation dramatically affects collagen type 1 deposition, causing intracellular procollagen 1 accumulation. We thus conclude that the levels of ERp44 are crucial for efficient collagen deposition.
    Keywords:  Biochemistry; Developmental biology; Molecular biology
    DOI:  https://doi.org/10.1016/j.isci.2026.115736
  38. Nat Commun. 2026 May 07.
    A conserved ER protein prevents lipotoxicity by stimulating the key enzyme in glycerolipid synthesis.
    Yan Li, Siwei Huang, Lam Shing Chan, Xuesong Li, Ning-Sum To, Xue Zhao, Kwangsek Jung, Xingyu Yang, Yu Chung Tse, Ningyi Xu, Yu Xia, Tom H Cheung, Jianan Qu, Ho Yi Mak.
      The synthesis of glycerolipid is essential to prevent the toxic effects of excess fatty acids. Glycerolipids are generated by the sequential attachment of acyl-CoA to glycerol by endoplasmic reticulum (ER)-localized acyltransferases, ultimately yielding non-toxic triacylglycerol that can be stored in lipid droplets. The key acyltransferase GPAT4 associates with the CHP1 protein, but the regulation of GPAT4 remains poorly understood. Here, we have used genetic, biochemical, and imaging techniques to identify TMEM120A as GPAT4-activating protein. We show that ER-localized TMEM120A and CHP1 synergistically activate GPAT4 and promote the incorporation of medium and long chain acyl-CoA into glycerolipid. C. elegans mutants of TMEM120A or CHP1 ortholog are susceptible to high-fat diet induced sterility, in part due to their deficiency in lipid droplet expansion. In mammalian cells, fatty acid supplementation and myristoylated CHP1 enhance the association of TMEM120A with GPAT4. Together, our results reveal an unexpected mechanism that alleviates lipotoxicity.
    DOI:  https://doi.org/10.1038/s41467-026-72786-x
  39. J Cell Biol. 2026 Jul 06. pii: e202411196. [Epub ahead of print]225(7):
    Mitochondrially tethered Mmm1 can function as a sole lipid transporter at ER-mitochondria contacts.
    Christian Covill-Cooke, Takashi Hirashima, Shin Kawano, Joe Ganellin, Andrew Moody, Sabine N S van Schie, Arun T John Peter, Chika Horie Saito, Toshiya Endo, Benoît Kornmann.
      Yeast mitochondria receive the majority of their lipids from the ER via the heterotetrameric ERMES lipid transport complex. This complex is thought to establish a lipid-transporting bridge of fixed composition spanning the space between both organelles. Intriguingly, however, some of the lipid-transporting components of the complex can be replaced by an artificial ER-mitochondria tether without lipid transport activity, questioning ERMES' relevance in lipid transport. Here, we show that Mmm1, one of the four ERMES subunits, alone is sufficient to support ERMES function when it is artificially tethered to mitochondria, provided its lipid-binding domain is intact. Combined with our previous finding that the absence of Mdm12 and Mdm34 can be rescued by the presence of Mmm1 and the artificial tethering protein ChiMERA, our results suggest that Mmm1 can act as the sole lipid transporter at the ER-mitochondrial contact sites, provided that Mdm10 is present, even in the absence of the other two subunits. Thus, our work reconciles ERMES' importance in lipid transport with the fact that the lipid transport activity of some of its components is not strictly necessary for function.
    DOI:  https://doi.org/10.1083/jcb.202411196
  40. bioRxiv. 2026 Apr 21. pii: 2026.04.20.719509. [Epub ahead of print]
    Ribosome biogenesis bottlenecks reveal vulnerabilities in cancer.
    Lifei Jiang, Qiwei Yu, Sofia A Quinodoz, Jordy F Botello, Sabreen Alam, Jing Xia, Jonida Trako, Troy J Comi, Aya A Abu-Alfa, Yong Wei, Andrej Košmrlj, Yibin Kang, Clifford P Brangwynne.
      Cell growth requires elevated protein synthesis, which depends on the production of ribosomes. Ribosome biogenesis is a complex, multi-step pathway in which newly transcribed precursor ribosomal RNA (rRNA) undergoes coordinated processing and assembly in the nucleolus to produce the small and large ribosomal subunits (SSU and LSU). 1-3 Oncogene activation stimulates rRNA transcription and processing, giving rise to enlarged nucleoli that produce thousands of ribosomes every minute. 4,5 However, efficient ribosome production requires tight coordination across numerous maturation steps, and it remains unclear if elevated rDNA transcription is proportionally converted into mature ribosomes, or whether imperfect coordination constrains the output yield. Here, we quantify pre-rRNA transcription (input) and compare it with newly-assembled cytoplasmic ribosomes (output), revealing that oncogene activation reduces the efficiency of ribosome production. Using a quantitative pulse-chase sequencing approach with mathematical modeling to resolve rRNA maturation kinetics, we found that oncogene activation creates late-stage processing bottlenecks, characterized by delayed precursor maturation and increased degradation. Perturbation of late-stage ribosome biogenesis factors preferentially impaired oncogene-driven cell growth, and limited tumor growth in mouse models, suggesting that these bottlenecks represent selective vulnerabilities in cancer, created by imbalanced biosynthetic flux. Together, these findings reveal that oncogene-driven ribosome production is imperfectly coordinated across maturation steps, and suggest that capacity limits in multi-step assembly pathways may be therapeutically exploitable in cancer and other diseases.
    DOI:  https://doi.org/10.64898/2026.04.20.719509
  41. bioRxiv. 2026 Apr 24. pii: 2026.04.21.719983. [Epub ahead of print]
    HSF1-mediated Proteostasis Decline Links Aging and Sleep Disruption.
    Shintaro Yamazaki, Akhilesh B Reddy.
      Sleep disruption increases with age and is associated with adverse age-related outcomes, yet the molecular mechanisms linking these phenomena remain unclear. Here, through integrative analysis of human and mouse transcriptomic and proteomic datasets, we identify proteostasis-related pathways whose aging trajectories align with transcriptional responses to chronic sleep disruption across tissues and cell types. In the human prefrontal cortex, gene expression exhibits coherent age-associated directional shifts. Across human peripheral blood following sleep restriction and multiple aging mouse tissues and cell types, proteostasis pathways exhibit concordant downregulation. Among these, heat shock response pathways emerge as the most persistent and cross-modal signatures, with components of the heat shock factor 1 (HSF1)-mediated proteostasis network displaying diminished inducibility with age and chronic sleep insufficiency, in contrast to transient activation following short-term sleep deprivation. This attenuation is particularly pronounced in neurons, where age-associated suppression of HSF1 target programs indicates selective vulnerability of neuronal proteostasis. Spatial and single-cell analyses map this vulnerability to hippocampal circuits during aging and to superficial cortical layers and glutamatergic neurons in Alzheimer's disease. These findings support a model in which repeated sleep disruption progressively reduces the inducible capacity of proteostatic stress responses, shifting from adaptive activation to progressive attenuation and accelerating age-related decline in proteome maintenance. Consistent with emerging functional evidence, this identifies HSF1-mediated proteostasis as an integrative axis linking sleep stability and molecular aging, suggesting a self-reinforcing relationship in which sleep disruption and proteostasis decline reciprocally exacerbate one another. These results connect transient molecular responses to sleep perturbations with long-term aging trajectories, revealing a systems-level mechanism through which cumulative sleep disruption may increase vulnerability during aging.
    DOI:  https://doi.org/10.64898/2026.04.21.719983
  42. J Am Chem Soc. 2026 May 06.
    Interface Architecture of a VHL-PROTAC Complex with and without Cullin-2.
    Evan N Whitford, Joshua D Gilbert, Marius M Kostelic, Aaron C Ehlinger, Tiffany A Thibaudeau, Shaun M McLoughlin, Vicki H Wysocki.
      Proteolysis Targeting Chimeras (PROTACs) are bispecific molecules that link a target protein to an E3 ligase, leading to ubiquitination and subsequent degradation. Their efficacy depends on their ability to form ternary complexes for target ubiquitination, which is influenced by protein-protein interactions. Native mass spectrometry combined with surface-induced dissociation (SID) is a sensitive technique for rapidly assessing protein structures, including stoichiometry and interfacial strengths. Native mass spectrometry can also capture a variety of conformational states in the gas phase, reflecting the intrinsic flexibility of many protein assemblies. This ability to resolve structural heterogeneity and transient subpopulations provides complementary insights not as readily accessible through crystallography, cryo-EM, or other ensemble-averaging assays. By coupling native mass spectrometry with surface-induced dissociation, topological features, specifically relative interfacial strengths and subcomplex arrangements, were probed with and without the scaffold protein Cullin-2 added to a PROTAC-mediated ternary complex. PROTAC-mediated ternary complexes yield rich SID fragmentation into several subcomplexes. The extensive fragmentation observed for the PROTAC-assembled complex lacking Cullin-2 suggests that this Cullin-free ternary complex is more conformationally flexible, enabling multiple accessible subcomplex topologies. Although PROTACs facilitate strong, noncovalent interactions between the target protein and the E3 ligase, the addition of Cullin-2 reduced the conformational flexibility of the E3 ligase complex. This results in a pronounced reduction in fragmentation and offers critical insight into the hierarchical connectivity of the ternary complex.
    DOI:  https://doi.org/10.1021/jacs.6c01509
  43. Nat Struct Mol Biol. 2026 May 07.
    Membrane insertion of mitochondrial-encoded proteins regulates ribosome decoding speed.
    Thomas Schöndorf, Valentyn Petrychenko, Ilgin Kotan, Drishan Dahal, Natalia Napieraj, Luis Daniel Cruz-Zaragoza, Cong Wang, Oliver Urbach, Tanja Gall, Sven Dennerlein, Günter Kramer, Niels Fischer, Peter Rehling.
      The human mitochondrial genome encodes 13 subunits of the oxidative phosphorylation system essential for energy metabolism to drive cellular activities. Translation of 11 mRNAs by membrane-bound ribosomes is coupled to insertion of the nascent polypeptides into the inner membrane aided by the OXA1L insertase. To this end, the mechanism of membrane insertion of nascent polypeptides and the functional link to the translation process are not sufficiently understood. Here, we applied ribosome profiling to assess translation dynamics in combination with cryo-electron microscopy analysis of a COX1 ribosome-nascent chain complex to visualize cotranslational folding of the nascent chain. We find that the membrane topology of the translation product impacts translation speed and that positioning of amphipathic helices in the ribosome vestibule induces structural changes, correlating with translation pausing events. Thus, our findings reveal a link between translation process and folding and membrane insertion of nascent polypeptides at the inner mitochondrial membrane.
    DOI:  https://doi.org/10.1038/s41594-026-01803-w
  44. Sci Adv. 2026 May 08. 12(19): eaee2303
    A unified mechanism for tubulin cofactors catalyzing α/β-tubulin biogenesis and degradation.
    Aryan Taheri, Md Ashaduzzaman, Vishv Gill, Julian A Eskin, Jawdat Al-Bassam.
      Microtubules polymerize from cytoplasmic pools of soluble αβ-tubulin heterodimers that support diverse cellular functions. The tubulin cofactors, TBCC, TBCD, and TBCE and the Arl2 GTPase, form TBC-DEG assemblies that regulate the assembly of α- and β-tubulin into heterodimers and their disassembly, yet their underlying mechanisms remain incompletely understood. Here, we reconstitute the human TBC-DE and TBC-DEG assemblies from eukaryotic cells copurified with monomeric β-tubulin intermediates and determine their cryo-EM structures. The structures reveal that TBC-DEG disassembles αβ-tubulin by releasing α-tubulin through a lever arm-like rotation in TBCE coupled to major conformational change in Arl2 upon its nucleotide release, while TBCD tightly holds β-tubulin. TBCD dissociates α-tubulin by refolding the β-tubulin H10-S8 loop at its intradimer interface. The TBC-DEG-β-tubulin or TBC-DE-β-tubulin assemblies undergo extensive back-to-back dimerization mediated by β-β-tubulin homodimers, formed through their dissociated H8 helices at unoccupied intradimer interfaces. Structural comparisons demonstrate that TBCE's mechanical rotation, driven by the Arl2 GTPase cycle, either delivers α-tubulin or removes it from beneath the TBCD-bound β-tubulin and is directionally regulated by TBCC stabilizing αβ-tubulin interfaces. Our findings suggest that TBC-DEG/TBCC catalyzing heterodimerization of α-tubulin with β-tubulin may have evolved to counteract β-tubulin's intrinsic tendency to form off-pathway toxic homodimers through its exposed α-tubulin-binding intradimer interface.
    DOI:  https://doi.org/10.1126/sciadv.aee2303
  45. bioRxiv. 2026 Apr 27. pii: 2026.04.26.720784. [Epub ahead of print]
    Mechanism of nucleolytic degradation of human ribosomes.
    Frances F Diehl, Allen R Buskirk, Rachel Green.
      Stresses like starvation trigger degradation of mature 40S ribosomes, requiring the coordinated breakdown of large and stable RNA-protein complexes. The atypical kinase RIOK3 orchestrates degradation by binding ubiquitylated 40S ribosomes and promoting rRNA decay. However, the mechanisms and factors that mediate rRNA decay remain unknown. Here we find that in response to starvation, RIOK3 recruits the terminal uridylyl-transferase TUT7 and the exonuclease DIS3L2 to 40S ribosomes. Sequencing analyses show that TUT7 adds oligo(uridine) tails to the 3' end of the 18S rRNA in these ribosomes. DIS3L2 subsequently recognizes uridylated 18S rRNA and carries out 3'-5' decay. We identify major decay intermediates that undergo further uridylation in a process of iterative uridylation and decay. Loss of DIS3L2 impairs 18S rRNA decay during starvation and leads to accumulation of uridylated 18S rRNA. Together these findings define a mechanism for ribosome degradation in which 3' oligo(uridine) tailing drives decay of rRNA from ribosomes.
    DOI:  https://doi.org/10.64898/2026.04.26.720784
  46. Nat Commun. 2026 May 07.
    Signal peptide peptidase-like proteases OsSPPL1 and OsSPPL2 facilitate ER-associated protein degradation in rice.
    Hai-Ping Lu, Jian-Hang Xu, Jia-Xin Chang, Hui-Dan Luo, Jian-Xiang Liu.
      Signal peptide peptidases (SPPs) play a critical role in intramembrane proteolysis of signal peptides in mammals. However, their function in plants remains poorly understood. Here, we uncover the critical role of two rice SPP-like proteins, OsSPPL1/ 2, in ER-associated degradation (ERAD). Their expression is directly upregulated by OsbZIP50 under ER stress conditions. Mutations in OsSPPL1/2 result in increased ER stress sensitivity, whereas their overexpression enhance ER stress tolerance. We further demonstrate that OsSPPL1/2 localize in ER, and physically interact with the ERAD components OsDER1/2, indicating their involvement in ERAD. Using a GFP protein fused with a segment of maize floury-2 protein defective in signal peptide cleavage (ZmFL2m-GFP), we show that OsSPPL1/2 interact with ZmFL2m-GFP in ER and facilitate its degradation in tobacco leaves and rice plants. Additionally, OsSPPL1/2 double mutants exhibit exaggerated thermal sensitivity, while OsSPPL1/2-overexpressing plants display improved thermotolerance. Together, our findings identify OsSPPL1/2 as components of ERAD and highlight the importance of ERAD in plant thermotolerance.
    DOI:  https://doi.org/10.1038/s41467-026-72830-w
  47. bioRxiv. 2026 Apr 30. pii: 2026.04.27.721160. [Epub ahead of print]
    An integrated RNA-centric imaging and omics approach reveals distinct properties and composition of neuronal RNA granules.
    Jackson A Rogow, Ella Doron-Mandel, Ronald Cutler, Leti Núñez, Ricardo Vazquez, Laura Harris, Marko Jovanovic, Robert H Singer, Sulagna Das.
      RNA granules are essential regulators of post-transcriptional gene expression, enabling mRNA transport, localization, and local translation in neurons. The localized transcriptome is diverse; however, how different mRNAs are organized into granules for efficient localization and translation remains unknown. Here, we combine real-time endogenous single RNA imaging with protein and RNA proximity labeling to investigate two distinct endogenous neuronal mRNA granule populations, Actb and Arc , in stimulated primary hippocampal neurons. Using orthogonal RNA labeling systems in a dual knock-in mouse model, we show that Actb and Arc mRNAs are packaged into spatially segregated granules with distinct trafficking dynamics, localization kinetics, and responses to synaptic stimulation. Actb granules displayed rapid and sustained localization, whereas Arc granules showed delayed, transient recruitment, consistent with their respective roles in structural and activity-dependent plasticity. Proximity labeling reveals that these granules are distinct in their mRNA composition, despite sharing core RNA-binding proteins, suggesting that shared cis-regulatory elements within mRNA 3'UTR regions drive selective co-packaging of mRNAs into unique granules. Together, these findings demonstrate that neuronal mRNAs are differentially sorted into molecularly and functionally distinct granules, providing a framework for understanding how precise spatio-temporal control of mRNA localization and translation is achieved across complex neuronal arbors.
    DOI:  https://doi.org/10.64898/2026.04.27.721160
  48. Nat Struct Mol Biol. 2026 May 08.
    Evaluating generalization in protein-ligand cofolding methods.
    Peter Škrinjar, Jérôme Eberhardt, Gabriel Studer, Gerardo Tauriello, Torsten Schwede, Janani Durairaj.
      Deep learning has driven major breakthroughs in protein structure prediction; however, one of the next critical steps forward is accurately predicting how proteins interact with small-molecule ligands, to enable real-world applications such as drug discovery. Recent cofolding methods aim to address this challenge, but evaluating their performance has been inconclusive because of the lack of relevant benchmarking datasets. Here we present a comprehensive evaluation of four leading all-atom cofolding methods using our newly introduced benchmark dataset, Runs N' Poses. Runs N' Poses comprises 2,600 high-resolution protein-ligand systems released after the training cutoff used by these methods. We demonstrate that current cofolding approaches largely memorize ligand poses from their training data, hindering their use for de novo drug design. With this assessment and benchmark dataset, we aim to accelerate progress in the field by allowing for a more realistic assessment of the current state-of-the-art deep learning methods for predicting protein-ligand interactions.
    DOI:  https://doi.org/10.1038/s41594-026-01797-5
  49. bioRxiv. 2026 May 01. pii: 2026.04.28.721421. [Epub ahead of print]
    A sterol-binding pocket in iRhom1 underlies paralog-specific regulation of the sheddase ADAM17.
    Fangfang Lu, Hongtu Zhao, Yaxin Dai, Chia-Hsueh Lee, Matthew Freeman.
      ADAM17, the major sheddase in mammalian cells, releases membrane-tethered EGFR ligands and inflammatory cytokines, and is a central regulator of cell signalling. The rhomboid pseudoproteases, iRhom1 and iRhom2, function as essential cofactors of ADAM17, controlling its maturation and activation. In contrast to the well-characterized iRhom2, the mechanism and regulation of its ubiquitously expressed paralog iRhom1 remain undefined. Here, we present a 2.5 angstrom cryo-EM structure of the full-length human iRhom1/ADAM17 complex, revealing a previously unrecognized sterol-binding pocket located between TMD2 and TMD5. Structure-guided mutagenesis and pharmacological perturbation of sterol binding demonstrate that sterol binding is required to stabilize the iRhom1/ADAM17 complex and sustain its shedding activity. Strikingly, this regulation is paralog-specific: iRhom2 precludes sterol binding and instead stabilizes ADAM17 through direct intramolecular interactions. Furthermore, two human iRhom1 variants associated with cardiac disease localize adjacent to the sterol-binding pocket and disrupt ADAM17 maturation and activity. Together, these findings uncover mechanistic divergence between iRhom paralogs and establish a sterol-binding pocket in iRhom1 as a critical determinant of ADAM17 stability, revealing a potential avenue for paralog-selective therapeutic targeting.
    DOI:  https://doi.org/10.64898/2026.04.28.721421
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