bims-proteo Biomed News
on Proteostasis
Issue of 2026–03–29
fifty-one papers selected by
Eric Chevet, INSERM
  1. The coordinated action of UFMylation and the RQC pathways clears arrested polypeptides at the ER.
  2. NAC promotes co-translational protein folding at the ribosomal tunnel exit.
  3. The E3-ome gene-centric compendium reveals the human E3 ligase landscape.
  4. A molecular switch in NAC prevents mitochondrial protein mistargeting by SRP.
  5. Dynamic translocation of Inside-Out proteins to the cell surface underlies cellular adaptation to cancer-induced stress.
  6. RNF25 confers mRNA damage tolerance by curbing activation of the integrated stress response.
  7. Cytosol-dwelling bacteria engage in a ubiquitination race to avoid antibacterial autophagy.
  8. An Optimized RNF126-Targeting Covalent Handle for Molecular Glue Degraders.
  9. Ribosome Molecular Aging Shapes Translation Dynamics.
  10. Receptor-ubiquitination-targeting antibody-drug conjugates for enhanced endocytosis and lysosomal delivery.
  11. Survey of the human proteostasis network: the ubiquitin-proteasome system.
  12. Systems-level organization of extracellular proteostasis.
  13. The Human Autophagy Core Complexes.
  14. Structural dynamics of the midnolin-proteasome during ubiquitin-independent substrate turnover.
  15. Small-molecule degraders for oncogenic KRASG12C and pan-KRAS mutations.
  16. Gcn2 deficiency triggers anemia and hypoxic intolerance in zebrafish.
  17. High-Throughput Platform for Discovery of Chemical Inhibitors of Heat Shock Protein 70 (Hsp70): Adaptation for the Specialized Bacterial HscA-HscB-IscU Complex.
  18. Cnpy1 is a candidate endoplasmic reticulum chaperone of vomeronasal type 2 GPCRs.
  19. RanBP2-dependent annulate lamellae drive nuclear pore assembly and nuclear expansion.
  20. MCTP1 and MCTP2 promote ER-PM contact sites and regulate PI4P homeostasis and cell migration.
  21. The Erlin1/2 complex is a dynamic scaffold for membrane microdomain assembly on the endoplasmic reticulum.
  22. Structural transitions in the stepwise assembly of proteasome core particles.
  23. CAND1 and CAND2 drive CUL4 substrate receptor exchange with largely comparable biochemical efficiency, unlike their relative effects on CUL1.
  24. Stress Responses Tied to Metastasis and Immune Evasion.
  25. Mechanism of ribosome stalling by the AMD1 C-terminal tail arrest peptide.
  26. Substrate-interacting pore loops of two ATPase subunits determine the degradation efficiency of the 26S proteasome.
  27. Salmonella Typhi asparaginase-dependent activation of GCN2 promotes bacterial killing in murine macrophages.
  28. Hsp70-Targeting Chimeras Enable Dual Proteasomal and Lysosomal Degradation of Intracellular and Extracellular Proteins.
  29. Structure-function analysis of the bacterial ClpE/ClpP AAA+ protease.
  30. Nonsense-mediated mRNA decay safeguards telomeres in pluripotent stem cells.
  31. STING signaling modulation by COPII cargo recognition.
  32. UFMylation-dependent inhibition of AKT signaling by PHLDA3 in lung adenocarcinoma.
  33. A quantitative cell-based reporter links TDP-43 aggregation and dysfunction to define pathogenic mechanisms.
  34. Repair condensates and lipid domains in lysosome integrity.
  35. NLRP1B is an integrated decoy that subverts Shigella flexneri E3 ligase activity to promote effector-triggered immunity.
  36. Protocol for quantifying silent ribosome induction in yeast and mammalian cells using polysome profiling.
  37. Stress-Encoded Mitochondrial Plasticity: ATF4 Control of Mega-Mitochondria and Nanotunnel Communication.
  38. Stress-induced OMA1-mediated cleavage of AIFM1 suppresses cell growth by controlling mitochondrial OXPHOS activity.
  39. UFMylation of Pyruvate Dehydrogenase Regulates Mitochondrial Metabolism.
  40. Molecular determinants and therapeutic targeting of stop codon readthrough in eukaryotic translation.
  41. Cellular Repair and Removal of Protein-Damage Modifications.
  42. Proteasome inhibition promotes Foxn1 expression in thymic epithelial cells and induces thymic regeneration in mice.
  43. Optineurin calibrates STING-mediated type I interferon response.
  44. Common and rare genetic variants show network convergence for a majority of human traits.
  45. ULK1 drives NDP52-mediated selective autophagic degradation of MHC-I to promote immune evasion in HPV-positive head and neck cancer.
  46. A molecular grammar for programmable multiphase protein-RNA vesicles.
  47. VAMP8 function reveals tight linkage between endocytic recycling and endocytosis.
  48. Structural and evolutionary insights into the eukaryotic RNase MRP ribonucleoprotein complex.
  49. USP25 aggravates liver cancer development and impairs chemosensitivity by limiting LATS1 activation.
  50. Structural basis of receptor retro-translocation in peroxisomal protein import.
  51. Roles of DNA Damage Response Pathway in the Regulation of the Nuclear Envelope.
  1. EMBO J. 2026 Mar 25.
    The coordinated action of UFMylation and the RQC pathways clears arrested polypeptides at the ER.
    Milica Mihailovic, Aleksandra S Anisimova, Bu Erte, Ni Zhan, Ioanna Styliara, Yasin Dagdas, Gülsün Elif Karagöz.
      Clearance of arrested nascent polypeptides resulting from ribosomal stalling is essential for proteostasis. Stalled endoplasmic reticulum (ER)-bound ribosomes are marked by ubiquitin-fold modifier 1 (UFM1) on the large ribosomal subunit protein RPL26, but the precise role of this modification in ribosome-associated quality control (RQC) remains poorly understood. Here, we define the interplay between the UFMylation machinery and the RQC in clearing arrested polypeptides upon ribosome stalling at the ER. Proteomic analysis shows that RQC factors associate with UFMylated ribosomes. Functional assays demonstrate that ribosome rescue factors ZNF598 and ASC-1 recognize and split stalled ribosomes at the ER, a prerequisite for RPL26 UFMylation. The UFM1 E3 ligase complex then binds and UFMylates the post-split 60S-peptidyl-tRNA complex, facilitating access of RQC factors. Depletion of the NEMF/LTN1 complex leads to accumulation of UFMylated ribosomes, whereas impaired UFMylation weakens NEMF/LTN1 binding to ER-stalled ribosomes, supporting a physical link between these pathways. These findings demonstrate that RQC cooperates with the UFMylation machinery to overcome the topological constraints of clearing the arrested polypeptides at the ER.
    Keywords:  Endoplasmic Reticulum; Ribosome Stalling; Ribosome-associated Quality Control; Translation; UFMylation
    DOI:  https://doi.org/10.1038/s44318-026-00753-9
  2. Mol Cell. 2026 Mar 23. pii: S1097-2765(26)00136-X. [Epub ahead of print]
    NAC promotes co-translational protein folding at the ribosomal tunnel exit.
    Jaime Santos, Manuel Günnigmann, Radoslaw J Gora, Marija Iljina, Masa Predin, Ilgin Eser Kotan, Pratiman De, Dhawal Choudhary, Juwon Jang, Frank Tippmann, Christopher Hins, Nenad Ban, Sander J Tans, Shu-Ou Shan, Günter Kramer, Bernd Bukau.
      The nascent polypeptide-associated complex (NAC) coordinates enzymatic modifications and membrane targeting of nascent chains during translation. While the role of NAC as a dynamic hub for other factors is well established, its direct role in co-translational folding is unclear. By proteome-wide profiling of co-translational NAC interactions in human cells, we found that NAC recognizes emerging segments enriched in hydrophobicity and α-helical propensity within folded domains of cytonuclear proteins. Single-molecule and structural analyses reveal that NAC, via its β-barrel domain, dynamically interacts with nascent chains at the ribosomal tunnel exit and is capable of promoting on-pathway folding. Compartment-specific nascent chain interactions of NAC further elucidate its role in targeting to the endoplasmic reticulum and in mitochondrial membrane protein biogenesis. Together, these findings show that human NAC acts as a bona fide co-translational chaperone that directly promotes early protein folding at the ribosomal tunnel exit, expanding its functional repertoire in protein biogenesis.
    Keywords:  NAC; chaperone; co-translational protein folding; cryo-electron microscopy; nascent chain; optical tweezers; proteostasis; ribosome; ribosome profiling; single-molecule microscopy
    DOI:  https://doi.org/10.1016/j.molcel.2026.02.022
  3. Cell. 2026 Mar 20. pii: S0092-8674(26)00116-9. [Epub ahead of print]
    The E3-ome gene-centric compendium reveals the human E3 ligase landscape.
    Ngee Kiat Chua, Tania J González-Robles, Cameron J Reddington, Jane Dudley-Fraser, Richard W Birkinshaw, Jiru Han, Ashleigh Solano, Soon Wei Wong, Tomasz Kochańczyk, Joshua J Peter, Mark A Nakasone, Florian Aust, Jacob Munro, Yeh Huei Tong, Julie Iskander, Waruni Abeysekera, Alex Garnham, Hannah Huckstep, Matthew E Ritchie, Ingrid Wertz, Sarah Hymowitz, Sharad Kumar, Ron C Conaway, Gilbert G Privé, Alex N Bullock, Jeffrey J Babon, Rachel E Klevit, Sonja Lorenz, Alessio Ciulli, Eric S Fischer, Nicolas H Thomä, Radosław P Nowak, Brenda A Schulman, Michael Rapé, Katrin Rittinger, Julia K Pagan, Melanie Bahlo, Joel P Mackay, Peter D Mace, Christopher D Lima, Ronald T Hay, David Komander, Bernhard C Lechtenberg, Claudio A P Joazeiro, Michele Pagano, Kay Hofmann, Rebecca Feltham.
      To define and systematically characterize the human E3 ubiquitin ligase (E3) landscape, we generated the E3-ome, a compendium of E3s encoded by the human genome. The E3-ome integrates experimental data, bioinformatics, and published research, revealing 672 high-confidence E3s. We standardized E3 classifications to create a unified framework for annotation and comparative analysis. The E3-ome identified several previously unrecognized domains, motifs, E3 candidates, and relationships, expanding the diversity of E3s. Furthermore, the E3-ome mapped the spatial and physiological organization of E3s across human tissues and cell types, revealing context-dependent E3s. Genetic analyses identified disease-associated variants across the E3-ome, linking E3s to diverse human pathologies. Together, these analyses define the human E3 landscape at high resolution and deliver a foundational resource to drive mechanistic and therapeutic discovery.
    DOI:  https://doi.org/10.1016/j.cell.2026.01.029
  4. Nat Commun. 2026 Mar 27.
    A molecular switch in NAC prevents mitochondrial protein mistargeting by SRP.
    Emir Maldosevic, Radoslaw Jakub Gora, Liangguang Leo Lin, Linyao Elina Zhou, Zexin Jason Li, Yelena Peskova, Ling Qi, Shu-Ou Shan, Ahmad Jomaa.
      The nascent polypeptide-associated complex (NAC) co-translationally screens all nascent proteins and regulates their access to signal recognition particle (SRP) to ensure the fidelity of protein targeting to the endoplasmic reticulum (ER). However, the mechanism by which NAC prevents the mistargeting of nascent mitochondrial proteins remains unclear. Here, we identify a molecular switch in NAC that allows its central barrel domain to adopt a stabilized conformation on ribosomes exposing a mitochondrial targeting sequence (MTS). Mutations of the MTS on the nascent chain or in the NAC switch region increase NAC barrel dynamics and reduce its binding to the ribosome. This impairs the ability of NAC to prevent mistargeting by SRP and causes ER stress in human cells. Our work reveals how NAC detects nascent mitochondrial proteins early in translation and prevents their promiscuous access to SRP, elucidating the structural basis that underlies this role and providing mechanistic insights into protein targeting fidelity with broader implications for cellular proteostasis.
    DOI:  https://doi.org/10.1038/s41467-026-71061-3
  5. Proc Natl Acad Sci U S A. 2026 Mar 31. 123(13): e2529493123
    Dynamic translocation of Inside-Out proteins to the cell surface underlies cellular adaptation to cancer-induced stress.
    Tomasz Slezak, Kelly M O'Leary, Tanya Guevara Avella, Natalia Musial, Jinyang Li, Anna Andrzejczak, Elizabeth F Scott, Duc Anh Le, Anthony A Kossiakoff.
      Inside-Out (I-O) protein display, the noncanonical surface localization of intracellular proteins, represents an underexplored feature of tumor cell biology. Here, we map the molecular landscape and trafficking mechanisms that control the presentation of I-O proteins on cancer cell membranes. Employing APEX2-mediated proximity biotinylation and a custom antibody generation and validation platform, we identified approximately 140 high-confidence I-O proteins, primarily ribosomal, proteasomal, chaperone, and translation factors, notably enriched in protein families associated with stress-response pathways. Validation of 500 antibodies encompassing 40 I-O targets across seven tumor cell lines confirmed selective and robust surface localization, while in vivo imaging in mouse xenografts demonstrated pronounced and tumor-specific antibody accumulation. I-O proteins were absent on peripheral blood mononuclear cells (PBMCs) and in normal tissues, indicating cancer cell selectivity. Functional analyses revealed that I-O protein tethering to the membrane is dependent on heparan sulfate interactions; enzymatic removal of these glycans led to the clearance of I-O proteins from the cell surface. Notably, the removed proteins returned to baseline levels within 6 h, indicating a dynamic balance related to Endoplasmic Reticulum (ER)-Golgi trafficking and cellular stress. Nearly half of these I-O proteins overlapped with known stress granule (SG) components; however, stress elements that promote SG formation do not similarly affect surface display of I-O proteins. Furthermore, I-O proteins are present on standard cancer cell lines under lower stress levels needed to induce SG formation, suggesting parallel yet mechanistically distinct aspects of the stress response. These findings position I-O display as a paradigm in protein trafficking, different from traditional secretion pathways and closely linked to stress response.
    Keywords:  Inside-Out proteins; cancer immunotherapy; cell surface proteome; tumor-specific biomarkers
    DOI:  https://doi.org/10.1073/pnas.2529493123
  6. Mol Cell. 2026 Mar 23. pii: S1097-2765(26)00138-3. [Epub ahead of print]
    RNF25 confers mRNA damage tolerance by curbing activation of the integrated stress response.
    Shubo Zhao, Chloe S Palma-Chaundler, Carla M Engel, Jacqueline Cordes, Daniel Nixdorf, Michael Y Luo, Selay Kaya, Aldwin Suryo Rahmanto, Diana van den Heuvel, Timur Mackens-Kiani, Pedro Weickert, Simon Lam, Vipul Gupta, Julia Philippou-Massier, Ivan Bagarić, Jonathan Bohlen, Graeme Hewitt, Martijn S Luijsterburg, Roland Beckmann, Petra Beli, Danny D Nedialkova, Christopher J Carnie, Marion Subklewe, Stephen P Jackson, Julian Stingele.
      Excessive RNA damage activates cellular stress responses, triggering cell death. However, pathways that negatively regulate RNA damage responses are largely uncharacterized. Using genetic screens, we find that the ubiquitin ligase RNF25 provides tolerance to RNA damage caused by the nucleoside analogue azacytidine, a chemotherapeutic agent used to treat acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). Mechanistically, we show that azacytidine is incorporated into mRNA, where it causes lesions that stall elongating ribosomes, leading to cytotoxic activation of the GCN2-dependent integrated stress response (ISR). Furthermore, we establish that RNF25 prevents ISR hyperactivation by ubiquitylation of ribosomal protein eS31, thereby suppressing cell death upon azacytidine treatment. Our study reveals an mRNA damage tolerance mechanism that determines cellular survival in response to azacytidine, highlighting RNA damage-induced stress response as a potentially critical component of chemosensitivity in AML and MDS.
    Keywords:  GCN1; GCN2; RNA damage; RNF25; acute myeloid leukemia; azacytidine; chemotherapy; integrated stress response; ribosome collisions; ubiquitylation
    DOI:  https://doi.org/10.1016/j.molcel.2026.02.024
  7. Autophagy. 2026 Apr;22(4): 645-647
    Cytosol-dwelling bacteria engage in a ubiquitination race to avoid antibacterial autophagy.
    Hana Popelka, Daniel J Klionsky.
      One of the defense mechanisms of host cells against bacterial pathogens is antibacterial macroautophagy/autophagy that relies on ubiquitination of a pathogen for recognition by specific receptors that deliver the pathogen to phagophores. RNF213 is an E3 ligase that mediates ubiquitination of lipopolysaccharides (LPS) on bacteria dwelling in the host cytosol. However, one type of cytosol-invading bacteria, Shigella flexneri, evolved a mechanism through which it can avoid LPS ubiquitination. S. flexneri employs IpaH1.4, an effector protein with E3 ligase activity that ubiquitinates RNF213 for proteasomal degradation. Here, we discuss a study that discovered this S. flexneri strategy, and revealed by cryo-EM that the IpaH1.4 leucine-rich repeat recognizes and binds the RNF213 RING domain. The mass spectrometry data showed that IpaH1.4 targets several other RING-containing E3 ligases implicated in inflammation and immunity, which opens a new field for xenophagy.Abbreviations: cryo-EM, cryo-electron microscopy; LPS, lipopolysaccharide; LRR, leucine-rich repeat; LUBAC, linear ubiquitin chain assembly complex; NEL, novel E3 ligase; OPTN, optineurin.
    Keywords:  Cryo-EM; IpaH; RNF213 RING finger; Shigella flexneri; lipopolysaccharides
    DOI:  https://doi.org/10.1080/15548627.2026.2624823
  8. bioRxiv. 2026 Mar 07. pii: 2026.03.06.709959. [Epub ahead of print]
    An Optimized RNF126-Targeting Covalent Handle for Molecular Glue Degraders.
    Aman Modi, Ethan S Toriki, Christian E Stieger, Emily A Lau, Claire Song, Alyssa Chew, Amy Tsao, Kaila Nishikawa, Jeffrey McKenna, Daniel K Nomura.
      Molecular glue degraders represent a powerful modality for targeting proteins that are refractory to traditional inhibition. However, rational design principles for molecular glue degraders remain poorly defined. Previously, we reported a chemistry-centric strategy to identify covalent degradative handles that, when appended to established ligands, convert non-degradative inhibitors into molecular glue degraders by engaging permissive E3 ligases. This effort identified a fumarate-based electrophilic handle that covalently modified the E3 ligase RNF126, enabling degradation of multiple protein targets when transplanted across diverse ligands. Despite its conceptual impact, the high intrinsic reactivity and cytotoxicity of the fumarate handle limited its translational utility. Here, we report the development of an optimized and metabolically stabilized RNF126-targeting covalent handle incorporating a trans -cyclobutane linker that exhibits reduced glutathione reactivity and diminished cytotoxicity while retaining robust degradative activity. When appended to the BET bromodomain inhibitor JQ1, this optimized handle yielded a potent and selective BRD4 degrader whose activity was dependent on RNF126. Importantly, transplantation of this handle onto a previously non-inhibitory ligand targeting the androgen receptor (AR) and its truncation variant, AR-V7, enabled selective degradation of both AR and AR-V7 in androgen-independent prostate cancer cells, thereby robustly inhibiting AR transcriptional activity beyond the established AR antagonist enzalutamide. Collectively, these findings demonstrate an optimized RNF126-based covalent handle for the rational development of molecular glue degraders against transcriptional regulators, including undruggable variants such as AR-V7.
    DOI:  https://doi.org/10.64898/2026.03.06.709959
  9. bioRxiv. 2026 Mar 09. pii: 2026.03.08.710403. [Epub ahead of print]
    Ribosome Molecular Aging Shapes Translation Dynamics.
    Jordy F Botello, Lifei Jiang, Peter J Metzger, Troy J Comi, Aya A Abu-Alfa, Qiwei Yu, Margaret S Ebert, Minkyu Lee, Lennard W Wiesner, Maya Butani, Claire J Weaver, Andrej Košmrlj, Ileana M Cristea, Clifford P Brangwynne.
      Cellular homeostasis relies on continual renewal of cellular components, yet some complexes like ribosomes persist for long periods, raising the question of whether extended molecular age impacts functional fidelity. Here, we introduce a spatiotemporal mapping strategy to resolve biomolecular life stages, and show that intracellular ribosome aging alters translational dynamics at specific transcripts. Molecularly aged ribosomes exhibit impaired elongation at basic amino acid-rich sequences, leading to increased pausing, premature termination, and ribosome collisions. By profiling ribosomal RNA modifications, we find that molecular aging increases the collision propensity of specific ribosome subpopulations. Consistent with our findings, enrichment of aged ribosomes in cells amplifies molecular age-dependent translation defects. In vivo labeling of ribosomes in aged C. elegans demonstrates that molecularly aged ribosomes shape translational dynamics during organismal aging. These findings identify ribosome molecular age as a determinant of translational dynamics, and link molecular aging of a core gene-expression complex to organismal aging.
    HIGHLIGHTS: A pulse-chase labeling strategy enables mapping subcellular demographics of macromolecular complexes in space and time.Molecular aging of ribosomes drives differential mRNA translation and shapes elongation dynamics.The collision propensity of specific ribosome subpopulations increases with molecular age.Older ribosomes shape translation dynamics during organismal aging.
    DOI:  https://doi.org/10.64898/2026.03.08.710403
  10. Cell Chem Biol. 2026 Mar 25. pii: S2451-9456(26)00070-X. [Epub ahead of print]
    Receptor-ubiquitination-targeting antibody-drug conjugates for enhanced endocytosis and lysosomal delivery.
    Xinlei Zhuang, Li Lin, Jingchao Li, Gang Yu, Bin Chen, Yingchun Xu, Shuqing Chen, Wen Yi, Liqiang Pan.
      Endocytosis and lysosomal degradation are critical pathways that determine the intracellular trafficking and therapeutic efficacy of antibody-drug conjugates (ADCs). However, inefficient internalization and lysosomal trafficking often limit ADC potency. Here, we introduce receptor-ubiquitination-targeting ADCs (ubitaADCs), a class of ADCs engineered to simultaneously bind target receptors and E3 ubiquitin ligases, thereby inducing receptor ubiquitination to enhance endocytosis and lysosomal delivery. Using engineered ubitaADC targeting epidermal growth factor receptor (EGFR), we demonstrate that promoting receptor ubiquitination accelerates internalization and lysosomal trafficking, leading to enhanced intracellular drug release and improved tumor cell killing. Mechanistic studies reveal that E3 ligase recruitment facilitates receptor ubiquitination, triggering endocytosis and subsequent lysosomal degradation. In vivo, ubitaADCs exhibit superior antitumor efficacy compared to conventional ADCs. This study establishes receptor ubiquitination as a powerful strategy to optimize ADC function and provides a generalizable approach for improving targeted protein degradation in therapeutic applications.
    Keywords:  E3 ligase; antibody-drug conjugate; colorectal cancer; internalization; lysosomal trafficking; receptor ubiquitination; targeted protein degradation
    DOI:  https://doi.org/10.1016/j.chembiol.2026.02.015
  11. bioRxiv. 2026 Mar 16. pii: 2026.03.13.711689. [Epub ahead of print]
    Survey of the human proteostasis network: the ubiquitin-proteasome system.
    Suzanne Elsasser, Evan T Powers, Thomas Stoeger, Xiaojing Sui, Roy D Kurtzbard, Patricia Martínez-Botía, Margaret A Wangeline, Alejandro Rodriguez Gama, Edward L Huttlin, Lisa P Elia, Jeffery W Kelly, Jason E Gestwicki, Judith Frydman, Steven Finkbeiner, Eugenia M Clerico, Richard I Morimoto, Miguel A Prado, Alfred C O Vertegaal, Kay Hofmann, Daniel Finley.
      Modification by ubiquitination governs the half-lives of thousands of proteins that are fated for elimination by either the proteasome or autophagy pathways, depending on the intricate architectures of ubiquitin modification. This system mediates quality control for individual proteins, protein complexes, and organelles, as well as myriad purely regulatory functions. Here we provide a comprehensive survey of the ubiquitin-proteasome system (UPS), the scope of which is at present poorly defined. The UPS, with the inclusion of pathways involving ubiquitin-like modifiers, comprises in our estimate over 1400 distinct proteins in humans, a vast set of activities whose collective impact on the biology of the cell is pervasive. The UPS is an integral component of the proteostasis network (PN), the remainder of which we have also surveyed in recent studies. With the addition of molecular chaperones, proteins from autophagy-lysosome pathway, and related activities, the PN includes in total over 3100 components by our estimates. Comprehensive and systematic definition of these pathways should support a range of ongoing investigations in the areas of genomics, proteomics, biochemistry, cell biology, and disease research.
    DOI:  https://doi.org/10.64898/2026.03.13.711689
  12. Science. 2026 Mar 26. 391(6792): 1332-1338
    Systems-level organization of extracellular proteostasis.
    Cláudio M Gomes, Michele Vendruscolo.
      One defining feature of complex organisms is the ability to maintain protein homeostasis beyond cellular boundaries. We review how extracellular proteostasis is organized as a hierarchical network spanning pericellular, tissue, and systemic tiers. At each tier, secreted chaperones, proteases, vesicles, receptors, immune sentinels, and clearance organs cooperate to recognize, buffer, and eliminate misfolded proteins. Feedback through immune signaling, stress-induced protein secretion, and glymphatic and lymphatic transport adjusts capacity to proteotoxic load. We illustrate how failures in this stratified defense underlie neurodegenerative disorders and systemic amyloidoses, and we highlight strategies that stabilize extracellular proteins, augment clearance pathways, or enhance fluid transport. Viewing extracellular proteostasis as an integrated systems-level network reveals opportunities for combinatorial and preventive therapies.
    DOI:  https://doi.org/10.1126/science.aed3712
  13. Annu Rev Biochem. 2026 Mar 25.
    The Human Autophagy Core Complexes.
    James H Hurley.
      The autophagy core machinery carries out the fundamental reactions of autophagosome biogenesis across all forms of bulk and selective macroautophagy. In humans, the core complexes consist of the ULK1 complex (ULK1C), the class III phosphatidylinositol 3-kinase complex I (PI3KC3-C1), the ATG8 proteins and the ATG8ylation machinery, the phosphatidylinositol 3-phosphate (PI3P)-sensing WIPI proteins, the lipid transporter ATG2, and the lipid scramblase and initiation scaffold ATG9. These complexes form a web of interactions that can be initiated by clustering of the FIP200 subunit of ULK1C but also by PI3KC3-C1 or WIPI2. Upon autophagy induction, these interactions are intensified by feed-forward signaling loops. These loops are amplified by WIPI-PI3P interactions and the conjugation of ATG8 proteins to the membrane by the ATG12-ATG5-ATG16L1 complex. Autophagosomes are seeded by ATG9 vesicles, which accrue initiation machinery on their surface and dock onto a PI3P-positive domain of the endoplasmic reticulum known as the omegasome. The omegasome contact site is the focal point for autophagosome growth, which is fed by lipid transport through the ATG2 bridge-like lipid transporter. The core complexes function in a dynamic manner, which makes autophagy vulnerable to stalling when dynamism fails. Disassembly and dissociation of the machinery, which is promoted at least in part by ULK1, is likely to be as important as assembly.
    DOI:  https://doi.org/10.1146/annurev-biochem-072425-030036
  14. Nat Commun. 2026 Mar 27. pii: 2800. [Epub ahead of print]17(1):
    Structural dynamics of the midnolin-proteasome during ubiquitin-independent substrate turnover.
    Chuanda Zhu, Lu Qin, Zonglin Dai, Peng Zuo, Ao Yang, Lijun Zhong, Zhiqiang Lin, Ling Liang.
      The 26S proteasome typically degrades proteins marked by ubiquitin chains. However, a distinct, ubiquitin-independent degradation pathway for nuclear proteins exists, mediated by the adaptor protein midnolin, yet its molecular mechanism remains poorly understood. Here, we present nine cryo-electron microscopy structures of the human 26S proteasome in complex with midnolin, which collectively delineate a near-complete catalytic cycle. Our structures reveal that midnolin binds to the proteasome via the RPN1 subunit by its C-terminal helix. Unexpectedly, its ubiquitin-like domain interacts with the RPN11 deubiquitinase in a non-catalytic role. This interaction positions the adjacent Catch domain, which is responsible for substrate binding, directly above the proteasomal entrance, potentially facilitating substrate entry into the proteasome. Furthermore, we observe four consecutive spiral staircase conformations of the AAA+ ATPase hexamer during substrate translocation. These findings provide insights into the mechanisms underlying ubiquitin-independent nuclear protein degradation and may help develop strategies for targeting nuclear proteins via direct proteasomal degradation.
    DOI:  https://doi.org/10.1038/s41467-026-71002-0
  15. Nat Commun. 2026 Mar 26.
    Small-molecule degraders for oncogenic KRASG12C and pan-KRAS mutations.
    Jianxiong Deng, Shujun Shen, Lei Huang, Fang Xu, Weizhen Huang, Chaoming Huang, Zhang Zhang, Tongzheng Liu, Yi Tan, Zhengqiu Li.
      KRAS, a frequently mutated oncogene, has been challenging to target therapeutically. Although covalent inhibitors like sotorasib against KRASG12C have been developed, their efficacy is often limited by acquired resistance. Targeted protein degradation offers a potential solution but has largely relied on large PROTAC molecules. Here, we report DJX-A-KM, a small-molecule degrader of KRASG12C, designed by incorporating an acrylamide warhead into the MRTX849 scaffold. It induces potent and sustained degradation of KRASG12C in cells and in vivo. Mechanistic investigation reveal that degradation is mediated by the ubiquitin-proteasome system, facilitated by covalent engagement with a E3 ligase, FBXO28, at cysteine 98. Antiproliferation assays demonstrate its potent inhibitory effects across multiple KRASG12C-mutant cancer models. This strategy also enables the development of pan-KRAS degraders against a broader spectrum of KRAS mutations. Our work presents a small-molecule degrader recruiting FBXO28 and provides a blueprint for exploring E3 ligases in protein degradation.
    DOI:  https://doi.org/10.1038/s41467-026-71093-9
  16. Cell Rep. 2026 Mar 26. pii: S2211-1247(26)00270-6. [Epub ahead of print]45(4): 117192
    Gcn2 deficiency triggers anemia and hypoxic intolerance in zebrafish.
    Chengdong Liu, Chenxi Wang, Jican Zhao, Weiyi Xia, Wanjuan Yu, Huihui Zhou, Xiya Wu, Mingjun Tang, Huan Zeng, Yanfei Tang, Ranran Zhao, Ling Lu, Xuan Wang, Kangsen Mai, Gen He.
      The integrated stress response (ISR) is a conserved signaling hub that orchestrates cellular adaptation to diverse stressors to maintain intracellular homeostasis. However, the specific role of the ISR in regulating hypoxic adaptation and redox homeostasis remains poorly defined. Here, we identify general control nonderepressible 2 (GCN2) as an essential factor for maintaining redox balance and suppressing ferroptosis. Gcn2-deficient zebrafish exhibit hypersensitivity to hypoxia, characterized by excessive heme degradation and mitochondrial damage. Loss of Gcn2 leads to upregulation of hmox1a, reduced erythrocyte numbers, and elevated levels of free ionic iron, collectively contributing to the development of anemia. Mechanistically, loss of Gcn2 downregulates slc3a2b, resulting in disturbed cysteine metabolism. This defect impairs glutathione biosynthesis, triggering ferroptosis characterized by elevated oxidative stress and iron-dependent lipid peroxidation. GCN2 deficiency also induces ferroptosis in HeLa cells. Our findings elucidate a critical role for GCN2 in protecting against ferroptosis and promoting hypoxic tolerance.
    Keywords:  CP: cell biology; CP: metabolism; GCN2; SLC3A2; ferroptosis; hypoxia; integrated stress response; redox homeostasis; zebrafish
    DOI:  https://doi.org/10.1016/j.celrep.2026.117192
  17. Chem Biol Drug Des. 2026 Mar;107(3): e70281
    High-Throughput Platform for Discovery of Chemical Inhibitors of Heat Shock Protein 70 (Hsp70): Adaptation for the Specialized Bacterial HscA-HscB-IscU Complex.
    Arielle Shkedi, Aneta Grabinska-Rogala, Jason Hernandez, Rafał Dutkiewicz, Jaroslaw Marszalek, Jason E Gestwicki.
      Adenosine triphosphatases (ATPases) power essential cellular processes, but they commonly achieve full activity only within multi-protein assemblies, where cofactors and partner proteins tune their function. Yet, most high-throughput screening (HTS) campaigns that target ATPases tend to use highly purified enzymes without these important partners. Here we present a high-throughput platform for discovering small-molecule modulators of the bacterial heat shock protein (Hsp70) system: HscA-HscB-IscU, a promising anti-bacterial target. In this multi-protein complex, HscA has ATPase activity that is stimulated by HscB and IscU, such that inhibitors might act at either the enzyme active site or at protein-protein interactions (PPIs). To enable discovery of such molecules, we reconstituted purified HscA, HscB, and IscU, optimized their ratios to favor the active complex and then miniaturized a quinaldine red-based, phosphate detection assay to 384-well plates (Z' = 0.68). A pilot screen of ~2000 bioactive compounds identified 253 primary hits, suggesting an abnormally high hit rate (13.6%); however, many of these signals were attributable to compound insolubility and could be triaged using aggregation-detection strategies. Collectively, this workflow establishes a scalable platform for discovering chemical probes of the HscA-HscB-IscU system. More broadly, this work provides the foundation for HTS campaigns targeting reconstituted, multi-protein complexes containing ATPase activity.
    DOI:  https://doi.org/10.1111/cbdd.70281
  18. Proc Natl Acad Sci U S A. 2026 Mar 31. 123(13): e2528466123
    Cnpy1 is a candidate endoplasmic reticulum chaperone of vomeronasal type 2 GPCRs.
    G V S Devakinandan, Abdul Rishad, Nandana Nanda, Syed Dastagir Hussain, Sishir Subedi, Adish Dani.
      Mouse vomeronasal sensory neurons are continuously generated from stem cells and differentiate to express either V1R or V2R G protein-coupled receptors (GPCRs), along with their respective Gαi2 or Gαo G-protein subunits. We previously reported that Gαo-type neurons exhibit elevated expression of endoplasmic reticulum (ER) chaperones and a distinctive hypertrophic, gyroid ER architecture, suggesting specialized proteostatic demands. Here, we identify a transcript for the mouse Canopy1 (Cnpy1) gene that yields full-length Cnpy1 protein selectively expressed in and localized to the ER of Gαo neurons. Immunoprecipitation coupled with mass spectrometry revealed that Cnpy1 associates specifically with V2R GPCRs and multiple ER chaperones. Cnpy1 deletion resulted in mice that were deficient in Gαo neuronal activation upon exposure to vomeronasal stimuli and a marked reduction in male-male aggressive behavior. In the absence of Cnpy1, Gαo neurons develop normally till birth but undergo selective, progressive apoptosis during postnatal development. Unexpectedly, Cnpy1-null vomeronasal neurons displayed neither an obvious unfolded protein response nor defects in V2R GPCR traffic to dendritic tips, indicating that Cnpy1 is required for V2R assembly or functional maturation but dispensable for their ER export. Together, these findings identify Cnpy1 as a component of an ER chaperone complex that is essential for Gαo neuron signaling and survival.
    Keywords:  Cnpy1; GPCR; endoplasmic reticulum; sensory neurons; vomeronasal
    DOI:  https://doi.org/10.1073/pnas.2528466123
  19. Nat Commun. 2026 Mar 25.
    RanBP2-dependent annulate lamellae drive nuclear pore assembly and nuclear expansion.
    Junyan Lin, Arantxa Agote-Aran, Yongrong Liao, Mehdi Cloarec, Leonid Andronov, Rafael L Schoch, Paolo Ronchi, Victor Cochard, Rui Zhu, Erwan Grandgirard, Xiaotian Liu, Marianne Victoria Lemée, Charlotte Kleiss, Christelle Golzio, Marc Ruff, Guillaume Chevreux, Yannick Schwab, Bruno P Klaholz, Izabela Sumara.
      Nuclear pore complexes (NPCs) enable nucleocytoplasmic transport. While NPCs primarily localize to the nuclear envelope (NE), they also appear in cytoplasmic endoplasmic reticulum (ER) membranes called annulate lamellae (AL). Though discovered in the mid-20th century, AL's function and biogenesis remain unclear. Previously considered exclusive to embryonic and malignant cells, we find AL in somatic mammalian cells. Under normal conditions, AL store pre-assembled AL-NPCs that integrate into the NE, producing approximately one-third of newly formed nuclear pores and supporting nuclear expansion during G1. Upon pathological stimuli, AL transfer to the NE is impaired, leading to their cytoplasmic accumulation. RanBP2 (Nup358) is essential for AL biogenesis, with its phenylalanine-glycine repeats promoting AL-NPC scaffold oligomerization. ER-associated Climp63 (CKAP4) directs AL-NPCs to ER sheets and the NE. This AL-driven nuclear pore formation is complementary to the canonical routes, constituting a distinct NPC assembly pathway. Our work uncovers the biogenesis mechanism of AL and the nuclear function of this key cellular organelle.
    DOI:  https://doi.org/10.1038/s41467-026-71101-y
  20. Mol Biol Cell. 2026 Mar 25. mbcE25090445
    MCTP1 and MCTP2 promote ER-PM contact sites and regulate PI4P homeostasis and cell migration.
    Suganthan Amirthagunanathan, Maxime Boutry, Vasudeva Tati, Dibyayan Maity, Caroline Chapman, Madhura R Pandkar, Brian Raught, Peter K Kim, Amit S Joshi.
      Endoplasmic reticulum-plasma membrane (ER-PM) contact sites play important roles in maintaining lipid homeostasis at plasma membrane (PM), cellular calcium homeostasis and cell signaling. Here, we show that MCTP1 and MCTP2 are at ER subdomains that form membrane contact sites (MCS) with multiple organelles using proximity labelling assay. MCTPs are three C2 domain-containing transmembrane proteins. We show that upon overexpression, MCTPs promote ER-PM contact sites in C2 domain dependent manner. MCTP C2 domains bind to PI(4)P and PI(4,5)P2, phosphoinositides that are enriched in the PM. Furthermore, we show that deletion of MCTP1 or MCTP2 increases PI(4)P levels in the PM and promote cell migration. Thus, our study identifies MCTPs as multiple ER-organelle contact site proteins and establishes its role at ER-PM contact sites in regulating lipid homeostasis and cell migration.
    DOI:  https://doi.org/10.1091/mbc.E25-09-0445
  21. Mol Cell. 2026 Mar 25. pii: S1097-2765(26)00157-7. [Epub ahead of print]
    The Erlin1/2 complex is a dynamic scaffold for membrane microdomain assembly on the endoplasmic reticulum.
    Lu Yan, Zihong Xu, Yuanhang Yao, Tadsanee Awang, Xiaoting Wang, Yonglun Wang, Chengying Ma, Ningning Li, Chen Song, Xiao-Wei Chen, Ning Gao.
      The SPFH (stomatin, prohibitin, flotillin, and HflK/C) family proteins are proposed scaffolds for organizing functional membrane microdomains (FMMs) on various cellular membranes. Erlin1 and Erlin2, two endoplasmic reticulum (ER)-residing SPFH members, as heteromeric complexes, participate in ER-associated protein degradation (ERAD). However, the mechanisms underlying Erlin-mediated FMM organization and ERAD regulation remain poorly understood. Here, through cryoelectron microscopy (cryo-EM), we find that the human Erlin1/2 complex forms a 26-mer cage assembly, defining a nanometer-sized microdomain on the luminal leaflet. The intramembrane region of each subunit constitutes a specific phosphatidylinositol-binding pocket. ER proteins can be recruited to both the interior and exterior of these cages. By caging cargoes, the Erlin1/2 complex physically secludes them from their substrates or binding partners, conferring another layer of regulation on their functions. Moreover, individual cages can cluster to organize FMMs of different sizes. These dynamic properties underscore a general regulatory role of Erlin1/2 in various ER-related biological processes, including coronaviral replication.
    Keywords:  ERAD; Erlin1/2; SPFH; cryo-EM; cryo-electron microscopy; endoplasmic reticulum-associated degradation; functional membrane microdomain; lipid raft; phosphatidylinositol; β-coronavirus
    DOI:  https://doi.org/10.1016/j.molcel.2026.03.001
  22. Nat Commun. 2026 Mar 24. pii: 2582. [Epub ahead of print]17(1):
    Structural transitions in the stepwise assembly of proteasome core particles.
    Eric Mark, Paula C Ramos, Maria M Nunes, Ana C Matias, R Jürgen Dohmen, Petra Wendler.
      20S catalytic core particles (CP) of eukaryotic 26S proteasomes are composed of two identical halves comprising 14 distinct subunits. 15S precursor complexes (PC) represent detectable half-CPs assembly intermediates lacking the β7-subunit but containing assembly chaperones Ump1 and Pba1-Pba2. Incorporation of β7 drives 15S-PC dimerisation and further CP maturation. Our cryo-EM structures of the yeast 15S-PC and all 13S-PC-derived intermediates suggest that assembly in yeast is not restricted to a single trajectory, but instead involves alternative, and potentially simultaneous pathways. Comparison of the intermediates reveals how Ump1 and β-subunits become structured with each additionally incorporated β-subunit, and how this prepares peptidase sites for auto-activation. We identify two transient interactions of Pba1 with the α-ring, which are important for an ordered progression of maturation. Pba1 loop 81-117 intercalates between subunits α3 and α4 in 13S-15S-PCs and is displaced upon 15S-PC dimerisation. The second interaction involves the α1 N-terminus, deletion of which leads to a defect in Pba1-Pba2 release. These findings indicate how changes in α-ring subunit conformations coordinate CP maturation with Pba1‑Pba2 release.
    DOI:  https://doi.org/10.1038/s41467-026-70525-w
  23. Structure. 2026 Mar 20. pii: S0969-2126(26)00056-0. [Epub ahead of print]
    CAND1 and CAND2 drive CUL4 substrate receptor exchange with largely comparable biochemical efficiency, unlike their relative effects on CUL1.
    Kankan Wang, Sebastian Kenny, Zhana Chagan, Lihong Li, Chittaranjan Das, Xing Liu.
      Cullin-RING ubiquitin ligases (CRLs) regulate diverse cellular processes by dynamically recruiting substrate receptors onto conserved cullin-RING scaffolds. CAND1 and CAND2 function as substrate receptor exchange factors for CRL1, but CAND2 displays reduced efficiency in CRL1 disassembly, exhibits tissue-specific expression, and shows distinct disease associations, raising questions about its function in other CRL subfamilies. Here, we define the regulatory roles of CAND1 and CAND2 in CRL4 remodeling. Using genetic perturbation, real-time kinetic analyses, and quantitative interaction proteomics, we show that both CAND proteins promote CRL4-mediated protein degradation and enhance the dynamic exchange of DDB1·DCAF substrate receptor modules, likely through conserved yet distinct structural features. In contrast to their differential efficiencies in CRL1 disassembly, CAND1 and CAND2 exhibit similar kinetic parameters and comparable exchange efficiencies across most of the CRL4 complexes. These findings establish CAND1 and CAND2 as bona fide CRL4 exchange factors and reveal biochemical distinctions between CRL4 and CRL1 regulation.
    Keywords:  CAND2; Cullin-RING ubiquitin ligases; dynamics of protein complexes; protein exchange factor
    DOI:  https://doi.org/10.1016/j.str.2026.02.015
  24. Cancer Discov. 2026 Mar 27. OF1
    Stress Responses Tied to Metastasis and Immune Evasion.
      Two studies show that cancer cells co-opt the integrated stress response, via the transcription factor ATF4, to drive both metastasis and immune evasion. Targeting this pathway or its downstream effectors, such as glutamine metabolism and the secreted protein LCN2, may offer a way to limit tumor spread and restore antitumor immunity.
    DOI:  https://doi.org/10.1158/2159-8290.CD-NW2026-0029
  25. Sci Adv. 2026 Mar 27. 12(13): eaec5067
    Mechanism of ribosome stalling by the AMD1 C-terminal tail arrest peptide.
    Emir Maldosevic, Fabio S Boiocchi, Michal I Swirski, Kyle A Meiklejohn, Martina M Yordanova, Pavel V Baranov, Ahmad Jomaa.
      AMD1 encodes adenosylmethionine decarboxylase 1 (AMD1), a key enzyme in polyamine biosynthesis. A subset of ribosomes translating the AMD1 coding sequence read through the stop codon and pause at a second in-frame stop 384 nucleotides downstream, producing a conserved C-terminal extension (C-tail). Despite growing evidence that such cis-acting elements regulate translation of their genes, the molecular mechanism by which the C-tail mediates ribosome stalling remains unclear. Here, we determined the structure of the ribosome nascent chain complex paused by the AMD1 C-tail which traps eukaryotic release factor 1 (eRF1) with the ATP-binding cassette subfamily E member 1 (ABCE1). The nascent chain forms a molecular clamp that positions an arginine hook in the peptidyl-transferase center, occluding the accommodation of the eRF1 GGQ motif thereby hampering translation termination. Analysis of aggregated ribosome profiling data revealed several genes with a pattern of stop codon readthrough followed by ribosome stalling at a specific location, suggesting that regulatory readthrough-stall mechanisms may not be limited to AMD1.
    DOI:  https://doi.org/10.1126/sciadv.aec5067
  26. Nat Commun. 2026 Mar 24.
    Substrate-interacting pore loops of two ATPase subunits determine the degradation efficiency of the 26S proteasome.
    Erika López-Alfonzo, Ayush Saurabh, Sahar Zarafshan, Connor Arkinson, Christine L Gee, Hao-Hsuan Hsieh, Steve Pressé, Andreas Martin.
      The 26S proteasome is the major eukaryotic protease responsible for the degradation of misfolded, damaged, and obsolete regulatory proteins. Commitment to degradation occurs when conserved pore loops in the heterohexameric ATPase motor of the proteasome engage the flexible initiation region of a polyubiquitinated protein substrate for subsequent mechanical unfolding and translocation into a proteolytic chamber. Here, we use in vitro biochemical assays, single-molecule FRET-based measurements, and cryo-EM structure determination to characterize how the pore-1 loops of individual ATPase subunits in the yeast 26S proteasome contribute to the different steps of substrate degradation and affect the proteasome conformational dynamics. We find that the pore-1 loops of the Rpt6 and Rpt4 ATPase subunits play particularly important, yet distinct roles in substrate capture and unfolding, and in holding the ATPase motor in a static state prior to substrate engagement. Interestingly, these pore-1 loop contributions correlate with the positions of ATPase subunits in spiral-staircase arrangements for the substrate-free and substrate-degrading proteasome, providing insights into the mechanisms of substrate processing by the 26S proteasome and related ATPase motors.
    DOI:  https://doi.org/10.1038/s41467-026-70426-y
  27. bioRxiv. 2026 Mar 17. pii: 2026.03.16.712107. [Epub ahead of print]
    Salmonella Typhi asparaginase-dependent activation of GCN2 promotes bacterial killing in murine macrophages.
    Zachary Powers, Michael McFadden, Gi Young Lee, Tracey L Schultz, Luiza Castro Jorge, Daniel Edwards, Simon Sanchez-Paiva, Jonathan Sexton, Katherine R Spindler, Jeongmin Song, Mary X O'Riordan.
      Many intracellular pathogens stimulate host cell stress by directly or indirectly causing an imbalance in host nutrients; depletion of amino acid pools in particular can act as a danger signal to infected cells. Using a restrictive host model of Salmonella enterica serovar Typhi (S. Typhi) infection, we identify early induction the integrated stress response (ISR) by viable bacteria, but not heat-killed bacteria. Genetic deletion of the amino acid sensing ISR kinase GCN2 (also known as EIF2AK4) prevented early ISR activation during S. Typhi infection, and murine macrophages lacking GCN2 show impaired bacterial clearance and decreased cytokine output. Supplementation of wildtype C57BL/6 murine macrophages with only the non-essential amino acid asparagine was sufficient to suppress S. Typhi-induced ISR activation and deletion of S. Typhi ansB, encoding an asparaginase, prevented ISR activation during infection. Pharmacological inhibition of mammalian target of rapamycin (mTOR), the other major amino acid sensing pathway in eukaryotic cells, prevented GCN2 activation and ISR induction in murine macrophages, indicating an upstream role for mTOR in signaling to GCN2. These findings suggest a role for the ISR in macrophage innate immune responses to S. Typhi infection and highlight a potential difference in nutrient-dependent signaling between the S. Typhi-susceptible human host and the restrictive murine host centered around asparagine, mTOR, and GCN2.
    DOI:  https://doi.org/10.64898/2026.03.16.712107
  28. J Med Chem. 2026 Mar 24.
    Hsp70-Targeting Chimeras Enable Dual Proteasomal and Lysosomal Degradation of Intracellular and Extracellular Proteins.
    Zihan Wang, Pengfei Li, Fangkui Yin, Hong Zhang, Siyao Wang, Yi Teng, Xiuwen Fan, Ke Wang, Yanxin Zhang, Haoxin Lun, Ting Song, Ziqian Wang, Zhichao Zhang.
      Developing targeted protein degradation (TPD) strategies with disease-specific mechanisms, modularity, and facile designability could ensure drug efficacy and selectivity. Herein, a small-molecule, Hsp70-based targeted protein degradation platform, termed Hsp70TAC, is described that enables tumor-selective degradation of both intracellular and extracellular proteins through distinct cellular pathways. By conjugating protein-of-interest (POI) ligands to Hsp70 inhibitors, Hsp70TACs exploits the chaperone functions of Hsp70 to enable protein degradation through both the ubiquitin-proteasome system and the endocytosis-lysosome pathway. As a proof of concept, Hsp70TACs induced efficient degradation of intracellular Bromodomain Protein 4 (BRD4) via the ubiquitin-proteasome system (DC50 = 0.67 μM) and membrane-bound Programmed Death Ligand 1 (PD-L1) via caveolin-mediated endocytosis-lysosomal processing (DC50 = 0.84 μM). Moreover, Hsp70TACs exploits the elevated expression of Hsp70 in tumor cells to preferentially accumulate in these cells, thereby enabling the tumor-selective degradation of POIs in Hsp70-enriched tumor cells.
    DOI:  https://doi.org/10.1021/acs.jmedchem.5c03784
  29. J Biol Chem. 2026 Mar 25. pii: S0021-9258(26)00273-5. [Epub ahead of print] 111403
    Structure-function analysis of the bacterial ClpE/ClpP AAA+ protease.
    Mariasole De Rosa, Lisa Maag, Dirk Flemming, Irmgard Sinning, Marta Carroni, Axel Mogk.
      General and regulatory proteolysis in bacteria is executed by a set of ATP-dependent proteases composed of hexameric ring-forming AAA+ proteins and associated peptidase barrels (e.g. ClpP). These AAA+ proteases play crucial roles in stress protection and bacterial virulence. Here, we provide the first biochemical characterization of the potential drug target ClpE/ClpP from Enterococcus faecalis. We show that ClpE/ClpP forms an autonomous and efficient protease, which degrades misfolded and aggregated model substrates and the stress-responsive transcriptional regulator CtsR. This qualifies ClpE/ClpP as central component of bacterial protein quality control systems and explains formerly reported stress-sensitive phenotypes of clpE mutants. ClpE substrate specificity is mediated by its N-terminal domain, which is crucial for targeting misfolded and aggregated proteins. ClpE assembles into a tetrahedral structure formed by four hexamers that interact via their coiled-coil M-domains. ClpP binding to ClpE tetrahedrons triggers the formation of large clusters of proteolytic complexes in vitro and in vivo. Such assembly in principle can allow for spatially confined proteolysis, separating the proteolytic activity of ClpE/ClpP complexes from other cellular processes. Indeed, ClpE M-domain mutants, which are deficient in cluster formation, exhibit increased toxicity in vivo.
    Keywords:  ATPase associated with diverse cellular activities (AAA); protein degradation; protein quality control
    DOI:  https://doi.org/10.1016/j.jbc.2026.111403
  30. Nat Cell Biol. 2026 Mar 24.
    Nonsense-mediated mRNA decay safeguards telomeres in pluripotent stem cells.
    Marta Markiewicz-Potoczny, Si Young Lee, Soniya Chatterjee, Justin W Mabin, Anna Zinsser, Ranjodh Sandhu, Gianna Tricola, J Robert Hogg, Eros Lazzerini Denchi.
      Telomeres are protective DNA caps at chromosome ends that prevent cells from mistakenly recognizing them as broken DNA. These structures are safeguarded by a protein complex called Shelterin, particularly through the TRF2 protein encoded by Trf2. Surprisingly, in mouse embryonic stem cells, TRF2 is not essential for telomere protection, suggesting that other mechanisms compensate for its loss. Here we show that a cellular quality control system called nonsense-mediated mRNA decay (NMD), which normally eliminates defective RNA molecules, plays an unexpected role in maintaining telomere integrity in pluripotent cells. Through a genome-wide genetic screen, we discovered that NMD is essential for cell survival when TRF2 is absent. NMD accomplishes this by degrading an aberrant form of the messenger RNA encoded by Trf1, which produces the TRF1 protein, another Shelterin component. Without NMD, this aberrant RNA produces a truncated, harmful version of TRF1 that interferes with normal telomere protection. Our findings reveal that embryonic stem cells use a unique strategy for chromosome end protection, linking RNA quality control to genome stability in a previously unrecognized way.
    DOI:  https://doi.org/10.1038/s41556-026-01912-0
  31. Cell. 2026 Mar 25. pii: S0092-8674(26)00267-9. [Epub ahead of print]
    STING signaling modulation by COPII cargo recognition.
    Heng Lyu, Cong Xing, Wanwan Huai, Kun Song, Devon Jeltema, Hui Zhang, Xuewu Zhang, Nan Yan.
      Stimulator of interferon genes (STING) activation requires coat protein complex II (COPII)-mediated endoplasmic reticulum (ER) exit, but the mechanism remains elusive. Here, we identify EEΦxΦ (339EEVTV343 in human STING) as the ER-exit motif recognized by SEC24 homolog C (SEC24C). Using AlphaFold3, we present a predicted structure of SEC24C binding to a STING dimer, revealing the EEΦxΦ motif in a previously structurally unresolved region. Mutations in this motif or the SEC24C cargo-binding site disrupt STING trafficking and signaling. Our findings support a STING oligomerization and avidity threshold model that explains regulated ER exit. The EEΦxΦ motif is conserved in vertebrate STING homologs and is sufficient to mediate ER exit of unrelated proteins. Interestingly, the STING ER-exit motif is suboptimal compared with known SEC24C cargos, which is crucial for preventing immune overactivation. An engineered "super-ER-exit" STING is constitutively active and induces potent antitumor immunity. Tandem repeats of this motif competitively inhibit endogenous STING signaling. Collectively, this study elucidates the STING-ER-exit mechanism and presents strategies for modulating STING signaling.
    Keywords:  COPII; ER exit; SEC24C; STING; cancer; inflammation; vesicle trafficking
    DOI:  https://doi.org/10.1016/j.cell.2026.02.029
  32. Cell Rep. 2026 Mar 25. pii: S2211-1247(26)00232-9. [Epub ahead of print]45(4): 117154
    UFMylation-dependent inhibition of AKT signaling by PHLDA3 in lung adenocarcinoma.
    Xiuqing Ma, Rui Wan, Xiao Yang, Jiaxin Tang, Yalei Wen, Lei Huang, Xinying Li, Yan Song, Yang Zhou, Shao-Hua Wang, Tongzheng Liu.
      UFMylation, a recently identified ubiquitin-like modification mediated by the E3 ligase UFL1, plays context-specific roles in cancers, but its substrates and functions in lung adenocarcinoma (LUAD) remain poorly defined. Here, we identify the AKT signaling repressor PHLDA3 as a substrate of UFL1 in LUAD. UFMylation of PHLDA3 at Lys51 and Lys106 promotes its membrane localization, thereby blocking AKT membrane recruitment and suppressing downstream signaling. Tumor-associated PHLDA3 mutations F41L, E82G, and K106N impair its UFMylation and membrane translocation, resulting in AKT hyperactivation and enhanced tumor growth. In samples from patients with LUAD, UFL1 expression inversely correlates with phospho-AKT levels. Functionally, the UFL1-PHLDA3 axis inhibits LUAD progression in both cell line-based and patient-derived xenograft models. These findings define a tumor-suppressive UFMylation pathway that modulates AKT activity and provides a mechanistic rationale for targeting UFL1-PHLDA3 signaling in LUAD.
    Keywords:  CP: cancer; PHLDA3; UFL1; UFMylation; lung adenocarcinoma
    DOI:  https://doi.org/10.1016/j.celrep.2026.117154
  33. PLoS Biol. 2026 Mar;24(3): e3003662
    A quantitative cell-based reporter links TDP-43 aggregation and dysfunction to define pathogenic mechanisms.
    Lohany Dias Mamede, Miwei Hu, Jaime Vaquer-Alicea, Amanda R Titus, Patricia M Passos, Erica Lantelme, Rachel L French, Paige A Kirschner, Marc I Diamond, Timothy M Miller, Yuna M Ayala.
      TDP-43 pathology is a hallmark of fatal neurodegenerative disorders, including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and limbic-predominant age-related TDP-43-encephalopathy (LATE). In affected patients, cytoplasmic TDP-43 aggregates are accompanied by disruption of its normal nuclear localization and function. Because TDP-43 is an RNA binding protein that controls transcript processing, including repression of cryptic exon splicing, its loss leads to dysregulation of gene expression. Despite its central significance in disease, the connection between TDP-43 aggregation and dysfunction remains poorly understood, and models to study the underlying mechanisms are limited. Here, we characterize a robust and quantitative cell-based reporter that captures both aggregation and the resulting loss of function. Using this human biosensor cell line, we show that aggregation initiated by prion-like seeding drives progressive depletion of nuclear TDP-43 and induces signature features of diminished TDP-43 activity, such as increased DNA damage and activation of cryptic exon splicing. We find that aggregate seeding also induces cryptic exon splicing in human neurons implying that this pathological link extends to disease-relevant models. The seeding model provides a platform for dissecting mechanisms that underlie TDP-43 pathology and for identifying factors that modulate the aggregation-to-dysfunction transition. Our data shows that aggregate seeding impacts TDP-43 autoregulation, initiating a toxic feed-forward mechanism that disrupts TDP-43 homeostasis. Furthermore, reducing ataxin-2 levels decreases aggregation and restores TDP-43 activity. Together, these findings reveal a molecularly guided strategy to directly impact TDP-43 activity by decreasing its misfolding and aggregation, highlighting approaches to prevent TDP-43 dysfunction and mitigate toxicity under pathological conditions.
    DOI:  https://doi.org/10.1371/journal.pbio.3003662
  34. Trends Cell Biol. 2026 Mar 25. pii: S0962-8924(26)00033-4. [Epub ahead of print]
    Repair condensates and lipid domains in lysosome integrity.
    Claudio Bussi, Weiping Li.
      Lysosomes are sophisticated signaling hubs whose function depends on membrane integrity. A breach of this barrier, known as lysosomal membrane permeabilization, triggers inflammation and cell death, driving pathologies from lysosomal storage disorders to neurodegeneration. Cells counter membrane damage with diverse repair mechanisms, including endosomal sorting complexes required for transport machinery, sphingomyelin scrambling, annexin-mediated scaffolding, lipid transport, and stress granule plugging. This diversity suggests singular strategies are insufficient, posing an 'orchestration challenge' regarding precise initiation, spatial organization, and temporal coordination. This opinion article proposes that biomolecular condensation, initiated by damage cues, acts as a primary organizing principle. We suggest lysosomal injury nucleates de novo 'repair condensates' that stabilize compromised membranes and serve as recruitment and organizational hubs for repair machinery.
    Keywords:  biomolecular condensates; lipids; lysophagy; lysosomes; membrane damage
    DOI:  https://doi.org/10.1016/j.tcb.2026.03.002
  35. Proc Natl Acad Sci U S A. 2026 Mar 31. 123(13): e2514645123
    NLRP1B is an integrated decoy that subverts Shigella flexneri E3 ligase activity to promote effector-triggered immunity.
    Siwon Chung, Hannah Hudson, Kaitlin A Stromberg, Andrew Sandstrom.
      Inflammasomes are cytosolic immune complexes that recognize pathogen-associated stimuli to initiate a potent inflammatory response. While some inflammasomes directly recognize pathogen-associated molecules, others, such as the NLRP1B inflammasome, respond to pathogen-associated activities. Specifically, the NLRP1B inflammasome senses the enzymatic activity of pathogen-secreted proteases and E3 ligases through a mechanism of "functional degradation"-effectors that promote the proteasomal degradation of NLRP1B induce activation of this inflammasome. However, why pathogens would target NLRP1B for degradation when doing so promotes a robust inflammatory response is unclear. We propose that NLRP1 acts as an integrated decoy receptor by mimicking other host proteins targeted for degradation by pathogens. Specifically, we hypothesize that NLRP1B encodes sequences and features such that these pathogen effectors are unable to distinguish between NLRP1B and their other targets. To test this hypothesis, we determine how the Shigella flexneri E3 ligase IpaH7.8 is recognized by NLRP1B and whether these interactions are equivalent to those between IpaH7.8 and its other substrates, the Gasdermin (GSDM) family of proteins. Here, we show that IpaH7.8 recognizes both the GSDMs and NLRP1B through a single shared interface and that NLRP1B presents a surface similar to that recognized by IpaH7.8 on the GSDMs. In this way, NLRP1B acts as a decoy for the GSDMs to subvert the activity of IpaH7.8 to promote inflammasome activation. These data demonstrate that NLRP1B acts as an integrated decoy receptor and establish the use of integrated decoy receptors by the vertebrate immune system.
    Keywords:  NLRP1; effector-triggered immunity; inflammasome; innate immunity
    DOI:  https://doi.org/10.1073/pnas.2514645123
  36. STAR Protoc. 2026 Mar 20. pii: S2666-1667(26)00100-0. [Epub ahead of print]7(2): 104447
    Protocol for quantifying silent ribosome induction in yeast and mammalian cells using polysome profiling.
    Sayanur Rahaman, Samuel Mondal, Nicole Schiffelholz, Attila Becskei.
      Translationally silent ribosomes lack bound mRNA and are difficult to quantify. Here, we present a protocol to measure silent ribosome induction under diverse conditions in yeast and mammalian cells. We describe steps to isolate polysome-profiling fractions, analyze ribosome-associated RNA by RNA sequencing with identification and removal of anomalously amplified rRNAs, and validate measurements by qPCR. For complete details on the use and execution of this protocol, please refer to Rahaman et al.1.
    Keywords:  Genomics; Molecular Biology; RNA-seq
    DOI:  https://doi.org/10.1016/j.xpro.2026.104447
  37. bioRxiv. 2026 Mar 04. pii: 2026.03.04.709625. [Epub ahead of print]
    Stress-Encoded Mitochondrial Plasticity: ATF4 Control of Mega-Mitochondria and Nanotunnel Communication.
    Amber Crabtree, Suraj Thapliyal, Mohd Mabood Khan, Edgar Garza Lopez, Andrea Marshall, Calixto Pablo Hernandez Perez, Oleg Kovtun, Jenny C Schafer, Dea Pulatani, Yuho Kim, Sepiso K Masenga, Annet Kirabo, Jeremiah Afolabi, Melanie McReynolds, Renata O Pereira, Prasanna Venkhatesh, Prasanna Katti, Brian Glancy, Antentor Hinton.
      Mitochondrial structural plasticity is a critical adaptive response to cellular stress, yet the transcriptional networks governing the formation of specialized mitochondrial architectures remain poorly defined. Here, we identified and demonstrated that activating transcription factor 4 (ATF4), the master regulator of the integrated stress response, directly regulates mitochondrial morphological remodeling through a novel ATF4-NRF1/Nrf2-MFN2 signaling axis. Using serial block-face scanning electron microscopy and three-dimensional reconstruction in Drosophila flight muscle, primary myotubes, and human skeletal muscle, we show that overexpression of ATF4 promotes significant mitochondrial elongation, increased cristae concentration, enhanced mitochondrial-endoplasmic reticulum contact site (MERC) formation, and the initiation of Mitochondrial Nanotunnels. In contrast, loss of ATF4 results in mitochondrial fragmentation and impaired aerobic capacity. Chromatin immunoprecipitation sequencing reveals direct ATF4 binding at the promoters of the genes encoding NRF1 and Nrf2, which in turn regulate MFN2 expression. Small-molecule inhibition studies further establish that activation of this hierarchical pathway is both necessary and sufficient for stress-induced mitochondrial structural adaptation. Together, these findings position ATF4 as a master regulator of mitochondrial architectural plasticity, providing a direct mechanistic link between cellular stress signaling and organelle remodeling.
    DOI:  https://doi.org/10.64898/2026.03.04.709625
  38. EMBO J. 2026 Mar 24.
    Stress-induced OMA1-mediated cleavage of AIFM1 suppresses cell growth by controlling mitochondrial OXPHOS activity.
    Mitsuhiro Nishigori, Serina Hirata, Hidetaka Kosako, Takeshi Ichinohe, Hendrik Nolte, Jan Riemer, Thomas Langer, Takumi Koshiba.
      Mitochondrial proteases regulate dynamic properties of organelle morphology and ensure functional plasticity at the cellular level. The metalloprotease OMA1 mediates constitutive and stress-inducible processing of its mitochondrial substrates, although only a few of its direct functional targets have been characterized. Using in vitro and in vivo multiproteomic and biochemical approaches, we here demonstrate that the membrane-anchored intermembrane space (IMS) protein AIFM1 serves as a mitochondrial stress-responsive OMA1 substrate. Under stress conditions, OMA1 cleaves AIFM1 in the IMS with slower kinetics than its conventional substrate, the dynamin-like GTPase OPA1. OMA1-mediated dislocation of cleaved AIFM1 from the mitochondrial inner membrane reduces its interaction with oxidative phosphorylation subunits, thereby decreasing respiratory activity and impairing cell growth. Furthermore, we reveal that under steady-state conditions AIFM1 broadly safeguards the mitochondrial proteome by mediating the import of proteins, particularly respiratory complex I subunits, via the TIM23 complex. Similar changes to the mitochondrial proteome occur in the lungs of virally infected mice, accompanied by stress-inducible AIFM1 processing. These findings identify OMA1 as a key integrator of mitochondrial stress and cellular energetics through AIFM1 remodeling.
    Keywords:  AIFM1; Mitochondrial Stress; OMA1; OXPHOS Activity; Proteolysis
    DOI:  https://doi.org/10.1038/s44318-026-00734-y
  39. bioRxiv. 2026 Mar 18. pii: 2026.03.18.712693. [Epub ahead of print]
    UFMylation of Pyruvate Dehydrogenase Regulates Mitochondrial Metabolism.
    Phong T Nguyen, Zheng Wu, Dohun Kim, Tamaratare Ogu, Siyu Yin, Varun Sondhi, Feng Cai, Trevor S Tippetts, Annie Jen, Evgenia Shishkova, Ling Cai, Dennis Dumesnil, Margaret Cervantes, Hongli Chen, Prashant Mishra, Joshua J Coon, Gerta Hoxhaj, Min Ni, Ralph J DeBerardinis.
      The ubiquitin-fold modifier 1 (UFM1) post-translational modification (PTM), or UFMylation, regulates protein homeostasis and is essential for human development. Yet the roles of the de-UFMylase, UFM1-specific peptidase 2 (UFSP2), which removes UFM1 from UFMylated proteins, remain poorly characterized. Here, we demonstrate that UFMylation and UFSP2 regulate mitochondrial metabolism. Quantitative proteomics in UFSP2-deficient cells revealed the accumulation of many proteins previously unknown to be impacted by UFMylation. These included components of the mitochondrial ribosome, electron transport chain (ETC), and pyruvate dehydrogenase (PDH) complex. Functional analyses demonstrated that excessive UFMylation in UFSP2-deficient cells increases mitochondrial respiration, glucose oxidation in the tricarboxylic acid (TCA) cycle, and PDH enzymatic activity. We identified dihydrolipoamide S-acetyltransferase (DLAT), the E2 component of PDH, as a direct UFMylation substrate, with lysine 118 (K118) as the primary conjugation site. Mutating K118 to arginine (K118R) abolished DLAT UFMylation and reduced pyruvate oxidation, identifying this modification as an activator of PDH. These findings reveal a UFMylation-based regulatory mechanism that controls mitochondrial function by inducing utilization of pyruvate as a TCA cycle fuel.
    DOI:  https://doi.org/10.64898/2026.03.18.712693
  40. J Mol Biol. 2026 Mar 24. pii: S0022-2836(26)00138-5. [Epub ahead of print] 169765
    Molecular determinants and therapeutic targeting of stop codon readthrough in eukaryotic translation.
    Wojciech Teodorowicz, Oliver Mühlemann.
      Accurate translation termination is essential for proteome integrity and is primarily governed by the release factors eRF1 and eRF3, which ensure precise recognition of stop codons and efficient release of nascent polypeptides. However, proteome integrity is challenged by mutations that generate premature termination codons (PTCs), leading to truncated, nonfunctional proteins and degradation of the aberrant transcript via nonsense-mediated mRNA decay (NMD). Collectively, these events account for ∼1800 human genetic diseases. Translational readthrough, the process by which near-cognate tRNAs decode stop codons and allow ribosomes to continue elongation beyond the stop codon, represents a possibility to suppress PTCs and restore full-length protein synthesis. Initially discovered in viruses as a mechanism to expand coding capacity, readthrough is now recognized as a regulated feature of eukaryotic gene expression influenced by both cis-acting sequence elements and trans-acting factors. Recent evidence highlights the remarkable context dependence of readthrough, revealing variation across transcripts, tissues, and developmental stages. In this review, we examine the molecular determinants that define stop codon recognition and readthrough efficiency, with particular emphasis on nucleotide context. We further discuss the mechanisms and binding sites of small molecules that promote PTC readthrough, and summarize the clinical development landscape of readthrough-inducing compounds for the treatment of diseases caused by nonsense mutations.
    Keywords:  Premature termination codon (PTC); nonsense-mediated mRNA decay (NMD); translation termination; translational readthrough (TR)
    DOI:  https://doi.org/10.1016/j.jmb.2026.169765
  41. Annu Rev Biochem. 2026 Mar 24.
    Cellular Repair and Removal of Protein-Damage Modifications.
    Abigail K D Porter, Christina M Woo.
      Protein aging, stress, or metabolism can lead to the accumulation of numerous nonenzymatic chemical alterations that can threaten protein stability and function, particularly in long-lived proteins. Eukaryotic cells recognize these protein-damage events through repair and removal pathways, whose loss can lead to adverse effects and contribute to age-related disease pathogenesis. Here, we review recent advances in understanding the formation, repair, and removal mechanisms of posttranslational modifications arising from protein damage, including dehydroamino acids, early-stage glycation, isoaspartate, C-terminal cyclic imides, and C-terminal amides. We emphasize the emerging role of E3 ubiquitin ligases in facilitating the degradation of proteins bearing these modifications, highlight the approaches used to make these discoveries, and discuss the potential functions of these modifications beyond protein damage. Mounting evidence that protein-damage events influence cellular signaling and metabolism suggests the existence of vast undiscovered regulatory networks, creating opportunities to uncover tissue-specific repair mechanisms and their roles in development, aging, and stress responses across diverse biological contexts.
    DOI:  https://doi.org/10.1146/annurev-biochem-051024-045733
  42. Cell Death Differ. 2026 Mar 26.
    Proteasome inhibition promotes Foxn1 expression in thymic epithelial cells and induces thymic regeneration in mice.
    Shirley Genah, Marsha Pellegrino, Manuela Giansanti, Angelica Mancusi, Alessio Taviani, Antonella Cardinale, Marco Rosichini, Sara Flamini, Maria Luigia Catanoso, Ezio Giorda, Gabriele Volpe, Michela Piccione, Francesca Nazio, Jarrod A Dudakov, Marcel R M van den Brink, Emmanuel de Billy, Franco Locatelli, Enrico Velardi.
      The thymus plays a critical role in sustaining T-cell immunity, although its function is highly vulnerable to acute injury and physiologically declines with age, resulting in compromised immune responses. Impaired thymic function represents a major clinical challenge, particularly in settings of immunosuppression associated with cancer therapy and aging. Yet, effective strategies to rejuvenate the thymus remain limited. To explore novel regenerative approaches, we focused on FOXN1, a master regulator of thymic epithelial cell (TEC) development and function. By developing a custom screening platform, we tested a library of FDA-approved compounds for their ability to induce FOXN1 in TECs. Proteasome inhibition emerged as a potent and previously unrecognized mechanism for upregulating FOXN1 in both murine and human primary TECs. Among the hits identified in the screening, the antiparasitic drug nitazoxanide (NTZ) stood out for its proteasome inhibitory activity and for inducing Foxn1 expression while preserving cell viability, unlike other proteasome inhibitors. Mechanistically, NTZ-induced proteasome inhibition triggered endoplasmic reticulum stress (ER) and the adaptive unfolded protein response (UPR), ultimately engaging autophagy in TECs. In this context, the induction of autophagy acted as a compensatory mechanism to support cell survival in response to proteasome inhibition. Notably, when administered in mice, NTZ significantly accelerated functional thymic recovery after radiation-induced damage, promoting restoration of thymic architecture and cellularity of both stromal and hematopoietic compartments without disrupting physiological T-cell selection or tolerance mechanisms. Consistent with our in vitro findings, NTZ treatment induced Foxn1 and its downstream targets in TECs in vivo and conferred protection to TECs following irradiation. These findings uncover proteasome inhibition and, more broadly, modulation of ER stress and UPR pathways as a previously unrecognized mechanism regulating Foxn1 expression and position NTZ as a promising pharmacological strategy to enhance immunity in patients experiencing T-cell deficiencies due to cancer-related immunosuppression, infections, and age-related thymic atrophy.
    DOI:  https://doi.org/10.1038/s41418-026-01724-7
  43. FEBS J. 2026 Mar 17.
    Optineurin calibrates STING-mediated type I interferon response.
    Sreeram Kaveti, Nishant Jain.
      Cyclic GMP-AMP synthase (cGAS) senses cytosolic self and microbial DNA to produce cyclic guanosine monophosphate-adenosine monophosphate (cGAMP), a secondary messenger that activates the endoplasmic reticulum-resident transmembrane protein, stimulator of interferon genes (STING). After binding to cGAMP, STING undergoes oligomerisation, exits the endoplasmic reticulum (ER), recruits tank-binding kinase 1 (TBK1) and interferon regulatory factor 3 (IRF3) on Golgi membranes, resulting in the activation of type I interferons (IFNs). STING is found to be a preformed dimer in the ER; however, it is yet unknown whether protein-protein interactions maintain STING in its resting state. Optineurin (OPTN) functions as an adaptor or a scaffold to coordinate autophagy, type I IFN response, vesicle trafficking, and mitophagy. TBK1 commonly binds OPTN and STING to activate type I IFNs in response to extracellular and intracellular cues. However, it remains unclear whether OPTN participates in STING-mediated type I interferon (IFN) response. As STING initiates inflammatory signalling and OPTN functions as an adaptor protein, we asked if OPTN is necessary for STING to mediate type I IFN response. To answer this question, we examined STING-mediated type I IFN response in human and mouse cells depleted of OPTN and elucidated STING-OPTN binding. We found that modulating OPTN levels alters STING-mediated type I IFN response. Further, the N-terminal domain of STING binds to the C-terminal ubiquitin-binding domain of OPTN. In addition, we found that OPTN engages with STING and TBK1. Thus, we conclude that OPTN calibrates STING-mediated type I IFN response. Based on our observations, approaches that include developing tailored molecular glue-like compounds binding STING-OPTN, and determining STING activation might be valuable avenues for understanding and treating autoimmune diseases.
    Keywords:  STING; TBK1; diABZI; optineurin; pSTING‐S‐366; type I IFN response
    DOI:  https://doi.org/10.1111/febs.70490
  44. EMBO Rep. 2026 Mar 26.
    Common and rare genetic variants show network convergence for a majority of human traits.
    Sarah N Wright, Jane Yang, Trey Ideker.
      While both common and rare variants contribute to the genetic etiology of complex traits, whether their impacts manifest through the same effector genes and molecular mechanisms is not well understood. Here, we systematically analyze common and rare variants associated with each of 373 phenotypic traits within a large biological knowledge network of gene and protein interactions. While common and rare variants implicate few shared genes, they converge on shared molecular networks for more than 75% of traits. We demonstrate that the strength of this convergence is influenced by core factors such as trait heritability, gene selective constraint, and tissue specificity. Using neuropsychiatric traits as examples, we show that common and rare variants impact genes with shared functions across multiple levels of biological organization. These findings underscore the importance of integrating variants across the frequency spectrum and establish a foundation for network-based investigations of the genetics of diverse human diseases and phenotypes.
    Keywords:  Common Variants; Complex Traits; Genetic Architecture; Network Biology; Rare Variants
    DOI:  https://doi.org/10.1038/s44319-026-00733-4
  45. bioRxiv. 2026 Mar 17. pii: 2026.03.14.711071. [Epub ahead of print]
    ULK1 drives NDP52-mediated selective autophagic degradation of MHC-I to promote immune evasion in HPV-positive head and neck cancer.
    Lexi Vu, Nicholas S Giacobbi, Mohamed I Khalil, Canchai Yang, William J Eckerman, Evelyn Gomez Recinos, Johnathon D Garber, Hyomin Son, Prerna Chahal, Dara M Villa, Tasha Srivastava, Abigail Z Bennett, Katie R Martin, Craig C Welbon, Caitlin Williamson, William C Spanos, Jeffrey P MacKeigan, Andrew J Olive, Dohun Pyeon.
      Antigen presentation by major histocompatibility complex class I (MHC-I) is critical for tumor cell killing by CD8 + T cells. Accordingly, tumor cells downregulate MHC-I expression through multiple mechanisms, thereby evading the immune response. Importantly, lower levels of MHC-I are associated with poor responses to immune checkpoint inhibitor therapy. Our recent study has shown that the human papillomavirus (HPV) oncoproteins induce MHC-I protein ubiquitination by membrane-associated Ring-CH-type finger 8 (MARCHF8) in HPV-positive head and neck cancer (HPV+ HNC). However, the mechanism by which ubiquitinated MHC-I is degraded remains elusive. By performing genome-wide CRISPR screens, we identified components of the ULK1 and PIK3C3 complexes for autophagy initiation complexes among the top negative regulators of cell-surface MHC-I expression in HPV+ HNC cells. We show that MHC-I is recruited from the ER to autophagosomes by the cargo receptor NDP52, decreasing MHC-I levels. Further, inhibiting the initiation or nucleation steps of autophagy before autophagosome formation is critical for restoring MHC-I levels on the cell surface. Finally, genetic inhibition of autophagy initiation suppresses HPV+ HNC tumor growth in vivo and enhances the CD8 + T cell-mediated antitumor response. Our findings suggest that autophagic degradation of MARCHF8-ubiquitinated MHC-I is a key immune evasion mechanism in HPV+ HNC.
    DOI:  https://doi.org/10.64898/2026.03.14.711071
  46. bioRxiv. 2026 Mar 05. pii: 2026.03.04.709570. [Epub ahead of print]
    A molecular grammar for programmable multiphase protein-RNA vesicles.
    V Ramachandran, D A Potoyan.
      Protein-RNA phase separation gives rise to biomolecular condensates with rich internal organization, yet the molecular rules that connect sequence-encoded interactions and composition to the emergent architecture of these condensates remain poorly defined. Here, using large-scale residue-level coarse-grained simulations, we identify a molecular grammar that governs the formation and stability of multiphase protein-RNA condensates. We show that asymmetries in protein-protein and protein-RNA interactions, together with protein stoichiometry, chain length, and condensate density, collectively determine whether condensates adopt homogeneous, layered, biphasic, or vesicle-like morphologies. Across a broad parameter space, these rules yield hollow multiphase vesicles with dense shells surrounding dilute interiors. Remarkably, vesicular condensates form spontaneously from well-mixed initial conditions, without requiring flux-driven oversaturation or extreme charge imbalance, distinguishing this mechanism from previously proposed routes to condensate hollowing. Our results establish minimal and general design principles for programming internal condensate architecture solely through sequence and composition, and provide a framework for engineering membrane-free vesicles and multilayered condensates with tunable permeability, encapsulation, and responsiveness.
    DOI:  https://doi.org/10.64898/2026.03.04.709570
  47. Proc Natl Acad Sci U S A. 2026 Mar 31. 123(13): e2602991123
    VAMP8 function reveals tight linkage between endocytic recycling and endocytosis.
    Ailing Liu, Yueping Li, Zheng Huang, Wen Chen, Peiliu Xu, Xiangying Wei, Guosheng Hu, Shuangquan Liu, Xiaoxia Liu, Yaohui He, Danling Wang, Sandra L Schmid, Zhiming Chen.
      Clathrin-mediated endocytosis (CME) is a multistage process that involves the initiation and stabilization of clathrin-coated pits (CCPs) that invaginate and finally detach from the plasma membrane to form clathrin-coated vesicles (CCVs). Given that Soluble N-ethylmaleimide-sensitive factor attachment receptor (SNARE) proteins are essential for downstream vesicle targeting and fusion events, their recruitment into nascent CCVs has been suggested to be a prerequisite for CME progression. However, which and how SNARE proteins regulate CME remains to be explored. Here, we showed that siRNA-mediated knockdown of the R-SNARE, vesicle-associated membrane protein 8 (VAMP8) impairs CCP initiation, stabilization, and invagination and strongly inhibits CME. Mechanistically, recruitment of VAMP8 to CCVs is not required for CME. Instead, depletion of VAMP8 inhibits recycling of endocytic cargoes and as exemplified here by transferrin receptor, skews their trafficking toward lysosomal degradation. VAMP8 depletion therefore indirectly impairs CCV formation and inhibits CME by depleting endocytic cargo. Overall, our study provides insights into the crosstalk between endocytosis and endocytic recycling of CME cargo and demonstrates the critical role for cargo recruitment in stabilizing nascent CCPs to regulate CME.
    Keywords:  SNARE; clathrin; endocytosis; recycling
    DOI:  https://doi.org/10.1073/pnas.2602991123
  48. Nat Commun. 2026 Mar 26.
    Structural and evolutionary insights into the eukaryotic RNase MRP ribonucleoprotein complex.
    Bin Zhou, Xiaozhu Wang, Futang Wan, Shaobai Li, Xiaoshuang Zhang, Yuanyuan Zhang, Ming Tan, Mi Cao, Yafeng Shen, Rui Gao, Yanjie Zhang, Pengfei Lan, Jian Wu, Ming Lei.
      RNase MRP is a conserved eukaryotic ribonucleoprotein essential for precursor-rRNA processing and ribosome assembly. Despite previous studies of yeast RNase MRP, the composition of RNase MRP and how it adapts to process flexible, single-stranded rRNA substrates in most eukaryotes remain enigmatic. Here, we perform an integrative structural, evolutionary, and functional dissection of human RNase MRP. Using structure-based bioinformatics and cryo-EM structural analyses, we identify NEPRO (RMP64) and C18orf21 (RMP24) as the bona fide subunits unique to RNase MRP, which are indispensable for precursor-rRNA cleavage, ribosome assembly, protein synthesis, and chondrogenesis. The structure of human RNase MRP reveals a unique 'double-anchor' substrate-binding mechanism that underlies evolutionary adaptations conferring broad substrate specificity. Our work on RNase MRP provides a unified evolutionary and mechanistic framework for this essential ancient ribozyme.
    DOI:  https://doi.org/10.1038/s41467-026-71007-9
  49. EMBO Rep. 2026 Mar 25.
    USP25 aggravates liver cancer development and impairs chemosensitivity by limiting LATS1 activation.
    Lei Li, Xinshu Wang, Yuntong Yang, YuJuan Zhou, ZeShan Jiang, Linhui Zhai, Xinru Zhao, Hanqiong Qiang, Jingyi Luo, Yanjun Ji, Jiakai Yao, Tingting Zhang, Yixian Wang, Ke Li, Lei Chen, Yuping Chen, Jian Yuan, Yunhui Li.
      Hepatocellular carcinoma (HCC) is a primary liver malignancy with high rates of morbidity and mortality, yet effective treatment options remain limited. Accumulating evidence indicates that large tumour suppressor kinase 1 (LATS1), a core kinase in the Hippo pathway, mediates the phosphorylation of downstream YAP/TAZ, thereby suppressing HCC progression. Although LATS1 protein stability has been reported to be modulated by ubiquitination, the specific mechanism controlling LATS1 kinase activity remains unknown. Here, we identify USP25 as a deubiquitinase that regulates LATS1 activity, independent of LATS1 protein stability. We demonstrated that USP25 is overexpressed in HCC and that USP25 depletion significantly suppresses HCC cell and tumour growth. Mechanistically, USP25 catalyses the removal of K63-linked ubiquitin at K688 of LATS1, which disrupts LATS1-MOB1 complex formation and promotes YAP-mediated transcriptional activation. Furthermore, we successfully developed a cell-penetrating peptide that disrupts the USP25-LATS1 interaction, which increases p-YAP expression and synergizes with chemotherapy in xenograft and patient-derived organoid and xenograft models. Collectively, our findings reveal a mechanism through which USP25 regulates LATS1 activity and provide a potential therapeutic strategy for HCC treatment.
    Keywords:  Chemoresponse; Deubiquitinase USP25; Hepatocellular Carcinoma (HCC); Large Tumour Suppressor Kinase 1 (LATS1); Therapeutic Strategy
    DOI:  https://doi.org/10.1038/s44319-026-00749-w
  50. bioRxiv. 2026 Mar 20. pii: 2026.03.18.712702. [Epub ahead of print]
    Structural basis of receptor retro-translocation in peroxisomal protein import.
    Nathaniel W M Dempsey, Laurie Wang, Ningjian Gao, Kangting Zhao, Jessica Cope, Eunyong Park.
      Peroxisomes import all matrix proteins post-translationally from the cytosol, a process that requires recycling of cargo receptors across the peroxisomal membrane. The membrane-embedded ubiquitin ligase, composed of Pex2, Pex10, and Pex12, is central to this process, but its mechanism remains unclear. Here we determined cryo-electron microscopy structures of the Saccharomyces cerevisiae Pex2-10-12 complex in closed and open states bound to Pex8, an essential factor of previously undefined function. The structures reveal how Pex2-10-12 gates its retro-translocation pore to control receptor entry and how the closed-to-open transition repositions the Pex10 RING domain to enable receptor mono-ubiquitination. Pex8 docks onto Pex2-10-12 from the matrix and guides receptors into the pore. Functional analyses show that the receptor's N-terminal segment downstream of its mono-ubiquitination site initiates a loop insertion into the pore. These findings establish how Pex2-10-12 coordinates receptor recognition, retro-translocation, and ubiquitination, providing the molecular basis for receptor recycling in peroxisomal protein import.
    DOI:  https://doi.org/10.64898/2026.03.18.712702
  51. Curr Issues Mol Biol. 2026 Feb 24. pii: 240. [Epub ahead of print]48(3):
    Roles of DNA Damage Response Pathway in the Regulation of the Nuclear Envelope.
    Yasunao Kamikawa, Zuqian Wu, Kenshiro Fujise, Kazunori Imaizumi, Atsushi Saito.
      The nuclear envelope (NE) functions as a barrier between the cytoplasm and nucleus. Over the past decade, NE has revealed unexpectedly divergent structural alterations. NE rupture triggers the uncontrollable exchange of macromolecules across the NE and potentially causes DNA damage. Conversely, a recent study demonstrated that DNA damage induces NE rupture and that one of the major kinases in the DNA damage response (DDR) pathway, ataxia telangiectasia and Rad3-related protein, ATR, is a key molecule in these events. Here, we review the role of the DDR pathway in NE regulation, with a focus mainly on ATR.
    Keywords:  ATR; DNA damage response; cell cycle; lamin; nuclear envelope; nuclear envelope rupture; nuclear lamina
    DOI:  https://doi.org/10.3390/cimb48030240
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