bims-proteo Biomed News
on Proteostasis
Issue of 2026–03–08
forty-five papers selected by
Eric Chevet, INSERM
  1. Global profiling of nascent chain interactors reveals TRIM25 as a co-translational E3 ubiquitin ligase.
  2. GCN2 in proteostasis: structural logic, signalling networks and disease.
  3. Inhibition of FicD-mediated AMPylation and deAMPylation by isoprenoid diphosphates.
  4. GlueFinder: A Data-Driven Framework for the Rational Discovery of Molecular Glues.
  5. Structural remodeling of the mitochondrial protein biogenesis machinery under proteostatic stress.
  6. MondoA mediates transcriptional coordination between the MYC network and the integrated stress response in pancreatic cancer.
  7. Active Site Assembly by SMG5 as a Mechanism for SMG6 Endonuclease Licencing in Nonsense-mediated mRNA Decay.
  8. The Ubiquitin Ligase Zinc Finger SWIM Domain-Containing Protein 8 Regulates Oligodendrocyte Development Through the Argonaute2/MicroRNA-7 Axis.
  9. Global analysis of protein degradation reveals instability of diverse regulators in Escherichia coli.
  10. The accessory adapters FAF1, FAF2, and UBXN7 accelerate proteasomal degradation by increasing prior p97-mediated substrate unfolding.
  11. Lysine-11 ubiquitination drives type-I/III interferon induction by cGAS-STING and Toll-like receptors 3 and 4.
  12. Brucella Omp25 activates the unfolded protein response to promote intracellular proliferation and inflammation.
  13. Neurons with granulovacuolar degeneration bodies are resilient to tau-induced protein synthesis impairment.
  14. CD44-Assisted Transcytosable Chimeras for Extracellular Protein Depletion in Deep Tumors.
  15. Activation of Unfolded Protein Response Pathways Promotes Keratinocyte Differentiation and Ameliorates Psoriasis Phenotypes.
  16. Functions of J-domain proteins in mitochondrial protein biogenesis.
  17. Chemical Synthesis of Ubiquitinated Proteins and Ubiquitin Probes for Biochemical and Functional Analysis.
  18. PROTAC-mediated degradation of peroxisomal d-aspartate oxidase: A novel strategy to modulate d-aspartate homeostasis for schizophrenia treatment.
  19. RNA-specific local translation is patterned by condensates for multinucleate cell growth.
  20. Immune activation reprograms growth mRNA stability to shape plant growth-defense trade-offs.
  21. Rab14 restricts pathogens by promoting V-ATPase lysosomal delivery to drive lysosomal acidification.
  22. OTUD3-mediated deubiquitination licenses TEX264 to orchestrate ER-phagy for KDM5B degradation in teniposide lung cancer therapy.
  23. Reconstitution approaches for understanding cellular lipid dynamics.
  24. Mapping the inter- and intra-genic codon-usage landscape in Homo sapiens.
  25. ALG8-Driven Metabolic Reprogramming in Polycystic Kidney Disease: A Systematic Synthesis of Evidence Linking Glycosylation Defects to Metabolic Signaling.
  26. Citrate clearance is a major function of aconitase 2 in the canonical TCA cycle.
  27. Cryo-EM structures of UBA6 reveal mechanisms of E1-E2 specificity and dual FAT10/ubiquitin thioester transfer.
  28. USP7 deubiquitinase stabilizes FAN1 to support DNA crosslink repair and suppress CAG repeat expansion.
  29. Unifying Constraints Linking Protein Folding and Native Dynamics Decoded from AlphaFold.
  30. PA200 differentially regulates the proteasome and inhibits migration of NSCLC cells.
  31. Targeting tRNA-dependent tyrosine usage unveils a metabolic vulnerability in hepatocellular carcinoma.
  32. Mitochondrial complex-derived ROS induces lysosomal dysfunction and impairs autophagic flux in human cells carrying the APOE4 allele.
  33. Efficient amyloid-β degradation in Alzheimer's disease using SPYTACs.
  34. 5PSeq explorer: interactive analysis of Co-translational mRNA decay and ribosome dynamics.
  35. Need for speed: Advances in the era of high throughput interaction proteomics.
  36. Lipid Pocket Binders Impose Allosteric Changes of Protein Dynamics Around the Active Site of the Protein Kinase p38α.
  37. Function and regulation of the mitochondrial stress response.
  38. SLC4A1 mutations that cause distal renal tubular acidosis alter cytoplasmic pH and cellular autophagy.
  39. Large adipocytes increase vesicle-mediated lipid release and promote breast cancer malignancy.
  40. Single-cell thiol profiling enabled by live-cell labeling reveals metabolic heterogeneity in ferroptosis.
  41. Structural heterogeneity and substrate engagement mechanism of the bacterial proteasome activator Bpa.
  42. Functional landscape of non-canonical open reading frames in coordinating cell fate.
  43. The lncRNA DAMER selectively guides m6A-dependent regulation of ATF4 and asparagine metabolism under nutrient stress in cancer.
  44. A Modular Toolkit for Nanoscale Interrogation of Multiprotein Assemblies Inside Living Cells.
  45. A proteome-wide dependency map of protein interaction motifs.
  1. Mol Cell. 2026 Mar 03. pii: S1097-2765(26)00102-4. [Epub ahead of print]
    Global profiling of nascent chain interactors reveals TRIM25 as a co-translational E3 ubiquitin ligase.
    Wenfeng Xiong, Zheng Ser, Radoslaw Mikolaj Sobota, Zhewang Lin.
      Nascent polypeptide chains emerging from the ribosome engage a range of co-translational factors at distinct phases of translation. These co-translational interactions are crucial for proper protein biogenesis and quality control pathways to maintain protein homeostasis. Hence, the systematic identification of these co-translational interactors provides insights into how distinct polypeptide fates are determined. Here, we developed nascent-chain interactor profiling (NCIP), a metabolic-labeling- and chemical-crosslinking-enabled proteomics method to identify proteins interacting with nascent polypeptide chains at a proteome-wide scale. Results from NCIP support the co-translational assembly model of multiple protein complexes and reveal TRIM25 as a co-translational E3 ubiquitin ligase. TRIM25 ubiquitinates misfolded nascent chains for quality control at the ribosome. Our results provide a generalizable framework to systematically profile co-translational interactors.
    Keywords:  co-translational E3 ubiquitin ligase; nascent chain interactors; protein quality control
    DOI:  https://doi.org/10.1016/j.molcel.2026.02.007
  2. FEBS J. 2026 Mar 04.
    GCN2 in proteostasis: structural logic, signalling networks and disease.
    JiaYi Zhu, Stefan J Marciniak.
      Proteostasis is the finely tuned balance of protein synthesis, folding and degradation essential for cellular health. When this equilibrium is disrupted, misfolded proteins accumulate, triggering adaptive stress responses such as the unfolded protein response and the integrated stress response (ISR). Central to the ISR is the kinase GCN2, a sensor of amino acid deprivation and ribosomal stress. Upon activation, GCN2 phosphorylates eIF2α, dampening global translation while selectively enhancing the synthesis of the stress-responsive transcription factors ATF4 and CHOP. ATF4 orchestrates a broad transcriptional programme that supports amino acid metabolism, redox homeostasis, autophagy and proteasomal degradation, which are key processes for restoring proteostasis. Beyond its canonical role, GCN2 interfaces with other regulatory networks modulating mTORC1 to promote autophagic clearance of damaged proteins and organelles, facilitating stress granule formation, and integrating signals from oxidative and endoplasmic reticulum stress to rebalance the proteome. Dysregulated GCN2 activity has been implicated in diverse pathologies including neurodegeneration, cancer and pulmonary vascular disease, positioning it as a promising therapeutic target. In this review, we explore how GCN2 links nutrient sensing to translational control and metabolic adaptation, and how its central role in proteostasis may inform new strategies for treating diseases driven by protein misfolding and stress pathway imbalance.
    Keywords:  GCN2; amino acid sensing; integrated stress response; proteostasis; translational control
    DOI:  https://doi.org/10.1111/febs.70480
  3. Proc Natl Acad Sci U S A. 2026 Mar 10. 123(10): e2533457123
    Inhibition of FicD-mediated AMPylation and deAMPylation by isoprenoid diphosphates.
    Aubrie M Blevins, Wei Peng, Lisa N Kinch, Zihan Monshad, Andrea G Paredes, Christina Volz, Jared Rutter, Amanda K Casey, Kevin G Hicks, Kim Orth.
      FicD regulates Unfolded Protein Response (UPR) through reversible AMPylation and deAMPylation of BiP, an HSP70 chaperone and master regulator of the UPR. FicD activity is regulated by endoplasmic reticulum-stress, catalyzing BiP AMPylation under low stress conditions to hold inactive chaperone in reserve. In stressed cells, FicD deAMPylates BiP, acutely increasing its active pool to assist in protein folding. Variants in UPR machinery, including those in the FicD gene, are linked to hereditary diseases. Despite the known role of FicD in UPR, in-vivo regulation of its activity remains elusive, and identifying metabolites that alter FicD activity could prove useful pharmaceutically. We applied an unbiased high-throughput screening platform, known as Mass spectrometry Integrated with equilibrium Dialysis for the discovery of Allostery Systematically (MIDAS), to identify small molecule metabolites that might regulate FicD activity. MIDAS revealed interactions between FicD and two mevalonate pathway intermediates: geranyl-pyrophosphate and farnesyl-pyrophosphate. Biochemical characterization indicates that both potently inhibit FicD-mediated AMPylation and deAMPylation. The crystal structure of FicD bound to farnesyl-pyrophosphate demonstrates a competitive inhibition mechanism, with the pyrophosphate adopting the alpha and beta phosphate positions of adenosine triphosphate (ATP) and the hydrocarbon chain filling the nucleoside pocket. FicD variants previously appeared as biochemically indistinguishable, yet lead to different human pathologies. We demonstrate farnesyl-pyrophosphate inhibits FicDR374H and FicDR374C variants implicated in causing hereditary spastic paraplegia, but not the FicDR371S variant associated with neonatal diabetes. This study furthers our understanding of FicD inhibitors and distinguishes disease causing variants, providing insight into pharmacological targeting of UPR activity.
    Keywords:  AMPylation; FicD; PTM; isoprenoid diphosphates; unfolded protein response
    DOI:  https://doi.org/10.1073/pnas.2533457123
  4. J Chem Inf Model. 2026 Mar 02.
    GlueFinder: A Data-Driven Framework for the Rational Discovery of Molecular Glues.
    Jeffrey Skolnick, Bharath Srinivasan, Hongyi Zhou.
      Molecular glues drive targeted protein degradation by stabilizing ternary complexes between proteins of interest and E3 ubiquitin ligases, but their rational design has lagged due to a limited understanding of the rules for interface recognition and an overreliance on a few ligases (e.g., VHL or Cereblon). We introduce GlueFinder, a systematic, unbiased platform that leverages structural bioinformatics to mine the Protein Data Bank for ligand-binding pockets adjacent to the protein interface which are ligandable sites that can nucleate glue-mediated complex formation. After validating its performance on a benchmark of experimentally solved dimeric structures with known and predicted glues, we applied GlueFinder to three therapeutically important targets, EGFR, HER2, and KRAS, and predicted candidate glues that recruit 24, 111, and 148 distinct E3 ligases to these targets, respectively. We further demonstrate that GlueFinder can promote the formation of non-native EGFR complexes with a variety of diverse proteins, possibly enabling ternary assemblies that would not form on their own. These results establish a general, computation-guided experimental prioritization strategy for molecular glue discovery that decouples design from legacy degrader scaffolds and specific ligase dependencies, expands the usable E3 ligase repertoire, and enables rational targeting of interfacial binding pockets.
    DOI:  https://doi.org/10.1021/acs.jcim.5c03232
  5. Sci Adv. 2026 Mar 06. 12(10): eaed3579
    Structural remodeling of the mitochondrial protein biogenesis machinery under proteostatic stress.
    Kenneth Ehses, Jorge P López-Alonso, Odetta Antico, Yannik Lang, Till Rudack, Abdussalam Azem, Miratul M K Muqit, Iban Ubarretxena-Belandia, Rubén Fernández-Busnadiego.
      Cells have evolved organelle-specific responses to maintain protein homeostasis (proteostasis). During proteostatic stress, mitochondria down-regulate translation and enhance protein folding, yet the underlying mechanisms remain poorly defined. Here, we used cryo-electron tomography to observe the structural consequences of mitochondrial proteostatic stress within human cells. We detected protein aggregates within the mitochondrial matrix, accompanied by a marked remodeling of cristae architecture. Concomitantly, the number of mitochondrial ribosome complexes was significantly reduced. Mitochondrial Hsp60 (mHsp60), a key protein folding machine, underwent major conformational changes to favor complexes with its co-chaperone mHsp10. We visualized the interactions of mHsp60 with native substrate proteins and determined in vitro mHsp60 cryo-electron microscopy structures enabling nucleotide state assignment of the in situ structures. These data converge on a model of the mHsp60 functional cycle and its essential role in mitochondrial proteostasis. More broadly, our findings reveal structural mechanisms governing mitochondrial protein biosynthesis and their remodeling under proteostatic stress.
    DOI:  https://doi.org/10.1126/sciadv.aed3579
  6. Proc Natl Acad Sci U S A. 2026 Mar 10. 123(10): e2524659123
    MondoA mediates transcriptional coordination between the MYC network and the integrated stress response in pancreatic cancer.
    Erin L Ramsey, Stephanie Dobersch, Brian Freie, Nan Hyung Hong, Xiaoying Wu, Sita Kugel, Robert N Eisenman, Patrick A Carroll.
      MYC amplification contributes to poor survival and outcome in pancreatic ductal adenocarcinoma (PDAC). Here we show that in PDAC cell lines with amplified MYC, MondoA is required for viability, facilitating proliferation while suppressing apoptosis in vitro and in vivo. Transcriptional and genomic profiling demonstrates that loss of MondoA leads to altered expression of direct MondoA targets as well as MYC target genes and is accompanied by shifts in genomic occupancy of MYC, MNT, and the MondoA paralog ChREBP. This altered genomic binding by MYC network members is associated with transcriptional perturbation of multiple metabolic and stress pathways, as well as global changes in N6-methyladenosine modification (m6A) of messenger RNA (mRNA). MondoA inhibition disrupts coordination between MYC network members and the Integrated Stress Response (ISR), resulting in decreased translation of ATF4 mRNA, discordant gene regulation of shared targets of MYC and ATF4 and, ultimately, apoptosis. Reestablishing ATF4 protein expression rescues the diminished viability due to loss of MondoA expression or activity, providing direct evidence of a link between deregulated MYC and the transcriptional machinery of the ISR. Last, we find that small-molecule inhibition of MondoA is lethal in a subset of PDAC cell lines, including patient-derived organoids, suggesting that the ability to target MYC via chemical inhibition of MondoA transcriptional activity may have broad efficacy.
    Keywords:  MYC network; MondoA inhibitor; MondoA/MLXIP; pancreatic cancer; stress response
    DOI:  https://doi.org/10.1073/pnas.2524659123
  7. J Mol Biol. 2026 Feb 26. pii: S0022-2836(26)00107-5. [Epub ahead of print] 169734
    Active Site Assembly by SMG5 as a Mechanism for SMG6 Endonuclease Licencing in Nonsense-mediated mRNA Decay.
    Enes S Arpa, Michael Taschner, Mara De Matos, Stefanie Jonas, David Gatfield.
      Nonsense-mediated mRNA decay (NMD) is a conserved eukaryotic surveillance pathway that eliminates transcripts containing premature termination codons (PTCs). Substantial progress has been made in defining the transcript features that mark aberrant translation termination for NMD activation, yet key mechanistic steps remain incompletely understood - including how recruitment of the central NMD factor UPF1 is coupled to the downstream effector phase in which targeted mRNAs are nucleolytically degraded. In metazoans, NMD employs an endonucleolytic route mediated by SMG6, a PIN-domain nuclease, alongside SMG5 and SMG7, which act downstream of PTC recognition. SMG5 has recently been proposed to licence SMG6 activity, yet the molecular basis of this licencing has remained elusive. Here, we combine AlphaFold structural predictions with biochemical assays to investigate interactions among human SMG5, SMG6, and SMG7. Structural models predict a high-confidence interface between SMG5 and SMG6 PIN domains that forms a composite active site: a conserved SMG5 aspartate (D893) complements the SMG6 acidic triad to reinstate the canonical tetrad required for PIN-domain catalysis. In vitro, SMG6 alone exhibits weak endonucleolytic activity, which is enhanced ∼10-fold by the SMG5 PIN domain. Mutational analyses confirm that conserved residues from both proteins are essential for this composite configuration. Our findings reveal that the SMG5 PIN domain, previously considered catalytically inert, plays a critical role in activating SMG6 by completing its active site. This work provides mechanistic insight into the SMG5-dependent licencing step and uncovers a composite PIN nuclease architecture at the heart of the metazoan NMD effector phase.
    Keywords:  PIN domain; SMG5-SMG6 interaction; UPF1 phosphorylation; endonucleolytic decay; nonsense-mediated mRNA decay (NMD)
    DOI:  https://doi.org/10.1016/j.jmb.2026.169734
  8. Glia. 2026 May;74(5): e70142
    The Ubiquitin Ligase Zinc Finger SWIM Domain-Containing Protein 8 Regulates Oligodendrocyte Development Through the Argonaute2/MicroRNA-7 Axis.
    Jing Lei, Siming Zhong, Rong Fan, Xin Shu, Guan Wang, Jiansheng Guo, Shuting Xue, Luqian Zheng, Aiming Ren, Junfang Ji, Bing Yang, Shumin Duan, Zhiping Wang, Xing Guo.
      Proteostasis of proteins with intrinsically disordered regions (IDRs) is of particular importance to the development and function of the central nervous system (CNS). The conserved ZSWIM8 ubiquitin ligase, an essential regulator of mammalian brain development, is known to target IDR proteins involved in neuronal cell migration. Here we show that ZSWIM8 is also indispensable for oligodendrocyte maturation and myelination in the CNS. Loss of ZSWIM8 in the brain causes gross accumulation of IDR-rich proteins including many RNA-binding proteins (RBPs). Substrate recognition by ZSWIM8 requires its own IDRs, while ZSWIM8-mediated ubiquitination of AGO2 also depends on microRNA binding. AGO2 stabilization in ZSWIM8-null tissues disrupts target-directed microRNA degradation (TDMD) of MiR7, leading to altered gene expressions and myelination defects in vivo. Together, these results not only establish ZSWIM8 as a versatile regulator of IDR proteins but also highlight the crucial roles of RBP/miRNA homeostasis in oligodendrocyte development.
    Keywords:   AGO2 ; ELAV1 ; MiR7 ; ZSWIM8 ; E3 ubiquitin ligase; intrinsically disordered region; myelination; oligodendrocyte development; oligodendrocyte progenitor cells
    DOI:  https://doi.org/10.1002/glia.70142
  9. Proc Natl Acad Sci U S A. 2026 Mar 10. 123(10): e2515265123
    Global analysis of protein degradation reveals instability of diverse regulators in Escherichia coli.
    Elliot J MacKrell, Brett Lomenick, Yanping Qiu, Hannah Jeckel, Jeff Jones, Tsui-Fen Chou, David A Tirrell.
      Regulated protein degradation underlies the timely execution of essential gene expression programs in bacteria. Here, we deployed time-resolved chemoproteomics, text mining of the PubMed and EcoCyc knowledge bases, and machine learning classification to identify proteolytic regulation in exponential and stationary phase Escherichia coli cultures. We experimentally validated the instability of diverse homeostatic and stress response regulators, including the principal cyclic-di-GMP phosphodiesterase PdeH, the N-end rule substrate chaperone ClpS, and all four A-type domain iron-sulfur cluster carriers, IscA, ErpA, NfuA, and SufA. Mutagenesis of the PdeH N-terminal extension abolished ClpXP recognition, thereby impairing stationary phase depletion of PdeH and altering macrocolony biofilm surface morphology. Unstable proteins synthesized in stationary phase such as the morphology regulator BolA, RNA polymerase ω subunit, and the biofilm regulator BssR were implicated in quiescence. Finally, machine learning-assisted substrate identification revealed Lon-mediated degradation of two opposing key regulators of surface adhesion, the RpoS antagonist FliZ and the major biofilm regulator CsgD, suggesting proteolysis may hasten transitions between motility and sessility. Together, these results highlight the role of regulated proteolysis in driving physiological adaptation for this model organism.
    Keywords:  BONCAT; Escherichia coli; machine learning; protein degradation; proteomics
    DOI:  https://doi.org/10.1073/pnas.2515265123
  10. Sci Adv. 2026 Mar 06. 12(10): eaea7381
    The accessory adapters FAF1, FAF2, and UBXN7 accelerate proteasomal degradation by increasing prior p97-mediated substrate unfolding.
    Matthias Kracht, Alexander Kröning, Johannes van den Boom, Pinki Gahlot, Sandra Koska, Leo Kiss, Hemmo Meyer.
      The AAA-ATPase VCP/p97 with its adapter Ufd1-Npl4 unfolds ubiquitylated substrate proteins to prepare degradation in the proteasome; however, the function of critical accessory factors remains unclear. Here, we show in the mammalian system that efficient protein degradation in the proteasome requires accessory adapters that boost p97-mediated unfolding likely by positioning Ufd1 for substrate loading. In a reaction that reconstitutes p97-Ufd1-Npl4-mediated unfolding coupled to proteasomal degradation, degradation was inefficient but stimulated by accessory adapters FAF1, FAF2, or UBXN7. Stimulation of proteasomal degradation was largely caused by an increase of p97 unfolding rates, conveyed by a helix-UBX segment in FAF1/2 that tethered the UT3 ubiquitin binding module of Ufd1 to the p97 N-domain. Mutations that abrogated the helix-Ufd1 interaction reduced stimulation of degradation, suggesting that accessory adapters position Ufd1 within the p97 complex to organize proficient substrate loading. Our results define the function of accessory adapters in mammals and highlight the complexity of substrate loading onto p97 for efficient substrate processing.
    DOI:  https://doi.org/10.1126/sciadv.aea7381
  11. Nat Cell Biol. 2026 Mar 06.
    Lysine-11 ubiquitination drives type-I/III interferon induction by cGAS-STING and Toll-like receptors 3 and 4.
    Alexis Betrancourt, M Talha Cinko, Ana Beatriz Varanda, Maykel Arias, Iratxe Uranga-Murillo, Natacha Peña, Lucia-Maria Kaps, Long Fung Chau, Bianca Buratti, Johannes Brägelmann, Diego de Miguel, Kerstin Becker, Ramona Casper, Rocio Martin, Antonio Alcami, Brian J Ferguson, Julian Pardo, Eva Rieser, Henning Walczak.
      Pattern recognition receptor (PRR)-induced interferon (IFN) is critical for effective immunity. The PRRs Toll-like receptor (TLR) 3, TLR4 and cyclic GMP-AMP synthase (cGAS), together with the stimulator of IFN genes (STING), signal through TANK-binding kinase 1 (TBK1), which activates the type-I/III IFN-inducing transcription factor interferon-response factor 3 (IRF3). The mechanism by which these PRRs activate TBK1 remains unresolved. Here we show that lysine-11 (K11)-linked ubiquitination drives TBK1 activation by these PRRs. The E3 ligase ANKIB1 attaches K11-linked ubiquitin chains to components of the TLR3- and cGAS-STING-induced signalosomes. This facilitates Optineurin recruitment to these complexes, in turn enabling recruitment and activation of TBK1 and IRF3, defining an uncharacterized signalling axis. In mice, ANKIB1 deficiency dampens IFN induction via TLR3 and cGAS-STING, reducing interferonopathy and compromising protection against HSV-1, respectively. Together, our results demonstrate an unanticipated and critical role for ANKIB1-generated K11-linked ubiquitination in the immune response activated by cGAS-STING, TLR3 and TLR4.
    DOI:  https://doi.org/10.1038/s41556-026-01886-z
  12. J Biol Chem. 2026 Feb 26. pii: S0021-9258(26)00203-6. [Epub ahead of print] 111333
    Brucella Omp25 activates the unfolded protein response to promote intracellular proliferation and inflammation.
    Jin-Ke Yang, Shuang Huang, Yuan-Pan Hou, Hui-Fei Yuan, Yue Wang, Mi Li, Li-Bo Cao, Tian Xia, Hong-Bing Shu, Xin Wu.
      Brucellosis is a widespread zoonotic disease caused by Brucella, a genus of facultative intracellular bacteria that infects livestock and humans. Brucella primarily replicates within the endoplasmic reticulum (ER) of host cells, where it establishes a specialized replicative niche. This ER localization disrupts ER structure and induces ER stress. The unfolded protein response (UPR) is a critical cellular pathway that maintains ER homeostasis by restoring protein-folding capacity and regulating stress responses. However, how Brucella manipulates host UPR pathways to promote its intracellular survival and pathogenesis remains poorly understood. Here, we identify the Brucella outer membrane protein Omp25 as a key factor in promoting its intracellular survival and proliferation by activating the host UPR. Omp25 directly binds to the ER chaperone Binding-immunoglobulin protein (BiP), inducing the release and activation of the UPR sensors PERK (PKR-like ER kinase), IRE1α (inositol requiring enzyme 1 alpha), and ATF6 (activating transcription factor 6), thereby modulating ER homeostasis to favor bacterial replication. Additionally, Omp25 enhances inflammatory cytokine expression via the BiP-IRE1α-NF-κB signaling axis. The omp25-deleted strains (Δomp25) show impaired intracellular replication and reduced UPR activation, and result in attenuated induction of inflammatory genes in infected cells compared to wild-type strains. In vivo, mice infected with an omp25 mutant strain exhibit lower bacterial burdens and milder tissue pathology compared to mice infected with the wild-type strain. These findings uncover a mechanism by which Omp25 facilitates Brucella intracellular proliferation through UPR modulation and highlight Omp25 as a potential target for therapeutic interventions and next-generation attenuated vaccines.
    Keywords:  BiP; Brucella; Omp25; inflammation; unfolded protein response (UPR)
    DOI:  https://doi.org/10.1016/j.jbc.2026.111333
  13. Sci Adv. 2026 Mar 06. 12(10): eaea8940
    Neurons with granulovacuolar degeneration bodies are resilient to tau-induced protein synthesis impairment.
    Jasper F M Smits, Thijmen W Ligthart, Marta Jorge-Oliva, Skip Middelhoff, Fleur Schipper, Débora Pita-Illobre, Ka Wan Li, Wiep Scheper.
      In Alzheimer's disease, many surviving neurons with tau pathology contain granulovacuolar degeneration bodies (GVBs), neuron-specific lysosomal structures induced by pathological tau assemblies. This could indicate a neuroprotective role for GVBs; however, the mechanism of GVB formation and its functional implications are elusive. Here, we demonstrate that casein kinase 1δ (CK1δ) activity is required for GVB formation. CK1δ is sequestered in the GVB during this process in an autophagy-dependent manner. We show that neurons with GVBs (GVB+) are resilient to tau-induced impairment of global protein synthesis and are protected against tau-mediated neurodegeneration. GVB+ neurons do not exhibit differential activation of transient translational stress responses but have increased ribosomal content. Unlike neurons without GVBs, GVB+ neurons fully retain the capacity to induce long-term potentiation-induced protein synthesis in the presence of tau pathology. Our results have identified CK1δ as a key regulator of GVB formation that confers a protective neuron-specific stress response to tau pathology. These findings provide opportunities for targeting neuronal resilience in tauopathies.
    DOI:  https://doi.org/10.1126/sciadv.aea8940
  14. Angew Chem Int Ed Engl. 2026 Mar 05. e21770
    CD44-Assisted Transcytosable Chimeras for Extracellular Protein Depletion in Deep Tumors.
    Xinlu Xu, Jingxing Si, Jingwen Xie, Jing Tan, Yumiao Guo, Gaoxia Ma, Shasha Yao, Yi Wang, Yuping Chen, Youqing Shen, Shiqun Shao.
      Extracellular targeted protein degradation (eTPD) typically uses antibody-derived bifunctional chimeras to direct extracellular targets toward lysosomal degradation. However, the requirements for antibody modification complicate degrader design, and their large size hinders tissue penetration. While small-molecule degraders provide enhanced tissue permeability, they suffer from poor pharmacokinetics and a limited target scope. Here we develop CD44-Assisted Transcytosable CHimeras (CATCHs), a plug-and-play platform that leverages CD44-mediated transcytosis for extracellular protein depletion in deep tumors. CATCHs are built on a hyaluronan-containing nanoparticle chassis, functionalized with IgG-affinitive tags to recruit unmodified antibodies. This design enables rapid generation of CATCHs against diverse targets. We show that CATCHs can drive near-complete depletion of cell-surface proteins, including PD-L1 and HER2, within 3 h at single-digit nanomolar antibody concentrations. Mechanistic studies reveal that CATCHs remove target proteins in a CD44-dependent manner through not only lysosomal proteolysis but also transcytosis of protein targets into extracellular spaces. The transcytosis-inducing activity also allows CATCHs to penetrate deep tumor tissues via consecutive transcytosis and effectuate depletion in otherwise inaccessible regions. We show that PD-L1-targeting CATCHs could induce potent antitumor immunity by depleting PD-L1 throughout tumor tissues. This platform promises a versatile eTPD tool with implications for both biomedical research and therapeutic drug discovery.
    Keywords:  CD44; extracellular targeted protein degradation; hyaluronic acid; lysosomal degradation; transcytosis
    DOI:  https://doi.org/10.1002/anie.202521770
  15. Cell Stress Chaperones. 2026 Feb 27. pii: S1355-8145(26)00019-2. [Epub ahead of print] 100163
    Activation of Unfolded Protein Response Pathways Promotes Keratinocyte Differentiation and Ameliorates Psoriasis Phenotypes.
    Zhibao Zhang, Mingyi Tan, Xin Liu, Wenhua Wang, Xiang Chen, Cong Peng, Shuang Zhao, Lisha Wu.
      Psoriasis is a chronic inflammatory skin disorder characterized by abnormal keratinocyte (KC) differentiation and proliferation, along with infiltration of various immune cells into the skin. Both internal and external perturbations can disrupt endoplasmic reticulum (ER) homeostasis, leading to ER stress and activation of the unfolded protein response (UPR) pathways. Although the UPR is known to participate in normal epidermal KC differentiation, its regulatory role in psoriasis remains poorly understood. In this study, we observed significant attenuation of UPR pathways specifically IRE1α-XBP1s and PERK signaling in psoriasis lesions. Administration of ER stress inducers (TM and BFA) alleviated psoriasis-like phenotypes in an imiquimod (IMQ)-induced mouse model. Furthermore, knockdown of Grp78 in KCs activated both IRE1α-XBP1s and PERK pathways, thereby improving KC differentiation in vitro. Notably, combining of Grp78 knockdown with ER stress inducers synergistically enhanced KC differentiation through UPR activation. Together, these findings indicate that the ER stress response promotes epidermal KC differentiation. Targeted activation of UPR pathways may thus represent a novel therapeutic strategy to improve KC differentiation in psoriasis.
    Keywords:  Endoplasmic Reticulum stress; Keratinocyte differentiation; Psoriasis; Unfolded Protein Response
    DOI:  https://doi.org/10.1016/j.cstres.2026.100163
  16. Protein Sci. 2026 Apr;35(4): e70516
    Functions of J-domain proteins in mitochondrial protein biogenesis.
    Vitasta Tiku, Georg Bossenz, Janine Kirstein, Thomas Becker.
      Mitochondrial biogenesis and functions depend on the import and assembly of more than 1000 proteins that are made as precursors on cytosolic ribosomes. The majority of these precursor proteins are transported from the ribosome to the translocase of the outer membrane (TOM complex), which constitutes the main entry site for mitochondrial precursors. The transient localization of mitochondrial precursor proteins in the cytosol represents a major burden for cellular proteostasis since these proteins can aggregate and accumulate in different cellular compartments, causing proteotoxic stress. Inside mitochondria, protein translocases sort the precursor proteins into the mitochondrial subcompartments-outer and inner membrane, the intermembrane space and matrix. The imported proteins have to be folded and efficiently assembled into functional protein complexes. Molecular chaperones such as Hsp70 monitor these processes to minimize proteotoxic stress. J-domain proteins stimulate the ATPase activity of Hsp70 and recruit the chaperones to their clients in the biogenesis of mitochondrial proteins. They ensure protein targeting to mitochondria, drive protein import into mitochondria, as well as folding and assembly of mitochondrial proteins. Here, we summarize the emerging view of how J-domain proteins guide mitochondrial precursor proteins from their synthesis in the cytosol until their folding into a mature protein and assembly into protein complexes in mitochondria.
    Keywords:  ER‐SURF; Hsp70; J‐domain protein; TOM complex; mitochondria; protein targeting
    DOI:  https://doi.org/10.1002/pro.70516
  17. Chemistry. 2026 Mar 04. e03578
    Chemical Synthesis of Ubiquitinated Proteins and Ubiquitin Probes for Biochemical and Functional Analysis.
    Chuntong Li, Luyu Shi, Lu-Jun Liang.
      Protein ubiquitination is a pivotal post-translational modification that plays vital roles in eukaryotic cellular regulation. Ubiquitination is orchestrated by a cascade of enzymes: E1 activating enzymes, E2 conjugating enzymes, and E3 ligases collectively facilitate ubiquitin conjugation, while ubiquitin-binding proteins interpret the ubiquitin signal. Deubiquitinases (DUBs) counterbalance this process by removing ubiquitin from substrate proteins, thereby reversing ubiquitination. In recent years, chemical protein synthesis-enabling the preparation of proteins with atomic-level precision-has emerged as a powerful approach to investigate protein ubiquitination. This review offers a comprehensive overview of recent progress in the development of strategies for the chemical synthesis of ubiquitinated proteins and the development of ubiquitin-based probes designed for covalent capturing of ubiquitin-modifying enzymes to facilitate biochemical and biophysical studies. We begin by outlining strategies for constructing native isopeptide-linked ubiquitinated proteins, covering both total chemical synthesis and semisynthetic routes. We also summarize existing methodologies for the semisynthesis of ubiquitinated proteins containing isopeptide bond mimics. Furthermore, we highlight recent advances in the design and synthesis of ubiquitin-based probes used to study ubiquitin-conjugating enzymes, ubiquitin-interacting proteins, and deubiquitinases. Finally, we offer perspectives on future directions, including the development of synthetic strategies for efficiently accessing more complex ubiquitinated proteins and studying noncanonical ubiquitination modification.
    Keywords:  activity‐based probe; chemical protein synthesis; deubiquitinases; protein ubiquitination; ubiquitin‐based probe
    DOI:  https://doi.org/10.1002/chem.202503578
  18. Eur J Med Chem. 2026 Feb 26. pii: S0223-5234(26)00165-0. [Epub ahead of print]309 118720
    PROTAC-mediated degradation of peroxisomal d-aspartate oxidase: A novel strategy to modulate d-aspartate homeostasis for schizophrenia treatment.
    Michela Galli, Valentina Rabattoni, Miriam Cavinato, Francesca Vasile, Irene Gado, Kainat Ulfat, Haidi Shehi, Alessandra Silvani, Daniele Passarella, Andrea Citarella, Loredano Pollegioni, Marco Nardini.
      D-Amino acids, once considered negligible in mammalian physiology, are now recognized as key neuromodulators. Among them, D-aspartate (D-Asp) regulates NMDAR and mGlu5 receptor function, influencing neurodevelopment, synaptic plasticity and cognition. In humans, postnatal brain D-Asp levels decline due to the upregulation of d-aspartate oxidase (hDASPO), the peroxisomal flavoenzyme responsible for D-Asp catabolism. Altered D-Asp homeostasis, characterized by reduced D-Asp and elevated hDASPO expression, has been associated with schizophrenia, supporting therapeutic strategies aimed at restoring physiological D-Asp levels. Although several small-molecule inhibitors of hDASPO have been reported, no potent or clinically viable candidates have emerged. Here, we investigated an alternative strategy based on targeted protein degradation to modulate hDASPO abundance. Guided by STD-NMR, we designed a series of heterobifunctional degraders integrating a hDASPO-binding ligand (olanzapine) with established E3 ligase recruiters (lenalidomide or VH032-Me) and aliphatic linkers of varying lengths. The resulting bifunctional compounds were synthesized and evaluated in biochemical assays for their ability to bind hDASPO. Most compounds retained micromolar inhibitory activity, indicating that derivatization at olanzapine position 10 preserves target engagement, with CRBN-recruiting analogues generally outperforming their VHL-based counterparts. Selected compounds were further investigated in cellular models, where PROTAC 17 demonstrated robust target engagement, positive cooperativity in ternary complex formation and dose-dependent degradation of hDASPO. Together, these findings establish the first proof-of-concept for hDASPO degradation via the PROTAC approach and provide a foundation for therapeutic strategies aimed at re-establishing D-Asp homeostasis in neuropsychiatric disorders characterized by NMDAR dysregulation.
    Keywords:  D-amino acid catabolism; D-aminoacid; Medicinal chemistry; NMDA receptors; Organic chemistry; Protein degradation
    DOI:  https://doi.org/10.1016/j.ejmech.2026.118720
  19. Nat Cell Biol. 2026 Mar 02.
    RNA-specific local translation is patterned by condensates for multinucleate cell growth.
    Zachary M Geisterfer, Ameya P Jalihal, Sierra J Cole, Amy S Gladfelter.
      Coordination between growth and nuclear division is a common cell feature. In some syncytia, nuclei divide asynchronously throughout the cell but growth occurs only at discrete locations, raising the question how the processes are locally regulated and globally coordinated. In the syncytial fungus Ashbya gossypii, both cell cycle progression and hyphal elongation require condensates formed by the protein Whi3 in complex with distinct mRNA species. Here we show that Whi3 condensates are enriched for translation regulators and are associated with local, spatially patterned translation of specific target RNAs near nuclei and growth sites. Whi3-RNA condensates can both promote and repress mRNA translation in an RNA- and condensate size-dependent manner in vitro. Condensate interfaces are sites of translation, tunable by condensate composition, RNA valency and protein charge state in vitro. Together, these data suggest that Whi3 condensates can generate a continuum of translation states that vary depending on the subcellular location and resident RNA sequences.
    DOI:  https://doi.org/10.1038/s41556-026-01887-y
  20. Cell Host Microbe. 2026 Feb 27. pii: S1931-3128(26)00052-1. [Epub ahead of print]
    Immune activation reprograms growth mRNA stability to shape plant growth-defense trade-offs.
    Guilong Zhou, Ruixia Niu, Sitao Zhu, Hui Wang, Zhijuan Tang, Wanzhen Wang, Sirui Xiong, Jiawei Long, Yulu Zhou, Yongjia Tong, Hongchun Yang, Guoyong Xu.
      Immune activation enhances defense gene expression but often suppresses plant growth, creating a fundamental trade-off that limits durable resistance. While selective translation of defense mRNAs has been reported, how growth mRNAs are regulated after transcription during immune responses remains poorly understood. Here, using network-level analyses in Arabidopsis, we identify an RNA-binding protein-dependent mechanism that selectively destabilizes growth-related mRNAs upon immune activation. We show that polypyrimidine tract-binding protein 3 (PTBP3) recognizes a pyrimidine-rich RNA element, undergoes immune-induced condensation, and assembles an mRNA degradation hub that preferentially targets growth genes, including growth-regulating factors. Experimental disruption of this pathway-either by impairing PTBP3 function or by restoring growth gene expression-unexpectedly enhances disease resistance while improving growth resilience under immune stress. These findings reveal post-transcriptional control of growth mRNA stability as a regulatory layer shaping growth-defense balance and suggest a strategy for achieving stronger and safer plant immunity without constitutive defense activation.
    Keywords:  RNA degradation; RNA regulon; RNA-binding proteins; gene expression; growth mRNA; growth resilience; growth-defense trade-off; plant immune strategy; post-transcriptional control; translational control
    DOI:  https://doi.org/10.1016/j.chom.2026.02.007
  21. Nat Commun. 2026 Mar 02.
    Rab14 restricts pathogens by promoting V-ATPase lysosomal delivery to drive lysosomal acidification.
    Zehui Lei, Lihua Qiang, Pupu Ge, Yuyun Qiang, Tergel Sun, Qiyao Chai, Yiru Wang, Shan Lv, Changgen Qiu, Zhe Lu, Mengyuan Zhao, Zhuo Zhao, You Wu, Xinwen Zhang, Yanzhao Zhong, Bingxi Li, Lingqiang Zhang, Jing Wang, Cui Hua Liu.
      Host restriction factors mediate intrinsic immunity against infections, thus serving as promising targets for host-directed therapy (HDT) against drug-resistant pathogens. While restriction factors counteracting viruses have been extensively studied, those targeting bacteria, particularly those with broad-spectrum activity, remain largely unexplored. Here, through screening for host factors promoting lysosomal acidification, a crucial process clearing pathogens, we identify the host small GTPase Rab14 as a restriction factor with broad-spectrum activity against multiple bacteria and viruses. Mechanistically, upon pathogen infections, GTP-bound Rab14 increases and binds to the calcium/calmodulin-dependent protein kinase type 2 delta (CAMK2D), suppressing CAMK2D-mediated phosphorylation of V0a1, the critical subunit determining V-ATPase localization, thus promoting V0a1 binding to the COPⅡ complex to facilitate V-ATPase trafficking from the endoplasmic reticulum to lysosomes, resulting in lysosomal acidification and pathogen clearance. Taken together, our data demonstrate an unrecognized intrinsic immune mechanism mediated by Rab14-CAMK2D-V-ATPase axis, which might be a promising target for infectious diseases.
    DOI:  https://doi.org/10.1038/s41467-026-70258-w
  22. Eur J Pharmacol. 2026 Feb 26. pii: S0014-2999(26)00167-6. [Epub ahead of print] 178685
    OTUD3-mediated deubiquitination licenses TEX264 to orchestrate ER-phagy for KDM5B degradation in teniposide lung cancer therapy.
    Ning Han, Xin-Ran Yu, Liu-Gen Li, Jun Hu, Fan Leng, Lei Wang, Ting-Ting Yu, Hua-Zhen Xu, Hongyao Huang, Tong-Fei Li, Xiao Chen.
      High expression of Lysine-Specific Demethylase 5B (KDM5B) in lung cancer drives tumorigenesis and immunosuppression. KDM5B is negatively correlated with endoplasmic reticulum (ER)-phagy receptors such as TEX264, indicating that selective induction of ER-phagy may degrade KDM5B. Our work revealed that chemotherapeutic drug Teniposide (Ten) was a potent anti-lung cancer agent, which could increase the stability of TEX264. The present study aims to elucidate the critical target and mechanism by which Ten inhibits KDM5B through TEX264-associated ER-phagy against lung cancer. Ten exhibited potent lung cancer suppression ability, as evidenced by the weakened proliferation of organoids and tumor grafts in mice along with activation of the immune microenvironment. Highly-expressed KDM5B demonstrated down-regulation upon Ten treatment, which may be attributed to its degradation via ER-phagy. Blockage of ER-phagy weakened Ten-mediated KDM5B degradation. Insightful investigations discovered that Ten activated OTUD3, a deubiquitylase, which stabilized TEX264, a crucial receptor for ER-phagy. Notably, genetic knockdown of TOP2A impacted little on the Ten-mediated ER-phagy. OTUD3 silencing dampened Ten-driven ER-phagy and KDM5B inhibition. To summarize, these findings demonstrate that Ten effectively inhibits lung cancer and activates immunocytes by KDM5B inhibition, which is regulated by TEX264-associated ER-phagy. Most importantly, OTUD3 serves as an essential target for enhancement of TEX264 stabilization.
    Keywords:  ER-Phagy; KDM5B; Lung cancer; OTUD3; TEX264; Teniposide (Ten)
    DOI:  https://doi.org/10.1016/j.ejphar.2026.178685
  23. Methods Enzymol. 2026 ;pii: S0076-6879(25)00526-9. [Epub ahead of print]727 233-251
    Reconstitution approaches for understanding cellular lipid dynamics.
    Dazhi Li, Justin L Korfhage, Karin M Reinisch.
      Lipid transport is essential for membrane biogenesis and maintenance. Newly synthesized phospholipids are produced on the cytosolic leaflet of the endoplasmic reticulum (ER). Redistribution of lipids in cells is achieved by lipid scramblases across the lipid bilayer or alternatively, by lipid transport proteins (LTPs) to other organelles. Despite their important functions, the molecular identities and mechanisms of these proteins are only now emerging. Here, we describe reconstitution approaches with purified proteins and artificial membranes to study lipid dynamics in vitro, including a fluorescence-based assay to identify lipid scrambling activity and a fluorescence resonance energy transfer (FRET)-based assay to assess protein-mediated lipid transfer between liposomes or between liposomes and lipid monolayers. Together, these methods enable mechanistic studies of cellular lipid dynamics regulated by proteins.
    Keywords:  Artificial lipid droplets; Lipid scramblase assay; Lipid transfer assay; Liposomes
    DOI:  https://doi.org/10.1016/bs.mie.2025.11.022
  24. NAR Genom Bioinform. 2026 Mar;8(1): lqag024
    Mapping the inter- and intra-genic codon-usage landscape in Homo sapiens.
    Maahil Arshad, Matthew Uchmanowicz, Vanshika Rana, Brett Trost, Stephen W Scherer, Muhammad Arshad Rafiq.
      Although the genetic code is degenerate, codon selection is nonrandom and reflects significant functional constraints. Codon-usage bias (CUB) acts as a layer of post-transcriptional regulation, influencing messenger RNA (mRNA) stability, translation kinetics, and co-translational protein folding. While CUB is well-characterized in unicellular organisms, its regulatory scope and functional consequences in humans remain complex and less defined. Our study offers a comprehensive evaluation of human codon usage. We report that genes exhibiting the strongest codon bias are enriched in high-stoichiometry biological processes, such as skin development and oxygen/carbon dioxide transport, and harbor significantly fewer synonymous variants than expected (ρ = -0.24, P < 2.2 × 10-16). Furthermore, we find that codon optimization is structurally distinct: it is significantly more pronounced in structured protein domains compared to intrinsically disordered regions (IDRs) (Cliff's Δ= 0.26, P < 2.2 × 10-16). Consistent with translational selection, the most frequently used codons are supported by higher transfer RNA (tRNA) gene copy numbers (ρ = 0.49, P < 6.4 × 10-4). Finally, by correcting for GC3 content, we reveal that the apparent correlation between effective number of codon and adaptation indices (CAI/tAI) vanishes, allowing us to disentangle mutational pressure from translational selection. Collectively, our findings position CUB as a central, evolutionarily conserved regulator of translation and protein folding in humans. Our results provide a comprehensive and integrated view of intergenic and intragenic CUB in humans, reinforcing the biological relevance of synonymous codon choice in shaping translational dynamics and protein biogenesis. This provides a refined framework for interpreting synonymous variation and guiding functional genomics.
    DOI:  https://doi.org/10.1093/nargab/lqag024
  25. IUBMB Life. 2026 Mar;78(3): e70091
    ALG8-Driven Metabolic Reprogramming in Polycystic Kidney Disease: A Systematic Synthesis of Evidence Linking Glycosylation Defects to Metabolic Signaling.
    Xiaoran Wang, Zhili Huang, Wen Zhang.
      Endoplasmic reticulum glycosyltransferase ALG8 controls metabolic fate in autosomal dominant polycystic kidney disease (ADPKD). In this paper, we summarize human genetics, cell-based, and organ-based evidence to investigate whether ALG8 variants affect cyst initiation and metabolic states of ADPKD. Population screening showed ALG8 variant enrichment in ADPKD cohorts (OR = 9.75, P0.001); loss-of-function alleles interact with PKD1 mutations to accelerate cystogenesis. ALG8 deficiency leads to metabolic collapse by several mechanisms. Impaired polycystin-1 glycosylation disrupts ER-to-cilium trafficking, prevents PC1/PC2 complex assembly, and impedes calcium-dependent ATP production. Deficient LRP6 glycosylation activates Wnt/-catenin signaling. This shifts metabolism toward aerobic glycolysis, leading to Warburg-like reprogramming seen in malignancy. Single cell analysis showed ALG8 deficient cystic epithelium has tumor-like metabolic signatures, such as increased glucose uptake, suppressed oxidative phosphorylation, and glutamine dependence. Chemical chaperones that restore folding capacity or glycosylation inhibitors that lower anabolic demand both suppressed cyst formation in ALG8/PKD1-deficient organoids. The connection from ALG8 loss to "oncogenic-like" metabolism remains incomplete. Study-to-study variability in model system, genotype, and endpoint still limits cross-cohort comparison. This dual vulnerability-of protein folding and glycosylation-is due to the fragile metabolic balance in cystogenesis. These results recast ADPKD as a metabolic disorder where glycosylation defects link ciliary dysfunction to oncogenic transformation. We focus on three areas: (i) convergence with multiple lines of evidence, (ii) disagreement, and (iii) testable predictions for future studies and trials. The overlap between cystogenic and tumorigenic metabolic programs suggests cancer metabolic inhibitors may be reused for ADPKD in near-term translation. By defining ALG8 as a metabolic checkpoint in polycystic disease, we uncover targets at the glycosylation-metabolism interface.
    Keywords:  ALG8 glycosyltransferase; N‐glycosylation; Warburg effect; autosomal dominant polycystic kidney disease (ADPKD); metabolic reprogramming
    DOI:  https://doi.org/10.1002/iub.70091
  26. Cell. 2026 Feb 27. pii: S0092-8674(26)00115-7. [Epub ahead of print]
    Citrate clearance is a major function of aconitase 2 in the canonical TCA cycle.
    Abigail Xie, Julia S Brunner, Sangita Chakraborty, Angela M Montero, Anna E Bridgeman, Katrina I Paras, Ruobing Cui, Maider Fagoaga-Eugui, Monika Komza, Paige K Arnold, Benjamin T Jackson, Santiago Noriega Madrazo, Mohamed I Atmane, Sebastian E Carrasco, Lydia W S Finley.
      The tricarboxylic acid (TCA) cycle couples nutrient oxidation with the generation of reducing equivalents that power oxidative phosphorylation. Nevertheless, the requirement for components of the TCA cycle is context-specific, raising the question of which TCA cycle outputs support cell fitness. Here, we demonstrate that citrate clearance is an essential function of the TCA cycle. As citrate production increases, so do TCA cycle activity and dependence upon aconitase 2 (ACO2), the enzyme that initiates citrate catabolism in the TCA cycle. Disrupting citrate catabolism activates the integrated stress response and impairs cell fitness, and these effects are reversed by preventing citrate production or promoting mitochondrial citrate efflux. In vivo, ACO2 deficiency induces citrate accumulation and triggers tubular degeneration in the kidney, a tissue that physiologically takes up circulating citrate. Thus, intracellular citrate accumulation can be a metabolic liability, and citrate clearance is a major function of ACO2 in the TCA cycle.
    Keywords:  ACO2; TCA cycle; cell metabolism; citrate; integrated stress response
    DOI:  https://doi.org/10.1016/j.cell.2026.01.028
  27. Nat Commun. 2026 Feb 28.
    Cryo-EM structures of UBA6 reveal mechanisms of E1-E2 specificity and dual FAT10/ubiquitin thioester transfer.
    Digant Nayak, Lijia Jia, Priscila Dos Santos Bury, Eliza A Ruben, Ankita Shukla, Anindita Nayak, Caleb M Stratton, Pirouz Ebadi, Hee Cho, Anna A Tumanova, Joyce T Varughese, Lingmin Yuan, Fei Gao, Kristin E Cano, Christopher Davies, Patrick Sung, Michaela U Gack, Elizabeth V Wasmuth, Shaun K Olsen.
      UBA1 and UBA6 define parallel ubiquitin (Ub) activation systems that perform non-overlapping roles in Ub and ubiquitin-like protein (Ubl) signaling. Whereas UBA1 supports the canonical Ub pathway, UBA6 also activates the Ubl FAT10, linking Ub signaling to immune-regulated proteostasis. In addition to selective Ub/Ubl activation, UBA1 and UBA6 engage distinct sets of E2s, yet how these enzymes achieve selective E2 engagement has remained unclear. Using chemical trapping and high-resolution cryo-EM, we determine four structures of UBA6-E2 complexes representing the thioester-transfer step with either FAT10 or Ub, revealing how this E1 distinguishes its cognate partners. UBA6 achieves E2 specificity through coordinated contributions of the UFD and SCCH domains, a dual-domain mechanism that contrasts with the UFD-dominated selectivity of UBA1. The structures further show that an existing inositol hexakisphosphate (InsP₆)-binding site, unique to UBA6, stabilizes an expanded SCCH cleft that pre-organizes the enzyme for selective engagement of UBA6-specific E2s. These findings define principles for E1-E2 recognition and identify InsP₆ as a cofactor shaping specificity within the Ub-like conjugation network.
    DOI:  https://doi.org/10.1038/s41467-026-69882-3
  28. Nat Commun. 2026 Mar 06.
    USP7 deubiquitinase stabilizes FAN1 to support DNA crosslink repair and suppress CAG repeat expansion.
    Giulio Collotta, Marco Gatti, Irina-Maria Ungureanu, Vanessa van Ackeren, Emilie Rannou, Francesca Vivalda, Diego Gomez Vieito, Keri M Fishwick, Christine von Aesch, Antonio Porro, Kyra Ungerleider, Ailin Heidari, Raphaël Guérois, Rachel J Harding, Sylvain Bischof, Gabriel Balmus, Alessandro A Sartori.
      Human FAN1 is a structure-specific endonuclease implicated in the repair of DNA interstrand crosslinks (ICLs) and the excision of extrahelical CAG repeats-whose pathological expansion underlies Huntington's disease (HD), a progressive and currently incurable neurodegenerative disorder. However, mechanisms of post-translational regulation of FAN1 are still largely unknown. Here, we identify the ubiquitin-specific protease 7 (USP7) as an interactor of FAN1. USP7 stabilizes FAN1 protein levels in a deubiquitination-dependent manner, preventing FAN1 from proteasomal degradation. Consequently, we demonstrate that USP7 depletion leads to reduced chromatin association of FAN1 and increased cellular hypersensitivity following ICL damage. Moreover, loss of USP7 accelerates CAG repeat expansion in an RPE-1 cell model stably expressing mutant huntingtin (mHTT) exon 1 containing 129 CAG repeats (RPE-1HTT-CAG129). Collectively, our findings uncover a link between USP7 and FAN1 in mechanisms that preserve genome stability and influence repeat instability.
    DOI:  https://doi.org/10.1038/s41467-026-70051-9
  29. Phys Rev Lett. 2026 Feb 13. 136(6): 068401
    Unifying Constraints Linking Protein Folding and Native Dynamics Decoded from AlphaFold.
    Zecheng Zhang, Weitong Ren, Liangxu Xie, Yuxiang Zheng, Xingyue Guan, Jun Wang, Wenfei Li, Qian-Yuan Tang.
      The interplay between protein folding and native dynamics remains a central question in biophysics. Analyzing an extensive set of AlphaFold-predicted structures, we uncover a robust relationship between folding topology (contact order) and native dynamics (fluctuation entropy), showing that long-range contacts that slow folding also restrict conformational flexibility across protein sizes and taxonomic groups. Scaling analysis reveals that this relationship, together with its chain-length dependence, is consistent with power-law-like trends, reflecting common organizing constraints of protein architecture. Across species, increasing organismal complexity is associated with proteome-wide shifts toward lower contact order and higher fluctuation entropy. Together, evidence from folding, stability, and functional dynamics converges on unifying constraints, revealing an intrinsic physical organizing principle captured by AI models.
    DOI:  https://doi.org/10.1103/7j2j-f8f7
  30. J Cell Sci. 2026 Feb 15. pii: jcs264683. [Epub ahead of print]139(4):
    PA200 differentially regulates the proteasome and inhibits migration of NSCLC cells.
    Ayse S Yazgili, Georgia A Giotopoulou, Sabine J Behrend, Frauke Koops, Vanessa Neiens, Thomas Meul, Linda Zemke, Norbert Reiling, Torsten Goldmann, Georgios T Stathopoulos, Silke Meiners.
      Proteasome activator 200 (PA200; also known as PSME4) is upregulated in non-small cell lung cancer (NSCLC) and linked to poor prognosis. We have previously demonstrated that the overexpression of PA200 in NSCLC is associated with immune evasion and reduced responsiveness to immune checkpoint inhibitors. The cell autonomous function of PA200 in cancer growth, however, has not been solved. We here demonstrate that deletion of PA200 in two distinct lung cancer cell lines induced cell-specific alterations in proteasome composition and activities with a minor direct impact on overall proteasome activity. Deficiency of PA200 in lung cancer cells did not consistently alter tumor cell growth in vitro and in vivo. However, we observed concerted inhibition of tumor cell migration and invasion with conserved downregulation of the integrin ITGB3 and transcriptional dysregulation of multiple cell adhesion and extracellular matrix regulators. Our transcriptome profiling revealed a striking disparity in the transcriptional response to PA200 deletion in the two lung cancer cell lines. Together with our PA200 interactome analysis that uncovered an unexpected cell-dependent profile of PA200-interacting proteins, our data indicate that the function of PA200 is cell specific and depends on the cellular context. In conclusion, we here demonstrate that PA200 cell-autonomously regulates the invasive capacities of tumor cells thereby potentially promoting lung cancer spread and metastasis formation. This mechanism might add to PA200-related immune evasion and contribute to the observed poor prognosis of individuals with PA200-overexpressing lung cancer.
    Keywords:  Lung cancer; PA200; PSME4; Proteasome
    DOI:  https://doi.org/10.1242/jcs.264683
  31. Nat Commun. 2026 Mar 06. pii: 2244. [Epub ahead of print]17(1):
    Targeting tRNA-dependent tyrosine usage unveils a metabolic vulnerability in hepatocellular carcinoma.
    Hongli Zhang, Zixuan Wang, Yiqi Zhao, Xiya Deng, Jian Zhang, Fei Shang, Hongjie Zhang, Yan Liu, Hongbo Wang, Yating Yang, Huiyu Lin, Bo Zhang, Ce Liu, Fan Guo, Ruolin Zhang, Qipeng Yuan, Yue Feng, Shi-Zhong Luo, Wei-Dong Chen, Yan-Dong Wang.
      Cancer cells reprogramme translation and metabolism to fuel tumorigenesis. Here, we show that hepatocellular carcinoma (HCC) paradoxically maintains low tyrosine levels despite increased uptake and reduced metabolism, redirecting tyrosine to translation via MYC-driven upregulation of tyrosyl-tRNA synthetase 1 (YARS1) and tRNA-TyrGUA. Restricting tyrosine translation availability (RTTA) via dietary limitation, YARS1/tRNA-TyrGUA ablation, tyrosine degradation (TAL), or YARS1 inhibition (tyrosinol) disturbs this adaptation, leading to the mitigation of tumorigenesis and extension of survival. Mechanistically, RTTA reduces tyrosine codon-dependent translation of mitochondrial complex I subunit NDUFB8 and lipid regulator SCD1, causing complex I misassembly, oxidative phosphorylation failure, and lipid peroxidation-induced ferroptosis. Genome-wide CRISPR screening identifies that loss of GPX4 and BCL2 by genetic manipulation or pharmacological treatment enhances the ability of RTTA to inhibit hepatocellular carcinogenesis. Our findings establish RTTA as a therapeutic strategy targeting tyrosine dependency and highlight combinatorial targeting of translation-metabolism crosstalk and ferroptosis pathways in liver cancer.
    DOI:  https://doi.org/10.1038/s41467-026-70112-z
  32. Biochim Biophys Acta Mol Basis Dis. 2026 Mar 03. pii: S0925-4439(26)00060-8. [Epub ahead of print] 168211
    Mitochondrial complex-derived ROS induces lysosomal dysfunction and impairs autophagic flux in human cells carrying the APOE4 allele.
    Sandra A Niño, Oskar Barrios-Camus, Eduardo Silva-Pavez, J César Cárdenas, Christian González-Billault.
      The APOE4 allele is the strongest genetic risk factor for sporadic Alzheimer's disease (sAD), yet its cell-autonomous effects remain poorly understood. While young, asymptomatic APOE4 carriers exhibit abnormal brain metabolism, the mechanistic link between mitochondrial dysfunction and lysosomal-autophagic failure remains unclear. In this study, we conducted a comprehensive analysis of primary human fibroblasts from APOE3 controls, APOE4, and sAD donors to assess mitochondrial bioenergetics, oxidative stress, autophagy, and lysosomal function. APOE4 fibroblasts displayed increased mitochondrial content-associated markers (PGC1α, mtDNA) accompanied by reduced respiratory capacity, elevated proton leak, and excessive mitochondrial ROS. In parallel, APOE4 fibroblasts showed impaired autophagic flux and reduced LC3-TOMM20 colocalization, indicating defective mitophagy. Lysosomal proteolytic activity, assessed using DQ-BSA, was significantly reduced and remained unresponsive under to starvation, in contrast to the partial recovery observed in sAD cells. Pharmacological targeting of mitochondrial ROS with site-specific inhibitors revealed that complex III-derived ROS is the predominant driver of redox stress in APOE4 fibroblasts, while complex I contributes primarily in sAD. Notably, selective inhibition of complex III-derived ROS with S3QEL restored lysosomal degradation, autophagic flux, and mitochondrial respiration in APOE4 cells. Together, these findings demonstrate that mitochondrial oxidative stress disrupts the mitochondria-lysosome axis in an APOE4-specific manner, revealing early and mechanistically distinct vulnerabilities that may precede neurodegeneration. Our results challenge the notion that APOE4 merely amplifies AD pathology and instead identity site-specific redox signaling as a promising target for allele-informed interventions.
    Keywords:  APOE4; Autophagy; Human fibroblasts; Lysosome; Mitochondria; Mitochondrial complex III; S3QEL
    DOI:  https://doi.org/10.1016/j.bbadis.2026.168211
  33. Cell. 2026 Mar 04. pii: S0092-8674(26)00162-5. [Epub ahead of print]
    Efficient amyloid-β degradation in Alzheimer's disease using SPYTACs.
    Fei Teng, Jing Liu, Tongtong Cui, Xiangtian Tan, Kailun Liu, Zongren Hou, Li Zhou, Yuanzhi Xie, Rongqi Li, Da Li, Bojin Li, Dongmei Wang, Qi Zhou, Baoyang Hu, Wei Li.
      Clearance of aberrant cerebral amyloid-β (Aβ) deposits represents a promising therapeutic strategy for Alzheimer's disease (AD), yet current anti-Aβ immunotherapy raises safety concerns due to frequent adverse effects. Extracellular targeted protein degradation (eTPD) offers an approach for safe and efficient clearance of disease-causing proteins. Here, we develop a next-generation eTPD platform, synthetic peptide-programmed lysosome-targeting chimeras (SPYTACs), using entirely synthesized bispecific peptides. Leveraging low-density lipoprotein receptor-related protein 1 (LRP1), SPYTACs effectively facilitate targeted degradation of extracellular proteins and enable transcytosis across the blood-brain barrier. In vivo administration of SPYTACs effectively reduces peripheral and cerebral Aβ burden, attenuates synapse loss, and improves cognitive function in 5×FAD mice at both prodromal and symptomatic stages. Notably, SPYTAC treatment shows fewer side effects, including intracerebral hemorrhage and inflammation, compared with conventional immunotherapies. The high modularity and genetic encodability enable SPYTACs to target customized disease-causing proteins, underscoring their therapeutic versatility and translational promise across diverse diseases driven by pathogenic proteins.
    Keywords:  AD; Alzheimer’s disease; Aβ; SPYTAC; amyloid-β; eTPD; extracellular targeted protein degradation
    DOI:  https://doi.org/10.1016/j.cell.2026.01.034
  34. RNA Biol. 2026 Mar 06.
    5PSeq explorer: interactive analysis of Co-translational mRNA decay and ribosome dynamics.
    Irene Stevens, Vicent Pelechano.
       BACKGROUND: Co-translational mRNA decay occurs when 5'to 3' exonucleases follow the last translating ribosome, generating in vivo ribosome protected fragments. Degradome sequencing ;(5PSeq) therefore offers unique insights into ribosome dynamics. Despite its potential, resources for systematic analysis of 5'P mRNA decay intermediates and associated features, such as ribosome stalls and collisions, are scarce.
    FINDINGS: We introduce 5PSeq Explorer, a web-based platform built from 773 uniformly processed 5PSeq datasets across 23 species in bacteria and Ascomycota suitable for exploring ribosome dynamics in vivo at codon, amino acid, and transcript levels.
    CONCLUSIONS: By integrating normalized counts, structured metadata, and scalable visualization tools, 5PSeq Explorer provides a framework for studying the crosstalk between mRNA decay and ribosome dynamics. To ensure reproducibility and accessibility, we offer both a public web interface and a Docker-based plug-and-play local version.URL: https://fivepseq-explorer.serve.scilifelab.se/app/fivepseq-explorer.
    Keywords:  5PSeq; Ribosome dynamics; mRNA decay
    DOI:  https://doi.org/10.1080/15476286.2026.2639616
  35. Mol Omics. 2026 Mar 07. pii: aaiag012. [Epub ahead of print]
    Need for speed: Advances in the era of high throughput interaction proteomics.
    Fabian Frommelt, Uliana Federico, Ruedi Aebersold, Andrea Fossati.
      Protein-protein interactions are central to virtually all biological processes, forming intricate networks that operate in a highly regulated manner. These interactions are not permanent but rather continuously adapt to environmental changes, developmental cues, or disease-related stress. Understanding which protein interactions are present in a specific cellular state and how they adapt to specific stimuli is one of the long-standing goals of modern systems biology. Mass spectrometry-based proteomics has emerged as the primary tool for charting these networks. Over the past two decades, continuous advances in instrumentation, sample preparation, and data analysis have enabled researchers to explore the protein interaction landscape with increasing depth and accuracy. This has led to important discoveries in areas ranging from fundamental cell signaling to the identification of new therapeutic targets. We present the current state of MS-based protein interaction analysis, focusing on the three most widely utilized approaches: affinity purification, proximity labeling and co-fractionation mass spectrometry. For each we discuss the fundamental approach, technical considerations, limitations and highlight the potential integration with future technologies and datasets. Recent innovations such as short-gradient chromatography and faster data acquisition have further improved sensitivity and throughput. Together, these developments are bringing researchers closer to mapping the dynamic, context-dependent architecture of protein networks in unprecedented detail.
    Keywords:  co-fractionation; protein complex profiling; protein complexes; protein-protein interactions
    DOI:  https://doi.org/10.1093/molecular-omics/aaiag012
  36. Angew Chem Int Ed Engl. 2026 Mar 01. e22665
    Lipid Pocket Binders Impose Allosteric Changes of Protein Dynamics Around the Active Site of the Protein Kinase p38α.
    Sara Medina Gómez, Laurin T Homberg, Mike Bührmann, Daniel Rauh, Rasmus Linser.
      Protein kinases represent major pharmaceutical targets, but the development of selective modulators remains challenging. In search of allosteric sites in the serine/threonine kinase p38α, a "lipid pocket" in the C-lobe has been found to bear prospects for the binding of small molecules. A pharmacological potential of those low-affinity binders found initially has not become obvious, however, raising the overarching question whether any sort of communication between this pocket and the enzyme's functional sites exists. Here, we use NMR spectroscopy to reveal an effective connectivity of these sites in spite of their spatial distance. The data reveal a clear interdependency of protein dynamics between the different structural elements through dynamic allostery, together suggesting a pharmacological avenue for the development of suitable lipid pocket binders to allosterically alter enzymatic functionality in a disease context.
    Keywords:  NMR spectroscopy; allosteric inhibitors; drug discovery; medicinal chemistry
    DOI:  https://doi.org/10.1002/anie.202522665
  37. Nat Struct Mol Biol. 2026 Mar 05.
    Function and regulation of the mitochondrial stress response.
    Joshua B Sheetz, Srividya Chandrasekhar, Michael Rapé.
      As mitochondria have crucial roles in metabolism and signaling, their structure and function must be continuously monitored and rapidly adjusted to meet cellular demands. Critical to this regulation is a conserved stress response that detects and alleviates challenges to mitochondrial integrity. Recent work has shown that mitochondrial stress often elicits simultaneous protective reactions that act in a coordinated and tightly regulated fashion to preserve this essential organelle. Here we review components, coordination and control within this comprehensive stress response and discuss how increased understanding of mitochondrial stress signaling is beginning to inform therapeutic approaches directed against diseases of high unmet need.
    DOI:  https://doi.org/10.1038/s41594-026-01769-9
  38. Elife. 2026 Mar 04. pii: RP108253. [Epub ahead of print]14
    SLC4A1 mutations that cause distal renal tubular acidosis alter cytoplasmic pH and cellular autophagy.
    Grace Essuman, Midhat Rizvi, Ensaf Almomani, Shahid A K M Ullah, Sarder M A Hasib, Forough Chelangarimiyandoab, Priyanka Mungara, Manfred J Schmitt, Marguerite Hureaux, Rosa Vargas-Poussou, Nicolas Touret, Emmanuelle Cordat.
      Distal renal tubular acidosis (dRTA) is a disorder characterized by the inability of the collecting duct system to secrete acids during metabolic acidosis. The pathophysiology of dominant or recessive SLC4A1 variant-related dRTA has been linked with the mis-trafficking defect of mutant kAE1 protein. However, in vivo studies in kAE1 R607H dRTA mice and humans have revealed a complex pathophysiology implicating a loss of kAE1-expressing intercalated cells and intracellular relocation of the H+-ATPase in the remaining type-A intercalated cells. These cells also displayed accumulation of ubiquitin and p62 autophagy markers. The highly active transport properties of collecting duct cells require the maintenance of cellular energy and homeostasis, a process dependent on intracellular pH. Therefore, we hypothesized that the expression of dRTA variants affects intracellular pH and autophagy pathways. In this study, we report the characterization of newly identified dRTA variants and provide evidence of abnormal autophagy and degradative pathways in mouse inner medullary collecting duct cells and kidneys from mice expressing kAE1 R607H dRTA mutant protein. We show that reduced transport activity of the kAE1 variants correlated with increased cytosolic pH, reduced ATP synthesis, attenuated downstream autophagic pathways pertaining to the fusion of autophagosomes and lysosomes and/or lysosomal degradative activity. Our study elucidated a close relationship between the expression of defective kAE1 proteins, reduced mitochondrial activity, and decreased autophagy and protein degradative flux.
    Keywords:  cell biology; kidney; mouse; transgenic animals
    DOI:  https://doi.org/10.7554/eLife.108253
  39. Cell Rep. 2026 Mar 05. pii: S2211-1247(26)00139-7. [Epub ahead of print]45(3): 117061
    Large adipocytes increase vesicle-mediated lipid release and promote breast cancer malignancy.
    Garrett F Beeghly, Irina Kopyeva, Jenny Deng, Marlee I Pincus, Rohan R Varshney, Dilip D Giri, Domenick J Falcone, Michael C Rudolph, Marc A Antonyak, Neil M Iyengar, Claudia Fischbach.
      Primary adipocytes exhibit striking variability in size, yet the functional consequences of adipocyte hypertrophy remain unclear due to insufficient experimental approaches to control for cell size. Here, we establish methods to culture large and small primary adipocytes isolated from the same adipose depot, enabling size-resolved analyses independent of systemic obesity. Using transcriptomic, lipidomic, and functional profiling across two mouse models of obesity, as well as human clinical samples, we show that adipocyte size-rather than body weight-drives distinct phenotypic cell states. Notably, large adipocytes increase extracellular vesicle-mediated lipid release. In coculture assays, this shift enhances lipid uptake, migration, and proliferation of breast cancer cells through fatty acid oxidation. Consistent with these findings, individuals with larger mammary adipocytes exhibit elevated fasting triglycerides independent of body mass index. Together, our results identify adipocyte size as a key determinant of adipose tissue function with implications for both metabolic disease and cancer progression.
    Keywords:  CP: cancer; CP: metabolism; adipocyte; adipose tissue; breast cancer; extracellular vesicles; hypertrophy; lipid metabolism; obesity; tumor microenvironment
    DOI:  https://doi.org/10.1016/j.celrep.2026.117061
  40. Nat Commun. 2026 Mar 03.
    Single-cell thiol profiling enabled by live-cell labeling reveals metabolic heterogeneity in ferroptosis.
    Daiyu Miao, Qiuning Li, Yi Zhang, Shaojie Qin, Ying Wang, Xiaoyun Liu, Yu Bai.
      Thiols serve indispensable biochemical functions across catalysis, redox homeostasis and energy metabolism. However, profiling multiple thiols at the single-cell level remains challenging due to their trace amount and susceptibility to oxidation. Herein, we report an integrated strategy for thiol profiling at the single-cell level which combines live-cell labeling with organic mass cytometry. The live-cell labeling strategy facilitates the comprehensive measurement of intrinsic thiols with expanded coverage and improved sensitivity, while organic mass cytometry enables simultaneous quantification of 27 labeled thiols and 355 other metabolites from single cells. Assessment of metabolic fluctuation upon stimulation demonstrates practicability and accuracy of this integrated methodology which is capable of pathway activity monitoring, metabolic network mapping and untargeted metabolome profiling. Further application of this method in investigating RSL3-triggered ferroptosis reveals that RSL3 inhibits glutathione synthesis via nuclear factor E2-related factor 2- glutathione axis and results in heterogenous glutathione metabolism between subtypes.
    DOI:  https://doi.org/10.1038/s41467-026-70336-z
  41. Nat Commun. 2026 Mar 02.
    Structural heterogeneity and substrate engagement mechanism of the bacterial proteasome activator Bpa.
    Bradley T V Davis, Enrico Rennella, Anisha Haris, Jakub Ujma, David Bruton, Keith Richardson, Kevin Giles, Lewis E Kay, Siavash Vahidi.
      Bacterial proteasomal activator (Bpa) is a regulatory particle of the Mycobacterium tuberculosis proteasome that facilitates the recruitment of substrates and their subsequent degradation by the 20S core particle. Substrate-bound structures of Bpa are unavailable, leaving its recruitment mechanism incompletely understood. Here, we use mass spectrometry and NMR to show that Bpa reversibly assembles into dodecamers from dimers/tetramers in a temperature-dependent manner in vitro, and map the oligomerization interfaces during assembly. To overcome the limitations posed by the poor solubility of natural Bpa substrates, we establish the DNA-binding domain of hTRF1 as a model substrate. We quantify the affinity and stoichiometry of the Bpa-hTRF1 interaction using methyl-TROSY NMR, identifying a 12 Bpa subunit: 3 hTRF1 binding ratio with micromolar affinity that is modulated by salt concentration. Our work maps the Bpa-hTRF1 interface at atomic resolution, identifies determinants of substrate engagement, and introduces a tractable substrate for dissecting proteasomal recognition in mycobacteria.
    DOI:  https://doi.org/10.1038/s41467-026-69978-w
  42. Mol Cell. 2026 Mar 04. pii: S1097-2765(26)00105-X. [Epub ahead of print]
    Functional landscape of non-canonical open reading frames in coordinating cell fate.
    Kaiyuan Zhu, Wan-Chen Li, Jamin Liu, Benjamin A Yang, Elmer Guzman, Morgane Guzman, Rene Sit, Jia Yan, Anastasiya Granat, Shi-An A Chen, Udit Parekh, Mia Pulos-Holmes, Yeyun Ouyang, Charlotte Dietzel, Sandra C A Nielsen, Maya Yamazaki, Carla Mulas, Renato Minopoli, Stefka Tyanova, Daniel N Itzhak, Diego Acosta-Alvear, Jin Chen.
      The human genome harbors thousands of unannotated short open reading frames (sORFs) with the potential to encode microproteins, yet their physiological roles remain largely unexplored. Here, we developed sORF-seq, a functional screen that identified hundreds of sORF-encoded microproteins regulating cellular differentiation. Among these, we discovered lncPRESS1 as a critical regulator of cell fate, and remarkably, it acts as a bifunctional RNA. In the nucleus, lncPRESS1 functions as a long non-coding RNA (lncRNA), guiding the genomic distribution of SWI/SNF and orchestrating developmental gene expression programs. In the cytoplasm, lncPRESS1 acts as an mRNA, translated into a microprotein that directs lineage commitment through Sonic hedgehog (SHH) signaling pathways and interactions with the primary cilium. This dual functionality allows lncPRESS1 to coordinate nuclear and cytoplasmic regulatory networks, shaping early embryogenesis and human brain development. Our findings unveil an unexpected paradigm of non-canonical ORFs in choreographing complex pathways, expanding our understanding of the functional genome beyond traditional coding genes.
    Keywords:  bifunctional RNA; de novo gene; embryonic development; lineage commitment; lncRNA; microprotein; moonlighting; sORF-seq
    DOI:  https://doi.org/10.1016/j.molcel.2026.02.010
  43. Nat Cell Biol. 2026 Mar 06.
    The lncRNA DAMER selectively guides m6A-dependent regulation of ATF4 and asparagine metabolism under nutrient stress in cancer.
    Tianyu Tao, Xianming Feng, Yi Yang, Bangdong Liu, Jiaer Liang, Zishuo Chen, Shuqi Wang, Jiaqi Zhao, Xiuxiu Yang, Liyun Huo, Youhong Zhang, Zhen Gan, Weibin Wu, Jiayu Zeng, Yi Huang, Yaokai Ye, Xuemei Xu, Jianchen Yu, Ruohui Hong, Hongyu Guan, Jueheng Wu, Laixin Xia, Weiling He, Bo Li, Junchao Cai, Mengfeng Li.
      How cancer cells couple metabolic stress sensing to orchestrate specific survival programmes is a key question. Here we show a long non-coding RNA (lncRNA)-guided epitranscriptomic mechanism orchestrating metabolic adaptation by controlling the stability of master stress regulator ATF4. Glucose or glutamine deprivation induces endoplasmic reticulum stress via reactive oxygen species-NRF2-dependent transcription of the lncRNA DAMER. Following its demethylation and nuclear retention by the m6A-eraser ALKBH5, DAMER acts as a scaffold, guiding ALKBH5 to demethylate and stabilize ATF4 mRNA through specific base-pairing. This provides an alternative post-transcriptional pathway for ATF4 upregulation, rewiring asparagine metabolism to promote cancer cell survival under stress. Furthermore, we identified the US FDA-approved drug elbasvir as a potent inhibitor of the DAMER-ALKBH5 interaction. Elbasvir dismantles this adaptive programme, targeting tumour asparagine dependency and exhibiting potent antitumour effects in preclinical models. Our findings reveal a paradigm for lncRNA-guided RNA demethylation that solves a target specificity enigma and offers a strategy targeting metabolic adaptation in cancer.
    DOI:  https://doi.org/10.1038/s41556-026-01905-z
  44. ACS Nano. 2026 Mar 06.
    A Modular Toolkit for Nanoscale Interrogation of Multiprotein Assemblies Inside Living Cells.
    Arthur Felker, Michael Philippi, Michael Holtmannspötter, Christoph Drees, Evelin Schäfer, Martin Steinhart, Rainer Kurre, Changjiang You, Jacob Piehler.
      Quantitative analysis of protein interactions and the formation of higher-order assemblies in living cells remain major challenges. Here, we introduce a versatile nanopatterning toolbox that employs capillary nanostamping of functionalized polymers to generate high-contrast biofunctionalized nanodot arrays (bNDAs) with diameters below 500 nm. By leveraging orthogonal adaptor designs, we achieve robust immobilization of diverse fluorescent protein fusions, enabling simultaneous and selective spatially controlled enrichment of cytosolic proteins into high-density cytosolic nanodot arrays (cNDAs). Focusing on the assembly of the multimeric myddosome complex, we demonstrate density-dependent recruitment and colocalization of the core components MyD88, IRAK4, IRAK1, and TRAF6 within cNDAs. Super-resolution microscopy revealed the distinct nanoscale clustering of MyD88 and IRAK4 and uncovered the ultrastructural architecture of IRAK4 oligomers. These analyses highlight the spatial organization and hierarchical assembly of the myddosome at the nanoscale in the native cellular context. Collectively, our findings establish cNDAs as a powerful platform for reconstituting and analyzing intricate multiprotein assemblies in live cells, offering exciting opportunities for elucidating the mechanistic principles underlying complex protein networks.
    Keywords:  capillary nanostamping; myddosome assembly; nanodot array; protein interaction analysis; super-resolution microscopy; surface biofunctionalization
    DOI:  https://doi.org/10.1021/acsnano.5c14657
  45. Nat Struct Mol Biol. 2026 Mar 06.
    A proteome-wide dependency map of protein interaction motifs.
    Sara M Ambjørn, Bob Meeusen, Johanna Kliche, Juanjuan Wang, Dimitriya H Garvanska, Thomas Kruse, Blanca Lopez Mendez, Matthias Mann, Niels Mailand, Emil P T Hertz, Norman E Davey, Jakob Nilsson.
      Short linear motifs (SLiMs) are the most ubiquitous protein interaction motifs within unstructured regions of the human proteome, yet their contribution to cellular homeostasis remains poorly understood. Here, to systematically assess SLiM function, we applied base editing to mutate all reported and a set of computationally predicted SLiMs defined by SLiM-like evolutionary patterns. By screening 7,293 SLiM-containing regions with 80,473 mutations in HAP1 cells, we define a SLiM dependency map identifying 450 reported and 264 predicted SLiMs required for normal cell proliferation. Mutational consequences were highly reproducible in RPE1 cells, with differences attributed to cell-line-specific gene essentiality. We show that many predicted SLiMs affecting proliferation do not belong to existing classes and identify binding partners for several of these, providing mechanistic insight into a disease-associated ANKRD17 mutation. Our study provides a proteome-wide resource on SLiM essentiality uncovering numerous uncharacterized essential SLiMs.
    DOI:  https://doi.org/10.1038/s41594-026-01762-2
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