bims-proteo 2025-05-11 papers

bims-proteo

Biomed News

on Proteostasis

Issue of 2025–05–11
43 papers selected by
Eric Chevet, INSERM

p97/VCP is required for piecemeal autophagy of aggresomes.
Molecular basis of SIFI activity in the integrated stress response.
The Erv41-Erv46 complex serves as a retrograde receptor to retrieve misfolded secretory proteins that have escaped from the ER.
m6A alters ribosome dynamics to initiate mRNA degradation.
Unveiling the intercompartmental signaling axis: Mitochondrial to ER Stress Response (MERSR) and its impact on proteostasis.
ER-to-lysosome-associated degradation.
Paraoxonase-like APMAP maintains endoplasmic-reticulum-associated lipid and lipoprotein homeostasis.
Biochemical investigation of LC3/GABARAP-ligand interaction as an important quality measure for LC3/GABARAP-targeting small molecules: addendum to the guidelines (4th edition).
Structural visualization of HECT-type E3 ligase Ufd4 accepting and transferring ubiquitin to form K29/K48-branched polyubiquitination.
E3Docker: a docking server for potential E3 binder discovery.
Unconventional secretion of PARK7 requires lysosomal delivery via chaperone-mediated autophagy and specialized SNARE complex.
Kinome screening identifies integrated stress response kinase EIF2AK1/HRI as a negative regulator of PINK1 mitophagy signaling.
Structural insights into the ubiquitin-independent midnolin-proteasome pathway.
AlphaFold2 SLiM screen for LC3-LIR interactions in autophagy.
mTORC1 cooperates with tRNA wobble modification to sustain the protein synthesis machinery.
Proteostasis and Protein Quality Control in chloroplasts: mechanisms and novel insights related to protein mis-localization.
Reduced Palmitoylation of SQSTM1/p62 in Huntington Disease Is Associated With Impaired Autophagy.
Primed for degradation: How weak protein interactions enable molecular glue degraders.
Chimeric deubiquitinase engineering reveals structural basis for specific inhibition of the mitophagy regulator USP30.
Nanoparticle-Mediated Targeted Protein Degradation: An Emerging Therapeutics Technology.
Autophagy-independent role of ATG9A vesicles as carriers for galectin-9 secretion.
ZNF574 is a quality control factor for defective ribosome biogenesis intermediates.
Fluorescence-Coupled Ubiquitination Assay as a High-Throughput Screening Strategy for Novel Cereblon Degraders.
BiDAC-dependent degradation of plasma membrane proteins by the endolysosomal system.
The Integrated Stress Response Pathway Coordinates Translational Control of Multiple Immune Checkpoints in Lung Cancer.
Expression of a protein disulfide isomerase A3 variant associated with amyotrophic lateral sclerosis triggers disease features in mice.
Emerging Patterns in Membrane Protein Folding Pathways.
Translational activity of 80S monosomes varies dramatically across different tissues.
Integrative proximal-ubiquitomics profiling for deubiquitinase substrate discovery applied to USP30.
Reticulon-dependent ER-phagy mediates adaptation to heat stress in C. elegans.
Patient-derived models of UBA5-associated encephalopathy identify defects in neurodevelopment and highlight potential therapeutic avenues.
A general assay platform to study protein pharmacology using ligand-dependent structural dynamics.
Endoplasmic reticulum protein 29 negatively regulates platelet functions and thrombosis in mice.
ER-PM tether Syt1 limits cell-to-cell connectivity via plasmodesmata during innate immune responses in Arabidopsis.
Palmitoylation prevents B7-H4 lysosomal degradation sustaining tumor immune evasion.
Reprograming gene expression in 'hibernating' C. elegans involves the IRE-1/XBP-1 pathway.
Broad Target Screening Reveals Abundance of FKBP12-Based Molecular Glues in Focused Libraries.
De novo design of porphyrin-containing proteins as efficient and stereoselective catalysts.
Detecting ribosome collisions with differential rRNA fragment analysis in ribosome profiling data.
Niemann Pick C1 mistargeting disrupts lysosomal cholesterol homeostasis contributing to neurodegeneration in a Batten disease model.
Biased regulation of protein synthesis and hypoxic death by a conditional raptor mutation.
VCP's nuclear journey: Initiated by interacting with KPNB1 to repair DNA damage.
HDAC1 is involved in the destabilization of the HSF2 protein under non-stress and stress conditions.

Nat Commun. 2025 May 07. 16(1): 4243

p97/VCP is required for piecemeal autophagy of aggresomes.

Maria Körner, Paul Müller, Hirak Das, Felix Kraus, Timo Pfeuffer, Sven Spielhaupter, Silke Oeljeklaus, Christina Schülein-Völk, J Wade Harper, Bettina Warscheid, Alexander Buchberger.

Metazoan cells adapt to the exhaustion of protein quality control (PQC) systems by sequestering aggregation-prone proteins in large, pericentriolar structures termed aggresomes. Defects in both aggresome formation and clearance affect proteostasis and have been linked to neurodegenerative diseases, but aggresome clearance pathways are still underexplored. Here we show that aggresomes comprising endogenous proteins are cleared via selective autophagy requiring the cargo receptor TAX1BP1. TAX1BP1 proximitomes reveal the presence of various PQC systems at aggresomes, including Hsp70 chaperones, the 26S proteasome, and the ubiquitin-selective unfoldase p97/VCP. While Hsp70 and p97/VCP with its cofactors UFD1-NPL4 and FAF1 play key roles in aggresome disassembly, the 26S proteasome is dispensable. We identify aggresomal client proteins that are degraded via different routes, in part in a p97/VCP-dependent manner via aggrephagy. Upon acute inhibition of p97/VCP, aggresomes fail to disintegrate and cannot be incorporated into autophagosomes despite the presence of factors critical for aggrephagosome formation, including p62/SQSTM1, TAX1BP1, and WIPI2. We conclude that the p97/VCP-mediated removal of ubiquitylated aggresomal clients is essential for the disintegration and subsequent piecemeal autophagy of aggresomes.

DOI: https://doi.org/10.1038/s41467-025-59556-x
Nature. 2025 May 06.

Molecular basis of SIFI activity in the integrated stress response.

Zhi Yang, Diane L Haakonsen, Michael Heider, Samuel R Witus, Alex Zelter, Tobias Beschauner, Michael J MacCoss, Michael Rapé.

Chronic stress response activation impairs cell survival and causes devastating degenerative di-seases 1-3. Organisms accordingly deploy silencing factors, such as the E3 ubiquitin ligase SIFI, to terminate stress response signaling and ensure cellular homeostasis 4. How a silencing factor can sense stress across cellular scales to elicit timely stress response inactivation is poorly understood. Here, we combine cryo-electron microscopy of endogenous SIFI with AlphaFold modeling and biochemical analyses to report the structural and mechanistic basis of integrated stress response silencing. SIFI detects both stress-indicators and stress response components through flexible domains within an easily accessible scaffold, before building linkage-specific ubiquitin chains at separate, sterically restricted elongation modules. Ubiquitin handover by a ubiquitin-like domain couples versatile substrate modification to linkage-specific ubiquitin polymer formation. Stress response silencing therefore exploits a catalytic mechanism that is geared towards processing many diverse proteins and hence allows a single enzyme to monitor and, if needed, modulate a complex cellular state.

DOI: https://doi.org/10.1038/s41586-025-09074-z
Mol Biol Cell. 2025 May 06. mbcE25020090

The Erv41-Erv46 complex serves as a retrograde receptor to retrieve misfolded secretory proteins that have escaped from the ER.

John A Fuesler, Jaime R Blais, Charles Barlowe.

The Erv41-Erv46 complex is a conserved transmembrane cargo receptor that returns ER resident proteins that have reached the Golgi complex back to the ER. Here we report that this retrograde receptor also retrieves misfolded secretory cargo that contain luminal domain lesions, such as CPY*. Cells lacking Erv41-Erv46 increase the cellular clearance of misfolded cargo proteins due to increased ER escape and transport to the cell surface or to the vacuole for degradation. Erv41-Erv46 displays selectivity in binding misfolded substrates compared to their folded counterparts. Binding experiments reconstituted with purified proteins demonstrate that Erv41-Erv46 complex binds directly to misfolded CPY* through a shared cargo binding site. These findings indicate that Erv41-Erv46 acts as a post-ER protein quality control checkpoint and expands the client range by which retrograde receptors ensure delivery of correctly folded secretory proteins.

DOI: https://doi.org/10.1091/mbc.E25-02-0090
Cell. 2025 May 05. pii: S0092-8674(25)00455-6. [Epub ahead of print]

m6A alters ribosome dynamics to initiate mRNA degradation.

Shino Murakami, Anthony O Olarerin-George, Jianheng Fox Liu, Sara Zaccara, Ben Hawley, Samie R Jaffrey.

  Degradation of mRNA containing N6-methyladenosine (m6A) is essential for cell growth, differentiation, and stress responses. Here, we show that m6A markedly alters ribosome dynamics and that these alterations mediate the degradation effect of m6A on mRNA. We find that m6A is a potent inducer of ribosome stalling, and these stalls lead to ribosome collisions that form a unique conformation unlike those seen in other contexts. We find that the degree of ribosome stalling correlates with m6A-mediated mRNA degradation, and increasing the persistence of collided ribosomes correlates with enhanced m6A-mediated mRNA degradation. Ribosome stalling and collision at m6A is followed by recruitment of YTHDF m6A reader proteins to promote mRNA degradation. We show that mechanisms that reduce ribosome stalling and collisions, such as translation suppression during stress, stabilize m6A-mRNAs and increase their abundance, enabling stress responses. Overall, our study reveals the ribosome as the initial m6A sensor for beginning m6A-mRNA degradation.

Keywords:  N(6)-methyladenosine; TimeLapse-seq; adaptive response; amino acid depletion; m(6)A; mRNA decay; mRNA degradation; mRNA stability; ribosome collision; ribosome stall

DOI:  https://doi.org/10.1016/j.cell.2025.04.020
PLoS Genet. 2025 May 08. 21(5): e1011700

Unveiling the intercompartmental signaling axis: Mitochondrial to ER Stress Response (MERSR) and its impact on proteostasis.

Jeson J Li, Nan Xin, Chunxia Yang, Bo G Kim, Larissa A Tavizon, Ruth Hong, Jina Park, Travis I Moore, Rebecca George Tharyan, Adam Antebi, Hyun-Eui Kim.

Maintaining protein homeostasis is essential for cellular health. Our previous research uncovered a cross-compartmental Mitochondrial to Cytosolic Stress Response, activated by the perturbation of mitochondrial proteostasis, which ultimately results in the improvement of proteostasis in the cytosol. Here, we found that this signaling axis also influences the unfolded protein response of the endoplasmic reticulum (UPRER), suggesting the presence of a Mitochondria to ER Stress Response (MERSR). During MERSR, the IRE1 branch of UPRER is inhibited, introducing a previously unknown regulatory component of MCSR. Moreover, proteostasis is enhanced through the upregulation of the PERK-eIF2α signaling pathway, increasing phosphorylation of eIF2α and improving the ER's ability to handle proteostasis. MERSR activation in both polyglutamine and amyloid-beta peptide-expressing C. elegans disease models also led to improvement in both aggregate burden and overall disease outcome. These findings shed light on the coordination between the mitochondria and the ER in maintaining cellular proteostasis and provide further evidence for the importance of intercompartmental signaling.

DOI: https://doi.org/10.1371/journal.pgen.1011700
Curr Biol. 2025 May 05. pii: S0960-9822(25)00384-7. [Epub ahead of print]35(9): R320-R322

ER-to-lysosome-associated degradation.

Maurizio Molinari.

Maurizio Molinari introduces ER-to-lysosome-associated degradation - the autophagic and non-autophagic pathways that deliver ERAD-resistant misfolded proteins to the lysosome for degradation to maintain cellular proteostasis.

DOI: https://doi.org/10.1016/j.cub.2025.03.068
Dev Cell. 2025 Apr 27. pii: S1534-5807(25)00210-2. [Epub ahead of print]

Paraoxonase-like APMAP maintains endoplasmic-reticulum-associated lipid and lipoprotein homeostasis.

Blessy Paul, Holly Merta, Rupali Ugrankar-Banerjee, Monica R Hensley, Son Tran, Goncalo Dias do Vale, Lauren Zacherias, Charles K Hewett, Jeffrey G McDonald, Joan Font-Burgada, Thomas P Mathews, Steven A Farber, W Mike Henne.

  Oxidative stress perturbs lipid homeostasis and contributes to metabolic diseases. Though ignored when compared with mitochondrial oxidation, the endoplasmic reticulum (ER) generates reactive oxygen species requiring antioxidant quality control. Using multi-organismal profiling featuring Drosophila, zebrafish, and mammalian hepatocytes, here we characterize the paraoxonase-like C20orf3/adipocyte plasma-membrane-associated protein (APMAP) as an ER-localized antioxidant that suppresses ER lipid oxidation to safeguard ER function. APMAP-depleted cells exhibit defective ER morphology, ER stress, and lipid peroxidation dependent on ER-oxidoreductase 1α (ERO1A), as well as sensitivity to ferroptosis and defects in ApoB-lipoprotein homeostasis. Similarly, organismal APMAP depletion in Drosophila and zebrafish perturbs ApoB-lipoprotein homeostasis. Strikingly, APMAP loss is rescued with chemical antioxidant N-acetyl-cysteine (NAC). Lipidomics identifies that APMAP loss elevates phospholipid peroxidation and boosts ceramides-signatures of lipid stress. Collectively, we propose that APMAP is an ER-localized antioxidant that promotes lipid and lipoprotein homeostasis in the ER network.

Keywords:  ER; PON; ceramide; endoplasmic reticulum; lipoprotein; paraoxonase; redox homeostasis

DOI:  https://doi.org/10.1016/j.devcel.2025.04.008
Autophagy. 2025 May 09. 1-5

Biochemical investigation of LC3/GABARAP-ligand interaction as an important quality measure for LC3/GABARAP-targeting small molecules: addendum to the guidelines (4th edition).

Martin P Schwalm, Christopher Lenz, Krishna Saxena, Daniel J Klionsky, Ewgenij Proschak, Stefan Knapp.

  Targeted protein degradation (TPD) represents a new therapeutic modality that allows the targeting of proteins that are considered undruggable by conventional small molecules. While TPD approaches via the ubiquitin-proteasome system are well established and validated, additional degradation pathways still require rigorous characterization. Here, we focus on macroautophagy/autophagy tethering compounds, a class of small molecules, designed to recruit cargo to LC3/GABARAP proteins for subsequent autophagosome-dependent degradation. We provide guidance for the biophysical and structural characterization of small molecule modulators for studying LC3/GABARAP-ligand interactions. In addition, we discuss potential limitations of autophagy-based TPD systems and emphasize the need for rigorous quality control in the development of LC3/GABARAP-targeting small molecules.Abbreviations: DSF: differential scanning fluorimetry; FP: fluorescence polarization; FRET: Förster/fluorescence resonance energy transfer; HTRF: homogeneous time-resolved fluorescence; ITC: isothermal titration calorimetry; LIR: LC3-interacting region; MGs: molecular glues; NMR: nuclear magnetic resonance; PROTACs: PROteolysis-TArgeting Chimeras; SPR: surface plasmon resonance; TPD: targeted protein degradation; TR-FRET: time-resolved Förster/fluorescence resonance energy transfer; UPS: ubiquitin-proteasome system.

Keywords:  ATTECs; AUTACs; Atg8; GABARAP; LC3

DOI:  https://doi.org/10.1080/15548627.2025.2498506
Nat Commun. 2025 May 09. 16(1): 4313

Structural visualization of HECT-type E3 ligase Ufd4 accepting and transferring ubiquitin to form K29/K48-branched polyubiquitination.

Xiangwei Wu, Huasong Ai, Junxiong Mao, Hongyi Cai, Lu-Jun Liang, Zebin Tong, Zhiheng Deng, Qingyun Zheng, Lei Liu, Man Pan.

The K29/K48-linked ubiquitination generated by the cooperative catalysis of E3 ligase Ufd4 and Ubr1 is an enhanced protein degradation signal, in which Ufd4 is responsible for introducing K29-linked ubiquitination to K48-linked ubiquitin chains to augment polyubiquitination. How HECT-E3 ligase Ufd4 mediates the ubiquitination event remains unclear. Here, we biochemically determine that Ufd4 preferentially catalyses K29-linked ubiquitination on K48-linked ubiquitin chains to generate K29/K48-branched ubiquitin chains and capture structural snapshots of Ub transfer cascades for Ufd4-mediated ubiquitination. The N-terminal ARM region and HECT domain C-lobe of Ufd4 are identified and characterized as key structural elements that together recruit K48-linked diUb and orient Lys29 of its proximal Ub to the active cysteine of Ufd4 for K29-linked branched ubiquitination. These structures not only provide mechanistic insights into the architecture of the Ufd4 complex but also provide structural visualization of branched ubiquitin chain formation by a HECT-type E3 ligase.

DOI: https://doi.org/10.1038/s41467-025-59569-6
Nucleic Acids Res. 2025 May 08. pii: gkaf391. [Epub ahead of print]

E3Docker: a docking server for potential E3 binder discovery.

Kejia Yan, Wangqiu He, Mingwei Pang, Xufeng Lu, Zhou Chen, Lianhua Piao, Han Zhang, Yu Wang, Shan Chang, Ren Kong.

Targeted protein degradation (TPD) has emerged as a promising therapeutic strategy for modulating protein levels in cells. Proteolysis-targeting chimeras and molecular glues facilitate the formation of a complex between the protein of interest (POI) and a specific E3 ligase, leading to POI ubiquitination and subsequent degradation by the proteasome. Considering over 600 E3s in the human genome, it is of great potential to find novel E3 binders and recruit new E3 ligase for TPD related drug discovery. Here we introduce E3Docker, an online computational tool for E3 binder discovery. A total of 1075 Homo sapiens E3 ligases are collected from databases and literature, and 4474 three-dimensional structures of these E3 ligases, in either apo or complex forms, are integrated into the web server. The druggable pockets for each E3 ligase are defined by experimentally bound ligand from PDB or predicted by using DeepPocket. CoDock-Ligand is employed as docking engine for potential E3 binder estimation. With a user-friendly interface, E3Docker facilitates the generation of binding poses and affinity scores for compounds with over 1000 kinds of E3 ligases and may benefit for novel E3 binder discovery. The E3Docker server and tutorials are freely available at https://e3docker.schanglab.org.cn/.

DOI: https://doi.org/10.1093/nar/gkaf391
Proc Natl Acad Sci U S A. 2025 May 13. 122(19): e2414790122

Unconventional secretion of PARK7 requires lysosomal delivery via chaperone-mediated autophagy and specialized SNARE complex.

Biplab Kumar Dash, Yasuomi Urano, Yuichiro Mita, Yuki Ashida, Ryoma Hirose, Noriko Noguchi.

  PARK7/DJ-1, a redox-sensitive protein implicated in neurodegeneration, cancer, and inflammation, exhibits increased secretion under stress. We previously demonstrated that, as a leaderless protein, PARK7 relies on an unconventional autophagy pathway for stress-induced secretion. The current study delves deeper into the mechanisms governing PARK7 secretion under oxidative stress triggered by the neurotoxin 6-hydroxydopamine (6-OHDA). Here, we revealed that 6-OHDA-induced autophagic flux is critical for PARK7 secretion. Downregulation of syntaxin 17 (STX17), a SNARE protein crucial for autophagosome-lysosome fusion and cargo degradation, hindered PARK7 secretion. Likewise, impairing lysosomal function with bafilomycin A1 (BafA1) or chloroquine (CQ) diminished PARK7 release, highlighting the importance of functional lysosomes, potentially in the form of secretory autolysosomes, in PARK7 release. We also found that 6-OHDA appeared to promote the unfolding of PARK7, allowing its selective recognition by the chaperone HSPA8 via KFERQ-like motifs, leading to PARK7 translocation to the lysosomal membrane through LAMP2 via chaperone-mediated autophagy (CMA). Additionally, a dedicated SNARE complex comprising Qabc-SNAREs (STX3/4, VTI1B, and STX8) and R-SNARE SEC22B mediates the fusion of PARK7-containing autolysosomes with the plasma membrane, facilitating the extracellular release of PARK7. Hence, this study uncovers a mechanism where 6-OHDA-induced autophagic flux drives the unconventional secretion of PARK7, involving CMA for PARK7 translocation to lysosomes and specialized SNARE complexes for membrane fusion events.

Keywords:  PARK7/DJ-1; SNAREs; chaperone-mediated autophagy; secretory autolysosome; unconventional secretion

DOI:  https://doi.org/10.1073/pnas.2414790122
Sci Adv. 2025 May 09. 11(19): eadn2528

Kinome screening identifies integrated stress response kinase EIF2AK1/HRI as a negative regulator of PINK1 mitophagy signaling.

Pawan K Singh, Shalini Agarwal, Ilaria Volpi, Léa P Wilhelm, Giada Becchi, Andrew Keenlyside, Thomas Macartney, Rachel Toth, Adrien Rousseau, Glenn R Masson, Ian G Ganley, Miratul M K Muqit.

Loss-of-function mutations in the PINK1 kinase lead to early-onset Parkinson's disease (PD). PINK1 is activated by mitochondrial damage to phosphorylate ubiquitin and Parkin, triggering mitophagy. PINK1 also indirectly phosphorylates Rab GTPases, such as Rab8A. Using an siRNA library targeting human Ser/Thr kinases in HeLa cells, we identified EIF2AK1 [heme-regulated inhibitor (HRI) kinase], a branch of the integrated stress response (ISR), as a negative regulator of PINK1. EIF2AK1 knockdown enhances mitochondrial depolarization-induced PINK1 stabilization and phosphorylation of ubiquitin and Rab8A. These results were confirmed in SK-OV-3, U2OS, and ARPE-19 cells. Knockdown of DELE1, an activator of EIF2AK1, produced similar effects. Notably, the ISR inhibitor ISRIB also enhanced PINK1 activation. In human cells with mito-QC mitophagy reporters, EIF2AK1 knockdown or ISRIB treatment increased PINK1-dependent mitophagy without affecting deferiprone-induced mitophagy. These findings suggest that the DELE1-EIF2AK1 ISR pathway is a negative regulator of PINK1-dependent mitophagy. Further evaluation in PD-relevant models is needed to assess the therapeutic potential of targeting this pathway.

DOI: https://doi.org/10.1126/sciadv.adn2528
Proc Natl Acad Sci U S A. 2025 May 13. 122(19): e2505345122

Structural insights into the ubiquitin-independent midnolin-proteasome pathway.

Nagesh Peddada, Xue Zhong, Yan Yin, Danielle Renee Lazaro, Jianhui Wang, Stephen Lyon, Jin Huk Choi, Xiao-Chen Bai, Eva Marie Y Moresco, Bruce Beutler.

  The protein midnolin (MIDN) augments proteasome activity in lymphocytes and dramatically facilitates the survival and proliferation of B-lymphoid malignancies. MIDN binds both to proteasomes and to substrates, but the mode of interaction with the proteasome is unknown, and the mechanism by which MIDN facilitates substrate degradation in a ubiquitin-independent manner is incompletely understood. Here, we present cryoelectron microscopy (cryo-EM) structures of the substrate-engaged, MIDN-bound human proteasome in two conformational states. MIDN induces proteasome conformations similarly to ubiquitinated substrates by using its ubiquitin-like domain to bind to the deubiquitinase RPN11 (PSMD14). By simultaneously binding to RPN1 (PSMD2) with its C-terminal α-helix, MIDN positions its substrate-carrying Catch domain above the proteasome ATPase channel through which substrates are translocated before degradation. Our findings suggest that both ubiquitin-like domain and C-terminal α-helix must bind to the proteasome for MIDN to stimulate proteasome activity.

Keywords:  MIDN; RPN1/PSMD2; RPN11/PSMD14; UBL domain; cryo-EM

DOI:  https://doi.org/10.1073/pnas.2505345122
Autophagy. 2025 May 04. 1-21

AlphaFold2 SLiM screen for LC3-LIR interactions in autophagy.

Jan Felix Maximilian Stuke, Gerhard Hummer.

  In selective macroautophagy/autophagy, cargo recruitment is mediated by MAP1LC3/LC3-interacting regions (LIRs)/Atg8-family interacting motifs (AIMs) in the cargo or cargo receptor proteins. The binding of these motifs to LC3/Atg8 proteins at the phagophore membrane is often modulated by post-translational modifications, especially phosphorylation. As a challenge for computational LIR predictions, sequences may contain the short canonical (W/F/Y)XX(L/I/V) motif without being functional. Conversely, LIRs may be formed by non-canonical but functional sequence motifs. AlphaFold2 has proven to be useful for LIR predictions, even if some LIRs are missed and proteins with thousands of residues reach the limits of computational feasibility. We present a fragment-based approach to address these limitations. We find that fragment length and phosphomimetic mutations modulate the interactions predicted by AlphaFold2. Systematic fragment screening for a range of target proteins yields structural models for interactions that AlphaFold2 and AlphaFold3 fail to predict for full-length targets. We provide guidance on fragment choice, sequence tuning, LC3 isoform effects, and scoring for optimal LIR screens. Finally, we also test the transferability of this general framework to SUMO-SIM interactions, another type of protein-protein interaction involving short linear motifs (SLiMs).Abbreviations: 2-HP-LIR: ncLIR binding either or both HPs with non-canonical residues; AIM: Atg8-family interacting motif; ap. LIR: antiparallel LIR; A.t.; Arabidopsis thaliana; AT5G06830/C53 (A.t.): CDK5RAP3-like protein; Atg8/ATG8: autophagy related 8, in yeast and plants, respectively; ATG8CL: ATG8C-like of Solanum tuberosum (potato); ATG8E: ATG8e of A.t.; Av. num. of contacts: average number of heavy atom contacts; BCL2: BCL2 apoptosis regulator; BNIP3: BCL2 interacting protein 3; CALCOCO2/NDP52: calcium binding and coiled-coil domain 2; CALR: calreticulin; can. LIR: canonical LIR; CDF: cumulative distribution function; CDK5RAP3/C53 (H.s.): CDK5 regulatory subunit associated protein 3; [DE]W[DE]-LIR: TRIM5-like ncLIR; DSK2A: ubiquitin domain-containing protein DSK2a; FUNDC1: FUN14 domain containing 1; GABARAP: GABA type A receptor-associated protein; HP0/1/2: hydrophobic pocket 0/1/2; HP0-LIR: ncLIR engaging HP0; H.s.; Homo sapiens; lcLIR: low-confidence LIR (ncLIR not similar to previously characterized ncLIRs); LDS: LIR-docking site; LIR: LC3-interacting region; LO score: length-weighted fraction of occurrence score; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MD: molecular dynamics; MEFV/pyrin: MEFV innate immunity regulator, pyrin; minPAE: minimum PAE; MSA: multiple sequence alignment; ncLIR: non-canonical LIR; NPC: nuclear pore complex; Nup159: nucleoporin 159; NUP214: nucleoporin 214; OPTN: optineurin; other@LDS: other interaction proximal to the LIR-docking site; PAE: predicted aligned error; PDCD6IP: programmed cell death 6 interacting protein; PDF: probability distribution function; pLDDT: predicted local-distance difference test; PLEKHM1: pleckstrin homology and RUN domain containing M1; PTM: post-translational modification; sAIM: shuffled AIM (ncLIR with shuffled motif); seq.: sequence; SIM: SUMO-interacting motif; SLiM: short linear motif; SMN1/SMN: survival of motor neuron 1, telomeric; ST: phosphomimetic; STBD1: starch binding domain 1; STK3: serine/threonine kinase 3; SUMO: small ubiquitin like modifier; TBC1D2/TBC1D2A: TBC1 domain family member 2; TEX264: testis expressed 264, ER-phagy receptor; TRIM5/TRIM5α: tripartite motif-containing protein 5; UDS: UIM-docking site; UIM: ubiquitin-interacting motif; UIMC1/RAP80: ubiquitin interaction motif containing 1; ULK1: unc-51 like autophagy activating kinase 1; ULK2: unc-51 like autophagy activating kinase 2; WT: wild type.

Keywords:  AIM; Atg8; SUMO-SIM interaction; phosphorylation; prediction; selective autophagy receptor

DOI:  https://doi.org/10.1080/15548627.2025.2493999
Nat Commun. 2025 May 06. 16(1): 4201

mTORC1 cooperates with tRNA wobble modification to sustain the protein synthesis machinery.

Julia Hermann, Toman Borteçen, Robert Kalis, Alexander Kowar, Catarina Pechincha, Vivien Vogt, Martin Schneider, Dominic Helm, Jeroen Krijgsveld, Fabricio Loayza-Puch, Johannes Zuber, Wilhelm Palm.

Synthesizing the cellular proteome is a demanding process that is regulated by numerous signaling pathways and RNA modifications. How precisely these mechanisms control the protein synthesis machinery to generate specific proteome subsets remains unclear. Here, through genome-wide CRISPR screens we identify genes that enable mammalian cells to adapt to inactivation of the kinase mechanistic target of rapamycin complex 1 (mTORC1), the central driver of protein synthesis. When mTORC1 is inactive, enzymes that modify tRNAs at wobble uridines (U34-enzymes), Elongator and Ctu1/2, become critically essential for cell growth in vitro and in tumors. By integrating quantitative nascent proteomics, steady-state proteomics and ribosome profiling, we demonstrate that the loss of U34-enzymes particularly impairs the synthesis of ribosomal proteins. However, when mTORC1 is active, this biosynthetic defect only mildly affects steady-state protein abundance. By contrast, simultaneous suppression of mTORC1 and U34-enzymes depletes cells of ribosomal proteins, globally inhibiting translation. Thus, mTORC1 cooperates with tRNA U34-enzymes to sustain the protein synthesis machinery and support the high translational requirements of cell growth.

DOI: https://doi.org/10.1038/s41467-025-59185-4
J Exp Bot. 2025 May 02. pii: eraf182. [Epub ahead of print]

Proteostasis and Protein Quality Control in chloroplasts: mechanisms and novel insights related to protein mis-localization.

Nicolaj Jeran, Maxime Mercier, Paolo Pesaresi, Luca Tadini.

  The dynamic rearrangement of the proteome and the maintenance of protein homeostasis (proteostasis) are crucial for the proper development and functionality of cellular compartments. Disruptions in proteostasis can severely compromise cellular health, leading to the accumulation of misfolded or mis-localized proteins prone to forming toxic aggregates. In chloroplasts, proteostasis presents unique challenges due to their endosymbiotic origin, complex sub-compartmentalization, and constant exposure to reactive oxygen species (ROS) generated during photosynthesis. To counteract these challenges, chloroplasts employ sophisticated quality control systems, including chaperones, proteases, and protein degradation pathways such as ubiquitination and autophagy-related mechanisms. Additionally, cytosolic systems play a crucial role in regulating nuclear-encoded, plastid-targeted proteins, ensuring their proper delivery or degradation when defective. Within chloroplasts, specialized proteases, chaperones, and the chloroplast unfolded protein response (cpUPR) oversee protein quality and resolve aggregates to maintain functional integrity. This review critically examines mechanisms governing intracellular trafficking of plastid-targeted proteins, emphasizing key pathways and regulatory bottlenecks that, when disrupted, lead to the accumulation of mis-localized or orphaned proteins. Particular focus is given to the signalling pathways that coordinate cytosolic and plastid effectors to sustain chloroplast function. Furthermore, we propose a novel role for PSBO, subunit of the Oxygen Evolving Complex associated with the Photosystem II, in linking proplastid-to-chloroplast differentiation with plastid quality control.

Keywords:  Chaperone and proteases; Chloroplast biology; Chloroplast degradation; Intracellular protein trafficking; Protein homeostasis; Signalling

DOI:  https://doi.org/10.1093/jxb/eraf182
FASEB J. 2025 May 15. 39(9): e70549

Reduced Palmitoylation of SQSTM1/p62 in Huntington Disease Is Associated With Impaired Autophagy.

F Abrar, M C Davies, Y Alshehabi, A Kumar, A Dang, Y T N Nguyen, J Collins, N S Caron, J S Choudhary, S S Sanders, M O Collins, M R Hayden, D D O Martin.

Disruption of autophagy has emerged as a common feature in many neurodegenerative diseases. Autophagy is a membrane-dependent pathway that requires many key regulators to quickly localize on and off membranes during induction, promoting membrane fusion. Previously, our bioinformatic approaches have shown that autophagy and Huntington disease (HD) are enriched in palmitoylated proteins. Palmitoylation involves the reversible addition of long-chain fatty acids to promote membrane binding. Herein, we show that inhibition of palmitoylation regulates the abundance of several key regulators of autophagy and leads to a partial block of autophagic flux. We confirm that the autophagy receptor SQSTM1/p62 (sequestosome 1) is palmitoylated and directed to the lysosome. Importantly, we report that SQSTM1 palmitoylation is significantly reduced in HD patient and mouse model brains. This finding reveals a novel mechanism contributing to the generation of empty autophagosomes previously seen in HD models and patient-derived cells.

DOI: https://doi.org/10.1096/fj.202401781R
Curr Opin Struct Biol. 2025 May 06. pii: S0959-440X(25)00070-3. [Epub ahead of print]92 103052

Primed for degradation: How weak protein interactions enable molecular glue degraders.

Alexander Hanzl, Clara Inghelram, Stefan Schmitt, Nicolas H Thomä.

Molecular glues are small drug-like molecules that induce de novo protein-protein interactions or facilitate pre-existing weak interactions between proteins. In the context of a ubiquitin ligase, such binding events frequently result in ubiquitination by proximity. Rational development of these transformative modalities, however, remains a major challenge. Here we review recent insights into molecular glues and the emerging design principles. Protein surfaces can similarly be complemented by mutations or compounds inducing binding and a resulting gain of functionality. When the interaction surface between two proteins is relatively small, or when the affinity between the proteins is otherwise weak, proportionally more binding energy will have to be provided by the compound to glue the proteins together. We suggest a simple thermodynamic model to rationalize molecular glue action facilitated by compounds and mutations.

DOI: https://doi.org/10.1016/j.sbi.2025.103052
Nat Struct Mol Biol. 2025 May 05.

Chimeric deubiquitinase engineering reveals structural basis for specific inhibition of the mitophagy regulator USP30.

Nafizul Haque Kazi, Nikolas Klink, Kai Gallant, Gian-Marvin Kipka, Malte Gersch.

The mitochondrial deubiquitinase ubiquitin-specific protease (USP) 30 negatively regulates PINK1-parkin-driven mitophagy. Whether enhanced mitochondrial quality control through inhibition of USP30 can protect dopaminergic neurons is currently being explored in a clinical trial for Parkinson's disease. However, the molecular basis for specific inhibition of USP30 by small molecules has remained elusive. Here we report the crystal structure of human USP30 in complex with a specific inhibitor, enabled by chimeric protein engineering. Our study uncovers how the inhibitor extends into a cryptic pocket facilitated by a compound-induced conformation of the USP30 switching loop. Our work underscores the potential of exploring induced pockets and conformational dynamics to obtain deubiquitinase inhibitors and identifies residues facilitating specific inhibition of USP30. More broadly, we delineate a conceptual framework for specific USP deubiquitinase inhibition based on a common ligandability hotspot in the Leu73 ubiquitin binding site and on diverse compound extensions. Collectively, our work establishes a generalizable chimeric protein-engineering strategy to aid deubiquitinase crystallization and enables structure-based drug design with relevance to neurodegeneration.

DOI: https://doi.org/10.1038/s41594-025-01534-4
Angew Chem Int Ed Engl. 2025 May 05. e202503958

Nanoparticle-Mediated Targeted Protein Degradation: An Emerging Therapeutics Technology.

Andrew G Baker, Adrian Pui Ting Ho, Laura S Itzhaki, Ljiljana Fruk.

  Targeted protein degradation (TPD) has emerged as a transformative therapeutic strategy for eliminating disease-associated proteins, with relevance across disorders ranging from cancer to neurodegeneration. Since its inception nearly two decades ago, TPD has attracted strong academic and commercial interest, with multiple candidates advancing into clinical trials. Despite this progress, the field faces persistent challenges, including limited solubility, poor cellular uptake, and unpredictable structure-activity relationship of small-molecule degraders, which complicate rational design. To address these limitations, alternative platforms such as nanoparticle-mediated protein degraders (NanoPDs) have gained attention. First reported 17 years ago, NanoPDs harness a diverse array of materials, degradation mechanisms, and linker chemistries to achieve protein clearance through novel pathways. Although promising, their clinical translation remains constrained by barriers such as lysosomal entrapment, protein corona formation, and biocompatibility concerns. In this review, we present a comprehensive overview of the current landscape of nanoparticle-mediated TPD. We emphasize the design principles underlying nano-bio interfaces and explore the role of proximity-induced biology as a mechanism for orchestrating protein interactions. Finally, we highlight critical challenges and key questions that must be addressed to fully realize the therapeutic potential of NanoPDs.

Keywords:  Lysosome‐targeting chimera; Nanomedicine; PROTAC; Proteolysis‐targeting chimera; Targeted protein degradation

DOI:  https://doi.org/10.1002/anie.202503958
Nat Commun. 2025 May 07. 16(1): 4259

Autophagy-independent role of ATG9A vesicles as carriers for galectin-9 secretion.

Wenting Zhang, Cuicui Ji, Xianghua Li, Tianlong He, Wei Jiang, Yukun Liu, Meiling Wu, Yunpeng Zhao, Xuechai Chen, Xiaoli Wang, Jian Li, Haolin Zhang, Juan Wang.

Galectins play vital roles in cellular processes such as adhesion, communication, and survival, yet the mechanisms underlying their unconventional secretion remain poorly understood. This study identifies ATG9A, a core autophagy protein, as a key regulator of galectin-9 secretion via a mechanism independent of classical autophagy, secretory autophagy, or the LC3-dependent extracellular vesicle loading and secretion pathway. ATG9A vesicles function as specialized carriers, with the N-terminus of ATG9A and both carbohydrate recognition domains of galectin-9 being critical for the process. TMED10 mediates the incorporation of galectin-9 into ATG9A vesicles, which then fuse with the plasma membrane via the STX13-SNAP23-VAMP3 SNARE complex. Furthermore, ATG9A regulates the secretion of other proteins, including galectin-4, galectin-8, and annexin A6, but not IL-1β, galectin-3, or FGF2. This mechanism is potentially conserved across other cell types, including monocytic cells, which underscores its broader significance in unconventional protein secretion.

DOI: https://doi.org/10.1038/s41467-025-59605-5
Mol Cell. 2025 Apr 30. pii: S1097-2765(25)00359-4. [Epub ahead of print]

ZNF574 is a quality control factor for defective ribosome biogenesis intermediates.

Jared F Akers, Michael LaScola, Adrian Bothe, Hanna Suh, Carmen Jung, Zachary D Stolp, Tanushree Ghosh, Liewei L Yan, Yuming Wang, Michelle Macurak, Amisha Devan, Mary C McKinney, Tarabryn S Grismer, Andres V Reyes, Eric J Ross, Tianyi Hu, Shou-Ling Xu, Nenad Ban, Kamena K Kostova.

  Eukaryotic ribosome assembly is an intricate process that involves four ribosomal RNAs, 80 ribosomal proteins, and over 200 biogenesis factors that participate in numerous interdependent steps. The complexity and essentiality of this process create opportunities for deleterious mutations to occur, accumulate, and impact downstream cellular processes. "Dead-end" ribosome intermediates that result from biogenesis errors are rapidly degraded, affirming the existence of quality control (QC) pathway(s) that monitor ribosome assembly. However, the factors that differentiate between on-path and dead-end intermediates are unknown. We engineered a system to perturb ribosome assembly in human cells and discovered that faulty ribosomes are degraded via the ubiquitin-proteasome system. We identified ZNF574 as a key component of a QC pathway, which we term the ribosome assembly surveillance pathway (RASP). In an animal model, loss of ZNF574 leads to developmental defects, emphasizing the importance of RASP in organismal health.

Keywords:  CRISPRi; development; quality control; ribosome assembly; ribosomopathy; ubiquitin-proteasome system

DOI:  https://doi.org/10.1016/j.molcel.2025.04.017
J Med Chem. 2025 May 07.

Fluorescence-Coupled Ubiquitination Assay as a High-Throughput Screening Strategy for Novel Cereblon Degraders.

Yanan Deng, Shiling Yang, Hesong Xu, Xiyao Ding, Ying Xu, Zhengzheng Ye, Yan Chen, Zemin Zhang, Jin Lin, Huan Xiong, Zizhong Zhang, Kun Yang, Yiran Hu, Ke Xu, Cheng Luo, Shijie Chen, Hua Lin, Zhihai Li.

Cereblon (CRBN)-based protein degradation, via molecular glue degraders (MGDs) and proteolysis-targeting chimeras (PROTACs), is a promising cancer treatment strategy in targeted protein degradation (TPD). However, novel degraders discovery remains limited due to the lack of robust, high-throughput screening (HTS) methods for processing pools of purified compounds or complex chemical synthesis mixtures. Here, we introduce an innovative HTS strategy that employs a highly sensitive, fluorescence-coupled ubiquitination assay to identify CRBN-based degraders. This approach tracks ubiquitinated target proteins via gel-based analyses, and thereby progressively narrows down the list of potential degrader molecules from large-scale compound libraries or chemical reaction mixtures. Using this strategy, we identified LL-BPTF-8, a promising lead compound of PROTAC degrader with high potency and selectivity that targets the bromodomain PHD finger transcription factor (BPTF). Overall, our method offers a low-cost, rapid, and versatile platform for the HTS of protein degrader candidates, significantly streamlining the discovery of novel degraders.

DOI: https://doi.org/10.1021/acs.jmedchem.5c00065
Nat Commun. 2025 May 10. 16(1): 4345

BiDAC-dependent degradation of plasma membrane proteins by the endolysosomal system.

Sammy Villa, Qumber Jafri, Julia R Lazzari-Dean, Manjot Sangha, Niclas Olsson, Austin E Y T Lefebvre, Mark E Fitzgerald, Katrina Jackson, Zhenghao Chen, Brian Y Feng, Aaron H Nile, David Stokoe, Kirill Bersuker.

The discovery of bifunctional degradation activating compounds (BiDACs) has led to the development of a new class of drugs that promote the clearance of their protein targets. BiDAC-induced ubiquitination is generally believed to direct cytosolic and nuclear proteins to proteolytic destruction by proteasomes. However, pathways that govern the degradation of other classes of BiDAC targets, such as integral membrane and intraorganellar proteins, have not been investigated in depth. In this study we use morphological profiling and CRISPR/Cas9 genetic screens to investigate the mechanisms by which BiDACs induce the degradation of plasma membrane receptor tyrosine kinases (RTKs) EGFR and Her2. We find that BiDAC-dependent ubiquitination triggers the trafficking of RTKs from the plasma membrane to lysosomes for degradation. Notably, functional proteasomes are required for endocytosis of RTKs upstream of the lysosome. Additionally, our screen uncovers a non-canonical function of the lysosome-associated arginine/lysine transporter PQLC2 in EGFR degradation. Our data show that BiDACs can target proteins to proteolytic machinery other than the proteasome and motivate further investigation of mechanisms that govern the degradation of diverse classes of BiDAC targets.

DOI: https://doi.org/10.1038/s41467-025-59627-z
Cancer Res. 2025 May 06.

The Integrated Stress Response Pathway Coordinates Translational Control of Multiple Immune Checkpoints in Lung Cancer.

Shayna Thomas-Jardin, Shruthy Suresh, Ariana Arce, Nicole Novaresi, Qing Deng, Emily Stein, Lisa Thomas, Cheryl Lewis, Chul Ahn, Bret M Evers, Esra A Akbay, Maria E Salvatierra, Wei Lu, Khaja Khan, Luisa M Solis Soto, Ignacio I Wistuba, John D Minna, Kathryn A O'Donnell.

The integrated stress response (ISR) is an adaptive pathway hijacked by cancer cells to survive cellular stresses in the tumor microenvironment. ISR activation potently induces PD-L1, leading to suppression of anti-tumor immunity. Here, we sought to uncover additional immune checkpoint proteins regulated by the ISR to elucidate mechanisms of tumor immune escape. ISR coordinately induced CD155 and PD-L1, enhancing translation of both immune checkpoint proteins through bypass of inhibitory upstream open reading frames in their 5' UTRs. Analysis of primary human lung tumors identified a significant correlation between expression of PD-L1 and CD155. ISR activation accelerated tumorigenesis and inhibited T cell function, which could be overcome by combining PD-1 and TIGIT blockade with the ISR inhibitor ISRIB. This study uncovers a mechanism by which two immune checkpoint proteins are coordinately regulated and suggests a therapeutic strategy for lung cancer patients.

DOI: https://doi.org/10.1158/0008-5472.CAN-24-3844
Neurobiol Dis. 2025 May 07. pii: S0969-9961(25)00163-9. [Epub ahead of print] 106947

Expression of a protein disulfide isomerase A3 variant associated with amyotrophic lateral sclerosis triggers disease features in mice.

Martin Sepulveda, Francisca Martinez-Traub, Patricia Ojeda, Viviana Perez, Jorge Ojeda, Jessica Mella, Rodrigo Diaz, Pablo Rozas, Matías Mansilla-Jaramillo, Amparo Zuleta, Guillermo Diaz, Bredford Kerr, Ute Woehlbier, Juan Pablo Henríquez, Danilo B Medinas, Claudio Hetz.

  Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by loss of motoneurons and compromised proteostasis. Dysfunction of the endoplasmic reticulum (ER) has been identified as a transversal pathogenic mechanism associated with motoneurons vulnerability in ALS. Protein disulfide isomerases (PDIs) are key enzymes catalyzing protein folding at the ER that are altered in the disease, involving biochemical and genetic perturbations. In ALS cases, we previously identified variants in the gene encoding PDIA3 (also known as Grp58 or ERp57), which were associated with altered neurite outgrowth in cell culture and abnormal motoneuron connectivity in zebrafish. Here, we report the generation of transgenic mice expressing the ALS-associated PDIA3Q481K variant. Moderate PDIA3Q481K overexpression resulted in altered motor capacity accompanied by decreased motoneuron number. The adverse effects of PDIA3Q481K were associated with induction of ER stress in the spinal cord and subtle morphological changes in neuromuscular junctions. Our results suggest that the PDIA3Q481K variant is likely pathogenic and its overexpression in mice recapitulate some ALS features, further supporting the concept that altered proteostasis due to PDI dysfunction may predispose an individual to develop the disease.

Keywords:  Amyotrophic lateral sclerosis; Endoplasmic reticulum; Protein disulfide isomerase; Transgenic line

DOI:  https://doi.org/10.1016/j.nbd.2025.106947
Annu Rev Biophys. 2025 May;54(1): 141-162

Emerging Patterns in Membrane Protein Folding Pathways.

Sang Ah Kim, Hyun Gyu Kim, W C Bhashini Wijesinghe, Duyoung Min, Tae-Young Yoon.

  Studies of membrane protein folding have progressed from simple systems such as bacteriorhodopsin to complex structures such as ATP-binding cassette transporters and voltage-gated ion channels. Advances in techniques such as single-molecule force spectroscopy and in vivo force profiling now allow for the detailed examination of membrane protein folding pathways at amino acid resolutions. These proteins navigate rugged energy landscapes partly shaped by the absence of hydrophobic collapse and the viscous nature of the lipid bilayer, imposing biophysical limitations on folding speeds. Furthermore, many transmembrane (TM) helices display reduced hydrophobicity to support functional requirements, simultaneously increasing the energy barriers for membrane insertion, a manifestation of the evolutionary trade-off between functionality and foldability. These less hydrophobic TM helices typically insert and fold as helical hairpins, following the protein synthesis direction from the N terminus to the C terminus, with assistance from endoplasmic reticulum (ER) chaperones like the Sec61 translocon and the ER membrane protein complex. The folding pathways of multidomain membrane proteins are defined by allosteric networks that extend across various domains, where mutations and folding correctors affect seemingly distant domains. A common evolutionary strategy is likely to be domain specialization, where N-terminal domains enhance foldability and C-terminal domains enhance functionality. Thus, despite inherent biophysical constraints, evolution has finely tuned membrane protein sequences to optimize foldability, stability, and functionality.

Keywords:  helical hairpin; membrane protein folding; multidomain membrane protein; single-molecule force spectroscopy; templated folding

DOI:  https://doi.org/10.1146/annurev-biophys-070524-100658
Nucleic Acids Res. 2025 Apr 22. pii: gkaf292. [Epub ahead of print]53(8):

Translational activity of 80S monosomes varies dramatically across different tissues.

Albert Blandy, Tayah Hopes, Elton J R Vasconcelos, Amy Turner, Bulat Fatkhullin, Michaela Agapiou, Juan Fontana, Julie L Aspden.

Translational regulation at the stage of initiation can impact the number of ribosomes translating each mRNA molecule. However, the translational activity of single 80S ribosomes (monosomes) on mRNA is less well understood, even though these 80S monosomes represent the dominant ribosomal complexes in vivo. Here, we used cryo-EM to determine the translational activity of 80S monosomes across different tissues in Drosophila melanogaster. We discovered that while head and embryo 80S monosomes are highly translationally active, testis and ovary 80S monosomes are translationally inactive. RNA-Seq analysis of head monosome- and polysome-translated mRNAs, revealed that head 80S monosomes preferentially translate mRNAs with TOP motifs, short 5'-UTRs, short ORFs and are enriched for the presence of uORFs. Overall, these findings highlight that regulation of translation initiation and protein synthesis is mostly performed by monosomes in head and embryo, while polysomes are the main source of protein production in testis and ovary.

DOI: https://doi.org/10.1093/nar/gkaf292
Cell Chem Biol. 2025 Apr 30. pii: S2451-9456(25)00127-8. [Epub ahead of print]

Integrative proximal-ubiquitomics profiling for deubiquitinase substrate discovery applied to USP30.

Andreas Damianou, Hannah B L Jones, Athina Grigoriou, Mohammed A Akbor, Edward Jenkins, Philip D Charles, Iolanda Vendrell, Simon Davis, Benedikt M Kessler.

  The growing interest in deubiquitinases (DUBs) as drug targets for modulating critical molecular pathways in disease is fueled by the discovery of their specific cellular roles. A crucial aspect of this fact is the identification of DUB substrates. While mass spectrometry-based proteomic methods can be used to study global changes in cellular ubiquitination following DUB activity perturbation, these datasets often include indirect and downstream ubiquitination events. To enrich for the direct substrates of DUB enzymes, we have developed a proximal-ubiquitome workflow that combines proximity labeling methodology (ascorbate peroxidase-2 [APEX2]) with subsequent ubiquitination enrichment based on the K-ε-GG motif. We applied this technology to identify altered ubiquitination events in the vicinity of the DUB ubiquitin-specific protease 30 (USP30) upon its inhibition. Our findings reveal ubiquitination events previously associated with USP30 on TOMM20 and FKBP8, as well as the candidate substrate LETM1, which is deubiquitinated in a USP30-dependent manner.

Keywords:  APEX2; LETM1; USP30; deubiquitinase; mass spectrometry; proteomics; proximal-ubiquitomics; proximity labeling; ubiquitin-specific protease 30

DOI:  https://doi.org/10.1016/j.chembiol.2025.04.004
Curr Biol. 2025 May 02. pii: S0960-9822(25)00457-9. [Epub ahead of print]

Reticulon-dependent ER-phagy mediates adaptation to heat stress in C. elegans.

Claudia Serot, Vincent Scarcelli, Alexandre Pouget, Céline Largeau, Audrey Sagot, Kenza El-Hachami, Denis Dupuy, Emmanuel Culetto, Christophe Lefebvre, Renaud Legouis.

  The selective degradation of endoplasmic reticulum (ER) by autophagy, named ER-phagy, promotes the recovery of ER homeostasis after stress. Depending on the ER stress, different types of ER-phagy involve various selective autophagy receptors. In this study, we report a macroER-phagy induced by the fragmentation of tubular ER in response to acute heat stress. We identified a novel ER-phagy receptor encoded by the reticulon long isoform RET-1d. RET-1d is mainly expressed in the nervous system and the epidermis and colocalizes with the ubiquitin-like autophagy protein LGG-1/GABARAP during heat-stress-induced autophagy. Two LC3-interacting region (LIR) motifs in the long intrinsically disordered region of RET-1d mediate its interaction with the LGG-1 protein. The specific depletion of the RET-1d isoform or the mutations of the LIRs resulted in a defective ER-phagy and a decrease in the capacity of animals to adapt to heat stress. Our data revealed a RET-1d- and LGG-1-dependent ER-phagy mechanism that takes place in neurons and epidermis and participates in the adaptation of C. elegans to heat stress.

Keywords:  ER stress; LGG-1/Gabarap; LIR motif; RET-1 isoforms; autophagosomes; autophagy; development; endoplasmic reticulum; locomotion; neuron

DOI:  https://doi.org/10.1016/j.cub.2025.04.028
Sci Transl Med. 2025 May 07. 17(797): eadn8417

Patient-derived models of UBA5-associated encephalopathy identify defects in neurodevelopment and highlight potential therapeutic avenues.

Helen Chen, Christy W LaFlamme, Yong-Dong Wang, Aidan W Blan, Nikki Koehler, Renata Mendonca Moraes, Athena R Olszewski, Edith P Almanza Fuerte, Emily S Bonkowski, Richa Bajpai, Alfonso Lavado, Shondra M Pruett-Miller, Heather C Mefford.

UBA5 encodes for the E1 enzyme of the UFMylation cascade, which plays an essential role in endoplasmic reticulum (ER) homeostasis. The clinical phenotypes of UBA5-associated encephalopathy include developmental delays, epilepsy, and intellectual disability. To date, there is no humanized neuronal model to study the cellular and molecular consequences of UBA5 pathogenic variants. We developed and characterized patient-derived cortical organoid cultures from two patients with compound heterozygous variants in UBA5. Both shared the same missense variant, which encodes a hypomorphic allele (p.A371T), along with a nonsense variant (p.G267* or p.A123fs*4). Single-cell RNA sequencing of 100-day organoids identified defects in GABAergic interneuron development. We demonstrated aberrant neuronal firing and reduction in size of patient-derived organoids. Mechanistically, we showed that ER homeostasis is perturbed along with an exacerbated unfolded protein response pathway in engineered U87-MG cells and patient-derived organoids expressing UBA5 pathogenic variants. We also assessed two potential therapeutic modalities that augmented UBA5 protein abundance to rescue aberrant molecular and cellular phenotypes. We assessed SINEUP, a long noncoding RNA that augments translation efficiency, and CRISPRa, a modified CRISPR-Cas9 approach to augment transcription efficiency to increase UBA5 protein production. Our study provides a humanized model that allows further investigations of UBA5 variants in the brain and highlights promising approaches to alleviate cellular aberrations for this rare, developmental disorder.

DOI: https://doi.org/10.1126/scitranslmed.adn8417
Nat Commun. 2025 May 10. 16(1): 4342

A general assay platform to study protein pharmacology using ligand-dependent structural dynamics.

Daniel A Ciulla, Patricia K Dranchak, Mahesh Aitha, Renier H P van Neer, Divia Shah, Ravi Tharakan, Kelli M Wilson, Yuhong Wang, John C Braisted, James Inglese.

Drug design strategies represent a fundamental challenge in chemical biology that could benefit from the development of next-generation high-throughput assays. Here we demonstrate that structural dynamic changes induced by ligand binding can be transmitted to a sensor protein fused to a target protein terminus. Here, NanoLuc luciferase, used as the intact protein or its α-complementation peptide, was fused to seven proteins from distinct enzyme superfamilies resulting in sensitive ligand-dependent bioluminescent outputs. This finding allows a general non-competitive, function-independent, quantitative, isothermal gain-of-signal ligand binding readout. As applied to chemical library high throughput screening, we can observe multivariate pharmacologic outputs including cofactor-induced synergy in ligand binding, as well as an example of allosteric site binding. The structural dynamics response assay format described here can enable the investigation of proteins precluded from study due to cost-prohibitive, insensitive, or technically challenging assays, including from cell lysates containing endogenously expressed gene edited proteins.

DOI: https://doi.org/10.1038/s41467-025-59658-6
Thromb J. 2025 May 07. 23(1): 44

Endoplasmic reticulum protein 29 negatively regulates platelet functions and thrombosis in mice.

Xiaofeng Yan, Yishan Lu, Keyu Lv, Miao Jiang, Chao Fang, Yi Wu, Aizhen Yang.

   BACKGROUND: Several members of protein disulfide isomerase (PDI) family with the CXYC active motif such as PDI, ERp57, ERp72, ERp46, ERp5 and TMX1 have important roles in platelet functions and thrombosis. These members contribute to the network of redox regulation of platelet activities. However, whether other PDI family members without the CXYC motif such as ERp29, have a role in these processes remains unknown.
AIMS: To determine the role of ERp29 in platelet functions and thrombosis.
METHODS: The phenotypes of platelet-specific ERp29-deficient (Pf4-Cre/ERp29fl/fl) mice were evaluated using tail bleeding assay and laser-induced and FeCl3-induced arterial injury models, as well as venous thrombosis model. In vitro, the functions of ERp29-deficient platelets were assessed in respect to aggregation, adhesion, spreading, clot retraction, granule secretion and integrin αIIbβ3 activation measured by flow cytometry. Redox state of integrin αIIbβ3 thiols was detected using 3-(N-maleimido-propionyl) biotin (MPB) labeling.
RESULTS: Compared with WT mice, Pf4-Cre/ERp29fl/fl mice exhibited shortened tail-bleeding times, increased platelet accumulation in the two arterial thrombosis models, and enhanced thrombogenesis in the venous thrombosis model. ERp29-deficient platelets had enhanced response in aggregation, ATP release, spreading, clot retraction, αIIbβ3 activation, fibrinogen binding and P-selectin expression. As detected by MPB labeling, the free thiol content of integrin αIIbβ3 in ERp29-deficient platelets were increased compared with WT platelets, suggesting that the role of ERp29 is associated with oxidation of the functional disulfides of integrin αIIb and/or β3 subunits.
CONCLUSION(S): ERp29 is the first disulfide isomerase without the CXYC motif that negatively regulates platelet function. This study provides new insight into the redox network controlling thrombosis.

Keywords:  ERp29; Integrin αIIbβ3; Platelets; Redox regulation; Thrombosis

DOI:  https://doi.org/10.1186/s12959-025-00726-8
Cell Rep. 2025 May 03. pii: S2211-1247(25)00443-7. [Epub ahead of print]44(5): 115672

ER-PM tether Syt1 limits cell-to-cell connectivity via plasmodesmata during innate immune responses in Arabidopsis.

Jiajing Li, Pengfei Lu, Qing Pan, Bingxiao Wang, Youjun Wang, Jiejie Li.

  Upon perception of microbe-associated molecular patterns (MAMPs), plants close plasmodesmata (PD) as part of their innate immune responses. However, the signaling cascades and molecular mechanisms underlying MAMP-induced PD closure require further investigation. Here, we show that the endoplasmic reticulum (ER)-plasma membrane (PM) tether Synaptotagmin 1 (Syt1) modulates the response of PD to MAMPs. Following MAMP stimulation, Syt1 rapidly accumulates to PD and further recruits a putative calcium-permeable transporter, ANN4, to promote a localized, PD-associated Ca2+ elevation, leading to callose-dependent PD closure. Moreover, Syt1 can sense the increased level of PI(4,5)P2 at the PD-PM via its C2 domain. Disrupting the interaction between Syt1 and PM lipids by pharmaceutical approaches or site-directed mutagenesis leads to impaired PD response to MAMPs. Collectively, our findings reveal that Syt1 integrates phospholipid signaling from the PD-PM to regulate PD-localized Ca2+ elevation, thereby modulating intercellular communication for restricting the spread of bacterial infection.

Keywords:  CP: Cell biology; CP: Plants; ER-PM contact sites; plant innate immunity; plasmodesmata; symplasmic trafficking; synaptotagmin

DOI:  https://doi.org/10.1016/j.celrep.2025.115672
Nat Commun. 2025 May 08. 16(1): 4254

Palmitoylation prevents B7-H4 lysosomal degradation sustaining tumor immune evasion.

Yijian Yan, Jiali Yu, Weichao Wang, Ying Xu, Kole Tison, Rongxin Xiao, Sara Grove, Shuang Wei, Linda Vatan, Max Wicha, Ilona Kryczek, Weiping Zou.

B7-H4 functions as an immune checkpoint in the tumor microenvironment (TME). However, the post-translational modification (PTM) of B7-H4 and its translational potential in cancer remains incompletely understood. We find that ZDHHC3, a zinc finger DHHC-type palmitoyltransferase, palmitoylates B7-H4 at Cys130 in breast cancer cells, preventing its lysosomal degradation and sustaining B7-H4-mediated immunosuppression. Knockdown of ZDHHC3 in tumors results in robust anti-tumor immunity and reduces tumor progression in murine models. Moreover, abemaciclib, a CDK4/6 inhibitor, primes lysosome activation and promotes lysosomal degradation of B7-H4 independently of the tumor cell cycle. Treatment with abemaciclib results in T cell activation and mitigates B7-H4-mediated immune suppression via inducing B7-H4 degradation in preclinical tumor models. Thus, B7-H4 palmitoylation is an important PTM controlling B7-H4 protein stability and abemaciclib may be repurposed to promote B7-H4 degradation, thereby treating patients with B7-H4 expressing tumors.

DOI: https://doi.org/10.1038/s41467-025-58552-5
Elife. 2025 May 06. pii: RP101186. [Epub ahead of print]13

Reprograming gene expression in 'hibernating' C. elegans involves the IRE-1/XBP-1 pathway.

Melanie Lianne Engelfriet, Yanwu Guo, Andreas Arnold, Eivind Valen, Rafal Ciosk.

  In nature, many animals respond to cold by entering hibernation, while in clinical settings, controlled cooling is used in transplantation and emergency medicine. However, the molecular mechanisms that enable cells to survive severe cold are still not fully understood. One key aspect of cold adaptation is the global downregulation of protein synthesis. Studying it in the nematode Caenorhabditis elegans, we find that the translation of most mRNAs continues in the cold, albeit at a slower rate, and propose that cold-specific gene expression is regulated primarily at the transcription level. Supporting this idea, we found that the transcription of certain cold-induced genes is linked to the activation of unfolded protein response (UPR) through the conserved IRE-1/XBP-1 signaling pathway. Our findings suggest that this pathway is triggered by cold-induced perturbations in proteins and lipids within the endoplasmic reticulum, and that its activation is beneficial for cold survival.

Keywords:  C. elegans; ER stress; UPR; cell biology; cold dormancy; global translation; hibernation; hypothermia

DOI:  https://doi.org/10.7554/eLife.101186
J Med Chem. 2025 May 08. 68(9): 9525-9536

Broad Target Screening Reveals Abundance of FKBP12-Based Molecular Glues in Focused Libraries.

Johannes K Dreizler, Christian Meyners, Wisely Oki Sugiarto, Maximilian L Repity, Edvaldo V S Maciel, Patrick L Purder, Frederik Lermyte, Stefan Knapp, Felix Hausch.

Competitive (nondegradative) molecular glues represent a promising drug modality that remains underexplored primarily due to the lack of adequate hit identification approaches. In this study, we screened our historically grown FKBP-focused library containing >1000 drug-like molecules to identify FKBP-assisted molecular glues targeting a diverse panel of 57 proteins. In addition to establishing a robust and generalizable screening approach, we discovered three novel FKBP-dependent molecular glues targeting PTPRN, BRD4BD2, and STAT4. Our results demonstrate that molecular glues are more common than previously thought and that they can be identified by repurposing existing focused libraries. An optimized, highly cooperative FKBP12-BRD4BD2 glue demonstrated the involvement of the BD2 pocket and exhibited selectivity over the closely related BD1 domain. Our results underscore the value of FKBP12-assisted molecular glues to target challenging proteins with the potential for high selectivity.

DOI: https://doi.org/10.1021/acs.jmedchem.5c00220
Science. 2025 May 08. 388(6747): 665-670

De novo design of porphyrin-containing proteins as efficient and stereoselective catalysts.

Kaipeng Hou, Wei Huang, Miao Qi, Thomas H Tugwell, Turki M Alturaifi, Yuda Chen, Xingjie Zhang, Lei Lu, Samuel I Mann, Peng Liu, Yang Yang, William F DeGrado.

De novo design of protein catalysts with high efficiency and stereoselectivity provides an attractive approach toward the design of environmentally benign catalysts. Here, we design proteins that incorporate histidine-ligated synthetic porphyrin and heme ligands. Four of 10 designed proteins catalyzed cyclopropanation with an enantiomeric ratio greater than 99:1. A second class of proteins were designed to catalyze a silicon-hydrogen insertion and were optimized by directed evolution in whole cells. The evolved proteins incorporated features unlikely to be generated by computational design alone, including a proline in an α helix. Molecular dynamics simulations showed that as the proteins evolved toward higher activity, their conformational ensembles narrowed to favor more productive conformations. Our work demonstrates that efficient de novo protein catalysts are designable and should be useful for manifold chemical processes.

DOI: https://doi.org/10.1126/science.adt7268
NAR Genom Bioinform. 2025 Jun;7(2): lqaf045

Detecting ribosome collisions with differential rRNA fragment analysis in ribosome profiling data.

Edwin Sakyi Kyei-Baffour, Jitske Bak, Joana Silva, William J Faller, Ferhat Alkan.

It has become clear in recent years that ribosomes regularly stall during translation. Such translation impairment has many causes, including exposure to ribotoxic stress agents, the presence of specific RNA structures or sequences, or a shortage of amino acids or translation factors. If they are not resolved, stalled ribosomes can lead to ribosome collisions that are continuously surveilled by various sensor proteins. This in turn initiates a cascade of signalling events that can change the physiology and behaviour of cells. However, measuring changes in collision abundance has proved challenging, and as a result, the importance of collision-mediated biological responses is still unclear. Here, we show that computational analyses of standard ribosome profiling (Ribo-seq) data enable the prediction of changes in ribosome collisions between conditions. This is achieved by using the known 3D structure of collided ribosomes to define the ribosomal RNA (rRNA) positions that are differentially digested by RNases during the Ribo-seq protocol. Comparison of the relative rRNA reads at these positions allows the relative quantification of collisions between samples, an approach we call differential ribosome collisions by Analysis of rRNA Fragments (dricARF). When applied to public datasets across multiple organisms, our approach detects changes in collision events with unprecedented accuracy and sensitivity. In addition to providing supplementary evidence for ribosome collisions, our tool has the potential to uncover novel biological processes that are mediated by them. dricARF is available as part of the ARF R package and can be accessed through https://github.com/fallerlab/ARF.

DOI: https://doi.org/10.1093/nargab/lqaf045
Sci Adv. 2025 May 09. 11(19): eadr5703

Niemann Pick C1 mistargeting disrupts lysosomal cholesterol homeostasis contributing to neurodegeneration in a Batten disease model.

Abhilash P Appu, Maria B Bagh, Nisha Plavelil, Avisek Mondal, Tamal Sadhukhan, Satya P Singh, Neil J Perkins, Aiyi Liu, Anil B Mukherjee.

Neurodegeneration is a devastating manifestation in most lysosomal storage disorders (LSDs). Loss-of-function mutations in CLN1, encoding palmitoyl-protein thioesterase-1 (PPT1), cause CLN1 disease, a devastating neurodegenerative LSD that has no curative treatment. Numerous proteins in the brain require dynamic S-palmitoylation (palmitoylation-depalmitoylation) for trafficking to their destination. Although PPT1 depalmitoylates S-palmitoylated proteins and its deficiency causes CLN1 disease, the underlying pathogenic mechanism has remained elusive. We report that Niemann-Pick C1 (NPC1), a polytopic membrane protein mediating lysosomal cholesterol egress, requires dynamic S-palmitoylation for trafficking to the lysosome. In Cln1-/- mice, Ppt1 deficiency misroutes NPC1-dysregulating lysosomal cholesterol homeostasis. Along with this defect, increased oxysterol-binding protein (OSBP) promotes cholesterol-mediated activation of mechanistic target of rapamycin C1 (mTORC1), which inhibits autophagy contributing to neurodegeneration. Pharmacological inhibition of OSBP suppresses mTORC1 activation, rescues autophagy, and ameliorates neuropathology in Cln1-/- mice. Our findings reveal a previously unrecognized role of CLN1/PPT1 in lysosomal cholesterol homeostasis and suggest that suppression of mTORC1 activation may be beneficial for CLN1 disease.

DOI: https://doi.org/10.1126/sciadv.adr5703
Curr Biol. 2025 May 01. pii: S0960-9822(25)00504-4. [Epub ahead of print]

Biased regulation of protein synthesis and hypoxic death by a conditional raptor mutation.

Chun-Ling Sun, Cong Xu, Omar Itani, Elyse L Christensen, Harshitha Vijay, Jessica Ho, Abraham Correa-Medina, Christian B Klingler, Neal D Mathew, Stephane Flibotte, Ian R Humphreys, Diego Delgadillo Rubalcaba, Alison E Ritter, Muriel Desbois, Brock Grill, C Michael Crowder.

  Mechanistic target of rapamycin (mTOR) functions in mTOR complex 1 (mTORC1) with raptor to match metazoan metabolism to available nutrients to regulate multiple cellular, physiological, and pathological processes. Hypoxic cellular injury is influenced by the mTORC1 pathway, but whether its activity promotes or prevents injury is unclear, and which mTORC1-regulated mechanisms control hypoxic injury are obscure. Here, we report the discovery of a hypoxia-resistant, temperature-sensitive raptor mutant in an unbiased forward mutagenesis screen in C. elegans. This raptor mutant is both hypoxia resistant and long lived at intermediate temperatures, while unable to develop at higher temperatures. Temperature-shift experiments show that the conditional hypoxia resistance can be induced in the raptor mutant immediately prior to the hypoxic insult. At these intermediate temperatures, the raptor mutation selectively reduces protein synthesis without affecting autophagy, and epistasis experiments implicate mTOR-targeted translation regulators as components of the hypoxia resistance mechanism. Using the conditional developmental arrest phenotype in a selection for suppressors of raptor loss of function, we isolated multiple second-site raptor missense mutants, whose mutated residue is predicted to interact with RagA, a raptor-binding protein. These suppressor mutations restore normal protein synthesis, hypoxic sensitivity, and lifespan and thereby implicate raptor-RagA interactions as critical to these biological processes.

Keywords:  C. elegans; anoxia; autophagy; cell death; conditional mutant; mTOR; mTORC1; metabolism; rapamycin; translation

DOI:  https://doi.org/10.1016/j.cub.2025.04.040
Proc Natl Acad Sci U S A. 2025 May 13. 122(19): e2416045122

VCP's nuclear journey: Initiated by interacting with KPNB1 to repair DNA damage.

Zhichao Xing, Xiaoying Cai, Ting He, Peiheng Li, Jun He, Yuxuan Qiu, Na Li, Li Mi, Ruixi Li, Jingqiang Zhu, Zhihui Li, Anping Su, Haoyu Ye, Wenshuang Wu.

  DNA damage repair (DDR) is essential for cancer cell survival and treatment resistance, making it a critical target for tumor therapy. The eukaryotic AAA+ adenosine triphosphatase valosin-containing protein (VCP), which is transported from the cytoplasm into the nucleus, plays a critical role in the DDR process. However, the nuclear translocation and molecular mechanism of VCP for DDR remain elusive. Here, we define VCP as a KPNB1 interacting protein through a combination of chemical and immunoprecipitation mass spectrometry approaches. Further biochemical studies elucidate that KPNB1 directly transports VCP into the nucleus. We also identify withaferin A (WA) as a small molecule that can retard VCP nuclear localization via covalent binding to CYS 158 of KPNB1. Further studies verify WA as an effective antitumor drug candidate via blocking VCP nuclear localization to impact on the DDR pathway in vivo. Our findings underly the unclear VCP's role in DDR in a KPNB1-dependent manner and provide an important theoretical basis for developing small-molecule inhibitors targeting this process.

Keywords:  DNA damage repair; KPNB1; VCP; nuclear translocation; withaferin A

DOI:  https://doi.org/10.1073/pnas.2416045122
Cell Stress Chaperones. 2025 May 01. pii: S1355-8145(25)00020-3. [Epub ahead of print] 100079

HDAC1 is involved in the destabilization of the HSF2 protein under non-stress and stress conditions.

Kevin Daupin, Véronique Dubreuil, Johanna K Ahlskog, Annalisa Verrico, Lea Sistonen, Valérie Mezger, Aurélie de Thonel.

  Heat shock transcription factors 1 and 2 (HSF1 and HSF2) are the major regulators of the cellular response to stressors, notably to heat shock and to oxidative stress. HSF1 and HSF2 are also important contributors in devasting human pathologies like cancer, neurodegenerative disorders, and neurodevelopmental disorders. Under physiological conditions, nuclear HSF2 is detected in only a few cell types in human adult healthy tissues. In contrast, HSF2 protein levels are elevated at some embryonic stages, but greatly vary among cell types and fluctuates during the cell cycle in diverse cell lines. HSF2 is a short-lived protein whose rapid turnover is controlled by the components of the ubiquitin-proteasome degradation pathway and the stabilization of HSF2 constitutes an important step that regulates its DNA-binding activity and mediates its roles in non-stress, physiological processes. The control of HSF2 abundancy is therefore critical for its regulatory roles in stress responses as well as under physiological conditions. In this regard, the fetal brain cortex is a singular context where HSF2 is strikingly abundant, exhibits constitutive DNA-binding activity and, by controlling a specific repertoire of target genes that play important roles at multiple steps of neurodevelopment. Recently, we showed that the lysine-acetyl-transferases CBP and EP300 stabilize the HSF2 protein under both unstressed and stressed conditions and that the integrity of the CBP/EP300-HSF2 pathway is important for neurodevelopment. Here, we identify the lysine-deacetylase HDAC1 as a novel HSF2-interacting protein partner and regulator, in an unbiased manner, and show that HSF2 and HDAC1 localize in the same cells in the developing mouse cortex and human cerebral organoids (hCOs). We also demonstrate that HDAC1, through its catalytic activity, destabilizes the HSF2 protein, through HSF2 poly-ubiquitination and proteasomal degradation, under both normal and stress conditions.

Keywords:  Heat shock factors (HSFs) · histone/lysine deacetylases HDACs · HSF2 ubiquitin proteasome degradation · stress · neurodevelopment · human cerebral organoids

DOI:  https://doi.org/10.1016/j.cstres.2025.100079