bims-cemest 2025-05-11 papers

bims-cemest

Biomed News

on Cell metabolism and stress

Issue of 2025–05–11
eight papers selected by
Jessica Rosarda, Uniformed Services University

ER-to-lysosome-associated degradation.
Molecular basis of SIFI activity in the integrated stress response.
HDAC1 is involved in the destabilization of the HSF2 protein under non-stress and stress conditions.
Emerging Patterns in Membrane Protein Folding Pathways.
m6A alters ribosome dynamics to initiate mRNA degradation.
mTORC1 cooperates with tRNA wobble modification to sustain the protein synthesis machinery.
Kinome screening identifies integrated stress response kinase EIF2AK1/HRI as a negative regulator of PINK1 mitophagy signaling.
BiDAC-dependent degradation of plasma membrane proteins by the endolysosomal system.

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
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
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
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
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
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
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
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