bims-cemest 2025-08-10 papers

bims-cemest

Biomed News

on Cell metabolism and stress

Issue of 2025–08–10
nine papers selected by
Jessica Rosarda, Uniformed Services University

Integral Synthesis and Clearance Analysis via DIA (ISDia) Reveals Coordinated Protein Dynamics Regulation during Endoplasmic Reticulum Stress.
A Three-Stage Assembly Program Governing Pancreatic, Plasma, Pituitary, and Bone Secretory Cell Differentiation: A Strategy to Augment Protein Delivery.
Optogenetic Clustering of Human IRE1 Reveals Differential Regulation of Transcription and mRNA Splice Isoform Abundance by the UPR.
A light-resuming strategy as a screening method for selecting Sec61 inhibitors down-modulating PD-L1 expression.
Natural SEL1L variants rescue a model of NGLY1 deficiency and modify ERAD function and proteasome sensitivity.
The AMPK Pathway: Molecular Rejuvenation of Metabolism and Mitochondria.
CRISPR RiPCA for Investigating eIF4E-m7GpppX Capped mRNA Interactions.
NAC controls nascent chain fate through tunnel sensing and chaperone action.
Two successive oligomeric Munc13 assemblies scaffold vesicle docking and SNARE assembly to support neurotransmitter release.

bioRxiv. 2025 Jul 30. pii: 2025.07.23.666381. [Epub ahead of print]

Integral Synthesis and Clearance Analysis via DIA (ISDia) Reveals Coordinated Protein Dynamics Regulation during Endoplasmic Reticulum Stress.

Yue Dou, Danny Qiu, Vivien Li, Maja E Wierzbińska, Gregory R Keele, Wenpeng Liu, Jie Yang, Joao A Paulo, Ling Qi, Tian Zhang.

Endoplasmic Reticulum (ER) stress disrupts protein homeostasis and impacts protein dynamics, driving cellular responses critical for survival, development and disease. However, no current proteome-wide technology enables simultaneous identification of proteins undergoing altered synthesis and clearance and distinguish their relative contribution during ER stress. To fill this gap, we developed Integral Synthesis and clearance analysis via DIA (ISDia), a robust mass spectrometry-based platform that integrates pulsed-SILAC labeling with data-independent acquisition (DIA) to quantify heavy and light peptide changes and determine the drivers of protein dynamics with high proteome coverage under non-steady-state conditions. Using ISDia, we uncover diverse regulatory mechanisms by which protein synthesis and clearance are modulated to control protein abundances during ER stress, revealing PERK dependent and independent regulatory mechanisms across subcellular compartments, complexes and isoforms. These findings highlight the potential of ISDia as a powerful and widely applicable platform for elucidating protein dynamic regulatory mechanisms.

DOI: https://doi.org/10.1101/2025.07.23.666381
J Biol Chem. 2025 Aug 05. pii: S0021-9258(25)02413-5. [Epub ahead of print] 110562

A Three-Stage Assembly Program Governing Pancreatic, Plasma, Pituitary, and Bone Secretory Cell Differentiation: A Strategy to Augment Protein Delivery.

Joseph P Bidwell, Alexander G Robling, Ronald C Wek.

  Defective secretory cell function underlies many diseases, and recent therapeutic strategies have focused on enhancing protein synthesis and delivery by targeting the secretory machinery of mature cells. However, mature differentiated cells appear to have intrinsic limits to their secretory capacity. In this review, we propose new strategies for engineering these cells to overcome these limits on secretion. The integrated stress response (ISR) and the related unfolded protein response (UPR) are stress adaptation systems that modulate transcriptional and translational programs of gene expression. These programs drive remodeling of cellular architecture to boost protein production and trafficking but also play critical roles in the differentiation of secretory cells. This dual function suggests that the limits of the secretory capacity of mature cells are pre-programmed during development. A potentially more effective therapeutic approach to expand protein secretion may lie in reprogramming the secretory capacity early in differentiation. Two additional transcriptional programs work in concert with the ISR and UPR to shape differentiated cell identities, their secretory outputs, and production capacity. The first involves lineage-determining transcription factors that define both cell type and secretory products. The second involves 'scaling factors' that set the magnitude of the cell's protein synthesis and secretion capacity. We explore the mechanisms by which these three programs-lineage specification, scaling, and stress adaptation-interact to define and potentially enhance secretory capacity. We will illustrate this integrated model across several secretory cell types, including pancreatic, plasma, pituitary, and bone secretory cells, with emphasis on applications to improve therapeutic outcomes in osteoporosis.

Keywords:  Integrated stress response; lineage-determining factor; scaling factor; unfolded protein response

DOI:  https://doi.org/10.1016/j.jbc.2025.110562
bioRxiv. 2025 Jul 21. pii: 2025.07.16.665212. [Epub ahead of print]

Optogenetic Clustering of Human IRE1 Reveals Differential Regulation of Transcription and mRNA Splice Isoform Abundance by the UPR.

Jacob W Smith, Damien B Wilburn, Vladislav Belyy.

Inositol-requiring enzyme 1 (IRE1) is one of three known sensor proteins that respond to homeostatic perturbations in the metazoan endoplasmic reticulum. The three sensors collectively initiate an intertwined signaling network called the Unfolded Protein Response (UPR). Although IRE1 plays pivotal roles in human health and development, understanding its specific contributions to the UPR remains a challenge due to signaling crosstalk from the other two stress sensors. To overcome this problem, we engineered a light-activatable version of IRE1 and probed the transcriptomic effects of IRE1 activity in isolation from the other branches of the UPR. We demonstrate that 1) oligomerization alone is sufficient to activate IRE1 in human cells, 2) IRE1's transcriptional response evolves substantially under prolonged activation, and 3) the UPR induces major changes in mRNA splice isoform abundance in an IRE1-independent manner. Our data reveal previously unknown targets of IRE1 transcriptional regulation and direct degradation. Additionally, the tools developed here will be broadly applicable for precise dissection of signaling networks in diverse cell types, tissues, and organisms.

DOI: https://doi.org/10.1101/2025.07.16.665212
Nat Commun. 2025 Aug 06. 16(1): 7243

A light-resuming strategy as a screening method for selecting Sec61 inhibitors down-modulating PD-L1 expression.

Fulvia Vitale, Gianluca Scerra, Laura Marrone, Anna Di Micco, Magda Cannata Serio, Amarawan Intasiri, Giuseppina Amodio, Vittorio Cirillo, Paolo Remondelli, Antonietta Luongo, Raffaella Bonavita, Maria Gabriella Caporaso, Franck Perez, Maurizio Renna, Thomas W Bell, Simona Romano, Massimo D'Agostino.

The perturbation of protein translocation into the secretory pathway using Sec61 translocon inhibitors is a novel and promising strategy for tackling many pathological situations, including cancer and viral infections. However, a highly sensitive and direct screening platform for selecting Sec61 inhibitors is unavailable. Here, we develop a "resuming luminescence upon translocation interference" (RELITE) assay capable of selecting Sec61 inhibitors in a single round of screening. This assay exploits the inactivation of firefly luciferase, once translocated into the endoplasmic reticulum (ER), and the possibility of diverting and "re-lighting" luciferase into the cytosol by a Sec61 inhibitor. Using this method, we select small molecules capable of hampering the protein expression of the PD-L1 immune checkpoint by interfering with its ER translocation and delivering it for degradation. In conclusion, our screening method will greatly facilitate the selection of Sec61 inhibitors for down-modulating the expression of many disease-relevant proteins.

DOI: https://doi.org/10.1038/s41467-025-62439-w
PLoS Genet. 2025 Aug 07. 21(8): e1011823

Natural SEL1L variants rescue a model of NGLY1 deficiency and modify ERAD function and proteasome sensitivity.

Travis K Tu'ifua, Clement Y Chow.

N-glycanase 1 (NGLY1) deficiency is an ultra-rare disease caused by autosomal recessive loss-of-function mutations in the NGLY1 gene. NGLY1 removes N-linked glycans from glycoproteins in the cytoplasm and is thought to help clear misfolded proteins from the endoplasmic reticulum (ER) through the ER associated degradation (ERAD) pathway. Despite this, the physiological significance of NGLY1 in ERAD is not understood. The best characterized substrate of NGLY1 is NRF1, a transcription factor that upregulates proteasome expression and the proteasome bounce-back response. We previously performed a genetic modifier screen using a Drosophila model of NGLY1 deficiency and identified potential modifiers that alter the lethality of the model. We identified two protein-coding variants in Hrd3/SEL1L: S780P and Δ806-809. Both variants are localized to the SEL1L cytoplasmic tail, an uncharacterized domain. SEL1L is a component of the ERAD complex that retrotranslocates misfolded proteins from the ER to the cytoplasm for degradation. We used CRISPR to generate fly lines carrying these SEL1L variants in a common genetic background and tested them with our model of NGLY1 deficiency. Validating our previous screen, the SEL1LS780P and SEL1LΔ806-809 variants increased the survival of the NGLY1 deficiency model, compared to the SEL1LS780 variant. To determine how these SEL1L variants were modifying lethality in NGLY1 deficiency, we interrogated the ERAD and NRF1 signaling pathways. We found that the SEL1LS780P and SEL1LΔ806-809 variants improve resistance to ER stress, with enhanced ERAD function as a likely contributing mechanism. This effect depends on NGLY1 activity, further implicating NGLY1 in general ERAD function. We also found that, in heterozygous NGLY1 null flies, these variants protect against some defects like increased lethality caused by proteasome inhibition. These results provide new insights into the role of SEL1L in the disease pathogenesis of NGLY1 deficiency. SEL1L is a strong candidate modifier gene in patients, where variability in presentation is common.

DOI: https://doi.org/10.1371/journal.pgen.1011823
Annu Rev Cell Dev Biol. 2025 Aug 06.

The AMPK Pathway: Molecular Rejuvenation of Metabolism and Mitochondria.

Nazma Malik, Reuben J Shaw.

Cells must constantly adapt their metabolism to the availability of nutrients and signals from their environment. Under conditions of limited nutrients, cells need to reprogram their metabolism to rely on internal stores of glucose and lipid metabolites. From the emergence of eukaryotes to the mitochondria as the central source of ATP to hundreds of other metabolites required for cellular homeostasis, survival, and proliferation, cells had to evolve sensors to detect even modest changes in mitochondrial function in order to safeguard cellular integrity and prevent energetic catastrophe. Homologs of AMP-activated protein kinase (AMPK) are found in all eukaryotic species and serve as an ancient sensor of conditions of low cellular energy. Here we explore advances in how AMPK modulates core processes underpinning the mitochondrial life cycle and how it serves to restore mitochondrial health in parallel with other beneficial metabolic adaptations.

DOI: https://doi.org/10.1146/annurev-cellbio-120420-094431
ACS Chem Biol. 2025 Aug 06.

CRISPR RiPCA for Investigating eIF4E-m7GpppX Capped mRNA Interactions.

Gabriela Vega-Hernández, Jesse Duque, Brandon J C Klein, Dalia M Soueid, Jason C Rech, Hui Wang, Wenhui Zhou, Amanda L Garner.

Post-transcriptional modifications expand the information encoded by an mRNA. These dynamic and reversible modifications are specifically recognized by reader RNA-binding proteins (RBPs), which mediate the regulation of gene expression, RNA processing, localization, stability, and translation. Given their crucial functions, any disruptions in the normal activity of these readers can have significant implications for cellular health. Consequently, the dysregulation of these RBPs has been associated with neurodegenerative disorders, cancers, and viral infections. Therefore, there has been growing interest in targeting reader RBPs as a potential therapeutic strategy since developing molecules that restore proper RNA processing and function may offer a promising avenue for treating diseases. In this work, we coupled our previously established live-cell RNA-protein interaction (RPI) assay, RNA interaction with Protein-mediated Complementation Assay (RiPCA), with CRISPR technology to build a new platform, CRISPR RiPCA. As a model for development, we utilized the interaction of eukaryotic translation initiation factor 4E (eIF4E), a reader RBP that binds to the m7GpppX cap present at the 5' terminus of coding mRNAs, with an m7G capped RNA substrate. Using eIF4E CRISPR RiPCA, we demonstrate our technology's potential for measuring on-target activity of inhibitors of the eIF4E RPI of relevance to cancer drug discovery.

DOI: https://doi.org/10.1021/acschembio.5c00471
bioRxiv. 2025 Jul 31. pii: 2025.07.27.667080. [Epub ahead of print]

NAC controls nascent chain fate through tunnel sensing and chaperone action.

Jae Ho Lee, Laurenz Rabl, Martin Gamerdinger, Vaishali Goyal, Katrin Michaela Khakzar, Natalia Moreira Barbosa, Juliana Abramovich, Fabian Morales-Polanco, Ann-Kathrin Köhler, Ekaterina Samatova, Marina V Rodnina, Elke Deuerling, Judith Frydman.

The nascent polypeptide-associated complex (NAC) is a conserved ribosome-bound factor with essential yet incompletely understood roles in protein biogenesis. Here, we show that NAC is a multifaceted regulator that coordinates translation elongation, cotranslational folding, and organelle targeting through distinct interactions with nascent polypeptides both inside and outside the ribosome exit tunnel. Using NAC-selective ribosome profiling in C. elegans , we identify thousands of sequence-specific NAC binding events across the nascent proteome, revealing broad cotranslational engagement with hydrophobic and helical motifs in cytosolic, nuclear, ER, and mitochondrial proteins. Unexpectedly, we discover an intra-tunnel sensing mode, where NAC engages ribosomes with extremely short nascent polypeptides inside the exit tunnel in a sequence-specific manner. These early NAC interactions induce an early elongation slowdown that tunes ribosome flux and prevent ribosome collisions, linking NAC's chaperone activity to kinetic control of translation. We propose that NAC action protects aggregation-prone intermediates by shielding amphipathic helices thus promoting cytonuclear folding and supporting mitochondrial membrane protein biogenesis and ER targeting by early recognition of signal sequences and transmembrane domain. Our findings establish NAC as an early-acting, multifaceted orchestrator of cotranslational proteostasis, with distinct mechanisms of action on nascent chains depending on their sequence features and subcellular destinations.

DOI: https://doi.org/10.1101/2025.07.27.667080
Nat Commun. 2025 Aug 05. 16(1): 7222

Two successive oligomeric Munc13 assemblies scaffold vesicle docking and SNARE assembly to support neurotransmitter release.

Manindra Bera, Kirill Grushin, R Venkat Kalyana Sundaram, Jasmine S Hinzen, Joyce Chen, Atrouli Chatterjee, Abhijith Radhakrishnan, Seong Lee, Murugesh Padmanarayana, Jeff Coleman, Frédéric Pincet, James E Rothman, Jeremy S Dittman.

The critical protein Munc13 serves numerous roles in the docking and priming of synaptic vesicles. On the presynaptic plasma membrane, Munc13 is organized into nanoclusters corresponding to release sites where synaptic vesicles dock and fuse. However, it is currently not known whether there is any organization of Munc13 monomers within the nanoclusters. Recent work suggests that Munc13 may spontaneously self-organize into homo-oligomers, raising the possibility that synaptic nanoclusters comprise organized assemblies of Munc13. Here we investigate the functional impact of two distinct Munc13 core domain oligomers comprising C1-C2B-MUN-C2C both in vitro and in vivo. Interface mutations that specifically destabilized oligomeric assemblies of Munc13 disrupted vesicle docking, trans-SNARE formation, and Ca2+-triggered vesicle fusion in vitro and impaired neurotransmitter secretion and motor nervous system function in vivo. We suggest that a sequence of oligomeric Munc13 complexes rapidly couple vesicle docking to vesicle priming via the assembly of a precise number of SNAREs.

DOI: https://doi.org/10.1038/s41467-025-62420-7