bims-cemest 2025-04-06 papers

bims-cemest

Biomed News

on Cell metabolism and stress

Issue of 2025–04–06
twelve papers selected by
Jessica Rosarda, Uniformed Services University

Remodelling of Cellular Protein Homeostasis by Enhanced ER-Mitochondrial Tethering.
Stress-dependent activation of PQM-1 orchestrates a second-wave proteostasis response for organismal survival.
Defective anterograde protein-trafficking contributes to endoplasmic reticulum-stress in a CLN1 disease model.
Mild activation of the mitochondrial unfolded protein response increases lifespan without increasing resistance to stress.
At the crossroads of calcium signaling, protein synthesis and neuropeptide release.
iPAR: a new reporter for eukaryotic cytoplasmic protein aggregation.
tRNA synthetase activity is required for stress granule and P-body assembly.
New Insights on Protein Folding and Misfolding: Histidine Behaviors.
Conversion of glutamate into proline by the leucine analog BCH enhances biphasic insulin secretion in pancreatic β-cells.
Protein aggregation identified in olfactory neuronal cells is associated with cognitive impairments in a subset of living schizophrenia patients.
Mitochondrial heat production: the elephant in the lab….
Essential Biology of Lipid Droplets.

Contact (Thousand Oaks). 2025 Jan-Dec;8:8 25152564251329704

Remodelling of Cellular Protein Homeostasis by Enhanced ER-Mitochondrial Tethering.

Elisa Tonelli, Justyna Malecka, Elettra Barberis, Camilla Romano, Emanuela Pessolano, Maria Talmon, Armando A Genazzani, Claudio Casali, Marco Biggiogera, Marcello Manfredi, Laura Tapella, Dmitry Lim, Giulia Dematteis.

  Alterations of endoplasmic reticulum (ER)-mitochondrial interaction have been associated with different pathological conditions, including neurodegenerative diseases, characterized by dysregulation of protein homeostasis. However, little is known about how enhanced ER-mitochondrial tethering affects cellular proteostatic machinery. Here, we transiently overexpressed synthetic ER-mitochondrial linkers (EMLs), stabilizing the ER-mitochondrial distance at ≤5 nm (denominated as 5 nm-EML) and ∼10 nm (10 nm-EML), in HeLa cells. No alterations were found in cell growth, although metabolic activity and total ATP were significantly reduced. In EML-expressing cells, global protein synthesis was significantly reduced, accompanied by a reduction of total PERK and eIF2α protein levels, but increased p-eIF2α. Unfolded protein response (UPR) markers ATF4 and ATF6 were upregulated, suggesting that enhanced ER-mitochondrial tethering deranges protein synthesis and induces a low-grade ER stress/UPR. To further investigate ER-mitochondrial tethering-induced protein dyshomeostasis, we performed shotgun mass spectrometry proteomics followed by bioinformatic analysis. Analysis of highly changed proteins and the most significantly overrepresented gene ontology (GO) terms revealed that ≤5 nm tethering preferentially affected the expression of proteins involved in RNA processing and splicing and proteasomal protein degradation, while ∼10 nm tethering preferentially affected protein translation. Both EMLs affected expression of proteins involved in mitochondrial bioenergetics and metabolism, defense against oxidative stress, ER protein homeostasis, signaling and secretion. Finally, lipidomic analysis suggests that 5 nm-EML and 10 nm-EML differentially affect lipid homeostasis. Altogether, our results suggest that enhanced ER-mitochondrial tethering leads to a profound remodeling of cellular protein homeostasis, which may play a key role in pathogenesis of Alzheimer's and other neurodegenerative diseases.

Keywords:  MAMs; MERCS; mitochondria-ER contact sites; proteostasis

DOI:  https://doi.org/10.1177/25152564251329704
bioRxiv. 2025 Mar 14. pii: 2025.03.11.642454. [Epub ahead of print]

Stress-dependent activation of PQM-1 orchestrates a second-wave proteostasis response for organismal survival.

Laura Jones, Valeria Uvarova, Daniel O'Brien, Holly McIntyre, Natalie R Cohen, Robert H Dowen, Patricija van Oosten-Hawle.

Stress responses are controlled by specialized stress-responsive proteostasis transcription factors that rapidly upregulate protein quality components to re-establish protein homeostasis and safeguard survival. Here we show that the zinc finger transcription factor PQM-1 is crucial for stress survival in response to thermal and oxidative challenges. We provide mechanistic insight into the regulation of PQM-1 during stress that depends on ILS-DAF-16 signaling, as well as phosphorylation on threonine residue 268 that is located within a conserved AKT motif. Our data show that in reproductively mature adults and during well-fed conditions, PQM-1 induction requires DAF-16 and occurs during the recovery period post heat shock. Moreover, PQM-1 co-localizes with DAF-16 in the nucleus during the stress recovery phase. This regulatory dependency on DAF-16 is bypassed under dietary restriction, allowing PQM-1 to promote stress resilience independent of the ILS pathway. During both conditions, PQM-1 is crucial for the upregulation of cytosolic and endoplasmic reticulum stress response genes required for organismal recovery and stress resilience. Our transcriptional and bioinformatic analysis reveals that PQM-1 regulates a distinct set of target genes during the stress recovery phase, suggesting that PQM-1 may be involved in vital secondary wave stress response. Thus, our findings uncover a previously unrecognized mechanism of stress-dependent PQM-1 activation that integrates multiple environmental cues to ensure proteostasis and organismal survival.

DOI: https://doi.org/10.1101/2025.03.11.642454
Neurobiol Dis. 2025 Mar 28. pii: S0969-9961(25)00106-8. [Epub ahead of print] 106890

Defective anterograde protein-trafficking contributes to endoplasmic reticulum-stress in a CLN1 disease model.

Nisha Plavelil, Abhilash P Appu, K C Gopal, Avisek Mondal, Neil Perkins, Anil B Mukherjee.

  Lysosomal storage disorders (LSDs) represent 70 inherited metabolic diseases, in most of which neurodegeneration is a devastating manifestation. The CLN1 disease is a fatal neurodegenerative LSD, caused by inactivating mutations in the CLN1 gene encoding palmitoyl-protein thioesterase-1 (PPT1). S-palmitoylation, a reversable posttranslational modification by saturated fatty acids (generally palmitate) facilitates endosomal trafficking of many proteins, especially in the brain. While palmitoyl-acyltransferases (called ZDHHCs) catalyze S-palmitoylation, depalmitoylation is mediated by palmitoyl-protein thioesterases (PPTs). We previously reported that in Cln1-/- mice, which mimic human CLN1-disease, endoplasmic reticulum (ER)-stress leads to unfolded protein response (UPR) contributing to neurodegeneration. However, the mechanism underlying ER-stress has remained elusive. The anterograde (ER to Golgi) protein-trafficking is mediated via COPII (coat protein complex II) vesicles, whereas the retrograde transport (Golgi to ER) is mediated by COPI vesicles. We hypothesized that dysregulated anterograde protein-trafficking causing stagnation of proteins in the ER leads to ER-stress in Cln1-/- mice. We found that the levels of five COPII vesicle-associated proteins (i.e. Sar1, Sec23, Sec24, Sec13 and Sec31) are significantly higher in the ER-fractions of cortical tissues from Cln1-/- mice compared with those from their WT littermates. Remarkably, all COPII proteins, except Sec13, undergo S-palmitoylation. Moreover, CLN8, a Batten disease-protein, requires dynamic S-palmitoylation (palmitoylation-depalmitoylation) for ER-Golgi trafficking. Intriguingly, Ppt1-deficiency in Cln1-/- mice impairs ER-Golgi trafficking of Cln8-protein along with several other COPII-associated proteins. We propose that impaired anterograde trafficking causes excessive accumulation of proteins in the ER causing ER-stress and UPR contributing to neurodegeneration in CLN1 disease.

Keywords:  CLN1 disease; ER-stress; Lysosomal storage disease; Neurodegeneration; Palmitoyl-protein thioesterase-1; S-palmitoylation; Unfolded protein response

DOI:  https://doi.org/10.1016/j.nbd.2025.106890
Open Biol. 2025 Apr;15(4): 240358

Mild activation of the mitochondrial unfolded protein response increases lifespan without increasing resistance to stress.

Alexa Di Pede, Bokang Ko, Abdelrahman AlOkda, Aura A Tamez González, Shusen Zhu, Jeremy M Van Raamsdonk.

  The mitochondrial unfolded protein response (mitoUPR) is a stress response pathway that responds to mitochondrial insults by altering gene expression to recover mitochondrial homeostasis. The mitoUPR is mediated by the stress-activated transcription factor ATFS-1 (activating transcription factor associated with stress 1). Constitutive activation of ATFS-1 increases resistance to exogenous stressors but paradoxically decreases lifespan. In this work, we determined the optimal levels of expression of activated ATFS-1 with respect to lifespan and resistance to stress by treating constitutively active atfs-1(et17) worms with different concentrations of RNA interference (RNAi) bacteria targeting atfs-1. We observed the maximum lifespan of atfs-1(et17) worms at full-strength atfs-1 RNAi, which was significantly longer than wild-type lifespan. Under the conditions of maximum lifespan, atfs-1(et17) worms did not show enhanced resistance to stress, suggesting a trade-off between stress resistance and longevity. The maximum resistance to stress in atfs-1(et17) worms occurred on empty vector. Under these conditions, atfs-1(et17) worms are short-lived. This indicates that constitutive activation of ATFS-1 can increase lifespan or enhance resistance to stress but not both, at the same time. Overall, these results demonstrate that constitutively active ATFS-1 can extend lifespan when expressed at low levels and that this lifespan extension is not dependent on the ability of ATFS-1 to enhance resistance to stress.

Keywords:  ATFS-1; Caenorhabditis elegans; ageing; genetics; mitochondrial unfolded protein response; stress resistance

DOI:  https://doi.org/10.1098/rsob.240358
Elife. 2025 Apr 02. pii: e106553. [Epub ahead of print]14

At the crossroads of calcium signaling, protein synthesis and neuropeptide release.

Jakob Rupert, Dragomir Milovanovic.

  By influencing calcium homeostasis, local protein synthesis and the endoplasmic reticulum, a small protein called Rab10 emerges as a crucial cytoplasmic regulator of neuropeptide secretion.

Keywords:  Rab10; endoplasmic reticulum; exocytosis; mouse; neuropeptide; neuroscience; protein synthesis; synaptic transmission

DOI:  https://doi.org/10.7554/eLife.106553
BMC Methods. 2025 ;2(1): 5

iPAR: a new reporter for eukaryotic cytoplasmic protein aggregation.

Sarah Lecinski, Jamieson A L Howard, Chris MacDonald, Mark C Leake.

   Background: Cells employ myriad regulatory mechanisms to maintain protein homeostasis, termed proteostasis, to ensure correct cellular function. Dysregulation of proteostasis, which is often induced by physiological stress and ageing, often results in protein aggregation in cells. These aggregated structures can perturb normal physiological function, compromising cell integrity and viability, a prime example being early onset of several neurodegenerative diseases. Understanding aggregate dynamics in vivo is therefore of strong interest for biomedicine and pharmacology. However, factors involved in formation, distribution and clearance of intracellular aggregates are not fully understood.
Methods: Here, we report an improved methodology for production of fluorescent aggregates in model budding yeast which can be detected, tracked and quantified using fluorescence microscopy in live cells. This new openly-available technology, iPAR (inducible Protein Aggregation Reporter), involves monomeric fluorescent protein reporters fused to a ∆ssCPY* aggregation biomarker, with expression controlled under the copper-regulated CUP1 promoter.
Results: Monomeric tags overcome challenges associated with non-physiological reporter aggregation, whilst CUP1 provides more precise control of protein production. We show that iPAR and the associated bioimaging methodology enables quantitative study of cytoplasmic aggregate kinetics and inheritance features in vivo. We demonstrate that iPAR can be used with traditional epifluorescence and confocal microscopy as well as single-molecule precise Slimfield millisecond microscopy. Our results indicate that cytoplasmic aggregates are mobile and contain a broad range of number of iPAR molecules, from tens to several hundred per aggregate, whose mean value increases with extracellular hyperosmotic stress.
Discussion: Time lapse imaging shows that although larger iPAR aggregates associate with nuclear and vacuolar compartments, we show directly, for the first time, that these proteotoxic accumulations are not inherited by daughter cells, unlike nuclei and vacuoles. If suitably adapted, iPAR offers new potential for studying diseases relating to protein oligomerization processes in other model cellular systems.
Supplementary Information: The online version contains supplementary material available at 10.1186/s44330-025-00023-w.

Keywords:  Cell ageing; Confocal microscopy; Inheritance; Protein aggregation; Saccharomyces cerevisiae; Single-molecule

DOI:  https://doi.org/10.1186/s44330-025-00023-w
bioRxiv. 2025 Mar 13. pii: 2025.03.10.642431. [Epub ahead of print]

tRNA synthetase activity is required for stress granule and P-body assembly.

Max Baymiller, Noah S Helton, Benjamin Dodd, Stephanie L Moon.

In response to stress, translation initiation is suppressed and ribosome runoff via translation elongation drives mRNA assembly into ribonucleoprotein (RNP) granules including stress granules and P-bodies. Defects in translation elongation activate the integrated stress response. If and how stalled ribosomes are removed from mRNAs during translation elongation stress to drive RNP granule assembly is not clear. We demonstrate the integrated stress response is induced upon tRNA synthetase inhibition in part via ribosome collision sensing. However, saturating levels of tRNA synthetase inhibitors do not induce stress granules or P-bodies and prevent RNP granule assembly upon exogenous stress. The loss of tRNA synthetase activity causes persistent ribosome stalls that can be released with puromycin but are not rescued by ribosome-associated quality control pathways. Therefore, tRNA synthetase activity is required for ribosomes to run off mRNAs during stress to scaffold cytoplasmic RNP granules. Our findings suggest ribosome stalls can persist in human cells and uniquely uncouple ribonucleoprotein condensate assembly from the integrated stress response.

DOI: https://doi.org/10.1101/2025.03.10.642431
ACS Chem Neurosci. 2025 Apr 02.

New Insights on Protein Folding and Misfolding: Histidine Behaviors.

Yue Sun, Hu Shi.

  Protein folding is crucial as it determines the three-dimensional structure and function of proteins, which are essential for biological processes, while misfolding can lead to the formation of aggregates and dysfunctional proteins, often associated with diseases. Histidine behaviors have been identified as a contributing factor to protein folding and misfolding due to changes in net charge and the diverse orientations of N/N-H groups on imidazole rings. In this viewpoint, we discuss misfolding diseases, the fundamental principles of histidine behaviors, and relevant studies in this field. Our current study helps elucidate histidine behaviors and their impact on secondary structure and aggregation characteristics, offering new insights into the mechanisms of histidine-related protein folding and misfolding.

Keywords:  Histidine behaviors; aggregation mechanism; deprotonated and protonated states; pathogenesis; protein folding and misfolding

DOI:  https://doi.org/10.1021/acschemneuro.5c00167
J Biol Chem. 2025 Mar 26. pii: S0021-9258(25)00298-4. [Epub ahead of print] 108449

Conversion of glutamate into proline by the leucine analog BCH enhances biphasic insulin secretion in pancreatic β-cells.

Sevda Gheibi, Luis Rodrigo Cataldo, Hamidreza Ardalani, Lisa Nocquet, Peter Spégel, Susanne G Straub, Geoffrey W G Sharp, Malin Fex, Hindrik Mulder.

  Biphasic insulin secretion, which fails in Type 2 Diabetes, can be provoked by various nutrient stimuli, glucose being the superior physiological one. To identify pathways that may play a role in β-cell stimulus-secretion coupling, we compared β-cell and islet functional, secretory, and metabolic responses to glucose and 2-aminobicyclo-(2,2,1)-heptane-2-carboxylic acid (BCH), a leucine analog, that acts as an allosteric activator of glutamate dehydrogenase (GDH). We employed a range of techniques, including insulin secretion assays, mitochondrial activity measurements, ATP/ADP ratio assessments, and cytosolic Ca2+ level quantifications. Metabolomics was used to analyze cellular metabolite profiles in response to glucose and BCH. Additionally, we investigated the role of proline synthesis by silencing ALDH18A1, encoding proline 5-carboxylate (P5C) synthase, in both clonal β-cells and human islets. BCH and glucose similarly induced a biphasic insulin response in INS-1 832/13 cells, parallelled by increased mitochondrial activity and raised ATP/ADP ratios, plasma membrane depolarization, and elevated cytosolic Ca2+ levels. Metabolomics revealed that proline levels increased significantly only in BCH-stimulated β-cells. Silencing ALDH18A1 disrupted insulin secretion in response to both glucose and BCH, accompanied by reduced cytosolic Ca2+ levels, ATP/ADP ratios, and mitochondrial activity. Our findings demonstrated that BCH-induced activation of GDH leads to the conversion of glutamate into proline, which apparently enhances β-cell stimulus-secretion coupling. This work identifies a previously unrecognized role of proline metabolism in β-cell function and provides novel insights into the complex regulation of insulin secretion.

Keywords:  BCH; Insulin secretion; glutamate dehydrogenase; proline; β-cells

DOI:  https://doi.org/10.1016/j.jbc.2025.108449
Mol Psychiatry. 2025 Apr 03.

Protein aggregation identified in olfactory neuronal cells is associated with cognitive impairments in a subset of living schizophrenia patients.

Leslie G Nucifora, Koko Ishizuka, Nagat El Demerdash, Brian J Lee, Michael T Imai, Carlos Ayala-Grosso, Gayane Yenokyan, Nicola G Cascella, Sandra Lin, David J Schretlen, Philip D Harvey, Russell L Margolis, Christopher A Ross, Akira Sawa, Frederick C Nucifora.

Schizophrenia is a heterogeneous disorder, and likely results from multiple pathophysiological mechanisms. Protein aggregation, resulting from disruption of protein homeostasis (proteostasis), has been implicated in many diseases, including cancer, cardiac and pulmonary diseases, muscle diseases, and neurodegenerative disorders, but is a relatively new pathophysiological hypothesis for schizophrenia. Genetic findings implicate proteostasis in schizophrenia, and individual proteins associated with the disorder may undergo aggregation. While there is some evidence of associations between genetic variants and protein aggregation, the extent to which genetic variations influence protein aggregation remains unknown. We have previously reported increased protein insolubility and increased ubiquitination of the insoluble protein fraction, two markers of protein aggregation, in human postmortem brains from a subset of patients with schizophrenia. In the present study, we investigate whether protein aggregation is observed in an independent model system, olfactory neuronal cells derived from living patients with schizophrenia, and examine the relationship between aggregation and patient clinical and cognitive status. We demonstrate that, as in postmortem brain, olfactory neurons from a subset of patients with schizophrenia exhibit protein aggregation, identified by increased protein insolubility and ubiquitination of the insoluble protein fraction, and by ubiquitin positive protein aggregates. Patients with protein aggregation exhibit more severe cognitive deficits than those without aggregation, as revealed by between-group comparisons and correlational analyses. Understanding the mechanisms of the aggregation process, the factors that differentiate individuals who develop aggregates from those who do not, and the relationship between aggregation and cell function, has important implications for the pathophysiology of schizophrenia, and may provide insight into disease heterogeneity and novel therapeutic targets.

DOI: https://doi.org/10.1038/s41380-025-02956-8
Trends Biochem Sci. 2025 Mar 31. pii: S0968-0004(25)00051-9. [Epub ahead of print]

Mitochondrial heat production: the elephant in the lab….

Pierre Rustin, Howard T Jacobs, Mügen Terzioglu, Paule Bénit.

  It has long been established that heat represents a major part of the energy released during the oxidation of mitochondrial substrates. However, with a few exceptions, the release of heat is rarely mentioned other than as being produced at the expense of ATP, without having any specific function. Here, after briefly surveying the literature on mitochondrial heat production, we argue for its cellular and organismal importance, sharing our opinions as to what could account for this unbalanced portrayal of mitochondrial energy transactions.

Keywords:  ATP; H(+)-ATPase; heat diffusion; mitochondria; nanoscale; respiratory chain

DOI:  https://doi.org/10.1016/j.tibs.2025.03.002
Annu Rev Biochem. 2025 Apr 01.

Essential Biology of Lipid Droplets.

Robert V Farese, Tobias C Walther.

Lipid droplets (LDs), long overlooked as inert cellular storage organelles, are now recognized for their complex and rich biology as membraneless organelles integral to cell metabolism. Significant advances have revealed that LDs are crucial for cellular processes that include the storage and retrieval of lipids for metabolic energy and membrane synthesis and the detoxification of lipids by sequestering them in the organelle's core. Here, we review current key aspects of LD biology, emphasizing insights into fundamental mechanisms of their formation, the mechanisms of protein targeting, new insights into LD turnover, and how LDs integrate into cellular metabolism. Where possible, we describe how these processes are important in physiology and how alterations in LD biology can lead to metabolic disease. We highlight unresolved questions and key challenges to be addressed for further advancing our understanding of LD biology and its implications for health and disease.

DOI: https://doi.org/10.1146/annurev-biochem-091724-013733