bims-celmim Biomed News
on Cellular and mitochondrial metabolism
Issue of 2025–05–11
twenty-six papers selected by
Marc Segarra Mondejar
  1. A lipid in transit - the journey of cholesterol into the heart of mitochondrial research.
  2. Exploring cellular metabolic kinetics through spectroscopic analysis of extracellular environments.
  3. The role of mitochondrial mRNA translation in cellular communication.
  4. A hidden cysteine in Fis1 targeted to prevent excessive mitochondrial fission and dysfunction under oxidative stress.
  5. Metabolic reprogramming driven by Ant2 deficiency augments T Cell function and anti-tumor immunity in mice.
  6. Mechanism and application of thiol-disulfide redox biosensors with a fluorescence-lifetime readout.
  7. Phase separation in mitochondrial fate and mitochondrial diseases.
  8. Dysregulated mast cell activation induced by diabetic milieu exacerbates the progression of diabetic peripheral neuropathy in mice.
  9. Msp1 and Pex19-Pex3 cooperate to achieve correct localization of Pex15 to peroxisomes.
  10. The oncoprotein SET promotes serine-derived one-carbon metabolism by regulating SHMT2 enzymatic activity.
  11. Astrocytic GLUT1 deletion in adult mice enhances glucose metabolism and resilience to stroke.
  12. SIRT2-mediated ACSS2 K271 deacetylation suppresses lipogenesis under nutrient stress.
  13. Endothelial cell metabolism in cardiovascular physiology and disease.
  14. Cryo-EM of Mitochondrial Complex I and ATP Synthase.
  15. Design of diverse, functional mitochondrial targeting sequences across eukaryotic organisms using variational autoencoder.
  16. Agent-based modeling of neuronal mitochondrial dynamics using intrinsic variables of individual mitochondria.
  17. RSEA: A Web Server for Pathway Enrichment Analysis of Metabolic Reaction Sets.
  18. A red-emitting, microenvironment-insensitive fluorophore for lysosome-specific imaging in live cells.
  19. Unveiling the intercompartmental signaling axis: Mitochondrial to ER Stress Response (MERSR) and its impact on proteostasis.
  20. Endoplasmic reticulum Nogo drives AgRP neuronal activation and feeding behavior.
  21. Unconventional secretion of PARK7 requires lysosomal delivery via chaperone-mediated autophagy and specialized SNARE complex.
  22. ANXA2 regulates mitochondrial function and cellular senescence of PDLCs via AKT/eNOS signaling pathway under high glucose conditions.
  23. Mechanistic study of modulating mitochondrial fission and fusion to ameliorate neuropathic pain in mice.
  24. Paraoxonase-like APMAP maintains endoplasmic-reticulum-associated lipid and lipoprotein homeostasis.
  25. Modular activation of macrophage-like cells by beta-2-microglobulin via mitochondria and the cGAS-STING pathway.
  26. Annexin A5 controls VDAC1-dependent mitochondrial Ca2+ homeostasis and determines cellular susceptibility to apoptosis.
  1. J Cell Sci. 2025 May 01. pii: jcs263907. [Epub ahead of print]138(9):
    A lipid in transit - the journey of cholesterol into the heart of mitochondrial research.
    Thomas Simmen, Luca Pellegrini.
      Mitochondrial cholesterol biology in non-steroidogenic tissues remains understudied in cell science. Although detecting cholesterol in mitochondria is challenging due to isolation difficulties, studies using mitoplasts (mitochondria stripped of their outer membrane) and imaging approaches confirm its presence in the inner mitochondrial membrane. Through analysis of published evidence and first-principles reasoning, we advance a model of cholesterol trafficking into and out of mitochondria via phospholipids at mitochondria-associated membranes (MAMs), challenging the traditional view of protein-driven transport. In this model, cholesterol enters mitochondria alongside phosphatidylserine and exits with phosphatidylethanolamine - either unchanged or in a hydroxylated form after modification by the enzyme CYP27A1. Strong cholesterol-phospholipid binding energies, ∼17 kcal/mol (71.128 kJ/mol), support this lipid-mediated mechanism, suggesting it complements protein-based pathways. Future research should explore how these mechanisms collaborate to regulate mitochondrial cholesterol trafficking. By rethinking cholesterol dynamics, we raise the possibility that cholesterol plays a larger role in mitochondrial biology, influencing membrane-dependent functions like cristae structure, respiratory efficiency and inter-organelle communication. This Perspective also highlights the potential of mitochondria to regulate both dietary and endogenous cholesterol flux and homeostasis across the cell.
    Keywords:  Lipid biology; Membrane trafficking; Organelles
    DOI:  https://doi.org/10.1242/jcs.263907
  2. Spectrochim Acta A Mol Biomol Spectrosc. 2025 May 01. pii: S1386-1425(25)00614-6. [Epub ahead of print]340 126308
    Exploring cellular metabolic kinetics through spectroscopic analysis of extracellular environments.
    Zohreh Mirveis, Nitin Patil, Hugh J Byrne.
      Studying the kinetics of metabolic pathways, such as glycolysis and glutaminolysis, is valuable due to their fundamental links to various diseases, including cancer. This study explores the potential of Attenuated Total Reflectance-Fourier Transform Infrared (ATR-FTIR) spectroscopy for analysing low concentrations of metabolites in extracellular media. It also evaluates the use of the Multivariate Curve Resolution-Alternating Least Squares (MCR-ALS) method to data mine the kinetic evolution of the spectroscopic signatures of the glycolysis metabolic pathway and to explore the impact of the presence of glutamine on it. By extracting samples at specific time intervals and drying them on the ATR crystal, ATR-FTIR could effectively measure individual metabolites of glucose, glutamine and lactate at low concentrations, providing clear spectra with strong correlations between peak absorbance and metabolite concentrations. In data mining, MCR-ALS successfully resolved two components, glucose and lactate, from time-series data of cellular glucose metabolism (glycolysis), showing approximately 28 % glucose consumption and 1 mM lactate production at a constant rate of 0.0016 min-1. However, when glutamine was introduced as a third component, the overlap of the peaks of glutamine and lactate limited the method's ability to deconvolute the data, highlighting constraints of MCR-ALS in complex mixtures.
    Keywords:  ATR-FTIR spectroscopy; Glutaminolysis; Glycolysis; MCR-ALS data analysis; Metabolic pathways kinetics; Spectral data mining
    DOI:  https://doi.org/10.1016/j.saa.2025.126308
  3. J Cell Sci. 2025 May 01. pii: jcs263753. [Epub ahead of print]138(9):
    The role of mitochondrial mRNA translation in cellular communication.
    Eleonora Zilio, Tim Schlegel, Marta Zaninello, Elena I Rugarli.
      Mitochondria are dynamic and heterogeneous organelles that rewire their network and metabolic functions in response to changing cellular needs. To this end, mitochondria integrate a plethora of incoming signals to influence cell fate and survival. A crucial and highly regulated node of cell-mitochondria communication is the translation of nuclear-encoded mitochondrial mRNAs. By controlling and monitoring the spatio-temporal translation of these mRNAs, cells can rapidly adjust mitochondrial function to meet metabolic demands, optimise ATP production and regulate organelle biogenesis and turnover. In this Review, we focus on how RNA-binding proteins that recognise nuclear-encoded mitochondrial mRNAs acutely modulate the rate of translation in response to nutrient availability. We further discuss the relevance of localised translation of these mRNAs for subsets of mitochondria in polarised cells. Finally, we highlight quality control mechanisms that monitor the translation process at the mitochondrial surface and their connections to mitophagy and stress responses. We propose that these processes collectively contribute to mitochondrial specialisation and signalling function.
    Keywords:  Cell signalling; Mitochondria; RNA-binding proteins; Ribosome quality control; Translation; mRNA
    DOI:  https://doi.org/10.1242/jcs.263753
  4. Nat Commun. 2025 May 06. 16(1): 4187
    A hidden cysteine in Fis1 targeted to prevent excessive mitochondrial fission and dysfunction under oxidative stress.
    Suman Pokhrel, Gwangbeom Heo, Irimpan Mathews, Shun Yokoi, Tsutomu Matsui, Ayori Mitsutake, Soichi Wakatsuki, Daria Mochly-Rosen.
      Fis1-mediated mitochondrial localization of Drp1 and excessive mitochondrial fission occur in human pathologies associated with oxidative stress. However, it is not known how Fis1 detects oxidative stress and what structural changes in Fis1 enable mitochondrial recruitment of Drp1. We find that conformational change involving α1 helix in Fis1 exposes its only cysteine, Cys41. In the presence of oxidative stress, the exposed Cys41 in activated Fis1 forms a disulfide bridge and the Fis1 covalent homodimers cause increased mitochondrial fission through increased Drp1 recruitment to mitochondria. Our discovery of a small molecule, SP11, that binds only to activated Fis1 by engaging Cys41, and data from genetically engineered cell lines lacking Cys41 strongly suggest a role of Fis1 homodimerization in Drp1 recruitment to mitochondria and excessive mitochondrial fission. The structure of activated Fis1-SP11 complex further confirms these insights related to Cys41 being the sensor for oxidative stress. Importantly, SP11 preserves mitochondrial integrity and function in cells during oxidative stress and thus may serve as a candidate molecule for the development of treatment for diseases with underlying Fis1-mediated mitochondrial fragmentation and dysfunction.
    DOI:  https://doi.org/10.1038/s41467-025-59434-6
  5. Nat Commun. 2025 May 08. 16(1): 4292
    Metabolic reprogramming driven by Ant2 deficiency augments T Cell function and anti-tumor immunity in mice.
    Omri Yosef, Leonor Cohen-Daniel, Oded Shamriz, Zahala Bar-On, Wajeeh Salaymeh, Amijai Saragovi, Ifat Abramovich, Bella Agranovich, Veronika Lutz, Joseph Tam, Anna Permyakova, Eyal Gottlieb, Magdalena Huber, Michael Berger.
      T cell activation requires a substantial increase in NAD+ production, often exceeding the capacity of oxidative phosphorylation (OXPHOS). To investigate how T cells adapt to this metabolic challenge, we generate T cell-specific ADP/ATP translocase-2 knockout (Ant2-/-) mice. Loss of Ant2, a crucial protein mediating ADP/ATP exchange between mitochondria and cytoplasm, induces OXPHOS restriction by limiting ATP synthase activity, thereby impeding NAD+ regeneration. Interestingly, Ant2-/- naïve T cells exhibit enhanced activation, proliferation and effector functions compared to wild-type controls. Metabolic profiling reveals that these T cells adopt an activated-like metabolic program with increased mitobiogenesis and anabolism. Lastly, pharmacological inhibition of ANT in wild-type T cells recapitulates the Ant2-/- phenotype and improves adoptive T cell therapy of cancer in mouse models. Our findings thus suggest that Ant2-deficient T cells bypass the typical metabolic reprogramming required for activation, leading to enhanced T cell function and highlighting the therapeutic potential of targeting ANT for immune modulation.
    DOI:  https://doi.org/10.1038/s41467-025-59310-3
  6. Proc Natl Acad Sci U S A. 2025 May 13. 122(19): e2503978122
    Mechanism and application of thiol-disulfide redox biosensors with a fluorescence-lifetime readout.
    Paul C Rosen, Andrew Glaser, Juan R Martínez-François, Daniel C Lim, Daniel J Brooks, Panhui Fu, Erica Kim, Dorothee Kern, Gary Yellen.
      Genetically encoded biosensors with changes in fluorescence lifetime (as opposed to fluorescence intensity) can quantify small molecules in complex contexts, even in vivo. However, lifetime-readout sensors are poorly understood at a molecular level, complicating their development. Although there are many sensors that have fluorescence-intensity changes, there are currently only a few with fluorescence-lifetime changes. Here, we optimized two biosensors for thiol-disulfide redox (RoTq-Off and RoTq-On) with opposite changes in fluorescence lifetime in response to oxidation. Using biophysical approaches, we showed that the high-lifetime states of these sensors lock the chromophore more firmly in place than their low-lifetime states do. Two-photon fluorescence lifetime imaging of RoTq-On fused to a glutaredoxin (Grx1) enabled robust, straightforward monitoring of cytosolic glutathione redox state in acute mouse brain slices. The motional mechanism described here is probably common and may inform the design of other lifetime-readout sensors; the Grx1-RoTq-On fusion sensor will be useful for studying glutathione redox in physiology.
    Keywords:  conformational change; fluorescence lifetime; genetically encoded fluorescent biosensor; glutathione redox
    DOI:  https://doi.org/10.1073/pnas.2503978122
  7. Proc Natl Acad Sci U S A. 2025 May 27. 122(21): e2422255122
    Phase separation in mitochondrial fate and mitochondrial diseases.
    Qingyi Chen, Sanqi An, Chuanlong Wang, Yanshuang Zhou, Xingguo Liu, Wenkai Ren.
      Mitochondria are central metabolic organelles that control cell fate and the development of mitochondrial diseases. Traditionally, phase separation directly regulates cell functions by driving RNA, proteins, or other molecules to concentrate into lipid droplets. Recent studies show that phase separation regulates cell functions and diseases through the regulation of subcellular organelles, particularly mitochondria. In fact, phase separation is involved in various mitochondrial activities including nucleoid assembly, autophagy, and mitochondria-related inflammation. Here, we outline the key mechanisms through which phase separation influences mitochondrial activities and the development of mitochondrial diseases. Insights into how phase separation regulates mitochondrial activities and diseases will help us develop interventions for related diseases.
    Keywords:  mitochondrial disease; mitochondrial dynamics; mitophagy; nucleoid assembly; phase separation
    DOI:  https://doi.org/10.1073/pnas.2422255122
  8. Nat Commun. 2025 May 05. 16(1): 4170
    Dysregulated mast cell activation induced by diabetic milieu exacerbates the progression of diabetic peripheral neuropathy in mice.
    Xiangyun Yao, Xin Wang, Rui Zhang, Lingchi Kong, Cunyi Fan, Yun Qian.
      Diabetic peripheral neuropathy (DPN), a common disorder in diabetes, is associated with severe microenvironment imbalance due to immunometabolic stress. However, the underlying mechanistic drivers remain unclear. Here, we generate a single-cell atlas of human peripheral nerves and identify cell-specific transcriptional changes in DPN as well as aberrant amplification of mast cells. Using streptozotocin-induced mouse diabetes models, we further find that glucose uptake mediated by GLUT3 in high-glucose (HG) diabetic milieu upregulates ERK1/2 phosphorylation in mouse mast cells. Sustained HG stimulation also induces aberrant mTOR hyperactivity, resulting in endoplasmic reticulum stress and mitochondrial oxidative stress, thereby impairing mitochondrial functions of mast cells. Dysregulated mast cells then degranulate and release histamine, tryptase and inflammatory factors into neural microenvironment to cause neuropathy in diabetic mice. Lastly, mice with mast cell deficiency are protected from the immune imbalance in nerves and progression of neuropathy. Our findings thus implicate dysregulated activation of mast cells as a potential driver in the progression of DPN.
    DOI:  https://doi.org/10.1038/s41467-025-59562-z
  9. FEBS J. 2025 May 09.
    Msp1 and Pex19-Pex3 cooperate to achieve correct localization of Pex15 to peroxisomes.
    Shunsuke Matsumoto, Yoshiki Kogure, Suzuka Ono, Tomoyuki Numata, Toshiya Endo.
      Yeast Msp1 is a dual-localized AAA-ATPase on the mitochondrial outer membrane (OM) and peroxisomal membrane. We previously showed that Msp1 transfers mistargeted tail-anchored (TA) proteins from mitochondria to the endoplasmic reticulum (ER) for degradation or delivery to their original destinations. However, the mechanism by which Msp1 in mitochondria and peroxisomes handles authentic peroxisomal TA proteins remains unclear. We show that newly synthesized Pex15 is targeted to peroxisomes primarily via the Pex19- and Pex3-dependent pathway. Mistargeted Pex15 on the mitochondrial OM is extracted by mitochondrial Msp1 and transferred to the ER via the guided-entry of TA proteins pathway for degradation or to peroxisomes via the Pex19-Pex3 pathway. Intriguingly, endogenous Pex15 localized in peroxisomes is also extracted from the membranes by peroxisomal Msp1 but returns to peroxisomes via the Pex19-Pex3 pathway. These results suggest that correct Pex15 localization to peroxisomes relies on not only the initial targeting by Pex19-Pex3 but also the constant re-routing by Msp1 and Pex19-Pex3.
    Keywords:  Msp1; Pex15; Pex19‐Pex3; mitochondria; peroxisome
    DOI:  https://doi.org/10.1111/febs.70132
  10. Proc Natl Acad Sci U S A. 2025 May 13. 122(19): e2412854122
    The oncoprotein SET promotes serine-derived one-carbon metabolism by regulating SHMT2 enzymatic activity.
    Zishan Jiao, Mi Zhang, Jingyuan Ning, Han Yao, Xiaojun Yan, Zhen Wu, Dexuan Wu, Yajing Liu, Meng Zhang, Lin Wang, Donglai Wang.
      Cancer cells frequently reprogram one-carbon metabolic pathways to fulfill their vigorous demands of biosynthesis and antioxidant defense for survival and proliferation. Dysfunction of oncogenes or tumor suppressor genes is critically involved in this process, but the precise mechanisms by which cancer cells actively trigger one-carbon metabolic alterations remain incompletely elucidated. Here, by using untargeted metabolomic analysis, we identify the oncoprotein SE translocation (SET) as a key regulator of one-carbon metabolism in cancer cells. SET physically interacts with mitochondrial SHMT2 and facilitates SHMT2 enzymatic activity. Loss of SET profoundly suppresses serine-derived one-carbon metabolic flux, whereas reexpression of ectopic SET leads to the opposite effect. Notably, although the presence of SHMT2 is critical for SET-mediated one-carbon metabolic alterations, the depletion of SHMT2 alone is insufficient to antagonize SET-induced tumor growth, probably due to functional compensation by its cytosolic isozyme SHMT1 upon SHMT2 knockdown. Instead, pharmacological targeting of cellular SHMT (including both SHMT1 and SHMT2) activity results in dramatic suppression of SET-induced tumor growth. Moreover, by using a Kras/Lkb1 mutation-driven lung tumor mouse model, we demonstrate that the loss of SET compromises both tumor formation and intratumoral SHMT2 enzymatic activity. Clinically, the overexpression of SET and SHMT2 is observed in lung tumors, both of which correlate with poor prognosis. Our study reveals a SET-SHMT2 axis in regulating serine-derived one-carbon metabolism and uncovers one-carbon metabolic reprogramming as a mechanism for SET-driven tumorigenesis.
    Keywords:  SET; SHMT2; enzymatic activity; one-carbon metabolism; tumor
    DOI:  https://doi.org/10.1073/pnas.2412854122
  11. Nat Commun. 2025 May 06. 16(1): 4190
    Astrocytic GLUT1 deletion in adult mice enhances glucose metabolism and resilience to stroke.
    Laetitia Thieren, Henri S Zanker, Jeanne Droux, Urvashi Dalvi, Matthias T Wyss, Rebecca Waag, Pierre-Luc Germain, Lukas M von Ziegler, Zoe J Looser, Ladina Hösli, Luca Ravotto, E Dale Abel, Johannes Bohacek, Susanne Wegener, L Felipe Barros, Mohamad El Amki, Bruno Weber, Aiman S Saab.
      Brain activity relies on a steady supply of blood glucose. Astrocytes express glucose transporter 1 (GLUT1), considered their primary route for glucose uptake to sustain metabolic and antioxidant support for neurons. While GLUT1 deficiency causes severe developmental impairments, its role in adult astrocytes remains unclear. Here, we show that astrocytes and neurons tolerate the inducible, astrocyte-specific deletion of GLUT1 in adulthood. Sensorimotor and memory functions remain intact in male GLUT1 cKO mice, indicating that GLUT1 loss does not impair behavior. Despite GLUT1 loss, two-photon glucose sensor imaging reveals that astrocytes maintain normal resting glucose levels but exhibit a more than two-fold increase in glucose consumption, indicating enhanced metabolic activity. Notably, male GLUT1 cKO mice display reduced infarct volumes following stroke, suggesting a neuroprotective effect of increased astrocytic glucose metabolism. Our findings reveal metabolic adaptability in astrocytes, ensuring glucose uptake and neuronal support despite the absence of their primary transporter.
    DOI:  https://doi.org/10.1038/s41467-025-59400-2
  12. Elife. 2025 May 07. pii: RP97019. [Epub ahead of print]13
    SIRT2-mediated ACSS2 K271 deacetylation suppresses lipogenesis under nutrient stress.
    Rezwana Karim, Wendi Teng, Cameron D Behram, Hening Lin.
      De novo lipogenesis is associated with the development of human diseases such as cancer, diabetes, and obesity. At the core of lipogenesis lies acetyl coenzyme A (CoA), a metabolite that plays a crucial role in fatty acid synthesis. One of the pathways contributing to the production of cytosolic acetyl-CoA is mediated by acetyl-CoA synthetase 2 (ACSS2). Here, we reveal that when cells encounter nutrient stress, particularly a deficiency in amino acids, Sirtuin 2 (SIRT2) catalyzes the deacetylation of ACSS2 at the lysine residue K271. This results in K271 ubiquitination and subsequently proteasomal degradation of ACSS2. Substitution of K271 leads to decreased ubiquitination of ACSS2, increased ACSS2 protein level, and thus increased lipogenesis. Our study uncovers a mechanism that cells employ to efficiently manage lipogenesis during periods of nutrient stress.
    Keywords:  SIRT2; acetyl-CoA synthetase 2; acetylation; biochemistry; cell biology; chemical biology; human; lipogenesis; mouse; nutrient stress; ubiquitylation
    DOI:  https://doi.org/10.7554/eLife.97019
  13. Nat Rev Cardiol. 2025 May 09.
    Endothelial cell metabolism in cardiovascular physiology and disease.
    Alessandra Pasut, Eleonora Lama, Amaryllis H Van Craenenbroeck, Jeffrey Kroon, Peter Carmeliet.
      Endothelial cells are multifunctional cells that form the inner layer of blood vessels and have a crucial role in vasoreactivity, angiogenesis, immunomodulation, nutrient uptake and coagulation. Endothelial cells have unique metabolism and are metabolically heterogeneous. The microenvironment and metabolism of endothelial cells contribute to endothelial cell heterogeneity and metabolic specialization. Endothelial cell dysfunction is an early event in the development of several cardiovascular diseases and has been shown, at least to some extent, to be driven by metabolic changes preceding the manifestation of clinical symptoms. Diabetes mellitus, hypertension, obesity and chronic kidney disease are all risk factors for cardiovascular disease. Changes in endothelial cell metabolism induced by these cardiometabolic stressors accelerate the accumulation of dysfunctional endothelial cells in tissues and the development of cardiovascular disease. In this Review, we discuss the diversity of metabolic programmes that control endothelial cell function in the cardiovascular system and how these metabolic programmes are perturbed in different cardiovascular diseases in a disease-specific manner. Finally, we discuss the potential and challenges of targeting endothelial cell metabolism for the treatment of cardiovascular diseases.
    DOI:  https://doi.org/10.1038/s41569-025-01162-x
  14. Annu Rev Biophys. 2025 May;54(1): 209-226
    Cryo-EM of Mitochondrial Complex I and ATP Synthase.
    Werner Kühlbrandt, Luis A M Carreira, Özkan Yildiz.
      Cryo-electron microscopy (cryo-EM) is the method of choice for investigating the structures of membrane protein complexes at high resolution under near-native conditions. This review focuses on recent cryo-EM work on mitochondrial complex I and ATP synthase. Single-particle cryo-EM structures of complex I from mammals, plants, and fungi extending to a resolution of 2 Å show different functional states, indicating consistent conformational changes of loops near the Q binding site, clusters of internal water molecules in the membrane arm, and an α-π transition in a membrane-spanning helix that opens and closes the proton transfer path. Cryo-EM structures of ATP synthase dimers from mammalian, yeast, and Polytomella mitochondria show several rotary states at a resolution of 2.7 to 3.5 Å. The new structures of complex I and ATP synthase are important steps along the way toward understanding the detailed molecular mechanisms of both complexes. Cryo-electron tomography and subtomogram averaging have the potential to resolve their high-resolution structures in situ.
    Keywords:  ATP synthase; complex I; cryo-electron microscopy; cryo-electron tomography; mitochondria; respiratory chain
    DOI:  https://doi.org/10.1146/annurev-biophys-060724-110838
  15. Nat Commun. 2025 May 04. 16(1): 4151
    Design of diverse, functional mitochondrial targeting sequences across eukaryotic organisms using variational autoencoder.
    Aashutosh Girish Boob, Shih-I Tan, Airah Zaidi, Nilmani Singh, Xueyi Xue, Shuaizhen Zhou, Teresa A Martin, Li-Qing Chen, Huimin Zhao.
      Mitochondria play a key role in energy production and metabolism, making them a promising target for metabolic engineering and disease treatment. However, despite the known influence of passenger proteins on localization efficiency, only a few protein-localization tags have been characterized for mitochondrial targeting. To address this limitation, we leverage a Variational Autoencoder to design novel mitochondrial targeting sequences. In silico analysis reveals that a high fraction of the generated peptides (90.14%) are functional and possess features important for mitochondrial targeting. We characterize artificial peptides in four eukaryotic organisms and, as a proof-of-concept, demonstrate their utility in increasing 3-hydroxypropionic acid titers through pathway compartmentalization and improving 5-aminolevulinate synthase delivery by 1.62-fold and 4.76-fold, respectively. Moreover, we employ latent space interpolation to shed light on the evolutionary origins of dual-targeting sequences. Overall, our work demonstrates the potential of generative artificial intelligence for both fundamental research and practical applications in mitochondrial biology.
    DOI:  https://doi.org/10.1038/s41467-025-59499-3
  16. iScience. 2025 May 16. 28(5): 112390
    Agent-based modeling of neuronal mitochondrial dynamics using intrinsic variables of individual mitochondria.
    Garrett M Fogo, Francisco J Torres Torres, Reagan L Speas, Anthony R Anzell, Thomas H Sanderson.
      Mitochondrial networks undergo remodeling to regulate form and function. The dynamic nature of mitochondria is maintained by the dueling processes of mitochondrial fission and fusion. Dysfunctional mitochondrial dynamics have been linked to debilitating diseases and injuries, suggesting mitochondrial dynamics as a promising therapeutic target. Increasing our understanding of the factors influencing mitochondrial dynamics will help inform therapeutic development. Utilizing live imaging of primary neurons, we analyzed how intrinsic properties of individual mitochondria influence their behavior. We found that size, shape, mitochondrial membrane potential, and protein oxidation predict mitochondrial fission and fusion. We constructed an agent-based model of mitochondrial dynamics, the mitochondrial dynamics simulation (MiDyS). In silico experiments of neuronal ischemia/reperfusion injury and antioxidant treatment illustrate the utility of MiDyS for testing hypothesized mechanisms of injury progression and evaluating therapeutic strategies. We present MiDyS as a framework for leveraging in silico experimentation to inform and improve the design of therapeutic trials.
    Keywords:  Cell biology; Molecular biology; Neuroscience
    DOI:  https://doi.org/10.1016/j.isci.2025.112390
  17. Biotechnol Bioeng. 2025 May 09.
    RSEA: A Web Server for Pathway Enrichment Analysis of Metabolic Reaction Sets.
    Merve Yarıcı, Furkan Cantürk, Serdar Dursun, Hatice Nur Aydın, Muhammed Erkan Karabekmez.
      Changes in biological pathways provide essential clues about metabolism. Genome-scale metabolic models (GEM) are network-based templates that computationally describe all stoichiometric associations and gene-protein reaction (GPR) relations found in an organism for all its metabolic genes and metabolites. Using reaction stoichiometry as input, GEMs mathematically simulate metabolic reaction fluxes occurring in an organism and predict changes in the metabolic system under the relevant condition. Multiple tools and approaches in the literature can capture fluxes sensitive to a given condition by using GEMs. However, functional enrichment analysis of these reaction lists in a systems biology perspective is not straightforward. Here, we introduce RSEA to annotate given reaction sets to significantly related metabolic pathways: Reaction Set Enrichment Analysis web server tool. RSEA converts given reaction list derived from GEMs into proper reaction identifiers and statistically analyze its enrichment in metabolic pathways. RSEA is designed to provide researchers with a practical and user-friendly platform to explore and interpret sets of reactions in biological pathways and freely available online (https://rseatool.com/).
    Keywords:  GPR rules; Genome‐Scale metabolic models; functional enrichment; metabolic pathways
    DOI:  https://doi.org/10.1002/bit.29020
  18. J Mater Chem B. 2025 May 08.
    A red-emitting, microenvironment-insensitive fluorophore for lysosome-specific imaging in live cells.
    Shabnam Mansuri, Subhadra Ojha, Sriram Kanvah.
      Lysosomes and the endoplasmic reticulum (ER) are vital for cellular homeostasis, degradation, and signaling, making them key imaging targets. However, existing fluorescent probes suffer from limitations such as pH sensitivity, poor photostability, and cytotoxicity. To overcome these challenges, we developed two red-emitting fluorophores, DM and MM, based on a rigid DCM scaffold with morpholine linkers. DM rapidly localizes to lysosomes within 10 minutes, exhibiting exceptional photostability, pH insensitivity, and resilience in live and fixed cells. MM initially targets the ER before redistributing to lysosomes, enabling studies of inter-organelle dynamics and lysosomal maturation. Both probes, excitable at 561 nm, emit in the red spectral region, reducing autofluorescence and phototoxicity while allowing deep tissue imaging. DM efficiently tracks lysosomal dynamics under normal and stressed conditions, including mitophagy and lysosome-mitochondria interactions. MM's dual-targeting behavior provides insights into ER-lysosome crosstalk, crucial for cellular signaling. Both dyes exhibit negligible cytotoxicity (up to 100 μM), ensuring prolonged imaging without disrupting the cellular function. Their rigid scaffold imparts high stability, making them versatile tools for studying lysosomal and ER-associated processes. DM and MM set a new standard for dynamic organelle imaging, advancing biomedical research on lysosomal biology and disease mechanisms.
    DOI:  https://doi.org/10.1039/d5tb00296f
  19. 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
  20. Cell Metab. 2025 Apr 30. pii: S1550-4131(25)00215-3. [Epub ahead of print]
    Endoplasmic reticulum Nogo drives AgRP neuronal activation and feeding behavior.
    Sungho Jin, Nal Ae Yoon, Mian Wei, Tilla Worgall, Luisa Rubinelli, Tamas L Horvath, Wei Min, Nadia Diano, Annarita di Lorenzo, Sabrina Diano.
      Lipid sensing in the hypothalamus contributes to the control of feeding and whole-body metabolism. However, the mechanism responsible for this nutrient-sensing process is ill-defined. Here, we show that Nogo-A, encoded by reticulon 4 (Rtn4) gene and associated with brain development and synaptic plasticity, regulates feeding and energy metabolism by controlling lipid metabolism in Agouti-related protein (AgRP) neurons. Nogo-A expression was upregulated in AgRP neurons of fasted mice and was associated with a significant downregulation of enzymes involved in sphingolipid de novo biosynthesis and the upregulation of key enzymes in intracellular lipid transport and fatty acid oxidation. Deletion of Rtn4 in AgRP neurons reduced body weight, ghrelin-induced AgRP activity and food intake, and fasting-induced AgRP activation, together with an increase in ceramide levels. Finally, high-fat-diet-induced obesity induced a significant downregulation of Rtn4 and increased ceramide levels in AgRP neurons, suggesting a role for Nogo in AgRP dysregulation in obesity. Taken together, our data reveal that Nogo-A drives AgRP neuronal activity and associated feeding behavior by controlling mitochondrial function and cellular lipid metabolism.
    Keywords:  AgRP; ceramides; endoplasmic reticulum; feeding behavior; hypothalamus; lipid metabolism; mitochondria
    DOI:  https://doi.org/10.1016/j.cmet.2025.04.005
  21. 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
  22. Sci Rep. 2025 May 06. 15(1): 15843
    ANXA2 regulates mitochondrial function and cellular senescence of PDLCs via AKT/eNOS signaling pathway under high glucose conditions.
    Yanlin Huang, Zejing Qiu, Chunhui Jiang, Qian Fang, Jiaye Wang, Mingfang Han, Yizhao Liu, Zehui Li.
      Diabetes mellitus is one of the risk factors for periodontitis. Patients with diabetes mellitus possess higher prevalence of periodontitis, more severe periodontal destruction, yet the underlying mechanisms of action are not yet clear. Annexin A2 (ANXA2) is a calcium-dependent phospholipid-binding protein widely involved in membrane repair, cytokinesis, and endocytosis. In this study, we explore whether ANXA2 is one of the associative links between diabetes and periodontitis and find out its underlying mechanisms. Cellular senescence and mitochondrial functions (ROS, mitochondrial morphology, mitochondrial autophagy) were observed. We observed that ANXA2 expression was down-regulated in Periodontal ligament cells (PDLCs) under high glucose conditions. Furthermore, overexpression of ANXA2 delayed high glucose-induced cellular senescence and mitochondrial dysfunction. β-galactosidase activity and the mRNA levels of the senescence-relative genes(p21,p16) were decreased, mitochondrial fracture and ROS release were reduced, and the expression of mitochondrial autophagy-related proteins (LC3,p62,Parkin) was enhanced. expression was enhanced. Mechanistically, we demonstrated that it can regulate the AKT/eNOS signaling pathway by knockdown and overexpression of ANXA2 which was measured using Western blotting (WB) assay to measure the expression of eNOS, p-eNOS Ser1177, Akt and p-Akt Ser473 proteins in PDLCs. After that, we used AKT and eNOS inhibitors to demonstrate the protective effect of ANXA2 on PDLCs under high glucose conditions. The above results suggest that ANXA2 has an anti-aging protective effect, attenuates high glucose-induced cellular senescence in PDLCs, and maintains mitochondrial homeostasis. Therefore, it would be valuable to further explore its role in the link between diabetes and periodontitis in future experiments.
    Keywords:  Cellular senescence; Diabetes; Mitochondria; Mitophagy; Periodontitis
    DOI:  https://doi.org/10.1038/s41598-025-00950-2
  23. Sci Rep. 2025 May 04. 15(1): 15571
    Mechanistic study of modulating mitochondrial fission and fusion to ameliorate neuropathic pain in mice.
    Liu Xie, Jing Cao, Yiran Xu, Qingqing Yang, Wanting Chang, Linna Song, Yanyan Sun.
      The emergence of neuropathic pain is significantly influenced by the impairment of mitochondrial processes. Ensuring the stability of mitochondrial activity requires a delicate equilibrium between the processes of mitochondrial fission and fusion. However, the specific alterations in mitochondrial activity across different models of neuropathic pain and the underlying mechanisms remain largely unclear. We developed a persistent compression injury (CCI) model targeting the sciatic nerve in mice. CCI induced pain like behaviors in mice, which were associated with increased levels of dynamin related protein 1 (Drp1) and decreased expression of the fusion protein OPA1 and an increase in the percentage of DRG nerve cell mitochondria in the fission form, and a decrease in percentage in the fusion form. Ultrastructural analysis showed that mitochondria in CCI mice were smaller in perimeter and area, adopting a more circular shape. Overexpression of OPA1 mediated by AAV attenuated pain hypersensitivity, lowered oxidative stress, and expanded mitochondrial circumference and area. Mdivi-1 treatment reduced pain, whereas blocking fusion with MYLS22 augmented pain and oxidative stress and further led to increased mitochondrial fragmentation. Our results illustrate that Mitochondria in DRG nerve cell are highly sensitive to neuropathic pain. Modulating mitochondrial fission and fusion through targeted gene overexpression and pharmacological inhibitors restores mitochondrial dynamics, reduces oxidative stress, and alleviates neuropathic pain in mice. These findings position mitochondrial dynamics as promising therapeutic targets for pain management.
    Keywords:  DRG; Fission and fusion; Mitochondrial; Neuropathic pain; Oxidative stress
    DOI:  https://doi.org/10.1038/s41598-025-99300-5
  24. 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
  25. Cell Immunol. 2025 May 05. pii: S0008-8749(25)00047-4. [Epub ahead of print]413 104962
    Modular activation of macrophage-like cells by beta-2-microglobulin via mitochondria and the cGAS-STING pathway.
    Josefine Kofoed Corneliussen, Helena Borland Madsen, Nadia Thaulov Zelander, Mogens Holst Nissen, Claus Desler.
      Beta-2-microglobulin (β2m) is a component of the major histocompatibility complex class I. β2m is released into cellular fluids in response to various stimuli, including pro-inflammatory cytokines. Elevated β2m levels have been found associated with autoimmune diseases such as rheumatoid arthritis, systemic lupus erythematosus, and Crohn's disease, as well as in various hematological cancers and viral infections. Despite an established correlation between immune activation of especially monocytes and macrophages, and circulating β2m levels, the causative relationship remains unclear. Here, we investigate the effects of exogenous β2m and a complement C1s cleaved form, dK58β2m, on two murine macrophage-like cell lines J774 and RAW. We demonstrate that β2m, and to a greater extent dK58β2m, can affect mitochondrial activity. Furthermore, the presence of IFN-γ amplifies the effect, causing altered bioenergetics, and increased production of mitochondrial reactive oxygen species and nitric oxide. In addition, we found activation of the cGAS-STING pathway by β2m and dK58β2m in the presence of IFN-γ. Only dK58β2m in combination with IFN-γ caused apoptosis and cell death. Our findings highlight the modular nature of a β2m-induced macrophage response, potentiated by dK58β2m and IFN-γ, and provide information on the underlying mechanisms responsible for the immune activation properties of β2m.
    Keywords:  Apoptosis; IFN-γ; Macrophage activation; Mitochondria; beta-2-microglobulin
    DOI:  https://doi.org/10.1016/j.cellimm.2025.104962
  26. EMBO J. 2025 May 09.
    Annexin A5 controls VDAC1-dependent mitochondrial Ca2+ homeostasis and determines cellular susceptibility to apoptosis.
    Furkan E Oflaz, Alexander I Bondarenko, Michael Trenker, Markus Waldeck-Weiermair, Benjamin Gottschalk, Eva Bernhart, Zhanat Koshenov, Snježana Radulović, Rene Rost, Martin Hirtl, Johannes Pilic, Aditya Karunanithi Nivedita, Adlet Sagintayev, Gerd Leitinger, Bent Brachvogel, Susanne Summerauer, Varda Shoshan-Barmatz, Roland Malli, Wolfgang F Graier.
      Annexin A5 (AnxA5) is a Ca2+-dependent phospholipid-binding protein associated with the regulation of intracellular Ca2+ homeostasis. However, the precise role of AnxA5 in controlling mitochondrial Ca2+ signaling remains elusive. Here, we introduce a novel function of AnxA5 in regulating mitochondrial Ca2+ signaling. Our investigation revealed that AnxA5 localizes at and in the mitochondria and orchestrates intermembrane space Ca2+ signaling upon high Ca2+ elevations induced by ER Ca2+ release. Proximity ligation assays and co-immunoprecipitation revealed a close association but no direct contact of AnxA5 with the voltage-dependent anion channel (VDAC1) in the outer mitochondrial membrane (OMM). In single-cell mitochondrial Ca2+ measurements and electrophysiological recordings, AnxA5 was found to enhance Ca2+ flux through the OMM by promoting the Ca2+-permeable state of VDAC1. By modulating intermembrane space Ca2+ signaling, AnxA5 shapes mitochondrial ultrastructure and influences the dynamicity of the mitochondrial Ca2+ uniporter. Furthermore, by controlling VDAC1's oligomeric state, AnxA5 is protective against cisplatin and selenite-induced apoptotic cell death. Our study uncovers AnxA5 as an integral regulator of VDAC1 in physiological and pathological conditions.
    Keywords:  Annexin-A5; Apoptotic Cell Death; Intermembrane Space Ca2⁺ Signaling; VDAC1 Ca2+ Permeability
    DOI:  https://doi.org/10.1038/s44318-025-00454-9
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