bims-celmim 2025-03-23 papers

bims-celmim

Biomed News

on Cellular and mitochondrial metabolism

Issue of 2025–03–23
28 papers selected by
Marc Segarra Mondejar

Mitochondrial fission - changing perspectives for future progress.
Unspliced XBP1 enhences metabolic reprogramming in colorectal cancer cells by interfering with the mitochondrial localization of MGME1.
Highly spatial-temporal electrochemical profiling of molecules trafficking at a single mitochondrion in one living cell.
A splendid molecular factory: De- and reconstruction of the mammalian respiratory chain.
Mitochondria: An overview of their origin, genome, architecture, and dynamics.
Exploring Human Brain Metabolism via Genome-Scale Metabolic Modeling with Highlights on Multiple Sclerosis.
TMBIM-2 orchestrates systemic mitochondrial stress response via facilitating Ca2+ oscillations.
Moonlighting Enzymes at the Interface Between Metabolism and Epigenetics.
Protein succinylation mechanisms and potential targeted therapies in urinary disease.
Mitoregulin, a tiny protein at the crossroads of mitochondrial functioning, stress, and disease.
In-cell architecture of the mitochondrial respiratory chain.
Bioengineering the metabolic network of CAR T cells with GLP-1 and Urolithin A increases persistence and long-term anti-tumor activity.
Emerging Approaches for Studying Lipid Dynamics, Metabolism, and Interactions in Cells.
Septin5 deletion enhances β-cell exocytosis by releasing microtubule-tethered insulin granules onto plasma membrane.
Mitochondrial reactive oxygen species regulate acetyl-CoA flux between cytokine production and fatty acid synthesis in effector T cells.
A metabolic shift to the serine pathway induced by lipids fosters epigenetic reprogramming in nontransformed breast cells.
Ubiquinol-mediated suppression of mitochondria-associated ferroptosis is a targetable function of lactate dehydrogenase B in cancer.
Pak1 dysregulates Pyruvate metabolism in PDAC cells by exerting a phosphorylation-mediated regulatory effect on PDHA1.
Dynamics of Neuronal and Astrocytic Energy Molecules in Epilepsy.
Decoding in-cell respiratory enzyme dynamics by label-free in situ electrochemistry.
Acute diacylglycerol production activates critical membrane-shaping proteins leading to mitochondrial tubulation and fission.
Quantitative mapping of key glucose metabolic rates in the human brain using dynamic deuterium magnetic resonance spectroscopic imaging.
Organelle-Specific Quantum Thermometry Using Fluorescent Nanodiamonds: Insights into Cellular Metabolic Thermodynamics.
STIM1/2 maintain signaling competence at ER-PM contact sites during neutrophil spreading.
Integrative single-cell metabolomics and phenotypic profiling reveals metabolic heterogeneity of cellular oxidation and senescence.
Definition of the human mitochondrial TOM interactome reveals TRABD as new interacting protein.
Metabolic Reprogramming into a Glycolysis Phenotype Induced by Extracellular Vesicles Derived from Prostate Cancer Cells.
Proteasome dynamics in response to metabolic changes.

J Cell Sci. 2025 May 01. pii: jcs263640. [Epub ahead of print]138(9):

Mitochondrial fission - changing perspectives for future progress.

Sukrut C Kamerkar, Ao Liu, Henry N Higgs.

  Mitochondrial fission is important for many aspects of cellular homeostasis, including mitochondrial distribution, stress response, mitophagy, mitochondrially derived vesicle production and metabolic regulation. Several decades of research has revealed much about fission, including identification of a key division protein - the dynamin Drp1 (also known as DNM1L) - receptors for Drp1 on the outer mitochondrial membrane (OMM), including Mff, MiD49 and MiD51 (also known as MIEF2 and MIEF1, respectively) and Fis1, and important Drp1 regulators, including post-translational modifications, actin filaments and the phospholipid cardiolipin. In addition, it is now appreciated that other organelles, including the endoplasmic reticulum, lysosomes and Golgi-derived vesicles, can participate in mitochondrial fission. However, a more holistic understanding of the process is lacking. In this Review, we address three questions that highlight knowledge gaps. First, how do we quantify mitochondrial fission? Second, how does the inner mitochondrial membrane (IMM) divide? Third, how many 'types' of fission exist? We also introduce a model that integrates multiple regulatory factors in mammalian mitochondrial fission. In this model, three possible pathways (cellular stimulation, metabolic switching or mitochondrial dysfunction) independently initiate Drp1 recruitment at the fission site, followed by a shared second step in which Mff mediates subsequent assembly of a contractile Drp1 ring. We conclude by discussing some perplexing issues in fission regulation, including the effects of Drp1 phosphorylation and the multiple Drp1 isoforms.

Keywords:  Drp1 receptors; Dynamin related protein-1; Inner mitochondrial membrane division; Mitochondrial fission

DOI:  https://doi.org/10.1242/jcs.263640
Biochem Biophys Res Commun. 2025 Mar 11. pii: S0006-291X(25)00327-4. [Epub ahead of print]757 151613

Unspliced XBP1 enhences metabolic reprogramming in colorectal cancer cells by interfering with the mitochondrial localization of MGME1.

Jiandong Zhang, Suyang Zhang, Fei Yu, Yuting Wan, Mingyue Wu, Can Huang.

  Tumor cells undergo metabolic reprogramming, which makes them tend to utilize anaerobic glycolysis rather than oxidation to rapidly produce energy and intermediate products required for proliferation. In this process, mitochondria inevitably undergo corresponding alterations; however, the specific alterations in mitochondria across different cancer types and the mechanisms governing these changes remain poorly understood. This study demonstrated that unspliced X-box binding protein 1 (XBP1-u) inhibits the translocation of mitochondrial genome maintenance exonuclease 1 (MGME1) into mitochondria by binding to the mitochondrial targeting sequence (MTS) of MGME1. This interaction results in the accumulation of mitochondrial 7sDNA, a reduction in mitochondrial DNA copy number, and a decrease in mitochondrial abundance. Consequently, this shift enhances the production of glycolysis and pentose phosphate pathway intermediates, thereby promoting the proliferation of colorectal cancer (CRC) cells. Our findings elucidated the critical mechanism by which XBP1-u enhances metabolic reprogramming by modulating mitochondrial biogenesis, and uncovered a novel role of MGME1 in the progression of CRC.

Keywords:  MGME1; Metabolic reprogramming; Mitochondrial number; Warburg effect; XBP1-u

DOI:  https://doi.org/10.1016/j.bbrc.2025.151613
Proc Natl Acad Sci U S A. 2025 Mar 25. 122(12): e2424591122

Highly spatial-temporal electrochemical profiling of molecules trafficking at a single mitochondrion in one living cell.

Kang Liu, Lina Wu, Yuanyuan Ma, Desheng Chen, Rujia Liu, Xiaobo Zhang, Dechen Jiang, Rongrong Pan.

  Simultaneous profiling of multiple molecules trafficking at a single organelle and the surrounding cytosol within a living cell is crucial for elucidating their functions, necessitating advanced techniques that provide high spatial-temporal resolution and molecule specificity. In this study, we present an electrochemical nanodevice based on a θ-nanopipette designed to coanalyze calcium ions (Ca2+) and reactive oxygen species (ROS) at a single mitochondrion and its surrounding cytosol, thereby enhancing our understanding of their trafficking within the signaling pathways of cellular autophagy. Two independent nanosensors integrated within the channels of the θ-nanopipette spatially isolate a single target mitochondrion from the cytosol and simultaneously measure the release of Ca2+ and ROS with high spatial-temporal resolution. Dynamic tracking reveals the direct trafficking of lysosomal Ca2+ to the mitochondrion rather than to the cytosol, which triggers ROS-induced ROS release within the mitochondria. Furthermore, highly temporal and concurrent observations revealed a second burst of Ca2+ in both the mitochondrion and the cytosol, which is not consistent with the change in ROS. These dynamic data elucidate the potential role of a beneficial feedback loop between the Ca2+ signaling pathway and the subsequent generation of mitochondrial ROS in ML-SA-induced autophagy. More importantly, this innovative platform facilitates detailed profiling of the molecular interactions between trafficking molecules within the mitochondria and the adjacent cytosolic environment, which is hardly realized using the current superresolution optical microscopy.

Keywords:  electrochemical analysis; highly spatial–temporal profiling; molecule trafficking; single living cell; single mitochondrion

DOI:  https://doi.org/10.1073/pnas.2424591122
Proc Natl Acad Sci U S A. 2025 Mar 25. 122(12): e2416162122

A splendid molecular factory: De- and reconstruction of the mammalian respiratory chain.

Lukas Rimle, Ben P Phillips, Isabela M Codo Costa Barra, Noëlle Arnold, Charlie Hennebert, Thomas Meier, Christoph von Ballmoos.

  Mitochondrial respiratory complexes I to IV and the F1Fo-ATP synthase (complex V) are large protein assemblies producing the universal cellular energy currency adenosine triphosphate (ATP). Individual complexes have been extensively studied in vitro, but functional co-reconstitution of several mammalian complexes into proteoliposomes, in particular, the combination of a primary pump with the ATP synthase, is less well understood. Here, we present a generic and scalable strategy to purify mammalian respiratory complexes I, III and the ATP synthase from enriched mitochondria in enzymatically fully active form, and procedures to reassemble the complexes into liposomes. A robust functionality can be shown by in situ monitoring of ATP synthesis rates and by using selected inhibitors of the respiratory chain complexes. By inclusion of cytochrome c oxidase, our procedures allowed us to reconstruct the entire mitochondrial respiratory chain (complexes I, III, IV, and V) in ubiquinone Q10 containing liposomes, demonstrating oxidative phosphorylation by nicotinamide adenine dinucleotide hydrogen driven ATP synthesis. The system was fully coupled at all levels and was used to probe cardiolipin as an essential component to activate the mammalian respiratory chain. Structural characterization using electron cryomicroscopy allowed us to resolve apo-state complex III and complex V at high and medium resolution, respectively, using in silico particle sorting, confirming the presence of all protein subunits and cofactors in native stoichiometry and conformation. The reported findings will facilitate future endeavors to characterize or modulate these key bioenergetic processes.

Keywords:  artificial ATP production; cryo-EM; mitochondria; oxidative phosphorylation; respiratory chain

DOI:  https://doi.org/10.1073/pnas.2416162122
Biochim Biophys Acta Mol Basis Dis. 2025 Mar 19. pii: S0925-4439(25)00148-6. [Epub ahead of print] 167803

Mitochondria: An overview of their origin, genome, architecture, and dynamics.

João P Moura, Paulo J Oliveira, Ana M Urbano.

  Mitochondria are traditionally viewed as the powerhouses of most eukaryotic cells, i.e., the main providers of the metabolic energy required to maintain their viability and function. However, the role of these ubiquitous intracellular organelles far extends energy generation, encompassing a large suite of functions, which they can adjust to changing physiological conditions. These functions rely on a sophisticated membrane system and complex molecular machineries, most of which imported from the cytosol through intricate transport systems. In turn, mitochondrial plasticity is rooted on mitochondrial biogenesis, mitophagy, fusion, fission, and movement. Dealing with all these aspects and terminology can be daunting for newcomers to the field of mitochondria, even for those with a background in biological sciences. The aim of the present educational article, which is part of a special issue entitled "Mitochondria in aging, cancer and cell death", is to present these organelles in a simple and concise way. Complex molecular mechanisms are deliberately omitted, as their inclusion would defeat the stated purpose of the article. Also, considering the wide scope of the article, coverage of each topic is necessarily limited, with the reader directed to excellent reviews, in which the different topics are discussed in greater depth than is possible here. In addition, the multiple cell type-specific genotypic and phenotypic differences between mitochondria are largely ignored, focusing instead on the characteristics shared by most of them, with an emphasis on mitochondria from higher eukaryotes. Also ignored are highly degenerate mitochondrion-related organelles, found in various anaerobic microbial eukaryotes lacking canonical mitochondria.

Keywords:  Educational article; Mitochondrial endosymbiosis; Mitochondrial function; Mitochondrial morphology; Mitochondrial plasticity and dynamics; mtDNA

DOI:  https://doi.org/10.1016/j.bbadis.2025.167803
ACS Chem Neurosci. 2025 Mar 17.

Exploring Human Brain Metabolism via Genome-Scale Metabolic Modeling with Highlights on Multiple Sclerosis.

Mustafa Sertbas, Kutlu O Ulgen.

  Cerebral dysfunctions give rise to a wide range of neurological diseases due to the structural and functional complexity of the human brain stemming from the interactive cellular metabolism of its specific cells, including neurons and glial cells. In parallel with advances in isolation and measurement technologies, genome-scale metabolic models (GEMs) have become a powerful tool in the studies of systems biology to provide critical insights into the understanding of sophisticated eukaryotic systems. In this study, brain cell-specific GEMs were reconstructed for neurons, astrocytes, microglia, oligodendrocytes, and oligodendrocyte precursor cells by integrating single-cell RNA-seq data and global Human1 via a task-driven integrative network inference for tissues (tINIT) algorithm. Then, intercellular reactions among neurons, astrocytes, microglia, and oligodendrocytes were added to generate a combined brain model, iHumanBrain2690. This brain network was used in the prediction of metabolic alterations in glucose, ketone bodies, oxygen change, and reporter metabolites. Glucose supplementation increased the subsystems' activities in glycolysis, and ketone bodies elevated those in the TCA cycle and oxidative phosphorylation. Reporter metabolite analysis identified L-carnitine and arachidonate as the top reporter metabolites in gray and white matter microglia in multiple sclerosis (MS), respectively. Carbamoyl-phosphate was found to be the top reporter metabolite in primary progressive MS. Taken together, single and integrated iHumanBrain2690 metabolic networks help us elucidate complex metabolism in brain physiology and homeostasis in health and disease.

Keywords:  brain metabolism; flux balance analysis; genome-scale metabolic modeling; multiple sclerosis; reporter metabolites

DOI:  https://doi.org/10.1021/acschemneuro.5c00006
J Cell Biol. 2025 May 05. pii: e202408050. [Epub ahead of print]224(5):

TMBIM-2 orchestrates systemic mitochondrial stress response via facilitating Ca2+ oscillations.

Jiasheng Li, Jimeng Cui, Xinyu Li, Di Zhu, Zhenhua Chen, Xiahe Huang, Yingchun Wang, Qingfeng Wu, Ye Tian.

Neuronal mitochondrial function is critical for orchestrating inter-tissue communication essential for overall fitness. Despite its significance, the molecular mechanism underlying the impact of prolonged mitochondrial stresses on neuronal activity and how they orchestrate metabolism and aging remains elusive. Here, we identified the evolutionarily conserved transmembrane protein XBX-6/TMBIM-2 as a key mediator in the neuronal-to-intestinal mitochondrial unfolded protein response (UPRmt). Our investigations reveal that intrinsic neuronal mitochondrial stress triggers spatiotemporal Ca2+ oscillations in a TMBIM-2-dependent manner through the Ca2+ efflux pump MCA-3. Notably, persistent Ca2+ oscillations at synapses of ADF neurons are critical for facilitating serotonin release and the subsequent activation of the neuronal-to-intestinal UPRmt. TMBIM2 expression diminishes with age; however, its overexpression counteracts the age-related decline in aversive learning behavior and extends the lifespan of Caenorhabditis elegans. These findings underscore the intricate integration of chronic neuronal mitochondrial stress into neurotransmission processes via TMBIM-2-dependent Ca2+ equilibrium, driving metabolic adaptation and behavioral changes for the regulation of aging.

DOI: https://doi.org/10.1083/jcb.202408050
Annu Rev Biochem. 2025 Mar 17.

Moonlighting Enzymes at the Interface Between Metabolism and Epigenetics.

Jan A van der Knaap, C Peter Verrijzer.

Metabolism and gene regulation are vital processes that need to be tightly coordinated to maintain homeostasis or to enable growth and development. Recent research has begun to reveal the surprisingly interlaced relationship between metabolism and gene expression control. Because key metabolites are cofactors or cosubstrates of chromatin-modifying enzymes, changes in their concentrations can modulate chromatin states and gene expression. Additionally, an increasing number of key metabolic enzymes are found to directly regulate chromatin and transcription in response to changes in metabolic state. These include enzymes that fuel chromatin-associated metabolism and moonlighting enzymes that function as transcription factors, independent of their enzymatic activity. Conversely, accumulating evidence suggests that chromatin itself serves key metabolic functions, independent of transcriptional regulation. Here, we discuss the bidirectional interface between metabolism and chromatin and its corruption in cancer cells.

DOI: https://doi.org/10.1146/annurev-biochem-030122-044718
Cell Signal. 2025 Mar 14. pii: S0898-6568(25)00157-3. [Epub ahead of print]131 111744

Protein succinylation mechanisms and potential targeted therapies in urinary disease.

Yuanquan Lou, Caitao Dong, Qinhong Jiang, Ziqi He, Sixing Yang.

  Succinylation is a relatively common post-translational modification. It occurs in the cytoplasm, mitochondria, and the nucleus, where its essential precursor, succinyl-CoA, is present, allowing for the modification of non-histone and histone proteins. In normal cells, succinylation levels are carefully regulated to sustain a dynamic balance, necessitating the involvement of various regulatory mechanisms, including non-enzymatic reactions, succinyltransferases, and desuccinylases. Among these regulatory factors, sirtuin 5, the first identified desuccinylase, plays a significant role and has been extensively researched. The level of succinylation has a significant effect on multiple metabolic pathways, including the tricarboxylic acid cycle, redox balance, and fatty acid metabolism. Dysregulated succinylation can contribute to the progression or exacerbation of various urinary diseases. Succinylation predominantly affects disease progression by altering the expression of key genes and modulating the activity of enzymes involved in vital metabolic processes. Desuccinylases primarily affect enzymes associated with Warburg's effect, thereby affecting the energy supply of tumor cells, while succinyltransferases can regulate gene transcription to alter cell phenotype, thereby involving the development of urinary diseases. Considering these effects, targeting succinylation-related enzymes to regulate metabolic pathways or gene expression may offer a promising therapeutic strategy for treating urinary diseases.

Keywords:  Metabolic pathways; Post-translational modification; Succinylation; Targeted therapies; Urinary disease

DOI:  https://doi.org/10.1016/j.cellsig.2025.111744
Front Cell Dev Biol. 2025 ;13 1545359

Mitoregulin, a tiny protein at the crossroads of mitochondrial functioning, stress, and disease.

Petr Sergiev, Olga Averina, Julia Golubeva, Mikhail Vyssokikh, Olga Dontsova.

  Mitoregulin (Mtln) is a small mitochondrial protein that was only recently identified. Despite this, a substantial number of studies on its function have already been published. Although sometimes contradictory, these studies have revealed the localization of Mtln, its protein and lipid partners, and its role in lipid homeostasis, energy metabolism, oxidative stress, and other aspects of mitochondrial functioning. Moreover, research using knockout and transgenic mouse models has revealed the important role of Mtln in mammalian physiology. Metabolic changes, along with muscle, kidney, and fat-related phenotypes, have been linked to Mtln dysfunction. In this review, we summarize a comprehensive set of published data on Mtln. While controversies remain, we seek to offer a unified view of its functions, spanning molecular mechanisms to organism-level effects.

Keywords:  Mtln; cardiolipin; membrane; mitochondria; respiration; small peptide

DOI:  https://doi.org/10.3389/fcell.2025.1545359
Science. 2025 Mar 21. 387(6740): 1296-1301

In-cell architecture of the mitochondrial respiratory chain.

Florent Waltz, Ricardo D Righetto, Lorenz Lamm, Thalia Salinas-Giegé, Ron Kelley, Xianjun Zhang, Martin Obr, Sagar Khavnekar, Abhay Kotecha, Benjamin D Engel.

Mitochondria regenerate adenosine triphosphate (ATP) through oxidative phosphorylation. This process is carried out by five membrane-bound complexes collectively known as the respiratory chain, working in concert to transfer electrons and pump protons. The precise organization of these complexes in native cells is debated. We used in situ cryo-electron tomography to visualize the native structures and organization of several major mitochondrial complexes in Chlamydomonas reinhardtii cells. ATP synthases and respiratory complexes segregate into curved and flat crista membrane domains, respectively. Respiratory complexes I, III, and IV assemble into a respirasome supercomplex, from which we determined a native 5-angstrom (Å) resolution structure showing binding of electron carrier cytochrome c. Combined with single-particle cryo-electron microscopy at 2.4-Å resolution, we model how the respiratory complexes organize inside native mitochondria.

DOI: https://doi.org/10.1126/science.ads8738
Cell Rep Med. 2025 Mar 18. pii: S2666-3791(25)00094-1. [Epub ahead of print]6(3): 102021

Bioengineering the metabolic network of CAR T cells with GLP-1 and Urolithin A increases persistence and long-term anti-tumor activity.

Areej Akhtar, Md Shakir, Mohammad Sufyan Ansari, Divya, Md Imam Faizan, Varnit Chauhan, Aashi Singh, Ruquaiya Alam, Iqbal Azmi, Sheetal Sharma, Mehak Pracha, Insha Mohi Uddin, Uzma Bashir, Syeda Najidah Shahni, Rituparna Chaudhuri, Sarah Albogami, Rik Ganguly, Shakti Sagar, Vijay Pal Singh, Gaurav Kharya, Amit Kumar Srivastava, Ulaganathan Mabalirajan, Soumya Sinha Roy, Irfan Rahman, Tanveer Ahmad.

  Constant tumor antigen exposure disrupts chimeric antigen receptor (CAR) T cell metabolism, limiting their persistence and anti-tumor efficacy. To address this, we develop metabolically reprogrammed CAR (MCAR) T cells with enhanced autophagy and mitophagy. A compound screening identifies a synergy between GLP-1R agonist (semaglutide [SG]) and Urolithin A (UrA), which activate autophagy through mTOR (mechanistic target of rapamycin) inhibition and mitophagy via Atg4b activation, maintaining mitochondrial metabolism in CAR T cells (MCAR T-1). These changes increase CD8+ T memory cells (Tm), enhancing persistence and anti-tumor activity in vitro and in xenograft models. GLP-1R knockdown in CAR T cells diminishes autophagy/mitophagy induction, confirming its critical role. We further engineer GLP-1-secreting cells (MCAR T-2), which exhibited sustained memory, stemness, and long-term persistence, even under tumor re-challenge. MCAR T-2 cells also reduce cytokine release syndrome (CRS) risks while demonstrating potent anti-tumor effects. This strategy highlights the potential of metabolic reprogramming via targeting autophagy/mitophagy pathways to improve CAR T cell therapy outcomes, ensuring durability and efficacy.

Keywords:  CAR T cells; GLP-1 peptide; T cell persistence; Urolithin A; anti-tumor activity; autophagy; metabolism; mitochondrial health; mitophagy

DOI:  https://doi.org/10.1016/j.xcrm.2025.102021
Annu Rev Biochem. 2025 Mar 18.

Emerging Approaches for Studying Lipid Dynamics, Metabolism, and Interactions in Cells.

Lin Luan, Nathan P Frederick, Jeremy M Baskin.

Lipids are a major class of biological molecules, the primary components of cellular membranes, and critical signaling molecules that regulate cell biology and physiology. Due to their dynamic behavior within membranes, rapid transport between organelles, and complex and often redundant metabolic pathways, lipids have traditionally been considered among the most challenging biological molecules to study. In recent years, a plethora of tools bridging the chemistry-biology interface has emerged for studying different aspects of lipid biology. Here, we provide an overview of these approaches. We discuss methods for lipid detection, including genetically encoded biosensors, synthetic lipid analogs, and metabolic labeling probes. For targeted manipulation of lipids, we describe pharmacological agents and controllable enzymes, termed membrane editors, that harness optogenetics and chemogenetics. To conclude, we survey techniques for elucidating lipid-protein interactions, including photoaffinity labeling and proximity labeling. Collectively, these strategies are revealing new insights into the regulation, dynamics, and functions of lipids in cell biology.

DOI: https://doi.org/10.1146/annurev-biochem-083024-110827
Nat Commun. 2025 Mar 19. 16(1): 2725

Septin5 deletion enhances β-cell exocytosis by releasing microtubule-tethered insulin granules onto plasma membrane.

Li Xie, Fei Kang, Tairan Qin, Youhou Kang, Tao Liang, Huanli Xie, Carol D Froese, Hong Xie, Aaron Au, Christopher M Yip, William S Trimble, Herbert Y Gaisano.

Septin5 interacts with SNARE proteins to regulate exocytosis in neurons, but its role in pancreatic β-cells is unknown. Here, we report that Septin5 is abundant in rodent and human β-cells, deletion of which dramatically enhances biphasic glucose-stimulated insulin secretion, including in type 2 diabetes (T2D). Super-resolution imaging shows that Septin5 is preferentially assembled in microtubule-plasma membrane contact sites in a microtubule-dependent manner, which provides discrete harbor for secretory granule anchoring. By decreasing the stability of the cortical microtubule meshwork, Septin5 depletion increases insulin granule dynamics and access to the plasma membrane. Analysis of spatiotemporal coupling of fusion events and localized Ca2+ influx through L-type Ca2+ channels show that Septin5 depletion increases releasable granule pool clustering on Ca2+ channels, previously shown to be impaired in T2D, thus rectifying this T2D defect. Hence, inhibition of Septin5 can improve insulin secretion.

DOI: https://doi.org/10.1038/s41467-025-57421-5
Cell Rep. 2025 Mar 13. pii: S2211-1247(25)00201-3. [Epub ahead of print]44(3): 115430

Mitochondrial reactive oxygen species regulate acetyl-CoA flux between cytokine production and fatty acid synthesis in effector T cells.

Beibei Wu, Jin Seok Woo, Spyridon Hasiakos, Calvin Pan, Shawn Cokus, Cristiane Benincá, Linsey Stiles, Zuoming Sun, Matteo Pellegrini, Orian S Shirihai, Aldon J Lusis, Sonal Srikanth, Yousang Gwack.

  Genetic and environmental factors shape an individual's susceptibility to autoimmunity. To identify genetic variations regulating effector T cell functions, we used a forward genetics screen of inbred mouse strains and uncovered genomic loci linked to cytokine expression. Among the candidate genes, we characterized a mitochondrial inner membrane protein, TMEM11, as an important determinant of Th1 responses. Loss of TMEM11 selectively impairs Th1 cell functions, reducing autoimmune symptoms in mice. Mechanistically, Tmem11-/- Th1 cells exhibit altered cristae architecture, impaired respiration, and increased mitochondrial reactive oxygen species (mtROS) production. Elevated mtROS hindered histone acetylation while promoting neutral lipid accumulation. Further experiments using genetic, biochemical, and pharmacological tools revealed that mtROS regulate acetyl-CoA flux between histone acetylation and fatty acid synthesis. Our findings highlight the role of mitochondrial cristae integrity in directing metabolic pathways that influence chromatin modifications and lipid biosynthesis in Th1 cells, providing new insights into immune cell metabolism.

Keywords:  CP: Immunology; CP: Metabolism; EAE; MICOS complex; Th1 cells; cytokine production; histone acetylation; mitochondria; mitochondrial cristae architecture; neutral lipids; reactive oxygen species

DOI:  https://doi.org/10.1016/j.celrep.2025.115430
Sci Adv. 2025 Mar 21. 11(12): eads9182

A metabolic shift to the serine pathway induced by lipids fosters epigenetic reprogramming in nontransformed breast cells.

Mariana Bustamante Eduardo, Gannon Cottone, Curtis W McCloskey, Shiyu Liu, Flavio R Palma, Maria Paula Zappia, Abul B M M K Islam, Peng Gao, Joel Setya, Saya Dennis, Hongyu Gao, Qian Zhang, Xiaoling Xuei, Yuan Luo, Jason Locasale, Marcelo G Bonini, Rama Khokha, Maxim V Frolov, Elizaveta V Benevolenskaya, Navdeep S Chandel, Seema A Khan, Susan E Clare.

Lipid metabolism and the serine, one-carbon, glycine (SOG) and methionine pathways are independently and significantly correlated with estrogen receptor-negative breast cancer (ERneg BC). Here, we propose a link between lipid metabolism and ERneg BC through phosphoglycerate dehydrogenase (PHGDH), the rate-limiting enzyme in the de novo serine pathway. We demonstrate that the metabolism of the paradigmatic medium-chain fatty acid octanoic acid leads to a metabolic shift toward the SOG and methionine pathways. PHGDH plays a role in both the forward direction, contributing to the production of S-adenosylmethionine, and the reverse direction, generating the oncometabolite 2-hydroxyglutarate, leading to epigenomic reprogramming and phenotypic plasticity. The methionine cycle is closely linked to the transsulfuration pathway. Consequently, we observe that the shift increases the antioxidant glutathione, which mitigates reactive oxygen species (ROS), enabling survival of a subset of cells that have undergone DNA damage. These metabolic changes contribute to several hallmarks of cancer.

DOI: https://doi.org/10.1126/sciadv.ads9182
Nat Commun. 2025 Mar 16. 16(1): 2597

Ubiquinol-mediated suppression of mitochondria-associated ferroptosis is a targetable function of lactate dehydrogenase B in cancer.

Haibin Deng, Liang Zhao, Huixiang Ge, Yanyun Gao, Yan Fu, Yantang Lin, Mojgan Masoodi, Tereza Losmanova, Michaela Medová, Julien Ott, Min Su, Wenxiang Wang, Ren-Wang Peng, Patrick Dorn, Thomas Michael Marti.

Lactate dehydrogenase B (LDHB) fuels oxidative cancer cell metabolism by converting lactate to pyruvate. This study uncovers LDHB's role in countering mitochondria-associated ferroptosis independently of lactate's function as a carbon source. LDHB silencing alters mitochondrial morphology, causes lipid peroxidation, and reduces cancer cell viability, which is potentiated by the ferroptosis inducer RSL3. Unlike LDHA, LDHB acts in parallel with glutathione peroxidase 4 (GPX4) and dihydroorotate dehydrogenase (DHODH) to suppress mitochondria-associated ferroptosis by decreasing the ubiquinone (coenzyme Q, CoQ) to ubiquinol (CoQH2) ratio. Indeed, supplementation with mitoCoQH2 (mitochondria-targeted analogue of CoQH2) suppresses mitochondrial lipid peroxidation and cell death after combined LDHB silencing and RSL3 treatment, consistent with the presence of LDHB in the cell fraction containing the mitochondrial inner membrane. Addressing the underlying molecular mechanism, an in vitro NADH consumption assay with purified human LDHB reveals that LDHB catalyzes the transfer of reducing equivalents from NADH to CoQ and that the efficiency of this reaction increases by the addition of lactate. Finally, radiation therapy induces mitochondrial lipid peroxidation and reduces tumor growth, which is further enhanced when combined with LDHB silencing. Thus, LDHB-mediated lactate oxidation drives the CoQ-dependent suppression of mitochondria-associated ferroptosis, a promising target for combination therapies.

DOI: https://doi.org/10.1038/s41467-025-57906-3
J Biol Chem. 2025 Mar 14. pii: S0021-9258(25)00258-3. [Epub ahead of print] 108409

Pak1 dysregulates Pyruvate metabolism in PDAC cells by exerting a phosphorylation-mediated regulatory effect on PDHA1.

Sowmiya Murugan, Srikanth Swamy Swaroop B, Prarthana Gopinath, Roshni Saravanan, Sandhya Sundaram, Gouthaman Shanmugasundaram, Ganesh Venkatraman, Suresh Kumar Rayala.

  Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive form of pancreatic cancer with the worst prognosis. Treating PDAC poses significant challenges, as tumor cells adapt metabolic alterations to thrive in the hypoxic environment created by desmoplasia surrounding the tumor cells. p21-activated kinase (Pak1), a serine-threonine kinase is found to be upregulated in many solid tumors and promotes tumor progression via diverse signalling pathways. In this study, we focussed on exploring the role of Pak1 in mediating tumor cell metabolism. Deletion of the Pak1 gene reduced the tumorigenic potential of PDAC cells. Also, Pak1 regulated both glycolysis and mitochondrial respiration in PDAC cells, contributing to the Warburg phenomenon. Untargeted metabolomic analysis revealed that Pak1 was strongly associated with Pyruvate metabolism. Interestingly, we found that Pak1 interacted and phosphorylated Pyruvate dehydrogenase E1α (PDHA1) at Serine 152. This phosphorylation negatively regulates PDHA1 activity, implying the direct regulatory role of Pak1 in Pyruvate metabolism. Moreover, deleting the Pak1 gene altered the expression and activity of PDHA1 and LDHA, as both are involved in regulating the direction of pyruvate flux inside the cells. Our study demonstrated that Pak1 plays a significant role in PDAC metabolism and Warburg effect, partly by phosphorylating PDHA1.

Keywords:  PDAC; Pak1; Pyruvate dehydrogenase; Warburg effect

DOI:  https://doi.org/10.1016/j.jbc.2025.108409
J Neurochem. 2025 Mar;169(3): e70044

Dynamics of Neuronal and Astrocytic Energy Molecules in Epilepsy.

Kota Furukawa, Yoko Ikoma, Yusuke Niino, Yuichi Hiraoka, Kohichi Tanaka, Atsushi Miyawaki, Johannes Hirrlinger, Ko Matsui.

  The dynamics of energy molecules in the mouse brain during metabolic challenges induced by epileptic seizures were examined. A transgenic mouse line expressing a fluorescence resonance energy transfer (FRET)-based adenosine triphosphate (ATP) sensor, selectively expressed in the cytosol of neurons, was used. An optical fiber was inserted into the hippocampus, and changes in cytosolic ATP concentration were estimated using the fiber photometry method. To induce epileptic neuronal hyperactivity, a train of electrical stimuli was delivered to a bipolar electrode placed alongside the optical fiber. Although maintaining a steady cytosolic ATP concentration is crucial for cell survival, a single episode of epileptic neuronal hyperactivity drastically reduced neuronal ATP levels. Interestingly, the magnitude of ATP reduction did not increase with the exacerbation of epilepsy, but rather decreased. This suggests that the primary consumption of ATP during epileptic neuronal hyperactivity may not be solely directed toward restoring the Na+ and K+ ionic imbalance caused by action potential bursts. Cytosolic ATP concentration reflects the balance between supply and consumption. To investigate the metabolic flux leading to neuronal ATP production, a new FRET-based pyruvate sensor was developed and selectively expressed in the cytosol of astrocytes in transgenic mice. Upon epileptic neuronal hyperactivity, an increase in astrocytic pyruvate concentration was observed. Changes in the supply of energy molecules, such as glucose and oxygen, due to blood vessel constriction or dilation, as well as metabolic alterations in astrocyte function, may contribute to cytosolic ATP dynamics in neurons.

Keywords:  ATP; astrocyte; blood vessels; epilepsy; fiber photometry; pyruvate

DOI:  https://doi.org/10.1111/jnc.70044
Proc Natl Acad Sci U S A. 2025 Mar 25. 122(12): e2418926122

Decoding in-cell respiratory enzyme dynamics by label-free in situ electrochemistry.

Yoshihide Tokunou, Tomohiko Yamazaki, Takashi Fujikawa, Akihiro Okamoto.

  Deciphering metabolic enzyme catalysis in living cells remains a formidable challenge due to the limitations of in vivo assays, which focus on enzymes isolated from respiration. This study introduces an innovative whole-cell electrochemical assay to reveal the Michaelis-Menten landscape of respiratory enzymes amid complex molecular interactions. We controlled the microbial current generation's rate-limiting step, extracting in vivo kinetic parameters (Km, Ki, and kcat) for the periplasmic nitrite (NrfA) and fumarate (FccA) reductases. Notably, while NrfA kinetics mirrored those of its purified form, FccA exhibited unique kinetic behavior. Further exploration using a mutant strain lacking CymA, a periplasmic hub protein, revealed its crucial role in modulating FccA's kinetics, challenging the prevailing view that molecular crowding is the main cause of discrepancies between in vivo and in vitro enzyme kinetics. This platform offers a groundbreaking approach to studying cellular respiratory enzymatic kinetics, paving the way for future research in bioenergetics and medicine.

Keywords:  Michaelis–Menten equation; enzymatic activity; interprotein interaction

DOI:  https://doi.org/10.1073/pnas.2418926122
Nat Commun. 2025 Mar 19. 16(1): 2685

Acute diacylglycerol production activates critical membrane-shaping proteins leading to mitochondrial tubulation and fission.

Joshua G Pemberton, Krishnendu Roy, Yeun Ju Kim, Tara D Fischer, Vijay Joshi, Elizabeth Ferrer, Richard J Youle, Thomas J Pucadyil, Tamas Balla.

Mitochondrial dynamics are orchestrated by protein assemblies that directly remodel membrane structure, however the influence of specific lipids on these processes remains poorly understood. Here, using an inducible heterodimerization system to selectively modulate the lipid composition of the outer mitochondrial membrane (OMM), we show that local production of diacylglycerol (DAG) directly leads to transient tubulation and rapid fragmentation of the mitochondrial network, which are mediated by isoforms of endophilin B (EndoB) and dynamin-related protein 1 (Drp1), respectively. Reconstitution experiments on cardiolipin-containing membrane templates mimicking the planar and constricted OMM topologies reveal that DAG facilitates the membrane binding and remodeling activities of both EndoB and Drp1, thereby independently potentiating membrane tubulation and fission events. EndoB and Drp1 do not directly interact with each other, suggesting that DAG production activates multiple pathways for membrane remodeling in parallel. Together, our data emphasizes the importance of OMM lipid composition in regulating mitochondrial dynamics.

DOI: https://doi.org/10.1038/s41467-025-57439-9
PNAS Nexus. 2025 Mar;4(3): pgaf072

Quantitative mapping of key glucose metabolic rates in the human brain using dynamic deuterium magnetic resonance spectroscopic imaging.

Xin Li, Xiao-Hong Zhu, Yudu Li, Tao Wang, Guangle Zhang, Hannes M Wiesner, Zhi-Pei Liang, Wei Chen.

  Deuterium (2H) magnetic resonance spectroscopic imaging (DMRSI) is a newly developed technology for assessing glucose metabolism by simultaneously measuring deuterium-labeled glucose and its downstream metabolites (1) and has a potential to provide a powerful neurometabolic imaging tool for quantitative studies of cerebral glucose metabolism involving multiple metabolic pathways in the human brain. In this work, we developed a dynamic DMRSI method that combines advanced radiofrequency coil and postprocessing techniques to substantially improve the imaging signal-to-noise ratio for detecting deuterated metabolites and enable robust dynamic DMRSI of the human brain at 7 T with very high resolution (HR; 0.7 cc nominal voxel and 2.5 min/image) and whole-brain coverage. Utilizing this capability, we were able to map and differentiate metabolite contents and dynamics throughout the human brain following oral administration of deuterated glucose. Furthermore, by introducing a sophisticated kinetic model, we demonstrated that three key cerebral metabolic rates of glucose consumption (CMRGlc), lactate production (CMRLac), and tricarboxylic acid (TCA) cycle (V TCA), as well as the maximum apparent rate of forward glucose transport (T max) can be simultaneously imaged in the human brain through a single dynamic DMRSI measurement. The results clearly show that the glucose transport, neurotransmitter turnover, CMRGlc, and V TCA are significantly higher in gray matter than in white matter in the human brain; and the mean metabolic rates and their ratios measured in this study are consistent with the values reported in the literature. The HR dynamic DMRSI methodology presented herein is of great significance and value for the quantitative assessment of human brain glucose metabolism, aerobic glycolysis, and metabolic reprogramming under physiopathological conditions.

Keywords:  Biological; Health; aerobic glycolysis; and Medical Sciences/neuroscience; cerebral glucose metabolism; dynamic DMRSI; imaging human brain glucose metabolic rates

DOI:  https://doi.org/10.1093/pnasnexus/pgaf072
J Am Chem Soc. 2025 Mar 20.

Organelle-Specific Quantum Thermometry Using Fluorescent Nanodiamonds: Insights into Cellular Metabolic Thermodynamics.

Yoobeen Lee, Kiho Kim, Dohun Kim, Jin Seok Lee.

Intracellular thermometry is a powerful method for studying biological thermodynamics across various physiological contexts. In this study, we present an organelle-specific quantum thermometry utilizing nitrogen-vacancy (NV) centers in fluorescent nanodiamonds (FNDs) to obtain precise temperature measurements at the subcellular level. By conjugating antibodies, FNDs were selectively targeted to mitochondria, nuclei, and cell membranes in living fibroblasts, enabling real-time monitoring of temperature changes during adenosine triphosphate (ATP) synthesis and inhibition. The system integrates advanced bioconjugation and quantum sensing methodologies, thereby overcoming challenges, such as photobleaching and limited spatial resolution. Notably, mitochondria-targeted FNDs revealed significant temperature increases, revealing mitochondria as the primary site of thermogenesis during ATP inhibition. These findings establish a robust framework for investigating metabolic thermodynamics and offer a powerful tool for exploring the thermal regulation of cellular processes.

DOI: https://doi.org/10.1021/jacs.4c16365
J Cell Biol. 2025 May 05. pii: e202406053. [Epub ahead of print]224(5):

STIM1/2 maintain signaling competence at ER-PM contact sites during neutrophil spreading.

Camille Rabesahala de Meritens, Amado Carreras-Sureda, Nicolas Rosa, Robert Pick, Christoph Scheiermann, Nicolas Demaurex.

Neutrophils are highly motile leukocytes that migrate inside tissues to destroy invading pathogens. Ca2+ signals coordinate leukocytes migration, but whether Ca2+ fluxes mediated by Stim proteins at ER-PM contact sites regulate neutrophil actin-based motility is unclear. Here, we show that myeloid-specific Stim1/2 ablation decreases basal cytosolic Ca2+ levels and prevents adhesion-induced Ca2+ elevations in mouse neutrophils, reducing actin fiber formation and impairing spreading. Unexpectedly, more ER-PM contact sites were detected on the actin-poor adhesive membranes of Stim1/2-deficient neutrophils, which had reduced inositol-1,4,5-trisphosphate receptor (IP3R) immunoreactivity on confocal and immunogold micrographs despite preserved IP3R levels on western blots. Remarkably, Stim1/2-deficient neutrophils regained signaling and spreading competence in Ca2+-rich solutions and were recruited more effectively in mouse inflamed cremaster muscles in vivo. Our findings indicate that Stim1/2 preserve IP3R functionality in neutrophils, generating adhesion-dependent Ca2+ signals that control actin dynamics during neutrophil spreading. Stim proteins thus maintain IP3R signaling competence at adhesive membranes, enabling Ca2+-dependent actin remodeling during spreading in mouse neutrophils.

DOI: https://doi.org/10.1083/jcb.202406053
Nat Commun. 2025 Mar 20. 16(1): 2740

Integrative single-cell metabolomics and phenotypic profiling reveals metabolic heterogeneity of cellular oxidation and senescence.

Ziyi Wang, Siyuan Ge, Tiepeng Liao, Man Yuan, Wenwei Qian, Qi Chen, Wei Liang, Xiawei Cheng, Qinghua Zhou, Zhenyu Ju, Hongying Zhu, Wei Xiong.

Emerging evidence has unveiled heterogeneity in phenotypic and transcriptional alterations at the single-cell level during oxidative stress and senescence. Despite the pivotal roles of cellular metabolism, a comprehensive elucidation of metabolomic heterogeneity in cells and its connection with cellular oxidative and senescent status remains elusive. By integrating single-cell live imaging with mass spectrometry (SCLIMS), we establish a cross-modality technique capturing both metabolome and oxidative level in individual cells. The SCLIMS demonstrates substantial metabolomic heterogeneity among cells with diverse oxidative levels. Furthermore, the single-cell metabolome predicted heterogeneous states of cells. Remarkably, the pre-existing metabolomic heterogeneity determines the divergent cellular fate upon oxidative insult. Supplementation of key metabolites screened by SCLIMS resulted in a reduction in cellular oxidative levels and an extension of C. elegans lifespan. Altogether, SCLIMS represents a potent tool for integrative metabolomics and phenotypic profiling at the single-cell level, offering innovative approaches to investigate metabolic heterogeneity in cellular processes.

DOI: https://doi.org/10.1038/s41467-025-57992-3
J Cell Sci. 2025 Mar 19. pii: jcs.263576. [Epub ahead of print]

Definition of the human mitochondrial TOM interactome reveals TRABD as new interacting protein.

Metin Özdemir, Silke Oeljeklaus, Schendzielorz Alexander, Marcel Morgenstern, Anusha Valpadashi, Roya Yousefi, Bettina Warscheid, Sven Dennerlein.

  The mitochondrial proteome arises from dual genetic origin. Nuclear-encoded proteins need to be transported across or inserted into two distinguished membranes, and the TOM complex represents the main translocase in the outer mitochondrial membrane. Its composition and regulations have been extensively investigated within yeast cells. However, we have little knowledge of the TOM complex composition within human cells. Here, we have defined the TOM interactome in a comprehensive manner using biochemical approaches to isolate the TOM complex in combination with quantitative mass spectrometry analyses. Within these studies, we defined the pleiotropic nature of the human TOM complex, including new interactors, such as TRABD. Our studies provide a framework to understand the various biogenesis pathways that merge at the TOM complex within human cells.

Keywords:  Mitochondria; Mitochondrial Biogenesis; Mitochondrial protein import; Mitochondrial quality control; Protein transport; TOM complex

DOI:  https://doi.org/10.1242/jcs.263576
Mol Cell Proteomics. 2025 Mar 13. pii: S1535-9476(25)00042-8. [Epub ahead of print] 100944

Metabolic Reprogramming into a Glycolysis Phenotype Induced by Extracellular Vesicles Derived from Prostate Cancer Cells.

Yoon-Jin Lee, Chul Won Seo, Shinwon Chae, Chang Yeol Lee, Sang Soo Kim, Yoon-Hee Shin, Hyun-Mee Park, Yong Song Gho, Seongho Ryu, Sang-Han Lee, Dongsic Choi.

Most cancer cells adopt a less efficient metabolic process of aerobic glycolysis with high level of glucose uptake followed by lactic acid production, known as the Warburg effect. This phenotypic transition enables cancer cells to achieve increased cellular survival and proliferation in a harsh low-oxygen tumor microenvironment. Also, the resulting acidic microenvironment causes inactivation of the immune system such as T-cell impairment that favors escape by immune surveillance. While lots of studies have revealed that tumor-derived EVs can deliver parental materials to adjacent cells and contribute to oncogenic reprogramming, their functionality in energy metabolism is not well addressed. In this study, we established prostate cancer cells PC3-AcT resistant to cellular death in an acidic culture medium driven by lactic acid. Quantitative proteomics between EVs derived from PC-3 and PC-3AcT cells identified 935 confident EV proteins. According to cellular adaptation to lactic acidosis, we revealed 159 regulated EV proteins related to energy metabolism, cellular shape, and extracellular matrix. These EVs contained a high abundance of glycolytic enzymes. In particular, PC-3AcT EVs were enriched with apolipoproteins including apolipoprotein B100 (APOB). APOB on PC-3AcT EVs could facilitate their endocytic uptake depending on low density lipoprotein receptor of recipient PC-3 cells, encouraging increases of cellular proliferation and survival in acidic culture media via increased activity and expression of hexokinases and phosphofructokinase. The activation of recipient PC-3 cells can increase glucose consumption and ATP generation, representing an acquired metabolic reprogramming into the Warburg phenotype. Our study first revealed that EVs derived from prostate cancer cells could contribute to energy metabolic reprogramming and that the acquired metabolic phenotypic transition of recipient cells could favor cellular survival in tumor microenvironment.

DOI: https://doi.org/10.1016/j.mcpro.2025.100944
Front Cell Dev Biol. 2025 ;13 1523382

Proteasome dynamics in response to metabolic changes.

Cordula Enenkel, Oliver P Ernst.

  Proteasomes, essential protease complexes in protein homeostasis, adapt to metabolic changes through intracellular movements. As the executive arm of the ubiquitin-proteasome system, they selectively degrade poly-ubiquitinated proteins in an ATP-dependent process. The primary proteasome configuration involved in this degradation is the 26S proteasome, which is composed of a proteolytically active core particle flanked by two regulatory particles. In metabolically active cells, such as proliferating yeast and mammalian cancer cells, 26S proteasomes are predominantly nuclear and actively engaged in protein degradation. However, during nutrient deprivation or stress-induced quiescence, proteasome localization changes. In quiescent yeast, proteasomes initially accumulate at the nuclear envelope. During prolonged quiescence with decreased ATP levels, proteasomes exit the nucleus and are sequestered into cytoplasmic membraneless organelles, so-called proteasome storage granules (PSGs). In mammalian cells, starvation and stress trigger formation of membraneless organelles containing proteasomes and poly-ubiquitinated substrates. The proteasome condensates are motile, reversible, and contribute to stress resistance and improved fitness during aging. Proteasome condensation may involve liquid-liquid phase separation, a mechanism underlying the assembly of membraneless organelles.

Keywords:  metabolic regulation of proteasome localization; proteasome condensates in membraneless organelles; proteasome storage granules; protein homeostasis (proteostasis); ubiquitin 26S-proteasome system

DOI:  https://doi.org/10.3389/fcell.2025.1523382