bims-celmim 2025-03-09 papers

bims-celmim

Biomed News

on Cellular and mitochondrial metabolism

Issue of 2025–03–09
eightteen papers selected by
Marc Segarra Mondejar

Succinate Dehydrogenase loss causes cascading metabolic effects that impair pyrimidine biosynthesis.
Human adenovirus serotype 5 infection dysregulates cysteine, purine, and unsaturated fatty acid metabolism in fibroblasts.
Mitochondrial accumulation and lysosomal dysfunction result in mitochondrial plaques in Alzheimer's disease.
Structure of mitochondrial pyruvate carrier and its inhibition mechanism.
SNX10 functions as a modulator of piecemeal mitophagy and mitochondrial bioenergetics.
Deuterium metabolic imaging phenotypes mouse glioblastoma heterogeneity through glucose turnover kinetics.
Cytoplasmic ribosomes on mitochondria alter the local membrane environment for protein import.
Mitochondrial fusion and cristae reorganization facilitate acquisition of cardiomyocyte identity during reprogramming of murine fibroblasts.
Discovery of a novel alpha isoform of the long-known enzyme LDHA provides new insights into cancer research.
Ca2+ binding to Esyt modulates membrane contact site density in Drosophila photoreceptors.
Neuron-specific isoform of PGC-1α regulates neuronal metabolism and brain aging.
Proximity proteomics reveals a mechanism of fatty acid transfer at lipid droplet-mitochondria- endoplasmic reticulum contact sites.
Untargeted lipidomic analysis of metabolic dysfunction-associated steatohepatitis in women with morbid obesity.
Single-nucleus RNA sequencing uncovers metabolic dysregulation in the prefrontal cortex of major depressive disorder patients.
The alternative oxidase reconfigures the larval mitochondrial electron transport system to accelerate growth and development in Drosophila melanogaster.
A subcellular map of translational machinery composition and regulation at the single-molecule level.
iMetAct: An integrated systematic inference of metabolic activity for dissecting tumor metabolic preference and tumor-immune microenvironment.
State-dependent motion of a genetically encoded fluorescent biosensor.

bioRxiv. 2025 Feb 19. pii: 2025.02.18.638948. [Epub ahead of print]

Succinate Dehydrogenase loss causes cascading metabolic effects that impair pyrimidine biosynthesis.

Madeleine L Hart, Kristian Davidsen, Serwah Danquah, Eric Zheng, David Sokolov, Lucas B Sullivan.

  Impaired availability of the amino acid aspartate can be a metabolic constraint of cell proliferation in diverse biological contexts. However, the kinetics of aspartate depletion, and its ramifications on downstream metabolism and cell proliferation, remain poorly understood. Here, we deploy the aspartate biosensor jAspSnFR3 with live cell imaging to resolve temporal relationships between aspartate and cell proliferation from genetic, pharmacological, and nutritional manipulations. In cells with impaired aspartate acquisition from mitochondrial complex I inhibition or constrained uptake in aspartate auxotrophs, we find that the proliferation defects lag changes in aspartate levels and only manifest once aspartate levels fall below a critical threshold, supporting the functional link between aspartate levels and cell proliferation in these contexts. In another context of aspartate synthesis inhibition, impairing succinate dehydrogenase (SDH), we find a more complex metabolic interaction, with initial aspartate depletion followed by a rebound of aspartate levels over time. We find that this aspartate rebound effect results from SDH inhibition disproportionately impairing pyrimidine synthesis by inhibiting aspartate transcarbamoylase (ATCase) through the dual effect of diminishing aspartate substrate availability while accumulating succinate, which functions as a competitive inhibitor of aspartate utilization. Finally, we uncover that the nucleotide imbalance from SDH inhibition causes replication stress and introduces a vulnerability to ATR kinase inhibition. Altogether, these findings identify a mechanistic role for succinate in modulating nucleotide synthesis and demonstrate how cascading metabolic interactions can unfold to impact cell function.

Keywords:  SDH; aspartate; biosensor; cancer; metabolism; metabolomics; proliferation; pyrimidines

DOI:  https://doi.org/10.1101/2025.02.18.638948
FASEB J. 2025 Mar 15. 39(5): e70411

Human adenovirus serotype 5 infection dysregulates cysteine, purine, and unsaturated fatty acid metabolism in fibroblasts.

Bailey-J C Sanchez, Rudy M Ortiz, Juris A Grasis.

  Viral infections can cause cellular dysregulation of metabolic reactions. Viruses alter host metabolism to meet their replication needs. The impact of viruses on specific metabolic pathways is not well understood, even in well-studied viruses, such as human adenovirus. Adenoviral infection is known to influence cellular glycolysis and respiration; however, global effects on overall cellular metabolism in response to infection are unclear. Furthermore, few studies have employed an untargeted approach, combining emphasis on viral dosage and infection. To address this, we employed untargeted metabolomics to quantify the dynamic metabolic shifts in fibroblasts infected with human adenovirus serotype 5 (HAdV-5) at three dosages (0.5, 1.0, and 2.0 multiplicity of infection [MOI]) and across 4 time points (6-, 12-, 24-, and 36-h post-infection [HPI]). The greatest differences in individual metabolites were observed at 6- and 12-h post-infection, correlating with the early phase of the HAdV-5 infection cycle. In addition to its effects on glycolysis and respiration, adenoviral infection downregulates cysteine and unsaturated fatty acid metabolism while upregulating aspects of purine metabolism. These results reveal specific metabolic pathways dysregulated by adenoviral infection and the associated dynamic shifts in metabolism, suggesting that viral infections alter energetics via profound changes in lipid, nucleic acid, and protein metabolism. The results revealed previously unconsidered metabolic pathways disrupted by HAdV-5 that can alter cellular metabolism, thereby prompting further investigation into HAdV mechanisms and antiviral targeting.

Keywords:  adenovirus; fibroblasts; mass spectrometry; metabolomics

DOI:  https://doi.org/10.1096/fj.202402726R
bioRxiv. 2025 Feb 20. pii: 2025.02.19.639081. [Epub ahead of print]

Mitochondrial accumulation and lysosomal dysfunction result in mitochondrial plaques in Alzheimer's disease.

Xiuli Dan, Deborah L Croteau, Wenlong Liu, Xixia Chu, Paul D Robbins, Vilhelm A Bohr.

Dysfunctional mitophagy is a key component of Alzheimer's disease (AD) pathology, yet direct in vivo evidence and mechanistic insights remain limited. Using a mitophagy reporter in an AD mouse model ( APP / PSEN1 /mt-Keima), we identified mitochondrial plaques (MPs) composed of accumulated mitochondria within or outside lysosomes in AD, but not normal mouse brains. Similar structures were also found in AD human brains, but not in healthy controls. Abnormal mitochondrial accumulation in dystrophic neurites, defective mitophagy, and impaired lysosomal function disrupted proper mitochondrial degradation, resulting in excessive mitochondria accumulation both within and outside autophagic vesicles. The resulting intensive mitochondria-containing neurites coalesce into MPs, which co-develop with amyloid plaques to form mixed plaques. These findings establish MPs as novel pathological entity and a promising therapeutic target in AD.

DOI: https://doi.org/10.1101/2025.02.19.639081
Nature. 2025 Mar 05.

Structure of mitochondrial pyruvate carrier and its inhibition mechanism.

Zheng He, Jianxiu Zhang, Yan Xu, Eve J Fine, Carl-Mikael Suomivuori, Ron O Dror, Liang Feng.

The mitochondrial pyruvate carrier (MPC) governs the entry of pyruvate-a central metabolite that bridges cytosolic glycolysis with mitochondrial oxidative phosphorylation-into the mitochondrial matrix1-5. It thus serves as a pivotal metabolic gatekeeper and has fundamental roles in cellular metabolism. Moreover, MPC is a key target for drugs aimed at managing diabetes, non-alcoholic steatohepatitis and neurodegenerative diseases4-6. However, despite MPC's critical roles in both physiology and medicine, the molecular mechanisms underlying its transport function and how it is inhibited by drugs have remained largely unclear. Here our structural findings on human MPC define the architecture of this vital transporter, delineate its substrate-binding site and translocation pathway, and reveal its major conformational states. Furthermore, we explain the binding and inhibition mechanisms of MPC inhibitors. Our findings provide the molecular basis for understanding MPC's function and pave the way for the development of more-effective therapeutic reagents that target MPC.

DOI: https://doi.org/10.1038/s41586-025-08667-y
J Cell Biol. 2025 May 05. pii: e202404009. [Epub ahead of print]224(5):

SNX10 functions as a modulator of piecemeal mitophagy and mitochondrial bioenergetics.

Laura Trachsel-Moncho, Chiara Veroni, Benan John Mathai, Ana Lapao, Sakshi Singh, Nagham Theres Asp, Sebastian W Schultz, Serhiy Pankiv, Anne Simonsen.

We here identify the endosomal protein SNX10 as a negative regulator of piecemeal mitophagy of OXPHOS machinery components. In control conditions, SNX10 localizes to early endocytic compartments in a PtdIns3P-dependent manner and modulates endosomal trafficking but also shows dynamic connections with mitochondria. Upon hypoxia-mimicking conditions, SNX10 localizes to late endosomal structures containing selected mitochondrial proteins, including COX-IV and SAMM50, and the autophagy proteins SQSTM1/p62 and LC3B. The turnover of COX-IV was enhanced in SNX10-depleted cells, with a corresponding reduced mitochondrial respiration and citrate synthase activity. Importantly, zebrafish larvae lacking Snx10 show reduced levels of Cox-IV, as well as elevated ROS levels and ROS-mediated cell death in the brain, demonstrating the in vivo relevance of SNX10-mediated modulation of mitochondrial bioenergetics.

DOI: https://doi.org/10.1083/jcb.202404009
Elife. 2025 Mar 04. pii: RP100570. [Epub ahead of print]13

Deuterium metabolic imaging phenotypes mouse glioblastoma heterogeneity through glucose turnover kinetics.

Rui Vasco Simoes, Rafael Neto Henriques, Jonas L Olesen, Beatriz M Cardoso, Francisca F Fernandes, Mariana A V Monteiro, Sune N Jespersen, Tânia Carvalho, Noam Shemesh.

  Glioblastomas are aggressive brain tumors with dismal prognosis. One of the main bottlenecks for developing more effective therapies for glioblastoma stems from their histologic and molecular heterogeneity, leading to distinct tumor microenvironments and disease phenotypes. Effectively characterizing these features would improve the clinical management of glioblastoma. Glucose flux rates through glycolysis and mitochondrial oxidation have been recently shown to quantitatively depict glioblastoma proliferation in mouse models (GL261 and CT2A tumors) using dynamic glucose-enhanced (DGE) deuterium spectroscopy. However, the spatial features of tumor microenvironment phenotypes remain hitherto unresolved. Here, we develop a DGE Deuterium Metabolic Imaging (DMI) approach for profiling tumor microenvironments through glucose conversion kinetics. Using a multimodal combination of tumor mouse models, novel strategies for spectroscopic imaging and noise attenuation, and histopathological correlations, we show that tumor lactate turnover mirrors phenotype differences between GL261 and CT2A mouse glioblastoma, whereas recycling of the peritumoral glutamate-glutamine pool is a potential marker of invasion capacity in pooled cohorts, linked to secondary brain lesions. These findings were validated by histopathological characterization of each tumor, including cell density and proliferation, peritumoral invasion and distant migration, and immune cell infiltration. Our study bodes well for precision neuro-oncology, highlighting the importance of mapping glucose flux rates to better understand the metabolic heterogeneity of glioblastoma and its links to disease phenotypes.

Keywords:  cancer biology; deuterium metabolic imaging; glioblastoma; glycolysis; kinetic modeling; mitochondrial metabolism; mouse

DOI:  https://doi.org/10.7554/eLife.100570
J Cell Biol. 2025 Apr 07. pii: e202407110. [Epub ahead of print]224(4):

Cytoplasmic ribosomes on mitochondria alter the local membrane environment for protein import.

Ya-Ting Chang, Benjamin A Barad, Juliette Hamid, Hamidreza Rahmani, Brian M Zid, Danielle A Grotjahn.

Most of the mitochondria proteome is nuclear-encoded, synthesized by cytoplasmic ribosomes, and targeted to the mitochondria posttranslationally. However, a subset of mitochondrial-targeted proteins is imported co-translationally, although the molecular mechanisms governing this process remain unclear. We employ cellular cryo-electron tomography to visualize interactions between cytoplasmic ribosomes and mitochondria in Saccharomyces cerevisiae. We use surface morphometrics tools to identify a subset of ribosomes optimally oriented on mitochondrial membranes for protein import. This allows us to establish the first subtomogram average structure of a cytoplasmic ribosome at the mitochondrial surface in the native cellular context, which showed three distinct connections with the outer mitochondrial membrane surrounding the peptide exit tunnel. Further, this analysis demonstrated that cytoplasmic ribosomes primed for mitochondrial protein import cluster on the outer mitochondrial membrane at sites of local constrictions of the outer and inner mitochondrial membranes. Overall, our study reveals the architecture and the spatial organization of cytoplasmic ribosomes at the mitochondrial surface, providing a native cellular context to define the mechanisms that mediate efficient mitochondrial co-translational protein import.

DOI: https://doi.org/10.1083/jcb.202407110
Cell Rep. 2025 Mar 05. pii: S2211-1247(25)00148-2. [Epub ahead of print]44(3): 115377

Mitochondrial fusion and cristae reorganization facilitate acquisition of cardiomyocyte identity during reprogramming of murine fibroblasts.

Brian M Spurlock, Yifang Xie, Yiran Song, Shea N Ricketts, James Rock Hua, Haley R Chi, Meenakshi Nishtala, Rustem Salmenov, Jiandong Liu, Li Qian.

  Cardiomyocytes (CMs) rely on mitochondrial energy produced in highly interconnected mitochondrial networks. Direct reprogramming of cardiac fibroblasts (CFs) into induced CMs (iCMs) shows promise for treating cardiac injury, but little work has investigated mitochondrial energetics and morphology during the conversion of CFs to iCMs. We characterized mitochondria during direct cardiac reprogramming of murine neonatal CFs (mnCFs). Reprogramming increased mitochondrial respiration and interconnectivity but not to the levels of native CMs. We therefore investigated whether perturbations to mitochondrial dynamics impacted reprogramming. Mitochondrial fusion (joining) was essential for iCM generation, while various fission (dividing) genes were reprogramming barriers. In particular, the loss of mitochondrial fission regulator 1 like (Mtfr1l) significantly increased the yield of functionally mature iCMs and induced mitochondrial fusion and respiration. These changes were countered by the concomitant loss of fusion effector optical atrophy protein 1 (Opa1). The present study advances our understanding of mitochondrial barriers to and mechanisms of direct cardiac reprogramming.

Keywords:  CP: Metabolism; CP: Stem cell research; Mtfr1l; cell fate conversion; direct cardiac reprogramming; machine learning; mitochondria; mitochondrial dynamics; mitochondrial energetics; mitochondrial fission; mitochondrial fusion; regenerative medicine

DOI:  https://doi.org/10.1016/j.celrep.2025.115377
FEBS J. 2025 Mar 06.

Discovery of a novel alpha isoform of the long-known enzyme LDHA provides new insights into cancer research.

Wonyoung Park, Shibo Wei, Dongryeol Ryu, Ki-Tae Ha.

  Lactate dehydrogenase A is a key enzyme in energy metabolism, with significant roles in cancer progression. Huang et al. identified LDHAα, a novel LDHA isoform derived from an alternative transcript initiated at AUG198, producing a protein 3 kDa larger than canonical LDHA. LDHAα exhibits enhanced glycolytic activity and promotes glucose uptake, lactate production, and tumor growth more effectively than LDHA. Regulated by c-MYC and FOXM1, LDHAα is mainly cytoplasmic and serves as a potential cancer biomarker and therapeutic target. These findings highlight LDHAα's unique role in cancer metabolism and its potential for advancing targeted cancer therapies.

Keywords:  FOXM1; LDHA; LDHAα; c‐MYC; glycolysis

DOI:  https://doi.org/10.1111/febs.70058
J Cell Biol. 2025 May 05. pii: e202407190. [Epub ahead of print]224(5):

Ca2+ binding to Esyt modulates membrane contact site density in Drosophila photoreceptors.

Vaisaly R Nath, Harini Krishnan, Shirish Mishra, Padinjat Raghu.

Membrane contact sites (MCS) between the plasma membrane (PM) and endoplasmic reticulum (ER) regulate Ca2+ influx. However, the mechanisms by which cells modulate ER-PM MCS density are not understood, and the role of Ca2+, if any, in regulating these is unknown. We report that in Drosophila photoreceptors, MCS density is regulated by the Ca2+ channels, TRP and TRPL. Regulation of MCS density by Ca2+ is mediated by Drosophila extended synaptotagmin (dEsyt), a protein localized to ER-PM MCS and previously shown to regulate MCS density. We find that the Ca2+-binding activity of dEsyt is required for its function in vivo. dEsytCaBM, a Ca2+ non-binding mutant of dEsyt is unable to modulate MCS structure. Further, reconstitution of dEsyt null photoreceptors with dEsytCaBM is unable to rescue ER-PM MCS density and other key phenotypes. Thus, our data supports a role for Ca2+ binding to dEsyt in regulating ER-PM MCS density in photoreceptors thus tuning signal transduction during light-activated Ca2+ influx.

DOI: https://doi.org/10.1083/jcb.202407190
Nat Commun. 2025 Feb 28. 16(1): 2053

Neuron-specific isoform of PGC-1α regulates neuronal metabolism and brain aging.

Dylan C Souder, Eric R McGregor, Josef P Clark, Timothy W Rhoads, Tiaira J Porter, Kevin W Eliceiri, Darcie L Moore, Luigi Puglielli, Rozalyn M Anderson.

The brain is a high-energy tissue, and although aging is associated with dysfunctional inflammatory and neuron-specific functional pathways, a direct connection to metabolism is not established. Here, we show that isoforms of mitochondrial regulator PGC-1α are driven from distinct brain cell-type specific promotors, repressed with aging, and integral in coordinating metabolism and growth signaling. Transcriptional and proteomic profiles of cortex from male adult, middle age, and advanced age mice reveal an aging metabolic signature linked to PGC-1α. In primary culture, a neuron-exclusive promoter produces the functionally dominant isoform of PGC-1α. Using growth repression as a challenge, we find that PGC-1α is regulated downstream of GSK3β independently across promoters. Broad cellular metabolic consequences of growth inhibition observed in vitro are mirrored in vivo, including activation of PGC-1α directed programs and suppression of aging pathways. These data place PGC-1α centrally in a growth and metabolism network directly relevant to brain aging.

DOI: https://doi.org/10.1038/s41467-025-57363-y
Nat Commun. 2025 Mar 03. 16(1): 2135

Proximity proteomics reveals a mechanism of fatty acid transfer at lipid droplet-mitochondria- endoplasmic reticulum contact sites.

Ayenachew Bezawork-Geleta, Camille J Devereux, Stacey N Keenan, Jieqiong Lou, Ellie Cho, Shuai Nie, David P De Souza, Vinod K Narayana, Nicole A Siddall, Carlos H M Rodrigues, Stephanie Portelli, Tenghao Zheng, Hieu T Nim, Mirana Ramialison, Gary R Hime, Garron T Dodd, Elizabeth Hinde, David B Ascher, David A Stroud, Matthew J Watt.

Membrane contact sites between organelles are critical for the transfer of biomolecules. Lipid droplets store fatty acids and form contacts with mitochondria, which regulate fatty acid oxidation and adenosine triphosphate production. Protein compartmentalization at lipid droplet-mitochondria contact sites and their effects on biological processes are poorly described. Using proximity-dependent biotinylation methods, we identify 71 proteins at lipid droplet-mitochondria contact sites, including a multimeric complex containing extended synaptotagmin (ESYT) 1, ESYT2, and VAMP Associated Protein B and C (VAPB). High resolution imaging confirms localization of this complex at the interface of lipid droplet-mitochondria-endoplasmic reticulum where it likely transfers fatty acids to enable β-oxidation. Deletion of ESYT1, ESYT2 or VAPB limits lipid droplet-derived fatty acid oxidation, resulting in depletion of tricarboxylic acid cycle metabolites, remodeling of the cellular lipidome, and induction of lipotoxic stress. These findings were recapitulated in Esyt1 and Esyt2 deficient mice. Our study uncovers a fundamental mechanism that is required for lipid droplet-derived fatty acid oxidation and cellular lipid homeostasis, with implications for metabolic diseases and survival.

DOI: https://doi.org/10.1038/s41467-025-57405-5
PLoS One. 2025 ;20(3): e0318557

Untargeted lipidomic analysis of metabolic dysfunction-associated steatohepatitis in women with morbid obesity.

Laia Bertran, Jordi Capellades, Sonia Abelló, Cristóbal Richart.

Metabolic Dysfunction-Associated Steatohepatitis (MASH) represents the severe condition of Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD). Currently, there is a need to identify non-invasive biomarkers for an accurate diagnosis of MASH. Previously, omics studies identified alterations in lipid metabolites involved in MASLD. However, these studies require validation in other cohorts. In this sense, our aim was to perform lipidomics to identify the circulating lipid metabolite profile of MASH. We assessed a liquid chromatography coupled to a mass spectrometer-based untargeted lipidomic assay in serum samples of 216 women with morbid obesity that were stratified according to their hepatic diagnosis into Normal Liver (NL, n = 44), Simple Steatosis (SS, n = 66) and MASH (n = 106). First, we identified a profile of lipid metabolites that are increased in MASLD, composed of ceramides, triacylglycerols (TAG) and some phospholipids. Then, we identified that patients with SS have a characteristic profile of increased levels of ceramides, diacylglycerols DG (36:2) and DG (36:4), some TAG and a few phospholipids such as PC (32:1), PE (38:3), PE (40:6), PI (32:0) and PI (32:1). Later, in MASH patients, we found increased levels of ceramides, deoxycholic acid, a set of TAG, and some phospholipids such as PC, PE, PI and LPI; while we found decreased levels of the DG (36:0). Finally, we have reported a panel of lipid metabolites that might be used to differentiate patients with MASH from SS patients, made up of increased levels of 9-HODE some PC and PE, the LPI (16:0) and decreased levels of DG (36:0). To conclude, our investigation has suggested a lipid metabolite profile associated with MASLD and MASH. Specifically, a set of lipid metabolites seems to be discriminatory in MASH subjects compared to SS individuals. Thus, this panel of lipid metabolites could be used as a non-invasive diagnostic tool.

DOI: https://doi.org/10.1371/journal.pone.0318557
Sci Rep. 2025 Mar 03. 15(1): 7418

Single-nucleus RNA sequencing uncovers metabolic dysregulation in the prefrontal cortex of major depressive disorder patients.

Xiang-Yao Li, Yingbo Rao, Guo-Hao Li, Luxi He, Yaohan Wang, Wenli He, Ping Fang, Chenyu Pei, Lun Xi, Haiyan Xie, Yun-Rong Lu.

  Major depressive disorder (MDD) is a widespread psychiatric condition, recognized as the third leading cause of global disease burden in 2008. In the context of MDD, alterations in synaptic transmission within the prefrontal cortex (PFC) are associated with PFC hypoactivation, a key factor in cognitive function and mood regulation. Given the high energy demands of the central nervous system, these synaptic changes suggest a metabolic imbalance within the PFC of MDD patients. However, the cellular mechanisms underlying this metabolic dysregulation remain not fully elucidated. This study employs single-nucleus RNA sequencing (snRNA-seq) data to predict metabolic alterations in the dorsolateral PFC (DLPFC) of MDD patients. Our analysis revealed cell type-specific metabolic patterns, notably the disruption of oxidative phosphorylation and carbohydrate metabolism in the DLPFC of MDD patients. Gene set enrichment analysis based on human phenotype ontology predicted alterations in serum lactate levels in MDD patients, corroborated by the observed decrease in lactate levels in MDD patients compared to 47 age-matched healthy controls (HCs). This transcriptional analysis offers novel insights into the metabolic disturbances associated with MDD and the energy dynamics underlying DLPFC hypoactivation. These findings are instrumental for comprehending the pathophysiology of MDD and may guide the development of innovative therapeutic strategies.

Keywords:  Glycolysis; KEGG; Major depressive disorder; Serum lactate; SnRNA-Seq

DOI:  https://doi.org/10.1038/s41598-025-92030-8
bioRxiv. 2025 Feb 21. pii: 2025.02.20.639223. [Epub ahead of print]

The alternative oxidase reconfigures the larval mitochondrial electron transport system to accelerate growth and development in Drosophila melanogaster.

Geovana S Garcia, Murilo F Othonicar, Antonio Thiago P Campos, Eric A Kilbourn, Kenia C Bicego, Johannes Lerchner, Jason M Tennessen, Marcos T Oliveira.

The alternative oxidase (AOX) is naturally present in the mitochondrial electron transfer system (ETS) of many organisms but absent in vertebrates and most insects. AOX oxidizes coenzyme Q and reduces O 2 in H 2 O, partially replacing the ETS cytochrome c segment and alleviating the oxidative stress caused by ETS overload. As successfully demonstrated in animal models, AOX shows potential in mitigating mitochondrial diseases. However, its non-proton-pumping nature may uncouple mitochondria, leading to excessive heat generation and interference with normal metabolism and physiology. Here we show that AOX from the tunicate Ciona intestinalis accelerates development of Drosophila melanogaster , elevating larval biomass accumulation (primarily due to increased fat), mobility and food intake, without increasing body heat production. AOX intensifies Leak respiration and lowers oxidative phosphorylation efficiency through functional interactions with the mitochondrial glycerol-3-phosphate dehydrogenase (mGPDH). This is associated with increased complex I (CI)-driven respiration and supercomplex formation, higher cellular NAD+/NADH ratios, and an enhanced flux through the central carbon metabolism. Chemical uncouplers and rotenone confirm the roles of mitochondrial uncoupling and CI in the development of AOX-expressing larvae. Thus, AOX appears to be promoting increased growth by reinforcing the larval proliferative metabolic program via an intricate mechanism that reconfigures the larval ETS.

DOI: https://doi.org/10.1101/2025.02.20.639223
Science. 2025 Mar 07. 387(6738): eadn2623

A subcellular map of translational machinery composition and regulation at the single-molecule level.

Zijian Zhang, Adele Xu, Yunhao Bai, Yuxiang Chen, Kitra Cates, Craig Kerr, Abel Bermudez, Teodorus Theo Susanto, Kelsie Wysong, Fernando J García Marqués, Garry P Nolan, Sharon Pitteri, Maria Barna.

Millions of ribosomes are packed within mammalian cells, yet we lack tools to visualize them in toto and characterize their subcellular composition. In this study, we present ribosome expansion microscopy (RiboExM) to visualize individual ribosomes and an optogenetic proximity-labeling technique (ALIBi) to probe their composition. We generated a super-resolution ribosomal map, revealing subcellular translational hotspots and enrichment of 60S subunits near polysomes at the endoplasmic reticulum (ER). We found that Lsg1 tethers 60S to the ER and regulates translation of select proteins. Additionally, we discovered ribosome heterogeneity at mitochondria guiding translation of metabolism-related transcripts. Lastly, we visualized ribosomes in neurons, revealing a dynamic switch between monosomes and polysomes in neuronal translation. Together, these approaches enable exploration of ribosomal localization and composition at unprecedented resolution.

DOI: https://doi.org/10.1126/science.adn2623
Cell Rep. 2025 Mar 06. pii: S2211-1247(25)00146-9. [Epub ahead of print]44(3): 115375

iMetAct: An integrated systematic inference of metabolic activity for dissecting tumor metabolic preference and tumor-immune microenvironment.

Binxian Wang, Chao Huang, Xuan Liu, Zhenni Liu, Yilei Zhang, Wei Zhao, Qiuran Xu, Ping-Chih Ho, Zhengtao Xiao.

  Metabolic enzymes play a central role in cancer metabolic reprogramming, and their dysregulation creates vulnerabilities that can be exploited for therapy. However, accurately measuring metabolic enzyme activity in a high-throughput manner remains challenging due to the complex, multi-layered regulatory mechanisms involved. Here, we present iMetAct, a framework that integrates metabolic-transcription networks with an information propagation strategy to infer enzyme activity from gene expression data. iMetAct outperforms expression-based methods in predicting metabolite conversion rates by accounting for the effects of post-translational modifications. With iMetAct, we identify clinically significant subtypes of hepatocellular carcinoma with distinct metabolic preferences driven by dysregulated enzymes and metabolic regulators acting at both the transcriptional and non-transcriptional levels. Moreover, applying iMetAct to single-cell RNA sequencing data allows for the exploration of cancer cell metabolism and its interplay with immune regulation in the tumor microenvironment. An accompanying online platform further facilitates tumor metabolic analysis, patient stratification, and immune microenvironment characterization.

Keywords:  CP: Cancer; CP: Metabolism; hepatocellular carcinoma; information propagation; metabolic enzyme activity; tumor stratification; tumor-immune microenvironment

DOI:  https://doi.org/10.1016/j.celrep.2025.115375
Proc Natl Acad Sci U S A. 2025 Mar 11. 122(10): e2426324122

State-dependent motion of a genetically encoded fluorescent biosensor.

Paul C Rosen, Samantha M Horwitz, Daniel J Brooks, Erica Kim, Joseph A Ambarian, Lidia Waidmann, Katherine M Davis, Gary Yellen.

  Genetically encoded biosensors can measure biochemical properties such as small-molecule concentrations with single-cell resolution, even in vivo. Despite their utility, these sensors are "black boxes": Very little is known about the structures of their low- and high-fluorescence states or what features are required to transition between them. We used LiLac, a lactate biosensor with a quantitative fluorescence-lifetime readout, as a model system to address these questions. X-ray crystal structures and engineered high-affinity metal bridges demonstrate that LiLac exhibits a large interdomain twist motion that pulls the fluorescent protein away from a "sealed," high-lifetime state in the absence of lactate to a "cracked," low-lifetime state in its presence. Understanding the structures and dynamics of LiLac will help to think about and engineer other fluorescent biosensors.

Keywords:  genetically encoded fluorescent biosensor; metabolite biosensor; protein conformational change

DOI:  https://doi.org/10.1073/pnas.2426324122