bims-celmim 2024-12-01 papers

bims-celmim

Biomed News

on Cellular and mitochondrial metabolism

Issue of 2024–12–01
twenty papers selected by
Marc Segarra Mondejar

Energy metabolism in osteoprogenitors and osteoblasts: role of the Pentose Phosphate Pathway.
Mitochondrial Respiration Quantification in Yeast Whole Cells.
The nutrient-sensing Rag-GTPase complex in B cells controls humoral immunity via TFEB/TFE3-dependent mitochondrial fitness.
Dynamic remodelling of the endoplasmic reticulum for mitosis.
Enhancing mitochondrial one-carbon metabolism is neuroprotective in Alzheimer's disease models.
Loss of mitochondrial enzyme GPT2 leads to reprogramming of synaptic glutamate metabolism.
ER-tethered stress sensor CREBH regulates mitochondrial unfolded protein response to maintain energy homeostasis.
ACSS1-dependent acetate utilization rewires mitochondrial metabolism to support AML and melanoma tumor growth and metastasis.
New-to-nature CO2-dependent acetyl-CoA assimilation enabled by an engineered B12-dependent acyl-CoA mutase.
Cancer Therapies Targeting Cellular Metabolism.
Metabolic Chaos in Kidney Disease: Unraveling Energy Dysregulation.
Signaling Regulation of FAM134-Dependent ER-Phagy in Cells.
NFE2L2 and SLC25A39 drive cuproptosis resistance through GSH metabolism.
A framework for understanding collective microbiome metabolism.
Nuclear mTORC1 Live-Cell Sensor nTORSEL Reports Differential Nuclear mTORC1 Activity in Cell Lines.
Deep learning-enhanced automated mitochondrial segmentation in FIB-SEM images using an entropy-weighted ensemble approach.
Metabolism and mRNA translation: a nexus of cancer plasticity.
Comprehensive characterization of mitochondrial bioenergetics at different larval stages reveals novel insights about the developmental metabolism of Caenorhabditis elegans.
Mitochondrial calcium uptake declines during aging and is directly activated by oleuropein to boost energy metabolism and skeletal muscle performance.
Targeting Glucose Metabolism: A Novel Therapeutic Approach for Parkinson's Disease.

J Biol Chem. 2024 Nov 26. pii: S0021-9258(24)02518-3. [Epub ahead of print] 108016

Energy metabolism in osteoprogenitors and osteoblasts: role of the Pentose Phosphate Pathway.

Sarah E Catheline, Charles O Smith, Matthew McArthur, Chen Yu, Paul S Brookes, Roman A Eliseev.

  Bioenergetic preferences of osteolineage cells, including osteoprogenitors and osteoblasts (OB), are a matter of intense debate. Early studies pointed to OB reliance on glucose and aerobic glycolysis while more recent works indicated the importance of glutamine as a mitochondrial fuel. Aiming to clarify this issue, we performed metabolic tracing of 13C-labeled glucose and glutamine in human osteolineage cells: bone marrow stromal (a.k.a. mesenchymal stem) cells (BMSC) and BMSC-derived OBs. Glucose tracing showed non-canonical direction of glucose metabolism with high labeling of early glycolytic steps and the Pentose Phosphate Pathway (PPP) but very low labeling of late glycolytic steps and the Krebs cycle. Labeling of Krebs cycle and late steps of glycolysis was primarily from glutamine. These data suggest that in osteolineage cells, glucose is metabolized primarily via the PPP while glutamine is metabolized in the mitochondria, also feeding into the late steps of glycolysis likely via the malate-aspartate shuttle (MAS). This metabolic setup did not change after induction of differentiation. To evaluate the importance of this setup for osteolineage cells, we used the inhibitors of either PPP or MAS and observed a significant reduction in both cell growth and ability to differentiate. In sum, we observed a distinct metabolic wiring in osteolineage cells with high flux of glucose through the PPP and glutamine flux fueling both mitochondria and late steps of glycolysis. This wiring likely reflects their unique capacity to rapidly proliferate and produce extracellular matrix, e.g. after bone fracture.

Keywords:  Malate-Aspartate Shuttle; Mitochondria; Osteoblasts; Osteoprogenitors; Pentose Phosphate Pathway

DOI:  https://doi.org/10.1016/j.jbc.2024.108016
J Vis Exp. 2024 Nov 08.

Mitochondrial Respiration Quantification in Yeast Whole Cells.

Gerardo M Nava, Andres Carrillo-Garmendia, Juan Carlos González-Hernández, Luis Alberto Madrigal-Perez.

Metabolism is mainly coordinated by cellular energy availability and environmental conditions. Assays for knowing how cells adapt energetic metabolism to different nutritional and environmental conditions give valuable information to elucidate molecular mechanisms. Oxidative phosphorylation is the primary source of ATP in most cells, and mitochondrial respiration activity is a key component of oxidative phosphorylation, maintaining mitochondrial membrane potential for ATP synthesis. Mitochondrial respiration is often studied in isolated mitochondria that are missing the cellular context. Here, we present a method for quantifying mitochondrial respiration in yeast-intact cells. This method applies to any yeast species, although it has been generally used for Saccharomyces cerevisiae cells. First, the yeast growth in specific conditions is tested. Then, cells are washed and resuspended in deionized water with a 1:1 ratio (w/v). Cells are then placed in an oximeter chamber with constant stirring, and a Clark electrode is used to quantify oxygen consumption. Some molecules are sequentially placed into the chamber and selected according to this effect on the electron transport chain or ATP synthesis. ATPase inhibitor oligomycin is first added to measure respiration coupled to ATP synthesis. Afterward, an uncoupler is used to measure the maximal respiratory capacity. Finally, a mix of electron transport chain inhibitors is added to discard oxygen consumption unrelated to mitochondrial respiration. Data are analyzed using a linear regression to obtain the slope, representing the oxygen consumption rate. The advantage of this method is that it is specific for yeast mitochondrial respiration, maintaining the cellular context. It is essential to highlight that inhibitors used in mitochondrial respiration quantification could vary between yeast species.

DOI: https://doi.org/10.3791/67186
Nat Commun. 2024 Nov 23. 15(1): 10163

The nutrient-sensing Rag-GTPase complex in B cells controls humoral immunity via TFEB/TFE3-dependent mitochondrial fitness.

Xingxing Zhu, Yue Wu, Yanfeng Li, Xian Zhou, Jens O Watzlawik, Yin Maggie Chen, Ariel L Raybuck, Daniel D Billadeau, Virginia Smith Shapiro, Wolfdieter Springer, Jie Sun, Mark R Boothby, Hu Zeng.

Germinal center (GC) formation, which is an integrant part of humoral immunity, involves energy-consuming metabolic reprogramming. Rag-GTPases are known to signal amino acid availability to cellular pathways that regulate nutrient distribution such as the mechanistic target of rapamycin complex 1 (mTORC1) pathway and the transcription factors TFEB and TFE3. However, the contribution of these factors to humoral immunity remains undefined. Here, we show that B cell-intrinsic Rag-GTPases are critical for the development and activation of B cells. RagA/RagB deficient B cells fail to form GCs, produce antibodies, and to generate plasmablasts during both T-dependent (TD) and T-independent (TI) humoral immune responses. Deletion of RagA/RagB in GC B cells leads to abnormal dark zone (DZ) to light zone (LZ) ratio and reduced affinity maturation. Mechanistically, the Rag-GTPase complex constrains TFEB/TFE3 activity to prevent mitophagy dysregulation and maintain mitochondrial fitness in B cells, which are independent of canonical mTORC1 activation. TFEB/TFE3 deletion restores B cell development, GC formation in Peyer's patches and TI humoral immunity, but not TD humoral immunity in the absence of Rag-GTPases. Collectively, our data establish the Rag GTPase-TFEB/TFE3 pathway as a likely mTORC1 independent mechanism to coordinating nutrient sensing and mitochondrial metabolism in B cells.

DOI: https://doi.org/10.1038/s41467-024-54344-5
J Cell Sci. 2024 Nov 15. pii: jcs261444. [Epub ahead of print]137(22):

Dynamic remodelling of the endoplasmic reticulum for mitosis.

Suzan Kors, Anne-Lore Schlaitz.

  The endoplasmic reticulum (ER) is a dynamic and continuous membrane network with roles in many cellular processes. The importance and maintenance of ER structure and function have been extensively studied in interphase cells, yet recent findings also indicate crucial roles of the ER in mitosis. During mitosis, the ER is remodelled significantly with respect to composition and morphology but persists as a continuous network. The ER interacts with microtubules, actin and intermediate filaments, and concomitant with the mitotic restructuring of all cytoskeletal systems, ER dynamics and distribution change. The ER is a metabolic hub and several examples of altered ER functions during mitosis have been described. However, we lack an overall understanding of the ER metabolic pathways and functions that are active during mitosis. In this Review, we will discuss mitotic changes to the ER at different organizational levels to explore how the mitotic ER, with its distinct properties, might support cell division.

Keywords:  Cell division; ER; ER dynamics and morphology; ER–cytoskeleton contacts; Endoplasmic reticulum; Membrane contact sites; Mitosis

DOI:  https://doi.org/10.1242/jcs.261444
Cell Death Dis. 2024 Nov 24. 15(11): 856

Enhancing mitochondrial one-carbon metabolism is neuroprotective in Alzheimer's disease models.

Yizhou Yu, Civia Z Chen, Ivana Celardo, Bryan Wei Zhi Tan, James D Hurcomb, Nuno Santos Leal, Rebeka Popovic, Samantha H Y Loh, L Miguel Martins.

Alzheimer's disease (AD) is the most common form of age-related dementia. In AD, the death of neurons in the central nervous system is associated with the accumulation of toxic amyloid β peptide (Aβ) and mitochondrial dysfunction. Mitochondria are signal transducers of metabolic and biochemical information, and their impairment can compromise cellular function. Mitochondria compartmentalise several pathways, including folate-dependent one-carbon (1C) metabolism and electron transport by respiratory complexes. Mitochondrial 1C metabolism is linked to electron transport through complex I of the respiratory chain. Here, we analysed the proteomic changes in a fly model of AD by overexpressing a toxic form of Aβ (Aβ-Arc). We found that expressing Aβ-Arc caused alterations in components of both complex I and mitochondrial 1C metabolism. Genetically enhancing mitochondrial 1C metabolism through Nmdmc improved mitochondrial function and was neuroprotective in fly models of AD. We also found that exogenous supplementation with the 1C donor folinic acid improved mitochondrial health in both mammalian cells and fly models of AD. We found that genetic variations in MTHFD2L, the human orthologue of Nmdmc, were linked to AD risk. Additionally, Mendelian randomisation showed that increased folate intake decreased the risk of developing AD. Overall, our data suggest enhancement of folate-dependent 1C metabolism as a viable strategy to delay the progression and attenuate the severity of AD.

DOI: https://doi.org/10.1038/s41419-024-07179-3
Mol Brain. 2024 Nov 27. 17(1): 87

Loss of mitochondrial enzyme GPT2 leads to reprogramming of synaptic glutamate metabolism.

Ozan Baytas, Shawn M Davidson, Julie A Kauer, Eric M Morrow.

  Recessive loss-of-function mutations in the mitochondrial enzyme Glutamate Pyruvate Transaminase 2 (GPT2) cause intellectual disability in children. Given this cognitive disorder, and because glutamate metabolism is tightly regulated to sustain excitatory neurotransmission, here we investigate the role of GPT2 in synaptic function. GPT2 catalyzes a reversible reaction interconverting glutamate and pyruvate with alanine and alpha-ketoglutarate, a TCA cycle intermediate; thereby, GPT2 may play an important role in linking mitochondrial tricarboxylic acid (TCA) cycle with synaptic transmission. In mouse brain, we find that GPT2 is enriched in mitochondria of synaptosomes (isolated synaptic terminals). Loss of Gpt2 in mouse appears to lead to reprogramming of glutamate and glutamine metabolism, and to decreased glutamatergic synaptic transmission. Whole-cell patch-clamp recordings in pyramidal neurons of CA1 hippocampal slices from Gpt2-null mice reveal decreased excitatory post-synaptic currents (mEPSCs) without changes in mEPSC frequency, or importantly, changes in inhibitory post-synaptic currents (mIPSCs). Additional evidence of defective glutamate release included reduced levels of glutamate released from Gpt2-null synaptosomes measured biochemically. Glutamate release from synaptosomes was rescued to wild-type levels by alpha-ketoglutarate supplementation. Additionally, we observed evidence of altered metabolism in isolated Gpt2-null synaptosomes: decreased TCA cycle intermediates, and increased glutamate dehydrogenase activity. Notably, alterations in the TCA cycle and the glutamine pool were alleviated by alpha-ketoglutarate supplementation. In conclusion, our data support a model whereby GPT2 mitochondrial activity may contribute to glutamate availability in pre-synaptic terminals, thereby highlighting potential interactions between pre-synaptic mitochondrial metabolism and synaptic transmission.

Keywords:  Cognitive development; Disease; GPT2; Glutamate; Intellectual disability; Neurometabolic; Neurometabolism; Synapse; TCA cycle

DOI:  https://doi.org/10.1186/s13041-024-01154-x
Proc Natl Acad Sci U S A. 2024 Dec 03. 121(49): e2410486121

ER-tethered stress sensor CREBH regulates mitochondrial unfolded protein response to maintain energy homeostasis.

Hyunbae Kim, Qi Chen, Donghong Ju, Neeraja Purandare, Xuequn Chen, Lobelia Samavati, Li Li, Ren Zhang, Lawrence I Grossman, Kezhong Zhang.

  The Mitochondrial Unfolded Protein Response (UPRmt), a mitochondria-originated stress response to altered mitochondrial proteostasis, plays important roles in various pathophysiological processes. In this study, we revealed that the endoplasmic reticulum (ER)-tethered stress sensor CREBH regulates UPRmt to maintain mitochondrial homeostasis and function in the liver. CREBH is enriched in and required for hepatic Mitochondria-Associated Membrane (MAM) expansion induced by energy demands. Under a fasting challenge or during the circadian cycle, CREBH is activated to promote expression of the genes encoding the key enzymes, chaperones, and regulators of UPRmt in the liver. Activated CREBH, cooperating with peroxisome proliferator-activated receptor α (PPARα), activates expression of Activating Transcription Factor (ATF) 5 and ATF4, two major UPRmt transcriptional regulators, independent of the ER-originated UPR (UPRER) pathways. Hepatic CREBH deficiency leads to accumulation of mitochondrial unfolded proteins, decreased mitochondrial membrane potential, and elevated cellular redox state. Dysregulation of mitochondrial function caused by CREBH deficiency coincides with increased hepatic mitochondrial oxidative phosphorylation (OXPHOS) but decreased glycolysis. CREBH knockout mice display defects in fatty acid oxidation and increased reliance on carbohydrate oxidation for energy production. In summary, our studies uncover that hepatic UPRmt is activated through CREBH under physiological challenges, highlighting a molecular link between ER and mitochondria in maintaining mitochondrial proteostasis and energy homeostasis under stress conditions.

Keywords:  ER-mitochondria contact; cell metabolism; michondrial UPR; transcriptional regulation; unfolded protein response

DOI:  https://doi.org/10.1073/pnas.2410486121
Cell Rep. 2024 Nov 21. pii: S2211-1247(24)01339-1. [Epub ahead of print]43(12): 114988

ACSS1-dependent acetate utilization rewires mitochondrial metabolism to support AML and melanoma tumor growth and metastasis.

Sabina I Hlavaty, Kelsey N Salcido, Katherine A Pniewski, Dzmitry Mukha, Weili Ma, Toshitha Kannan, Joel Cassel, Yellamelli V V Srikanth, Qin Liu, Andrew Kossenkov, Joseph M Salvino, Qing Chen, Zachary T Schug.

  Cancer cells often use alternative nutrient sources to support their metabolism and proliferation. One important alternative nutrient source for many cancers is acetate. Acetate is metabolized into acetyl-coenzyme A (CoA) by acetyl-CoA synthetases 1 and 2 (ACSS1 and ACSS2), which are found in the mitochondria and cytosol, respectively. We show that ACSS1 and ACSS2 are differentially expressed in cancer. Melanoma, breast cancer, and acute myeloid leukemia cells expressing ACSS1 readily use acetate for acetyl-CoA biosynthesis and to fuel mitochondrial metabolism. ACSS1-dependent acetate metabolism decreases the relative contributions of glucose and glutamine to the tricarboxylic acid (TCA) cycle and alters the pentose phosphate pathway and redox state of cancer cells. ACSS1 knockdown decreases acute myeloid leukemia burden in vivo and inhibits melanoma tumor and metastatic growth. Our study highlights a key role for ACSS1-dependent acetate metabolism for cancer growth, raising the potential for ACSS1-targeting therapies in cancer.

Keywords:  ACSS1; ACSS2; ACSS2 inhibitor; AML; CP: Cancer; CP: Metabolism; acetate; cancer; melanoma; metabolism; metastasis

DOI:  https://doi.org/10.1016/j.celrep.2024.114988
Nat Commun. 2024 Nov 26. 15(1): 10235

New-to-nature CO2-dependent acetyl-CoA assimilation enabled by an engineered B12-dependent acyl-CoA mutase.

Helena Schulz-Mirbach, Philipp Wichmann, Ari Satanowski, Helen Meusel, Tong Wu, Maren Nattermann, Simon Burgener, Nicole Paczia, Arren Bar-Even, Tobias J Erb.

Acetyl-CoA is a key metabolic intermediate and the product of various natural and synthetic one-carbon (C1) assimilation pathways. While an efficient conversion of acetyl-CoA into other central metabolites, such as pyruvate, is imperative for high biomass yields, available aerobic pathways typically release previously fixed carbon in the form of CO2. To overcome this loss of carbon, we develop a new-to-nature pathway, the Lcm module, in this study. The Lcm module provides a direct link between acetyl-CoA and pyruvate, is shorter than any other oxygen-tolerant route and notably fixes CO2, instead of releasing it. The Lcm module relies on the new-to-nature activity of a coenzyme B12-dependent mutase for the conversion of 3-hydroxypropionyl-CoA into lactyl-CoA. We demonstrate Lcm activity of the scaffold enzyme 2-hydroxyisobutyryl-CoA mutase from Bacillus massiliosenegalensis, and further improve catalytic efficiency 10-fold by combining in vivo targeted hypermutation and adaptive evolution in an engineered Escherichia coli selection strain. Finally, in a proof-of-principle, we demonstrate the complete Lcm module in vitro. Overall, our work demonstrates a synthetic CO2-incorporating acetyl-CoA assimilation route that expands the metabolic solution space of central carbon metabolism, providing options for synthetic biology and metabolic engineering.

DOI: https://doi.org/10.1038/s41467-024-53762-9
Cold Spring Harb Perspect Med. 2024 Nov 25. pii: a041657. [Epub ahead of print]

Cancer Therapies Targeting Cellular Metabolism.

Benjamin Morris, Alejandro Gutierrez.

Cancer is caused by mutations that drive aberrant growth, proliferation, and invasion, thus overriding regulatory mechanisms that normally link these processes to organismal needs and cellular physiology. This imposes demands for the production of energy and biomass and for survival in microenvironments that are often nonphysiologic and nutrient-poor, which are met by rewiring of cellular metabolism. The resultant dependence of tumor cells on altered metabolism can induce sensitivity to specific metabolic perturbations that can be exploited for cancer therapy. Some cancers are caused by mutations that impart a novel function to metabolic enzymes, leading to the production of a tumor-promoting metabolite that is dispensable in normal cells, representing an ideal therapeutic target. Tumors can also exploit metabolic regulation of cellular immunity to evade antitumor immune responses, and deciphering this biology has revealed potential targets for therapeutic intervention. Here, we discuss a number of illustrative examples highlighting the therapeutic potential and the challenges of targeting metabolism for cancer therapy.

DOI: https://doi.org/10.1101/cshperspect.a041657
J Clin Med. 2024 Nov 11. pii: 6772. [Epub ahead of print]13(22):

Metabolic Chaos in Kidney Disease: Unraveling Energy Dysregulation.

Priya Gupta, Saiya Zhu, Yuan Gui, Dong Zhou.

   BACKGROUND: Acute kidney injury (AKI) and chronic kidney disease (CKD) share a fundamental disruption: metabolic dysfunction.
METHODS: A literature review was performed to determine the metabolic changes that occur in AKI and CKD as well as potential therapeutic targets related to these changes.
RESULTS: In AKI, increased energy demand in proximal tubular epithelial cells drives a shift from fatty acid oxidation (FAO) to glycolysis. Although this shift offers short-term support, it also heightens cellular vulnerability to further injury. As AKI progresses to CKD, metabolic disruption intensifies, with both FAO and glycolysis becoming downregulated, exacerbating cellular damage and fibrosis. These metabolic alterations are governed by shifts in gene expression and protein signaling pathways, which can now be precisely analyzed through advanced omics and histological methods.
CONCLUSIONS: This review examines these metabolic disturbances and their roles in disease progression, highlighting therapeutic interventions that may restore metabolic balance and enhance kidney function. Many metabolic changes that occur in AKI and CKD can be utilized as therapeutic targets, indicating a need for future studies related to the clinical utility of these therapeutics.

Keywords:  AKI; CKD; FAO; energy metabolism; glycolysis

DOI:  https://doi.org/10.3390/jcm13226772
J Cell Physiol. 2024 Nov 25. e31492

Signaling Regulation of FAM134-Dependent ER-Phagy in Cells.

Alessandro Palma, Alessio Reggio.

  The endoplasmic reticulum (ER) is a pivotal organelle responsible for protein and lipid synthesis, calcium homeostasis, and protein quality control within eukaryotic cells. To maintain cellular health, damaged or excess portions of the ER must be selectively degraded via a process known as selective autophagy, or ER-phagy. This specificity is driven by a network of protein receptors and regulatory mechanisms. In this review, we explore the molecular mechanisms governing ER-phagy, with a focus on the FAM134 family of ER-resident ER-phagy receptors. We discuss the molecular pathways and Posttranslational modifications that regulate receptor activation and clustering, and how these modifications fine-tune ER-phagy in response to stress. This review provides a concise understanding of how ER-phagy contributes to cellular homeostasis and highlights the need for further studies in models where ER stress and autophagy are dysregulated.

Keywords:  ER‐phagy; FAM134B; autophagy; endoplasmic reticulum; ubiquitination

DOI:  https://doi.org/10.1002/jcp.31492
Sci Rep. 2024 Nov 28. 14(1): 29579

NFE2L2 and SLC25A39 drive cuproptosis resistance through GSH metabolism.

Jiao Liu, Hu Tang, Fangquan Chen, Changfeng Li, Yangchun Xie, Rui Kang, Daolin Tang.

  Cuproptosis is a recently discovered form of regulated cell death triggered by mitochondrial copper accumulation and proteotoxic stress. Here, we provide the first evidence that glutathione (GSH), a major non-protein thiol in cells, acts as a cuproptosis inhibitor in pancreatic ductal adenocarcinoma (PDAC) cells. Mechanistically, GSH inhibits cuproptosis by chelating copper, contrasting its role in blocking ferroptosis by inhibiting lipid peroxidation. The classical cuproptosis inducer, ES-Cu (elesclomol plus copper), increases the protein stability of the transcription factor NFE2L2 (also known as NRF2), leading to the upregulation of gene expression of glutamate-cysteine ligase modifier subunit (GCLM) and glutamate-cysteine ligase catalytic subunit (GCLC). GCLM and GCLC are rate-limiting enzymes in GSH synthesis, and increased GSH is transported into mitochondria via the solute carrier family 25 member 39 (SLC25A39) transporter. Consequently, genetic inhibition of the NFE2L2-GSH-SLC25A39 pathway enhances cuproptosis-mediated tumor suppression in cell culture and in mouse tumor models. These findings not only reveal distinct mechanisms of GSH in inhibiting cuproptosis and ferroptosis, but also suggest a potential combination strategy to suppress PDAC tumor growth.

Keywords:  Copper; Cuproptosis; Elesclomol; Glutathione; NFE2L2; SLC25A39

DOI:  https://doi.org/10.1038/s41598-024-81317-x
Nat Microbiol. 2024 Dec;9(12): 3097-3109

A framework for understanding collective microbiome metabolism.

Matthias Huelsmann, Olga T Schubert, Martin Ackermann.

Microbiome metabolism underlies numerous vital ecosystem functions. Individual microbiome members often perform partial catabolism of substrates or do not express all of the metabolic functions required for growth. Microbiome members can complement each other by exchanging metabolic intermediates and cellular building blocks to achieve a collective metabolism. We currently lack a mechanistic framework to explain why microbiome members adopt partial metabolism and how metabolic functions are distributed among them. Here we argue that natural selection for proteome efficiency-that is, performing essential metabolic fluxes at a minimal protein investment-explains partial metabolism of microbiome members, which underpins the collective metabolism of microbiomes. Using the carbon cycle as an example, we discuss motifs of collective metabolism, the conditions under which these motifs increase the proteome efficiency of individuals and the metabolic interactions they result in. In summary, we propose a mechanistic framework for how collective metabolic functions emerge from selection on individuals.

DOI: https://doi.org/10.1038/s41564-024-01850-3
Int J Mol Sci. 2024 Nov 12. pii: 12117. [Epub ahead of print]25(22):

Nuclear mTORC1 Live-Cell Sensor nTORSEL Reports Differential Nuclear mTORC1 Activity in Cell Lines.

Yifan Wang, Canrong Li, Yingyi Ouyang, Xiaoduo Xie.

  The mammalian or mechanistic target of rapamycin complex 1 (mTORC1) is activated on the surface of lysosomes and phosphorylates substrates at various subcellular locations, including the lysosome, cytosol, and nucleus. However, the signaling and biological functions of nuclear mTORC1 (nmTORC1) are not well understood, primarily due to limited tools for monitoring mTORC1 activity in the nucleus. In this study, we developed a genetically encoded nmTORC1 sensor, termed nTORSEL, based on the phosphorylation of the eukaryotic initiation factor 4E (eIF4E) binding protein 1 (4EBP1) by mTORC1 within the nucleus. nTORSEL, like its predecessor TORSEL, exhibits a fluorescent punctate pattern in the nucleus through multivalent protein-protein interactions between oligomerized 4EBP1 and eIF4E when nmTORC1 activity is low. We validated nTORSEL using biochemical analyses and imaging techniques across representative cell lines with varying levels of nmTORC1 activity. Notably, nTORSEL specifically detects physiological, pharmacological, and genetic inhibition of nmTORC1 in mouse embryonic fibroblast (MEF) cells but not in HEK293T cells. Therefore, nTORSEL is an effective tool for investigating nuclear mTORC1 signaling in cell lines.

Keywords:  PI3K-AKT-mTOR pathway; amino acid; fluorescent reporter; live-cell sensor; nuclear mTORC1

DOI:  https://doi.org/10.3390/ijms252212117
PLoS One. 2024 ;19(11): e0313000

Deep learning-enhanced automated mitochondrial segmentation in FIB-SEM images using an entropy-weighted ensemble approach.

Yubraj Gupta, Rainer Heintzmann, Carlos Costa, Rui Jesus, Eduardo Pinho.

Mitochondria are intracellular organelles that act as powerhouses by breaking down nutrition molecules to produce adenosine triphosphate (ATP) as cellular fuel. They have their own genetic material called mitochondrial DNA. Alterations in mitochondrial DNA can result in primary mitochondrial diseases, including neurodegenerative disorders. Early detection of these abnormalities is crucial in slowing disease progression. With recent advances in data acquisition techniques such as focused ion beam scanning electron microscopy, it has become feasible to capture large intracellular organelle volumes at data rates reaching 4Tb/minute, each containing numerous cells. However, manually segmenting large data volumes (gigapixels) can be time-consuming for pathologists. Therefore, there is an urgent need for automated tools that can efficiently segment mitochondria with minimal user intervention. Our article proposes an ensemble of two automatic segmentation pipelines to predict regions of interest specific to mitochondria. This architecture combines the predicted outputs from both pipelines using an ensemble learning-based entropy-weighted fusion technique. The methodology minimizes the impact of individual predictions and enhances the overall segmentation results. The performance of the segmentation task is evaluated using various metrics, ensuring the reliability of our results. We used four publicly available datasets to evaluate our proposed method's effectiveness. Our proposed fusion method has achieved a high score in terms of the mean Jaccard index and dice coefficient for all four datasets. For instance, in the UroCell dataset, our proposed fusion method achieved scores of 0.9644 for the mean Jaccard index and 0.9749 for the Dice coefficient. The mean error rate and pixel accuracy were 0.0062 and 0.9938, respectively. Later, we compared it with state-of-the-art methods like 2D and 3D CNN algorithms. Our ensemble approach shows promising segmentation efficiency with minimal intervention and can potentially aid in the early detection and mitigation of mitochondrial diseases.

DOI: https://doi.org/10.1371/journal.pone.0313000
Trends Cell Biol. 2024 Nov 27. pii: S0962-8924(24)00225-3. [Epub ahead of print]

Metabolism and mRNA translation: a nexus of cancer plasticity.

Xinpu Tang, Kaixiu Li, Yuqing Wang, Stéphane Rocchi, Shensi Shen, Michael Cerezo.

  Tumors often face energy deprivation due to mutations, hypoxia, and nutritional deficiencies within the harsh tumor microenvironment (TME), and as an effect of anticancer treatments. This metabolic stress triggers adaptive reprogramming of mRNA translation, which in turn adjusts metabolic plasticity and associated signaling pathways to ensure tumor cell survival. Emerging evidence is beginning to reveal the complex interplay between metabolism and mRNA translation, shedding light on the mechanisms that synchronize ribosome assembly and reconfigure translation programs under metabolic stress. This review explores recent advances in our understanding of the coordination between metabolism and mRNA translation, offering insights that could inform therapeutic strategies targeting both cancer metabolism and translation, with the aim of disrupting cancer cell plasticity and survival.

Keywords:  cancer cell plasticity; mRNA translation; tumor metabolism

DOI:  https://doi.org/10.1016/j.tcb.2024.10.009
PLoS One. 2024 ;19(11): e0306849

Comprehensive characterization of mitochondrial bioenergetics at different larval stages reveals novel insights about the developmental metabolism of Caenorhabditis elegans.

Danielle F Mello, Luiza Perez, Christina M Bergemann, Katherine S Morton, Ian T Ryde, Joel N Meyer.

Mitochondrial bioenergetic processes are fundamental to development, stress responses, and health. Caenorhabditis elegans is widely used to study developmental biology, mitochondrial disease, and mitochondrial toxicity. Oxidative phosphorylation generally increases during development in many species, and genetic and environmental factors may alter this normal trajectory. Altered mitochondrial function during development can lead to both drastic, short-term responses including arrested development and death, and subtle consequences that may persist throughout life and into subsequent generations. Understanding normal and altered developmental mitochondrial biology in C. elegans is currently constrained by incomplete and conflicting reports on how mitochondrial bioenergetic parameters change during development in this species. We used a Seahorse XFe24 Extracellular Flux (XF) Analyzer to carry out a comprehensive analysis of mitochondrial and non-mitochondrial oxygen consumption rates (OCR) throughout larval development in C. elegans. We optimized and describe conditions for analysis of basal OCR, basal mitochondrial OCR, ATP-linked OCR, spare and maximal respiratory capacity, proton leak, and non-mitochondrial OCR. A key consideration is normalization, and we present and discuss results as normalized per individual worm, protein content, worm volume, mitochondrial DNA (mtDNA) count, nuclear DNA (ncDNA) count, and mtDNA:ncDNA ratio. Which normalization process is best depends on the question being asked, and differences in normalization explain some of the discrepancies in previously reported developmental changes in OCR in C. elegans. Broadly, when normalized to worm number, our results agree with previous reports in showing dramatic increases in OCR throughout development. However, when normalized to total protein, worm volume, or ncDNA or mtDNA count, after a significant 2-3-fold increase from L1 to L2 stages, we found small or no changes in most OCR parameters from the L2 to the L4 stage, other than a marginal increase at L3 in spare and maximal respiratory capacity. Overall, our results indicate an earlier cellular shift to oxidative metabolism than suggested in most previous literature.

DOI: https://doi.org/10.1371/journal.pone.0306849
Cell Metab. 2024 Nov 23. pii: S1550-4131(24)00417-0. [Epub ahead of print]

Mitochondrial calcium uptake declines during aging and is directly activated by oleuropein to boost energy metabolism and skeletal muscle performance.

Gaia Gherardi, Anna Weiser, Flavien Bermont, Eugenia Migliavacca, Benjamin Brinon, Guillaume E Jacot, Aurélie Hermant, Mattia Sturlese, Leonardo Nogara, Filippo Vascon, Agnese De Mario, Andrea Mattarei, Emma Garratt, Mark Burton, Karen Lillycrop, Keith M Godfrey, Laura Cendron, Denis Barron, Stefano Moro, Bert Blaauw, Rosario Rizzuto, Jerome N Feige, Cristina Mammucari, Umberto De Marchi.

  Mitochondrial calcium (mtCa2+) uptake via the mitochondrial calcium uniporter (MCU) couples calcium homeostasis and energy metabolism. mtCa2+ uptake via MCU is rate-limiting for mitochondrial activation during muscle contraction, but its pathophysiological role and therapeutic application remain largely uncharacterized. By profiling human muscle biopsies, patient-derived myotubes, and preclinical models, we discovered a conserved downregulation of mitochondrial calcium uniporter regulator 1 (MCUR1) during skeletal muscle aging that associates with human sarcopenia and impairs mtCa2+ uptake and mitochondrial respiration. Through a screen of 5,000 bioactive molecules, we identify the natural polyphenol oleuropein as a specific MCU activator that stimulates mitochondrial respiration via mitochondrial calcium uptake 1 (MICU1) binding. Oleuropein activates mtCa2+ uptake and energy metabolism to enhance endurance and reduce fatigue in young and aged mice but not in muscle-specific MCU knockout (KO) mice. Our work demonstrates that impaired mtCa2+ uptake contributes to mitochondrial dysfunction during aging and establishes oleuropein as a novel food-derived molecule that specifically targets MCU to stimulate mitochondrial bioenergetics and muscle performance.

Keywords:  MCU; MCUR1; aging; calcium signaling; endurance; energy; fatigue; mitochondria; polyphenols; sarcopenia; skeletal muscle

DOI:  https://doi.org/10.1016/j.cmet.2024.10.021
Cells. 2024 Nov 13. pii: 1876. [Epub ahead of print]13(22):

Targeting Glucose Metabolism: A Novel Therapeutic Approach for Parkinson's Disease.

Ahmed Tanvir, Junghyun Jo, Sang Myun Park.

  Glucose metabolism is essential for the maintenance and function of the central nervous system. Although the brain constitutes only 2% of the body weight, it consumes approximately 20% of the body's total energy, predominantly derived from glucose. This high energy demand of the brain underscores its reliance on glucose to fuel various functions, including neuronal activity, synaptic transmission, and the maintenance of ion gradients necessary for nerve impulse transmission. Increasing evidence shows that many neurodegenerative diseases, including Parkinson's disease (PD), are associated with abnormalities in glucose metabolism. PD is characterized by the progressive loss of dopaminergic neurons in the substantia nigra, accompanied by the accumulation of α-synuclein protein aggregates. These pathological features are exacerbated by mitochondrial dysfunction, oxidative stress, and neuroinflammation, all of which are influenced by glucose metabolism disruptions. Emerging evidence suggests that targeting glucose metabolism could offer therapeutic benefits for PD. Several antidiabetic drugs have shown promise in animal models and clinical trials for mitigating the symptoms and progression of PD. This review explores the current understanding of the association between PD and glucose metabolism, emphasizing the potential of antidiabetic medications as a novel therapeutic approach. By improving glucose uptake and utilization, enhancing mitochondrial function, and reducing neuroinflammation, these drugs could address key pathophysiological mechanisms in PD, offering hope for more effective management of this debilitating disease.

Keywords:  Parkinson’s disease; anti-diabetic drugs; drug repositioning; glucose metabolism; neurodegenerative disease

DOI:  https://doi.org/10.3390/cells13221876