bims-celmim 2024-01-28 papers

bims-celmim

Biomed News

on Cellular and mitochondrial metabolism

Issue of 2024–01–28
twenty-six papers selected by
Marc Segarra Mondejar, University of Cologne

Functional interplay of lipid droplets and mitochondria.
Recent Advances in Electrochemical Detection of Cell Energy Metabolism.
A comprehensive review on signaling attributes of serine and serine metabolism in health and disease.
AKT1 phosphorylation of cytoplasmic ME2 induces a metabolic switch to glycolysis for tumorigenesis.
Acetyltransferase P300 Regulates Glucose Metabolic Reprogramming through Catalyzing Succinylation in Lung Cancer.
Glutamine Metabolism Promotes Renal Fibrosis through Regulation of Mitochondrial Energy Generation and Mitochondrial Fission.
Phosphate starvation signaling increases mitochondrial membrane potential through respiration-independent mechanisms.
A mouse model to study glutathione limitation in vivo.
Mitochondrial choline import regulates purine nucleotide pools via SLC25A48.
p300 nucleocytoplasmic shuttling underlies mTORC1 hyperactivation in Hutchinson-Gilford progeria syndrome.
Innovative Cyanine-Based Fluorescent Dye for Targeted Mitochondrial Imaging and Its Utility in Whole-Brain Visualization.
Metabolic alterations in hereditary and sporadic renal cell carcinoma.
Oligodendroglial metabolic support of myelinated axons driven by K+ dynamics.
Motion of VAPB molecules reveals ER-mitochondria contact site subdomains.
Potassium Ions Decrease Mitochondrial Matrix pH: Implications for ATP Production and Reactive Oxygen Species Generation.
Amino Acid Transporters Proteins Involved in the Glutamate-Glutamine Cycle and Their Alterations in Murine Models of Alzheimer's Disease.
Nano-medicine therapy reprogramming metabolic network of tumor microenvironment: new opportunity for cancer therapies.
The Role of Amino Acids in Non-Enzymatic Antioxidant Mechanisms in Cancer: A Review.
Mitochondrial complex I inhibition triggers NAD+-independent glucose oxidation via successive NADPH formation, "futile" fatty acid cycling, and FADH2 oxidation.
Oligodendrocyte-axon metabolic coupling is mediated by extracellular K+ and maintains axonal health.
Mitochondria-targetable small molecule fluorescent probes for the detection of cancer-associated biomarkers: A review.
Comprehensive review of amino acid transporters as therapeutic targets.
A data-driven approach for timescale decomposition of biochemical reaction networks.
Protocol for measuring mitochondrial size in mouse and human liver tissues.
Metabolic heterogeneity in cancer.
A genetically-encoded fluorescent biosensor for visualization of acetyl-CoA in live cells.

FEBS Lett. 2024 Jan 24.

Functional interplay of lipid droplets and mitochondria.

Ludovic Enkler, Anne Spang.

  Our body stores energy mostly in form of fatty acids (FAs) in lipid droplets (LDs). From there the FAs can be mobilized and transferred to peroxisomes and mitochondria. This transfer is dependent on close opposition of LDs and mitochondria and peroxisomes and happens at membrane contact sites. However, the composition and the dynamics of these contact sites is not well understood, which is in part due to the dependence on the metabolic state of the cell and on the cell- and tissue-type. Here, we summarize the current knowledge on the contacts between lipid droplets and mitochondria both in mammals and in the yeast Saccharomyces cerevisiae, in which various contact sites are well studied. We discuss possible functions of the contact site and their implication in disease.

Keywords:  disease; fatty acids; mammals; metabolism; stress; yeast; β-oxidation

DOI:  https://doi.org/10.1002/1873-3468.14809
Biosensors (Basel). 2024 Jan 15. pii: 46. [Epub ahead of print]14(1):

Recent Advances in Electrochemical Detection of Cell Energy Metabolism.

Kyeong-Mo Koo, Chang-Dae Kim, Tae-Hyung Kim.

  Cell energy metabolism is a complex and multifaceted process by which some of the most important nutrients, particularly glucose and other sugars, are transformed into energy. This complexity is a result of dynamic interactions between multiple components, including ions, metabolic intermediates, and products that arise from biochemical reactions, such as glycolysis and mitochondrial oxidative phosphorylation (OXPHOS), the two main metabolic pathways that provide adenosine triphosphate (ATP), the main source of chemical energy driving various physiological activities. Impaired cell energy metabolism and perturbations or dysfunctions in associated metabolites are frequently implicated in numerous diseases, such as diabetes, cancer, and neurodegenerative and cardiovascular disorders. As a result, altered metabolites hold value as potential disease biomarkers. Electrochemical biosensors are attractive devices for the early diagnosis of many diseases and disorders based on biomarkers due to their advantages of efficiency, simplicity, low cost, high sensitivity, and high selectivity in the detection of anomalies in cellular energy metabolism, including key metabolites involved in glycolysis and mitochondrial processes, such as glucose, lactate, nicotinamide adenine dinucleotide (NADH), reactive oxygen species (ROS), glutamate, and ATP, both in vivo and in vitro. This paper offers a detailed examination of electrochemical biosensors for the detection of glycolytic and mitochondrial metabolites, along with their many applications in cell chips and wearable sensors.

Keywords:  cell chip; electrochemical biosensor; glycolytic metabolites; mitochondrial metabolites; wearable sensor

DOI:  https://doi.org/10.3390/bios14010046
Int J Biol Macromol. 2024 Jan 20. pii: S0141-8130(24)00410-0. [Epub ahead of print]260(Pt 2): 129607

A comprehensive review on signaling attributes of serine and serine metabolism in health and disease.

Di Wu, Kejia Zhang, Faheem Ahmed Khan, Nuruliarizki Shinta Pandupuspitasari, Kaifeng Guan, Fei Sun, Chunjie Huang.

  Serine is a metabolite with ever-expanding metabolic and non-metabolic signaling attributes. By providing one‑carbon units for macromolecule biosynthesis and functional modifications, serine and serine metabolism largely impinge on cellular survival and function. Cancer cells frequently have a preference for serine metabolic reprogramming to create a conducive metabolic state for survival and aggressiveness, making intervention of cancer-associated rewiring of serine metabolism a promising therapeutic strategy for cancer treatment. Beyond providing methyl donors for methylation in modulation of innate immunity, serine metabolism generates formyl donors for mitochondrial tRNA formylation which is required for mitochondrial function. Interestingly, fully developed neurons lack the machinery for serine biosynthesis and rely heavily on astrocytic l-serine for production of d-serine to shape synaptic plasticity. Here, we recapitulate recent discoveries that address the medical significance of serine and serine metabolism in malignancies, mitochondrial-associated disorders, and neurodegenerative pathologies. Metabolic control and epigenetic- and posttranslational regulation of serine metabolism are also discussed. Given the metabolic similarities between cancer cells, neurons and germ cells, we further propose the relevance of serine metabolism in testicular homeostasis. Our work provides valuable hints for future investigations that will lead to a deeper understanding of serine and serine metabolism in cellular physiology and pathology.

Keywords:  Cancer therapeutics; Mitochondrial-associated disorders; Neurodegenerative pathologies; Serine; Serine metabolic reprogramming

DOI:  https://doi.org/10.1016/j.ijbiomac.2024.129607
Nat Commun. 2024 Jan 23. 15(1): 686

AKT1 phosphorylation of cytoplasmic ME2 induces a metabolic switch to glycolysis for tumorigenesis.

Taiqi Chen, Siyi Xie, Jie Cheng, Qiao Zhao, Hong Wu, Peng Jiang, Wenjing Du.

Many types of tumors feature aerobic glycolysis for meeting their increased energetic and biosynthetic demands. However, it remains still unclear how this glycolytic phenomenon is achieved and coordinated with other metabolic pathways in tumor cells in response to growth stimuli. Here we report that activation of AKT1 induces a metabolic switch to glycolysis from the mitochondrial metabolism via phosphorylation of cytoplasmic malic enzyme 2 (ME2), named ME2fl (fl means full length), favoring an enhanced glycolytic phenotype. Mechanistically, in the cytoplasm, AKT1 phosphorylates ME2fl at serine 9 in the mitochondrial localization signal peptide at the N-terminus, preventing its mitochondrial translocation. Unlike mitochondrial ME2, which accounts for adjusting the tricarboxylic acid (TCA) cycle, ME2fl functions as a scaffold that brings together the key glycolytic enzymes phosphofructokinase (PFKL), glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and pyruvate kinase M2 (PKM2), as well as Lactate dehydrogenase A (LDHA), to promote glycolysis in the cytosol. Thus, through phosphorylation of ME2fl, AKT1 enhances the glycolytic capacity of tumor cells in vitro and in vivo, revealing an unexpected role for subcellular translocation switching of ME2 mediated by AKT1 in the metabolic adaptation of tumor cells to growth stimuli.

DOI: https://doi.org/10.1038/s41467-024-44772-8
Int J Mol Sci. 2024 Jan 15. pii: 1057. [Epub ahead of print]25(2):

Acetyltransferase P300 Regulates Glucose Metabolic Reprogramming through Catalyzing Succinylation in Lung Cancer.

Qingzhi Ma, Qingmei Zeng, Kun Wang, Meirui Qian, Jingzhuo Li, Hao Wang, Huijie Zhang, Jianli Jiang, Zhinan Chen, Wan Huang.

  Aberrant protein post-translational modification is a hallmark of malignant tumors. Lysine succinylation (Ksucc) plays a vital role in cell energy metabolism in various cancers. However, whether succinylation can be catalyzed by acetyltransferase p300 remains unclear. In this study, we unveiled that p300 is a "writer" for succinylation, and p300-mediated Ksucc promotes cell glycometabolism in lung adenocarcinoma (LUAD). Specifically, our succinylome data revealed that EP300 deficiency leads to the systemic reduction of Ksucc, and 79.55% of the p300-succinylated proteins were found in the cytoplasm, which were primarily enriched in the carbohydrate metabolism process. Interestingly, deleting EP300 led to a notable decrease in Ksucc levels on several glycolytic enzymes, especially Phosphoglycerate Kinase 1 (PGK1). Mutation of the succinylated site of PGK1 notably hindered cell glycolysis and lactic acid excretion. Metabolomics in vivo indicated that p300-caused metabolic reprogramming was mainly attributed to the altered carbohydrate metabolism. In addition, 89.35% of LUAD patients exhibited cytoplasmic localization of p300, with higher levels in tumor tissues than adjacent normal tissues. High levels of p300 correlated with advanced tumor stages and poor prognosis of LUAD patients. Briefly, we disclose the activity of p300 to catalyze succinylation, which contributes to cell glucose metabolic reprogramming and malignant progression of lung cancer.

Keywords:  EP300; PGK1; glucose metabolism; lung cancer; lysine succinylation

DOI:  https://doi.org/10.3390/ijms25021057
Int J Biol Sci. 2024 ;20(3): 987-1003

Glutamine Metabolism Promotes Renal Fibrosis through Regulation of Mitochondrial Energy Generation and Mitochondrial Fission.

Yang Cai, Beichen Tian, Yuanjun Deng, Lele Liu, Chunjiang Zhang, Wei Peng, Qian Li, Tianjing Zhang, Min Han, Gang Xu.

  Fibroblast activation and proliferation is an essential phase in the progression of renal fibrosis. Despite the recognized significance of glutamine metabolism in cellular growth and proliferation, its precise pathophysiological relevance in renal fibrosis remains uncertain. Therefore, this study aims to investigate the involvement of glutamine metabolism in fibroblast activation and its possible mechanism. Our findings highlight the importance of glutamine metabolism in fibroblast activation and reveal that patients with severe fibrosis exhibit elevated serum glutamine levels and increased expression of kidney glutamine synthetase. Furthermore, the deprivation of glutamine metabolism in vitro and in vivo could inhibit fibroblast activation, thereby ameliorating renal fibrosis. It was also detected that glutamine metabolism is crucial for maintaining mitochondrial function and morphology. These effects may partially depend on the metabolic intermediate α-ketoglutaric acid. Moreover, glutamine deprivation led to upregulated mitochondrial fission in fibroblasts and the activation of the mammalian target of rapamycin / mitochondrial fission process 1 / dynamin-related protein 1 pathway. Thus, these results provide compelling evidence that the modulation of glutamine metabolism initiates the regulation of mitochondrial function, thereby facilitating the progression of renal fibrosis. Consequently, targeting glutamine metabolism emerges as a novel and promising avenue for therapeutic intervention and prevention of renal fibrosis.

Keywords:  Fibroblasts; Glutamine; Mitochondria; Mitochondrial fission; Renal fibrosis; α-ketoglutaric acid

DOI:  https://doi.org/10.7150/ijbs.89960
Elife. 2024 Jan 22. pii: e84282. [Epub ahead of print]13

Phosphate starvation signaling increases mitochondrial membrane potential through respiration-independent mechanisms.

Yeyun Ouyang, Mi-Young Jeong, Corey N Cunningham, Jordan A Berg, Ashish G Toshniwal, Casey E Hughes, Kristina Seiler, Jonathan G Van Vranken, Ahmad A Cluntun, Geanette Lam, Jacob M Winter, Emel Akdoǧan, Katja K Dove, Sara M Nowinski, Matthew West, Greg Odorizzi, Steven P Gygi, Cory D Dunn, Dennis R Winge, Jared Rutter.

  Mitochondrial membrane potential directly powers many critical functions of mitochondria, including ATP production, mitochondrial protein import, and metabolite transport. Its loss is a cardinal feature of aging and mitochondrial diseases, and cells closely monitor membrane potential as an indicator of mitochondrial health. Given its central importance, it is logical that cells would modulate mitochondrial membrane potential in response to demand and environmental cues, but there has been little exploration of this question. We report that loss of the Sit4 protein phosphatase in yeast increases mitochondrial membrane potential, both through inducing the electron transport chain and the phosphate starvation response. Indeed, a similarly elevated mitochondrial membrane potential is also elicited simply by phosphate starvation or by abrogation of the Pho85-dependent phosphate sensing pathway. This enhanced membrane potential is primarily driven by an unexpected activity of the ADP/ATP carrier. We also demonstrate that this connection between phosphate limitation and enhancement of mitochondrial membrane potential is observed in primary and immortalized mammalian cells as well as in Drosophila. These data suggest that mitochondrial membrane potential is subject to environmental stimuli and intracellular signaling regulation and raise the possibility for therapeutic enhancement of mitochondrial function even in defective mitochondria.

Keywords:  D. melanogaster; S. cerevisiae; cell biology; human

DOI:  https://doi.org/10.7554/eLife.84282
bioRxiv. 2024 Jan 09. pii: 2024.01.08.574722. [Epub ahead of print]

A mouse model to study glutathione limitation in vivo.

Rebecca C Timson, Artem Khan, Beste Uygur, Marwa Saad, Hsi-Wen Yeh, Nicole DelGaudio, Ross Weber, Hanan Alwaseem, Jing Gao, Chingwen Yang, Kıvanç Birsoy.

Glutathione (GSH) is a highly abundant tripeptide thiol that performs diverse protective and biosynthetic functions in cells. While changes in GSH availability are linked to many diseases, including cancer and neurodegenerative disorders, determining the function of GSH in physiology and disease has been challenging due to its tight regulation. To address this, we generated cell and mouse models that express a bifunctional glutathione-synthesizing enzyme from Streptococcus Thermophilus (GshF). GshF expression allows efficient production of GSH in the cytosol and mitochondria and prevents cell death in response to GSH depletion, but not ferroptosis, indicating that GSH is not a limiting factor under lipid peroxidation. CRISPR screens using engineered enzymes revealed metabolic liabilities under compartmentalized GSH depletion. Finally, GshF expression in mice is embryonically lethal but sustains postnatal viability when restricted to adulthood. Overall, our work identifies a conditional mouse model to investigate the role of GSH availability in physiology and disease.

DOI: https://doi.org/10.1101/2024.01.08.574722
bioRxiv. 2024 Jan 01. pii: 2023.12.31.573776. [Epub ahead of print]

Mitochondrial choline import regulates purine nucleotide pools via SLC25A48.

Anthony R P Verkerke, Xu Shi, Ichitaro Abe, Robert E Gerszten, Shingo Kajimura.

Choline is an essential nutrient for cellular metabolism, including the biosynthesis of phospholipids, neurotransmitters, and one-carbon metabolism. A critical step of choline catabolism is the mitochondrial import and synthesis of chorine-derived methyl donors, such as betaine. However, the underlying mechanisms and the biological significance of mitochondrial choline catabolism remain insufficiently understood. Here, we report that a mitochondrial inner-membrane protein SLC25A48 controls mitochondrial choline transport and catabolism in vivo . We demonstrate that SLC25A48 is highly expressed in brown adipose tissue and required for whole-body cold tolerance, thermogenesis, and mitochondrial respiration. Mechanistically, choline uptake into the mitochondrial matrix via SLC25A48 facilitates betaine synthesis and one-carbon metabolism. Importantly, cells lacking SLC25A48 exhibited reduced synthesis of purine nucleotides and failed to initiate the G1-to-S phase transition, thereby leading to cell death. Taken together, the present study identified SLC25A48 as a mitochondrial carrier that mediates choline import and plays a critical role in mitochondrial respiratory capacity, purine nucleotide synthesis, and cell survival.
Key points: SLC25A48 is required for mitochondrial choline uptake.Mitochondrial choline uptake regulates one-carbon contribution to purine nucleotide synthesis.Brown fat thermogenesis requires mitochondrial choline catabolism for respiratory capacity.Cancer cells require mitochondrial choline uptake for cell survival.

DOI: https://doi.org/10.1101/2023.12.31.573776
Nat Cell Biol. 2024 Jan 24.

p300 nucleocytoplasmic shuttling underlies mTORC1 hyperactivation in Hutchinson-Gilford progeria syndrome.

Sung Min Son, So Jung Park, Sophia Y Breusegem, Delphine Larrieu, David C Rubinsztein.

The mechanistic target of rapamycin complex 1 (mTORC1) is a master regulator of cell growth, metabolism and autophagy. Multiple pathways modulate mTORC1 in response to nutrients. Here we describe that nucleus-cytoplasmic shuttling of p300/EP300 regulates mTORC1 activity in response to amino acid or glucose levels. Depletion of these nutrients causes cytoplasm-to-nucleus relocalization of p300 that decreases acetylation of the mTORC1 component raptor, thereby reducing mTORC1 activity and activating autophagy. This is mediated by AMP-activated protein kinase-dependent phosphorylation of p300 at serine 89. Nutrient addition to starved cells results in protein phosphatase 2A-dependent dephosphorylation of nuclear p300, enabling its CRM1-dependent export to the cytoplasm to mediate mTORC1 reactivation. p300 shuttling regulates mTORC1 in most cell types and occurs in response to altered nutrients in diverse mouse tissues. Interestingly, p300 cytoplasm-nucleus shuttling is altered in cells from patients with Hutchinson-Gilford progeria syndrome. p300 mislocalization by the disease-causing protein, progerin, activates mTORC1 and inhibits autophagy, phenotypes that are normalized by modulating p300 shuttling. These results reveal how nutrients regulate mTORC1, a cytoplasmic complex, by shuttling its positive regulator p300 in and out of the nucleus, and how this pathway is misregulated in Hutchinson-Gilford progeria syndrome, causing mTORC1 hyperactivation and defective autophagy.

DOI: https://doi.org/10.1038/s41556-023-01338-y
ACS Omega. 2024 Jan 16. 9(2): 2585-2596

Innovative Cyanine-Based Fluorescent Dye for Targeted Mitochondrial Imaging and Its Utility in Whole-Brain Visualization.

Xin Yan, Xinqian Chen, Zhiying Shan, Lanrong Bi.

Conducting in vivo brain imaging can be a challenging task due to the complexity of brain tissue and the strict requirements for safe and effective imaging agents. However, a new fluorescent dye called Cy5-PEG2 has been developed that selectively accumulates in mitochondria, enabling the visualization of these essential organelles in various cell lines. This dye is versatile and can be used for the real-time monitoring of mitochondrial dynamics in living cells. Moreover, it can cross the blood-brain barrier, making it a promising tool for noninvasive in vivo brain imaging. Based on the assessment of glial cell responses in the hippocampus and neocortex regions using GFAP and Iba1 biomarkers, Cy5-PEG2 seems to have minimal adverse effects on brain immune response or neuronal health. Therefore, this mitochondria-targeting fluorescent dye has the potential to advance our understanding of mitochondrial dynamics and function within the broader context of whole-brain physiology and disease progression. However, further research is needed to evaluate the safety and efficacy of Cy5-PEG2.

DOI: https://doi.org/10.1021/acsomega.3c07374
Nat Rev Nephrol. 2024 Jan 22.

Metabolic alterations in hereditary and sporadic renal cell carcinoma.

Nathan J Coffey, M Celeste Simon.

Kidney cancer is the seventh leading cause of cancer in the world, and its incidence is on the rise. Renal cell carcinoma (RCC) is the most common form and is a heterogeneous disease comprising three major subtypes that vary in their histology, clinical course and driver mutations. These subtypes include clear cell RCC, papillary RCC and chromophobe RCC. Molecular analyses of hereditary and sporadic forms of RCC have revealed that this complex and deadly disease is characterized by metabolic pathway alterations in cancer cells that lead to deregulated oxygen and nutrient sensing, as well as impaired tricarboxylic acid cycle activity. These metabolic changes facilitate tumour growth and survival. Specifically, studies of the metabolic features of RCC have led to the discovery of oncometabolites - fumarate and succinate - that can promote tumorigenesis, moonlighting functions of enzymes, and substrate auxotrophy owing to the disruption of pathways that enable the production of arginine and cholesterol. These metabolic alterations within RCC can be exploited to identify new therapeutic targets and interventions, in combination with novel approaches that minimize the systemic toxicity of metabolic inhibitors and reduce the risk of drug resistance owing to metabolic plasticity.

DOI: https://doi.org/10.1038/s41581-023-00800-2
Nat Neurosci. 2024 Jan 24.

Oligodendroglial metabolic support of myelinated axons driven by K+ dynamics.

DOI: https://doi.org/10.1038/s41593-023-01559-2
Nature. 2024 Jan 24.

Motion of VAPB molecules reveals ER-mitochondria contact site subdomains.

Christopher J Obara, Jonathon Nixon-Abell, Andrew S Moore, Federica Riccio, David P Hoffman, Gleb Shtengel, C Shan Xu, Kathy Schaefer, H Amalia Pasolli, Jean-Baptiste Masson, Harald F Hess, Christopher P Calderon, Craig Blackstone, Jennifer Lippincott-Schwartz.

To coordinate cellular physiology, eukaryotic cells rely on the rapid exchange of molecules at specialized organelle-organelle contact sites1,2. Endoplasmic reticulum-mitochondrial contact sites (ERMCSs) are particularly vital communication hubs, playing key roles in the exchange of signalling molecules, lipids and metabolites3,4. ERMCSs are maintained by interactions between complementary tethering molecules on the surface of each organelle5,6. However, due to the extreme sensitivity of these membrane interfaces to experimental perturbation7,8, a clear understanding of their nanoscale organization and regulation is still lacking. Here we combine three-dimensional electron microscopy with high-speed molecular tracking of a model organelle tether, Vesicle-associated membrane protein (VAMP)-associated protein B (VAPB), to map the structure and diffusion landscape of ERMCSs. We uncovered dynamic subdomains within VAPB contact sites that correlate with ER membrane curvature and undergo rapid remodelling. We show that VAPB molecules enter and leave ERMCSs within seconds, despite the contact site itself remaining stable over much longer time scales. This metastability allows ERMCSs to remodel with changes in the physiological environment to accommodate metabolic needs of the cell. An amyotrophic lateral sclerosis-associated mutation in VAPB perturbs these subdomains, likely impairing their remodelling capacity and resulting in impaired interorganelle communication. These results establish high-speed single-molecule imaging as a new tool for mapping the structure of contact site interfaces and reveal that the diffusion landscape of VAPB at contact sites is a crucial component of ERMCS homeostasis.

DOI: https://doi.org/10.1038/s41586-023-06956-y
Int J Mol Sci. 2024 Jan 19. pii: 1233. [Epub ahead of print]25(2):

Potassium Ions Decrease Mitochondrial Matrix pH: Implications for ATP Production and Reactive Oxygen Species Generation.

Jannatul Naima, Yoshihiro Ohta.

  Potassium (K+) is the most abundant cation in the cytosol and is maintained at high concentrations within the mitochondrial matrix through potassium channels. However, many effects of K+ at such high concentrations on mitochondria and the underlying mechanisms remain unclear. This study aims to elucidate these effects and mechanisms by employing fluorescence imaging techniques to distinguish and precisely measure signals inside and outside the mitochondria. We stained the mitochondrial matrix with fluorescent dyes sensitive to K+, pH, reactive oxygen species (ROS), and membrane potential in plasma membrane-permeabilized C6 cells and isolated mitochondria from C6 cells. Fluorescence microscopy facilitated the accurate measurement of fluorescence intensity inside and outside the matrix. Increasing extramitochondrial K+ concentration from 2 mM to 127 mM led to a reduction in matrix pH and a decrease in the generation of highly reactive ROS. In addition, elevated K+ levels electrically polarized the inner membrane of the mitochondria and promoted efficient ATP synthesis via FoF1-ATPase. Introducing protons (H+) into the matrix through phosphate addition led to further mitochondrial polarization, and this effect was more pronounced in the presence of K+. K+ at high concentrations, reaching sub-hundred millimolar levels, increased H+ concentration within the matrix, suppressing ROS generation and boosting ATP synthesis. Although this study does not elucidate the role of specific types of potassium channels in mitochondria, it does suggest that mitochondrial K+ plays a beneficial role in maintaining cellular health.

Keywords:  ATP production; ROS generation; matrix pH; mitochondria; potassium ions

DOI:  https://doi.org/10.3390/ijms25021233
Mol Neurobiol. 2024 Jan 26.

Amino Acid Transporters Proteins Involved in the Glutamate-Glutamine Cycle and Their Alterations in Murine Models of Alzheimer's Disease.

Diana Laura Vázquez-Durán, Arturo Ortega, Angelina Rodríguez.

  The brain's ability to integrate external stimuli and generate responses is highly complex. While these mechanisms are not completely understood, current evidence suggests that alterations in cellular metabolism and microenvironment are involved in some dysfunctions as complex as Alzheimer's disease. This pathology courses with defects in the establishment of chemical synapses, which is dependent on the production and supply of neurotransmitters like glutamate and its recycling through the glutamate-glutamine cycle. Alterations in the expression and function of the amino acid transporters proteins involved in this cycle have recently been reported in different stages of Alzheimer's disease. Most of these data come from patients in advanced stages of the disease or post-mortem, due to the ethical and technical limitations of human studies. Therefore, genetically modified mouse models have been an excellent tool to analyze metabolic and even behavioral parameters that are very similar to those that develop in Alzheimer's disease, even at presymptomatic stages. Hence, this paper analyzes the role of glutamate metabolism and its intercellular trafficking in excitatory synapses from different approaches using transgenic mouse models; such an analysis will contribute to our present understanding of AD.

Keywords:  Alzheimer’s disease; Amino acid transporter; Glutamate-Glutamine Cycle

DOI:  https://doi.org/10.1007/s12035-024-03966-3
J Drug Target. 2024 Jan 22. 1-47

Nano-medicine therapy reprogramming metabolic network of tumor microenvironment: new opportunity for cancer therapies.

Xiaojie Zhang, Min An, Juntao Zhang, Yumeng Zhao, Yanhua Liu.

  Metabolic heterogeneity is one of the characteristics of tumor cells. In order to adapt to the tumor microenvironment of hypoxia, acidity and nutritional deficiency, tumor cells have undergone extensive metabolic reprogramming. Metabolites involved in tumor cell metabolism are also very different from normal cells, such as a large number of lactate and adenosine. Metabolites play an important role in regulating the whole tumor microenvironment. Taking metabolites as the target, it aims to change the metabolic pattern of tumor cells again, destroy the energy balance it maintains, activate the immune system, and finally kill tumor cells. In this paper, the regulatory effects of metabolites such as lactate, glutamine, arginine, tryptophan, fatty acids and adenosine were reviewed, and the related targeting strategies of nano-medicines were summarized, and the future therapeutic strategies of nano-drugs were discussed. The abnormality of tumor metabolites caused by tumor metabolic remodeling not only changes the energy and material supply of tumor, but also participates in the regulation of tumor-related signal pathways, which plays an important role in the survival, proliferation, invasion and metastasis of tumor cells. Regulating the availability of local metabolites is a new aspect that affects tumor progress.

Keywords:  immune cells; metabolite; nano-medicine; tumor microenvironment

DOI:  https://doi.org/10.1080/1061186X.2024.2309565
Metabolites. 2023 Dec 31. pii: 28. [Epub ahead of print]14(1):

The Role of Amino Acids in Non-Enzymatic Antioxidant Mechanisms in Cancer: A Review.

Elena I Dyachenko, Lyudmila V Bel'skaya.

  Currently, the antioxidant properties of amino acids and their role in the physicochemical processes accompanying oxidative stress in cancer remain unclear. Cancer cells are known to extensively uptake amino acids, which are used as an energy source, antioxidant precursors that reduce oxidative stress in cancer, and as regulators of inhibiting or inducing tumor cell-associated gene expression. This review examines nine amino acids (Cys, His, Phe, Met, Trp, Tyr, Pro, Arg, Lys), which play a key role in the non-enzymatic oxidative process in various cancers. Conventionally, these amino acids can be divided into two groups, in one of which the activity increases (Cys, Phe, Met, Pro, Arg, Lys) in cancer, and in the other, it decreases (His, Trp, Tyr). The review examines changes in the metabolism of nine amino acids in eleven types of oncology. We have identified the main nonspecific mechanisms of changes in the metabolic activity of amino acids, and described direct and indirect effects on the redox homeostasis of cells. In the future, this will help to understand better the nature of life of a cancer cell and identify therapeutic targets more effectively.

Keywords:  amino acids; cancer; non-enzymatic antioxidant system; oxidative stress

DOI:  https://doi.org/10.3390/metabo14010028
Geroscience. 2024 Jan 25.

Mitochondrial complex I inhibition triggers NAD+-independent glucose oxidation via successive NADPH formation, "futile" fatty acid cycling, and FADH2 oxidation.

Roman Abrosimov, Marius W Baeken, Samuel Hauf, Ilka Wittig, Parvana Hajieva, Carmen E Perrone, Bernd Moosmann.

  Inhibition of mitochondrial complex I (NADH dehydrogenase) is the primary mechanism of the antidiabetic drug metformin and various unrelated natural toxins. Complex I inhibition can also be induced by antidiabetic PPAR agonists, and it is elicited by methionine restriction, a nutritional intervention causing resistance to diabetes and obesity. Still, a comprehensible explanation to why complex I inhibition exerts antidiabetic properties and engenders metabolic inefficiency is missing. To evaluate this issue, we have systematically reanalyzed published transcriptomic datasets from MPP-treated neurons, metformin-treated hepatocytes, and methionine-restricted rats. We found that pathways leading to NADPH formation were widely induced, together with anabolic fatty acid biosynthesis, the latter appearing highly paradoxical in a state of mitochondrial impairment. However, concomitant induction of catabolic fatty acid oxidation indicated that complex I inhibition created a "futile" cycle of fatty acid synthesis and degradation, which was anatomically distributed between adipose tissue and liver in vivo. Cofactor balance analysis unveiled that such cycling would indeed be energetically futile (-3 ATP per acetyl-CoA), though it would not be redox-futile, as it would convert NADPH into respirable FADH2 without any net production of NADH. We conclude that inhibition of NADH dehydrogenase leads to a metabolic shift from glycolysis and the citric acid cycle (both generating NADH) towards the pentose phosphate pathway, whose product NADPH is translated 1:1 into FADH2 by fatty acid cycling. The diabetes-resistant phenotype following hepatic and intestinal complex I inhibition is attributed to FGF21- and GDF15-dependent fat hunger signaling, which remodels adipose tissue into a glucose-metabolizing organ.

Keywords:  Diabetes; FGF21; Metformin; Methionine restriction; NADH dehydrogenase; Peroxisome proliferator-activated receptor

DOI:  https://doi.org/10.1007/s11357-023-01059-y
Nat Neurosci. 2024 Jan 24.

Oligodendrocyte-axon metabolic coupling is mediated by extracellular K+ and maintains axonal health.

Zoe J Looser, Zainab Faik, Luca Ravotto, Henri S Zanker, Ramona B Jung, Hauke B Werner, Torben Ruhwedel, Wiebke Möbius, Dwight E Bergles, L Felipe Barros, Klaus-Armin Nave, Bruno Weber, Aiman S Saab.

The integrity of myelinated axons relies on homeostatic support from oligodendrocytes (OLs). To determine how OLs detect axonal spiking and how rapid axon-OL metabolic coupling is regulated in the white matter, we studied activity-dependent calcium (Ca2+) and metabolite fluxes in the mouse optic nerve. We show that fast axonal spiking triggers Ca2+ signaling and glycolysis in OLs. OLs detect axonal activity through increases in extracellular potassium (K+) concentrations and activation of Kir4.1 channels, thereby regulating metabolite supply to axons. Both pharmacological inhibition and OL-specific inactivation of Kir4.1 reduce the activity-induced axonal lactate surge. Mice lacking oligodendroglial Kir4.1 exhibit lower resting lactate levels and altered glucose metabolism in axons. These early deficits in axonal energy metabolism are associated with late-onset axonopathy. Our findings reveal that OLs detect fast axonal spiking through K+ signaling, making acute metabolic coupling possible and adjusting the axon-OL metabolic unit to promote axonal health.

DOI: https://doi.org/10.1038/s41593-023-01558-3
Anal Chim Acta. 2024 Feb 08. pii: S0003-2670(23)01281-3. [Epub ahead of print]1289 342060

Mitochondria-targetable small molecule fluorescent probes for the detection of cancer-associated biomarkers: A review.

Xue Yu, Yunong Huang, Yunqi Tao, Li Fan, Yuewei Zhang.

  Cancer represents a global threat to human health, and effective strategies for improved cancer early diagnosis and treatment are urgently needed. The detection of tumor biomarkers has been one of the important auxiliary means for tumor screening and diagnosis. Mitochondria are crucial subcellular organelles that produce most chemical energy used by cells, control metabolic processes, and maintain cell function. Evidence suggests the close involvement of mitochondria with cancer development. As a consequence, the identification of cancer-associated biomarker expression levels in mitochondria holds significant importance in the diagnosis of early-stage diseases and the monitoring of therapy efficacy. Small-molecule fluorescent probes are effective for the identification and visualization of bioactive entities within biological systems, owing to their heightened sensitivity, expeditious non-invasive analysis and real-time detection capacities. The design principles and sensing mechanisms of mitochondrial targeted fluorescent probes are summarized in this review. Additionally, the biomedical applications of these probes for detecting cancer-associated biomarkers are highlighted. The limitations and challenges of fluorescent probes in vivo are also considered and some future perspectives are provided. This review is expected to provide valuable insights for the future development of novel fluorescent probes for clinical imaging, thereby contributing to the advancement of cancer diagnosis and treatment.

Keywords:  Biomarkers; Cancer; Fluorescent probes; Mitochondria; Organelle targeting

DOI:  https://doi.org/10.1016/j.aca.2023.342060
Int J Biol Macromol. 2024 Jan 23. pii: S0141-8130(24)00449-5. [Epub ahead of print]260(Pt 2): 129646

Comprehensive review of amino acid transporters as therapeutic targets.

Ran Xia, Hai-Feng Peng, Xing Zhang, Hong-Sheng Zhang.

  The solute carrier (SLC) family, with more than 400 membrane-bound proteins, facilitates the transport of a wide array of substrates such as nutrients, ions, metabolites, and drugs across biological membranes. Amino acid transporters (AATs) are membrane transport proteins that mediate transfer of amino acids into and out of cells or cellular organelles. AATs participate in many important physiological functions including nutrient supply, metabolic transformation, energy homeostasis, redox regulation, and neurological regulation. Several AATs have been found to significantly impact the progression of human malignancies, and dysregulation of AATs results in metabolic reprogramming affecting tumor growth and progression. However, current clinical therapies that directly target AATs have not been developed. The purpose of this review is to highlight the structural and functional diversity of AATs, the molecular mechanisms in human diseases such as tumors, kidney diseases, and emerging therapeutic strategies for targeting AATs.

Keywords:  SLC transporter; amino acid transporter; cancer therapy; targeted therapy

DOI:  https://doi.org/10.1016/j.ijbiomac.2024.129646
mSystems. 2024 Jan 23. e0100123

A data-driven approach for timescale decomposition of biochemical reaction networks.

Amir Akbari, Zachary B Haiman, Bernhard O Palsson.

  Understanding the dynamics of biological systems in evolving environments is a challenge due to their scale and complexity. Here, we present a computational framework for the timescale decomposition of biochemical reaction networks to distill essential patterns from their intricate dynamics. This approach identifies timescale hierarchies, concentration pools, and coherent structures from time-series data, providing a system-level description of reaction networks at physiologically important timescales. We apply this technique to kinetic models of hypothetical and biological pathways, validating it by reproducing analytically characterized or previously known concentration pools of these pathways. Moreover, by analyzing the timescale hierarchy of the glycolytic pathway, we elucidate the connections between the stoichiometric and dissipative structures of reaction networks and the temporal organization of coherent structures. Specifically, we show that glycolysis is a cofactor-driven pathway, the slowest dynamics of which are described by a balance between high-energy phosphate bond and redox trafficking. Overall, this approach provides more biologically interpretable characterizations of network dynamics than large-scale kinetic models, thus facilitating model reduction and personalized medicine applications. IMPORTANCE Complex interactions within interconnected biochemical reaction networks enable cellular responses to a wide range of unpredictable environmental perturbations. Understanding how biological functions arise from these intricate interactions has been a long-standing problem in biology. Here, we introduce a computational approach to dissect complex biological systems' dynamics in evolving environments. This approach characterizes the timescale hierarchies of complex reaction networks, offering a system-level understanding at physiologically relevant timescales. Analyzing various hypothetical and biological pathways, we show how stoichiometric properties shape the way energy is dissipated throughout reaction networks. Notably, we establish that glycolysis operates as a cofactor-driven pathway, where the slowest dynamics are governed by a balance between high-energy phosphate bonds and redox trafficking. This approach enhances our understanding of network dynamics and facilitates the development of reduced-order kinetic models with biologically interpretable components.

Keywords:  coherent structures; data-driven approach; dynamic-mode decomposition; kinetic models; timescale decomposition

DOI:  https://doi.org/10.1128/msystems.01001-23
STAR Protoc. 2024 Jan 18. pii: S2666-1667(24)00007-8. [Epub ahead of print]5(1): 102842

Protocol for measuring mitochondrial size in mouse and human liver tissues.

Balamurugan Ramatchandirin, Miho Iijima, Arisa Ikeda, Alexia Pearah, Sally Radovick, Fredric E Wondisford, Hiromi Sesaki, Ling He.

  Mitochondrial dynamic process is important for cell viability, metabolic activity, and mitochondria health. Here, we present a protocol for measuring mitochondrial size through immunofluorescence staining, confocal imaging, and analysis in ImageJ. We describe the steps for tissue processing, antigen retrieval, mitochondrial staining using an integrating immunofluorescence assay, and computerized image analysis to measure each mitochondrial size in mouse and human liver tissues. This protocol reduces tissue sample volume and processing time for the preparation of primary cells. For complete details on the use and execution of this protocol, please refer to Pearah et al.1.

Keywords:  Cell Biology; Health Sciences; Metabolism

DOI:  https://doi.org/10.1016/j.xpro.2024.102842
Nat Metab. 2024 Jan 24.

Metabolic heterogeneity in cancer.

Margherita Demicco, Xiao-Zheng Liu, Katharina Leithner, Sarah-Maria Fendt.

Cancer cells rewire their metabolism to survive during cancer progression. In this context, tumour metabolic heterogeneity arises and develops in response to diverse environmental factors. This metabolic heterogeneity contributes to cancer aggressiveness and impacts therapeutic opportunities. In recent years, technical advances allowed direct characterisation of metabolic heterogeneity in tumours. In addition to the metabolic heterogeneity observed in primary tumours, metabolic heterogeneity temporally evolves along with tumour progression. In this Review, we summarize the mechanisms of environment-induced metabolic heterogeneity. In addition, we discuss how cancer metabolism and the key metabolites and enzymes temporally and functionally evolve during the metastatic cascade and treatment.

DOI: https://doi.org/10.1038/s42255-023-00963-z
bioRxiv. 2024 Jan 01. pii: 2023.12.31.573774. [Epub ahead of print]

A genetically-encoded fluorescent biosensor for visualization of acetyl-CoA in live cells.

Joseph J Smith, Taylor R Valentino, Austin H Ablicki, Riddhidev Banerjee, Adam R Colligan, Debra M Eckert, Gabrielle A Desjardins, Katharine L Diehl.

Acetyl-coenzyme A is a central metabolite that participates in many cellular pathways. Evidence suggests that acetyl-CoA production and consumption are highly compartmentalized in mammalian cells. Yet methods to measure acetyl-CoA in living cells are lacking. In this work, we engineer an acetyl-CoA biosensor from the bacterial protein PanZ and circularly permuted green fluorescent protein (cpGFP). We biochemically characterize the sensor and demonstrate its selectivity for acetyl-CoA over other CoA species. We then deploy the biosensor in E. coli and HeLa cells to demonstrate its utility in living cells. In E. coli , we show that the biosensor enables detection of rapid changes in acetyl-CoA levels. In human cells, we show that the biosensor enables subcellular detection and reveals the compartmentalization of acetyl-CoA metabolism.

DOI: https://doi.org/10.1101/2023.12.31.573774