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Leung A, Rangamani P. Computational modeling of AMPK and mTOR crosstalk in glutamatergic synapse calcium signaling. NPJ Syst Biol Appl 2023; 9:34. [PMID: 37460570 DOI: 10.1038/s41540-023-00295-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/29/2023] [Indexed: 07/20/2023] Open
Abstract
Neuronal energy consumption is vital for information processing and memory formation in synapses. The brain consists of just 2% of the human body's mass, but consumes almost 20% of the body's energy budget. Most of this energy is attributed to active transport in ion signaling, with calcium being the canonical second messenger of synaptic transmission. Here, we develop a computational model of synaptic signaling resulting in the activation of two protein kinases critical in metabolic regulation and cell fate, AMP-Activated protein kinase (AMPK) and mammalian target of rapamycin (mTOR) and investigate the effect of glutamate stimulus frequency on their dynamics. Our model predicts that frequencies of glutamate stimulus over 10 Hz perturb AMPK and mTOR oscillations at higher magnitudes by up to 36% and change the area under curve (AUC) by 5%. This dynamic difference in AMPK and mTOR activation trajectories potentially differentiates high frequency stimulus bursts from basal neuronal signaling leading to a downstream change in synaptic plasticity. Further, we also investigate the crosstalk between insulin receptor and calcium signaling on AMPK and mTOR activation and predict that the pathways demonstrate multistability dependent on strength of insulin signaling and metabolic consumption rate. Our predictions have implications for improving our understanding of neuronal metabolism, synaptic pruning, and synaptic plasticity.
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Affiliation(s)
- A Leung
- Chemical Engineering Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - P Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, USA.
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2
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Barros LF, Ruminot I, Sandoval PY, San Martín A. Enlightening brain energy metabolism. Neurobiol Dis 2023:106211. [PMID: 37352985 DOI: 10.1016/j.nbd.2023.106211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/06/2023] [Accepted: 06/20/2023] [Indexed: 06/25/2023] Open
Abstract
Brain tissue metabolism is distributed across several cell types and subcellular compartments, which activate at different times and with different temporal patterns. The introduction of genetically-encoded fluorescent indicators that are imaged using time-lapse microscopy has opened the possibility of studying brain metabolism at cellular and sub-cellular levels. There are indicators for sugars, monocarboxylates, Krebs cycle intermediates, amino acids, cofactors, and energy nucleotides, which inform about relative levels, concentrations and fluxes. This review offers a brief survey of the metabolic indicators that have been validated in brain cells, with some illustrative examples from the literature. Whereas only a small fraction of the metabolome is currently accessible to fluorescent probes, there are grounds to be optimistic about coming developments and the application of these tools to the study of brain disease.
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Affiliation(s)
- L F Barros
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Facultad de Medicina y Ciencia, Universidad San Sebastián, Valdivia, Chile.
| | - I Ruminot
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Facultad de Ciencias para el Cuidado de La Salud, Universidad San Sebastián, Valdivia, Chile
| | - P Y Sandoval
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Facultad de Ciencias para el Cuidado de La Salud, Universidad San Sebastián, Valdivia, Chile
| | - A San Martín
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Facultad de Ciencias para el Cuidado de La Salud, Universidad San Sebastián, Valdivia, Chile
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3
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Fan G, Liu M, Liu J, Huang Y. The initiator of neuroexcitotoxicity and ferroptosis in ischemic stroke: Glutamate accumulation. Front Mol Neurosci 2023; 16:1113081. [PMID: 37033381 PMCID: PMC10076579 DOI: 10.3389/fnmol.2023.1113081] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/06/2023] [Indexed: 04/11/2023] Open
Abstract
Glutamate plays an important role in excitotoxicity and ferroptosis. Excitotoxicity occurs through over-stimulation of glutamate receptors, specifically NMDAR, while in the non-receptor-mediated pathway, high glutamate concentrations reduce cystine uptake by inhibiting the System Xc-, leading to intracellular glutathione depletion and resulting in ROS accumulation, which contributes to increased lipid peroxidation, mitochondrial damage, and ultimately ferroptosis. Oxidative stress appears to crosstalk between excitotoxicity and ferroptosis, and it is essential to maintain glutamate homeostasis and inhibit oxidative stress responses in vivo. As researchers work to develop natural compounds to further investigate the complex mechanisms and regulatory functions of ferroptosis and excitotoxicity, new avenues will be available for the effective treatment of ischaemic stroke. Therefore, this paper provides a review of the molecular mechanisms and treatment of glutamate-mediated excitotoxicity and ferroptosis.
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Affiliation(s)
- Genhao Fan
- Graduate School, Tianjin University of Chinese Medicine, Tianjin, China
| | - Menglin Liu
- Graduate School, Tianjin University of Chinese Medicine, Tianjin, China
| | - Jia Liu
- Department of Clinical Pharmacology, The Second Affiliated Hospital of Tianjin University of Chinese Medicine, Tianjin, China
| | - Yuhong Huang
- Department of Clinical Pharmacology, The Second Affiliated Hospital of Tianjin University of Chinese Medicine, Tianjin, China
- *Correspondence: Yuhong Huang,
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San Martín A, Arce-Molina R, Aburto C, Baeza-Lehnert F, Barros LF, Contreras-Baeza Y, Pinilla A, Ruminot I, Rauseo D, Sandoval PY. Visualizing physiological parameters in cells and tissues using genetically encoded indicators for metabolites. Free Radic Biol Med 2022; 182:34-58. [PMID: 35183660 DOI: 10.1016/j.freeradbiomed.2022.02.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 02/07/2023]
Abstract
The study of metabolism is undergoing a renaissance. Since the year 2002, over 50 genetically-encoded fluorescent indicators (GEFIs) have been introduced, capable of monitoring metabolites with high spatial/temporal resolution using fluorescence microscopy. Indicators are fusion proteins that change their fluorescence upon binding a specific metabolite. There are indicators for sugars, monocarboxylates, Krebs cycle intermediates, amino acids, cofactors, and energy nucleotides. They permit monitoring relative levels, concentrations, and fluxes in living systems. At a minimum they report relative levels and, in some cases, absolute concentrations may be obtained by performing ad hoc calibration protocols. Proper data collection, processing, and interpretation are critical to take full advantage of these new tools. This review offers a survey of the metabolic indicators that have been validated in mammalian systems. Minimally invasive, these indicators have been instrumental for the purposes of confirmation, rebuttal and discovery. We envision that this powerful technology will foster metabolic physiology.
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Affiliation(s)
- A San Martín
- Centro de Estudios Científicos (CECs), Valdivia, Chile.
| | - R Arce-Molina
- Centro de Estudios Científicos (CECs), Valdivia, Chile
| | - C Aburto
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Universidad Austral de Chile, Valdivia, Chile
| | | | - L F Barros
- Centro de Estudios Científicos (CECs), Valdivia, Chile
| | - Y Contreras-Baeza
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Universidad Austral de Chile, Valdivia, Chile
| | - A Pinilla
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Universidad Austral de Chile, Valdivia, Chile
| | - I Ruminot
- Centro de Estudios Científicos (CECs), Valdivia, Chile
| | - D Rauseo
- Centro de Estudios Científicos (CECs), Valdivia, Chile; Universidad Austral de Chile, Valdivia, Chile
| | - P Y Sandoval
- Centro de Estudios Científicos (CECs), Valdivia, Chile
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Zhang X, Dash RK, Clough AV, Xie D, Jacobs ER, Audi SH. Integrated Computational Model of Lung Tissue Bioenergetics. Front Physiol 2019; 10:191. [PMID: 30906264 PMCID: PMC6418344 DOI: 10.3389/fphys.2019.00191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 02/15/2019] [Indexed: 11/29/2022] Open
Abstract
Altered lung tissue bioenergetics plays a key role in the pathogenesis of lung diseases. A wealth of information exists regarding the bioenergetic processes in mitochondria isolated from rat lungs, cultured pulmonary endothelial cells, and intact rat lungs under physiological and pathophysiological conditions. However, the interdependence of those processes makes it difficult to quantify the impact of a change in a single or multiple process(es) on overall lung tissue bioenergetics. Integrated computational modeling provides a mechanistic and quantitative framework for the bioenergetic data at different levels of biological organization. The objective of this study was to develop and validate an integrated computational model of lung bioenergetics using existing experimental data from isolated perfused rat lungs. The model expands our recently developed computational model of the bioenergetics of mitochondria isolated from rat lungs by accounting for glucose uptake and phosphorylation, glycolysis, and the pentose phosphate pathway. For the mitochondrial region of the model, values of kinetic parameters were fixed at those estimated in our recent model of the bioenergetics of mitochondria isolated from rat lungs. For the cytosolic region of the model, intrinsic parameters such as apparent Michaelis constants were determined based on previously published enzyme kinetics data, whereas extrinsic parameters such as maximal reaction and transport velocities were estimated by fitting the model solution to published data from isolated rat lungs. The model was then validated by assessing its ability to predict existing experimental data not used for parameter estimation, including relationships between lung nucleotides content, lung lactate production rate, and lung energy charge under different experimental conditions. In addition, the model was used to gain novel insights on how lung tissue glycolytic rate is regulated by exogenous substrates such as glucose and lactate, and assess differences in the bioenergetics of mitochondria isolated from lung tissue and those of mitochondria in intact lungs. To the best of our knowledge, this is the first model of lung tissue bioenergetics. The model provides a mechanistic and quantitative framework for integrating available lung tissue bioenergetics data, and for testing novel hypotheses regarding the role of different cytosolic and mitochondrial processes in lung tissue bioenergetics.
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Affiliation(s)
- Xiao Zhang
- Department of Biomedical Engineering, Marquette University, Milwaukee, WI, United States
| | - Ranjan K Dash
- Department of Biomedical Engineering, Marquette University, Milwaukee, WI, United States.,Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI, United States.,Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Anne V Clough
- Zablocki V. A. Medical Center, Milwaukee, WI, United States.,Department of Mathematics, Statistics, and Computer Science, Marquette University, Milwaukee, WI, United States
| | - Dexuan Xie
- Department of Mathematical Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, United States
| | - Elizabeth R Jacobs
- Zablocki V. A. Medical Center, Milwaukee, WI, United States.,Division of Pulmonary and Critical Care Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
| | - Said H Audi
- Department of Biomedical Engineering, Marquette University, Milwaukee, WI, United States.,Department of Biomedical Engineering, Medical College of Wisconsin, Milwaukee, WI, United States.,Zablocki V. A. Medical Center, Milwaukee, WI, United States.,Division of Pulmonary and Critical Care Medicine, Medical College of Wisconsin, Milwaukee, WI, United States
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Haeseler FV, Rudolph N, Findeisen R, Huber HJ. Parameter Estimation for Signal Transduction Networks from Experimental Time Series Using Picard Iteration. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.ifacol.2018.09.298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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7
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Pelosse M, Cottet-Rousselle C, Grichine A, Berger I, Schlattner U. Genetically Encoded Fluorescent Biosensors to Explore AMPK Signaling and Energy Metabolism. ACTA ACUST UNITED AC 2017; 107:491-523. [PMID: 27812993 DOI: 10.1007/978-3-319-43589-3_20] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Maintenance of energy homeostasis is a basic requirement for cell survival. Different mechanisms have evolved to cope with spatial and temporal mismatch between energy-providing and -consuming processes. Among these, signaling by AMP-activated protein kinase (AMPK) is one of the key players, regulated by and itself regulating cellular adenylate levels. Further understanding its complex cellular function requires deeper insight into its activation patterns in space and time at a single cell level. This may become possible with an increasing number of genetically encoded fluorescent biosensors, mostly based on fluorescence resonance energy transfer, which have been engineered to monitor metabolic parameters and kinase activities. Here, we review basic principles of biosensor design and function and the advantages and limitations of their use and provide an overview on existing FRET biosensors to monitor AMPK activation, ATP concentration, and ATP/ADP ratios, together with other key metabolites and parameters of energy metabolism.
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Affiliation(s)
- Martin Pelosse
- Laboratory of Fundamental and Applied Bioenergetics (LBFA) and SFR Environmental and Systems Biology (BEeSy), University Grenoble Alpes, Grenoble, France.,Inserm, U1055 and U1209, Grenoble, France
| | - Cécile Cottet-Rousselle
- Laboratory of Fundamental and Applied Bioenergetics (LBFA) and SFR Environmental and Systems Biology (BEeSy), University Grenoble Alpes, Grenoble, France.,Inserm, U1055 and U1209, Grenoble, France
| | - Alexei Grichine
- Inserm, U1055 and U1209, Grenoble, France.,Institute for Advanced Biosciences, University Grenoble Alpes, Grenoble, France
| | | | - Uwe Schlattner
- Laboratory of Fundamental and Applied Bioenergetics (LBFA) and SFR Environmental and Systems Biology (BEeSy), University Grenoble Alpes, Grenoble, France. .,Inserm, U1055 and U1209, Grenoble, France.
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iTRAQ-based proteomics analysis of hippocampus in spatial memory deficiency rats induced by simulated microgravity. J Proteomics 2017; 160:64-73. [PMID: 28341594 DOI: 10.1016/j.jprot.2017.03.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Revised: 03/02/2017] [Accepted: 03/17/2017] [Indexed: 01/27/2023]
Abstract
It has been demonstrated that simulated microgravity (SM) may lead to cognitive dysfunction. However, the underlying mechanism remains unclear. In present study, tail-suspension (30°) rat was employed to explore the effects of 28 days of SM on hippocampus-dependent learning and memory capability and the underlying mechanisms. We found that 28-day tail-suspension rats displayed decline of learning and memory ability in Morris water maze (MWM) test. Using iTRAQ-based proteomics analysis, a total of 4774 proteins were quantified in hippocampus. Of these identified proteins, 147 proteins were differentially expressed between tail-suspension and control group. Further analysis showed these differentially expressed proteins (DEPs) involved in different molecular function categories, and participated in many biological processes. Based on the results of PANTHER pathway analysis and further western blot verification, we observed the expression of glutamate receptor 1 (GluR1) and glutamate receptor 4 (GluR4) which involved in metabotropic glutamate receptor group III pathway and ionotropic glutamate receptor pathway were significantly induced by SM. Moreover, an increased concentration of glutamic acid (Glu) was also found in hippocampus while the concentrations of 5-hydroxytryptamine (5-HT), dopamine (DA), γ-amino acid butyric acid (GABA) and epinephrine (E) were decreased. Our finding confirms that 28-day SM exposure can cause degrading of the spatial learning and memory capability and the possible mechanisms might be related with glutamate excitotoxicity and imbalances in specific neurotransmitters. BIOLOGICAL SIGNIFICANCE The goal of sending astronauts farther into space and extending the duration of spaceflight missions from months to years will challenge the current capabilities of bioastronautics. The investigation of the physiological and pathological changes induced by spaceflight will be critical in developing countermeasures to ensure astronauts to complete spaceflight mission accurately and effectively and return to earth safely. It has been demonstrated that spaceflight may lead to impairments in cognitive function which is crucial for mission success. Here we show that long-term simulated microgravity, the most potent environment risk factor during spaceflight, impairs the spatial learning and memory of rats and the underlying mechanism may be involved in glutamate excitotoxicity and imbalances in specific neurotransmitters release in hippocampus, which may provide new insight for the countermeasures of cognitive impairment during spaceflight.
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