Visualization of ATP levels inside single living cells with fluorescence resonance energy transfer-based genetically encoded indicators

Emission based sensing of phosphate ions and ATP via a newly synthesized Cu(II) chelated tetra N-phenyl carbazole porphyrin derivative

In this work spectral properties and sensor characteristics of a newly synthesized porphyrin derivative were investigated by absorption, excitation and emission spectroscopy. We also treated this molecule as a metal-ion chelation based fluorescent probe and investigated its response for PO43- and hydrolyzed adenosine triphosphate. Tetra-N-phenyl-carbazole-porphyrin derivative (TN-PCP) equipped with four symmetrical carbazole units via phenyl linkages exhibited high quantum yield in DMSO (Ф=0.55.1). We reported effect of the Cu (II) and Ag (I) ions on the fluorescence of the TN-PCP considering general sensor parameters including calibration studies, selectivity and LOD values. Metal chelation by Cu (II) and Ag (I) quenched the fluorescence of the probe with I0/I100 ratios of 20.1 and 2.5, respectively. Considering the higher magnitude and effectiveness of the Cu(II)-induced quenching, we tested some analytes that could restore the emission of Cu[TN-PCP], thereby signaling the analytes including chelating anions. Among them, phosphate ion exhibited an exceptional and selective response towards the Cu[ TN-PCP] complex at pH 12.0 in a buffered solution. We measured 14.0 and 2.0-fold increase in emission intensity of the dye at 360 and 687 nm, upon phosphate binding, respectively. Additionally, we reported a very promising and selective response for the ATP molecule (I0/I100 = 50.0) for a concentration range; 1.8*10-4 M -1.7*10-2 M, at 420 nm, which can easily determine the ATP levels in bacteria, yeast, mammalian cells, muscle cells and even in intercellular spaces. The LOD value of the probe was found to be 2.1*10-5 M for the ATP molecule. We have also demonstrated that the proposed probe can be used as an emission-based sensor capable of exhibiting good detection limits for these two metal cations.

The glycosomal ATP-dependent phosphofructokinase of Trypanosoma brucei operates also in the gluconeogenic direction

In the glucose-free environment of the midgut of the tsetse fly vector, the procyclic forms of Trypanosoma brucei primarily consume proline to feed its central carbon and energy metabolism. In this context, the parasite produces through gluconeogenesis, glucose 6-phosphate (G6P), the precursor of essential metabolic pathways, from proline catabolism. We show here that the parasite uses three different enzymes to perform the key gluconeogenic reaction producing fructose 6-phosphate (F6P) from fructose 1,6-bisphosphate, (i) fructose-1,6-bisphosphatase (FBPase), the canonical enzyme performing this reaction, (ii) sedoheptulose-1,7-bisphosphatase (SBPase), and (iii) more surprisingly ATP-dependent phosphofructokinase (PFK), an enzyme considered to irreversibly catalyze the opposite reaction involved in glycolysis. These three enzymes, as well as six other glycolytic/gluconeogenic enzymes, are located in peroxisome-related organelles, named glycosomes. Incorporation of 13C-enriched glycerol (a more effective alternative to proline for monitoring gluconeogenic activity) into F6P and G6P was more affected in the PFK null mutant than in the FBPase null mutant, suggesting the PFK contributes at least as much as FBPase to gluconeogenesis. We also showed that glucose deprivation did not affect the quantities of PFK substrates and products, whereas an approximately 500-fold increase in the substrate/product ratio was expected for PFK to carry out the gluconeogenic reaction. In conclusion, we show for the first time that ATP-dependent PFK can function in vivo in the gluconeogenic direction, even in the presence of FBPase activity. This particular feature, which precludes loss of ATP through a futile cycle involving PFK and FBPase working simultaneously in the glycolytic and gluconeogenic directions, respectively, is possibly due to the supramolecular organization of the metabolic pathway within glycosomes to overcome thermodynamic barriers through metabolic channeling.

Pools of Independently Cycling Inositol Phosphates Revealed by Pulse Labeling with 18O-Water

Inositol phosphates control many central processes in eukaryotic cells including nutrient availability, growth, and motility. Kinetic resolution of a key modulator of their signaling functions, the turnover of the phosphate groups on the inositol ring, has been hampered by slow uptake, high dilution, and constraining growth conditions in radioactive pulse-labeling approaches. Here, we demonstrate a rapid (seconds to minutes) and nonradioactive labeling strategy of inositol polyphosphates through 18O-water in yeast, human cells, and amoeba, which can be applied in any media. In combination with capillary electrophoresis and mass spectrometry, 18O-water labeling simultaneously dissects the in vivo phosphate group dynamics of a broad spectrum of even rare inositol phosphates. The good temporal resolution allowed us to discover vigorous phosphate group exchanges in some inositol polyphosphates and pyrophosphates, whereas others remain remarkably inert. We propose a model in which the biosynthetic pathway of inositol polyphosphates and pyrophosphates is organized in distinct, kinetically separated pools. While transfer of compounds between those pools is slow, each pool undergoes rapid internal phosphate cycling. This might enable the pools to perform distinct signaling functions while being metabolically connected.

Role of macrophage ATP metabolism disorder in SiO2‑induced pulmonary fibrosis: a review

Silicosis, a chronic lung disease, results from prolonged inhalation of silica dust (SiO2) in occupational environments, and its pathogenesis remains incompletely elucidated. Studies have shown that alveolar macrophages (AMs) play a pivotal role in its development. These AMs phagocytose the inhaled SiO2, which leads to morphological, structural, and functional abnormalities that result in lung fibrosis. During this process, adenosine triphosphate (ATP) not only provides energy for the physiological and pathological activities but also acts as a key intracellular and extracellular signaling molecule and regulates cytokine synthesis and secretion. This complex process has not been systematically summarized. In this study, first, the current data on ATP metabolism in the development of SiO2-induced pulmonary fibrosis are introduced. ATP metabolism disorder, caused by impaired production, utilization, or distribution of ATP, disrupts macrophage energy homeostasis. Then, how ATP metabolism disorder affects macrophage morphology and function and the inflammatory and fibrotic processes of the lungs by activating the P2X7 receptor-mediated ATP signaling pathway are discussed. Finally, current therapeutic strategies targeting ATP metabolism disorder and ATP signaling pathways in silicosis are summarized. In conclusion, SiO2-induced ATP metabolism disorder indirectly accelerates the progression of silicosis fibrosis.

Spreading depolarizations exhaust neuronal ATP in a model of cerebral ischemia

Spreading depolarizations (SDs) have been identified in various brain pathologies. SDs increase the cerebral energy demand and, concomitantly, oxygen consumption, which indicates enhanced synthesis of adenosine triphosphate (ATP) by oxidative phosphorylation. Therefore, SDs are considered particularly detrimental during reduced supply of oxygen and glucose. However, measurements of intracellular neuronal ATP ([ATP]i), ultimately reporting the balance of ATP synthesis and consumption during SDs, have not yet been conducted. Here, we investigated neuronal ATP homeostasis during SDs using two-photon imaging in acute brain slices from adult mice expressing the ATP sensor ATeam1.03YEMK in neurons. SDs were induced by application of potassium chloride or by oxygen and glucose deprivation (OGD) and detected by recording the local field potential, extracellular potassium, as well as the intrinsic optical signal. We found that, in the presence of oxygen and glucose, SDs were accompanied by a substantial but transient drop in neuronal ATP sensor signals, corresponding to a drop in ATP. OGD, which prior to SDs was accompanied by only a slight reduction in ATP signals, led to a large, terminal drop in ATP signals during SDs. Subsequently, we investigated whether neurons could still regenerate ATP if oxygen and glucose were promptly resupplied following SD detection, and show that ATP depletion was essentially reversible in most cells. Our findings indicate that SDs are accompanied by a substantial increase in ATP consumption beyond production. This, under conditions that mimic reduced blood supply, leads to a breakdown of [ATP]i. Therefore, our findings support therapeutic strategies targeting SDs after cerebral ischemia.

Annexin A5 controls VDAC1-dependent mitochondrial Ca2+ homeostasis and determines cellular susceptibility to apoptosis

Annexin A5 (AnxA5) is a Ca2+-dependent phospholipid-binding protein associated with the regulation of intracellular Ca2+ homeostasis. However, the precise role of AnxA5 in controlling mitochondrial Ca2+ signaling remains elusive. Here, we introduce a novel function of AnxA5 in regulating mitochondrial Ca2+ signaling. Our investigation revealed that AnxA5 localizes at and in the mitochondria and orchestrates intermembrane space Ca2+ signaling upon high Ca2+ elevations induced by ER Ca2+ release. Proximity ligation assays and co-immunoprecipitation revealed a close association but no direct contact of AnxA5 with the voltage-dependent anion channel (VDAC1) in the outer mitochondrial membrane (OMM). In single-cell mitochondrial Ca2+ measurements and electrophysiological recordings, AnxA5 was found to enhance Ca2+ flux through the OMM by promoting the Ca2+-permeable state of VDAC1. By modulating intermembrane space Ca2+ signaling, AnxA5 shapes mitochondrial ultrastructure and influences the dynamicity of the mitochondrial Ca2+ uniporter. Furthermore, by controlling VDAC1's oligomeric state, AnxA5 is protective against cisplatin and selenite-induced apoptotic cell death. Our study uncovers AnxA5 as an integral regulator of VDAC1 in physiological and pathological conditions.

The role of human Shu complex in ATP-dependent regulation of RAD51 filaments during homologous recombination-associated DNA damage response

Error-free DNA lesion bypass is an important pathway in DNA damage tolerance. The Shu complex facilitates this process by promoting homologous recombination (HR) to bypass DNA damage. Biochemical analysis of the human Shu complex homolog, hSWS1-SWSAP1, offers valuable insights into the HR-associated DNA damage response. Here, we biochemically characterized the human Shu complex and examined its interactions with RAD51 filaments, which are essential in HR. Using fluorescence polarization assays, we first revealed that hSWS1-SWSAP1 preferentially binds DNA with an exposed 5' end in the presence of adenine nucleotides. We then investigated and validated the DNA-stimulated ATPase activity of hSWS1-SWSAP1 through site-specific mutagenesis, revealing that DNA with an exposed 5' end is the most efficient in enhancing this activity. Furthermore, we showed that hSWS1-SWSAP1 initially interacts with RAD51 filaments at the 5' end and modulates the properties of the nucleoprotein filaments using fluorescence-based assays. Our findings revealed that hSWS1-SWSAP1 induces conformational changes in RAD51 filaments in an ATP-hydrolysis-dependent manner, while its stabilization of the filaments depends on ATP binding. This work provides mechanistic insights into the regulation of RAD51 filaments in HR-associated DNA damage tolerance.

A novel ratiometric luminescent probe based on a ruthenium(II) complex-rhodamine scaffold for ATP detection in cancer cells

Adenosine 5'-triphosphate (ATP) plays a pivotal role as an essential intermediate in energy metabolism, influencing nearly all biological metabolic processes. Cancer cells predominantly rely on glycolysis for ATP production, differing significantly from normal cells. Real-time in situ monitoring and rapid response to intracellular ATP levels offers more valuable insights into cancer cell physiology. Herein, we report a novel ratiometric luminescent probe, Ru-Rho, comprised of a ruthenium(II)-based complex and rhodamine 6G (Rho 6G) with excellent water solubility and photostability. Notably, Ru-Rho selectively responds to ATP at acidic conditions, matching the need of monitoring ATP under the acidic intracellular environment of cancer cells. Moreover, the fast ratiometric detection and imaging of ATP under single wavelength excitation improve the detection accuracy. Ru-Rho has been effectively utilized not only for ratio imaging ATP in cells and zebrafish, but also for assessing the efficacy of glycolysis-inhibiting anticancer drugs in intracellular levels, which accelerates the screening process for anticancer drugs and supports the development of new therapeutic agents. The design strategy based on transition metal ruthenium(II) complexes opens a new pathway for constructing ATP luminescent probes, allowing for better adaptation to complex detection requirements.

Death-Associated Protein 3 Triggers Intrinsic Apoptosis via Miro1 Upon Inducing Intracellular Calcium Changes

Mitochondrial homeostasis is essential for cell survival and function, necessitating quality control mechanisms to ensure a healthy mitochondrial network. Death-associated protein 3 (DAP3) serves as a subunit of the mitochondrial ribosome, playing a pivotal role in the translation of mitochondrial-encoded proteins. Apart from its involvement in protein synthesis, DAP3 has been implicated in the process of cell death and mitochondrial dynamics. In this study, we demonstrate that DAP3 mediates cell death via intrinsic apoptosis by triggering excessive mitochondrial fragmentation, loss of mitochondrial membrane potential (ΔΨm), ATP decline, and oxidative stress. Notably, DAP3 induces mitochondrial fragmentation through the Mitochondrial Rho GTPase 1 (Miro1), independently of the canonical fusion/fission machinery. Mechanistically, DAP3 promotes mitochondrial calcium accumulation through the MCU complex, leading to decreased cytosolic Ca2+ levels. This reduction in cytosolic Ca2+ is sensed by Miro1, which subsequently drives mitochondrial fragmentation. Depletion of Miro1 or MCU alleviates mitochondrial fragmentation, oxidative stress, and cell death. Collectively, our findings reveal a novel function of the mitoribosomal protein DAP3 in regulating calcium signalling and maintaining mitochondrial homeostasis.

Atypical plume-like events contribute to glutamate accumulation in metabolic stress conditions

Neural glutamate homeostasis is important for health and disease. Ischemic conditions, like stroke, cause imbalances in glutamate release and uptake due to energy depletion and depolarization. We here used the glutamate sensor SF-iGluSnFR(A184V) to probe how chemical ischemia affects the extracellular glutamate dynamics in slice cultures from mouse cortex. SF-iGluSnFR imaging showed spontaneous glutamate release indicating synchronous network activity, similar to calcium imaging with GCaMP6f. Glutamate imaging further revealed local, atypically large, and long-lasting plume-like release events. Plumes occurred with low frequency, independent of network activity, and persisted in tetrodotoxin (TTX). Blocking glutamate uptake with TFB-TBOA favored plumes, whereas blocking ionotropic glutamate receptors (iGluRs) suppressed plumes. During chemical ischemia plumes became more pronounced, overly abundant and contributed to large-scale glutamate accumulation. Similar plumes were previously observed in cortical spreading depression and migraine models, and they may thus be a more general consequence of glutamate uptake dysfunctions in neurological and neurodegenerative diseases.

Metal-based immunogenic cell death inducers for cancer immunotherapy

Immunogenic cell death (ICD) has attracted enormous attention over the past decade due to its unique characteristics in cancer cell death and its role in activating innate and adaptive immune responses against tumours. Many efforts have been dedicated to screening, identifying and discovering ICD inducers, resulting in the validation of several based on metal complexes. In this review, we provide a comprehensive summary of current metal-based ICD inducers, their molecular mechanisms for triggering ICD initiation and subsequent protective antitumour immune responses, along with considerations for validating ICD both in vitro and in vivo. We also aim to offer insights into the future development of metal complexes with enhanced ICD-inducing properties and their applications in potentiating antitumour immunity.

Lactate activates trained immunity by fueling the tricarboxylic acid cycle and regulating histone lactylation

Trained immunity refers to the long-term memory of the innate immune cells. However, little is known about how environmental nutrient availability influences trained immunity. This study finds that physiologic carbon sources impact glucose contribution to the tricarboxylic acid (TCA) cycle and enhance cytokine production of trained monocytes. Our experiments demonstrate that trained monocytes preferentially employe lactate over glucose as a TCA cycle substrate, and lactate metabolism is required for trained immune cell responses to bacterial and fungal infection. Except for the contribution to the TCA cycle, endogenous lactate or exogenous lactate also supports trained immunity by regulating histone lactylation. Further transcriptome analysis, ATAC-seq, and CUT&Tag-seq demonstrate that lactate enhance chromatin accessibility in a manner dependent histone lactylation. Inhibiting lactate-dependent metabolism by silencing lactate dehydrogenase A (LDHA) impairs both lactate fueled the TCA cycle and histone lactylation. These findings suggest that lactate is the hub of immunometabolic and epigenetic programs in trained immunity.

Glycolysis-enhancing α1-adrenergic antagonists are neuroprotective in Alzheimer's disease

Terazosin (TZ) is an α 1 -adrenergic receptor antagonist that enhances glycolysis by activating the enzyme phosphoglycerate kinase 1 (PGK1). Epidemiological data suggest that TZ may be neuroprotective in Parkinson's disease and in dementia with Lewy bodies and that glycolysis-enhancing drugs might be protective in other neurodegenerative diseases involving protein aggregation, such as Alzheimer's disease (AD). We investigated TZ in AD and report four main results. First, we found that TZ increased ATP levels in a Saccharomyces cerevisiae mutant with impaired energy homeostasis and reduced the aggregation of the AD-associated protein, amyloid beta (Aβ) 42. Second, in an AD transgenic mouse model (5xFAD) we found that TZ attenuated amyloid pathology in the hippocampus and rescued cognitive impairments in spatial memory and interval timing behavioral assays. Third, using the Alzheimer's Disease Neuroimaging Initiative (ADNI) database, we found that AD patients newly started on TZ or related glycolysis-enhancing drugs had a slower progression of both cognitive dysfunction and neuroimaging biomarkers, such as 18 F-fluorodeoxyglucose positron emission tomography (FDG-PET), a measure of brain metabolism. Finally, in a large human administrative dataset, we found that patients taking TZ or related glycolysis-enhancing drugs had a lower hazard of being diagnosed with AD compared to those taking tamsulosin or 5-alpha reductase inhibitors. These data further implicate metabolism in neurodegenerative diseases and suggest that glycolysis-enhancing drugs may be neuroprotective in AD.

Deletion of fbiC in Streptomyces venezuelae removes autofluorescence in the excitation-emission range of cyan fluorescent protein

Autofluorescence poses an impediment to fluorescence microscopy of biological samples. In the Gram-positive, soil-dwelling bacteria of the genus Streptomyces, sources of autofluorescence have not been examined systematically to date. Here, we show that the model organism for the genus, Streptomyces venezuelae, shows autofluorescence in two of the commonly used fluorescence channels for visualizing cyan and green/yellow fluorescent proteins. We identify the source of autofluorescence in the cyan fluorescence channel as redox cofactor factor 420 (F420) and target its synthesis to remove it. By deleting the vnz15170 (fbiC) gene, which is a key biosynthetic gene for the production of F420, we were able to create an autofluorescence-free strain in the cyan range of fluorescence excitation-emission. We demonstrate the usefulness of this strain by imaging the mTurquoise-tagged polar growth-related protein DivIVA and the cell division-related protein FtsZ in the fbiC deletion background. Using live-cell imaging to follow the dynamics of DivIVA and FtsZ, we demonstrate an improved signal-to-noise ratio in the mutant strain. We show that this strain can be a suitable tool for visualizing the localization of proteins in Streptomyces spp. and can facilitate the utilization of multi-colour imaging and fluorescence resonance energy transfer-based imaging.

A2B adenosine receptor signaling and regulation

The A2B adenosine receptor (A2BR) is one of the four adenosine-activated G protein-coupled receptors. In addition to adenosine, protein kinase C (PKC) was recently found to activate the A2BR. The A2BR is coupled to both Gs and Gi, as well as Gq proteins in some cell types. Many primary cells and cell lines, such as bladder and breast cancer, bronchial smooth muscle, skeletal muscle, and fat cells, express the A2BR endogenously at high levels, suggesting its potentially important role in asthma, cancer, diabetes, and other conditions. The A2BR has been characterized as both pro- and anti-inflammatory, inducing cell type-dependent secretion of IL-6, IL-8, and IL-10. Theophylline and enprofylline have long been used for asthma treatment, although it is still not entirely clear if their A2BR antagonism contributes to their therapeutic effects or side effects. The A2BR is required in ischemic cardiac preconditioning by adenosine. Both A2BR and protein kinase C (PKC) contribute to cardioprotection, and both modes of A2BR signaling can be blocked by A2BR antagonists. Inhibitors of PKC and A2BR are in clinical cancer trials. Sulforaphane and other isothiocyanates from cruciferous vegetables such as broccoli and cauliflower have been reported to inhibit A2BR signaling via reaction with an intracellular A2BR cysteine residue (C210). A full, A2BR-selective agonist, critical to elucidate many controversial roles of the A2BR, is still not available, although agonist-bound A2BR structures have recently been reported.

An optical BOD biosensor based on intracellular ATP measurements in genetically modified Saccharomyces cerevisiae

A biosensor for biochemical oxygen demand (BOD) was developed based on intracellular 5'-adenosine triphosphate (ATP) measurements in Saccharomyces cerevisiae. Intracellular ATP was measured using an engineered protein named ATeam, comprising a bacterial F0F1-ATP synthase ε subunit sandwiched between cyan fluorescent protein and mVenus, a modified yellow fluorescent protein. Because the binding of ATP to ATeam induces changes in the fluorescence spectra owing to Fӧrster resonance energy transfer, S. cerevisiae expressing ATeam is expected to show spectral changes owing to the intracellular ATP produced by the metabolism of the BOD sample. A glycogen phosphorylase knockout S. cerevisiae strain expressing ATeam was prepared, and the fluorescence spectra of the strain were analyzed. Changes in the fluorescence spectra of glucose in the medium were observed, which exhibited a linear relationship with the glucose concentration (0-100 mg/L, R2 = 0.970). Responses to lactose, fructose, sucrose, Glu, Asp, His, and Gly were evaluated and compared with typical BOD measurements. The results of this comparison suggest that a BOD biosensor based on intracellular ATP can be used for BOD measurements. A BOD standard solution comprising glucose and glutamic acid (GGA) was calibrated across a concentration range of 0 to 100 mg/L. Finally, simulated real samples were prepared using real pond water and GGA was measured. The correlation between the BOD value evaluated using intracellular ATP and that evaluated using the 5-day BOD test showed a linear relationship with R2 = 0.944.

Optimal Neuromuscular Performance Requires Motor Neuron Phosphagen Kinases

Phosphagen systems are crucial for muscle bioenergetics - rapidly regenerating ATP to support the high metabolic demands of intense musculoskeletal activity. However, their roles in motor neurons that drive muscle contraction have received little attention. Here, we knocked down expression of the primary phosphagen kinase [Arginine Kinase 1; ArgK1] in Drosophila larval motor neurons and assessed the impact on presynaptic energy metabolism and neurotransmission in situ . Fluorescent metabolic probes showed a deficit in presynaptic energy metabolism and some glycolytic compensation. Glycolytic compensation was revealed through a faster elevation in lactate at high firing frequencies, and the accumulation of pyruvate subsequent to firing. Our performance assays included two tests of endurance: enforced cycles of presynaptic calcium pumping, and, separately, enforced body-wall contractions for extended periods. Neither test of endurance revealed deficits when ArgK1 was knocked down. The only performance deficits were detected at firing frequencies that approached, or exceeded, twice the firing frequencies recorded during fictive locomotion, where both electrophysiology and SynaptopHluorin imaging showed an inability to sustain neurotransmitter release. Our computational modeling of presynaptic bioenergetics indicates that the phosphagen system's contribution to motor neuron performance is likely through the removal of ADP in microdomains close to sites of ATP hydrolysis, rather than the provision of a deeper reservoir of ATP. Taken together, these data demonstrate that, as in muscle fibers, motor neurons rely on phosphagen systems during activity that imposes intense energetic demands.

Exogenously and Endogenously Sequential Regulation of DNA Nanodevices Enables Organelle-Specific Signal Amplification in Subcellular ATP Profiling

Adenosine triphosphate (ATP), the primary energy currency in cells, is dynamically regulated across different subcellular compartments. The ATP interplay between mitochondria and endoplasmic reticulum (ER) underscores their coordinated roles in various biochemical processes, highlighting the necessity for precise profiling of subcellular ATP dynamics. Here we present an exogenously and endogenously dual-regulated DNA nanodevice for spatiotemporally selective, subcellular-compartment specific signal amplification in ATP sensing. The system allows for exogenous NIR light-controlled spatiotemporal localization and activation of the aptamer sensor in mitochondria or ER, while a specific endogenous enzyme in the organelles further drives signal amplification via the consumption of molecular beacon fuels, resulting in significantly enhanced sensitivity and spatial precision for the subcellular ATP profiling in the organelle of interest. Furthermore, we demonstrate the application of this system for robust monitoring of ATP fluctuations in mitochondria and ER following drug interventions. This advancement provides a powerful tool for improving our understanding of cellular energetics at the subcellular level and holds potential for the development of targeted therapeutics.

Hypoxia induced mitophagy generates reversible metabolic and redox heterogeneity with transient cell death switch driving tumorigenesis

Tumor hypoxia determines tumor growth, metastasis, drug resistance, and tumor heterogeneity through multiple mechanisms, largely dependent on the extent of hypoxia, further modulated by re-oxygenation events. In order to track the cell fates under hypoxia and re-oxygenation, we have developed a sensor cell for real-time tracking of apoptotic, necrotic, and surviving mitophagy cells under hypoxia and re-oxygenation. The study using this sensor revealed a cell death switch from apoptosis to necrosis by hypoxia-exposed cells under re-oxygenation, where mitophagy plays a key role in acquiring temporally evolving functional phenotypes, including metabolic heterogeneity and mitochondrial redox heterogeneity. RNA transcriptomics also revealed a temporally evolving genomic landscape supporting the complex transcriptional plasticity of cells as a non-genetic adaptive event. Interestingly, cells regained from these distinct stages retained their metastatic potential despite slow growth in animal models. Overall, the study demonstrated that cells acquire distinct functions by tumor hypoxia and re-oxygenation, secondarily acquiring transient functional traits and metabolic heterogeneity governed by cell inherent mitochondrial dynamics. Such cell autonomous temporal alterations in cell states governed by organelle integrity with distinct cell proliferation and apoptosis-necrosis switch may be advantageous for the growing tumor to evolve under complex microenvironmental stress, further contributing to tumorigenesis.

Energetic diversity in retinal ganglion cells is modulated by neuronal activity and correlates with resilience to degeneration

Neuronal function requires high energy expenditure that is likely customized to meet specific signaling demands. However, little is known about diversity of metabolic homeostasis among divergently-functioning types of neurons. To this end, we examined retinal ganglion cells (RGCs), a population of closely related, yet electrophysiologically distinct excitatory projection neurons. Using in vivo 2-photon imaging to measure ATP with single cell resolution, we identified differential homeostatic energy maintenance in the RGC population that correspond to distinct RGC types. In the presence of circuit activity, the most active RGC type (Alpha RGCs), had lower homeostatic ATP levels than other types and exhibited the greatest magnitude of ATP decline when ATP synthesis was inhibited. By simultaneously manipulating circuit activity and mitochondrial function, we found that while oxidative phosphorylation was required to meet ATP demands during circuit activity, it was expendable to maintain resting ATP levels. We also examined ATP signatures associated with survival and injury response after axotomy and report a correlation between low homeostatic ATP and increased survival. In addition, we observed transient ATP increases in RGCs following axon injury. Together, these findings identify diversity of energy handling capabilities of dynamically active neurons with implications for neuronal resilience.

Raptin, a sleep-induced hypothalamic hormone, suppresses appetite and obesity

Sleep deficiency is associated with obesity, but the mechanisms underlying this connection remain unclear. Here, we identify a sleep-inducible hypothalamic protein hormone in humans and mice that suppresses obesity. This hormone is cleaved from reticulocalbin-2 (RCN2), and we name it Raptin. Raptin release is timed by the circuit from vasopressin-expressing neurons in the suprachiasmatic nucleus to RCN2-positive neurons in the paraventricular nucleus. Raptin levels peak during sleep, which is blunted by sleep deficiency. Raptin binds to glutamate metabotropic receptor 3 (GRM3) in neurons of the hypothalamus and stomach to inhibit appetite and gastric emptying, respectively. Raptin-GRM3 signaling mediates anorexigenic effects via PI3K-AKT signaling. Of note, we verify the connections between deficiencies in the sleeping state, impaired Raptin release, and obesity in patients with sleep deficiency. Moreover, humans carrying an RCN2 nonsense variant present with night eating syndrome and obesity. These data define a unique hormone that suppresses food intake and prevents obesity.

Dynamics of Neuronal and Astrocytic Energy Molecules in Epilepsy

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

Genetically Encoded Single-Wavelength Sensor with High Specificity for Imaging ATP in Living Cells

Adenosine 5'-triphosphate (ATP) plays an essential role in regulating many metabolic activities. Therefore, developing tools to directly measure ATP in real time will help us understand its underlying functions. Here, we report an optimized genetically encoded ATP sensor (OAS1.0) with a high specificity for ATP detection. OAS1.0 can be genetically targeted to specific cell types and subcellular compartments to monitor ATP production and consumption. We also used OAS1.0 to visualize metabolic-activity-dependent changes in ATP in normal and tumor cell lines and ATP consumption during the virus-host interaction process. OAS1.0 also worked well with a Ca2+ sensor to concurrently monitor ATP and Ca2+ dynamics in living cells. Thus, OAS1.0 represents a promising tool for ATP imaging under both physiological and pathophysiological conditions.

Charcot Marie Tooth disease pathology is associated with mitochondrial dysfunction and lower glutathione production

Charcot Marie Tooth (CMT) or hereditary motor and sensory neuropathy is a heterogeneous neurological disorder leading to nerve damage and muscle weakness. Although multiple mutations associated with CMT were identified, the cellular and molecular mechanisms of this pathology are still unclear, although most of the subtype of this disease involve mitochondrial dysfunction and oxidative stress in the mechanism of pathology. Using patients' fibroblasts of autosomal recessive, predominantly demyelinating form of CMT-CMT4B3 subtype, we studied the effect of these mutations on mitochondrial metabolism and redox balance. We have found that CMT4B3-associated mutations decrease mitochondrial membrane potential and mitochondrial NADH redox index suggesting an increase rate of mitochondrial respiration in these cells. However, mitochondrial dysfunction had no profound effect on the overall levels of ATP and on the energy capacity of these cells. Although the rate of reactive oxygen species production in mitochondria and cytosol in fibroblasts with CMT4B3 pathology was not significantly higher than in control, the level of GSH was significantly lower. Lower level of glutathione was most likely induced by the lower level of NADPH production, which was used for a GSH cycling, however, expression levels and activity of the major NADPH producing enzyme Glucose-6-Phosphate Dehydrogenase (G6PDH) was not altered. Low level of GSH renders the fibroblast with CMT4B3 pathology more sensitive to oxidative stress and further treatment of cells with hydroperoxide increases CMT patients' fibroblast death rates compared to control. Thus, CMT4B3 pathology makes cells vulnerable to oxidative stress due to the lack of major endogenous antioxidant GSH.

Inhibition of mitochondrial energy production leads to reorganization of the plant endomembrane system

Mitochondria have generated the bulk of ATP to fuel cellular activities, including membrane trafficking, since the beginning of eukaryogenesis. How inhibition of mitochondrial energy production will affect the form and function of the endomembrane system and whether such changes are specific in today's cells remain unclear. Here, we treated Arabidopsis thaliana with antimycin A (AA), a potent inhibitor of the mitochondrial electron transport chain (mETC), as well as other mETC inhibitors and an uncoupler. We investigated the effects of AA on different endomembrane organelles connected by vesicle trafficking via anterograde and retrograde routes that heavily rely on ATP and GTP provision for SNARE and RAB/GEF function, respectively, in root cells. Similar to previous reports, AA inhibited root growth mainly by shortening the elongation zone (EZ) in an energy- and auxin-dependent way. We found that PIN-FORMED 2 (PIN2) and REQUIRES HIGH BORON 1 (BOR1), key proteins for EZ establishment and cell expansion, undergo accelerated endocytosis and accumulate at enlarged multivesicular bodies (MVBs) after AA treatment. Such accumulation is consistent with the observation that the central vacuole becomes fragmented and spherical and that the Arabidopsis Rab7 homolog RABG3f, a master regulator of MVB and vacuolar function, localizes to the tonoplast, likely in a GTP-bound form. We further examined organelles and vesicle populations along the secretory pathway and found that the Golgi apparatus-in particular, the endoplasmic reticulum-Golgi intermediate compartment (ERGIC)-cannot be maintained when mETC is inhibited. Our findings reveal the importance and specific impact of mitochondrial energy production on endomembrane homeostasis.

Non-thermal atmospheric pressure plasma-irradiated cysteine protects cardiac ischemia/reperfusion injury by preserving supersulfides

Ischemic heart disease is the main global cause of death in the world. Abnormal sulfide catabolism, especially hydrogen sulfide accumulation, impedes mitochondrial respiration and worsens the prognosis after ischemic insults, but the substantial therapeutic strategy has not been established. Non-thermal atmospheric pressure plasma irradiation therapy is attracted attention as it exerts beneficial effects by producing various reactive molecular species. Growing evidence has suggested that supersulfides, formed by catenation of sulfur atoms, contribute to various biological processes involving electron transfer in cells. Here, we report that non-thermal plasma-irradiated cysteine (Cys∗) protects mouse hearts against ischemia/reperfusion (I/R) injury by preventing supersulfide catabolism. Cys∗ has a weak but long-lasting supersulfide activity, and the treatment of rat cardiomyocytes with Cys∗ prevents mitochondrial dysfunction after hypoxic stress. Cys∗ increases sulfide-quinone oxidoreductase (SQOR), and silencing SQOR abolishes Cys∗-induced supersulfide formation and cytoprotection. Local administration of mouse hearts with Cys∗ significantly reduces infarct size with preserving supersulfide levels after I/R. These results suggest that maintaining supersulfide formation through SQOR underlies cardioprotection by Cys∗ against I/R injury.

The Dose-Dependent Effects of Fluorocitrate on the Metabolism and Activity of Astrocytes and Neurons

BACKGROUND

Fluorocitrate (FC) ranging from 5 μM to 5 mM is often used as a specific metabolic inhibitor of the astrocytes to study astrocytic functions. Whether FC at such concentrations may affect neuronal metabolism and function in vivo remains unclear.

METHODS

We examined the effects of FC on the ATP levels and Ca2+ activity of the astrocytes and neurons in the motor cortices of living mice using two-photon microscopy.

RESULTS

We found that 25 μM and 250 μM of FC decreased the intracellular ATP levels and Ca2+ activity in the astrocytes in the motor cortex. Equally, 250 μM of FC, but not 25 μM of FC, reduced the intracellular ATP levels in the dendritic processes of the layer 5 pyramidal neurons. However, 25 μM of FC increased the neuronal Ca2+ activity, whereas ≥250 μM of FC decreased it. To test whether the differential effects of FC on neuronal Ca2+ activity reflect the direct effect of FC on the neurons or its indirect effect on the astrocytes, we used the CNO-hM3Dq chemogenetic approach to block astrocytic Ca2+ activity and examined the effect of FC. In the absence of astrocytic Ca2+ activity, 25 μM of FC still increased and ≥250 μM of FC reduced the dendritic Ca2+ activity of the neurons, respectively, suggesting a direct effect of 250 μM of FC on inhibiting neuronal Ca2+ activity. Further, 250 μM, but not 25 μM, of FC increased the size of the dendritic spines over 2 h.

CONCLUSIONS

Our findings suggest that FC at high concentrations (≥250 μM) is not a specific inhibitor of astrocytic functions, as it directly affects neuronal metabolism and synaptic plasticity in vivo.

Genetically Encoded Fluorogenic DNA Aptamers for Imaging Metabolite in Living Cells

Genetically encoded fluorescent protein and fluorogenic RNA sensors are indispensable tools for imaging biomolecules in cells. To expand the toolboxes and improve the generalizability and stability of this type of sensor, we report herein a genetically encoded fluorogenic DNA aptamer (GEFDA) sensor by linking a fluorogenic DNA aptamer for dimethylindole red with an ATP aptamer. The design enhances red fluorescence by 4-fold at 650 nm in the presence of ATP. Additionally, upon dimerization, it improves the signal-to-noise ratio by 2-3 folds. We further integrated the design into a plasmid to create a GEFDA sensor for sensing ATP in live bacterial and mammalian cells. This work expanded genetically encoded sensors by employing fluorogenic DNA aptamers, which offer enhanced stability over fluorogenic proteins and RNAs, providing a novel tool for real-time monitoring of an even broader range of small molecular metabolites in biological systems.

Mitochondrial bioenergetics stimulates autophagy for pathological MAPT/Tau clearance in tauopathy neurons

Hyperphosphorylation and aggregation of MAPT (microtubule-associated protein tau) is a pathogenic hallmark of tauopathies and a defining feature of Alzheimer disease (AD). Pathological MAPT/tau is targeted by macroautophagy/autophagy for clearance after being sequestered within autophagosomes, but autophagy dysfunction is indicated in tauopathy. While mitochondrial bioenergetic deficits have been shown to precede MAPT/tau pathology in tauopathy brains, it is unclear whether energy metabolism deficiency is involved in the pathogenesis of autophagy defects. Here, we reveal that stimulation of anaplerotic metabolism restores defective oxidative phosphorylation (OXPHOS) in tauopathy neurons which, strikingly, leads to pronounced MAPT/tau clearance by boosting autophagy functionality through enhancements of mitochondrial biosynthesis and supply of phosphatidylethanolamine for autophagosome biogenesis. Furthermore, early anaplerotic stimulation of OXPHOS elevates autophagy activity and attenuates MAPT/tau pathology, thereby counteracting memory impairment in tauopathy mice. Taken together, our study sheds light on a pivotal role of mitochondrial bioenergetic deficiency in tauopathy-related autophagy defects and suggests a new therapeutic strategy to prevent the buildup of pathological MAPT/tau in AD and other tauopathy diseases.Abbreviation: AA: antimycin A; AD, Alzheimer disease; ATP, adenosine triphosphate; AV, autophagosome/autophagic vacuole; AZ, active zone; Baf-A1: bafilomycin A1; CHX, cycloheximide; COX, cytochrome c oxidase; DIV, days in vitro; DRG, dorsal root ganglion; ETN, ethanolamine; FRET, Förster/fluorescence resonance energy transfer; FTD, frontotemporal dementia; Gln, glutamine; HA: hydroxylamine; HsMAPT/Tau, human MAPT; IMM, inner mitochondrial membrane; LAMP1, lysosomal-associated membrane protein 1; LIs, lysosomal inhibitors; MDAV, mitochondria-derived autophagic vacuole; MmMAPT/Tau, murine MAPT; NFT, neurofibrillary tangle; OCR, oxygen consumption rate; Omy: oligomycin; OXPHOS, oxidative phosphorylation; PPARGC1A/PGC-1alpha: peroxisome proliferative activated receptor, gamma, coactivator 1 alpha; PE, phosphatidylethanolamine; phospho-MAPT/tau, hyperphosphorylated MAPT; PS, phosphatidylserine; PISD, phosphatidylserine decarboxylase;SQSTM1/p62, sequestosome 1; STX1, syntaxin 1; SYP, synaptophysin; Tg, transgenic; TCA, tricarboxylic acid; TEM, transmission electron microscopy.

Monitoring Cellular Energy Balance in Single Cells Using Fluorescent Biosensors for AMPK

5'-Adenosine monophosphate-activated protein kinase (AMPK) senses cellular metabolic status and reflects the balance between ATP production and ATP usage. This balance varies from cell to cell and changes over time, creating a need for methods that can capture cellular heterogeneity and temporal dynamics. Fluorescent biosensors for AMPK activity offer a unique approach to measure metabolic status nondestructively in single cells in real time. In this chapter, we provide a brief rationale for using live-cell biosensors to measure AMPK activity, survey the current AMPK biosensors, and discuss considerations for using this approach. We provide methodology for introducing AMPK biosensors into a cell line of choice, setting up experiments for live-cell fluorescent microscopy of AMPK activity, and calibrating the biosensors using immunoblot data.

FRET-Based Sensor for Measuring Adenine Nucleotide Binding to AMPK

AMP-activated protein kinase (AMPK) has evolved to detect a critical increase in cellular AMP/ATP and ADP/ATP concentration ratios as a signal for limiting energy supply. Such energy stress then leads to AMPK activation and downstream events that maintain cellular energy homeostasis. AMPK activation by AMP, ADP, or pharmacological activators involves a conformational switch within the AMPK heterotrimeric complex. We have engineered an AMPK-based sensor, AMPfret, which translates the activating conformational switch into a fluorescence signal, based on increased fluorescence resonance energy transfer (FRET) between donor and acceptor fluorophores. Here we describe how this sensor can be used to analyze direct AMPK activation by small molecules in vitro using a fluorimeter, or to estimate changes in the energy state of cells using standard fluorescence or confocal microscopy.

Live imaging of paracrine signaling: Advances in visualization and tracking techniques

Live imaging techniques have revolutionized our understanding of paracrine signaling, a crucial form of cell-to-cell communication in biological processes. This review examines recent advances in visualizing and tracking paracrine factors through four key stages: secretion from producing cells, diffusion through extracellular space, binding to target cells, and activation of intracellular signaling within target cells. Paracrine factor secretion can be directly visualized by fluorescent protein tagging to ligand, or indirectly by visualizing the cleavage of the transmembrane pro-ligands or plasma membrane fusion of endosomes comprising the paracrine factors. Diffusion of paracrine factors has been studied using techniques such as fluorescence correlation spectroscopy (FCS), fluorescence recovery after photobleaching (FRAP), fluorescence decay after photoactivation (FDAP), and single-molecule tracking. Binding of paracrine factors to target cells has been visualized through various biosensors, including GPCR-activation-based (GRAB) sensors and Förster resonance energy transfer (FRET) probes for receptor tyrosine kinases. Finally, activation of intracellular signaling is monitored within the target cells by biosensors for second messengers, transcription factors, and so on. In addition to the imaging tools, the review also highlights emerging optogenetic and chemogenetic tools for triggering the release of paracrine factors, which is essential for associating the paracrine factor secretion to biological outcomes during the bioimaging of paracrine factor signaling.Key words: paracrine signaling, live imaging, biosensors, optogenetics, chemogenetics.

Insulin and leptin acutely modulate the energy metabolism of primary hypothalamic and cortical astrocytes

Astrocytes constitute a heterogeneous cell population within the brain, contributing crucially to brain homeostasis and playing an important role in overall brain function. Their function and metabolism are not only regulated by local signals, for example, from nearby neurons, but also by long-range signals such as hormones. Thus, two prominent hormones primarily known for regulating the energy balance of the whole organism, insulin, and leptin, have been reported to also impact astrocytes within the brain. In this study, we investigated the acute regulation of astrocytic metabolism by these hormones in cultured astrocytes prepared from the mouse cortex and hypothalamus, a pivotal region in the context of nutritional regulation. Utilizing genetically encoded, fluorescent nanosensors, the cytosolic concentrations of glucose, lactate, and ATP, along with glycolytic rate and the NADH/NAD+ redox state were measured. Under basal conditions, differences between the two populations of astrocytes were observed for glucose and lactate concentrations as well as the glycolytic rate. Additionally, astrocytic metabolism responded to insulin and leptin in both brain regions, with some unique characteristics for each cell population. Finally, both hormones influenced how cells responded to elevated extracellular levels of potassium ions, a common indicator of neuronal activity. In summary, our study provides evidence that insulin and leptin acutely regulate astrocytic metabolism within minutes. Additionally, while astrocytes from the hypothalamus and cortex share similarities in their metabolism, they also exhibit distinct properties, further underscoring the growing recognition of astrocyte heterogeneity.

The Shu complex is an ATPase that regulates Rad51 filaments during homologous recombination in the DNA damage response

Rad51 filaments are Rad51-coated single-stranded DNA and essential in homologous recombination (HR). The yeast Shu complex (Shu) is a conserved regulator of homologous recombination, working through its modulation on Rad51 filaments to direct HR-associated DNA damage response. However, the biochemical properties of Shu remain unclear, which hinders molecular insights into Shu's role in HR and the DNA damage response. In this work, we biochemically characterized Shu and analyzed its molecular actions on single-stranded DNA and Rad51 filaments. First, we revealed that Shu preferentially binds fork-shaped DNA with 20nt ssDNA components. Then, we identified and validated, through site-specific mutagenesis, that Shu is an ATPase and hydrolyzes ATP in a DNA-dependent manner. Furthermore, we showed that Shu interacts with ssDNA and Rad51 filaments and alters the properties of ssDNA and the filaments with a 5'-3' polarity. The alterations depend on the ATP hydrolysis of Shu, suggesting that the ATPase activity of Shu is important in regulating its functions. The preference of Shu for acting on the 5' end of Rad51 filaments aligns with the observation that Shu promotes lesion bypass at the lagging strand of a replication fork. Our work on Shu, a prototype modulator of Rad51 filaments in eukaryotes, provides a general molecular mechanism for Rad51-mediated error-free DNA lesion bypass.

Efficient Electrochemical Coupling of Aptamer to Nanoelectrode for In Situ Detection of ATP in Single Cells

Nanoelectrodes, renowned for their small size, rapid mass transport, fast response, and high spatiotemporal resolution, have been recognized as a powerful tool in biosensing, especially for single-cell analysis. However, the nanoelectrode itself has no selectivity and cannot respond to nonelectroactive substances, limiting its wide application to some extent. Herein, we propose a simple and efficient electrochemical conjugation strategy to develop an electrochemical aptamer-coupled (E-AC) sensor for detecting adenosine triphosphate (ATP) in single living cells. Through simple electrochemical conjugation, ferrocene-labeled aptamers could be stably and efficiently coupled onto the surface of carbon fiber electrodes within 5 min. The small size (ca. 400 nm) and biocompatibility of the functionalized nanoelectrodes enabled the E-AC sensors to noninvasively and continuously monitor ATP content in single HeLa cells over 20 min, as well as the cellular ATP fluctuations under glucose starvation. Furthermore, the E-AC sensors exhibit superior specificity, sensitivity, and universality in the application of analysis of ATP in single living Hela cells and MCF-7 cells. They were also versatile for sensing other nonelectroactive targets through modification of the corresponding electroactive marker-labeled aptamers, showing great potential in cell-related physiological processes and drug screening.

Tools to understand hypoxia responses in plant tissues

Our understanding of how low oxygen (O2) conditions arise in plant tissues and how they shape specific responses has seen major advancement in recent years. Important drivers have been (1) the discovery of the molecular machinery that underpins plant O2 sensing; and (2) a growing set of dedicated tools to define experimental conditions and assess plant responses with increasing accuracy and resolution. While some of those tools, such as the Clark-type O2 electrode, were established decades ago, recent customization has set entirely new standards and enabled novel research avenues in plant hypoxia research. Other tools, such as optical hypoxia reporters and O2 biosensor systems, have been introduced more recently. Yet, their adoption into plant hypoxia research has started to generate novel insight into hypoxia physiology at the tissue and cellular levels. The aim of this update is to provide an overview of the currently available and emerging tools for O2 hypoxia measurements in plants, with an emphasis on high-resolution analyses in living plant tissues and cells. Furthermore, it offers directions for future development and deployment of tools to aid progress with the most pressing questions in plant hypoxia research.

Local glycolysis supports injury-induced axonal regeneration

Successful axonal regeneration following injury requires the effective allocation of energy. How axons withstand the initial disruption in mitochondrial energy production caused by the injury and subsequently initiate regrowth is poorly understood. Transcriptomic data showed increased expression of glycolytic genes after optic nerve crush in retinal ganglion cells with the co-deletion of Pten and Socs3. Using retinal cultures in a multicompartment microfluidic device, we observed increased regrowth and enhanced mitochondrial trafficking in the axons of Pten and Socs3 co-deleted neurons. While wild-type axons relied on mitochondrial metabolism, after injury, in the absence of Pten and Socs3, energy production was supported by local glycolysis. Specific inhibition of lactate production hindered injury survival and the initiation of regrowth while slowing down glycolysis upstream impaired regrowth initiation, axonal elongation, and energy production. Together, these observations reveal that glycolytic ATP, combined with sustained mitochondrial transport, is essential for injury-induced axonal regrowth, providing new insights into the metabolic underpinnings of axonal regeneration.

Exploring the landscape of FRET-based molecular sensors: Design strategies and recent advances in emerging applications

Probing biological processes in living organisms that could provide one-of-a-kind insights into real-time alterations of significant physiological parameters is a formidable task that calls for specialized analytic devices. Classical biochemical methods have significantly aided our understanding of the mechanisms that regulate essential biological processes. These methods, however, are typically insufficient for investigating transient molecular events since they focus primarily on the end outcome. Fluorescence resonance energy transfer (FRET) microscopy is a potent tool used for exploring non-invasively real-time dynamic interactions between proteins and a variety of biochemical signaling events using sensors that have been meticulously constructed. Due to their versatility, FRET-based sensors have enabled the rapid and standardized assessment of a large array of biological variables, facilitating both high-throughput research and precise subcellular measurements with exceptional temporal and spatial resolution. This review commences with a brief introduction to FRET theory and a discussion of the fluorescent molecules that can serve as tags in different sensing modalities for studies in chemical biology, followed by an outlining of the imaging techniques currently utilized to quantify FRET highlighting their strengths and shortcomings. The article also discusses the various donor-acceptor combinations that can be utilized to construct FRET scaffolds. Specifically, the review provides insights into the latest real-time bioimaging applications of FRET-based sensors and discusses the common architectures of such devices. There has also been discussion of FRET systems with multiplexing capabilities and multi-step FRET protocols for use in dual/multi-analyte detections. Future research directions in this exciting field are also mentioned, along with the obstacles and opportunities that lie ahead.

TND1128, a 5-deazaflavin derivative with auto-redox ability, facilitates polarization of mitochondrial membrane potential (ΔΨm) and on-demand ATP synthesis in mice brain slices

TND1128, a 5-deazaflavin derivative, is a drug with self-redox ability. We examined the effect of TND1128 on the level of mitochondrial membrane potential (ΔΨm), which is the most critical motive power for the biosynthesis of ATP. We prepared brain slices from mice pretreated with TND1128 (0.1-10 mg/kg, intraperitoneally) and detected ΔΨm level with JC-1, a fluorescence ΔΨm indicator. We further examined the depolarization of ΔΨm under 5-min exposure to 25 mM KCl-ACSF (25K-ACSF), which activated neuronal voltage-dependent Ca2+ channels. We evaluated the effect of TND1128 by using the inverse number of the ΔΨm value as the ATP synthesis index (ASI). The level of ΔΨm increased significantly by 24-h pretreatment with TND1128 (10 mg/kg), and significantly higher depolarization of the ΔΨm was observed with 25K-ACSF exposure than in non-treated control. We found a significant decrease in 25K-ACSF induced [Ca2+]c and [Ca2+]m levels in the TND1128-pretreated preparations. We confirmed the dose and time-dependent facilitatory effects of TND1128 on the ASI. This study suggested that TND1128 could be incorporated into the TCA cycle and electron transfer chains to facilitate the polarization of ΔΨm and activate on-demand ATP synthesis. TND1128 might rescue neurons in various brain diseases caused by energy defects. (198).

A multiplexed high throughput screening assay using flow cytometry identifies glycolytic molecular probes in bloodstream form Trypanosoma brucei

Kinetoplastid organisms, including Trypanosoma brucei, are a significant health burden in many tropical and semitropical countries. Much of their metabolism is poorly understood. To better study kinetoplastid metabolism, chemical probes that inhibit kinetoplastid enzymes are needed. To discover chemical probes, we have developed a high-throughput flow cytometry screening assay that simultaneously measures multiple glycolysis-relevant metabolites in live T. brucei bloodstream form parasites. We transfected parasites with biosensors that measure glucose, ATP, or glycosomal pH. The glucose and ATP sensors were FRET biosensors, while the pH sensor was a GFP-based biosensor. The pH sensor exhibited a different fluorescent profile from the FRET sensors, allowing us to simultaneously measure pH and either glucose or ATP. Cell viability was measured in tandem with the biosensors using thiazole red. We pooled sensor cell lines, loaded them onto plates containing a compound library, and then analyzed them by flow cytometry. The library was analyzed twice, once with the pooled pH and glucose sensor cell lines and once with the pH and ATP sensor cell lines. Multiplexing sensors provided some internal validation of active compounds and gave potential clues for each compound's target(s). We demonstrated this using the glycolytic inhibitor 2-deoxyglucose and the alternative oxidase inhibitor salicylhydroxamic acid. Individual biosensor-based assays exhibited a Z'-factor value acceptable for high-throughput screening, including when multiplexed. We tested assay performance in a pilot screen of 14,976 compounds from the Life Chemicals Compound Library. We obtained hit rates from 0.2 to 0.4% depending on the biosensor, with many compounds impacting multiple sensors. We rescreened 44 hits, and 28 (64%) showed repeatable activity for one or more sensors. One compound exhibited EC50 values in the low micromolar range against two sensors. We expect this method will enable the discovery of glycolytic chemical probes to improve metabolic studies in kinetoplastid parasites.

Unraveling Diabetic Kidney Disease: The Roles of Mitochondrial Dysfunction and Immunometabolism

Mitochondria are essential for cellular energy production and are implicated in numerous diseases, including diabetic kidney disease (DKD). Current evidence indicates that mitochondrial dysfunction results in alterations in several metabolic pathways within kidney cells, thereby contributing to the progression of DKD. Furthermore, mitochondrial dysfunction can engender an inflammatory milieu, leading to the activation and recruitment of immune cells to the kidney tissue, potentially perturbing intrarenal metabolism. In addition, this inflammatory microenvironment has the potential to modify immune cell metabolism, which may further accentuate the immune-mediated kidney injury. This understanding has led to the emerging field of immunometabolism, which views DKD as not just a metabolic disorder caused by hyperglycemia but also one with significant immune contributions. Targeting mitochondrial function and immunometabolism may offer protective effects for the kidneys, complementing current therapies and potentially mitigating the risk of DKD progression. This comprehensive review examines the impact of mitochondrial dysfunction and the potential role of immunometabolism in DKD. We also discuss tools for investigating these mechanisms and propose avenues for integrating this research with existing therapies. These insights underscore the modulation of mitochondrial function and immunometabolism as a critical strategy for decelerating DKD progression.

Molecular Spies in Action: Genetically Encoded Fluorescent Biosensors Light up Cellular Signals

Cellular function is controlled through intricate networks of signals, which lead to the myriad pathways governing cell fate. Fluorescent biosensors have enabled the study of these signaling pathways in living systems across temporal and spatial scales. Over the years there has been an explosion in the number of fluorescent biosensors, as they have become available for numerous targets, utilized across spectral space, and suited for various imaging techniques. To guide users through this extensive biosensor landscape, we discuss critical aspects of fluorescent proteins for consideration in biosensor development, smart tagging strategies, and the historical and recent biosensors of various types, grouped by target, and with a focus on the design and recent applications of these sensors in living systems.

Understanding metabolic plasticity at single cell resolution

It is increasingly clear that cellular metabolic function varies not just between cells of different tissues, but also within tissues and cell types. In this essay, we envision how differences in central carbon metabolism arise from multiple sources, including the cell cycle, circadian rhythms, intrinsic metabolic cycles, and others. We also discuss and compare methods that enable such variation to be detected, including single-cell metabolomics and RNA-sequencing. We pay particular attention to biosensors for AMPK and central carbon metabolites, which when used in combination with metabolic perturbations, provide clear evidence of cellular variance in metabolic function.

Development of fluorescence lifetime biosensors for ATP, cAMP, citrate, and glucose using the mTurquoise2-based platform

Single-fluorescent protein (FP)-based FLIM (fluorescence lifetime imaging microscopy) biosensors can visualize intracellular processes quantitatively. They require a single wavelength for detection, which facilitates multi-color imaging. However, their development has been limited by the absence of a general design framework and complex screening processes. In this study, we engineered FLIM biosensors for ATP (adenosine triphosphate), cAMP (cyclic adenosine monophosphate), citrate, and glucose by inserting each sensing domain into mTurquoise2 (mTQ2) between Tyr-145 and Phe-146 using peptide linkers. Fluorescence intensity-based screening yielded FLIM biosensors with a 0.5 to 1.0 ns dynamic range upon analyte binding, demonstrating that the mTQ2(1-145)-GT-X-EF-mTQ2(146-238) backbone is a versatile platform for FLIM biosensors, allowing for simple intensity-based screening while providing dual-functional biosensors for both FLIM and intensity-based imaging. As a proof of concept, we monitored cAMP and Ca2+ dynamics simultaneously in living cells by dual-color imaging. Our results complement recent studies, establishing mTQ2 as a valuable framework for developing FLIM biosensors.

Elucidating the spatiotemporal dynamics of glucose metabolism with genetically encoded fluorescent biosensors

Glucose metabolism has been well understood for many years, but some intriguing questions remain regarding the subcellular distribution, transport, and functions of glycolytic metabolites. To address these issues, a living cell metabolic monitoring technology with high spatiotemporal resolution is needed. Genetically encoded fluorescent sensors can achieve specific, sensitive, and spatiotemporally resolved metabolic monitoring in living cells and in vivo, and dozens of glucose metabolite sensors have been developed recently. Here, we highlight the importance of tracking specific intermediate metabolites of glycolysis and glycolytic flux measurements, monitoring the spatiotemporal dynamics, and quantifying metabolite abundance. We then describe the working principles of fluorescent protein sensors and summarize the existing biosensors and their application in understanding glucose metabolism. Finally, we analyze the remaining challenges in developing high-quality biosensors and the huge potential of biosensor-based metabolic monitoring at multiple spatiotemporal scales.

Mitochondrial ATP synthesis is essential for efficient gametogenesis in Plasmodium falciparum

Plasmodium male and female gametocytes are the gatekeepers of human-to-mosquito transmission, therefore essential for propagation of malaria within a population. Whilst dormant in humans, their divergent roles during transmission become apparent soon after mosquito feeding with a rapid transformation into gametes - males forming eight motile sperm-like cells aiming to fertilise a single female gamete. Little is known about how the parasite fuels this abrupt change, and the potential role played by their large and elaborate cristate mitochondrion. Using a sex-specific antibody and functional mitochondrial labelling, we show that the male gametocyte mitochondrion is less active than that of female gametocytes and more sensitive to antimalarials targeting mitochondrial energy metabolism. Rather than a vestigial organelle discarded during male gametogenesis, we demonstrate that mitochondrial ATP synthesis is essential for its completion. Additionally, using a genetically encoded ratiometric ATP sensor, we show that gametocytes can maintain cytoplasmic ATP homeostasis in the absence of mitochondrial respiration, indicating the essentiality of the gametocyte mitochondrion for transmission alone. Together, this reveals how gametocytes responsively balance the conflicting demands of a dormant and active lifestyle, highlighting the mitochondria as a rich source of transmission-blocking targets for future drug development.

Breast cancer cells utilize T3 to trigger proliferation through cellular Ca2+ modulation

High levels of thyroid hormones are linked to increased risk and advanced stages of breast cancer. Our previous work demonstrated that the biologically active triiodothyronine (T3) facilitates mitochondrial ATP production by upregulating Ca2+ handling proteins, thereby boosting mitochondrial Ca2+ uptake and Krebs cycle activity. In this study, different cell types were utilized to investigate whether T3 activates a Ca2+-induced signaling pathway to boost cancer cell proliferation. Using live-cell imaging, biochemical assays, and molecular profiling, differences in intracellular signaling among MCF7 and MDA-MB-468 breast cancer cells, non-cancerous breast cells hTERT-HME1, and PC3 prostate carcinoma cells, previously found to be insensitive to thyroid hormones in terms of proliferation, were investigated. Our findings revealed that T3 upregulates 1,4,5-trisphosphate receptor 3 via thyroid hormone receptor α. This boosts mitochondrial Ca2+ uptake, reduction equivalent yield, and mitochondrial ATP production, supporting the viability and proliferation of breast cancer cells without affecting non-cancerous hTERT-HME1 or PC3 prostate carcinoma cells. Understanding the interplay between T3 signaling, organellar interaction, and breast cancer metabolism could lead to targeted therapies that exploit cancer cell vulnerabilities. Our findings highlight T3 as a crucial regulator of cancer metabolism, reinforcing its potential as a therapeutic target in breast cancer.

Recent advances in fluorescent probes for ATP imaging

Adenosine-5'-triphosphate (ATP) is a critical biological molecule that functions as the primary energy currency within cells. ATP synthesis occurs in the mitochondria, and variations in its concentration can significantly influence mitochondrial and cellular performance. Prior studies have established a link between ATP levels and a variety of diseases, such as cancer, neurodegenerative conditions, ischemia, and hypoglycemia. Consequently, researchers have developed many fluorescent probes for ATP detection, recognizing the importance of monitoring intracellular ATP levels to understand cellular processes. These probes have been effectively utilized for visualizing ATP in living cells and biological samples. In this comprehensive review, we categorize fluorescent sensors developed in the last five years for ATP detection. We base our classification on fluorophores, structure, multi-response channels, and application. We also evaluate the challenges and potential for advancing new generations of fluorescence imaging probes for monitoring ATP in living cells. We hope this summary motivates researchers to design innovative and effective probes tailored to ATP sensing. We foresee imminent progress in the development of highly sophisticated ATP probes.

Proviral and antiviral roles of phosphofructokinase family of glycolytic enzymes in TBSV replication

Positive-strand RNA viruses build viral replication organelles (VROs) with the help of co-opted host factors. The biogenesis of the membranous VROs requires major metabolic changes in infected cells. Previous studies showed that tomato bushy stunt virus (TBSV) hijacks several glycolytic enzymes to produce ATP locally within VROs. In this work, we demonstrate that the yeast Pfk2p phosphofructokinase, which performs a rate-limiting and highly regulated step in glycolysis, interacts with the TBSV p33 replication protein. Deletion of PFK2 reduced TBSV replication in yeast, suggesting proviral role for Pfk2p. TBSV also co-opted two plant phosphofructokinases, which supported viral replication and ATP production within VROs, thus acting as proviral factors. Three other phosphofructokinases inhibited TBSV replication and they reduced ATP production within VROs, thus functioning as antiviral factors. Altogether, different phosphofructokinases have proviral or antiviral roles. This suggests on-going arms race between tombusviruses and their hosts to control glycolysis pathway in infected cells.

Autonomous multicolor bioluminescence imaging in bacteria, mammalian, and plant hosts

Bioluminescence imaging has become a valuable tool in biological research, offering several advantages over fluorescence-based techniques, including the absence of phototoxicity and photobleaching, along with a higher signal-to-noise ratio. Common bioluminescence imaging methods often require the addition of an external chemical substrate (luciferin), which can result in a decrease in luminescence intensity over time and limit prolonged observations. Since the bacterial bioluminescence system is genetically encoded for luciferase-luciferin production, it enables autonomous bioluminescence (auto-bioluminescence) imaging. However, its application to multiple reporters is restricted due to a limited range of color variants. Here, we report five-color auto-bioluminescence system named Nano-lanternX (NLX), which can be expressed in bacterial, mammalian, and plant hosts, thereby enabling auto-bioluminescence in various living organisms. Utilizing spectral unmixing, we achieved the successful observation of multicolor auto-bioluminescence, enabling detailed single-cell imaging across both bacterial and mammalian cells. We have also expanded the applications of the NLX system, such as multiplexed auto-bioluminescence imaging for gene expression, protein localization, and dynamics of biomolecules within living mammalian cells.