High-energy Phosphate Bonds Research Articles

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

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

The dynamic relationship between inorganic polyphosphate and adenosine triphosphate in human non-small cell lung cancer H1299 cells.

Inorganic polyphosphate (polyP) plays a vital role in cellular energy metabolism and signaling, owing to its structure and high-energy phosphate bonds. Intracellular ATP functions both as a cellular energy source and a key factor in cell death, and ATP dynamics in tumor cells are crucial for advancing cancer therapy. In this study, we explored the interplay between polyP and ATP in cellular energy metabolism. Treatment with polyP did not affect cell proliferation of human non-small cell lung cancer H1299 and human glioblastoma T98G cell lines as compared to their respective control cells until 72 h post-treatment. The mitochondrial membrane potential (MMP) in polyP-treated cells was low, contrasting with the time-dependent increase observed in control cells. While the ATP content increased over time in untreated and Na-phosphate-treated control cells, it remained unchanged in polyP-treated cells. Furthermore, the addition of cyclosporine A, a mitochondrial permeability transition pore (mPTP) inhibitor, failed to restore ATP levels in polyP-treated cells. We performed lactate assays and western blot analysis to evaluate the effect of polyP on glucose metabolism and found no significant differences in lactate secretion or glucose-6-phosphate dehydrogenase (G6PD) activity between polyP-treated and control cells. Additional pyruvate restored MMP but had no effect on the cellular ATP content in polyP-treated cells. We observed no correlation between the Warburg effect and glucose metabolism during ATP depletion in polyP-treated cells. Further investigation is warranted to explore the roles of polyP and ATP in cancer cell energy metabolism, which might offer potential avenues for therapeutic interventions.

Polyphosphate kinase 1 is involved in formation, the morphology and ultramicrostructure of biofilm of Mycobacterium smegmatis and its survivability in macrophage

The most unique characteristic of Mycobacterium tuberculosis is persistence in the human host, and the biofilm formation is related to the persistance. Polyphosphate (polyP) kinase 1 (PPK1) is conserved in Mycobacteria and is responsible for polyP synthesis. polyP is a chain molecule linked by high-energy phosphate bonds, which is considered to play a very important role in bacterial persistence. However, the relationship of PPK1 and mycobacterial biofilm formation is still adequately unclear. In current study, ppk1-deficient mutant (MT), ppk1-complemented (CT) and wild-type strains of M. smegmatis mc2 155 were used to investigate the formation, morphology and ultramicrostructure of the biofilm and to analyze the lipid levels and susceptibility to vancomycin antibiotic. And then WT, MT and CT strains were used to infect macrophages and to analyze the expression levels of various inflammatory factors, respectively. We found that PPK1 was required for M. smegmatis polyP production in vivo and polyP deficiency not only attenuated the biofilm formation, but also altered the phenotype and ultramicrostructure of the biofilm and reduced the cell lipid composition (except for C16.1 and C17.1, most of the fatty acid components from C8–C24). Moreover, the ppk1-deficient mutant was also significantly more sensitive to vancomycin which targets the cell wall, and its ability to survive in macrophages was decreased, which was related to the change of the expression level of inflammatory factors in macrophage. This study demonstrates that the PPK1 can affect the biofilm structure through affecting the content of short chain fatty acid and promote intracellular survival of M. smegmatis by altering the expression of inflammatory factors. These findings establish a basis for investigating the role of PPK1 in the persistence of M. tuberculosis, and provide clues for treating latent infection of M. tuberculosis with PPK1 as a potential drug target.

Metabolic mechanism and function of cyanobacterial polyphosphate in lakes

大规模蓝藻水华暴发对湖泊水生态系统健康和饮用水安全产生巨大危害，而湖泊水体磷是影响蓝藻水华暴发程度的重要生源要素。应对水体不同磷酸盐浓度，蓝藻高效运行磷酸盐转运系统和磷酸盐特殊转运系统，并合成多聚磷酸盐（聚磷）。蓝藻胞内存在颗粒态、胶体态和可溶态3种形态的聚磷，且不同形态的聚磷分布位置不同。不同蓝藻合成聚磷颗粒的大小、数量和合成期均有所差异。多聚磷酸盐激酶、多聚磷酸盐外切酶、多聚磷酸盐内切酶和P-AMP-磷酸转移酶分别催化聚磷的合成与分解。多聚磷酸盐是二价阳离子的螯合剂，也是磷酸盐及高能磷酸键的储藏库，为细胞生存提供阳离子、磷酸盐和能量，满足蓝藻生命活动过程中生理生化活动所需，具有抵御高温、高pH、紫外线和营养盐缺乏等环境胁迫的生理功能，提升其在不利环境中的生存能力。同时，在蓝藻水华持续暴发、湖泊藻型生境稳态和磷生物地球化学循环过程中聚磷发挥重要的生态功能。因此，蓝藻合成聚磷的分子生物学机制及生态功能研究能够阐明聚磷的存在如何改变湖泊水体-沉积物磷分配、食物网中磷传递等。而开展调控聚磷合成的技术研究，通过控制蓝藻合成聚磷来减轻蓝藻水华暴发规模，将为湖泊水体良性生态系统的重构提供新方法。;Cyanobacterial blooms pose a huge harm to lake aquatic ecosystems health and drinking water safety, and the high phosphorus concentration of lake water bodies is an important inducement for the frequent outbreak of cyanobacterial blooms in lakes. The efficient operation of cyanobacterial intracellular inorganic phosphate transport system and the phosphate special transport system and polyphosphate (polyP) synthesis in cyanobacteria ensures the absorption of phosphate and its survival in phosphorus fluctuating environment. Three forms of polyP including granular, colloidal and soluble polyP, appear in cyanbacterial cells. The subcellular locations of different polyP forms are varied. The size, quantity and the growth period of polyP synthesized are different in different cyanobacterial species. The synthesis and decomposition of polyP are catalyzed by polyphosphate kinase, polyphosphate exonuclease, polyphosphate endonuclease and P-AMP-phosphate transferase, respectively. PolyP is also a chelating agent of divalent cations and a reservoir of phosphate and high-energy phosphate bonds, providing cations, phosphate and energy for cell survival. Cyanobacterial synthesizing polyP is a response to environmental stresses such as high temperature, peroxidation, and nutrient salt deficiency, which improves the viability of cyanobacteria. Therefore, the synthesis of polyP is required for physiological and biochemical activities in the life activities of cyanobacteria. In addition, the synthesis of polyP plays an important ecological function in the continuous outbreak of cyanobacterial blooms and the maintenance of the homeostasis of algal eco-environments. Therefore, it should strengthen the research on the molecular biological mechanism and the ecological function of cyanobacterial polyP synthesis. How the presence of polyphosphorus changes the phosphorus distribution in lake water-sediment and phosphorus transfer in food webs should also be elucidated. The techniques to control large-scale outbreaks of cyanobacterial blooms by controlling the synthesis of polyP in cyanobacteria may provide new methods to reconstruct benign ecosystems in lake waters.

Dextran-coated Gd-based ultrasmall nanoparticles as phosphatase-like nanozyme to increase ethanol yield via reduction of yeast intracellular ATP level

Nanozymes—functional materials that possess intrinsic enzyme-like characteristics—have gained tremendous attention in recent years owing to their unique advantages; however, further research is required to understand their scope in biological applications. In this study, dextran-coated nanogadolinia (DCNG) was synthesised, and its phosphatase mimetic activity was demonstrated. Specifically, the dephosphorylation of adenosine triphosphate (ATP), an important biomolecule, by DCNG was investigated. The results showed that DCNG could selectively catalyse the hydrolysis of the terminal high-energy phosphate bonds of ATP under physiological conditions. Furthermore, the biocompatible DCNG, with remarkable phosphatase mimicking activity, decreased the intracellular ATP content by dephosphorylation and increased ethanol yield during glucose fermentation by S. cerevisiae. These results indicate potential alternatives for improving ethanol yields and exploring novel biological applications of nanozymes.

Approaches to monitor ATP levels in living cells: where do we stand?

ATP is the most universal and essential energy molecule in cells. This is due to its ability to store cellular energy in form of high-energy phosphate bonds, which are extremely stable and readily usable by the cell. This energy is key for a variety of biological functions such as cell growth and division, metabolism, and signaling, and for the turnover of biomolecules. Understanding how ATP is produced and hydrolyzed with a spatiotemporal resolution is necessary to understand its functions both in physiological and in pathological contexts. In this review, first we will describe the organization of the electron transport chain and ATP synthase, the main molecular motor for ATP production in mitochondria. Second, we will review the biochemical assays currently available to estimate ATP quantities in cells, and we will compare their readouts, strengths, and weaknesses. Finally, we will explore the palette of genetically encoded biosensors designed for microscopy-based approaches, and show how their spatiotemporal resolution opened up the possibility to follow ATP levels in living cells.

Polyphosphate (PolyP) for alveolar cleft repair: study protocol for a pilot randomized controlled trial

ObjectiveBone grafting is an important surgical procedure to restore missing bone in patients with alveolar cleft lip/palate, aiming to stabilize either sides of the maxillary segments by inducing new bone formation, and in bilateral cleft cases also to stabilize the pre-maxilla. Polyphosphate (PolyP), a physiological polymer composed of orthophosphate units linked together with high-energy phosphate bonds, is a naturally existing compound in platelets which, when complexed with calcium as Ca-polyP microparticles (Ca-polyP MPs), was proven to have osteoinductive properties in preclinical studies.AimTo evaluate the feasibility, safety, and osteoinductivity of Ca-polyP MPs as a bone-inducing graft material in humans.MethodsThis prospective non-blinded first-in-man clinical pilot study shall consist of 8 alveolar cleft patients of 13 years or older to evaluate the feasibility and safety of Ca-PolyP MPs as a bone-inducing graft material. Patients will receive Ca-polyP graft material only or Ca-polyP in combination with biphasic calcium phosphate (BCP) as a bone substitute carrier. During the trial, the participants will be investigated closely for safety parameters using radiographic imaging, regular blood tests, and physical examinations. After 6 months, a hollow drill will be used to prepare the implantation site to obtain a biopsy. The radiographic imaging will be used for clinical evaluation; the biopsy will be processed for histological/histomorphometric evaluation of bone formation.DiscussionThis is the first-in-man study evaluating the safety and feasibility of the polyP as well as the potential regenerative capacity of polyP using an alveolar cleft model.Trial registrationIndonesian Trial Registry INA-EW74C1N. Registered on 12 June 2020

Effects of guanidinoacetic acid supplementation on nitrogen retention and methionine flux in cattle.

Creatine stores high-energy phosphate bonds in muscle and is synthesized in the liver through methylation of guanidinoacetic acid (GAA). Supplementation of GAA may therefore increase methyl group requirements, and this may affect methyl group utilization. Our experiment evaluated the metabolic responses of growing cattle to postruminal supplementation of GAA, in a model where methionine (Met) was deficient, with and without Met supplementation. Seven ruminally cannulated Holstein steers (161 kg initial body weight [BW]) were limit-fed a soybean hull-based diet (2.7 kg/d dry matter) and received continuous abomasal infusions of an essential amino acid (AA) mixture devoid of Met to ensure that no AA besides Met limited animal performance. To provide energy without increasing the microbial protein supply, all steers received ruminal infusions of 200 g/d acetic acid, 200 g/d propionic acid, and 50 g/d butyric acid, as well as abomasal infusions of 300 g/d glucose. Treatments, provided abomasally, were arranged as a 2 × 3 factorial in a split-plot design, and included 0 or 6 g/d of l-Met and 0, 7.5, and 15 g/d of GAA. The experiment included six 10-d periods. Whole body Met flux was measured using continuous jugular infusion of 1-13C-l-Met and methyl-2H3-l-Met. Nitrogen retention was elevated by Met supplementation (P < 0.01). Supplementation with GAA tended to increase N retention when it was supplemented along with Met, but not when it was supplemented without Met. Supplementing GAA linearly increased plasma concentrations of GAA and creatine (P < 0.001), but treatments did not affect urinary excretion of GAA, creatine, or creatinine. Supplementation with Met decreased plasma homocysteine (P < 0.01). Supplementation of GAA tended (P = 0.10) to increase plasma homocysteine when no Met was supplemented, but not when 6 g/d Met was provided. Protein synthesis and protein degradation were both increased by GAA supplementation when no Met was supplemented, but decreased by GAA supplementation when 6 g/d Met were provided. Loss of Met through transsulfuration was increased by Met supplementation, whereas synthesis of Met from remethylation of homocysteine was decreased by Met supplementation. No differences in transmethylation, transsulfuration, or remethylation reactions were observed in response to GAA supplementation. The administration of GAA, when methyl groups are not limiting, has the potential to improve lean tissue deposition and cattle growth.

The Autotrophic Core: An Ancient Network of 404 Reactions Converts H2, CO2, and NH3 into Amino Acids, Bases, and Cofactors.

The metabolism of cells contains evidence reflecting the process by which they arose. Here, we have identified the ancient core of autotrophic metabolism encompassing 404 reactions that comprise the reaction network from H2, CO2, and ammonia (NH3) to amino acids, nucleic acid monomers, and the 19 cofactors required for their synthesis. Water is the most common reactant in the autotrophic core, indicating that the core arose in an aqueous environment. Seventy-seven core reactions involve the hydrolysis of high-energy phosphate bonds, furthermore suggesting the presence of a non-enzymatic and highly exergonic chemical reaction capable of continuously synthesizing activated phosphate bonds. CO2 is the most common carbon-containing compound in the core. An abundance of NADH and NADPH-dependent redox reactions in the autotrophic core, the central role of CO2, and the circumstance that the core’s main products are far more reduced than CO2 indicate that the core arose in a highly reducing environment. The chemical reactions of the autotrophic core suggest that it arose from H2, inorganic carbon, and NH3 in an aqueous environment marked by highly reducing and continuously far from equilibrium conditions. Such conditions are very similar to those found in serpentinizing hydrothermal systems.

Role of Inositols and Inositol Phosphates in Energy Metabolism.

Recently, inositols, especially myo-inositol and inositol hexakisphosphate, also known as phytic acid or IP6, with their biological activities received much attention for their role in multiple health beneficial effects. Although their roles in cancer treatment and prevention have been extensively reported, interestingly, they may also have distinctive properties in energy metabolism and metabolic disorders. We review inositols and inositol phosphate metabolism in mammalian cells to establish their biological activities and highlight their potential roles in energy metabolism. These molecules are known to decrease insulin resistance, increase insulin sensitivity, and have diverse properties with importance from cell signaling to metabolism. Evidence showed that inositol phosphates might enhance the browning of white adipocytes and directly improve insulin sensitivity through adipocytes. In addition, inositol pyrophosphates containing high-energy phosphate bonds are considered in increasing cellular energetics. Despite all recent advances, many aspects of the bioactivity of inositol phosphates are still not clear, especially their effects on insulin resistance and alteration of metabolism, so more research is needed.

Intrinsic Apyrase-Like Activity of Cerium-Based Metal-Organic Frameworks (MOFs): Dephosphorylation of Adenosine Tri- and Diphosphate.

Apyrase is an important family of extracellular enzymes that catalyse the hydrolysis of high-energy phosphate bonds (HEPBs) in ATP and ADP, thereby modulating many physiological processes and driving life activities. Herein, we report an unexpected discovery that cerium-based metal-organic frameworks (Ce-MOFs) of UiO-66(Ce) have intrinsic apyrase-like activity for ATP/ADP-related physiological processes. The abundant CeIII /CeIV couple sites of Ce-MOFs endow them with the ability to selectively catalyse the hydrolysis of HEPBs of ATP and ADP under physiological conditions. Compared to natural enzymes, they could resist extreme pH and temperature, and present a broad range of working conditions. Based on this finding, a significant inhibitory effect on ADP-induced platelet aggregation was observed upon exposing the platelet-rich plasma (PRP) to the biomimetic UiO-66(Ce) films, prefiguring their wide application potentials in medicine and biotechnology.

Intrinsic Apyrase‐Like Activity of Cerium‐Based Metal–Organic Frameworks (MOFs): Dephosphorylation of Adenosine Tri‐ and Diphosphate

AbstractApyrase is an important family of extracellular enzymes that catalyse the hydrolysis of high‐energy phosphate bonds (HEPBs) in ATP and ADP, thereby modulating many physiological processes and driving life activities. Herein, we report an unexpected discovery that cerium‐based metal–organic frameworks (Ce‐MOFs) of UiO‐66(Ce) have intrinsic apyrase‐like activity for ATP/ADP‐related physiological processes. The abundant CeIII/CeIV couple sites of Ce‐MOFs endow them with the ability to selectively catalyse the hydrolysis of HEPBs of ATP and ADP under physiological conditions. Compared to natural enzymes, they could resist extreme pH and temperature, and present a broad range of working conditions. Based on this finding, a significant inhibitory effect on ADP‐induced platelet aggregation was observed upon exposing the platelet‐rich plasma (PRP) to the biomimetic UiO‐66(Ce) films, prefiguring their wide application potentials in medicine and biotechnology.

Effect of post-ruminal guanidinoacetic acid supplementation on creatine synthesis and plasma homocysteine concentrations in cattle.

Creatine stores high-energy phosphate bonds in muscle, which is critical for muscle activity. In animals, creatine is synthesized in the liver from guanidinoacetic acid (GAA) with methylation by S-adenosylmethionine. Because methyl groups are used for the conversion of GAA to creatine, methyl group deficiency may occur as a result of GAA supplementation. With this study, the metabolic responses of cattle to post-ruminal supplementation of GAA were evaluated with and without methionine (Met) supplementation as a source of methyl groups. Six ruminally cannulated Holstein heifers (520 kg) were used in a split-plot design with treatments arranged as a 2 × 5 factorial. The main plot treatments were 0 or 12 g/d of l-Met arranged in a completely randomized design; three heifers received each main plot treatment throughout the entire experiment. Subplot treatments were 0, 10, 20, 30, and 40 g/d of GAA, with GAA treatments provided in sequence from lowest to highest over five 6-d periods. Treatments were infused continuously to the abomasum. Heifers were limit-fed twice daily a diet consisting of (dry matter basis) 5.3 kg/d rolled corn, 3.6 kg/d alfalfa hay, and 50 g/d trace-mineralized salt. Plasma Met increased (P < 0.01) when Met was supplemented, but it was not affected by supplemental GAA. Supplementing GAA linearly increased plasma arginine (% of total amino acids) and plasma concentrations of GAA and creatinine (P < 0.001). Plasma creatine was increased at all levels of GAA except when 40 g/d of GAA was supplemented with no Met (GAA-quadratic × Met, P = 0.07). Plasma homocysteine was not affected by GAA supplementation when heifers received 12 g/d Met, but it was increased when 30 or 40 g/d of GAA was supplemented without Met (GAA-linear × Met, P = 0.003); increases were modest and did not suggest a dangerous hyperhomocysteinemia. Urinary concentrations of GAA and creatine were increased by all levels of GAA when 12 g/d Met was supplemented; increasing GAA supplementation up to 30 g/d without Met increased urinary GAA and creatine concentrations, but 40 g/d GAA did not affect urine concentrations of GAA and creatine when no Met was supplemented. Overall, post-ruminal GAA supplementation increased creatine supply to cattle. A methyl group deficiency, demonstrated by modest increases in plasma homocysteine, became apparent when 30 or 40 g/d of GAA was supplemented, but it was ameliorated by 12 g/d Met.

Mathematical absurdities in the California net energy system.

Net energy systems, such as the California Net Energy System (CNES), are useful for prediction of input:output relationships not because of fidelity to the laws of thermodynamics, but because they were designed to predict well. Unless model descriptions of input:output relationships are consistent with the laws of thermodynamics, conclusions regarding those relationships may be incorrect. Heat energy (HE) + recovered energy (RE) = ME intake (MEI) is basic to descriptions of energy utilization found in the CNES and is consistent with the laws of thermodynamics; it may be the only relationship described in the CNES consistent with the first law of thermodynamics. In the CNES, efficiencies of ME utilization for maintenance (km) and gain (kg) were estimated using ordinary least squares (OLS) equations. Efficiencies thus estimated using static linear models are often inconsistent with the biochemistry of processes underlying maintenance and gain. Reactions in support of oxidative mitochondrial metabolism are thermodynamically favorable and irreversible; these reactions yield ATP, or other high-energy phosphate bonds, used for what is generally termed maintenance. Synthesis of biomass (gain) is less thermodynamically favorable; reactions do not proceed unless coupled with hydrolysis of high-energy phosphate bonds and lie closer to equilibrium than those in support of oxidative mitochondrial metabolism. The opposite is described in the CNES (km > kg) due to failure of partitioning of HE; insufficient HE is accounted for in maintenance. Efficiencies of ME utilization (km and kg) as described in the CNES are variable. Further neither km nor kg are uniformly monotonic f (ME, Mcal/kg); for ME (Mcal/kg) <0.512 or >4.26, km are inconsistent with thermodynamically allowed values for efficiencies (>1.0); kg are a monotonically positive f (ME) concentration (Mcal/kg) for ME <3.27 Mcal/kg. For ME <1.42 Mcal/kg, kg are not in the range of thermodynamically allowed values for efficiencies (0 to 1.0). Variable efficiencies of ME utilization require that the first law may not be observed in all cases. The CNES is an excellent empirical tool for prediction of input:output relationship, but many CNES parameter estimates evaluated in this study lack consistency with biology and the laws of thermodynamics.

Influence of Mesenchymal Stem Cells on Qualitative and Quantitative Characteristics of Energy Transformation in Muscle Tissue of Lower Extremity in Ischemia.

Energy transformation required for the performance of multiple energy dependent functions of the body, i.e. mechanical, chemical, and electrical, is important part of cell activity. Energy dependent functions become slower at intracellular level due to decreased ATP by 10–15% and stops completely with 25–30% decrease in ATP in the cell. Adenylic nucleotide concentration measures the mismatch between the energy demand and energy production in the cell's mitochondrial oxidative phosphorylation.A study was done with pubescent Wistar rats with body mass of 160–200 grams. The ischemia of the lower extremities was achieved by ligation of femoral artery. Bone marrow was taken from femoral, humoral and tibial bones. Cell culture was grown in Eagle medium IGLA MEM, enriched with L‐glutamine, 10% calf embryo serum with antibiotics added and 5 million of cell were injected intramuscularly in the experimental animals. The concentration of ATP, ADP and AMP in the gastrocnemius muscle measured by means of thin‐layer filtration on silica gel plates on 3rd, 5th, 7th, 14th, 21st and 28th day after injection of mesenchymal stem cells (MSC).The concentration of ATP decreased significantly in the control group after ischemia in consecutive study on specified days. It has been proved that MSC ejection redistributes the pool of adenylic nucleotides towards the increased ATP biosynthesis, so that such parameters of energy metabolism as energy charge, energy potential, thermodynamic control of respiration are increased and the correlation between the components of adenylate kinase reaction is decreased.This study showed that the ability of MSC provide protective action on energy homeostasis by means of the synthesis of large amount of cytokines and growth factors which stimulate the synthesis of glycolytic and Krebs cycle enzymes, increase glucose utilisation and ATP synthesis. Thus, activation of ATP synthesis restores the level of ATP and high energy phosphate bonds.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Using high-energy phosphate as energy-donor and nucleus growth-inhibitor to prepare carbon dots for hydrogen peroxide related biosensing

The various synthetic routes of carbon dots (C-dots) feature a considerable step toward their potential use in sensors and biotechnology. Herein, by coupling pyrophosphate introduction with high-energy phosphate bond design, the fluorescence performance of C-dots is improved greatly. The introduction of pyrophosphate acts as the nucleus growth-inhibitor to protect C-dots from assembling and growing into large carbon particles. The high-energy phosphate bond is designed as an energy-donor to provide energy for synthesizing C-dots. The C-dots exhibit enhanced fluorescence with a high quantum yield of 24.8%. Then the C-dots are employed as the fluorescent probe to develop hydrogen peroxide (H2O2)-related biosensors. The mechanism is based on the fluorescence quenching of C-dots caused by the highly reactive OH and Fe3+ during the Fenton reaction. A wide linear range (0.5–100 μM) and a low detection limit (0.195 μM) are achieved for H2O2 detection. Moreover, the probe can be applied to H2O2-related biosensing in the presence of oxidase. As a proof-of-concept, a glucose sensor is developed with glucose oxidase. The presented glucose sensor exhibits good selectivity and high sensitivity with a detection limit of 0.254 μM. Additionally, the practical application of the proposed biosensor has been confirmed by detecting glucose in human serum samples.

Biosynthetic energy cost of potentially highly expressed proteins vary with niche in selected actinobacteria.

Amino acid and protein biosynthesis requires a number of high energy phosphate bonds and includes a dual energy cost for the synthesis of chemical intermediates during the fueling reactions and the conversion of precursor molecules to final products. One popular hypothesis is that the proteins encoded by putative highly expressed genes (hence called PHXPs) generally utilize low energy consuming amino acids to reduce the biosynthetic cost of the essential proteins. In our study, we found that this idea was not supported in the case of actinobacteria. With the actinobacteria, the energy costs of PHXPs varied in relation to their niche. Free-living, including aquatic, soil and extremophilic, and plant-associated actinobacteria were found to use energetically expensive amino acids in their PHXPs. An exception occurred with some animal-host-associated actinobacteria that used energy efficient amino acids. One explanation for these results may be due to the diverse metabolic patterns exhibited by actinobacteria under varied niches influenced by nutritional availability and physical environment.

Abnormal high-energy phosphate molecule metabolism during regional brain activation in patients with bipolar disorder.

Converging evidence suggests bioenergetic abnormalities in bipolar disorder (BD). In the brain, phosphocreatine (PCr) acts a reservoir of high-energy phosphate (HEP) bonds, and creatine kinases (CK) catalyze the transfer of HEP from adenosine triphosphate (ATP) to PCr and from PCr back to ATP, at times of increased need. This study examined the activity of this mechanism in BD by measuring the levels of HEP molecules during a stimulus paradigm that increased local energy demand. Twenty-three patients diagnosed with BD-I and 22 healthy controls (HC) were included. Levels of phosphorus metabolites were measured at baseline and during visual stimulation in the occipital lobe using (31)P magnetic resonance spectroscopy at 4T. Changes in metabolite levels showed different patterns between the groups. During stimulation, HC had significant reductions in PCr but not in ATP, as expected. In contrast, BD patients had significant reductions in ATP but not in PCr. In addition, PCr/ATP ratio was lower at baseline in patients, and there was a higher change in this measure during stimulation. This pattern suggests a disease-related failure to replenish ATP from PCr through CK enzyme catalysis during tissue activation. Further studies measuring the CK flux in BD are required to confirm and extend this finding.

Adenine nucleotide metabolism and a role for AMP in modulating flagellar waveforms in mouse sperm.

While most ATP, the main energy source driving sperm motility, is derived from glycolysis and oxidative phosphorylation, the metabolic demands of the cell require the efficient use of power stored in high-energy phosphate bonds. In times of high energy consumption, adenylate kinase (AK) scavenges one ATP molecule by transphosphorylation of two molecules of ADP, simultaneously yielding one molecule of AMP as a by-product. Either ATP or ADP supported motility of detergent-modeled cauda epididymal mouse sperm, indicating that flagellar AKs are functional. However, the ensuing flagellar waveforms fueled by ATP or ADP were qualitatively different. Motility driven by ATP was rapid but restricted to the distal region of the sperm tail, whereas ADP produced slower and more fluid waves that propagated down the full flagellum. Characterization of wave patterns by tracing and superimposing the images of the flagella, quantifying the differences using digital image analysis, and computer-assisted sperm analysis revealed differences in the amplitude, periodicity, and propagation of the waves between detergent-modeled sperm treated with either ATP or ADP. Surprisingly, addition of AMP to the incubation medium containing ATP recapitulated the pattern of sperm motility seen with ADP alone. In addition to AK1 and AK2, which we previously demonstrated are present in outer dense fibers and mitochondrial sheath of the mouse sperm tail, we show that another AK, AK8, is present in a third flagellar compartment, the axoneme. These results extend the known regulators of sperm motility to include AMP, which may be operating through an AMP-activated protein kinase.

Purine metabolite and energy charge analysis of Trypanosoma brucei cells in different growth phases using an optimized ion-pair RP-HPLC/UV for the quantification of adenine and guanine pools

Human African Trypanosomiasis (HAT) is caused by the protozoan parasite Trypanosoma brucei. Although trypanosomes are well-studied model organisms, only little is known about their adenine and guanine nucleotide pools. Besides being building blocks of RNA and DNA, these nucleotides are also important modulators of diverse biochemical cellular processes. Adenine nucleotides also play an important role in the regulation of metabolic energy. The energetic state of cells is evaluated by the energy charge which gives information about how much energy is available in form of high energy phosphate bonds of adenine nucleotides. A sensitive and reproducible ion-pair RP-HPLC/UV method was developed and optimized, allowing the quantification of guanine and adenine nucleosides/nucleotides in T. brucei. With this method, the purine levels and their respective ratios were investigated in trypanosomes during logarithmic, stationary and senescent growth phases. Results of this study showed that all adenine and guanine purines under investigation were in the low mM range. The energy charge was found to decrease from logarithmic to static and to senescent phase whereas AMP/ATP, ADP/ATP and GDP/GTP ratios increased in the same order. In addition, the AMP/ATP ratio varied as the square of the ADP/ATP ratio, indicating AMP to be the key energy sensor molecule in trypanosomes.