Pentose Cycle Research Articles

Fructose metabolism is unregulated in cancers and placentae.

Fructose and lactate are present in high concentrations in uterine luminal fluid, fetal fluids and fetal blood of ungulates and cetaceans, but their roles have been ignored and they have been considered waste products of pregnancy. This review provides evidence for key roles of both fructose and lactate in support of key metabolic pathways required for growth and development of fetal-placental tissues, implantation and placentation. The uterus and placenta of ungulates convert glucose to fructose via the polyol pathway. Fructose is sequestered within the uterus and cannot be transported back into the maternal circulation. Fructose is phosphorylated by ketohexokinase to fructose-1-PO4 (F1P) by that is metabolized via the fructolysis pathway to yield dihydoxyacetone phosphate and glyceraldehyde-3-PO4 that are downstream of phosphofructokinase. Thus, there is no inhibition of the fructolysis pathway by low pH, citrate or ATP which allows F1P to continuously generate substrates for the pentose cycle, hexosamine biosynthesis pathway, one-carbon metabolism and tricarboxylic acid cycle, as well as lactate. Lactate sustains the activity of hypoxia-inducible factor alpha and its downstream targets such as vascular endothelial growth factor to increase utero-placental blood flow critical to growth and development of the fetal-placental tissues and a successful outcome of pregnancy. Pregnancy has been referred to as a controlled cancer and this review addresses similarities regarding metabolic aspects of tumors and the placenta.

Metabolic pathways for glucose and fructose: I synthesis and metabolism of fructose by ovine conceptuses†.

Fructose, the most abundant hexose sugar in fetal fluids and the blood of sheep and other ungulates and cetaceans, is synthesized from glucose via the polyol pathway in trophectoderm and chorion. However, the cell-specific and temporal expression of enzymes for the synthesis and metabolism of fructose in sheep conceptuses (embryo and placental membranes) and placentomes has not been characterized. This study characterized key enzymes involved in fructose synthesis and metabolism by ovine conceptuses throughout pregnancy. Day 17 conceptuses expressed mRNAs for the polyol pathway (SORD and AKR1B1) and glucose and fructose metabolism (HK1, HK2, G6PD, OGT, and FBP), but not those required for gluconeogenesis (G6Pase or PCK). Ovine placentomes also expressed mRNAs for SORD, AKR1B1, HK1, and OGT. Fructose can be metabolized via the ketohexokinase (KHK) pathway, and isoforms, KHK-A and KHK-C, were expressed in ovine conceptuses from Day 16 of pregnancy and placentomes during pregnancy in a cell-specific manner. The KHK-A protein was more abundant in the trophectoderm and cotyledons of placentomes, while KHK-C protein was more abundant in the endoderm of Day 16 conceptuses and the chorionic epithelium in placentomes. Expression of KHK mRNAs in placentomes was greatest at Day 30 of pregnancy (P < 0.05), but not different among days later in gestation. These results provide novel insights into the synthesis and metabolism of fructose via the uninhibited KHK pathway in ovine conceptuses to generate ATP via the tricarboxylic cycle, as well as substrates for the pentose cycle, hexosamine biosynthesis pathway, and one-carbon metabolism required for conceptus development throughout pregnancy.

Oxidative stress in animals exposed to cypermethrin: mechanisms of development and possible risks

The purpose of the study is to establish the mechanisms of development of oxidative stress during long-term low-dose exposure to cypermethrin on the animal organism and to substantiate possible risks. The work was carried out using Wistar rats, which were intragastrically injected daily with cypermethrin at a dose of 1/1000 LD50 for 60 and 120 days. At the same time, control animals received an appropriate volume of saline solution inside. When removing animals from the experiment, blood was taken to determine the number of red blood cells, the concentration of hemoglobin, glucose, lactic and uric acids, and total bilirubin. In the study of erythrocytes and liver, biochemical parameters characterizing carbohydrate and purine metabolism, processes of xenobiotics biotransformation, pro- and antioxidant processes were determined. Long-term lowdose exposure to cypermethrin for 60 days causes hematotoxic effects in animals, enhancement of xenobiotic biotransformation processes, and slight compensatory restructuring of metabolic processes in the liver. Exposure to 1/1000 LD50 of cypermethrin for 120 days, in addition to the above effects, causes the development of acidosis, enhances pro-oxidant processes, and suppresses the function of the antioxidant defense system and the pentose cycle. The decrease in the activity of the liver antioxidant system is due to glutathione deficiency due to the activation of xenobiotic biotransformation systems and suppression of the activity of glutathione reductase and glucose-6- phosphate dehydrogenase, which ultimately leads to the development of oxidative stress. Long-term exposure of animals to low doses of cypermethrin causes hemolysis of erythrocytes, lactic acidosis, activation of prooxidant systems, and inhibition of the antioxidant defense system. Deficiency of carbohydrates and suppression of the activity of the pentose cycle indicate a decrease in the functional activity of the liver and an increased risk of immunosuppression.

Trigger Mechanisms of Cypermethrin-Induced Changes of Metabolism: An Experimental Study

Background: The purpose of this work was to study the triggering mechanisms of metabolic changes in experimental animals after a single injection of cypermethrin at a dose of 55 mg/kg of body weight. Methods and Results: Sixty rats were randomly divided into four groups (15 rats in each group). Rats of the control groups (G1 and G3) were injected with saline into the stomach. Animals of the experimental groups (G2 and G4) were injected once with the synthetic pyrethroid cypermethrin at a dose of 55 mg/kg of body weight, which is 1/5 LD50. Before being withdrawn from the experiment, blood was taken in vivo under anesthesia, and the liver was removed. The glucose, lactate, uric acid, and total bilirubin concentrations were determined in blood serum by unified research methods. The content of glutathione (GSH), malondialdehyde (MDA), and activity of glucose-6-phosphate dehydrogenase (G6PDH) was determined in erythrocyte hemolysates. In liver homogenates, the content of total protein, glycogen, uric acid, and inorganic phosphorus (Pi) was determined by unified methods, as well as MDA, GSH, activity of G6PDH, microsomal oxygenase, glutathione-S-transferase (GST), glutathione peroxidase (GPx), and glutathione reductase (GR). Administration of cypermethrin to laboratory rats at a dose of 1/5 LD50 causes adaptive changes in metabolism. After one day, there was an increase in the content of glucose in the blood serum against the background of a deficiency of carbohydrates in the liver tissue. At the same time, there was an increase in anaerobic oxidation and an increase in purine catabolism, which was associated with the activation of lipid peroxidation (LP) of cell membranes and the depletion of the pool of antioxidants. GSH deficiency was exacerbated by an increase in the activity of antioxidant enzymes and xenobiotic biotransformation systems. Seven days after the administration of cypermethrin, rats retained a high rate of breakdown of purines to uric acid. This process was enhanced by a decrease in the RBC, a deficiency of carbohydrates, and inhibition of the activity of G6PDH, GPx, and GR. This ultimately led to the development of oxidative stress. Conclusion: The triggers for the development of oxidative stress under cypermethrin exposure are lactic acidosis and increased catabolism of purine mononucleotides, accompanied by an increase in the production of free radicals and inhibition of the function of the antioxidant system. A decrease in the blood RBC, carbohydrate deficiency, and suppression of the activity of the pentose cycle 7 days after the administration of cypermethrin aggravate this condition.

Ovine conceptus tissue metabolizes fructose for metabolic support during the peri-implantation period of pregnancy†.

Roles of fructose in elongating ovine conceptuses are poorly understood, despite it being the major hexose sugar in fetal fluids and plasma throughout gestation. Therefore, we determined if elongating ovine conceptuses utilize fructose via metabolic pathways for survival and development. Immunohistochemical analyses revealed that trophectoderm and extra-embryonic endoderm express ketohexokinase and aldolase B during the peri-implantation period of pregnancy for conversion of fructose into fructose-1-phosphate for entry into glycolysis and related metabolic pathways. Conceptus homogenates were cultured with 14C-labeled glucose and/or fructose under oxygenated and hypoxic conditions to assess contributions of glucose and fructose to the pentose cycle (PC), tricarboxylic acid cycle, glycoproteins, and lipid synthesis. Results indicated that both glucose and fructose contributed carbons to each of these pathways, except for lipid synthesis, and metabolized to pyruvate and lactate, with lactate being the primary product of glycolysis under oxygenated and hypoxic conditions. We also found that (1) conceptuses preferentially oxidized glucose over fructose (P &lt; 0.05); (2) incorporation of fructose and glucose at 4mM each into the PC by Day 16 conceptus homogenates was similar in the presence or absence of glucose, but incorporation of glucose into the PC was enhanced by the presence of fructose (P &lt; 0.05); (3) incorporation of fructose into the PC in the absence of glucose was greater under oxygenated conditions (P &lt; 0.01); and (4) incorporation of glucose into the PC under oxygenated conditions was greater in the presence of fructose (P = 0.05). These results indicate that fructose is an important metabolic substrate for ovine conceptuses.

Switching to the cyclic pentose phosphate pathway powers the oxidative burst in activated neutrophils

Neutrophils are cells at the frontline of innate immunity that can quickly activate effector functions to eliminate pathogens upon stimulation. However, little is known about the metabolic adaptations that power these functions. Here we show rapid metabolic alterations in neutrophils upon activation, particularly drastic reconfiguration around the pentose phosphate pathway, which is specifically and quantitatively coupled to an oxidative burst. During this oxidative burst, neutrophils switch from glycolysis-dominant metabolism to a unique metabolic mode termed ‘pentose cycle’, where all glucose-6-phosphate is diverted into oxidative pentose phosphate pathway and net flux through upper glycolysis is reversed to allow substantial recycling of pentose phosphates. This reconfiguration maximizes NADPH yield to fuel superoxide production via NADPH oxidase. Disruptions of pentose cycle greatly suppress oxidative burst, the release of neutrophil extracellular traps and pathogen killing by neutrophils. Together, these results demonstrate the remarkable metabolic flexibility of neutrophils, which is essential for their functions as the first responders in innate immunity.

Towards Cancer Theory – Circadian and 11-Day Biological Clocks

Background: In the current study, we used the information-hierarchical system approach to examine human metabolism. Metabolism hierarchical structure, beginning from enzyme level, is controlled by the established information principle and divine section numbers. This structure represents a key mechanism of the hierarchical biological clock (HBC) of human body. Time cycles of HBC hierarchical levels are nested into each other according to strict dynamics schemes. The cycles form the HBC scales of 1, 6, 42 seconds, 24 hours (circadian rhythm), and 11 days and jointly make up the precision HBC similar to the conventional countdown (1 s, 1 m, 1 hr, 1 day, and 1 month). Method: Diagnostic/prognostic studies of cancer require a detailed analysis of metabolic HBC disorders. We utilized the information-hierarchical system approach and the information principle in order to analyze HBC run under different dietary patterns. Results: We characterized hierarchical metabolic systems with 24-hour and 11-day operation times. The 24-hour circadian rhythm comprised citrate, pentose, and fatty acid (anabolic or catabolic) biochemical cycles individually. The 11-day cyclicity referred to these cycles combined into a ternary system of the higher-rank hierarchical level. Disorder of systems operation should lead to a radical change in HBC run with subsequent transformation of normal cells into cancer cells. Conclusion: Mutations of metabolic enzyme genes can damage HBC run, thereby leading to cancer and other chronobiological disorders. Organized rhythmicity of external factors (everyday food intake, 11-day periodical dietary pattern, and so forth) made it possible to heal cancer cells per se. Applying a particular kind of diet, the human lifespan could significantly increase. The proposed direction of cancer prevention and treatment can be called a cancer metabolism chronotherapy.

Deuterium Depletion Inhibits Cell Proliferation, RNA and Nuclear Membrane Turnover to Enhance Survival in Pancreatic Cancer.

The effects of deuterium-depleted water (DDW) containing deuterium (D) at a concentration of 25 parts per million (ppm), 50 ppm, 105 ppm and the control at 150 ppm were monitored in MIA-PaCa-2 pancreatic cancer cells by the real-time cell impedance detection xCELLigence method. The data revealed that lower deuterium concentrations corresponded to lower MiA PaCa-2 growth rate. Nuclear membrane turnover and nucleic acid synthesis rate at different D-concentrations were determined by targeted [1,2-13C2]-D-glucose fate associations. The data showed severely decreased oxidative pentose cycling, RNA ribose 13C labeling from [1,2-13C2]-D-glucose and nuclear membrane lignoceric (C24:0) acid turnover. Here, we treated advanced pancreatic cancer patients with DDW as an extra-mitochondrial deuterium-depleting strategy and evaluated overall patient survival. Eighty-six (36 male and 50 female) pancreatic adenocarcinoma patients were treated with conventional chemotherapy and natural water (control, 30 patients) or 85 ppm DDW (56 patients), which was gradually decreased to preparations with 65 ppm and 45 ppm deuterium content for each 1 to 3 months treatment period. Patient survival curves were calculated by the Kaplan-Meier method and Pearson correlation was taken between medial survival time (MST) and DDW treatment in pancreatic cancer patients. The MST for patients consuming DDW treatment (n = 56) was 19.6 months in comparison with the 6.36 months’ MST achieved with chemotherapy alone (n = 30). There was a strong, statistically significant Pearson correlation (r = 0.504, p < 0.001) between survival time and length and frequency of DDW treatment.

Different Bacteroides Species Colonise Human and Chicken Intestinal Tract.

Bacteroidaceae are common gut microbiota members in all warm-blooded animals. However, if Bacteroidaceae are to be used as probiotics, the species selected for different hosts should reflect the natural distribution. In this study, we therefore evaluated host adaptation of bacterial species belonging to the family Bacteroidaceae. B. dorei, B. uniformis, B. xylanisolvens, B. ovatus, B. clarus, B. thetaiotaomicron and B. vulgatus represented human-adapted species while B. gallinaceum, B. caecigallinarum, B. mediterraneensis, B. caecicola, M. massiliensis, B. plebeius and B. coprocola were commonly detected in chicken but not human gut microbiota. There were 29 genes which were present in all human-adapted Bacteroides but absent from the genomes of all chicken isolates, and these included genes required for the pentose cycle and glutamate or histidine metabolism. These genes were expressed during an in vitro competitive assay, in which human-adapted Bacteroides species overgrew the chicken-adapted isolates. Not a single gene specific for the chicken-adapted species was found. Instead, chicken-adapted species exhibited signs of frequent horizontal gene transfer, of KUP, linA and sugE genes in particular. The differences in host adaptation should be considered when the new generation of probiotics for humans or chickens is designed.

Inhibition effects of some antidepressant drugs on pentose phosphate pathway enzymes

The glucose metabolism in the pentose cycle is essential to the source of NADPH. Deficiency of these enzymes have been linked to depression and psychotic disorders. Depression is an increasingly prevalent mental disorder which may cause loss of labor. Antidepressant drugs are commonly employed in treatments of mood disorders and anxiety treatment. The purpose of this study is to investigate the effects of aripiprazole, mirtazapine, risperidone, escitalopram and haloperidol on the activity of 6-phosphogluconate dehydrogenase (6PGD) and glucose-6-phosphate dehydrogenase (G6PD) enzymes purified from human erythrocytes. It was found that aripiprazole, mirtazapine, risperidone, escitalopram and haloperidol show effective inhibitor properties on purified G6PD and 6PGD enzymes. The IC50 values of these drugs were found in the range of 26.34 μM-5.78 mM for 6PGD and 16.26 μM-3.85 mM for G6PD. The Ki values of the drugs were found in the range of 30.21 ± 4.31 μM-4.51 ± 1.83 mM for 6PGD and 14.12 ± 3.48 μM-4.98 ± 1.14 mM for G6PD. Usage of drugs with significant biological effects may be a hazard in some conditions.

Heat shock induces the cellular antioxidant defenses peroxiredoxin, glutathione and glucose 6-phosphate dehydrogenase through Nrf2

Hyperthermia is a promising anticancer treatment used in combination with radiotherapy and/or chemotherapy. Heat (42–45 °C) can kill cancer cells. Low doses of heat at milder temperatures (39–41 °C) induce thermotolerance, an adaptive survival response that upregulates defense molecules to protect cells against subsequent exposure to toxic stress. Although hyperthermia has proven effective in clinical trials, there is still much to learn about its cellular mechanisms. This study aims to understand the role of reactive oxygen species (ROS), antioxidants and the antioxidant transcription factor Nrf2 in cellular stress responses to mild and lethal heat shock. Mild thermotolerance (40 °C) and hyperthermia (42–43 °C) caused increased expression of the antioxidants peroxiredoxin-3 (Prx3) and Prx2, and its hyperoxidized form Prx-SO3. Cellular levels of superoxide and peroxides increased at 40 °C and 42 °C. Heat shock (42 °C)-induced increases in Prx3 and Prx-SO3 were inhibited by antioxidants (PEG-catalase, MnTBAP) and a Nrf2 shRNA. Glucose metabolism by the pentose phosphate pathway produces NADPH, which maintains the antioxidant glutathione in its reduced form, GSH. Heat shock (40°C–42 °C) increased GSH levels, expression of glucose transporter GLUT1, and enzymatic activity and expression of glucose 6-phosphate dehydrogenase (G6PD), the rate-limiting enzyme in the pentose cycle. Heat-induced increases in GSH levels and G6PD expression were inhibited by antioxidants and Nrf2 knockdown. These results suggest that heat shock-generated ROS were involved in induction of cellular defense molecules Prxs, GSH and G6PD through Nrf2 activation. Our study sheds new light on the role of Nrf2 and antioxidants in cellular responses to heat shock at mild and lethal temperatures.

Synergistic substrate cofeeding stimulates reductive metabolism.

Advanced bioproduct synthesis via reductive metabolism requires coordinating carbons, ATP and reducing agents, which are generated with varying efficiencies depending on metabolic pathways. Substrate mixtures with direct access to multiple pathways may optimally satisfy these biosynthetic requirements. However, native regulation favouring preferential use precludes cells from co-metabolizing multiple substrates. Here we explore mixed substrate metabolism and tailor pathway usage to synergistically stimulate carbon reduction. By controlled cofeeding of superior ATP and NADPH generators as 'dopant' substrates to cells primarily using inferior substrates, we circumvent catabolite repression and drive synergy in two divergent organisms. Glucose doping in Moorella thermoacetica stimulates CO2 reduction (2.3 g gCDW-1 h-1) into acetate by augmenting ATP synthesis via pyruvate kinase. Gluconate doping in Yarrowia lipolytica accelerates acetate-driven lipogenesis (0.046 g gCDW-1 h-1) by obligatory NADPH synthesis through the pentose cycle. Together, synergistic cofeeding produces CO2-derived lipids with 38% energy yield and demonstrates the potential to convert CO2 into advanced bioproducts. This work advances the systems-level control of metabolic networks and CO2 use, the most pressing and difficult reduction challenge.

An early stage in T4-induced hyperthyroidism is related to systemic oxidative stress but does not influence the pentose cycle in erythrocytes and systemic inflammatory status.

Hyperthyroidism causes many injuries in its target organs and the consequences are reflected systemically. As systemic alterations in hyperthyroidism at earlier stages have received partial attention, this study aimed to investigate systemic redox and inflammatory status at an early stage of T4-induced hyperthyroidism. Male Wistar rats were assigned to control and hyperthyroid groups (n = 7/group). The hyperthyroid group received L-thyroxine (12 mg/L) in their drinking water for 14 days whereas control group received only the vehicle. Body weight was measured on the 1st and 14th day of the protocol. On the 14th day, animals were anaesthetized. Blood was then collected from the retro-orbital venous plexus and then the animals were euthanised. The blood was separated into plasma and erythrocytes. Plasma was used to measure ROS levels, sulfhydryl compounds, IL-10, TNF-α and LDH levels; erythrocytes were used for the analysis of thioredoxin reductase activity, glutaredoxin content, and pentose cycle enzymes (total G6PD, G6PD and 6PGD). Hyperthyroid animals presented body weight gain and final body weight reduction, which was associated with increased ROS levels and decreased sulfhydryl content in plasma. Thioredoxin reductase activity, glutaredoxin content, and pentose cycle enzymes levels in erythrocytes, as well as IL-10, TNF-α and LDH plasma levels were unaltered. Taken together, our results suggest an impairment in corporal mass associated with systemic oxidative stress at this stage of hyperthyroidism. Meanwhile, the pentose cycle was not influenced and systemic inflammation and tissue damage seem to be absent at this stage of hyperthyroidism.

Abstract A35: Ovarian cancer stem cells subvert tumor-specific T cells by disrupting T cells’ metabolic fitness

Abstract Cancer stem cells (CSCs) are defined by their unlimited self-renewal ability and their capacity to initiate and maintain malignancy, traits that are not found in most cells that compose the tumor. These stem cells have been shown to be relatively resistant to conventional chemotherapeutic regimens and radiation. Previously, we have reported that spheroid cells derived from 3D epithelial ovarian cancer cells are enriched with cancer stem cells by in vitro and in vivo experiments. In addition, we have demonstrated that CSCs adopt unique metabolic pathways by routing glucose predominantly to anaerobic glycolysis and pentose cycle to the detriment of rerouting glucose for anabolic purposes. In the current study, we hypothesized that CSCs may contribute to the immunosuppressive microenvironment of ovarian cancer by disrupting the metabolic fitness of infiltrating T cells. We isolated fresh spheroid cells from ovarian cancer patients’ ascites and examined their effect on T-cell responses ex vivo. In addition, other than ovarian cancer, we generated more spheroid cells from pancreatic cancer and breast cancer cells. Compared to nonspheroid cells, these spheroid cells have upregulated stem cell gene expression, higher ALDH activity, and more tumor-initiating capacities in SCID mice, indicating CSCs enrichment in spheroid cells. Seahorse XF analysis revealed a glycolytic metabolic phenotype of spheroid cells with increased extracellular acidification rate (ECAR) compared to nonspheroid cells. Spheroid cells suppress the response of cocultured T cells to TCR stimulation by inhibiting T-cell activation, growth, proliferation, and function independent of cell-cell contact determined by transwell assay and supernatant incubation. After spheroid cells treatment, activated T cells metabolically shifted from energetic to quiescence phenotype, which is reversely correlated with increased glycolysis in spheroid cells, indicating that highly glycolytic spheroid cells suppress T-cell response through reprogramming T-cell metabolic status. Furthermore, we found that spheroid cells dampen T cells’ response by inhibiting Erk-AKT-mTor signaling and by activating the integrated stress response pathway. This study provides novel insights into the relationship between cancer stem cells and T cells’ response and has clinical implications for cancer therapy. Citation Format: Feng Qian, Jianqun Liao, Anthony J. Miliotto, Katherine A. Collins, Kunle Odunsi. Ovarian cancer stem cells subvert tumor-specific T cells by disrupting T cells’ metabolic fitness. [abstract]. In: Proceedings of the AACR Conference: Addressing Critical Questions in Ovarian Cancer Research and Treatment; Oct 1-4, 2017; Pittsburgh, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(15_Suppl):Abstract nr A35.

Erythritol Availability in Bovine, Murine and Human Models Highlights a Potential Role for the Host Aldose Reductase during Brucella Infection.

Erythritol is the preferential carbon source for most brucellae, a group of facultative intracellular bacteria that cause a worldwide zoonosis. Since this polyol is abundant in genital organs of ruminants and swine, it is widely accepted that erythritol accounts at least in part for the characteristic genital tropism of brucellae. Nevertheless, proof of erythritol availability and essentiality during Brucella intracellular multiplication has remained elusive. To investigate this relationship, we compared ΔeryH (erythritol-sensitive and thus predicted to be attenuated if erythritol is present), ΔeryA (erythritol-tolerant but showing reduced growth if erythritol is a crucial nutrient) and wild type B. abortus in various infection models. This reporting system indicated that erythritol was available but not required for B. abortus multiplication in bovine trophoblasts. However, mice and humans have been considered to lack erythritol, and we found that it was available but not required for B. abortus multiplication in human and murine trophoblastic and macrophage-like cells, and in mouse spleen and conceptus (fetus, placenta and envelopes). Using this animal model, we found that B. abortus infected cells and tissues contained aldose reductase, an enzyme that can account for the production of erythritol from pentose cycle precursors.

A guide to the effects of a large portion of the residues of triosephosphate isomerase on catalysis, stability, druggability, and human disease.

Triosephosphate isomerase (TIM) is a ubiquitous enzyme, which appeared early in evolution. TIM is responsible for obtaining net ATP from glycolysis and producing an extra pyruvate molecule for each glucose molecule, under aerobic and anaerobic conditions. It is placed in a metabolic crossroad that allows a quick balance of the triose phosphate aldolase produced by glycolysis, and is also linked to lipid metabolism through the alternation of glycerol-3-phosphate and the pentose cycle. TIM is one of the most studied enzymes with more than 199 structures deposited in the PDB. The interest for this enzyme stems from the fact that it is involved in glycolysis, but also in aging, human diseases and metabolism. TIM has been a target in the search for chemical compounds against infectious diseases and is a model to study catalytic features. Until February 2017, 62% of all residues of the protein have been studied by mutagenesis and/or using other approaches. Here, we present a detailed and comprehensive recompilation of the reported effects on TIM catalysis, stability, druggability and human disease produced by each of the amino acids studied, contributing to a better understanding of the properties of this fundamental protein. The information reviewed here shows that the role of the noncatalytic residues depend on their molecular context, the delicate balance between the short and long-range interactions in concerted action determining the properties of the protein. Each protein should be regarded as a unique entity that has evolved to be functional in the organism to which it belongs. Proteins 2017; 85:1190-1211. © 2017 Wiley Periodicals, Inc.

Updates to a 13C metabolic flux analysis model for evaluating energy metabolism in cultured cerebellar granule neurons from neonatal rats

A hexose phosphate recycling model previously developed to infer fluxes through the major glucose consuming pathways in cultured cerebellar granule neurons (CGNs) from neonatal rats metabolizing [1,2–13C2]glucose was revised by considering reverse flux through the non-oxidative pentose phosphate pathway (PPP) and symmetrical succinate oxidation within the tricarboxylic acid (TCA) cycle. The model adjusts three flux ratios to effect 13C distribution in the hexose, pentose, and triose phosphate pools, and in TCA cycle malate to minimize the error between predicted and measured 13C labeling in exported lactate (i.e., unlabeled, single-, double-, and triple-labeled; M, M1, M2, and M3, respectively). Inclusion of reverse non-oxidative PPP flux substantially increased the number of calculations but ultimately had relatively minor effects on the labeling of glycolytic metabolites. From the error-minimized solution in which the predicted M-M3 lactate differed by 0.49% from that measured by liquid chromatography-triple quadrupole mass spectrometry, the neurons exhibited negligible forward non-oxidative PPP flux. Thus, no glucose was used by the pentose cycle despite explicit consideration of hexose phosphate recycling. Mitochondria consumed only 16% of glucose while 45% was exported as lactate by aerobic glycolysis. The remaining 39% of glucose was shunted to pentose phosphates presumably for de novo nucleotide synthesis, but the proportion metabolized through the oxidative PPP vs. the reverse non-oxidative PPP could not be determined. The lactate exported as M1 (2.5%) and M3 (1.2%) was attributed to malic enzyme, which was responsible for 7.8% of pyruvate production (vs. 92.2% by glycolysis). The updated model is more broadly applicable to different cell types by considering bi-directional flux through the non-oxidative PPP. Its application to cultured neurons utilizing glucose as the sole exogenous substrate has demonstrated substantial oxygen-independent glucose utilization by aerobic glycolysis as well as the oxidative PPP and/or reverse non-oxidative PPP, but negligible glucose consumption by the pentose cycle.

13C metabolic flux analysis in neurons utilizing a model that accounts for hexose phosphate recycling within the pentose phosphate pathway

Glycolysis, mitochondrial substrate oxidation, and the pentose phosphate pathway (PPP) are critical for neuronal bioenergetics and oxidation–reduction homeostasis, but quantitating their fluxes remains challenging, especially when processes such as hexose phosphate (i.e., glucose/fructose-6-phosphate) recycling in the PPP are considered. A hexose phosphate recycling model was developed which exploited the rates of glucose consumption, lactate production, and mitochondrial respiration to infer fluxes through the major glucose consuming pathways of adherent cerebellar granule neurons by replicating [13C]lactate labeling from metabolism of [1,2-13C2]glucose. Flux calculations were predicated on a steady-state system with reactions having known stoichiometries and carbon atom transitions. Non-oxidative PPP activity and consequent hexose phosphate recycling, as well as pyruvate production by cytoplasmic malic enzyme, were optimized by the model and found to account for 28 ± 2% and 7.7 ± 0.2% of hexose phosphate and pyruvate labeling, respectively. From the resulting fluxes, 52 ± 6% of glucose was metabolized by glycolysis, compared to 19 ± 2% by the combined oxidative/non-oxidative pentose cycle that allows for hexose phosphate recycling, and 29 ± 8% by the combined oxidative PPP/de novo nucleotide synthesis reactions. By extension, 62 ± 6% of glucose was converted to pyruvate, the metabolism of which resulted in 16 ± 1% of glucose oxidized by mitochondria and 46 ± 6% exported as lactate. The results indicate a surprisingly high proportion of glucose utilized by the pentose cycle and the reactions synthesizing nucleotides, and exported as lactate. While the in vitro conditions to which the neurons were exposed (high glucose, no lactate or other exogenous substrates) limit extrapolating these results to the in vivo state, the approach provides a means of assessing a number of metabolic fluxes within the context of hexose phosphate recycling in the PPP from a minimal set of measurements.

Fructose Alters Intermediary Metabolism of Glucose in Human Adipocytes and Diverts Glucose to Serine Oxidation in the One-Carbon Cycle Energy Producing Pathway.

Increased consumption of sugar and fructose as sweeteners has resulted in the utilization of fructose as an alternative metabolic fuel that may compete with glucose and alter its metabolism. To explore this, human Simpson-Golabi-Behmel Syndrome (SGBS) preadipocytes were differentiated to adipocytes in the presence of 0, 1, 2.5, 5 or 10 mM of fructose added to a medium containing 5 mM of glucose representing the normal blood glucose concentration. Targeted tracer [1,2-13C2]-d-glucose fate association approach was employed to examine the influence of fructose on the intermediary metabolism of glucose. Increasing concentrations of fructose robustly increased the oxidation of [1,2-13C2]-d-glucose to 13CO2 (p < 0.000001). However, glucose-derived 13CO2 negatively correlated with 13C labeled glutamate, 13C palmitate, and M+1 labeled lactate. These are strong markers of limited tricarboxylic acid (TCA) cycle, fatty acid synthesis, pentose cycle fluxes, substrate turnover and NAD+/NADP+ or ATP production from glucose via complete oxidation, indicating diminished mitochondrial energy metabolism. Contrarily, a positive correlation was observed between glucose-derived 13CO2 formed and 13C oleate and doses of fructose which indicate the elongation and desaturation of palmitate to oleate for storage. Collectively, these results suggest that fructose preferentially drives glucose through serine oxidation glycine cleavage (SOGC pathway) one-carbon cycle for NAD+/NADP+ production that is utilized in fructose-induced lipogenesis and storage in adipocytes.

The Warburg effect: a balance of flux analysis.

Cancer metabolism is characterized by increased macromolecular syntheses through coordinated increases in energy and substrate metabolism. The observation that cancer cells produce lactate in an environment of oxygen sufficiency (aerobic glycolysis) is a central theme of cancer metabolism known as the Warburg effect. Aerobic glycolysis in cancer metabolism is accompanied by increased pentose cycle and anaplerotic activities producing energy and substrates for macromolecular synthesis. How these processes are coordinated is poorly understood. Recent advances have focused on molecular regulation of cancer metabolism by oncogenes and tumor suppressor genes which regulate numerous enzymatic steps of central glucose metabolism. In the past decade, new insights in cancer metabolism have emerged through the application of stable isotopes particularly from 13C carbon tracing. Such studies have provided new evidence for system-wide changes in cancer metabolism in response to chemotherapy. Interestingly, experiments using metabolic inhibitors on individual biochemical pathways all demonstrate similar system-wide effects on cancer metabolism as in targeted therapies. Since biochemical reactions in the Warburg effect place competing demands on available precursors, high energy phosphates and reducing equivalents, the cancer metabolic system must fulfill the condition of balance of flux (homeostasis). In this review, the functions of the pentose cycle and of the tricarboxylic acid (TCA) cycle in cancer metabolism are analyzed from the balance of flux point of view. Anticancer treatments that target molecular signaling pathways or inhibit metabolism alter the invasive or proliferative behavior of the cancer cells by their effects on the balance of flux (homeostasis) of the cancer metabolic phenotype.