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Marín-Hernández Á, Saavedra E. Metabolic control analysis as a strategy to identify therapeutic targets, the case of cancer glycolysis. Biosystems 2023; 231:104986. [PMID: 37506818 DOI: 10.1016/j.biosystems.2023.104986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 07/30/2023]
Abstract
The use of kinetic modeling and metabolic control analysis (MCA) to identify possible therapeutic targets and to investigate the controlling and regulatory mechanisms in cancer glycolysis is here reviewed. The glycolytic pathway has been considered a target to decrease cancer cell growth; however, its occurrence in normal cells makes it difficult to design therapeutic strategies that target this pathway in pathological cells. Notwithstanding, the over-expression of all enzymes and transporters, as well as the expression of isoenzymes with different kinetic and regulatory properties in cancer cells, suggested a different distribution of the control of glycolytic flux than that observed in normal cells. Kinetic models of glycolysis are constructed with enzyme kinetics experimental data, validated with the steady-state metabolite concentrations and glycolytic fluxes; applying MCA, permitted us to identify the steps with the highest control of glycolysis in cancer cells, but low control in normal cells. The cancer glycolysis main controlling steps under several metabolic conditions were: glucose transport, hexokinase and hexose-6-phosphate isomerase (HPI); whereas in normal cells were: the first two and phosphofructokinase-1. HPI is the best therapeutic target because it exerts high control in cancer glycolytic flux, but not in normal cells. Furthermore, kinetic modeling also contributed to identifying new feed-back and feed-forward regulatory loops in cancer cells glycolysis, and to understanding the mode of metabolic action of glycolytic inhibitors. Thus, MCA and metabolic modeling allowed to propose new strategies for inhibiting glycolysis in cancer cells.
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Affiliation(s)
- Álvaro Marín-Hernández
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, 14080, Mexico.
| | - Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, 14080, Mexico
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2
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Wesel J, Ingram-Smith C. Glycogen Metabolism and Its Role in Growth and Encystation in Entamoeba histolytica. Life (Basel) 2023; 13:1529. [PMID: 37511904 PMCID: PMC10381564 DOI: 10.3390/life13071529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/03/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Entamoeba histolytica is a parasitic protozoan that causes diarrheal disease in approximately 100 million people worldwide every year. E. histolytica has two forms, the growing trophozoite and the infectious cyst. Trophozoites colonizing the large intestine form cysts that are released into the environment. The ingestion of the cysts in contaminated food and water continues the disease cycle. Here, we investigated the role of glycogen in trophozoite growth and encystation. Glycogen is thought to provide precursors for the synthesis of chitin, a major component of the protective cyst wall. We propose that glycogen also serves as an energy source during metabolic adaptation to different nutrient environments. We examined the role of glycogen in E. histolytica by analyzing the growth and encystation of RNAi strains with reduced expression of the single gene-encoding glycogen synthase (GYS) or two of three genes encoding glycogen phosphorylase (PYG). The GYS RNAi strain had a greatly reduced glycogen accumulation, and both the GYS and PYG RNAi strains exhibited reduced growth in the glucose-poor medium. Both RNAi strains also showed reduced cyst production. Our results suggest glycogen synthesis and degradation are vital to the growth and adaptation of E. histolytica to a low-glucose environment such as that encountered in the large intestine.
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Affiliation(s)
- Jordan Wesel
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, SC 29634, USA
| | - Cheryl Ingram-Smith
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
- Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, SC 29634, USA
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3
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Lo-Thong-Viramoutou O, Charton P, Cadet XF, Grondin-Perez B, Saavedra E, Damour C, Cadet F. Non-linearity of Metabolic Pathways Critically Influences the Choice of Machine Learning Model. Front Artif Intell 2022; 5:744755. [PMID: 35757298 PMCID: PMC9226554 DOI: 10.3389/frai.2022.744755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
The use of machine learning (ML) in life sciences has gained wide interest over the past years, as it speeds up the development of high performing models. Important modeling tools in biology have proven their worth for pathway design, such as mechanistic models and metabolic networks, as they allow better understanding of mechanisms involved in the functioning of organisms. However, little has been done on the use of ML to model metabolic pathways, and the degree of non-linearity associated with them is not clear. Here, we report the construction of different metabolic pathways with several linear and non-linear ML models. Different types of data are used; they lead to the prediction of important biological data, such as pathway flux and final product concentration. A comparison reveals that the data features impact model performance and highlight the effectiveness of non-linear models (e.g., QRF: RMSE = 0.021 nmol·min-1 and R2 = 1 vs. Bayesian GLM: RMSE = 1.379 nmol·min-1 R2 = 0.823). It turns out that the greater the degree of non-linearity of the pathway, the better suited a non-linear model will be. Therefore, a decision-making support for pathway modeling is established. These findings generally support the hypothesis that non-linear aspects predominate within the metabolic pathways. This must be taken into account when devising possible applications of these pathways for the identification of biomarkers of diseases (e.g., infections, cancer, neurodegenerative diseases) or the optimization of industrial production processes.
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Affiliation(s)
- Ophélie Lo-Thong-Viramoutou
- University of Paris, BIGR—Biologie Intégrée du Globule Rouge, Inserm, UMR_S1134, Paris, France
- Laboratory of Excellence GR-Ex, Paris, France
- Laboratory DSIMB, UMR_S1134, BIGR, Inserm, Faculty of Sciences and Technology, University of La Reunion, Saint-Denis, France
| | - Philippe Charton
- University of Paris, BIGR—Biologie Intégrée du Globule Rouge, Inserm, UMR_S1134, Paris, France
- Laboratory of Excellence GR-Ex, Paris, France
- Laboratory DSIMB, UMR_S1134, BIGR, Inserm, Faculty of Sciences and Technology, University of La Reunion, Saint-Denis, France
| | | | - Brigitte Grondin-Perez
- EnergyLab, EA 4079, Faculty of Sciences and Technology, University of La Reunion, Saint-Denis, France
| | - Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Cédric Damour
- EnergyLab, EA 4079, Faculty of Sciences and Technology, University of La Reunion, Saint-Denis, France
| | - Frédéric Cadet
- University of Paris, BIGR—Biologie Intégrée du Globule Rouge, Inserm, UMR_S1134, Paris, France
- Laboratory of Excellence GR-Ex, Paris, France
- Laboratory DSIMB, UMR_S1134, BIGR, Inserm, Faculty of Sciences and Technology, University of La Reunion, Saint-Denis, France
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Oxygen levels are key to understanding "Anaerobic" protozoan pathogens with micro-aerophilic lifestyles. Adv Microb Physiol 2021; 79:163-240. [PMID: 34836611 DOI: 10.1016/bs.ampbs.2021.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Publications abound on the physiology, biochemistry and molecular biology of "anaerobic" protozoal parasites as usually grown under "anaerobic" culture conditions. The media routinely used are poised at low redox potentials using techniques that remove O2 to "undetectable" levels in sealed containers. However there is growing understanding that these culture conditions do not faithfully resemble the O2 environments these organisms inhabit. Here we review for protists lacking oxidative energy metabolism, the oxygen cascade from atmospheric to intracellular concentrations and relevant methods of measurements of O2, some well-studied parasitic or symbiotic protozoan lifestyles, their homeodynamic metabolic and redox balances, organism-drug-oxygen interactions, and the present and future prospects for improved drugs and treatment regimes.
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Salgado-Martínez AI, Avila-Bonilla RG, Ramírez-Moreno E, Castañón-Sánchez CA, López-Camarillo C, Marchat LA. Unraveling the relevance of the polyadenylation factor EhCFIm25 in Entamoeba histolytica through proteomic analysis. FEBS Open Bio 2021; 11:2819-2835. [PMID: 34486252 PMCID: PMC8487052 DOI: 10.1002/2211-5463.13287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/06/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022] Open
Abstract
We recently reported that silencing of the polyadenylation factor EhCFIm25 in Entamoeba histolytica, the protozoan which causes human amoebiasis, affects trophozoite proliferation, death, and virulence, suggesting that EhCFIm25 may have potential as a new biochemical target. Here, we performed a shotgun proteomic analysis to identify modulated proteins that could explain this phenotype. Data are available via ProteomeXchange with identifier PXD027784. Our results revealed changes in the abundance of 75 proteins. Interestingly, STRING analysis, functional GO‐term annotations, KEGG analyses, and literature review showed that modulated proteins are mainly related to glycolysis and carbon metabolism, cytoskeleton dynamics, and parasite virulence, as well as gene expression and protein modifications. Further studies are needed to confirm the hypotheses emerging from this proteomic analysis, to thereby acquire a comprehensive view of the molecular mechanisms involved.
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Affiliation(s)
| | | | - Esther Ramírez-Moreno
- Laboratorio de Biomedicina Molecular II, ENMH, Instituto Politécnico Nacional, Mexico City, Mexico
| | | | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México (UACM), Mexico
| | - Laurence A Marchat
- Laboratorio de Biomedicina Molecular II, ENMH, Instituto Politécnico Nacional, Mexico City, Mexico
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Shirley DA, Sharma I, Warren CA, Moonah S. Drug Repurposing of the Alcohol Abuse Medication Disulfiram as an Anti-Parasitic Agent. Front Cell Infect Microbiol 2021; 11:633194. [PMID: 33777846 PMCID: PMC7991622 DOI: 10.3389/fcimb.2021.633194] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 02/18/2021] [Indexed: 01/24/2023] Open
Abstract
Parasitic infections contribute significantly to worldwide morbidity and mortality. Antibiotic treatment is essential for managing patients infected with these parasites since control is otherwise challenging and there are no vaccines available for prevention. However, new antimicrobial therapies are urgently needed as significant problems exist with current treatments such as drug resistance, limited options, poor efficacy, as well as toxicity. This situation is made worse by the challenges of drug discovery and development which is costly especially for non-profitable infectious diseases, time-consuming, and risky with a high failure rate. Drug repurposing which involves finding new use for existing drugs may help to more rapidly identify therapeutic candidates while drastically cutting costs of drug research and development. In this perspective article, we discuss the importance of drug repurposing, review disulfiram pharmacology, and highlight emerging data that supports repurposing disulfiram as an anti-parasitic, exemplified by the major diarrhea-causing parasite Entamoeba histolytica.
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Affiliation(s)
- Debbie-Ann Shirley
- Division of Pediatric Infectious Diseases, Department of Pediatrics, University of Virginia, Charlottesville, VA, United States
| | - Ishrya Sharma
- Division of Infectious Diseases & International Health, Department of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Cirle A Warren
- Division of Infectious Diseases & International Health, Department of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Shannon Moonah
- Division of Infectious Diseases & International Health, Department of Medicine, University of Virginia, Charlottesville, VA, United States
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7
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Lo-Thong O, Charton P, Cadet XF, Grondin-Perez B, Saavedra E, Damour C, Cadet F. Identification of flux checkpoints in a metabolic pathway through white-box, grey-box and black-box modeling approaches. Sci Rep 2020; 10:13446. [PMID: 32778715 PMCID: PMC7417601 DOI: 10.1038/s41598-020-70295-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 07/27/2020] [Indexed: 11/29/2022] Open
Abstract
Metabolic pathway modeling plays an increasing role in drug design by allowing better understanding of the underlying regulation and controlling networks in the metabolism of living organisms. However, despite rapid progress in this area, pathway modeling can become a real nightmare for researchers, notably when few experimental data are available or when the pathway is highly complex. Here, three different approaches were developed to model the second part of glycolysis of E. histolytica as an application example, and have succeeded in predicting the final pathway flux: one including detailed kinetic information (white-box), another with an added adjustment term (grey-box) and the last one using an artificial neural network method (black-box). Afterwards, each model was used for metabolic control analysis and flux control coefficient determination. The first two enzymes of this pathway are identified as the key enzymes playing a role in flux control. This study revealed the significance of the three methods for building suitable models adjusted to the available data in the field of metabolic pathway modeling, and could be useful to biologists and modelers.
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Affiliation(s)
- Ophélie Lo-Thong
- University of Paris, UMR_S1134, BIGR, Inserm, 75015, Paris, France.,DSIMB, UMR_S1134, BIGR, Inserm, Laboratory of Excellence GR-Ex, Faculty of Sciences and Technology, University of La Reunion, 97715, Saint-Denis, France
| | - Philippe Charton
- University of Paris, UMR_S1134, BIGR, Inserm, 75015, Paris, France.,DSIMB, UMR_S1134, BIGR, Inserm, Laboratory of Excellence GR-Ex, Faculty of Sciences and Technology, University of La Reunion, 97715, Saint-Denis, France
| | - Xavier F Cadet
- PEACCEL, Artificial Intelligence Department, 6 square Albin Cachot, box 42, 75013, Paris, France
| | - Brigitte Grondin-Perez
- LE2P, Laboratory of Energy, Electronics and Processes EA 4079, Faculty of Sciences and Technology, University of La Reunion, 97444, St Denis cedex, France
| | - Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, 14080, Mexico City, Mexico
| | - Cédric Damour
- LE2P, Laboratory of Energy, Electronics and Processes EA 4079, Faculty of Sciences and Technology, University of La Reunion, 97444, St Denis cedex, France
| | - Frédéric Cadet
- University of Paris, UMR_S1134, BIGR, Inserm, 75015, Paris, France. .,DSIMB, UMR_S1134, BIGR, Inserm, Laboratory of Excellence GR-Ex, Faculty of Sciences and Technology, University of La Reunion, 97715, Saint-Denis, France.
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8
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Saavedra E, González-Chávez Z, Moreno-Sánchez R, Michels PA. Drug Target Selection for Trypanosoma cruzi Metabolism by Metabolic Control Analysis and Kinetic Modeling. Curr Med Chem 2019; 26:6652-6671. [DOI: 10.2174/0929867325666180917104242] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 08/17/2018] [Accepted: 08/17/2018] [Indexed: 11/22/2022]
Abstract
In the search for therapeutic targets in the intermediary metabolism of trypanosomatids
the gene essentiality criterion as determined by using knock-out and knock-down genetic
strategies is commonly applied. As most of the evaluated enzymes/transporters have
turned out to be essential for parasite survival, additional criteria and approaches are clearly
required for suitable drug target prioritization. The fundamentals of Metabolic Control
Analysis (MCA; an approach in the study of control and regulation of metabolism) and kinetic
modeling of metabolic pathways (a bottom-up systems biology approach) allow quantification
of the degree of control that each enzyme exerts on the pathway flux (flux control coefficient)
and metabolic intermediate concentrations (concentration control coefficient). MCA
studies have demonstrated that metabolic pathways usually have two or three enzymes with
the highest control of flux; their inhibition has more negative effects on the pathway function
than inhibition of enzymes exerting low flux control. Therefore, the enzymes with the highest
pathway control are the most convenient targets for therapeutic intervention. In this review,
the fundamentals of MCA as well as experimental strategies to determine the flux control coefficients
and metabolic modeling are analyzed. MCA and kinetic modeling have been applied
to trypanothione metabolism in Trypanosoma cruzi and the model predictions subsequently
validated in vivo. The results showed that three out of ten enzyme reactions analyzed
in the T. cruzi anti-oxidant metabolism were the most controlling enzymes. Hence, MCA and
metabolic modeling allow a further step in target prioritization for drug development against
trypanosomatids and other parasites.
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Affiliation(s)
- Emma Saavedra
- Departamento de Bioquimica, Instituto Nacional de Cardiologia Ignacio Chavez. Mexico City, Mexico
| | - Zabdi González-Chávez
- Departamento de Bioquimica, Instituto Nacional de Cardiologia Ignacio Chavez. Mexico City, Mexico
| | - Rafael Moreno-Sánchez
- Departamento de Bioquimica, Instituto Nacional de Cardiologia Ignacio Chavez. Mexico City, Mexico
| | - Paul A.M. Michels
- Centre for Immunity, Infection and Evolution (CIIE) and Centre for Translational and Chemical Biology (CTCB), School of Biological Sciences, The University of Edinburgh, Edinburgh, Scotland
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Mechanisms of natural resistance of Balb/c mice to experimental liver amoebiasis. Biosci Rep 2019; 39:BSR20182333. [PMID: 30979831 PMCID: PMC6500896 DOI: 10.1042/bsr20182333] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 04/03/2019] [Accepted: 04/10/2019] [Indexed: 11/24/2022] Open
Abstract
Entamoeba histolytica is the parasite responsible for human amoebiasis. The analysis of the natural resistance mechanisms of some rodents to amoebic liver abscess (ALA) may reveal alternative pathogenicity mechanisms to those previously discovered in the experimental model of ALA in hamsters. In this work the natural resistance of BALB/c mice to ALA was explored by performing: (i) in vivo chemotaxis analysis with a specifically designed chamber; (ii) in vitro amoebic survival in fresh and decomplemented serum; (iii) histological temporal course analysis of ALA development in mice with different treatments (hypocomplementemic, hyperimmune and treated with iNOS and NADPH oxidase inhibitors) and (iv) mouse liver amoebic infection by both in situ implantation of ALA from hamsters and inoculation of parasites into the peritoneal cavity. The results show that E. histolytica clearance from the mouse liver is related to a low chemotactic activity of complement, which results in poor inflammatory response and parasite inability to cause tissue damage. Also, the absence of amoebic tropism for the mouse liver is correlated with resistance to experimental liver amoebiasis.
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Control and regulation of the pyrophosphate-dependent glucose metabolism in Entamoeba histolytica. Mol Biochem Parasitol 2019; 229:75-87. [PMID: 30772421 DOI: 10.1016/j.molbiopara.2019.02.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/31/2019] [Accepted: 02/09/2019] [Indexed: 01/10/2023]
Abstract
Entamoeba histolytica has neither Krebs cycle nor oxidative phosphorylation activities; therefore, glycolysis is the main pathway for ATP supply and provision of carbon skeleton precursors for the synthesis of macromolecules. Glucose is metabolized through fermentative glycolysis, producing ethanol as its main end-product as well as some acetate. Amoebal glycolysis markedly differs from the typical Embden-Meyerhof-Parnas pathway present in human cells: (i) by the use of inorganic pyrophosphate, instead of ATP, as the high-energy phospho group donor; (ii) with one exception, the pathway enzymes can catalyze reversible reactions under physiological conditions; (iii) there is no allosteric regulation and sigmoidal kinetic behavior of key enzymes; and (iv) the presence of some glycolytic and fermentation enzymes similar to those of anaerobic bacteria. These peculiarities bring about alternative mechanisms of control and regulation of the PPi-dependent fermentative glycolysis in the parasite in comparison to the ATP-dependent and allosterically regulated glycolysis in many other eukaryotic cells. In this review, the current knowledge of the carbohydrate metabolism enzymes in E. histolytica is analyzed. Thermodynamics and stoichiometric analyses indicate 2 to 3.5 ATP yield per glucose metabolized, instead of the often presumed 5 ATP/glucose ratio. PPi derived from anabolism seems insufficient for PPi-glycolysis; hence, alternative ways of PPi supply are also discussed. Furthermore, the underlying mechanisms of control and regulation of the E. histolytica carbohydrate metabolism, analyzed by applying integral and systemic approaches such as Metabolic Control Analysis and kinetic modeling, contribute to unveiling alternative and promising drug targets.
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Angelani CR, Carabias P, Cruz KM, Delfino JM, de Sautu M, Espelt MV, Ferreira-Gomes MS, Gómez GE, Mangialavori IC, Manzi M, Pignataro MF, Saffioti NA, Salvatierra Fréchou DM, Santos J, Schwarzbaum PJ. A metabolic control analysis approach to introduce the study of systems in biochemistry: the glycolytic pathway in the red blood cell. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2018; 46:502-515. [PMID: 30281891 DOI: 10.1002/bmb.21139] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 06/05/2018] [Indexed: 06/08/2023]
Abstract
Metabolic control analysis (MCA) is a promising approach in biochemistry aimed at understanding processes in a quantitative fashion. Here the contribution of enzymes and transporters to the control of a given pathway flux and metabolite concentrations is determined and expressed quantitatively by means of numerical coefficients. Metabolic flux can be influenced by a wide variety of modulators acting on one or more metabolic steps along the pathway. We describe a laboratory exercise to study metabolic regulation of human erythrocytes (RBCs). Within the framework of MCA, students use these cells to determine the sensitivity of the glycolytic flux to two inhibitors (iodoacetic acid: IA, and iodoacetamide: IAA) known to act on the enzyme glyceraldehyde-3-phosphate-dehydrogenase. Glycolytic flux was estimated by determining the concentration of extracellular lactate, the end product of RBC glycolysis. A low-cost colorimetric assay was implemented, that takes advantage of the straightforward quantification of the absorbance signal from the photographic image of the multi-well plate taken with a standard digital camera. Students estimate flux response coefficients for each inhibitor by fitting an empirical function to the experimental data, followed by analytical derivation of this function. IA and IAA exhibit qualitatively different patterns, which are thoroughly analyzed in terms of the physicochemical properties influencing their action on the target enzyme. IA causes highest glycolytic flux inhibition at lower concentration than IAA. This work illustrates the feasibility of using the MCA approach to study key variables of a simple metabolic system, in the context of an upper level biochemistry course. © 2018 International Union of Biochemistry and Molecular Biology, 46(5):502-515, 2018.
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Affiliation(s)
- Carla R Angelani
- Departamento de Química Biológica and Institute of Biochemistry and Biophysics (IQUIFIB, UBA-CONICET), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires. Junín 956, C1113AAD, Buenos Aires, Argentina
| | - Pablo Carabias
- Departamento de Química Biológica and Institute of Biochemistry and Biophysics (IQUIFIB, UBA-CONICET), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires. Junín 956, C1113AAD, Buenos Aires, Argentina
| | - Karen M Cruz
- Departamento de Química Biológica and Institute of Biochemistry and Biophysics (IQUIFIB, UBA-CONICET), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires. Junín 956, C1113AAD, Buenos Aires, Argentina
| | - José M Delfino
- Departamento de Química Biológica and Institute of Biochemistry and Biophysics (IQUIFIB, UBA-CONICET), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires. Junín 956, C1113AAD, Buenos Aires, Argentina
| | - Marilina de Sautu
- Departamento de Química Biológica and Institute of Biochemistry and Biophysics (IQUIFIB, UBA-CONICET), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires. Junín 956, C1113AAD, Buenos Aires, Argentina
| | - María V Espelt
- Departamento de Química Biológica and Institute of Biochemistry and Biophysics (IQUIFIB, UBA-CONICET), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires. Junín 956, C1113AAD, Buenos Aires, Argentina
| | - Mariela S Ferreira-Gomes
- Departamento de Química Biológica and Institute of Biochemistry and Biophysics (IQUIFIB, UBA-CONICET), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires. Junín 956, C1113AAD, Buenos Aires, Argentina
| | - Gabriela E Gómez
- Departamento de Química Biológica and Institute of Biochemistry and Biophysics (IQUIFIB, UBA-CONICET), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires. Junín 956, C1113AAD, Buenos Aires, Argentina
| | - Irene C Mangialavori
- Departamento de Química Biológica and Institute of Biochemistry and Biophysics (IQUIFIB, UBA-CONICET), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires. Junín 956, C1113AAD, Buenos Aires, Argentina
| | - Malena Manzi
- Departamento de Química Biológica and Institute of Biochemistry and Biophysics (IQUIFIB, UBA-CONICET), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires. Junín 956, C1113AAD, Buenos Aires, Argentina
| | - María F Pignataro
- Departamento de Química Biológica and Institute of Biochemistry and Biophysics (IQUIFIB, UBA-CONICET), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires. Junín 956, C1113AAD, Buenos Aires, Argentina
| | - Nicolás A Saffioti
- Departamento de Química Biológica and Institute of Biochemistry and Biophysics (IQUIFIB, UBA-CONICET), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires. Junín 956, C1113AAD, Buenos Aires, Argentina
| | - Damiana M Salvatierra Fréchou
- Departamento de Química Biológica and Institute of Biochemistry and Biophysics (IQUIFIB, UBA-CONICET), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires. Junín 956, C1113AAD, Buenos Aires, Argentina
| | - Javier Santos
- Departamento de Química Biológica and Institute of Biochemistry and Biophysics (IQUIFIB, UBA-CONICET), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires. Junín 956, C1113AAD, Buenos Aires, Argentina
| | - Pablo J Schwarzbaum
- Departamento de Química Biológica and Institute of Biochemistry and Biophysics (IQUIFIB, UBA-CONICET), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires. Junín 956, C1113AAD, Buenos Aires, Argentina
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12
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Pineda E, Perdomo D. Entamoeba histolytica under Oxidative Stress: What Countermeasure Mechanisms Are in Place? Cells 2017; 6:cells6040044. [PMID: 29160807 PMCID: PMC5755502 DOI: 10.3390/cells6040044] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 11/17/2017] [Accepted: 11/17/2017] [Indexed: 02/06/2023] Open
Abstract
Entamoeba histolytica is the causative agent of human amoebiasis; it affects 50 million people worldwide and causes approximately 100,000 deaths per year. Entamoeba histolytica is an anaerobic parasite that is primarily found in the colon; however, for unknown reasons, it can become invasive, breaching the gut barrier and migrating toward the liver causing amoebic liver abscesses. During the invasive process, it must maintain intracellular hypoxia within the oxygenated human tissues and cellular homeostasis during the host immune defense attack when it is confronted with nitric oxide and reactive oxygen species. But how? This review will address the described and potential mechanisms available to counter the oxidative stress generated during invasion and the possible role that E. histolytica’s continuous endoplasmic reticulum (Eh-ER) plays during these events.
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Affiliation(s)
- Erika Pineda
- Laboratory of Fundamental Microbiology and Pathogenicity (MFP), University of Bordeaux, CNRS UMR-5234, 33000 Bordeaux, France.
| | - Doranda Perdomo
- Laboratory of Fundamental Microbiology and Pathogenicity (MFP), University of Bordeaux, CNRS UMR-5234, 33000 Bordeaux, France.
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Pineda E, Vázquez C, Encalada R, Nozaki T, Sato E, Hanadate Y, Néquiz M, Olivos-García A, Moreno-Sánchez R, Saavedra E. Roles of acetyl-CoA synthetase (ADP-forming) and acetate kinase (PPi-forming) in ATP and PPi supply in Entamoeba histolytica. Biochim Biophys Acta Gen Subj 2016; 1860:1163-72. [PMID: 26922831 DOI: 10.1016/j.bbagen.2016.02.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 02/03/2016] [Accepted: 02/21/2016] [Indexed: 10/22/2022]
Abstract
BACKGROUND Acetate is an end-product of the PPi-dependent fermentative glycolysis in Entamoeba histolytica; it is synthesized from acetyl-CoA by ADP-forming acetyl-CoA synthetase (ACS) with net ATP synthesis or from acetyl-phosphate by a unique PPi-forming acetate kinase (AcK). The relevance of these enzymes to the parasite ATP and PPi supply, respectively, are analyzed here. METHODS The recombinant enzymes were kinetically characterized and their physiological roles were analyzed by transcriptional gene silencing and further metabolic analyses in amoebae. RESULTS Recombinant ACS showed higher catalytic efficiencies (Vmax/Km) for acetate formation than for acetyl-CoA formation and high acetyl-CoA levels were found in trophozoites. Gradual ACS gene silencing (49-93%) significantly decreased the acetate flux without affecting the levels of glycolytic metabolites and ATP in trophozoites. However, amoebae lacking ACS activity were unable to reestablish the acetyl-CoA/CoA ratio after an oxidative stress challenge. Recombinant AcK showed activity only in the acetate formation direction; however, its substrate acetyl-phosphate was undetected in axenic parasites. AcK gene silencing did not affect acetate production in the parasites but promoted a slight decrease (10-20%) in the hexose phosphates and PPi levels. CONCLUSIONS These results indicated that the main role of ACS in the parasite energy metabolism is not ATP production but to recycle CoA for glycolysis to proceed under aerobic conditions. AcK does not contribute to acetate production but might be marginally involved in PPi and hexosephosphate homeostasis. SIGNIFICANCE The previous, long-standing hypothesis that these enzymes importantly contribute to ATP and PPi supply in amoebae can now be ruled out.
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Affiliation(s)
- Erika Pineda
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez. Mexico D.F. 14080, Mexico
| | - Citlali Vázquez
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez. Mexico D.F. 14080, Mexico
| | - Rusely Encalada
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez. Mexico D.F. 14080, Mexico
| | - Tomoyoshi Nozaki
- Department of Parasitology, National Institute of Infectious Diseases. Tokyo 162-8640, Japan
| | - Emi Sato
- Department of Parasitology, National Institute of Infectious Diseases. Tokyo 162-8640, Japan
| | - Yuki Hanadate
- Department of Parasitology, National Institute of Infectious Diseases. Tokyo 162-8640, Japan
| | - Mario Néquiz
- Departamento de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México. Mexico D.F. 04510, Mexico
| | - Alfonso Olivos-García
- Departamento de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México. Mexico D.F. 04510, Mexico
| | - Rafael Moreno-Sánchez
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez. Mexico D.F. 14080, Mexico
| | - Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez. Mexico D.F. 14080, Mexico.
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Matt J, Duchêne M. Molecular and biochemical characterization of Entamoeba histolytica fructokinase. Parasitol Res 2015; 114:1939-47. [PMID: 25700717 PMCID: PMC4412284 DOI: 10.1007/s00436-015-4383-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 02/05/2015] [Indexed: 11/23/2022]
Abstract
Entamoeba histolytica is the causative agent of amoebic dysentery and liver abscess. The medium for its axenic culture contains glucose as energy source, and we addressed the question whether E. histolytica can also use fructose instead. As the amoebic hexokinases do not phosphorylate fructose, a separate fructokinase is essential. The genome project revealed a single candidate gene encoding an E. histolytica homolog of bacterial fructokinases. This gene was cloned, and the recombinant enzyme had a magnesium-dependent fructose 6-kinase activity (EC 2.7.1.4) with a Km for fructose of 0.156 mM and a Vmax of 131 U/mg protein. Recombinant fructokinase also showed a much weaker mannokinase activity, but no activity with glucose or galactose. The amoebae could be switched from glucose to fructose medium without any detectable consequence on doubling time. Fructokinase messenger RNA (mRNA) was modestly but significantly upregulated in amoebae switched to fructose medium as well as in fructose-adapted E. histolytica.
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Affiliation(s)
- Julia Matt
- Institute of Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Kinderspitalgasse 15, 1090, Vienna, Austria
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