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Understanding bistability in yeast glycolysis using general properties of metabolic pathways. Math Biosci 2014; 255:33-42. [PMID: 24956444 DOI: 10.1016/j.mbs.2014.06.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 06/03/2014] [Accepted: 06/04/2014] [Indexed: 11/23/2022]
Abstract
UNLABELLED Glycolysis is the central pathway in energy metabolism in the majority of organisms. In a recent paper, van Heerden et al. showed experimentally and computationally that glycolysis can exist in two states, a global steady state and a so-called imbalanced state. In the imbalanced state, intermediary metabolites accumulate at low levels of ATP and inorganic phosphate. It was shown that Baker's yeast uses a peculiar regulatory mechanism--via trehalose metabolism--to ensure that most yeast cells reach the steady state and not the imbalanced state. RESULTS Here we explore the apparent bistable behaviour in a core model of glycolysis that is based on a well-established detailed model, and study in great detail the bifurcation behaviour of solutions, without using any numerical information on parameter values. CONCLUSION We uncover a rich suite of solutions, including so-called imbalanced states, bistability, and oscillatory behaviour. The techniques employed are generic, directly suitable for a wide class of biochemical pathways, and could lead to better analytical treatments of more detailed models.
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van Heerden JH, Wortel MT, Bruggeman FJ, Heijnen JJ, Bollen YJM, Planqué R, Hulshof J, O'Toole TG, Wahl SA, Teusink B. Lost in transition: start-up of glycolysis yields subpopulations of nongrowing cells. Science 2014; 343:1245114. [PMID: 24436182 DOI: 10.1126/science.1245114] [Citation(s) in RCA: 221] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cells need to adapt to dynamic environments. Yeast that fail to cope with dynamic changes in the abundance of glucose can undergo growth arrest. We show that this failure is caused by imbalanced reactions in glycolysis, the essential pathway in energy metabolism in most organisms. The imbalance arises largely from the fundamental design of glycolysis, making this state of glycolysis a generic risk. Cells with unbalanced glycolysis coexisted with vital cells. Spontaneous, nongenetic metabolic variability among individual cells determines which state is reached and, consequently, which cells survive. Transient ATP (adenosine 5'-triphosphate) hydrolysis through futile cycling reduces the probability of reaching the imbalanced state. Our results reveal dynamic behavior of glycolysis and indicate that cell fate can be determined by heterogeneity purely at the metabolic level.
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Affiliation(s)
- Johan H van Heerden
- Systems Bioinformatics/Amsterdam Institute for Molecules, Medicines and Systems (AIMMS)/Netherlands Institute for Systems Biology, VU University, De Boelelaan 1085, 1081 HV Amsterdam, Netherlands
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Claeyssen É, Dorion S, Clendenning A, He JZ, Wally O, Chen J, Auslender EL, Moisan MC, Jolicoeur M, Rivoal J. The futile cycling of hexose phosphates could account for the fact that hexokinase exerts a high control on glucose phosphorylation but not on glycolytic rate in transgenic potato (Solanum tuberosum) roots. PLoS One 2013; 8:e53898. [PMID: 23382859 PMCID: PMC3557296 DOI: 10.1371/journal.pone.0053898] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 12/04/2012] [Indexed: 11/18/2022] Open
Abstract
The metabolism of potato (Solanum tuberosum) roots constitutively over- and underexpressing hexokinase (HK, EC 2.7.1.1) was examined. An 11-fold variation in HK activity resulted in altered root growth, with antisense roots growing better than sense roots. Quantification of sugars, organic acids and amino acids in transgenic roots demonstrated that the manipulation of HK activity had very little effect on the intracellular pools of these metabolites. However, adenylate and free Pi levels were negatively affected by an increase in HK activity. The flux control coefficient of HK over the phosphorylation of glucose was measured for the first time in plants. Its value varied with HK level. It reached 1.71 at or below normal HK activity value and was much lower (0.32) at very high HK levels. Measurements of glycolytic flux and O2 uptake rates demonstrated that the differences in glucose phosphorylation did not affect significantly glycolytic and respiratory metabolism. We hypothesized that these results could be explained by the existence of a futile cycle between the pools of hexose-Ps and carbohydrates. This view is supported by several lines of evidence. Firstly, activities of enzymes capable of catalyzing these reactions were detected in roots, including a hexose-P phosphatase. Secondly, metabolic tracer experiments using 14C-glucose as precursor showed the formation of 14C-fructose and 14C-sucrose. We conclude that futile cycling of hexose-P could be partially responsible for the differences in energetic status in roots with high and low HK activity and possibly cause the observed alterations in growth in transgenic roots. The involvement of HK and futile cycles in the control of glucose-6P metabolism is discussed.
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Affiliation(s)
- Éric Claeyssen
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Sonia Dorion
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Audrey Clendenning
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Jiang Zhou He
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Owen Wally
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Jingkui Chen
- Department of Chemical Engineering, École Polytechnique de Montréal, Montréal, Québec, Canada
| | - Evgenia L. Auslender
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Marie-Claude Moisan
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
| | - Mario Jolicoeur
- Department of Chemical Engineering, École Polytechnique de Montréal, Montréal, Québec, Canada
| | - Jean Rivoal
- Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Québec, Canada
- * E-mail:
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Teusink B, Westerhoff HV, Bruggeman FJ. Comparative systems biology: from bacteria to man. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2011; 2:518-532. [PMID: 20836045 DOI: 10.1002/wsbm.74] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Comparative analyses, as carried out by comparative genomics and bioinformatics, have proven extremely powerful to obtain insight into the identity of specific genes that underlie differences and similarities across species. The central concept developed in this chapter is that important aspects of the functional differences between organisms derive not only from the differences in genetic components (which underlies comparative genomics) but also from dynamic, molecular (physical) interactions. Approaches that aim at identifying such network-based rather than component-based homologies between species we shall call Comparative Systems Biology. It will be illustrated by a number of examples from metabolic networks from prokaryotes, via yeast, to man. The potential for species comparisons, at the genome-scale using classical approaches and at the more detailed level of dynamic molecular networks will be illustrated. In our opinion, comparative systems biology, as a marriage between bioinformatics and systems biology, will offer new insights into the nature of organisms for the benefit of medicine, biotechnology, and drug design. As dynamic modeling is becoming more mainstream in cell biology, the potential of comparative systems biology will become more evident.
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Affiliation(s)
- Bas Teusink
- Systems BioInformatics, Center for Integrative Bioinformatics VU (IBIVU), VU University Amsterdam, The Netherlands.,Netherlands Institute Systems Biology (NISB), The Netherlands.,Kluyver Center for Genomics of Industrial Fermentation, The Netherlands
| | - Hans V Westerhoff
- Netherlands Institute Systems Biology (NISB), The Netherlands.,Molecular Cell Physiology, VU University Amsterdam, The Netherlands.,Manchester Centre for Integrative Systems Biology, University of Manchester, UK
| | - Frank J Bruggeman
- Systems BioInformatics, Center for Integrative Bioinformatics VU (IBIVU), VU University Amsterdam, The Netherlands.,Regulatory Networks Group, NISB, The Netherlands.,Life Sciences, Centre for Mathematics and Computer Science (CWI) Amsterdam, The Netherlands
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Papp B, Teusink B, Notebaart RA. A critical view of metabolic network adaptations. HFSP JOURNAL 2008; 3:24-35. [PMID: 19492021 DOI: 10.2976/1.3020599] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2008] [Accepted: 10/20/2008] [Indexed: 01/16/2023]
Abstract
There has been considerable recent interest in deciphering the adaptive properties underlying the structure and function of metabolic networks. Various features of metabolic networks such as the global topology, distribution of fluxes, and mutational robustness, have been proposed to have adaptive significance and hence reflect design principles. However, whether evolutionary processes alternative to direct selection on the trait under investigation also play a role is often ignored and the selection pressures maintaining a given metabolic trait often remain speculative. Some systems-level traits might simply arise as by-products of selection on other traits or even through random genetic drift. Here, we ask which systems-level aspects of metabolism are likely to have adaptive utility and which could be better explained as by-products of other evolutionary forces. We conclude that the global topological characteristics of metabolic networks and their mutational robustness are unlikely to be directly shaped by natural selection. Conversely, models of optimal design revealed that various aspects of individual pathways and the behavior of the whole network show signs of adaptations, even though the exact selective forces often remain elusive. Comparative and experimental approaches, which so far have been relatively rarely employed, could help to distinguish between alternative adaptive scenarios.
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Steuer R, Junker BH. Computational Models of Metabolism: Stability and Regulation in Metabolic Networks. ADVANCES IN CHEMICAL PHYSICS 2008. [DOI: 10.1002/9780470475935.ch3] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Faradji RN, Havari E, Chen Q, Gray J, Tornheim K, Corkey BE, Mulligan RC, Lipes MA. Glucose-induced toxicity in insulin-producing pituitary cells that coexpress GLUT2 and glucokinase. Implications for metabolic engineering. J Biol Chem 2001; 276:36695-702. [PMID: 11443115 DOI: 10.1074/jbc.m102542200] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We have shown that intermediate lobe (IL) pituitary cells can be engineered to produce sufficient amounts of insulin (ins) to cure diabetes in nonobese diabetic mice but, unlike transplanted islets, ILins cells evade immune attack. To confer glucose-sensing capabilities into these cells, they were further modified with recombinant adenoviruses to express high levels of GLUT2 and the beta-cell isoform of glucokinase (GK). Although expression of GLUT2 alone had negligible effects on glucose usage and lactate production, expression of GK alone resulted in approximately 2-fold increase in glycolytic flux within the physiological (3-20 mm) glucose range. GLUT2/GK coexpression further increased glycolytic flux at 20 mm glucose but disproportionately increased flux at 3 mm glucose. Despite enhanced glycolytic fluxes, GLUT2/GK-coexpressing cells showed glucose dose-dependent accumulation of hexose phosphates, depletion of intracellular ATP, and severe apoptotic cell death. These studies demonstrate that glucose-sensing properties can be introduced into non-islet cells by the single expression of GK and that glucose responsiveness can be augmented by the coexpression of GLUT2. However, in the metabolic engineering of surrogate beta cells, it is critical that the levels of the components be closely optimized to ensure their physiological function and to avoid the deleterious consequences of glucose-induced toxicity.
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Affiliation(s)
- R N Faradji
- Joslin Diabetes Center, Department of Medicine, Harvard Medical School, Boston, Massachusetts 02215, USA
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Bakker BM, Mensonides FI, Teusink B, van Hoek P, Michels PA, Westerhoff HV. Compartmentation protects trypanosomes from the dangerous design of glycolysis. Proc Natl Acad Sci U S A 2000; 97:2087-92. [PMID: 10681445 PMCID: PMC15758 DOI: 10.1073/pnas.030539197] [Citation(s) in RCA: 150] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Unlike in other organisms, in trypanosomes and other Kinetoplastida the larger part of glycolysis takes place in a specialized organelle, called the glycosome. At present it is impossible to remove the glycosome without changing much of the rest of the cell. It would seem impossible, therefore, to assess the metabolic consequences of this compartmentation. Therefore, we here develop a computer experimentation approach, which we call computational cell biology. A validated molecular kinetic computer replica was built of glycolysis in the parasite Trypanosoma brucei. Removing the glycosome membrane in that replica had little effect on the steady-state flux, which argues against the prevalent speculation that glycosomes serve to increase flux by concentrating the enzymes. Removal of the membrane did cause (i) the sugar phosphates to rise to unphysiologically high levels, which must have pathological effects, and (ii) a failure to recover from glucose deprivation. We explain these effects on the basis of the biochemical organization of the glycosome. We conclude (i) that the glycosome protects trypanosomes from the negative side effects of the "turbo" structure of glycolysis and (ii) that computer experimentation based on solid molecular data is a powerful tool to address questions that are not, or not yet, accessible to experimentation.
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Affiliation(s)
- B M Bakker
- Molecular Cell Physiology, BioCentrum Amsterdam, Vrije Universiteit, De Boelelaan 1087, NL-1081 HV Amsterdam, The Netherlands
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Affiliation(s)
- K L Manchester
- Dept of Biochemistry, University of the Witwatersrand, Johannesburg, Wits 2050, South Africa
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