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Volumn 279, Issue 17, 2012, Pages 3192-3202

Detecting and investigating substrate cycles in a genome-scale human metabolic network

Author keywords

elementary flux modes; futile cycle; genome scale metabolic models; human metabolic model; substrate cycle

Indexed keywords

ADENOSINE TRIPHOSPHATE;

EID: 84865224842     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2012.08700.x     Document Type: Article
Times cited : (22)

References (55)
  • 1
    • 33645873573 scopus 로고    scopus 로고
    • Thermogenic mechanisms and their hormonal regulation
    • Silva JE, (2006) Thermogenic mechanisms and their hormonal regulation. Physiol Rev 86, 435-464.
    • (2006) Physiol Rev , vol.86 , pp. 435-464
    • Silva, J.E.1
  • 2
    • 0347989317 scopus 로고    scopus 로고
    • Brown adipose tissue: Function and physiological significance
    • Cannon B, &, Nedergaard J, (2004) Brown adipose tissue: function and physiological significance. Physiol Rev 84, 277-359.
    • (2004) Physiol Rev , vol.84 , pp. 277-359
    • Cannon, B.1    Nedergaard, J.2
  • 3
    • 0015850193 scopus 로고
    • Estimation of the fructose diphosphatase-phosphofructokinase substrate cycle in the flight muscle of Bombus affinis
    • Clark MG, Bloxham DP, Holland PC, &, Lardy HA, (1973) Estimation of the fructose diphosphatase-phosphofructokinase substrate cycle in the flight muscle of Bombus affinis. Biochem J 134, 589-597.
    • (1973) Biochem J , vol.134 , pp. 589-597
    • Clark, M.G.1    Bloxham, D.P.2    Holland, P.C.3    Lardy, H.A.4
  • 4
    • 0017154480 scopus 로고
    • Substrate cycles in metabolic regulation and in heat generation
    • Newsholme EA, &, Crabtree B, (1976) Substrate cycles in metabolic regulation and in heat generation. Biochem Soc Symp 41, 61-109.
    • (1976) Biochem Soc Symp , vol.41 , pp. 61-109
    • Newsholme, E.A.1    Crabtree, B.2
  • 6
    • 70349559115 scopus 로고    scopus 로고
    • Metabolic systems maintain stable non-equilibrium via thermodynamic buffering
    • Igamberdiev AU, &, Kleczkowski LA, (2009) Metabolic systems maintain stable non-equilibrium via thermodynamic buffering. BioEssays 31, 1091-1099.
    • (2009) BioEssays , vol.31 , pp. 1091-1099
    • Igamberdiev, A.U.1    Kleczkowski, L.A.2
  • 7
    • 0028853442 scopus 로고
    • The contribution of glucose cycling to the maintenance of steady-state levels of lactate by hepatocytes during glycolysis and gluconeogenesis
    • Phillips JW, Clark DG, Henly DC, &, Berry MN, (1995) The contribution of glucose cycling to the maintenance of steady-state levels of lactate by hepatocytes during glycolysis and gluconeogenesis. Eur J Biochem 227, 352-358.
    • (1995) Eur J Biochem , vol.227 , pp. 352-358
    • Phillips, J.W.1    Clark, D.G.2    Henly, D.C.3    Berry, M.N.4
  • 8
    • 0017828650 scopus 로고
    • Analysis of futile cycles in metabolism
    • Stein RB, &, Blum JJ, (1978) Analysis of futile cycles in metabolism. J Theor Biol 72, 487-522.
    • (1978) J Theor Biol , vol.72 , pp. 487-522
    • Stein, R.B.1    Blum, J.J.2
  • 9
    • 0034680782 scopus 로고    scopus 로고
    • In vivo quantification of parallel and bidirectional fluxes in the anaplerosis of Corynebacterium glutamicum
    • Petersen S, de Graaf AA, Eggeling L, Mollney M, Wiechert W, &, Sahm H, (2000) In vivo quantification of parallel and bidirectional fluxes in the anaplerosis of Corynebacterium glutamicum. J Biol Chem 275, 35932-35941.
    • (2000) J Biol Chem , vol.275 , pp. 35932-35941
    • Petersen, S.1    De Graaf, A.A.2    Eggeling, L.3    Mollney, M.4    Wiechert, W.5    Sahm, H.6
  • 10
    • 85039312210 scopus 로고
    • Quantitative interrelationship between rates of glucose-metabolism and futile cycling of fructose 6-phosphate in rat-liver in-vivo
    • Clark MG, Bloxham DP, Holland PC, &, Lardy HA, (1973) Quantitative interrelationship between rates of glucose-metabolism and futile cycling of fructose 6-phosphate in rat-liver in-vivo. J Cell Biol 59, A56-A56.
    • (1973) J Cell Biol , vol.59
    • Clark, M.G.1    Bloxham, D.P.2    Holland, P.C.3    Lardy, H.A.4
  • 11
    • 0017818713 scopus 로고
    • Futile cycling in glucose-metabolism
    • Katz J, &, Rognstad R, (1978) Futile cycling in glucose-metabolism. Trends Biochem Sci 3, 171-174.
    • (1978) Trends Biochem Sci , vol.3 , pp. 171-174
    • Katz, J.1    Rognstad, R.2
  • 12
    • 0018961091 scopus 로고
    • Co-ordinate control of phosphofructokinase and pyruvate kinase by fructose diphosphate: A mechanism for amplification and step changes in the regulation of glycolysis in liver
    • Tornheim K, (1980) Co-ordinate control of phosphofructokinase and pyruvate kinase by fructose diphosphate: a mechanism for amplification and step changes in the regulation of glycolysis in liver. J Theor Biol 85, 199-222.
    • (1980) J Theor Biol , vol.85 , pp. 199-222
    • Tornheim, K.1
  • 13
    • 0022363123 scopus 로고
    • Activation of muscle phosphofructokinase by fructose 2,6-bisphosphate and fructose 1,6-bisphosphate is differently affected by other regulatory metabolites
    • Tornheim K, (1985) Activation of muscle phosphofructokinase by fructose 2,6-bisphosphate and fructose 1,6-bisphosphate is differently affected by other regulatory metabolites. J Biol Chem 260, 7985-7989.
    • (1985) J Biol Chem , vol.260 , pp. 7985-7989
    • Tornheim, K.1
  • 14
    • 0023610603 scopus 로고
    • On the analysis of substrate cycles in large metabolic systems
    • Leiser J, &, Blum JJ, (1987) On the analysis of substrate cycles in large metabolic systems. Cell Biophys 11, 123-138.
    • (1987) Cell Biophys , vol.11 , pp. 123-138
    • Leiser, J.1    Blum, J.J.2
  • 17
    • 0020972416 scopus 로고
    • Gluconeogenesis and related aspects of glycolysis
    • Hers HG, &, Hue L, (1983) Gluconeogenesis and related aspects of glycolysis. Annu Rev Biochem 52, 617-653.
    • (1983) Annu Rev Biochem , vol.52 , pp. 617-653
    • Hers, H.G.1    Hue, L.2
  • 19
    • 17644375240 scopus 로고    scopus 로고
    • The PEP-pyruvate-oxaloacetate node as the switch point for carbon flux distribution in bacteria
    • Sauer U, &, Eikmanns BJ, (2005) The PEP-pyruvate-oxaloacetate node as the switch point for carbon flux distribution in bacteria. FEMS Microbiol Rev 29, 765-794.
    • (2005) FEMS Microbiol Rev , vol.29 , pp. 765-794
    • Sauer, U.1    Eikmanns, B.J.2
  • 20
    • 0031401211 scopus 로고    scopus 로고
    • Carbon partitioning during sucrose accumulation in sugarcane internodal tissue
    • Whittaker A, &, Botha FC, (1997) Carbon partitioning during sucrose accumulation in sugarcane internodal tissue. Plant Physiol 115, 1651-1659.
    • (1997) Plant Physiol , vol.115 , pp. 1651-1659
    • Whittaker, A.1    Botha, F.C.2
  • 21
    • 0035448427 scopus 로고    scopus 로고
    • Analysis of sucrose accumulation in the sugar cane culm on the basis of in vitro kinetic data
    • Rohwer JM, &, Botha FC, (2001) Analysis of sucrose accumulation in the sugar cane culm on the basis of in vitro kinetic data. Biochem J 358, 437-445.
    • (2001) Biochem J , vol.358 , pp. 437-445
    • Rohwer, J.M.1    Botha, F.C.2
  • 22
    • 0025210437 scopus 로고
    • Regulation of 5-phosphoribosyl 1-pyrophosphate and of hypoxanthine uptake and release in human erythrocytes by oxypurine cycling
    • Berman PA, &, Human L, (1990) Regulation of 5-phosphoribosyl 1-pyrophosphate and of hypoxanthine uptake and release in human erythrocytes by oxypurine cycling. J Biol Chem 265, 6562-6568.
    • (1990) J Biol Chem , vol.265 , pp. 6562-6568
    • Berman, P.A.1    Human, L.2
  • 23
    • 0036691976 scopus 로고    scopus 로고
    • Reaction routes in biochemical reaction systems: Algebraic properties, validated calculation procedure and example from nucleotide metabolism
    • Schuster S, Hilgetag C, Woods JH, &, Fell DA, (2002) Reaction routes in biochemical reaction systems: algebraic properties, validated calculation procedure and example from nucleotide metabolism. J Math Biol 45, 153-181.
    • (2002) J Math Biol , vol.45 , pp. 153-181
    • Schuster, S.1    Hilgetag, C.2    Woods, J.H.3    Fell, D.A.4
  • 24
    • 0023682912 scopus 로고
    • Biochemical markers of aging
    • Stadtman ER, (1988) Biochemical markers of aging. Exp Gerontol 23, 327-347.
    • (1988) Exp Gerontol , vol.23 , pp. 327-347
    • Stadtman, E.R.1
  • 25
    • 0034626735 scopus 로고    scopus 로고
    • Oxidants, oxidative stress and the biology of ageing
    • Finkel T, &, Holbrook NJ, (2000) Oxidants, oxidative stress and the biology of ageing. Nature 408, 239-247.
    • (2000) Nature , vol.408 , pp. 239-247
    • Finkel, T.1    Holbrook, N.J.2
  • 26
    • 0033785071 scopus 로고    scopus 로고
    • Uncoupling to survive? the role of mitochondrial inefficiency in ageing
    • Brand MD, (2000) Uncoupling to survive? The role of mitochondrial inefficiency in ageing. Exp Gerontol 35, 811-820.
    • (2000) Exp Gerontol , vol.35 , pp. 811-820
    • Brand, M.D.1
  • 27
    • 0029765443 scopus 로고    scopus 로고
    • Role of uncoupled and non-coupled oxidations in maintenance of safely low levels of oxygen and its one-electron reductants
    • Skulachev VP, (1996) Role of uncoupled and non-coupled oxidations in maintenance of safely low levels of oxygen and its one-electron reductants. Q Rev Biophys 29, 169-202.
    • (1996) Q Rev Biophys , vol.29 , pp. 169-202
    • Skulachev, V.P.1
  • 29
    • 77958154730 scopus 로고    scopus 로고
    • Insulin action in hyperthyroidism: A focus on muscle and adipose tissue
    • Mitrou P, Raptis SA, &, Dimitriadis G, (2010) Insulin action in hyperthyroidism: a focus on muscle and adipose tissue. Endocr Rev 31, 663-679.
    • (2010) Endocr Rev , vol.31 , pp. 663-679
    • Mitrou, P.1    Raptis, S.A.2    Dimitriadis, G.3
  • 30
    • 0033080396 scopus 로고    scopus 로고
    • Detection of elementary flux modes in biochemical networks: A promising tool for pathway analysis and metabolic engineering
    • Schuster S, Dandekar T, &, Fell DA, (1999) Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. Trends Biotechnol 17, 53-60.
    • (1999) Trends Biotechnol , vol.17 , pp. 53-60
    • Schuster, S.1    Dandekar, T.2    Fell, D.A.3
  • 31
    • 0034064689 scopus 로고    scopus 로고
    • A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks
    • Schuster S, Fell DA, &, Dandekar T, (2000) A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat Biotechnol 18, 326-332.
    • (2000) Nat Biotechnol , vol.18 , pp. 326-332
    • Schuster, S.1    Fell, D.A.2    Dandekar, T.3
  • 32
    • 34548302044 scopus 로고    scopus 로고
    • Petri net modelling of biological networks
    • Chaouiya C, (2007) Petri net modelling of biological networks. Brief Bioinform 8, 210-219.
    • (2007) Brief Bioinform , vol.8 , pp. 210-219
    • Chaouiya, C.1
  • 33
    • 16344381707 scopus 로고    scopus 로고
    • Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber
    • Koch I, Junker BH, &, Heiner M, (2005) Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber. Bioinformatics 21, 1219-1226.
    • (2005) Bioinformatics , vol.21 , pp. 1219-1226
    • Koch, I.1    Junker, B.H.2    Heiner, M.3
  • 34
    • 69049113081 scopus 로고    scopus 로고
    • Modeling and analyzing the metabolism of riboflavin production using Petri nets
    • Ding DW, &, Li LN, (2009) Modeling and analyzing the metabolism of riboflavin production using Petri nets. J Biol Syst 17, 479-490.
    • (2009) J Biol Syst , vol.17 , pp. 479-490
    • Ding, D.W.1    Li, L.N.2
  • 36
    • 33846015888 scopus 로고    scopus 로고
    • Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model
    • Teusink B, Wiersma A, Molenaar D, Francke C, de Vos WM, Siezen RJ, &, Smid EJ, (2006) Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model. J Biol Chem 281, 40041-40048.
    • (2006) J Biol Chem , vol.281 , pp. 40041-40048
    • Teusink, B.1    Wiersma, A.2    Molenaar, D.3    Francke, C.4    De Vos, W.M.5    Siezen, R.J.6    Smid, E.J.7
  • 38
    • 77649270909 scopus 로고    scopus 로고
    • A note on the complexity of finding and enumerating elementary modes
    • Acuña V, Marchetti-Spaccamela A, Sagot M-F, &, Stougie L, (2010) A note on the complexity of finding and enumerating elementary modes. Biosystems 99, 210-214.
    • (2010) Biosystems , vol.99 , pp. 210-214
    • Acuña, V.1    Marchetti-Spaccamela, A.2    Sagot, M.-F.3    Stougie, L.4
  • 41
    • 84856560417 scopus 로고    scopus 로고
    • EFMEvolver: Computing elementary flux modes in genome-scale metabolic networks
    • In (Grosse I., Neumann S., Posch S., Schreiber F. & Stadler P.F., eds), pp. Gesellschaft f. Informatik e.V., Bonn
    • Kaleta C, de Figueiredo LF, Behre J, &, Schuster S, (2009) EFMEvolver: computing elementary flux modes in genome-scale metabolic networks. In Proceedings of the 14th German Conference on Bioinformatics (GCB) (, Grosse I, Neumann S, Posch S, Schreiber F, &, Stadler PF, eds), pp. 180-190. Gesellschaft f. Informatik e.V., Bonn.
    • (2009) Proceedings of the 14th German Conference on Bioinformatics (GCB) , pp. 180-190
    • Kaleta, C.1    De Figueiredo, L.F.2    Behre, J.3    Schuster, S.4
  • 42
    • 52949098408 scopus 로고    scopus 로고
    • Large-scale computation of elementary flux modes with bit pattern trees
    • Terzer M, &, Stelling J, (2008) Large-scale computation of elementary flux modes with bit pattern trees. Bioinformatics 24, 2229-2235.
    • (2008) Bioinformatics , vol.24 , pp. 2229-2235
    • Terzer, M.1    Stelling, J.2
  • 44
    • 33746929855 scopus 로고    scopus 로고
    • The fractional contributions of elementary modes to the metabolism of Escherichia coli and their estimation from reaction entropies
    • Wlaschin AP, Trinh CT, Carlson R, &, Srienc F, (2006) The fractional contributions of elementary modes to the metabolism of Escherichia coli and their estimation from reaction entropies. Metab Eng 8, 338-352.
    • (2006) Metab Eng , vol.8 , pp. 338-352
    • Wlaschin, A.P.1    Trinh, C.T.2    Carlson, R.3    Srienc, F.4
  • 46
    • 77956417789 scopus 로고    scopus 로고
    • Computational reconstruction of tissue-specific metabolic models: Application to human liver metabolism
    • Jerby L, Shlomi T, &, Ruppin E, (2010) Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism. Mol Syst Biol 6, 401.
    • (2010) Mol Syst Biol , vol.6 , pp. 401
    • Jerby, L.1    Shlomi, T.2    Ruppin, E.3
  • 47
    • 9544253891 scopus 로고    scopus 로고
    • Genome-scale models of microbial cells: Evaluating the consequences of constraints
    • Price ND, Reed JL, &, Palsson BA, (2004) Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol 2, 886-897.
    • (2004) Nat Rev Microbiol , vol.2 , pp. 886-897
    • Price, N.D.1    Reed, J.L.2    Palsson, B.3
  • 48
    • 77956649528 scopus 로고    scopus 로고
    • Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks
    • Ruppin E, Papin JA, de Figueiredo LF, &, Schuster S, (2010) Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks. Curr Opin Biotechnol 21, 502-510.
    • (2010) Curr Opin Biotechnol , vol.21 , pp. 502-510
    • Ruppin, E.1    Papin, J.A.2    De Figueiredo, L.F.3    Schuster, S.4
  • 49
    • 33747856186 scopus 로고    scopus 로고
    • Metatool 5.0: Fast and flexible elementary modes analysis
    • von Kamp A, &, Schuster S, (2006) Metatool 5.0: fast and flexible elementary modes analysis. Bioinformatics 22, 1930-1931.
    • (2006) Bioinformatics , vol.22 , pp. 1930-1931
    • Von Kamp, A.1    Schuster, S.2
  • 50
    • 13244292328 scopus 로고    scopus 로고
    • Computation of elementary modes: A unifying framework and the new binary approach
    • Gagneur J, &, Klamt S, (2004) Computation of elementary modes: a unifying framework and the new binary approach. BMC Bioinformatics 5, 175.
    • (2004) BMC Bioinformatics , vol.5 , pp. 175
    • Gagneur, J.1    Klamt, S.2
  • 51
    • 77954791900 scopus 로고    scopus 로고
    • Compartmentalization of the Edinburgh Human Metabolic Network
    • Hao T, Ma HW, Zhao XM, &, Goryanin I, (2010) Compartmentalization of the Edinburgh Human Metabolic Network. BMC Bioinformatics 11, 393.
    • (2010) BMC Bioinformatics , vol.11 , pp. 393
    • Hao, T.1    Ma, H.W.2    Zhao, X.M.3    Goryanin, I.4
  • 53
    • 78049445175 scopus 로고    scopus 로고
    • Drug off-target effects predicted using structural analysis in the context of a metabolic network model
    • Chang RL, Xie L, Xie L, Bourne PE, &, Palsson BA, (2010) Drug off-target effects predicted using structural analysis in the context of a metabolic network model. PLoS Comput Biol 6, e1000938.
    • (2010) PLoS Comput Biol , vol.6
    • Chang, R.L.1    Xie, L.2    Xie, L.3    Bourne, P.E.4    Palsson, B.5
  • 54
    • 1242274402 scopus 로고    scopus 로고
    • Flux coupling analysis of genome-scale metabolic network reconstructions
    • Burgard AP, Nikolaev EV, Schilling CH, &, Maranas CD, (2004) Flux coupling analysis of genome-scale metabolic network reconstructions. Genome Res 14, 301-312.
    • (2004) Genome Res , vol.14 , pp. 301-312
    • Burgard, A.P.1    Nikolaev, E.V.2    Schilling, C.H.3    Maranas, C.D.4


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