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Volumn 117, Issue 1, 2014, Pages 68-76

Elucidating the adaptation and temporal coordination of metabolic pathways using in-silico evolution

Author keywords

Evolutionary algorithms; Flux balance analysis; Metabolic oscillations; Metabolism; Systems biology

Indexed keywords

ADAPTATION; METABOLISM; NUTRIENT AVAILABILITY; RESOURCE ALLOCATION; TOPOLOGY;

EID: 84894106291     PISSN: 03032647     EISSN: 18728324     Source Type: Journal    
DOI: 10.1016/j.biosystems.2013.12.006     Document Type: Article
Times cited : (9)

References (36)
  • 1
    • 34547887655 scopus 로고    scopus 로고
    • Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity
    • Beg Q.K., Vazquez A., Ernst J., de Menezes M.A., Bar-Joseph Z., Barabási A.-L., Oltvai Z.N. Intracellular crowding defines the mode and sequence of substrate uptake by Escherichia coli and constrains its metabolic activity. Proc. Natl. Acad. Sci. U.S.A. 2007, 104(31 Jul):12663-12668. http://dx.doi.org/10.1073/pnas.0609845104.
    • (2007) Proc. Natl. Acad. Sci. U.S.A. , vol.104 , Issue.31 JUL , pp. 12663-12668
    • Beg, Q.K.1    Vazquez, A.2    Ernst, J.3    de Menezes, M.A.4    Bar-Joseph, Z.5    Barabási, A.-L.6    Oltvai, Z.N.7
  • 3
    • 57649168862 scopus 로고
    • The carbohydrate metabolism of certain pathological overgrowths
    • Crabtree H.G. The carbohydrate metabolism of certain pathological overgrowths. Biochem. J. 1928, 22(5):1289-1298.
    • (1928) Biochem. J. , vol.22 , Issue.5 , pp. 1289-1298
    • Crabtree, H.G.1
  • 4
    • 5644236684 scopus 로고    scopus 로고
    • Preliminary studies on the in silico evolution of biochemical networks
    • Deckard A., Sauro H.M. Preliminary studies on the in silico evolution of biochemical networks. Chembiochem 2004, 5(10):1423-1431. http://dx.doi.org/10.1002/cbic.200400178.
    • (2004) Chembiochem , vol.5 , Issue.10 , pp. 1423-1431
    • Deckard, A.1    Sauro, H.M.2
  • 5
    • 0034973362 scopus 로고    scopus 로고
    • Evolutionary optimization of metabolic pathways. theoretical reconstruction of the stoichiometry of ATP and NADH producing systems
    • Ebenhöh O., Heinrich R. Evolutionary optimization of metabolic pathways. theoretical reconstruction of the stoichiometry of ATP and NADH producing systems. Bull. Math. Biol. 2001, 63(1):21-55. http://dx.doi.org/10.1006/bulm.2000.0197.
    • (2001) Bull. Math. Biol. , vol.63 , Issue.1 , pp. 21-55
    • Ebenhöh, O.1    Heinrich, R.2
  • 7
    • 0029096741 scopus 로고
    • Genetic-algorithm selection of a regulatory structure that directs flux in a simple metabolic model
    • Gilman A., Ross J. Genetic-algorithm selection of a regulatory structure that directs flux in a simple metabolic model. Biophys. J. 1995, 69(4):1321-1333. http://dx.doi.org/10.1016/S0006-3495(95)79999-4.
    • (1995) Biophys. J. , vol.69 , Issue.4 , pp. 1321-1333
    • Gilman, A.1    Ross, J.2
  • 8
    • 84868367714 scopus 로고    scopus 로고
    • Metabolic shifts: a fitness perspective for microbial cell factories
    • Goel A., Wortel M.T., Molenaar D., Teusink B. Metabolic shifts: a fitness perspective for microbial cell factories. Biotechnol. Lett. 2012, 34(12):2147-2160. http://dx.doi.org/10.1007/s10529-012-1038-9.
    • (2012) Biotechnol. Lett. , vol.34 , Issue.12 , pp. 2147-2160
    • Goel, A.1    Wortel, M.T.2    Molenaar, D.3    Teusink, B.4
  • 10
    • 84864386279 scopus 로고    scopus 로고
    • Multi-criteria optimization of regulation in metabolic networks
    • Higuera C., Villaverde A.F., Banga J.R., Ross J., Morn F. Multi-criteria optimization of regulation in metabolic networks. PLoS ONE 2012, 7(7):e41122. http://dx.doi.org/10.1371/journal.pone.0041122.
    • (2012) PLoS ONE , vol.7 , Issue.7
    • Higuera, C.1    Villaverde, A.F.2    Banga, J.R.3    Ross, J.4    Morn, F.5
  • 11
    • 0037079023 scopus 로고    scopus 로고
    • Escherichia coli k-12 undergoes adaptive evolution to achieve in silico predicted optimal growth
    • Ibarra R.U., Edwards J.S., Palsson B.O. Escherichia coli k-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 2002, 420(6912):186-189. http://dx.doi.org/10.1038/nature01149.
    • (2002) Nature , vol.420 , Issue.6912 , pp. 186-189
    • Ibarra, R.U.1    Edwards, J.S.2    Palsson, B.O.3
  • 12
    • 0032729822 scopus 로고    scopus 로고
    • Competition for enzymes in metabolic pathways: implications for optimal distributions of enzyme concentrations and for the distribution of flux control
    • Klipp E., Heinrich R. Competition for enzymes in metabolic pathways: implications for optimal distributions of enzyme concentrations and for the distribution of flux control. BioSystems 1999, 54:1-14.
    • (1999) BioSystems , vol.54 , pp. 1-14
    • Klipp, E.1    Heinrich, R.2
  • 14
    • 33746463692 scopus 로고    scopus 로고
    • The temporal architecture of eukaryotic growth
    • Lloyd D., Murray D.B. The temporal architecture of eukaryotic growth. FEBS Lett. 2006, 580(12 May):2830-2835. http://dx.doi.org/10.1016/j.febslet.2006.02.066.
    • (2006) FEBS Lett. , vol.580 , Issue.12 MAY , pp. 2830-2835
    • Lloyd, D.1    Murray, D.B.2
  • 15
    • 34248598677 scopus 로고    scopus 로고
    • Redox rhythmicity: clocks at the core of temporal coherence
    • Lloyd D., Murray D.B. Redox rhythmicity: clocks at the core of temporal coherence. Bioessays 2007, 29(5 May):465-473. http://dx.doi.org/10.1002/bies.20575.
    • (2007) Bioessays , vol.29 , Issue.5 MAY , pp. 465-473
    • Lloyd, D.1    Murray, D.B.2
  • 16
    • 84862003030 scopus 로고    scopus 로고
    • The yin and yang of yeast transcription: elements of a global feedback system between metabolism and chromatin
    • Machné R., Murray D.B. The yin and yang of yeast transcription: elements of a global feedback system between metabolism and chromatin. PLoS ONE 2012, 7(6):e37906. http://dx.doi.org/10.1371/journal.pone.0037906.
    • (2012) PLoS ONE , vol.7 , Issue.6
    • Machné, R.1    Murray, D.B.2
  • 17
    • 73149109962 scopus 로고    scopus 로고
    • Shifts in growth strategies reflect tradeoffs in cellular economics
    • Molenaar D., van Berlo R., de Ridder D., Teusink B. Shifts in growth strategies reflect tradeoffs in cellular economics. Mol. Syst. Biol. 2009, 5(323). http://dx.doi.org/10.1038/msb.2009.82.
    • (2009) Mol. Syst. Biol. , vol.5 , Issue.323
    • Molenaar, D.1    van Berlo, R.2    de Ridder, D.3    Teusink, B.4
  • 18
    • 84896713646 scopus 로고    scopus 로고
    • Enzyme allocation problems in kinetic metabolic networks: Optimal solutions are elementary flux modes
    • PMID: 24295962
    • Müller S., Regensburger G., Steuer R. Enzyme allocation problems in kinetic metabolic networks: Optimal solutions are elementary flux modes. J. Theor. Biol. 2013, PMID: 24295962. 10.1016/j.jtbi.2013.11.015.
    • (2013) J. Theor. Biol.
    • Müller, S.1    Regensburger, G.2    Steuer, R.3
  • 19
    • 77749320898 scopus 로고    scopus 로고
    • What is flux balance analysis?
    • Orth J.D., Thiele I., Palsson B.O. What is flux balance analysis?. Nat. Biotechnol. 2010, 28(3):245-248. http://dx.doi.org/10.1038/nbt.1614.
    • (2010) Nat. Biotechnol. , vol.28 , Issue.3 , pp. 245-248
    • Orth, J.D.1    Thiele, I.2    Palsson, B.O.3
  • 20
    • 84865972260 scopus 로고    scopus 로고
    • Extensive exometabolome analysis reveals extended overflow metabolism in various microorganisms
    • Paczia N., Nilgen A., Lehmann T., Gätgens J., Wiechert W., Noack S. Extensive exometabolome analysis reveals extended overflow metabolism in various microorganisms. Microb. Cell Fact. 2012, 11(122). http://dx.doi.org/10.1186/1475-2859-11-122.
    • (2012) Microb. Cell Fact. , vol.11 , Issue.122
    • Paczia, N.1    Nilgen, A.2    Lehmann, T.3    Gätgens, J.4    Wiechert, W.5    Noack, S.6
  • 22
    • 64049088538 scopus 로고    scopus 로고
    • A critical view of metabolic network adaptations
    • Papp B., Teusink B., Notebaart R.A. A critical view of metabolic network adaptations. HFSP J. 2009, 3(1):24-35. http://dx.doi.org/10.2976/1.3020599.
    • (2009) HFSP J. , vol.3 , Issue.1 , pp. 24-35
    • Papp, B.1    Teusink, B.2    Notebaart, R.A.3
  • 23
    • 22744439567 scopus 로고    scopus 로고
    • The evolution of connectivity in metabolic networks
    • Pfeiffer T., Soyer O.S., Bonhoeffer S. The evolution of connectivity in metabolic networks. PLoS Biol. 2005, 3(7 Jul):e228. http://dx.doi.org/10.1371/journal.pbio.0030228.
    • (2005) PLoS Biol. , vol.3 , Issue.7 JUL
    • Pfeiffer, T.1    Soyer, O.S.2    Bonhoeffer, S.3
  • 24
    • 77956649528 scopus 로고    scopus 로고
    • Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks
    • Ruppin E., Papin J.A., de Figueiredo L.F., Schuster S. Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks. Curr. Opin. Biotechnol. 2010, 21(4):502-510. http://dx.doi.org/10.1016/j.copbio.2010.07.002.
    • (2010) Curr. Opin. Biotechnol. , vol.21 , Issue.4 , pp. 502-510
    • Ruppin, E.1    Papin, J.A.2    de Figueiredo, L.F.3    Schuster, S.4
  • 25
    • 79960346732 scopus 로고    scopus 로고
    • Combining metabolic pathway analysis with evolutionary game theory: explaining the occurrence of low-yield pathways by an analytic optimization approach
    • Schuster S., de Figueiredo L.F., Schroeter A., Kaleta C. Combining metabolic pathway analysis with evolutionary game theory: explaining the occurrence of low-yield pathways by an analytic optimization approach. Biosystems 2011, 105(2):147-153. http://dx.doi.org/10.1016/j.biosystems.2011.05.007.
    • (2011) Biosystems , vol.105 , Issue.2 , pp. 147-153
    • Schuster, S.1    de Figueiredo, L.F.2    Schroeter, A.3    Kaleta, C.4
  • 26
    • 0034064689 scopus 로고    scopus 로고
    • A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks
    • Schuster S., Fell D.A., Dandekar T. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat. Biotechnol. 2000, 18(3):326-332. http://dx.doi.org/10.1038/73786.
    • (2000) Nat. Biotechnol. , vol.18 , Issue.3 , pp. 326-332
    • Schuster, S.1    Fell, D.A.2    Dandekar, T.3
  • 27
    • 43449132092 scopus 로고    scopus 로고
    • Is maximization of molar yield in metabolic networks favoured by evolution?
    • Schuster S., Pfeiffer T., Fell D.A. Is maximization of molar yield in metabolic networks favoured by evolution?. J. Theor. Biol. 2008, 252(3):497-504. http://dx.doi.org/10.1016/j.jtbi.2007.12.008.
    • (2008) J. Theor. Biol. , vol.252 , Issue.3 , pp. 497-504
    • Schuster, S.1    Pfeiffer, T.2    Fell, D.A.3
  • 28
    • 79953661070 scopus 로고    scopus 로고
    • Genome-scale metabolic modeling elucidates the role of proliferative adaptation in causing the Warburg effect
    • Shlomi T., Benyamini T., Gottlieb E., Sharan R., Ruppin E. Genome-scale metabolic modeling elucidates the role of proliferative adaptation in causing the Warburg effect. PLoS Comput. Biol. 2011, 7(3):e1002018. http://dx.doi.org/10.1371/journal.pcbi.1002018.
    • (2011) PLoS Comput. Biol. , vol.7 , Issue.3
    • Shlomi, T.1    Benyamini, T.2    Gottlieb, E.3    Sharan, R.4    Ruppin, E.5
  • 29
    • 33745739006 scopus 로고    scopus 로고
    • Simulating the evolution of signal transduction pathways
    • Soyer O.S., Pfeiffer T., Bonhoeffer S. Simulating the evolution of signal transduction pathways. J. Theor. Biol. 2006, 241(2):223-232. http://dx.doi.org/10.1016/j.jtbi.2005.11.024.
    • (2006) J. Theor. Biol. , vol.241 , Issue.2 , pp. 223-232
    • Soyer, O.S.1    Pfeiffer, T.2    Bonhoeffer, S.3
  • 30
    • 0033532830 scopus 로고    scopus 로고
    • Optimal stoichiometric designs of ATP-producing systems as determined by an evolutionary algorithm
    • Stephani A., Nuno J.C., Heinrich R. Optimal stoichiometric designs of ATP-producing systems as determined by an evolutionary algorithm. J. Theor. Biol. 1999, 199(1):45-61. http://dx.doi.org/10.1006/jtbi.1999.0942.
    • (1999) J. Theor. Biol. , vol.199 , Issue.1 , pp. 45-61
    • Stephani, A.1    Nuno, J.C.2    Heinrich, R.3
  • 31
    • 77954190195 scopus 로고    scopus 로고
    • Computational Models of Metabolism: Stability and Regulation in Metabolic Networks
    • John Wiley & Sons, Inc, Hoboken, NJ, USA
    • Steuer R., Junker B.H. Computational Models of Metabolism: Stability and Regulation in Metabolic Networks. Advances in Chemical Physics 2008, vol. 142. John Wiley & Sons, Inc, Hoboken, NJ, USA. 10.1002/9780470475935.ch3.
    • (2008) Advances in Chemical Physics , vol.142
    • Steuer, R.1    Junker, B.H.2
  • 33
    • 84858717996 scopus 로고    scopus 로고
    • Redox balance is key to explaining full vs. partial switching to low-yield metabolism
    • van Hoek M.J.A., Merks R.M.H. Redox balance is key to explaining full vs. partial switching to low-yield metabolism. BMC Syst. Biol. 2012, 6(22). http://dx.doi.org/10.1186/1752-0509-6-22.
    • (2012) BMC Syst. Biol. , vol.6 , Issue.22
    • van Hoek, M.J.A.1    Merks, R.M.H.2
  • 35
    • 84899416159 scopus 로고    scopus 로고
    • Metabolic states with maximal specific rate carry flux through an elementary flux mode
    • PMID:24460934
    • Wortel M.T., Peters H., Hulshof J., Teusink B., Bruggeman F.J. Metabolic states with maximal specific rate carry flux through an elementary flux mode. FEBS J. 2014, PMID:24460934. 10.1111/febs.12722.
    • (2014) FEBS J.
    • Wortel, M.T.1    Peters, H.2    Hulshof, J.3    Teusink, B.4    Bruggeman, F.J.5
  • 36
    • 79959610766 scopus 로고    scopus 로고
    • Economics of membrane occupancy and respiro-fermentation
    • Zhuang K., Vemuri G.N., Mahadevan R. Economics of membrane occupancy and respiro-fermentation. Mol. Syst. Biol. 2011, 7(500.). http://dx.doi.org/10.1038/msb.2011.34.
    • (2011) Mol. Syst. Biol. , vol.7 , Issue.500
    • Zhuang, K.1    Vemuri, G.N.2    Mahadevan, R.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.