메뉴 건너뛰기




Volumn 15, Issue 1, 2015, Pages

In silico evolution of diauxic growth

Author keywords

Diauxic growth; Glucose effect; Simulated evolution

Indexed keywords

ADAPTATION; BACTERIUM; BIOMASS; CARBON; CELLS AND CELL COMPONENTS; EVOLUTION; GENE EXPRESSION; GLUCOSE; GROWTH RESPONSE; METABOLISM; NUMERICAL MODEL; NUTRIENT UPTAKE;

EID: 84942432514     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/s12862-015-0492-0     Document Type: Article
Times cited : (11)

References (39)
  • 1
    • 0001639179 scopus 로고
    • The growth of bacterial cultures
    • 1:CAS:528:DyaG3cXlt1GitQ%3D%3D
    • Monod J. The growth of bacterial cultures. Annu Rev Microbiol. 1949; 3:371-49.
    • (1949) Annu Rev Microbiol , vol.3 , pp. 371-449
    • Monod, J.1
  • 2
    • 0033118267 scopus 로고    scopus 로고
    • Carbon catabolite repression in bacteria
    • 10322165 doi:10.1016/S1369-5274(99)80034-4
    • Stülke J, Hillen W. Carbon catabolite repression in bacteria. Curr Opin Microbiol. 1999; 2(2):195-201. doi: 10.1016/S1369-5274(99)80034-4.
    • (1999) Curr Opin Microbiol , vol.2 , Issue.2 , pp. 195-201
    • Stülke, J.1    Hillen, W.2
  • 3
    • 0037046271 scopus 로고    scopus 로고
    • Carbon catabolite repression in bacteria: Choice of the carbon source and autoregulatory limitation of sugar utilization
    • 12007797 doi:10.1016/S0378-1097(02)00559-1
    • Brückner R, Titgemeyer F. Carbon catabolite repression in bacteria: choice of the carbon source and autoregulatory limitation of sugar utilization. FEMS Microbiol Lett. 2002; 209(2):141-8. doi: 10.1016/S0378-1097(02)00559-1.
    • (2002) FEMS Microbiol Lett , vol.209 , Issue.2 , pp. 141-148
    • Brückner, R.1    Titgemeyer, F.2
  • 4
    • 84876989674 scopus 로고    scopus 로고
    • Single-cell dynamics reveals sustained growth during diauxic shifts
    • doi:10.1371/journal.pone.0061686
    • Boulineau S, Tostevin F, Kiviet D, ten Wolde P, Nghe P, Tans S. Single-cell dynamics reveals sustained growth during diauxic shifts. PLoS One. 2013; 8(4):61686. doi: 10.1371/journal.pone.0061686.
    • (2013) PLoS One , vol.8 , Issue.4 , pp. 61686
    • Boulineau, S.1    Tostevin, F.2    Kiviet, D.3    Ten Wolde, P.4    Nghe, P.5    Tans, S.6
  • 5
    • 84867738121 scopus 로고    scopus 로고
    • A non-linear deterministic model for regulation of diauxic lag on cellobiose by the pneumococcal multidomain transcriptional regulator celr
    • doi:10.1371/journal.pone.0047393
    • Boianelli A, Bidossi A, Gualdi L, Mulas L, Mocenni C, Pozzi G, et al. A non-linear deterministic model for regulation of diauxic lag on cellobiose by the pneumococcal multidomain transcriptional regulator celr. PLoS One. 2012; 7(10):47393. doi: 10.1371/journal.pone.0047393.
    • (2012) PLoS One , vol.7 , Issue.10 , pp. 47393
    • Boianelli, A.1    Bidossi, A.2    Gualdi, L.3    Mulas, L.4    Mocenni, C.5    Pozzi, G.6
  • 6
    • 0030089476 scopus 로고    scopus 로고
    • Mechanism responsible for glucose-lactose diauxie in Escherichia coli: Challenge to the cAMP model
    • 1:CAS:528:DyaK28XksFChtLY%3D 9133663
    • Inada T, Kimata K, Aiba H. Mechanism responsible for glucose-lactose diauxie in Escherichia coli: challenge to the cAMP model. Genes Cells. 1996; 1(3):293-301.
    • (1996) Genes Cells , vol.1 , Issue.3 , pp. 293-301
    • Inada, T.1    Kimata, K.2    Aiba, H.3
  • 7
    • 0022755363 scopus 로고
    • Investigation of bacterial growth on mixed substrates: Experimental evaluation of cybernetic models
    • 1:CAS:528:DyaL28XkslOmtro%3D doi:10.1002/bit.260280715
    • Kompala D, Ramkrishna D, Jansen N, Tsao G. Investigation of bacterial growth on mixed substrates: Experimental evaluation of cybernetic models. Biotech Bioeng. 1986; 28(7):1044-55. doi: 10.1002/bit.260280715.
    • (1986) Biotech Bioeng , vol.28 , Issue.7 , pp. 1044-1055
    • Kompala, D.1    Ramkrishna, D.2    Jansen, N.3    Tsao, G.4
  • 8
    • 84893765873 scopus 로고    scopus 로고
    • Different levels of catabolite repression optimize growth in stable and variable environments
    • doi:10.1371/journal.pbio.1001764
    • New A, Cerulus B, Govers S, Perez-Samper G, Zhu B, Boogmans S, et al. Different levels of catabolite repression optimize growth in stable and variable environments. PLoS Biology. 2014; 12(1):1001764. doi: 10.1371/journal.pbio.1001764.
    • (2014) PLoS Biology , vol.12 , Issue.1 , pp. 1001764
    • New, A.1    Cerulus, B.2    Govers, S.3    Perez-Samper, G.4    Zhu, B.5    Boogmans, S.6
  • 9
    • 33747178680 scopus 로고    scopus 로고
    • Comparative analysis of some models of gene regulation in mixed-substrate microbial growth
    • 1:CAS:528:DC%2BD28XotlCisbw%3D 16650437
    • Narang A. Comparative analysis of some models of gene regulation in mixed-substrate microbial growth. J Theor Biol. 2006; 242(2):489-501.
    • (2006) J Theor Biol , vol.242 , Issue.2 , pp. 489-501
    • Narang, A.1
  • 10
    • 33751169996 scopus 로고    scopus 로고
    • Bacterial gene regulation in diauxic and non-diauxic growth
    • 1:CAS:528:DC%2BD28Xht1Chs7rK 16989865 doi:10.1016/j.jtbi.2006.08.007
    • Narang A, Pilyugin S. Bacterial gene regulation in diauxic and non-diauxic growth. J Theor Biol. 2007; 244(2):326-48. doi: 10.1016/j.jtbi.2006.08.007.
    • (2007) J Theor Biol , vol.244 , Issue.2 , pp. 326-348
    • Narang, A.1    Pilyugin, S.2
  • 11
    • 58149165152 scopus 로고    scopus 로고
    • Catabolite repression in Escherichia coli- a comparison of modelling approaches
    • 1:CAS:528:DC%2BD1MXptV2ktw%3D%3D 19087189 doi:10.1111/j.1742-4658.2008.06810.x
    • Kremling A, Kremling S, Bettenbrock K. Catabolite repression in escherichia coli- a comparison of modelling approaches. FEBS J. 2009; 276(2):594-602. doi: 10.1111/j.1742-4658.2008.06810.x.
    • (2009) FEBS J , vol.276 , Issue.2 , pp. 594-602
    • Kremling, A.1    Kremling, S.2    Bettenbrock, K.3
  • 12
    • 42049092081 scopus 로고    scopus 로고
    • The mechanisms of carbon catabolite repression in bacteria
    • 1:CAS:528:DC%2BD1cXkvFahsro%3D 18359269 doi:10.1016/j.mib.2008.02.007
    • Deutscher J. The mechanisms of carbon catabolite repression in bacteria. Curr Opin Microbiol. 2008; 11(2):87-93. doi: 10.1016/j.mib.2008.02.007.
    • (2008) Curr Opin Microbiol , vol.11 , Issue.2 , pp. 87-93
    • Deutscher, J.1
  • 13
    • 77953170555 scopus 로고    scopus 로고
    • Computational limits to binary genes
    • 2871807 20007173 doi:10.1098/rsif.2009.0474
    • Zabet N, Chu D. Computational limits to binary genes. J R Soc Interface. 2010; 7(47):945-54. doi: 10.1098/rsif.2009.0474.
    • (2010) J R Soc Interface , vol.7 , Issue.47 , pp. 945-954
    • Zabet, N.1    Chu, D.2
  • 14
    • 23144432213 scopus 로고    scopus 로고
    • Optimality and evolutionary tuning of the expression level of a protein
    • 1:CAS:528:DC%2BD2MXmsFCgsLw%3D 16049495 doi:10.1038/nature03842
    • Dekel E, Alon U. Optimality and evolutionary tuning of the expression level of a protein. Nature. 2005; 436(7050):588-92. doi: 10.1038/nature03842.
    • (2005) Nature , vol.436 , Issue.7050 , pp. 588-592
    • Dekel, E.1    Alon, U.2
  • 15
    • 38049146129 scopus 로고    scopus 로고
    • Cost-benefit theory and optimal design of gene regulation functions
    • 1:CAS:528:DC%2BD2sXhtl2rt7vO 17991990
    • Kalisky T, Dekel E, Alon U. Cost-benefit theory and optimal design of gene regulation functions. Phys Biol. 2007; 4(4):229.
    • (2007) Phys Biol , vol.4 , Issue.4 , pp. 229
    • Kalisky, T.1    Dekel, E.2    Alon, U.3
  • 16
    • 2942555282 scopus 로고    scopus 로고
    • Stochastic gene expression in fluctuating environments
    • 1470854 15166174
    • Thattai M, van Oudenaarden A. Stochastic gene expression in fluctuating environments. Genetics. 2004; 167(1):523-30.
    • (2004) Genetics , vol.167 , Issue.1 , pp. 523-530
    • Thattai, M.1    Van Oudenaarden, A.2
  • 17
    • 34547418221 scopus 로고    scopus 로고
    • An experimental test of evolutionary trade-offs during temperature adaptation
    • 1876442 1:CAS:528:DC%2BD2sXlvFCqu7Y%3D 17494741 doi:10.1073/pnas.0702117104
    • Bennett A, Lenski R. An experimental test of evolutionary trade-offs during temperature adaptation. Proc Natl Acad Sci. 2007; 104(suppl 1):8649-54. doi: 10.1073/pnas.0702117104.
    • (2007) Proc Natl Acad Sci , vol.104 , pp. 8649-8654
    • Bennett, A.1    Lenski, R.2
  • 19
    • 79953757806 scopus 로고    scopus 로고
    • Optimal parameter settings for information processing in gene regulatory networks
    • 1:CAS:528:DC%2BC3MXksFentrY%3D 21256918 doi:10.1016/j.biosystems.2011.01.006
    • Chu D, Zabet N, Hone A. Optimal parameter settings for information processing in gene regulatory networks. BioSystems. 2011; 104:99-108. doi: 10.1016/j.biosystems.2011.01.006.
    • (2011) BioSystems , vol.104 , pp. 99-108
    • Chu, D.1    Zabet, N.2    Hone, A.3
  • 21
    • 61449155349 scopus 로고    scopus 로고
    • Models of transcription factor binding: Sensitivity of activation functions to model assumptions
    • 1:CAS:528:DC%2BD1MXisl2qsrc%3D 19121637 doi:10.1016/j.jtbi.2008.11.026
    • Chu D, Zabet N, Mitavskiy B. Models of transcription factor binding: sensitivity of activation functions to model assumptions. J Theor Biol. 2009; 257(3):419-29. doi: 10.1016/j.jtbi.2008.11.026.
    • (2009) J Theor Biol , vol.257 , Issue.3 , pp. 419-429
    • Chu, D.1    Zabet, N.2    Mitavskiy, B.3
  • 22
    • 0035917865 scopus 로고    scopus 로고
    • Cooperation and competition in the evolution of ATP-producing pathways
    • 1:CAS:528:DC%2BD3MXjtVemsrw%3D 11283355 doi:10.1126/science.1058079
    • Pfeiffer T, Schuster S, Bonhoeffer S. Cooperation and competition in the evolution of ATP-producing pathways. Science. 2001; 292(5516):504-7. doi: 10.1126/science.1058079.
    • (2001) Science , vol.292 , Issue.5516 , pp. 504-507
    • Pfeiffer, T.1    Schuster, S.2    Bonhoeffer, S.3
  • 23
    • 85050209693 scopus 로고
    • The molecular quasi-species
    • 1:CAS:528:DyaK3cXmtlOqtb0%3D
    • Eigen M, McCaskill J, Schuster P. The molecular quasi-species. Adv Chem Phys. 1989; 75:149-263.
    • (1989) Adv Chem Phys , vol.75 , pp. 149-263
    • Eigen, M.1    McCaskill, J.2    Schuster, P.3
  • 24
    • 84866839511 scopus 로고    scopus 로고
    • The yield of experimental yeast populations declines during selection
    • doi:10.1098/rspb.2012.1659
    • Jasmin J, Dillon MM, Zeyl C. The yield of experimental yeast populations declines during selection. Proc R Soc B Biol Sci. 2012; 279(1746):4382-8. doi: 10.1098/rspb.2012.1659. http://rspb.royalsocietypublishing.org/content/279/1746/4382.full.pdf+html.
    • (2012) Proc R Soc B Biol Sci , vol.279 , Issue.1746 , pp. 4382-4388
    • Jasmin, J.1    Dillon, M.M.2    Zeyl, C.3
  • 25
    • 73149109962 scopus 로고    scopus 로고
    • Shifts in growth strategies reflect tradeoffs in cellular economics
    • 2795476 19888218 doi:10.1038/msb.2009.82
    • 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. doi: 10.1038/msb.2009.82.
    • (2009) Mol Syst Biol , vol.5 , pp. 323
    • Molenaar, D.1    Van Berlo, R.2    De Ridder, D.3    Teusink, B.4
  • 26
    • 84894106291 scopus 로고    scopus 로고
    • Elucidating the adaptation and temporal coordination of metabolic pathways using in-silico evolution
    • 1:CAS:528:DC%2BC2cXjvFWis7c%3D 24440082 doi:10.1016/j.biosystems.2013.12.006
    • Gottstein W, Müller S, Herzel H, Steuer R. Elucidating the adaptation and temporal coordination of metabolic pathways using in-silico evolution. Biosystems. 2014; 117(0):68-76. doi: 10.1016/j.biosystems.2013.12.006.
    • (2014) Biosystems , vol.117 , pp. 68-76
    • Gottstein, W.1    Müller, S.2    Herzel, H.3    Steuer, R.4
  • 27
    • 0033552946 scopus 로고    scopus 로고
    • Robustness in bacterial chemotaxis
    • 1:CAS:528:DyaK1MXntV2rsw%3D%3D 9923680
    • Alon U, Surette M, Barkai N, Leibler S. Robustness in bacterial chemotaxis. Nature. 1999; 397:168-71.
    • (1999) Nature , vol.397 , pp. 168-171
    • Alon, U.1    Surette, M.2    Barkai, N.3    Leibler, S.4
  • 28
    • 0037078982 scopus 로고    scopus 로고
    • Control, exploitation and tolerance of intracellular noise
    • 1:CAS:528:DC%2BD38Xos1GnsbY%3D 12432408
    • Rao C, Wolf D, Arkin A. Control, exploitation and tolerance of intracellular noise. Nature. 2002; 420:231-7.
    • (2002) Nature , vol.420 , pp. 231-237
    • Rao, C.1    Wolf, D.2    Arkin, A.3
  • 29
    • 14044265753 scopus 로고    scopus 로고
    • Stochastic amplification and signaling in Enzymatic futile cycles through noise-induced Bistability with oscillations
    • 548975 1:CAS:528:DC%2BD2MXhvFKitro%3D 15701703
    • Samoilov M, Plyasunov S, Arkin A. Stochastic amplification and signaling in Enzymatic futile cycles through noise-induced Bistability with oscillations. Proc Natl Acad Sci USA. 2005; 102(7):2310-315.
    • (2005) Proc Natl Acad Sci USA , vol.102 , Issue.7 , pp. 2310-2315
    • Samoilov, M.1    Plyasunov, S.2    Arkin, A.3
  • 30
    • 1842687878 scopus 로고    scopus 로고
    • The yeast cell-cycle network is robustly designed
    • 387325 1:CAS:528:DC%2BD2cXjsFCjur4%3D 15037758
    • Li F, Lu Y, Tang C. The yeast cell-cycle network is robustly designed. Proc Natl Acad Sci USA. 2004; 101(14):4781-6.
    • (2004) Proc Natl Acad Sci USA , vol.101 , Issue.14 , pp. 4781-4786
    • Li, F.1    Lu, Y.2    Tang, C.3
  • 31
    • 0000746606 scopus 로고
    • On the nature and origin of complexity in discrete, homogeneous, locally-interacting systems
    • Bennett C. On the nature and origin of complexity in discrete, homogeneous, locally-interacting systems. Found Phys. 1986; 16(6):585-92.
    • (1986) Found Phys , vol.16 , Issue.6 , pp. 585-592
    • Bennett, C.1
  • 32
    • 84883430616 scopus 로고    scopus 로고
    • Evolutionary tradeoffs between economy and effectiveness in biological homeostasis systems
    • doi:10.1371/journal.pcbi.1003163
    • Szekely P, Sheftel H, Mayo A, Alon U. Evolutionary tradeoffs between economy and effectiveness in biological homeostasis systems. PLoS Comput Biol. 2013; 9(8):1003163. doi: 10.1371/journal.pcbi.1003163.
    • (2013) PLoS Comput Biol , vol.9 , Issue.8 , pp. 1003163
    • Szekely, P.1    Sheftel, H.2    Mayo, A.3    Alon, U.4
  • 33
    • 0038441327 scopus 로고    scopus 로고
    • Evolution experiments with microorganisms: The dynamics and genetic bases of adaptation
    • 1:CAS:528:DC%2BD3sXktFOgsLY%3D 12776215 doi:10.1038/nrg1088
    • Elena S, Lenski R. Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat Rev Genet. 2003; 4(6):457-69. doi: 10.1038/nrg1088.
    • (2003) Nat Rev Genet , vol.4 , Issue.6 , pp. 457-469
    • Elena, S.1    Lenski, R.2
  • 34
    • 0347635508 scopus 로고    scopus 로고
    • Design of genetic networks with specified functions by evolution in silico
    • 327190 1:CAS:528:DC%2BD2cXmsFGnuw%3D%3D 14704282
    • Francois P, Hakim V. Design of genetic networks with specified functions by evolution in silico. Proc Natl Acad Sci USA. 2004; 101(2):580-5. http://www.pnas.org/cgi/reprint/101/2/580.pdf.
    • (2004) Proc Natl Acad Sci USA , vol.101 , Issue.2 , pp. 580-585
    • Francois, P.1    Hakim, V.2
  • 35
    • 77956061862 scopus 로고    scopus 로고
    • De novo evolution of complex, global and hierarchical gene regulatory mechanisms
    • 2924499 1:CAS:528:DC%2BC3cXhtVCnt7%2FE 20680619
    • Jenkins D, Stekel D. De novo evolution of complex, global and hierarchical gene regulatory mechanisms. J Mol Evol. 2010; 71(2):128-40.
    • (2010) J Mol Evol , vol.71 , Issue.2 , pp. 128-140
    • Jenkins, D.1    Stekel, D.2
  • 36
    • 84866786886 scopus 로고    scopus 로고
    • Evolution of resource and energy management in biologically realistic gene regulatory network models
    • 1:CAS:528:DC%2BC3sXhsVWqsbs%3D 22821464
    • Stekel D, Jenkins D. Evolution of resource and energy management in biologically realistic gene regulatory network models. Adv Exp Med Biol. 2012; 751:301-28.
    • (2012) Adv Exp Med Biol , vol.751 , pp. 301-328
    • Stekel, D.1    Jenkins, D.2
  • 37
    • 84881596821 scopus 로고    scopus 로고
    • Replaying the tape of evolution: Evolving parameters for a simple bacterial metabolism
    • 2013 IEEE Congress On
    • Chu D. Replaying the tape of evolution: Evolving parameters for a simple bacterial metabolism. In: Evolutionary Computation (CEC), 2013 IEEE Congress On: 2013. p. 213-20. doi: 10.1109/CEC.2013.6557573.
    • (2013) Evolutionary Computation (CEC) , pp. 213-220
    • Chu, D.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.