메뉴 건너뛰기




Volumn 15, Issue 1, 2015, Pages

Applications of computational modeling in metabolic engineering of yeast

Author keywords

Biotechnology; Genome scale model; Kinetic model; Synthetic biology

Indexed keywords

ENZYME KINETICS; GENOME SCALE MODEL; METABOLIC ENGINEERING; METABOLIC REGULATION; MODEL; NONHUMAN; SHORT SURVEY; THERMODYNAMICS; YEAST; BIOLOGICAL MODEL; BIOTECHNOLOGY; COMPUTER SIMULATION; GENETICS; KINETICS; METABOLISM; PROCEDURES; SACCHAROMYCES CEREVISIAE; SYSTEMS BIOLOGY;

EID: 84943659706     PISSN: 15671356     EISSN: 15671364     Source Type: Journal    
DOI: 10.1111/1567-1364.12199     Document Type: Article
Times cited : (47)

References (122)
  • 3
    • 84863307952 scopus 로고    scopus 로고
    • Engineering of self-sustaining systems: substituting the yeast glucose transporter plus hexokinase for the Lactococcus lactis phosphotransferase system in a Lactococcus lactis network in silico
    • Adamczyk M, WesterhoffHV. Engineering of self-sustaining systems: substituting the yeast glucose transporter plus hexokinase for the Lactococcus lactis phosphotransferase system in a Lactococcus lactis network in silico. Biotechnol J 2012;7:877-83.
    • (2012) Biotechnol J , vol.7 , pp. 877-883
    • Adamczyk, M.1    Westerhoff, H.V.2
  • 4
    • 84875973063 scopus 로고    scopus 로고
    • The RAVEN toolbox and its use for generating a genomescale metabolic model for Penicillium chrysogenum
    • Agren R, Liu L, Shoaie S, Vongsangnak W, Nookaew I, Nielsen J. The RAVEN toolbox and its use for generating a genomescale metabolic model for Penicillium chrysogenum. PLoS Comput Biol 2013;9:e1002980.
    • (2013) PLoS Comput Biol , vol.9
    • Agren, R.1    Liu, L.2    Shoaie, S.3    Vongsangnak, W.4    Nookaew, I.5    Nielsen, J.6
  • 5
    • 84879236195 scopus 로고    scopus 로고
    • Genome-scale modeling enables metabolic engineering of Saccharomyces cerevisiae for succinic acid production
    • Agren R, Otero JM, Nielsen J. Genome-scale modeling enables metabolic engineering of Saccharomyces cerevisiae for succinic acid production. J Ind Microbiol Biotechnol 2013;40:735-47.
    • (2013) J Ind Microbiol Biotechnol , vol.40 , pp. 735-747
    • Agren, R.1    Otero, J.M.2    Nielsen, J.3
  • 6
    • 84896419256 scopus 로고    scopus 로고
    • Evolutionary engineering of Saccharomyces cerevisiae for enhanced tolerance to hydrolysates of lignocellulosic biomass
    • Almario MP, Reyes LH, Kao KC. Evolutionary engineering of Saccharomyces cerevisiae for enhanced tolerance to hydrolysates of lignocellulosic biomass. Biotechnol Bioeng 2013;110:2616-23.
    • (2013) Biotechnol Bioeng , vol.110 , pp. 2616-2623
    • Almario, M.P.1    Reyes, L.H.2    Kao, K.C.3
  • 8
    • 0344099105 scopus 로고    scopus 로고
    • Integration of kinetic information on yeast sphingolipid metabolism in dynamical pathway models
    • Alvarez-Vasquez F, Sims KJ, Hannun YA, Voit EO. Integration of kinetic information on yeast sphingolipid metabolism in dynamical pathway models. J Theor Biol 2004;226:265-91.
    • (2004) J Theor Biol , vol.226 , pp. 265-291
    • Alvarez-Vasquez, F.1    Sims, K.J.2    Hannun, Y.A.3    Voit, E.O.4
  • 9
    • 83355176573 scopus 로고    scopus 로고
    • Mathematical modeling and validation of the ergosterol pathway in Saccharomyces cerevisiae
    • Alvarez-Vasquez F, Riezman H, Hannun YA, Voit EO. Mathematical modeling and validation of the ergosterol pathway in Saccharomyces cerevisiae. PLoS One 2011;6:e28344.
    • (2011) PLoS One , vol.6
    • Alvarez-Vasquez, F.1    Riezman, H.2    Hannun, Y.A.3    Voit, E.O.4
  • 10
    • 84897581176 scopus 로고    scopus 로고
    • Total synthesis of a functional designer eukaryotic chromosome
    • Annaluru N, Muller H, Mitchell LA, et al. Total synthesis of a functional designer eukaryotic chromosome. Science 2014;344:55-8.
    • (2014) Science , vol.344 , pp. 55-58
    • Annaluru, N.1    Muller, H.2    Mitchell, L.A.3
  • 11
    • 70449592325 scopus 로고    scopus 로고
    • Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering
    • Asadollahi MA, Maury J, Patil KR, Schalk M, Clark A, Nielsen J. Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering. Metab Eng 2009;11:328-34.
    • (2009) Metab Eng , vol.11 , pp. 328-334
    • Asadollahi, M.A.1    Maury, J.2    Patil, K.R.3    Schalk, M.4    Clark, A.5    Nielsen, J.6
  • 12
    • 84863633909 scopus 로고    scopus 로고
    • Turbidostat culture of Saccharomyces cerevisiae W303-1A under selective pressure elicited by ethanol selects for mutations in SSD1 and UTH1
    • Avrahami-Moyal L, Engelberg D, Wenger JW, Sherlock G, Braun S. Turbidostat culture of Saccharomyces cerevisiae W303-1A under selective pressure elicited by ethanol selects for mutations in SSD1 and UTH1. FEMS Yeast Res 2012;12:521-33.
    • (2012) FEMS Yeast Res , vol.12 , pp. 521-533
    • Avrahami-Moyal, L.1    Engelberg, D.2    Wenger, J.W.3    Sherlock, G.4    Braun, S.5
  • 13
    • 0025895183 scopus 로고
    • Toward a science of metabolic engineering
    • Bailey J. Toward a science of metabolic engineering. Science 1991;252:1668-75.
    • (1991) Science , vol.252 , pp. 1668-1675
    • Bailey, J.1
  • 14
    • 25444467580 scopus 로고    scopus 로고
    • Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast
    • Blank LM, Kuepfer L, Sauer U. Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast. Genome Biol 2005;6:R49.
    • (2005) Genome Biol , vol.6 , pp. R49
    • Blank, L.M.1    Kuepfer, L.2    Sauer, U.3
  • 15
    • 78049304837 scopus 로고    scopus 로고
    • Sampling the solution space in genome-scale metabolic networks reveals transcriptional regulation in key enzymes
    • Bordel S, Agren R, Nielsen J. Sampling the solution space in genome-scale metabolic networks reveals transcriptional regulation in key enzymes. PLoS Comput Biol 2010;6:e1000859.
    • (2010) PLoS Comput Biol , vol.6
    • Bordel, S.1    Agren, R.2    Nielsen, J.3
  • 16
    • 33644832381 scopus 로고    scopus 로고
    • In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production
    • Bro C, Regenberg B, Förster J, Nielsen J. In silico aided metabolic engineering of Saccharomyces cerevisiae for improved bioethanol production. Metab Eng 2006;8:102-11.
    • (2006) Metab Eng , vol.8 , pp. 102-111
    • Bro, C.1    Regenberg, B.2    Förster, J.3    Nielsen, J.4
  • 19
    • 84857672615 scopus 로고    scopus 로고
    • Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism
    • Buescher JM, Liebermeister W, Jules M, et al. Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism. Science 2012;335:1099-103.
    • (2012) Science , vol.335 , pp. 1099-1103
    • Buescher, J.M.1    Liebermeister, W.2    Jules, M.3
  • 20
    • 0038293216 scopus 로고    scopus 로고
    • Optimization-based framework for inferring and testing hypothesized metabolic objective functions
    • Burgard AP, Maranas CD. Optimization-based framework for inferring and testing hypothesized metabolic objective functions. Biotechnol Bioeng 2003;82:670-7.
    • (2003) Biotechnol Bioeng , vol.82 , pp. 670-677
    • Burgard, A.P.1    Maranas, C.D.2
  • 22
    • 84883800631 scopus 로고    scopus 로고
    • Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiology constraints
    • Chakrabarti A, Miskovic L, Soh KC, Hatzimanikatis V. Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiology constraints. Biotechnol J 2013;8:1043-57.
    • (2013) Biotechnol J , vol.8 , pp. 1043-1057
    • Chakrabarti, A.1    Miskovic, L.2    Soh, K.C.3    Hatzimanikatis, V.4
  • 23
    • 77956289955 scopus 로고    scopus 로고
    • Classic and contemporary approaches to modeling biochemical reactions
    • Chen WW, Niepel M, Sorger PK. Classic and contemporary approaches to modeling biochemical reactions. Genes Dev 2010;24:1861-75.
    • (2010) Genes Dev , vol.24 , pp. 1861-1875
    • Chen, W.W.1    Niepel, M.2    Sorger, P.K.3
  • 24
    • 84865337008 scopus 로고    scopus 로고
    • Genomebased kinetic modeling of cytosolic glucose metabolism in industrially relevant cell lines: Saccharomyces cerevisiae and Chinese hamster ovary cells
    • Chen N, Koumpouras GC, Polizzi KM, Kontoravdi C. Genomebased kinetic modeling of cytosolic glucose metabolism in industrially relevant cell lines: Saccharomyces cerevisiae and Chinese hamster ovary cells. Bioprocess Biosyst Eng 2012;35:1023-33.
    • (2012) Bioprocess Biosyst Eng , vol.35 , pp. 1023-1033
    • Chen, N.1    Koumpouras, G.C.2    Polizzi, K.M.3    Kontoravdi, C.4
  • 25
    • 84894040387 scopus 로고    scopus 로고
    • Coupled incremental precursor and co-factor supply improves 3-hydroxypropionic acid production in Saccharomyces cerevisiae
    • Chen Y, Bao J, Kim I-K, Siewers V, Nielsen J. Coupled incremental precursor and co-factor supply improves 3-hydroxypropionic acid production in Saccharomyces cerevisiae. Metab Eng 2014;22:104-9.
    • (2014) Metab Eng , vol.22 , pp. 104-109
    • Chen, Y.1    Bao, J.2    Kim, I.-K.3    Siewers, V.4    Nielsen, J.5
  • 26
    • 79952104485 scopus 로고    scopus 로고
    • Tandem mass spectrometry: a novel approach for metabolic flux analysis
    • Choi J, Antoniewicz MR. Tandem mass spectrometry: a novel approach for metabolic flux analysis. Metab Eng 2011;13:225-33.
    • (2011) Metab Eng , vol.13 , pp. 225-233
    • Choi, J.1    Antoniewicz, M.R.2
  • 27
    • 63649099433 scopus 로고    scopus 로고
    • Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae
    • Christensen TS, Oliveira AP, Nielsen J. Reconstruction and logical modeling of glucose repression signaling pathways in Saccharomyces cerevisiae. BMC Syst Biol 2009;3:7.
    • (2009) BMC Syst Biol , vol.3 , pp. 7
    • Christensen, T.S.1    Oliveira, A.P.2    Nielsen, J.3
  • 29
    • 0035824029 scopus 로고    scopus 로고
    • Regulation of gene expression in flux balance models of metabolism
    • Covert MW, Schilling CH, Palsson B. Regulation of gene expression in flux balance models of metabolism. J Theor Biol 2001;213:73-88.
    • (2001) J Theor Biol , vol.213 , pp. 73-88
    • Covert, M.W.1    Schilling, C.H.2    Palsson, B.3
  • 30
    • 2342648924 scopus 로고    scopus 로고
    • Integrating high-throughput and computational data elucidates bacterial networks
    • Covert MW, Polakis P, Palsson BØ Integrating high-throughput and computational data elucidates bacterial networks. Nature 2004;429:92-6.
    • (2004) Nature , vol.429 , pp. 92-96
    • Covert, M.W.1    Polakis, P.2    Palsson, B.Ø.3
  • 31
    • 51749113592 scopus 로고    scopus 로고
    • Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli
    • Covert MW, Xiao N, Chen TJ, Karr JR. Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli. Bioinformatics 2008;24:2044-50.
    • (2008) Bioinformatics , vol.24 , pp. 2044-2050
    • Covert, M.W.1    Xiao, N.2    Chen, T.J.3    Karr, J.R.4
  • 32
    • 0036713452 scopus 로고    scopus 로고
    • Metabolic control analysis of glycerol synthesis in Saccharomyces cerevisiae
    • Cronwright GR, Rohwer JM, Prior BA. Metabolic control analysis of glycerol synthesis in Saccharomyces cerevisiae. Appl Environ Microbiol 2002;68:4448-56.
    • (2002) Appl Environ Microbiol , vol.68 , pp. 4448-4456
    • Cronwright, G.R.1    Rohwer, J.M.2    Prior, B.A.3
  • 33
    • 33748474370 scopus 로고    scopus 로고
    • Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution
    • Dantas G, Watters AL, Lundes BM, et al. Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution. J Mol Biol 2006;362:1004-24.
    • (2006) J Mol Biol , vol.362 , pp. 1004-1024
    • Dantas, G.1    Watters, A.L.2    Lundes, B.M.3
  • 34
    • 1542350073 scopus 로고    scopus 로고
    • Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae. A chemostat culture study
    • Daran-Lapujade P, Jansen ML, Daran J-M, van Gulik W, de Winde JH, Pronk JT. Role of transcriptional regulation in controlling fluxes in central carbon metabolism of Saccharomyces cerevisiae. A chemostat culture study. J Biol Chem 2004;279:9125-38.
    • (2004) J Biol Chem , vol.279 , pp. 9125-9138
    • Daran-Lapujade, P.1    Jansen, M.L.2    Daran, J.-M.3    van Gulik, W.4    de Winde, J.H.5    Pronk, J.T.6
  • 35
    • 35648972123 scopus 로고    scopus 로고
    • The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels
    • Daran-Lapujade P, Rossell S, Van Gulik WM, et al. The fluxes through glycolytic enzymes in Saccharomyces cerevisiae are predominantly regulated at posttranscriptional levels. P Natl Acad Sci USA 2007;104:15753-8.
    • (2007) P Natl Acad Sci USA , vol.104 , pp. 15753-15758
    • Daran-Lapujade, P.1    Rossell, S.2    Van Gulik, W.M.3
  • 36
    • 84879119602 scopus 로고    scopus 로고
    • Development of a D-xylose fermenting and inhibitor tolerant industrial Saccharomyces cerevisiae strain with high performance in lignocellulose hydrolysates using metabolic and evolutionary engineering
    • Demeke MM, Dietz H, Li Y, et al. Development of a D-xylose fermenting and inhibitor tolerant industrial Saccharomyces cerevisiae strain with high performance in lignocellulose hydrolysates using metabolic and evolutionary engineering. Biotechnol Biofuels 2013;6:89.
    • (2013) Biotechnol Biofuels , vol.6 , pp. 89
    • Demeke, M.M.1    Dietz, H.2    Li, Y.3
  • 37
    • 79955027266 scopus 로고    scopus 로고
    • Adaptation of Saccharomyces cerevisiae to saline stress through laboratory evolution
    • Dhar R, Sägesser R, Weikert C, Yuan J, Wagner A. Adaptation of Saccharomyces cerevisiae to saline stress through laboratory evolution. J Evol Biol 2011;24:1135-53.
    • (2011) J Evol Biol , vol.24 , pp. 1135-1153
    • Dhar, R.1    Sägesser, R.2    Weikert, C.3    Yuan, J.4    Wagner, A.5
  • 38
    • 52649136124 scopus 로고    scopus 로고
    • Integration of metabolic modeling and phenotypic data in evaluation and improvement of ethanol production using respiration-deficient mutants of Saccharomyces cerevisiae
    • Dikicioglu D, Pir P, Onsan ZI, Ulgen KO, Kirdar B, Oliver SG. Integration of metabolic modeling and phenotypic data in evaluation and improvement of ethanol production using respiration-deficient mutants of Saccharomyces cerevisiae. Appl Environ Microbiol 2008;74:5809-16.
    • (2008) Appl Environ Microbiol , vol.74 , pp. 5809-5816
    • Dikicioglu, D.1    Pir, P.2    Onsan, Z.I.3    Ulgen, K.O.4    Kirdar, B.5    Oliver, S.G.6
  • 39
    • 3843128481 scopus 로고    scopus 로고
    • Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model
    • Duarte NC, Herrgård MJ, Palsson BØ Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res 2004;14:1298-309.
    • (2004) Genome Res , vol.14 , pp. 1298-1309
    • Duarte, N.C.1    Herrgård, M.J.2    Palsson, B.Ø.3
  • 40
    • 80053132391 scopus 로고    scopus 로고
    • Synthetic chromosome arms function in yeast and generate phenotypic diversity by design
    • Dymond JS, Richardson SM, Coombes CE, et al. Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature 2011;477:471-6.
    • (2011) Nature , vol.477 , pp. 471-476
    • Dymond, J.S.1    Richardson, S.M.2    Coombes, C.E.3
  • 41
    • 0034688173 scopus 로고    scopus 로고
    • A synthetic oscillatory network of transcriptional regulators
    • Elowitz MB, Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature 2000;403:335-8.
    • (2000) Nature , vol.403 , pp. 335-338
    • Elowitz, M.B.1    Leibler, S.2
  • 42
    • 22144492269 scopus 로고    scopus 로고
    • The biological limitations of transcriptomics in elucidating stress and stress responses
    • Feder ME, Walser J-C. The biological limitations of transcriptomics in elucidating stress and stress responses. J Evol Biol 2005;18:901-10.
    • (2005) J Evol Biol , vol.18 , pp. 901-910
    • Feder, M.E.1    Walser, J.-C.2
  • 44
    • 78649832864 scopus 로고    scopus 로고
    • Unraveling condition-dependent networks of transcription factors that control metabolic pathway activity in yeast
    • Fendt S-M, Oliveira AP, Christen S, Picotti P, Dechant RC, Sauer U. Unraveling condition-dependent networks of transcription factors that control metabolic pathway activity in yeast. Mol Syst Biol 2010;6:432.
    • (2010) Mol Syst Biol , vol.6 , pp. 432
    • Fendt, S.-M.1    Oliveira, A.P.2    Christen, S.3    Picotti, P.4    Dechant, R.C.5    Sauer, U.6
  • 45
    • 0037313750 scopus 로고    scopus 로고
    • Genome-scale re-construction of the Saccharomyces cerevisiae metabolic network
    • Förster J, Famili I, Fu P, Palsson BØ, Nielsen J. Genome-scale re-construction of the Saccharomyces cerevisiae metabolic network. Genome Res 2003;13:244-53.
    • (2003) Genome Res , vol.13 , pp. 244-253
    • Förster, J.1    Famili, I.2    Fu, P.3    Palsson, B.Ø.4    Nielsen, J.5
  • 46
    • 27744491124 scopus 로고    scopus 로고
    • Characterization of the metabolic shift between oxidative and fermentative growth in Saccharomyces cerevisiae by comparative 13C flux analysis
    • Frick O, Wittmann C. Characterization of the metabolic shift between oxidative and fermentative growth in Saccharomyces cerevisiae by comparative 13C flux analysis. Microb Cell Fact 2005;4:30.
    • (2005) Microb Cell Fact , vol.4 , pp. 30
    • Frick, O.1    Wittmann, C.2
  • 47
    • 0025400371 scopus 로고
    • Fermentation pathway kinetics and metabolic flux control in suspended and immobilized Saccharomyces cerevisiae
    • Galazzo J, Bailey J. Fermentation pathway kinetics and metabolic flux control in suspended and immobilized Saccharomyces cerevisiae. Enzyme Microb Technol 1990;12:162-72.
    • (1990) Enzyme Microb Technol , vol.12 , pp. 162-172
    • Galazzo, J.1    Bailey, J.2
  • 48
    • 0034688174 scopus 로고    scopus 로고
    • Construction of a genetic toggle switch in Escherichia coli
    • Gardner TS, Cantor CR, Collins JJ. Construction of a genetic toggle switch in Escherichia coli. Nature 2000;403:339-42.
    • (2000) Nature , vol.403 , pp. 339-342
    • Gardner, T.S.1    Cantor, C.R.2    Collins, J.J.3
  • 49
    • 79960964285 scopus 로고    scopus 로고
    • Regulation and control of metabolic fluxes in microbes
    • Gerosa L, Sauer U. Regulation and control of metabolic fluxes in microbes. Curr Opin Biotechnol 2011;22:566-75.
    • (2011) Curr Opin Biotechnol , vol.22 , pp. 566-575
    • Gerosa, L.1    Sauer, U.2
  • 51
    • 0035140099 scopus 로고    scopus 로고
    • Network identification and flux quantification in the central metabolism of Saccharomyces cerevisiae under different conditions of glucose repression
    • Gombert AK, Moreira M, Christensen B, Nielsen J, Acteriol JB. Network identification and flux quantification in the central metabolism of Saccharomyces cerevisiae under different conditions of glucose repression. J Bacteriol 2001;183:1441-51.
    • (2001) J Bacteriol , vol.183 , pp. 1441-1451
    • Gombert, A.K.1    Moreira, M.2    Christensen, B.3    Nielsen, J.4    Acteriol, J.B.5
  • 54
    • 84890802554 scopus 로고    scopus 로고
    • Dynamic model-based analysis of furfural and HMF detoxification by pure and mixed batch cultures of S. cerevisiae and S. stipitis
    • Hanly TJ, Henson MA. Dynamic model-based analysis of furfural and HMF detoxification by pure and mixed batch cultures of S. cerevisiae and S. stipitis. Biotechnol Bioeng 2014;111:272-84.
    • (2014) Biotechnol Bioeng , vol.111 , pp. 272-284
    • Hanly, T.J.1    Henson, M.A.2
  • 56
    • 0034213671 scopus 로고    scopus 로고
    • Simultaneous genomic over-expression of seven glycolytic enzymes in the yeast Saccharomyces cerevisiae
    • Hauf J, Zimmermann FK, Müller S. Simultaneous genomic over-expression of seven glycolytic enzymes in the yeast Saccharomyces cerevisiae. Enzyme Microb Technol 2000;26:688-98.
    • (2000) Enzyme Microb Technol , vol.26 , pp. 688-698
    • Hauf, J.1    Zimmermann, F.K.2    Müller, S.3
  • 57
    • 25144492110 scopus 로고    scopus 로고
    • Approximative kinetic formats used in metabolic network modeling
    • Heijnen JJ. Approximative kinetic formats used in metabolic network modeling. Biotechnol Bioeng 2005;91:534-45.
    • (2005) Biotechnol Bioeng , vol.91 , pp. 534-545
    • Heijnen, J.J.1
  • 60
    • 53749085229 scopus 로고    scopus 로고
    • A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology
    • Herrgård MJ, Swainston N, Dobson P, et al. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nat Biotechnol 2008;26:1155-60.
    • (2008) Nat Biotechnol , vol.26 , pp. 1155-1160
    • Herrgård, M.J.1    Swainston, N.2    Dobson, P.3
  • 61
    • 66249096326 scopus 로고    scopus 로고
    • Steady-state and dynamic flux balance analysis of ethanol production by Saccharomyces cerevisiae
    • Hjersted JLL, Henson MA. Steady-state and dynamic flux balance analysis of ethanol production by Saccharomyces cerevisiae. IET Syst Biol 2009;3:167-79.
    • (2009) IET Syst Biol , vol.3 , pp. 167-179
    • Hjersted, J.L.L.1    Henson, M.A.2
  • 62
    • 79961072482 scopus 로고    scopus 로고
    • Unravelling evolutionary strategies of yeast for improving galactose utilization through integrated systems level analysis
    • Hong K-K, Vongsangnak W, Vemuri GN, Nielsen J. Unravelling evolutionary strategies of yeast for improving galactose utilization through integrated systems level analysis. P Natl Acad Sci USA 2011;108:12179-84.
    • (2011) P Natl Acad Sci USA , vol.108 , pp. 12179-12184
    • Hong, K.-K.1    Vongsangnak, W.2    Vemuri, G.N.3    Nielsen, J.4
  • 63
    • 0035846723 scopus 로고    scopus 로고
    • Full-scale model of glycolysis in Saccharomyces cerevisiae
    • Hynne F, Danø S, Sørensen PG. Full-scale model of glycolysis in Saccharomyces cerevisiae. Biophys Chem 2001;94:121-63.
    • (2001) Biophys Chem , vol.94 , pp. 121-163
    • Hynne, F.1    Danø, S.2    Sørensen, P.G.3
  • 64
    • 34247612307 scopus 로고    scopus 로고
    • Multiple high-throughput analyses monitor the response of E. coli to perturbations
    • Ishii N, Nakahigashi K, Baba T, et al. Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science 2007;316:593-7.
    • (2007) Science , vol.316 , pp. 593-597
    • Ishii, N.1    Nakahigashi, K.2    Baba, T.3
  • 65
    • 84861128104 scopus 로고    scopus 로고
    • System-level insights into yeast metabolism by thermodynamic analysis of elementary flux modes
    • Jol SJ, Kümmel A, Terzer M, Stelling J, Heinemann M. System-level insights into yeast metabolism by thermodynamic analysis of elementary flux modes. PLoS Comput Biol 2012;8:e1002415.
    • (2012) PLoS Comput Biol , vol.8
    • Jol, S.J.1    Kümmel, A.2    Terzer, M.3    Stelling, J.4    Heinemann, M.5
  • 67
    • 0018527496 scopus 로고
    • Molecular democracy: who shares the controls?
    • Kacser H, Burns J. Molecular democracy: who shares the controls?. Biochem Soc Trans 1979;7:1149-60.
    • (1979) Biochem Soc Trans , vol.7 , pp. 1149-1160
    • Kacser, H.1    Burns, J.2
  • 68
    • 0019869334 scopus 로고
    • The molecular basis of dominance
    • Kacser H, Burns J. The molecular basis of dominance. Genetics 1981;97:639-66.
    • (1981) Genetics , vol.97 , pp. 639-666
    • Kacser, H.1    Burns, J.2
  • 71
    • 84908074616 scopus 로고    scopus 로고
    • Adaptation of Bacillus subtilis carbon core metabolism to simultaneous nutrient limitation and osmotic challenge: a multi-omics perspective
    • Kohlstedt M, Sappa PK, Meyer H, et al. Adaptation of Bacillus subtilis carbon core metabolism to simultaneous nutrient limitation and osmotic challenge: a multi-omics perspective. Environ Microbiol 2014;16:1898-917.
    • (2014) Environ Microbiol , vol.16 , pp. 1898-1917
    • Kohlstedt, M.1    Sappa, P.K.2    Meyer, H.3
  • 72
    • 77949385752 scopus 로고    scopus 로고
    • Bacterial adaptation through distributed sensing of metabolic fluxes
    • Kotte O, Zaugg JB, Heinemann M. Bacterial adaptation through distributed sensing of metabolic fluxes. Mol Syst Biol 2010;6:1-9.
    • (2010) Mol Syst Biol , vol.6 , pp. 1-9
    • Kotte, O.1    Zaugg, J.B.2    Heinemann, M.3
  • 73
    • 25844463806 scopus 로고    scopus 로고
    • Metabolic functions of duplicate genes in Saccharomyces cerevisiae
    • Kuepfer L, Sauer U, Blank LM. Metabolic functions of duplicate genes in Saccharomyces cerevisiae. Genome Res 2005;15:1421-30.
    • (2005) Genome Res , vol.15 , pp. 1421-1430
    • Kuepfer, L.1    Sauer, U.2    Blank, L.M.3
  • 74
    • 36849002434 scopus 로고    scopus 로고
    • Systems metabolic engineering of Escherichia coli for L-threonine production
    • Lee KH, Park JH, Kim TY, Kim HU, Lee SY. Systems metabolic engineering of Escherichia coli for L-threonine production. Mol Syst Biol 2007;3:149.
    • (2007) Mol Syst Biol , vol.3 , pp. 149
    • Lee, K.H.1    Park, J.H.2    Kim, T.Y.3    Kim, H.U.4    Lee, S.Y.5
  • 75
    • 84858439602 scopus 로고    scopus 로고
    • Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods
    • Lewis NE, Nagarajan H, Palsson BO. Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat Rev Microbiol 2012;10:291-305.
    • (2012) Nat Rev Microbiol , vol.10 , pp. 291-305
    • Lewis, N.E.1    Nagarajan, H.2    Palsson, B.O.3
  • 76
    • 33846617808 scopus 로고    scopus 로고
    • Bringing metabolic networks to life: convenience rate law and thermodynamic constraints
    • Liebermeister W, Klipp E. Bringing metabolic networks to life: convenience rate law and thermodynamic constraints. Theor Biol Med Model 2006;3:41.
    • (2006) Theor Biol Med Model , vol.3 , pp. 41
    • Liebermeister, W.1    Klipp, E.2
  • 77
    • 77954196484 scopus 로고    scopus 로고
    • Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation
    • Liebermeister W, Uhlendorf J, Klipp E. Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation. Bioinformatics 2010;26:1528-34.
    • (2010) Bioinformatics , vol.26 , pp. 1528-1534
    • Liebermeister, W.1    Uhlendorf, J.2    Klipp, E.3
  • 78
    • 84877296949 scopus 로고    scopus 로고
    • Systematic identification of allosteric protein-metabolite interactions that control enzyme activity in vivo
    • Link H, Kochanowski K, Sauer U. Systematic identification of allosteric protein-metabolite interactions that control enzyme activity in vivo. Nat Biotechnol 2013;31:357-61.
    • (2013) Nat Biotechnol , vol.31 , pp. 357-361
    • Link, H.1    Kochanowski, K.2    Sauer, U.3
  • 79
    • 84901306814 scopus 로고    scopus 로고
    • Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism
    • Machado D, Herrgård M. Systematic evaluation of methods for integration of transcriptomic data into constraint-based models of metabolism. PLoS Comput Biol 2014;10:e1003580.
    • (2014) PLoS Comput Biol , vol.10
    • Machado, D.1    Herrgård, M.2
  • 80
    • 0032406131 scopus 로고    scopus 로고
    • Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation
    • Mendes P, Kell D. Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. Bioinformatics 1998;14:869-83.
    • (1998) Bioinformatics , vol.14 , pp. 869-883
    • Mendes, P.1    Kell, D.2
  • 81
    • 84919412893 scopus 로고    scopus 로고
    • Enzyme characterisation and kinetic modelling of the pentose phosphate pathway in yeast
    • Messiha H, Kent E, Malys N, Carroll K. Enzyme characterisation and kinetic modelling of the pentose phosphate pathway in yeast. PeerJ Prepr 2014;2:e146v4.
    • (2014) PeerJ Prepr , vol.2
    • Messiha, H.1    Kent, E.2    Malys, N.3    Carroll, K.4
  • 82
    • 84864318798 scopus 로고    scopus 로고
    • Continuous modeling of metabolic networks with gene regulation in yeast and in vivo determination of rate parameters
    • Moisset P, Vaisman D, Cintolesi A, Urrutia J, Rapaport I, Andrews BA, Asenjo JA. Continuous modeling of metabolic networks with gene regulation in yeast and in vivo determination of rate parameters. Biotechnol Bioeng 2012;109:2325-39.
    • (2012) Biotechnol Bioeng , vol.109 , pp. 2325-2339
    • Moisset, P.1    Vaisman, D.2    Cintolesi, A.3    Urrutia, J.4    Rapaport, I.5    Andrews, B.A.6    Asenjo, J.A.7
  • 84
    • 0031015551 scopus 로고    scopus 로고
    • Flux distributions in anaerobic, glucose-limited continuous cultures of Saccharomyces cerevisiae
    • Nissen TL, Schulze U, Nielsen J, Villadsen J. Flux distributions in anaerobic, glucose-limited continuous cultures of Saccharomyces cerevisiae. Microbiology 1997;143:203-18.
    • (1997) Microbiology , vol.143 , pp. 203-218
    • Nissen, T.L.1    Schulze, U.2    Nielsen, J.3    Villadsen, J.4
  • 86
    • 84857048791 scopus 로고    scopus 로고
    • The importance of post-translational modifications in regulating Saccharomyces cerevisiae metabolism
    • Oliveira AP, Sauer U. The importance of post-translational modifications in regulating Saccharomyces cerevisiae metabolism. FEMS Yeast Res 2012;12:104-17.
    • (2012) FEMS Yeast Res , vol.12 , pp. 104-117
    • Oliveira, A.P.1    Sauer, U.2
  • 88
    • 84864932596 scopus 로고    scopus 로고
    • Fifteen years of large scale metabolic modeling of yeast: developments and impacts
    • Osterlund T, Nookaew I, Nielsen J. Fifteen years of large scale metabolic modeling of yeast: developments and impacts. Biotechnol Adv 2012;30:979-88.
    • (2012) Biotechnol Adv , vol.30 , pp. 979-988
    • Osterlund, T.1    Nookaew, I.2    Nielsen, J.3
  • 89
    • 84872655172 scopus 로고    scopus 로고
    • Industrial systems biology of Saccharomyces cerevisiae enables novel succinic acid cell factory
    • Otero JM, Cimini D, Patil KR, Poulsen SG, Olsson L, Nielsen J. Industrial systems biology of Saccharomyces cerevisiae enables novel succinic acid cell factory. PLoS One 2013;8: e54144.
    • (2013) PLoS One , vol.8
    • Otero, J.M.1    Cimini, D.2    Patil, K.R.3    Poulsen, S.G.4    Olsson, L.5    Nielsen, J.6
  • 90
    • 84876784070 scopus 로고    scopus 로고
    • High-level semi-synthetic production of the potent antimalarial artemisinin
    • Paddon CJ, Westfall PJ, Pitera DJ, et al. High-level semi-synthetic production of the potent antimalarial artemisinin. Nature 2013;496:528-32.
    • (2013) Nature , vol.496 , pp. 528-532
    • Paddon, C.J.1    Westfall, P.J.2    Pitera, D.J.3
  • 91
    • 80052037221 scopus 로고    scopus 로고
    • Kinetic modelling reveals current limitations in the production of ethanol from xylose by recombinant Saccharomyces cerevisiae
    • Parachin NS, Bergdahl B, van Niel EWJ, Gorwa-Grauslund MF. Kinetic modelling reveals current limitations in the production of ethanol from xylose by recombinant Saccharomyces cerevisiae. Metab Eng 2011;13:508-17.
    • (2011) Metab Eng , vol.13 , pp. 508-517
    • Parachin, N.S.1    Bergdahl, B.2    van Niel, E.W.J.3    Gorwa-Grauslund, M.F.4
  • 92
    • 30044437327 scopus 로고    scopus 로고
    • Evolutionary programming as a platform for in silico metabolic engineering
    • Patil KR, Rocha I, Förster J, Nielsen J. Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinformatics 2005;6:308.
    • (2005) BMC Bioinformatics , vol.6 , pp. 308
    • Patil, K.R.1    Rocha, I.2    Förster, J.3    Nielsen, J.4
  • 93
    • 84901685293 scopus 로고    scopus 로고
    • Coordinated activation of PTA-ACS and TCA cycles strongly reduces overflow metabolism of acetate in Escherichia coli
    • Peebo K, Valgepea K, Nahku R, Riis G, Oun M, Adamberg K, Vilu R. Coordinated activation of PTA-ACS and TCA cycles strongly reduces overflow metabolism of acetate in Escherichia coli. Appl Microbiol Biotechnol 2014;98:5131-43.
    • (2014) Appl Microbiol Biotechnol , vol.98 , pp. 5131-5143
    • Peebo, K.1    Valgepea, K.2    Nahku, R.3    Riis, G.4    Oun, M.5    Adamberg, K.6    Vilu, R.7
  • 96
    • 41249087796 scopus 로고    scopus 로고
    • Yield optimization of regulated metabolic systems using deterministic branch-and-reduce methods
    • Polisetty PK, Gatzke EP, Voit EO. Yield optimization of regulated metabolic systems using deterministic branch-and-reduce methods. Biotechnol Bioeng 2008;99:1154-69.
    • (2008) Biotechnol Bioeng , vol.99 , pp. 1154-1169
    • Polisetty, P.K.1    Gatzke, E.P.2    Voit, E.O.3
  • 97
    • 0014649230 scopus 로고
    • Biochemical systems analysis: I. Some mathematical properties of the rate law for the component enzymatic reactions
    • Savageau MA. Biochemical systems analysis: I. Some mathematical properties of the rate law for the component enzymatic reactions. J Theor Biol 1969;25:365-9.
    • (1969) J Theor Biol , vol.25 , pp. 365-369
    • Savageau, M.A.1
  • 98
    • 79551662521 scopus 로고    scopus 로고
    • Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
    • Schellenberger J, Que R, Fleming RMT, et al. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc 2011;6:1290-307.
    • (2011) Nat Protoc , vol.6 , pp. 1290-1307
    • Schellenberger, J.1    Que, R.2    Fleming, R.M.T.3
  • 99
    • 84876522835 scopus 로고    scopus 로고
    • brenda in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in brenda
    • Schomburg I, Chang A, Placzek S, et al. brenda in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in brenda. Nucleic Acids Res 2013;41:D764-72.
    • (2013) Nucleic Acids Res , vol.41 , pp. D764-D772
    • Schomburg, I.1    Chang, A.2    Placzek, S.3
  • 100
    • 34447523907 scopus 로고    scopus 로고
    • Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
    • Schuetz R, Kuepfer L, Sauer U. Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Mol Syst Biol 2007;3:119.
    • (2007) Mol Syst Biol , vol.3 , pp. 119
    • Schuetz, R.1    Kuepfer, L.2    Sauer, U.3
  • 102
    • 0037069467 scopus 로고    scopus 로고
    • Analysis of optimality in natural and perturbed
    • Segre D, Vitkup D, Church GM. Analysis of optimality in natural and perturbed. P Natl Acad Sci USA 2002;99:15112-7.
    • (2002) P Natl Acad Sci USA , vol.99 , pp. 15112-15117
    • Segre, D.1    Vitkup, D.2    Church, G.M.3
  • 104
    • 84883049898 scopus 로고    scopus 로고
    • A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes
    • Smallbone K, Messiha HL, Carroll KM, et al. A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes. FEBS Lett 2013;587:2832-41.
    • (2013) FEBS Lett , vol.587 , pp. 2832-2841
    • Smallbone, K.1    Messiha, H.L.2    Carroll, K.M.3
  • 108
    • 58749106454 scopus 로고    scopus 로고
    • Ensemble modeling of metabolic networks
    • Tran LM, Rizk ML, Liao JC. Ensemble modeling of metabolic networks. Biophys J 2008;95:5606-17.
    • (2008) Biophys J , vol.95 , pp. 5606-5617
    • Tran, L.M.1    Rizk, M.L.2    Liao, J.C.3
  • 109
    • 84881087942 scopus 로고    scopus 로고
    • Escherichia coli achieves faster growth by increasing catalytic and translation rates of proteins
    • Valgepea K, Adamberg K, Seiman A, Vilu R. Escherichia coli achieves faster growth by increasing catalytic and translation rates of proteins. Mol BioSyst 2013;9:2344-58.
    • (2013) Mol BioSyst , vol.9 , pp. 2344-2358
    • Valgepea, K.1    Adamberg, K.2    Seiman, A.3    Vilu, R.4
  • 110
    • 84861131751 scopus 로고    scopus 로고
    • Testing biochemistry revisited: how in vivo metabolism can be understood from in vitro enzyme kinetics
    • Van Eunen K, Kiewiet JAL, WesterhoffHV, Bakker BM. Testing biochemistry revisited: how in vivo metabolism can be understood from in vitro enzyme kinetics. PLoS Comput Biol 2012;8:e1002483.
    • (2012) PLoS Comput Biol , vol.8
    • Van Eunen, K.1    Kiewiet, J.A.L.2    Westerhoff, H.V.3    Bakker, B.M.4
  • 111
    • 0028973161 scopus 로고
    • A metabolic network stoichiometry analysis of microbial growth and product formation
    • Van Gulik WM, Heijnen JJ. A metabolic network stoichiometry analysis of microbial growth and product formation. Biotechnol Bioeng 1995;48:681-98.
    • (1995) Biotechnol Bioeng , vol.48 , pp. 681-698
    • Van Gulik, W.M.1    Heijnen, J.J.2
  • 113
    • 0033107539 scopus 로고    scopus 로고
    • In vivo dynamics of the pentose phosphate pathway in Saccharomyces cerevisiae
    • Vaseghi S, Baumeister A, Rizzi M, Reuss M. In vivo dynamics of the pentose phosphate pathway in Saccharomyces cerevisiae. Metab Eng 1999;140:128-40.
    • (1999) Metab Eng , vol.140 , pp. 128-140
    • Vaseghi, S.1    Baumeister, A.2    Rizzi, M.3    Reuss, M.4
  • 114
    • 0141684666 scopus 로고    scopus 로고
    • Dynamic simulation and metabolic redesign of a branched pathway using linlog kinetics
    • Visser D, Heijnen JJ. Dynamic simulation and metabolic redesign of a branched pathway using linlog kinetics. Metab Eng 2003;5:164-76.
    • (2003) Metab Eng , vol.5 , pp. 164-176
    • Visser, D.1    Heijnen, J.J.2
  • 115
    • 84883050022 scopus 로고    scopus 로고
    • Biochemical systems theory: a review
    • Voit EO. Biochemical systems theory: a review. ISRN Biomath 2013;2013:1-53.
    • (2013) ISRN Biomath , vol.2013 , pp. 1-53
    • Voit, E.O.1
  • 116
    • 0034877874 scopus 로고    scopus 로고
    • The silicon cell, not dead but live!
    • WesterhoffHV. The silicon cell, not dead but live!. Metab Eng 2001;3:207-10.
    • (2001) Metab Eng , vol.3 , pp. 207-210
    • Westerhoff, H.V.1
  • 117
    • 84862214722 scopus 로고    scopus 로고
    • SABIO-RK-database for biochemical reaction kinetics
    • Wittig U, Kania R, Golebiewski M, et al. SABIO-RK-database for biochemical reaction kinetics. Nucleic Acids Res 2012;40:D790-6.
    • (2012) Nucleic Acids Res , vol.40 , pp. D790-D796
    • Wittig, U.1    Kania, R.2    Golebiewski, M.3
  • 118
    • 34548088923 scopus 로고    scopus 로고
    • Synthetic biology: lessons from the history of synthetic organic chemistry
    • Yeh BJ, Lim WA. Synthetic biology: lessons from the history of synthetic organic chemistry. Nat Chem Biol 2007;3:521-5.
    • (2007) Nat Chem Biol , vol.3 , pp. 521-525
    • Yeh, B.J.1    Lim, W.A.2
  • 119
    • 84884535181 scopus 로고    scopus 로고
    • Directed evolution of a highly efficient cellobiose utilizing pathway in an industrial Saccharomyces cerevisiae strain
    • Yuan Y, Zhao H. Directed evolution of a highly efficient cellobiose utilizing pathway in an industrial Saccharomyces cerevisiae strain. Biotechnol Bioeng 2013;110:2874-81.
    • (2013) Biotechnol Bioeng , vol.110 , pp. 2874-2881
    • Yuan, Y.1    Zhao, H.2
  • 120
    • 84901321053 scopus 로고    scopus 로고
    • Contribution of network connectivity in determining the relationship between gene expression and metabolite concentration changes
    • Zelezniak A, Sheridan S, Patil KR. Contribution of network connectivity in determining the relationship between gene expression and metabolite concentration changes. PLoS Comput Biol 2014;10:e1003572.
    • (2014) PLoS Comput Biol , vol.10
    • Zelezniak, A.1    Sheridan, S.2    Patil, K.R.3
  • 121
    • 84859633048 scopus 로고    scopus 로고
    • Design of a dynamic sensorregulator system for production of chemicals and fuels derived from fatty acids
    • Zhang F, Carothers JM, Keasling JD. Design of a dynamic sensorregulator system for production of chemicals and fuels derived from fatty acids. Nat Biotechnol 2012;30:354-9.
    • (2012) Nat Biotechnol , vol.30 , pp. 354-359
    • Zhang, F.1    Carothers, J.M.2    Keasling, J.D.3
  • 122
    • 84891711763 scopus 로고    scopus 로고
    • The yeast AMPK homolog SNF1 regulates acetyl coenzyme A homeostasis and histone acetylation
    • Zhang M, Galdieri L, Vancura A. The yeast AMPK homolog SNF1 regulates acetyl coenzyme A homeostasis and histone acetylation. Mol Cell Biol 2013;33:4701-17.
    • (2013) Mol Cell Biol , vol.33 , pp. 4701-4717
    • Zhang, M.1    Galdieri, L.2    Vancura, A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.