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Volumn 1152, Issue , 2014, Pages 281-294

Model-guided identifi cation of gene deletion targets for metabolic engineering in saccharomyces cerevisiae

Author keywords

Flux balance analysis; Genome scale metabolic reconstructions; Metabolic engineering; Minimization of metabolic adjustment; Minimization of metabolite balance; OptGene

Indexed keywords

SESQUITERPENE; VANILLIN;

EID: 84907832819     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-0563-8_17     Document Type: Article
Times cited : (2)

References (43)
  • 1
    • 75149129569 scopus 로고    scopus 로고
    • A protocol for generating a high-quality genome-scale metabolic reconstruction
    • Thiele I, Palsson BØ (2010) A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc 5:93–121
    • (2010) Nat Protoc , vol.5 , pp. 93-121
    • Thiele, I.1    Palsson, B.2
  • 2
    • 77951612556 scopus 로고    scopus 로고
    • BiGG, a biochemical genetic and genomic knowledgebase of large scale metabolic reconstructions
    • Schellenberger J, Park JO, Conrad TM, Palsson BØ (2010) BiGG, a biochemical genetic and genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinformatics 11:213
    • (2010) BMC Bioinformatics , vol.11 , pp. 213
    • Schellenberger, J.1    Park, J.O.2    Conrad, T.M.3    Palsson, B.4
  • 3
    • 73149122136 scopus 로고    scopus 로고
    • Applications of genome-scale metabolic reconstructions
    • Oberhardt MA, Palsson BØ, Papin JA (2009) Applications of genome-scale metabolic reconstructions. Mol Syst Biol 5:320
    • (2009) Mol Syst Biol , vol.5 , pp. 320
    • Oberhardt, M.A.1    Palsson, B.2    Papin, J.A.3
  • 4
    • 73149091660 scopus 로고    scopus 로고
    • Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator
    • Usaite R, Jewett MC, Oliveira AP et al (2009) Reconstruction of the yeast Snf1 kinase regulatory network reveals its role as a global energy regulator. Mol Syst Biol 5:319
    • (2009) Mol Syst Biol , vol.5 , pp. 319
    • Usaite, R.1    Jewett, M.C.2    Oliveira, A.P.3
  • 5
    • 14544268137 scopus 로고    scopus 로고
    • Uncovering transcriptional regulation of metabolism by using metabolic network topology
    • Patil KR, Nielsen J (2005) Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proc Natl Acad Sci U S A 102:2685–2689
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 2685-2689
    • Patil, K.R.1    Nielsen, J.2
  • 6
    • 2342648924 scopus 로고    scopus 로고
    • Integrating high-throughput and computational data elucidates bacterial networks
    • Covert MW, Knight EM, Reed JL et al (2004) Integrating high-throughput and computational data elucidates bacterial networks. Nature 429:92–96
    • (2004) Nature , vol.429 , pp. 92-96
    • Covert, M.W.1    Knight, E.M.2    Reed, J.L.3
  • 7
    • 84864795465 scopus 로고    scopus 로고
    • Recent advances in reconstruction and applications of genome-scale metabolic models
    • Kim TY, Sohn SB, Kim YB et al (2011) Recent advances in reconstruction and applications of genome-scale metabolic models. Curr Opin Biotechnol 23:1–7
    • (2011) Curr Opin Biotechnol , vol.23 , pp. 1-7
    • Kim, T.Y.1    Sohn, S.B.2    Kim, Y.B.3
  • 8
    • 84864932596 scopus 로고    scopus 로고
    • Fifteen years of large scale metabolic modeling of yeast, developments and impacts
    • Osterlund T, Nookaew I, Nielsen J (2011) Fifteen years of large scale metabolic modeling of yeast, developments and impacts. Biotechnol Adv 30:979–988
    • (2011) Biotechnol Adv , vol.30 , pp. 979-988
    • Osterlund, T.1    Nookaew, I.2    Nielsen, J.3
  • 10
    • 84864186953 scopus 로고    scopus 로고
    • Metabolic engineering of Saccharomyces cerevisiae, a key cell factory platform for future biorefi neries
    • Hong K-K, Nielsen J (2012) Metabolic engineering of Saccharomyces cerevisiae, a key cell factory platform for future biorefi neries. Cell Mol Life Sci 69:2671–2690
    • (2012) Cell Mol Life Sci , vol.69 , pp. 2671-2690
    • Hong, K.-K.1    Nielsen, J.2
  • 11
    • 1242283921 scopus 로고    scopus 로고
    • Use of genome-scale microbial models for metabolic engineering
    • Patil KR, Akesson M, Nielsen J (2004) Use of genome-scale microbial models for metabolic engineering. Curr Opin Biotechnol 15:64–69
    • (2004) Curr Opin Biotechnol , vol.15 , pp. 64-69
    • Patil, K.R.1    Akesson, M.2    Nielsen, J.3
  • 12
    • 0025895183 scopus 로고
    • Toward a science of metabolic engineering
    • Bailey JE (1991) Toward a science of metabolic engineering. Science 252:1668–1675
    • (1991) Science , vol.252 , pp. 1668-1675
    • Bailey, J.E.1
  • 13
    • 0027716622 scopus 로고
    • Metabolic capabilities of Escherichia coli. I. Synthesis of biosynthetic precursors and cofactors
    • Varma A, Palsson BØ (1993) Metabolic capabilities of Escherichia coli. I. Synthesis of biosynthetic precursors and cofactors. J Theor Biol 165:477–502
    • (1993) J Theor Biol , vol.165 , pp. 477-502
    • Varma, A.1    Palsson, B.2
  • 14
    • 0028108519 scopus 로고
    • Metabolic fl ux balancing, basic concepts scientifi c and practical use
    • Varma A, Palsson BØ (1994) Metabolic fl ux balancing, basic concepts scientifi c and practical use. Nat Biotechnol 12:994–998
    • (1994) Nat Biotechnol , vol.12 , pp. 994-998
    • Varma, A.1    Palsson, B.2
  • 16
    • 0035125986 scopus 로고    scopus 로고
    • In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data
    • Edwards JS, Ibarra RU, Palsson BØ (2001) In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol 19:125–130
    • (2001) Nat Biotechnol , vol.19 , pp. 125-130
    • Edwards, J.S.1    Ibarra, R.U.2    Palsson, B.3
  • 17
    • 0344824417 scopus 로고    scopus 로고
    • Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network
    • Famili I, Förster J, Nielsen J, Palsson BØ (2003) Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network. Proc Natl Acad Sci U S A 100: 13134–13139
    • (2003) Proc Natl Acad Sci U S A , vol.100 , pp. 13134-13139
    • Famili, I.1    Förster, J.2    Nielsen, J.3    Palsson, B.4
  • 19
    • 30044437327 scopus 로고    scopus 로고
    • Evolutionary programming as a platform for in silico metabolic engineering
    • Patil KR, Rocha I, Förster J, Nielsen J (2005) Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinformatics 6:308
    • (2005) BMC Bioinformatics , vol.6 , pp. 308
    • Patil, K.R.1    Rocha, I.2    Förster, J.3    Nielsen, J.4
  • 20
    • 0242487787 scopus 로고    scopus 로고
    • Optknock, a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
    • Burgard AP, Pharkya P, Maranas CD (2003) Optknock, a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng 84:647–657
    • (2003) Biotechnol Bioeng , vol.84 , pp. 647-657
    • Burgard, A.P.1    Pharkya, P.2    Maranas, C.D.3
  • 21
    • 70449592325 scopus 로고    scopus 로고
    • Enhancing sesquiterpene production in Saccha romyces cerevisiae through in silico driven metabolic engineering
    • Asadollahi M, Maury J, Patil KR et al (2009) Enhancing sesquiterpene production in Saccha romyces cerevisiae through in silico driven metabolic engineering. Metab Eng 11: 328–334
    • (2009) Metab Eng , vol.11 , pp. 328-334
    • Asadollahi, M.1    Maury, J.2    Patil, K.R.3
  • 22
    • 78049460641 scopus 로고    scopus 로고
    • Improved vanillin production in baker’s yeast through in silico design
    • Brochado AR, Matos C, Møller BL et al (2010) Improved vanillin production in baker’s yeast through in silico design. Microb Cell Fact 9:84
    • (2010) Microb Cell Fact , vol.9 , pp. 84
    • Brochado, A.R.1    Matos, C.2    Møller, B.L.3
  • 23
    • 0037313750 scopus 로고    scopus 로고
    • Genomescale reconstruction of the Saccharomyces cerevisiae metabolic network
    • Förster J, Famili I, Fu P et al (2003) Genomescale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res 13: 244–253
    • (2003) Genome Res , vol.13 , pp. 244-253
    • Förster, J.1    Famili, I.2    Fu, P.3
  • 24
    • 25844463806 scopus 로고    scopus 로고
    • Metabolic functions of duplicate genes in Saccharomyces cerevisiae
    • Kuepfer L, Sauer U, Blank LM (2005) Metabolic functions of duplicate genes in Saccharomyces cerevisiae. Genome Res 15:1421–1430
    • (2005) Genome Res , vol.15 , pp. 1421-1430
    • Kuepfer, L.1    Sauer, U.2    Blank, L.M.3
  • 25
    • 65649126379 scopus 로고    scopus 로고
    • Connecting extracellular metabolomic measurements to intracellular fl ux states in yeast
    • Mo ML, Palsson BØ, Herrgård MJ (2009) Connecting extracellular metabolomic measurements to intracellular fl ux states in yeast. BMC Syst Biol 3:37
    • (2009) BMC Syst Biol , vol.3 , pp. 37
    • Mo, M.L.1    Palsson, B.2    Herrgård, M.J.3
  • 26
    • 78650595350 scopus 로고    scopus 로고
    • Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data
    • Zomorrodi AR, Maranas CD (2010) Improving the iMM904 S. cerevisiae metabolic model using essentiality and synthetic lethality data. BMC Syst Biol 4:178
    • (2010) BMC Syst Biol , vol.4 , pp. 178
    • Zomorrodi, A.R.1    Maranas, C.D.2
  • 27
    • 84861744439 scopus 로고    scopus 로고
    • Yeast 5—an expanded reconstruction of the Saccharomyces cerevisiae metabolic network
    • Heavner BD, Smallbone K, Barker B et al (2012) Yeast 5—an expanded reconstruction of the Saccharomyces cerevisiae metabolic network. BMC Syst Biol 6:55
    • (2012) BMC Syst Biol , vol.6 , pp. 55
    • Heavner, B.D.1    Smallbone, K.2    Barker, B.3
  • 28
    • 34547676311 scopus 로고    scopus 로고
    • Optimization based automated curation of metabolic reconstructions
    • Kumar VS, Dasika MS, Maranas CD (2007) Optimization based automated curation of metabolic reconstructions. BMC Bioinformatics 8:212
    • (2007) BMC Bioinformatics , vol.8 , pp. 212
    • Kumar, V.S.1    Dasika, M.S.2    Maranas, C.D.3
  • 29
    • 63549108441 scopus 로고    scopus 로고
    • GrowMatch, an automated method for reconciling in silico/ in vivo growth predictions
    • Kumar VS, Maranas CD (2009) GrowMatch, an automated method for reconciling in silico/ in vivo growth predictions. PLoS Comput Biol 5:e1000308
    • (2009) PLoS Comput Biol , vol.e1000308 , pp. 5
    • Kumar, V.S.1    Maranas, C.D.2
  • 30
    • 0021750019 scopus 로고
    • Saccharomyces cerevisiae does not accumulate ethanol against concentration gradient
    • Guijarro JM, Lagunas R (1984) Saccharomyces cerevisiae does not accumulate ethanol against concentration gradient. J Bacteriol 160: 874–878
    • (1984) J Bacteriol , vol.160 , pp. 874-878
    • Guijarro, J.M.1    Lagunas, R.2
  • 31
    • 0037079023 scopus 로고    scopus 로고
    • Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth
    • Ibarra RU, Edwards JS, Palsson BØ (2002) Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420:20–23
    • (2002) Nature , vol.420 , pp. 20-23
    • Ibarra, R.U.1    Edwards, J.S.2    Palsson, B.3
  • 32
    • 0037069467 scopus 로고    scopus 로고
    • Analysis of optimality in natural and perturbed metabolic networks
    • Segrè D, Vitkup D, Church GM (2002) Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci U S A 99:15112–15117
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 15112-15117
    • Segrè, D.1    Vitkup, D.2    Church, G.M.3
  • 33
    • 19644386033 scopus 로고    scopus 로고
    • Regulatory on/off minimization of metabolic fl ux changes after genetic perturbations
    • Shlomi T, Berkman O, Ruppin E (2005) Regulatory on/off minimization of metabolic fl ux changes after genetic perturbations. Proc Natl Acad Sci U S A 102:7695–7700
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 7695-7700
    • Shlomi, T.1    Berkman, O.2    Ruppin, E.3
  • 34
    • 84870676608 scopus 로고    scopus 로고
    • Impact of stoichiometry representation on simulation of genotype-phenotype relationships in metabolic networks
    • Brochado AR, Andrejev S, Maranas CD, Patil KR (2012) Impact of stoichiometry representation on simulation of genotype-phenotype relationships in metabolic networks. PLoS Comput Biol 8:e1002758
    • (2012) PLoS Comput Biol , vol.8 , pp. e1002758
    • Brochado, A.R.1    Andrejev, S.2    Maranas, C.D.3    Patil, K.R.4
  • 35
    • 34447523907 scopus 로고    scopus 로고
    • Systematic evaluation of objective functions for predicting intracellular fl uxes in Escherichia coli
    • Schuetz R, Kuepfer L, Sauer U (2007) Systematic evaluation of objective functions for predicting intracellular fl uxes in Escherichia coli. Mol Syst Biol 3:119
    • (2007) Mol Syst Biol , vol.3 , pp. 119
    • Schuetz, R.1    Kuepfer, L.2    Sauer, U.3
  • 36
    • 33846061120 scopus 로고    scopus 로고
    • Metabolic networks in motion, 13C-based fl ux analysis
    • Sauer U (2006) Metabolic networks in motion, 13C-based fl ux analysis. Mol Syst Biol 2:62
    • (2006) Mol Syst Biol , vol.2 , pp. 62
    • Sauer, U.1
  • 37
    • 84866128045 scopus 로고    scopus 로고
    • Shrinking the metabolic solution space using experimental datasets
    • Reed JL (2012) Shrinking the metabolic solution space using experimental datasets. PLoS Comput Biol 8:e1002662
    • (2012) PLoS Comput Biol , vol.8 , pp. e1002662
    • Reed, J.L.1
  • 38
    • 1642457253 scopus 로고    scopus 로고
    • The effects of alternate optimal solutions in constraintbased genome-scale metabolic models
    • Mahadevan R, Schilling CH (2003) The effects of alternate optimal solutions in constraintbased genome-scale metabolic models. Metab Eng 5:264–276
    • (2003) Metab Eng , vol.5 , pp. 264-276
    • Mahadevan, R.1    Schilling, C.H.2
  • 39
    • 77950960250 scopus 로고    scopus 로고
    • OptFlux, an open-source software platform for in silico metabolic engineering
    • Rocha I, Maia P, Evangelista P et al (2010) OptFlux, an open-source software platform for in silico metabolic engineering. BMC Syst Biol 4:45
    • (2010) BMC Syst Biol , vol.4 , pp. 45
    • Rocha, I.1    Maia, P.2    Evangelista, P.3
  • 40
    • 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 (2011) Quantitative prediction of cellular metabolism with constraint-based models, the COBRA Toolbox v2. 0. Nat Protoc 6: 1290–1307
    • (2011) Nat Protoc , vol.6 , pp. 1290-1307
    • Schellenberger, J.1    Que, R.2    Fleming, R.M.T.3
  • 42
    • 77949495880 scopus 로고    scopus 로고
    • Predicting metabolic engineering knockout strategies for chemical production, accounting for competing pathways
    • Tepper N, Shlomi T (2010) Predicting metabolic engineering knockout strategies for chemical production, accounting for competing pathways. Bioinformatics 26:536–543
    • (2010) Bioinformatics , vol.26 , pp. 536-543
    • Tepper, N.1    Shlomi, T.2
  • 43
    • 77950863401 scopus 로고    scopus 로고
    • Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli
    • Feist AM, Zielinski CD, Orth JD et al (2010) Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli. Metab Eng 12: 173–186
    • (2010) Metab Eng , vol.12 , pp. 173-186
    • Feist, A.M.1    Zielinski, C.D.2    Orth, J.D.3


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