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Volumn 25, Issue 13, 2009, Pages 1702-1708

Genetic modification of flux for flux prediction of mutants

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIUM MUTANT; CORYNEBACTERIUM GLUTAMICUM; DNA MODIFICATION; ENZYME REGULATION; ESCHERICHIA COLI; GENE DELETION; GENE EXPRESSION PROFILING; GENE FUNCTION; GENE OVEREXPRESSION; GENETIC ALGORITHM; METABOLIC REGULATION; NONHUMAN; PHENOTYPE; PREDICTION; PRIORITY JOURNAL;

EID: 67649218402     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp298     Document Type: Article
Times cited : (19)

References (45)
  • 1
    • 6044265058 scopus 로고    scopus 로고
    • Integration of gene expression data into genome-scale metabolic models
    • Akesson,M. et al. (2004) Integration of gene expression data into genome-scale metabolic models. Metab. Eng., 6, 285-293.
    • (2004) Metab. Eng , vol.6 , pp. 285-293
    • Akesson, M.1
  • 2
    • 38049001166 scopus 로고    scopus 로고
    • Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels
    • Atsumi,S. et al. (2008) Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature, 451, 86-89.
    • (2008) Nature , vol.451 , pp. 86-89
    • Atsumi, S.1
  • 3
    • 27744506402 scopus 로고    scopus 로고
    • Amplified expression of fructose 1,6-bisphosphatase in Corynebacterium glutamicum increases in vivo flux through the pentose phosphate pathway and lysine production on different carbon sources
    • Becker,J. et al. (2005) Amplified expression of fructose 1,6-bisphosphatase in Corynebacterium glutamicum increases in vivo flux through the pentose phosphate pathway and lysine production on different carbon sources. Appl. Environ. Microbiol., 71, 8587-8596.
    • (2005) Appl. Environ. Microbiol , vol.71 , pp. 8587-8596
    • Becker, J.1
  • 4
    • 35348981360 scopus 로고    scopus 로고
    • Metabolic flux engineering of L-lysine production in Corynebacterium glutamicum - over expression and modification of G6P dehydrogenase
    • Becker,J. et al. (2007) Metabolic flux engineering of L-lysine production in Corynebacterium glutamicum - over expression and modification of G6P dehydrogenase. J. Biotechnol., 132, 99-109.
    • (2007) J. Biotechnol , vol.132 , pp. 99-109
    • Becker, J.1
  • 5
    • 2342419140 scopus 로고    scopus 로고
    • Metabolic pathway analysis of yeast strengthens the bridge between transcriptornics and metabolic networks
    • Çakir,T. et al. (2004a) Metabolic pathway analysis of yeast strengthens the bridge between transcriptornics and metabolic networks. Biotechnol. Bioeng., 86, 251-260.
    • (2004) Biotechnol. Bioeng , vol.86 , pp. 251-260
    • Çakir, T.1
  • 6
    • 8844231118 scopus 로고    scopus 로고
    • Metabolic pathway analysis of enzyme-deficient human red blood cells
    • Çakir,T. et al. (2004b) Metabolic pathway analysis of enzyme-deficient human red blood cells. Biosystems, 78, 49-67.
    • (2004) Biosystems , vol.78 , pp. 49-67
    • Çakir, T.1
  • 7
    • 38149142675 scopus 로고    scopus 로고
    • Effect of carbon source perturbations on transcriptional regulation of metabolic fluxes in Saccharomyces cerevisiae
    • Çakir,T. et al. (2007) Effect of carbon source perturbations on transcriptional regulation of metabolic fluxes in Saccharomyces cerevisiae. BMC Syst. Biol., 1, 18.
    • (2007) BMC Syst. Biol , vol.1 , pp. 18
    • Çakir, T.1
  • 8
    • 2342648924 scopus 로고    scopus 로고
    • Integrating high-throughput and computational data elucidates bacterial networks
    • Covert,M.W. 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
  • 9
    • 20044375201 scopus 로고    scopus 로고
    • Large-scale in vivo flux analysis shows rigidity and suboptimal performance of Bacillus subtilis metabolism
    • Fischer,E. and Sauer,U. (2005) Large-scale in vivo flux analysis shows rigidity and suboptimal performance of Bacillus subtilis metabolism. Nat. Genet., 37, 636-640.
    • (2005) Nat. Genet , vol.37 , pp. 636-640
    • Fischer, E.1    Sauer, U.2
  • 10
    • 0037200931 scopus 로고    scopus 로고
    • A functional genomics approach using metabolomics and in silico pathway analysis
    • Förster,J. et al. (2002) A functional genomics approach using metabolomics and in silico pathway analysis. Biotechnol. Bioeng., 79, 703-712.
    • (2002) Biotechnol. Bioeng , vol.79 , pp. 703-712
    • Förster, J.1
  • 11
    • 33750331573 scopus 로고    scopus 로고
    • Analysis of optimal phenotypic space using elementary modes as applied to Corynebacterium glutamicum
    • Gayen,K. and Venkatesh,K.V. (2006) Analysis of optimal phenotypic space using elementary modes as applied to Corynebacterium glutamicum. BMC Bioinformatics, 7, 445.
    • (2006) BMC Bioinformatics , vol.7 , pp. 445
    • Gayen, K.1    Venkatesh, K.V.2
  • 12
    • 0015989446 scopus 로고
    • A linear steady state treatment of enzymatic chains. General properties, control and effector strength
    • Heinrich,R. and Rapoport,T.A. (1974) A linear steady state treatment of enzymatic chains. General properties, control and effector strength. Eur. J. Biochem., 42, 89-95.
    • (1974) Eur. J. Biochem , vol.42 , pp. 89-95
    • Heinrich, R.1    Rapoport, T.A.2
  • 13
    • 0345529074 scopus 로고    scopus 로고
    • Responses of the central metabolism in Escherichia coli to phosphoglucose isomerase and glucose-6-phosphate dehydrogenase knockouts
    • Hua,Q. et al. (2003) Responses of the central metabolism in Escherichia coli to phosphoglucose isomerase and glucose-6-phosphate dehydrogenase knockouts. J. Bacteriol., 185, 7053-7067.
    • (2003) J. Bacteriol , vol.185 , pp. 7053-7067
    • Hua, Q.1
  • 14
    • 0035805255 scopus 로고    scopus 로고
    • Integrated genomic and proteomic analyses of a systematically perturbed metabolic network
    • Ideker,T. et al. (2001) Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science, 292 929-934.
    • (2001) Science , vol.292 , pp. 929-934
    • Ideker, T.1
  • 15
    • 34247612307 scopus 로고    scopus 로고
    • Multiple high-throughput analyses monitor the response of E. coli to perturbations
    • Ishii,N. et al. (2007) Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science, 316 593-597.
    • (2007) Science , vol.316 , pp. 593-597
    • Ishii, N.1
  • 16
    • 33644527950 scopus 로고    scopus 로고
    • The model organism as a system: Integrating 'omics' data sets
    • Joyce,A.R. and Palsson,B.O. (2006) The model organism as a system: integrating 'omics' data sets. Nat. Rev. Mol. Cell. Biol., 7 198-210.
    • (2006) Nat. Rev. Mol. Cell. Biol , vol.7 , pp. 198-210
    • Joyce, A.R.1    Palsson, B.O.2
  • 17
    • 0142122303 scopus 로고    scopus 로고
    • Advances in flux balance analysis
    • Kauffman,K.J. et al. (2003) Advances in flux balance analysis. Curr. Opin. Biotechnol., 14, 491-496.
    • (2003) Curr. Opin. Biotechnol , vol.14 , pp. 491-496
    • Kauffman, K.J.1
  • 18
    • 58249089508 scopus 로고    scopus 로고
    • In silico genome-scale reconstruction and validation of the Corynebacterium glutamicum metabolic network
    • Kjeldsen,K.R. and Nielsen,J. (2009) In silico genome-scale reconstruction and validation of the Corynebacterium glutamicum metabolic network. Biotechnol. Bioeng., 102, 583-597.
    • (2009) Biotechnol. Bioeng , vol.102 , pp. 583-597
    • Kjeldsen, K.R.1    Nielsen, J.2
  • 19
    • 34447551397 scopus 로고    scopus 로고
    • Klamt,S. et al. (2007) Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Syst. Biol., 1, 2.
    • Klamt,S. et al. (2007) Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Syst. Biol., 1, 2.
  • 20
    • 0242380634 scopus 로고    scopus 로고
    • CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle
    • Kurata,H. et al. (2003) CADLIVE for constructing a large-scale biochemical network based on a simulation-directed notation and its application to yeast cell cycle. Nucleic Acids Res. 2003, 31 4071-4084.
    • (2003) Nucleic Acids Res , vol.2003 , Issue.31 , pp. 4071-4084
    • Kurata, H.1
  • 21
    • 36749043657 scopus 로고    scopus 로고
    • Extended CADLIVE: A novel graphical notation for design of biochemical network maps and computational pathway analysis
    • Kurata,H. et al. (2007a) Extended CADLIVE: A novel graphical notation for design of biochemical network maps and computational pathway analysis. Nucleic Acids Res., 35, e134.
    • (2007) Nucleic Acids Res , vol.35
    • Kurata, H.1
  • 22
    • 34548546603 scopus 로고    scopus 로고
    • Kurata,H. et al. (2007b) Integration of enzyme activities into metabolic flux distributions by elementary mode analysis. BMC Syst. Biol., 1, 31.
    • Kurata,H. et al. (2007b) Integration of enzyme activities into metabolic flux distributions by elementary mode analysis. BMC Syst. Biol., 1, 31.
  • 23
    • 20644467467 scopus 로고    scopus 로고
    • Systems biotechnology for strain improvement
    • Lee,S.Y. et al. (2005) Systems biotechnology for strain improvement. Trends Biotechnol., 23, 349358.
    • (2005) Trends Biotechnol , vol.23 , pp. 349358
    • Lee, S.Y.1
  • 24
    • 34548623183 scopus 로고    scopus 로고
    • Response of the central metabolism of Escherichia coli to modified expression of the gene encoding the glucose-6-phosphate dehydrogenase
    • Nicolas,C. et al. (2007) Response of the central metabolism of Escherichia coli to modified expression of the gene encoding the glucose-6-phosphate dehydrogenase. FEBS Lett., 581, 3771-3776.
    • (2007) FEBS Lett , vol.581 , pp. 3771-3776
    • Nicolas, C.1
  • 25
    • 38349066180 scopus 로고    scopus 로고
    • Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli
    • Nishio,Y. et al. (2008) Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli. Mol. Syst. Biol., 4, 160.
    • (2008) Mol. Syst. Biol , vol.4 , pp. 160
    • Nishio, Y.1
  • 26
    • 11144261828 scopus 로고    scopus 로고
    • A novel gnd mutation leading to increased L-lysine production in Corynebacterium glutamicum
    • Ohnishi,J. et al. (2005) A novel gnd mutation leading to increased L-lysine production in Corynebacterium glutamicum. FEMS Microbiol. Lett., 242, 265-274.
    • (2005) FEMS Microbiol. Lett , vol.242 , pp. 265-274
    • Ohnishi, J.1
  • 27
    • 34249934691 scopus 로고    scopus 로고
    • Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation
    • Park,J.H. et al. (2007) Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation. Proc. Natl Acad. Sci. USA, 104, 7797-7802.
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 7797-7802
    • Park, J.H.1
  • 28
    • 2442707990 scopus 로고    scopus 로고
    • Metabolic flux analysis for a ppc mutant Escherichia coli based on C-13-labelling experiments together with enzyme activity assays and intracellular metabolite measurements
    • Peng,L.F. et al. (2004) Metabolic flux analysis for a ppc mutant Escherichia coli based on C-13-labelling experiments together with enzyme activity assays and intracellular metabolite measurements. FEMS Microbiol. Lett., 235, 17-23.
    • (2004) FEMS Microbiol. Lett , vol.235 , pp. 17-23
    • Peng, L.F.1
  • 29
    • 0036330798 scopus 로고    scopus 로고
    • Genome-scale metabolic model of Helicobacter pylori 26695
    • Schilling,C.H. et al. (2002) Genome-scale metabolic model of Helicobacter pylori 26695. J. Bacteriol., 184, 4582-4593.
    • (2002) J. Bacteriol , vol.184 , pp. 4582-4593
    • Schilling, C.H.1
  • 30
    • 34447523907 scopus 로고    scopus 로고
    • Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
    • Schuetz,R. et al. (2007) Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Mol. Syst. Biol., 3, 119.
    • (2007) Mol. Syst. Biol , vol.3 , pp. 119
    • Schuetz, R.1
  • 31
    • 0033080396 scopus 로고    scopus 로고
    • Detection of elementary flux modes in biochemical networks: A promising tool for pathway analysis and metabolic engineering
    • Schuster,S. et al. (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
  • 32
    • 0034064689 scopus 로고    scopus 로고
    • A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks
    • Schuster,S. et al. (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
  • 33
    • 43449132092 scopus 로고    scopus 로고
    • Is maximization of molar yield in metabolic networks favoured by evolution?
    • Schuster,S. et al. (2008) Is maximization of molar yield in metabolic networks favoured by evolution? J. Theor. Biol., 252 497-504.
    • (2008) J. Theor. Biol , vol.252 , pp. 497-504
    • Schuster, S.1
  • 34
    • 27544434362 scopus 로고    scopus 로고
    • A quadratic programming approach for decomposing steady-state metabolic flux distributions onto elementary modes
    • Schwartz,J.M. and Kanehisa,M. (2005) A quadratic programming approach for decomposing steady-state metabolic flux distributions onto elementary modes. Bioinformatics, 21 (Suppl 2), ii204-ii205.
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 2
    • Schwartz, J.M.1    Kanehisa, M.2
  • 35
    • 33746083686 scopus 로고    scopus 로고
    • Quantitative elementary mode analysis of metabolic pathways: The example of yeast glycolysis
    • Schwartz,J.M. and Kanehisa,M. (2006) Quantitative elementary mode analysis of metabolic pathways: The example of yeast glycolysis. BMC Bioinformatics, 7, 186.
    • (2006) BMC Bioinformatics , vol.7 , pp. 186
    • Schwartz, J.M.1    Kanehisa, M.2
  • 36
    • 0037069467 scopus 로고    scopus 로고
    • Analysis of optimality in natural and perturbed metabolic networks
    • Segrè,D. et al. (2002) Analysis of optimality in natural and perturbed metabolic networks. Proc. Natl Acad. Sci. USA, 99, 15112-15117.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 15112-15117
    • Segrè, D.1
  • 37
    • 19644386033 scopus 로고    scopus 로고
    • Regulatory on/off minimization of metabolic flux changes after genetic perturbations
    • Shlomi,T. et al. (2005) Regulatory on/off minimization of metabolic flux changes after genetic perturbations. Proc. Natl Acad. Sci. USA, 102, 7695-7700.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 7695-7700
    • Shlomi, T.1
  • 38
    • 2442675518 scopus 로고    scopus 로고
    • Effect of a pyruvate kinase (pyk -gene) knockout mutation on the control of gene expression and metabolic fluxes in Escherichia coli
    • Siddiquee,K.A. et al. (2004) Effect of a pyruvate kinase (pyk -gene) knockout mutation on the control of gene expression and metabolic fluxes in Escherichia coli. FEMS Microbiol. Lett., 235, 25-33.
    • (2004) FEMS Microbiol. Lett , vol.235 , pp. 25-33
    • Siddiquee, K.A.1
  • 39
    • 0027513359 scopus 로고
    • Responses of metabolic systems to large changes in enzyme activities and effectors. 1. The linear treatment of unbranched chains
    • Small,J.R. and Kacser,H. (1993) Responses of metabolic systems to large changes in enzyme activities and effectors. 1. The linear treatment of unbranched chains. Eur. J. Biochem., 213, 613-624.
    • (1993) Eur. J. Biochem , vol.213 , pp. 613-624
    • Small, J.R.1    Kacser, H.2
  • 40
    • 0037079050 scopus 로고    scopus 로고
    • Metabolic network structure determines key aspects of functionality and regulation
    • Stelling,J. et al. (2002) Metabolic network structure determines key aspects of functionality and regulation. Nature, 420, 190-193.
    • (2002) Nature , vol.420 , pp. 190-193
    • Stelling, J.1
  • 41
    • 33846950348 scopus 로고    scopus 로고
    • Challenges in engineering microbes for biofuels production
    • Stephanopoulos,G. (2007) Challenges in engineering microbes for biofuels production. Science, 315, 801-804.
    • (2007) Science , vol.315 , pp. 801-804
    • Stephanopoulos, G.1
  • 42
    • 0031746509 scopus 로고    scopus 로고
    • Effects of pyruvate decarboxylase overproduction on flux distribution at the pyruvate branch point in Saccharomyces cerevisiae
    • van Hoek,P. et al. (1998) Effects of pyruvate decarboxylase overproduction on flux distribution at the pyruvate branch point in Saccharomyces cerevisiae. Appl. Environ. Microbiol., 64, 2133-2140.
    • (1998) Appl. Environ. Microbiol , vol.64 , pp. 2133-2140
    • van Hoek, P.1
  • 43
    • 2342427580 scopus 로고    scopus 로고
    • Using metabolic flux data to further constrain the metabolic solution space and predict internal flux patterns: The Escherichia coli spectrum
    • Wiback,S.J. et al. (2004) Using metabolic flux data to further constrain the metabolic solution space and predict internal flux patterns: The Escherichia coli spectrum. Biotechnol. Bioeng. 86, 317-331.
    • (2004) Biotechnol. Bioeng , vol.86 , pp. 317-331
    • Wiback, S.J.1
  • 44
    • 58149279036 scopus 로고    scopus 로고
    • Maximum entropy decomposition of flux distribution at steady state to elementary modes
    • Zhao,Q. and Kurata,H. (2009) Maximum entropy decomposition of flux distribution at steady state to elementary modes. J. Biosci. Bioeng. 107, 84-89.
    • (2009) J. Biosci. Bioeng , vol.107 , pp. 84-89
    • Zhao, Q.1    Kurata, H.2
  • 45
    • 1642294491 scopus 로고    scopus 로고
    • Global metabolic response of Escherichia coli to gnd or zwf gene-knockout, based on C-13-labeling experiments and the measurement of enzyme activities
    • Zhao,J. et al. (2004) Global metabolic response of Escherichia coli to gnd or zwf gene-knockout, based on C-13-labeling experiments and the measurement of enzyme activities. Appl. Microbiol. Biotechnol., 64, 91-98.
    • (2004) Appl. Microbiol. Biotechnol , vol.64 , pp. 91-98
    • Zhao, J.1


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