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Volumn 8, Issue 5, 2013, Pages 595-604

Constraint-based strain design using continuous modifications (CosMos) of flux bounds finds new strategies for metabolic engineering

Author keywords

Constraint based modeling; Enzyme expression; Flux balance analysis; OptKnock; Strain design

Indexed keywords

CHEMICAL MODIFICATION; ESCHERICHIA COLI; METABOLISM; PRODUCT DESIGN; YEAST;

EID: 84877118199     PISSN: 18606768     EISSN: 18607314     Source Type: Journal    
DOI: 10.1002/biot.201200316     Document Type: Article
Times cited : (37)

References (27)
  • 1
    • 70449592325 scopus 로고    scopus 로고
    • Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering.
    • Asadollahi, M. A., Maury, J., Patil, K. R., Schalk, M. et al., Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering. Metab. Eng. 2009, 11, 328-334.
    • (2009) Metab. Eng. , vol.11 , pp. 328-334
    • Asadollahi, M.A.1    Maury, J.2    Patil, K.R.3    Schalk, M.4
  • 2
    • 0242487787 scopus 로고    scopus 로고
    • Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization.
    • Burgard, A. P., Pharkya, P., Maranas, C. D., Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol. Bioeng. 2003, 84, 647-657.
    • (2003) Biotechnol. Bioeng. , vol.84 , pp. 647-657
    • Burgard, A.P.1    Pharkya, P.2    Maranas, C.D.3
  • 3
    • 77951552860 scopus 로고    scopus 로고
    • OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains.
    • Kim, J., Reed, J. L., OptORF: Optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains. BMC Syst. Biol. 2010, 4, 53.
    • (2010) BMC Syst. Biol. , vol.4 , pp. 53
    • Kim, J.1    Reed, J.L.2
  • 4
    • 80052573483 scopus 로고    scopus 로고
    • Large-scale bi-level strain design approaches and mixed-integer programming solution techniques.
    • Kim, J., Reed, J. L., Maravelias, C. T., Large-scale bi-level strain design approaches and mixed-integer programming solution techniques. PloS ONE 2011, 6, e24162.
    • (2011) PloS ONE , vol.6
    • Kim, J.1    Reed, J.L.2    Maravelias, C.T.3
  • 5
    • 29544436058 scopus 로고    scopus 로고
    • An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems.
    • Pharkya, P., Maranas, C. D., An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems. Metab. Eng. 2006, 8, 1-13.
    • (2006) Metab. Eng. , vol.8 , pp. 1-13
    • Pharkya, P.1    Maranas, C.D.2
  • 6
    • 77954590959 scopus 로고    scopus 로고
    • OptForce: An optimization procedure for identifying all genetic manipulations leading to targeted overproductions.
    • Ranganathan, S., Suthers, P. F., Maranas, C. D., OptForce: An optimization procedure for identifying all genetic manipulations leading to targeted overproductions. PLoS Comput. Biol 2010, 6, e1000744.
    • (2010) PLoS Comput. Biol , vol.6
    • Ranganathan, S.1    Suthers, P.F.2    Maranas, C.D.3
  • 7
    • 77950960250 scopus 로고    scopus 로고
    • OptFlux: An open-source software platform for in silico metabolic engineering.
    • Rocha, I., Maia, P., Evangelista, P., Vilaca, P. et al., OptFlux: An open-source software platform for in silico metabolic engineering. BMC Syst. Biol. 2010, 4, 45.
    • (2010) BMC Syst. Biol. , vol.4 , pp. 45
    • Rocha, I.1    Maia, P.2    Evangelista, P.3    Vilaca, P.4
  • 8
    • 8744224466 scopus 로고    scopus 로고
    • OptStrain: A computational framework for redesign of microbial production systems.
    • Pharkya, P., Burgard, A. P., Maranas, C. D., OptStrain: A computational framework for redesign of microbial production systems. Genome Res. 2004, 14, 2367-2376.
    • (2004) Genome Res. , vol.14 , pp. 2367-2376
    • Pharkya, P.1    Burgard, A.P.2    Maranas, C.D.3
  • 10
    • 0037069467 scopus 로고    scopus 로고
    • Analysis of optimality in natural and perturbed metabolic networks.
    • Segre, D., Vitkup, D., Church, G. M., Analysis of optimality in natural and perturbed metabolic networks. Proc. Natl. Acad. Sci. USA 2002, 99, 15112-15117.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 15112-15117
    • Segre, D.1    Vitkup, D.2    Church, G.M.3
  • 11
    • 19644386033 scopus 로고    scopus 로고
    • Regulatory on/off minimization of metabolic flux changes after genetic perturbations.
    • Shlomi, T., Berkman, O., Ruppin, E., Regulatory on/off minimization of metabolic flux changes after genetic perturbations. Proc. Natl. Acad. Sci. USA 2005, 102, 7695-7700.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 7695-7700
    • Shlomi, T.1    Berkman, O.2    Ruppin, E.3
  • 12
    • 84866539049 scopus 로고    scopus 로고
    • RELATCH: Relative optimality in metabolic networks explains robust metabolic and regulatory responses to perturbations.
    • Kim, J., Reed, J. L., RELATCH: Relative optimality in metabolic networks explains robust metabolic and regulatory responses to perturbations. Genome Biol. 2012, 13, R78.
    • (2012) Genome Biol. , vol.13
    • Kim, J.1    Reed, J.L.2
  • 13
    • 77949495880 scopus 로고    scopus 로고
    • Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways.
    • Tepper, N., Shlomi, T., Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways. Bioinformatics 2010, 26, 536-543.
    • (2010) Bioinformatics , vol.26 , pp. 536-543
    • Tepper, N.1    Shlomi, T.2
  • 14
    • 77950863401 scopus 로고    scopus 로고
    • Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli.
    • Feist, A. M., Zielinski, D. C., Orth, J. D., Schellenberger, J. et al., Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli. Metab. Eng. 2010, 12, 173-186.
    • (2010) Metab. Eng. , vol.12 , pp. 173-186
    • Feist, A.M.1    Zielinski, D.C.2    Orth, J.D.3    Schellenberger, J.4
  • 15
    • 77957061890 scopus 로고    scopus 로고
    • Prediction of metabolic fluxes by incorporating genomic context and flux-converging pattern analyses.
    • Park, J. M., Kim, T. Y., Lee, S. Y., Prediction of metabolic fluxes by incorporating genomic context and flux-converging pattern analyses. Proc. Natl. Acad. Sci. USA 2010, 107, 14931-14936.
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 14931-14936
    • Park, J.M.1    Kim, T.Y.2    Lee, S.Y.3
  • 16
    • 58149154663 scopus 로고    scopus 로고
    • Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism.
    • Trinh, C. T., Wlaschin, A., Srienc, F., Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism. Appl. Microbiol. Biotechnol. 2009, 81, 813-826.
    • (2009) Appl. Microbiol. Biotechnol. , vol.81 , pp. 813-826
    • Trinh, C.T.1    Wlaschin, A.2    Srienc, F.3
  • 17
    • 1042269472 scopus 로고    scopus 로고
    • Minimal cut sets in biochemical reaction networks.
    • Klamt, S., Gilles, E. D., Minimal cut sets in biochemical reaction networks. Bioinformatics 2004, 20, 226-234.
    • (2004) Bioinformatics , vol.20 , pp. 226-234
    • Klamt, S.1    Gilles, E.D.2
  • 18
    • 74549189949 scopus 로고    scopus 로고
    • Flux design: In silico design of cell factories based on correlation of pathway fluxes to desired properties.
    • Melzer, G., Esfandabadi, M. E., Franco-Lara, E., Wittmann, C., Flux design: In silico design of cell factories based on correlation of pathway fluxes to desired properties. BMC Syst. Biol. 2009, 3, 120.
    • (2009) BMC Syst. Biol. , vol.3 , pp. 120
    • Melzer, G.1    Esfandabadi, M.E.2    Franco-Lara, E.3    Wittmann, C.4
  • 19
    • 1642457253 scopus 로고    scopus 로고
    • The effects of alternate optimal solutions in constraint-based genome-scale metabolic models.
    • Mahadevan, R., Schilling, C. H., The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab. Eng. 2003, 5, 264-276.
    • (2003) Metab. Eng. , vol.5 , pp. 264-276
    • Mahadevan, R.1    Schilling, C.H.2
  • 20
    • 9544253891 scopus 로고    scopus 로고
    • Genome-scale models of microbial cells: evaluating the consequences of constraints.
    • Price, N. D., Reed, J. L., Palsson, B. O., Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat. Revi. Microbiol. 2004, 2, 886-897.
    • (2004) Nat. Revi. Microbiol. , vol.2 , pp. 886-897
    • Price, N.D.1    Reed, J.L.2    Palsson, B.O.3
  • 21
    • 80054069179 scopus 로고    scopus 로고
    • A comprehensive genome-scale reconstruction of Escherichia coli metabolism-2011.
    • Orth, J. D., Conrad, T. M., Na, J., Lerman, J. A. et al., A comprehensive genome-scale reconstruction of Escherichia coli metabolism-2011. Mol. Syst. Biol. 2011, 7, 535.
    • (2011) Mol. Syst. Biol. , vol.7 , pp. 535
    • Orth, J.D.1    Conrad, T.M.2    Na, J.3    Lerman, J.A.4
  • 22
    • 65649126379 scopus 로고    scopus 로고
    • Connecting extracellular metabolomic measurements to intracellular flux states in yeast.
    • Mo, M. L., Palsson, B. O., Herrgard, M. J., Connecting extracellular metabolomic measurements to intracellular flux states in yeast. BMC Syst. Biol. 2009, 3, 37.
    • (2009) BMC Syst. Biol. , vol.3 , pp. 37
    • Mo, M.L.1    Palsson, B.O.2    Herrgard, M.J.3
  • 23
    • 0034798879 scopus 로고    scopus 로고
    • Minimal reaction sets for Escherichia coli metabolism under different growth requirements and uptake environments.
    • Burgard, A. P., Vaidyaraman, S., Maranas, C. D., Minimal reaction sets for Escherichia coli metabolism under different growth requirements and uptake environments. Biotechnol. Progr. 2001, 17, 791-797.
    • (2001) Biotechnol. Progr. , vol.17 , pp. 791-797
    • Burgard, A.P.1    Vaidyaraman, S.2    Maranas, C.D.3
  • 24
    • 34347332311 scopus 로고    scopus 로고
    • A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information.
    • Feist, A. M., Henry, C. S., Reed, J. L., Krummenacker, M. et al., A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Molecular Syst. Biol. 2007, 3, 121.
    • (2007) Molecular Syst. Biol. , vol.3 , pp. 121
    • Feist, A.M.1    Henry, C.S.2    Reed, J.L.3    Krummenacker, M.4
  • 25
    • 0033219023 scopus 로고    scopus 로고
    • Effects of a feedback-resistant aspartokinase III gene on L-isoleucine production in Escherichia coli K-12.
    • Hashiguchi, K., Matsui, H., Kurahashi, O., Effects of a feedback-resistant aspartokinase III gene on L-isoleucine production in Escherichia coli K-12. Biosci. Biotechnol. Biochem. 1999, 63, 2023-2024.
    • (1999) Biosci. Biotechnol. Biochem. , vol.63 , pp. 2023-2024
    • Hashiguchi, K.1    Matsui, H.2    Kurahashi, O.3
  • 26
    • 0041661883 scopus 로고    scopus 로고
    • Effect of cysteine desulfhydrase gene disruption on L-cysteine overproduction in Escherichia coli.
    • Awano, N., Wada, M., Kohdoh, A., Oikawa, T. et al., Effect of cysteine desulfhydrase gene disruption on L-cysteine overproduction in Escherichia coli. Appl. Microbiol. Biotechnol. 2003, 62, 239-243.
    • (2003) Appl. Microbiol. Biotechnol. , vol.62 , pp. 239-243
    • Awano, N.1    Wada, M.2    Kohdoh, A.3    Oikawa, T.4
  • 27
    • 33751545659 scopus 로고    scopus 로고
    • Genome-scale in silico aided metabolic analysis and flux comparisons of Escherichia coli to improve succinate production.
    • Wang, Q., Chen, X., Yang, Y., Zhao, X., Genome-scale in silico aided metabolic analysis and flux comparisons of Escherichia coli to improve succinate production. Appl. Microbiol. Biotechnol. 2006, 73, 887-894.
    • (2006) Appl. Microbiol. Biotechnol. , vol.73 , pp. 887-894
    • Wang, Q.1    Chen, X.2    Yang, Y.3    Zhao, X.4


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