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Volumn 13, Issue 3, 2010, Pages 344-349

The biomass objective function

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL GROWTH; BIOMASS; BIOSYNTHESIS; CATALYSIS; CELL ENERGY; CELL GROWTH; CELL METABOLISM; CELL SURVIVAL; CELL VIABILITY; ESCHERICHIA COLI; GROWTH RATE; MACROMOLECULE; MICROORGANISM; MOLECULAR BIOLOGY; MOLECULAR EVOLUTION; NONHUMAN; REVIEW; RNA TRANSCRIPTION; STOICHIOMETRY; WILD TYPE;

EID: 77952886804     PISSN: 13695274     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mib.2010.03.003     Document Type: Review
Times cited : (466)

References (48)
  • 1
    • 0028108519 scopus 로고
    • Metabolic flux balancing: basic concepts, scientific and practical use
    • Varma A., and Palsson B.O. Metabolic flux balancing: basic concepts, scientific and practical use. Nat Biotechnol 12 (1994) 994-998
    • (1994) Nat Biotechnol , vol.12 , pp. 994-998
    • Varma, A.1    Palsson, B.O.2
  • 2
    • 45149111660 scopus 로고    scopus 로고
    • The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli
    • Feist A.M., and Palsson B.O. The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol 26 (2008) 659-667
    • (2008) Nat Biotechnol , vol.26 , pp. 659-667
    • Feist, A.M.1    Palsson, B.O.2
  • 3
    • 73149122136 scopus 로고    scopus 로고
    • Applications of genome-scale metabolic reconstructions
    • Oberhardt M.A., Palsson B.O., and Papin J.A. Applications of genome-scale metabolic reconstructions. Mol Syst Biol 5 (2009) 320
    • (2009) Mol Syst Biol , vol.5 , pp. 320
    • Oberhardt, M.A.1    Palsson, B.O.2    Papin, J.A.3
  • 4
    • 4644220226 scopus 로고    scopus 로고
    • Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states
    • Reed J.L., and Palsson B.O. Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states. Genome Res 14 (2004) 1797-1805
    • (2004) Genome Res , vol.14 , pp. 1797-1805
    • Reed, J.L.1    Palsson, B.O.2
  • 6
    • 33644527950 scopus 로고    scopus 로고
    • The model organism as a system: integrating 'omics' data sets
    • Joyce A.R., and Palsson B.O. The model organism as a system: integrating 'omics' data sets. Nat Rev Mol Cell Biol 7 (2006) 198-210
    • (2006) Nat Rev Mol Cell Biol , vol.7 , pp. 198-210
    • Joyce, A.R.1    Palsson, B.O.2
  • 9
    • 75149129569 scopus 로고    scopus 로고
    • A protocol for generating a high-quality genome-scale metabolic reconstruction
    • Thiele I., and Palsson B.O. A protocol for generating a high-quality genome-scale metabolic reconstruction. Nat Protoc 5 (2010) 93-121
    • (2010) Nat Protoc , vol.5 , pp. 93-121
    • Thiele, I.1    Palsson, B.O.2
  • 10
    • 63549148162 scopus 로고    scopus 로고
    • Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization
    • Thiele I., Jamshidi N., Fleming R.M., and Palsson B.O. Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization. PLoS Comput Biol 5 (2009) e1000312
    • (2009) PLoS Comput Biol , vol.5
    • Thiele, I.1    Jamshidi, N.2    Fleming, R.M.3    Palsson, B.O.4
  • 11
    • 0026516223 scopus 로고
    • Network analysis of intermediary metabolism using linear optimization. I. Development of mathematical formalism
    • Savinell J.M., and Palsson B.O. Network analysis of intermediary metabolism using linear optimization. I. Development of mathematical formalism. J Theor Biol 154 (1992) 421-454
    • (1992) J Theor Biol , vol.154 , pp. 421-454
    • Savinell, J.M.1    Palsson, B.O.2
  • 12
    • 0026603416 scopus 로고
    • Network analysis of intermediary metabolism using linear optimization. II. Interpretation of hybridoma cell metabolism
    • Savinell J.M., and Palsson B.O. Network analysis of intermediary metabolism using linear optimization. II. Interpretation of hybridoma cell metabolism. J Theor Biol 154 (1992) 455-473
    • (1992) J Theor Biol , vol.154 , pp. 455-473
    • Savinell, J.M.1    Palsson, B.O.2
  • 13
    • 0343035686 scopus 로고    scopus 로고
    • Stoichiometric model of Escherichia coli metabolism: incorporation of growth-rate dependent biomass composition and mechanistic energy requirements
    • Pramanik J., and Keasling J.D. Stoichiometric model of Escherichia coli metabolism: incorporation of growth-rate dependent biomass composition and mechanistic energy requirements. Biotechnol Bioeng 56 (1997) 398-421
    • (1997) Biotechnol Bioeng , vol.56 , pp. 398-421
    • Pramanik, J.1    Keasling, J.D.2
  • 14
    • 0038293216 scopus 로고    scopus 로고
    • Optimization-based framework for inferring and testing hypothesized metabolic objective functions
    • Burgard A.P., and Maranas C.D. Optimization-based framework for inferring and testing hypothesized metabolic objective functions. Biotechnol Bioeng 82 (2003) 670-677
    • (2003) Biotechnol Bioeng , vol.82 , pp. 670-677
    • Burgard, A.P.1    Maranas, C.D.2
  • 15
    • 33847307148 scopus 로고    scopus 로고
    • Bayesian-based selection of metabolic objective functions
    • Knorr A.L., Jain R., and Srivastava R. Bayesian-based selection of metabolic objective functions. Bioinformatics 23 (2007) 351-357
    • (2007) Bioinformatics , vol.23 , pp. 351-357
    • Knorr, A.L.1    Jain, R.2    Srivastava, R.3
  • 16
    • 34447523907 scopus 로고    scopus 로고
    • Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli
    • Schuetz R., Kuepfer L., and Sauer U. Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. Mol Syst Biol 3 (2007)
    • (2007) Mol Syst Biol , vol.3
    • Schuetz, R.1    Kuepfer, L.2    Sauer, U.3
  • 18
    • 63549108441 scopus 로고    scopus 로고
    • GrowMatch: an automated method for reconciling in silico/in vivo growth predictions
    • Kumar V.S., and Maranas C.D. GrowMatch: an automated method for reconciling in silico/in vivo growth predictions. PLoS Comput Biol 5 (2009) e1000308
    • (2009) PLoS Comput Biol , vol.5
    • Kumar, V.S.1    Maranas, C.D.2
  • 19
    • 64549091131 scopus 로고    scopus 로고
    • Identification of cellular objective for elucidating the physiological state of plasmid-bearing Escherichia coli using genome-scale in silico analysis
    • Ow D.S., Lee D.Y., Yap M.G., and Oh S.K. Identification of cellular objective for elucidating the physiological state of plasmid-bearing Escherichia coli using genome-scale in silico analysis. Biotechnol Prog 25 (2009) 61-67
    • (2009) Biotechnol Prog , vol.25 , pp. 61-67
    • Ow, D.S.1    Lee, D.Y.2    Yap, M.G.3    Oh, S.K.4
  • 20
    • 0026254349 scopus 로고
    • Growth, metabolic, and antibody production kinetics of hybridoma cell culture. II. Effects of serum concentration, dissolved oxygen concentration, and medium pH in a batch reactor
    • Ozturk S.S., and Palsson B.O. Growth, metabolic, and antibody production kinetics of hybridoma cell culture. II. Effects of serum concentration, dissolved oxygen concentration, and medium pH in a batch reactor. Biotechnol Prog 7 (1991) 481-494
    • (1991) Biotechnol Prog , vol.7 , pp. 481-494
    • Ozturk, S.S.1    Palsson, B.O.2
  • 21
    • 9544253891 scopus 로고    scopus 로고
    • Genome-scale models of microbial cells: evaluating the consequences of constraints
    • Price N.D., Reed J.L., and Palsson B.O. Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol 2 (2004) 886-897
    • (2004) Nat Rev Microbiol , vol.2 , pp. 886-897
    • Price, N.D.1    Reed, J.L.2    Palsson, B.O.3
  • 22
    • 28444475529 scopus 로고    scopus 로고
    • Adaptive evolution of bacterial metabolic networks by horizontal gene transfer
    • Pal C., Papp B., and Lercher M.J. Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet 37 (2005) 1372-1375
    • (2005) Nat Genet , vol.37 , pp. 1372-1375
    • Pal, C.1    Papp, B.2    Lercher, M.J.3
  • 23
    • 27544449355 scopus 로고    scopus 로고
    • Horizontal gene transfer depends on gene content of the host
    • Pal C., Papp B., and Lercher M.J. Horizontal gene transfer depends on gene content of the host. Bioinformatics 21 Suppl 2 (2005) ii222-ii223
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 2
    • Pal, C.1    Papp, B.2    Lercher, M.J.3
  • 24
    • 33645460106 scopus 로고    scopus 로고
    • Chance and necessity in the evolution of minimal metabolic networks
    • Pal C., Papp B., Lercher M.J., Csermely P., Oliver S.G., and Hurst L.D. Chance and necessity in the evolution of minimal metabolic networks. Nature 440 (2006) 667-670
    • (2006) Nature , vol.440 , pp. 667-670
    • Pal, C.1    Papp, B.2    Lercher, M.J.3    Csermely, P.4    Oliver, S.G.5    Hurst, L.D.6
  • 25
    • 0347506028 scopus 로고    scopus 로고
    • It is all about metabolic fluxes
    • Nielsen J. It is all about metabolic fluxes. J Bacteriol 185 (2003) 7031-7035
    • (2003) J Bacteriol , vol.185 , pp. 7031-7035
    • Nielsen, J.1
  • 26
    • 0035125986 scopus 로고    scopus 로고
    • In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data
    • Edwards J.S., Ibarra R.U., and Palsson B.O. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol 19 (2001) 125-130
    • (2001) Nat Biotechnol , vol.19 , pp. 125-130
    • Edwards, J.S.1    Ibarra, R.U.2    Palsson, B.O.3
  • 27
    • 0037079023 scopus 로고    scopus 로고
    • Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth
    • Ibarra R.U., Edwards J.S., and Palsson B.O. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420 (2002) 186-189
    • (2002) Nature , vol.420 , pp. 186-189
    • Ibarra, R.U.1    Edwards, J.S.2    Palsson, B.O.3
  • 28
    • 6944224154 scopus 로고    scopus 로고
    • Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes
    • Fong S.S., and Palsson B.O. Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes. Nat Genet 36 (2004) 1056-1058
    • (2004) Nat Genet , vol.36 , pp. 1056-1058
    • Fong, S.S.1    Palsson, B.O.2
  • 29
    • 33846015888 scopus 로고    scopus 로고
    • Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model
    • Teusink B., Wiersma A., Molenaar D., Francke C., de Vos W.M., Siezen R.J., and Smid E.J. Analysis of growth of Lactobacillus plantarum WCFS1 on a complex medium using a genome-scale metabolic model. J Biol Chem 281 (2006) 40041-40048
    • (2006) J Biol Chem , vol.281 , pp. 40041-40048
    • Teusink, B.1    Wiersma, A.2    Molenaar, D.3    Francke, C.4    de Vos, W.M.5    Siezen, R.J.6    Smid, E.J.7
  • 30
    • 67650904950 scopus 로고    scopus 로고
    • Understanding the adaptive growth strategy of Lactobacillus plantarum by in silico optimisation
    • Teusink B., Wiersma A., Jacobs L., Notebaart R.A., and Smid E.J. Understanding the adaptive growth strategy of Lactobacillus plantarum by in silico optimisation. PLoS Comput Biol 5 (2009) e1000410
    • (2009) PLoS Comput Biol , vol.5
    • Teusink, B.1    Wiersma, A.2    Jacobs, L.3    Notebaart, R.A.4    Smid, E.J.5
  • 32
    • 75349114758 scopus 로고    scopus 로고
    • Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations
    • Conrad T.M., Joyce A.R., Applebee M.K., Barrett C.L., Xie B., Gao Y., and Palsson B.O. Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations. Genome Biol 10 (2009) R118
    • (2009) Genome Biol , vol.10
    • Conrad, T.M.1    Joyce, A.R.2    Applebee, M.K.3    Barrett, C.L.4    Xie, B.5    Gao, Y.6    Palsson, B.O.7
  • 33
    • 0242487787 scopus 로고    scopus 로고
    • Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
    • Burgard A.P., Pharkya P., and Maranas C.D. Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng 84 (2003) 647-657
    • (2003) Biotechnol Bioeng , vol.84 , pp. 647-657
    • Burgard, A.P.1    Pharkya, P.2    Maranas, C.D.3
  • 34
    • 8744224466 scopus 로고    scopus 로고
    • OptStrain: a computational framework for redesign of microbial production systems
    • Pharkya P., Burgard A.P., and Maranas C.D. OptStrain: a computational framework for redesign of microbial production systems. Genome Res 14 (2004) 2367-2376
    • (2004) Genome Res , vol.14 , pp. 2367-2376
    • Pharkya, P.1    Burgard, A.P.2    Maranas, C.D.3
  • 35
    • 30044437327 scopus 로고    scopus 로고
    • Evolutionary programming as a platform for in silico metabolic engineering
    • Patil K.R., Rocha I., Forster J., and Nielsen J. Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinformatics 6 (2005) 308
    • (2005) BMC Bioinformatics , vol.6 , pp. 308
    • Patil, K.R.1    Rocha, I.2    Forster, J.3    Nielsen, J.4
  • 36
    • 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., Herrgard M.J., and Palsson B.O. Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli. Metab Eng 12 (2010) 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    Herrgard, M.J.5    Palsson, B.O.6
  • 38
    • 0021801376 scopus 로고
    • Branch point control by the phosphorylation state of isocitrate dehydrogenase. A quantitative examination of fluxes during a regulatory transition
    • Walsh K.J., and Koshland D.E. Branch point control by the phosphorylation state of isocitrate dehydrogenase. A quantitative examination of fluxes during a regulatory transition. J Biol Chem 260 (1985) 8430-8437
    • (1985) J Biol Chem , vol.260 , pp. 8430-8437
    • Walsh, K.J.1    Koshland, D.E.2
  • 39
    • 0032838693 scopus 로고    scopus 로고
    • Quantitative analysis of metabolic fluxes in Escherichia coli, using two-dimensional NMR spectroscopy and complete isotopomer models
    • Schmidt K., Nielsen J., and Villadsen J. Quantitative analysis of metabolic fluxes in Escherichia coli, using two-dimensional NMR spectroscopy and complete isotopomer models. J Biotechnol 71 (1999) 175-189
    • (1999) J Biotechnol , vol.71 , pp. 175-189
    • Schmidt, K.1    Nielsen, J.2    Villadsen, J.3
  • 40
    • 0344328817 scopus 로고    scopus 로고
    • An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
    • R54.51-R54.12
    • Reed J.L., Vo T.D., Schilling C.H., and Palsson B.O. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol 4 (2003) R54.51-R54.12
    • (2003) Genome Biol , vol.4
    • Reed, J.L.1    Vo, T.D.2    Schilling, C.H.3    Palsson, B.O.4
  • 41
    • 17644369246 scopus 로고    scopus 로고
    • Impact of global transcriptional regulation by ArcA, ArcB, Cra, Crp, Cya, Fnr, and Mlc on glucose catabolism in Escherichia coli
    • Perrenoud A., and Sauer U. Impact of global transcriptional regulation by ArcA, ArcB, Cra, Crp, Cya, Fnr, and Mlc on glucose catabolism in Escherichia coli. J Bacteriol 187 (2005) 3171-3179
    • (2005) J Bacteriol , vol.187 , pp. 3171-3179
    • Perrenoud, A.1    Sauer, U.2
  • 42
    • 33144472889 scopus 로고    scopus 로고
    • Nonlinear dependency of intracellular fluxes on growth rate in miniaturized continuous cultures of Escherichia coli
    • Nanchen A., Schicker A., and Sauer U. Nonlinear dependency of intracellular fluxes on growth rate in miniaturized continuous cultures of Escherichia coli. Appl Environ Microbiol 72 (2006) 1164-1172
    • (2006) Appl Environ Microbiol , vol.72 , pp. 1164-1172
    • Nanchen, A.1    Schicker, A.2    Sauer, U.3
  • 44
    • 0035140099 scopus 로고    scopus 로고
    • Network identification and flux quantification in the central metabolism of Saccharomyces cerevisiae under different conditions of glucose repression
    • Gombert A.K., Moreira dos Santos M., Christensen B., and Nielsen J. Network identification and flux quantification in the central metabolism of Saccharomyces cerevisiae under different conditions of glucose repression. J Bacteriol 183 (2001) 1441-1451
    • (2001) J Bacteriol , vol.183 , pp. 1441-1451
    • Gombert, A.K.1    Moreira dos Santos, M.2    Christensen, B.3    Nielsen, J.4
  • 48
    • 33845315054 scopus 로고    scopus 로고
    • Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism
    • Wang Z., Xiang L., Shao J., Wegrzyn A., and Wegrzyn G. Effects of the presence of ColE1 plasmid DNA in Escherichia coli on the host cell metabolism. Microb Cell Fact 5 (2006) 34
    • (2006) Microb Cell Fact , vol.5 , pp. 34
    • Wang, Z.1    Xiang, L.2    Shao, J.3    Wegrzyn, A.4    Wegrzyn, G.5


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