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Volumn 23, Issue 7, 2005, Pages 349-358

Systems biotechnology for strain improvement

Author keywords

[No Author keywords available]

Indexed keywords

CELLS; COMPUTER SIMULATION; INDUSTRIAL APPLICATIONS; ITERATIVE METHODS; MATHEMATICAL MODELS; METABOLISM; STRAIN;

EID: 20644467467     PISSN: 01677799     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tibtech.2005.05.003     Document Type: Review
Times cited : (271)

References (52)
  • 1
    • 0033797405 scopus 로고    scopus 로고
    • Improvement of microbial strains and fermentation processes
    • S. Parekh Improvement of microbial strains and fermentation processes Appl. Microbiol. Biotechnol. 54 2000 287 301
    • (2000) Appl. Microbiol. Biotechnol. , vol.54 , pp. 287-301
    • Parekh, S.1
  • 2
    • 0037370373 scopus 로고    scopus 로고
    • Proteomics: The first decade and beyond
    • S.D. Patterson, and R.H. Aebersold Proteomics: the first decade and beyond Nat. Genet. 33 2003 311 323
    • (2003) Nat. Genet. , vol.33 , pp. 311-323
    • Patterson, S.D.1    Aebersold, R.H.2
  • 3
    • 0035989624 scopus 로고    scopus 로고
    • Metabolic engineering by genome shuffling
    • G. Stephanopoulos Metabolic engineering by genome shuffling Nat. Biotechnol. 20 2002 707 712
    • (2002) Nat. Biotechnol. , vol.20 , pp. 707-712
    • Stephanopoulos, G.1
  • 4
    • 0036331713 scopus 로고    scopus 로고
    • Functional genomics: High-throughput mRNA, protein, and metabolite analyses
    • D.J. Oliver Functional genomics: high-throughput mRNA, protein, and metabolite analyses Metab. Eng. 4 2002 98 106
    • (2002) Metab. Eng. , vol.4 , pp. 98-106
    • Oliver, D.J.1
  • 5
    • 3242726864 scopus 로고    scopus 로고
    • Impact of 'ome' analyses on inverse metabolic engineering
    • C. Bro, and J. Nielsen Impact of 'ome' analyses on inverse metabolic engineering Metab. Eng. 6 2004 204 211
    • (2004) Metab. Eng. , vol.6 , pp. 204-211
    • Bro, C.1    Nielsen, J.2
  • 6
    • 0346256835 scopus 로고    scopus 로고
    • Proteome profiling and its use in metabolic and cellular engineering
    • M-J. Han, and S.Y. Lee Proteome profiling and its use in metabolic and cellular engineering Proteomics 3 2003 2317 2324
    • (2003) Proteomics , vol.3 , pp. 2317-2324
    • Han, M.-J.1    Lee, S.Y.2
  • 7
    • 4644237025 scopus 로고    scopus 로고
    • Using functional genomics to improve productivity in the manufacture of industrial biochemicals
    • T. Hermann Using functional genomics to improve productivity in the manufacture of industrial biochemicals Curr. Opin. Biotechnol. 15 2004 444 448
    • (2004) Curr. Opin. Biotechnol. , vol.15 , pp. 444-448
    • Hermann, T.1
  • 8
    • 0035905782 scopus 로고    scopus 로고
    • Modelling cellular behaviour
    • D. Endy, and R. Brent Modelling cellular behaviour Nature 409 2001 391 395
    • (2001) Nature , vol.409 , pp. 391-395
    • Endy, D.1    Brent, R.2
  • 9
    • 0038730860 scopus 로고    scopus 로고
    • On the complete determination of biological systems
    • D.W. Selinger On the complete determination of biological systems Trends Biotechnol. 21 2003 251 254
    • (2003) Trends Biotechnol. , vol.21 , pp. 251-254
    • Selinger, D.W.1
  • 10
    • 4644268555 scopus 로고    scopus 로고
    • Mathematical models in microbial systems biology
    • J. Stelling Mathematical models in microbial systems biology Curr. Opin. Microbiol. 7 2004 513 518
    • (2004) Curr. Opin. Microbiol. , vol.7 , pp. 513-518
    • Stelling, J.1
  • 11
    • 0037075690 scopus 로고    scopus 로고
    • Modeling and simulation: Tools for metabolic engineering
    • W. Wiechert Modeling and simulation: tools for metabolic engineering J. Biotechnol. 94 2002 37 63
    • (2002) J. Biotechnol. , vol.94 , pp. 37-63
    • Wiechert, W.1
  • 12
    • 1242283921 scopus 로고    scopus 로고
    • Use of genome-scale microbial models for metabolic engineering
    • K.R. Patil Use of genome-scale microbial models for metabolic engineering Curr. Opin. Biotechnol. 15 2004 64 69
    • (2004) Curr. Opin. Biotechnol. , vol.15 , pp. 64-69
    • Patil, K.R.1
  • 13
    • 0036228521 scopus 로고    scopus 로고
    • Engineering a reduced Escherichia coli genome
    • V. Kolisnychenko Engineering a reduced Escherichia coli genome Genome Res. 12 2002 640 647
    • (2002) Genome Res. , vol.12 , pp. 640-647
    • Kolisnychenko, V.1
  • 14
    • 0036161274 scopus 로고    scopus 로고
    • A novel methodology employing Corynebacterium glutamicum genome information to generate a new L-lysine-producing mutant
    • J. Ohnishi A novel methodology employing Corynebacterium glutamicum genome information to generate a new L-lysine-producing mutant Appl. Microbiol. Biotechnol. 58 2002 217 223
    • (2002) Appl. Microbiol. Biotechnol. , vol.58 , pp. 217-223
    • Ohnishi, J.1
  • 15
    • 0043031143 scopus 로고    scopus 로고
    • Enhanced production of insulin-like growth factor I fusion protein in Escherichia coli by coexpression of the down-regulated genes identified by transcriptome profiling
    • J.H. Choi Enhanced production of insulin-like growth factor I fusion protein in Escherichia coli by coexpression of the down-regulated genes identified by transcriptome profiling Appl. Environ. Microbiol. 69 2003 4737 4742
    • (2003) Appl. Environ. Microbiol. , vol.69 , pp. 4737-4742
    • Choi, J.H.1
  • 16
    • 0035191291 scopus 로고    scopus 로고
    • Proteome analysis of metabolically engineered Escherichia coli cells producing poly(3-hydroxybutyrate)
    • M.J. Han Proteome analysis of metabolically engineered Escherichia coli cells producing poly(3-hydroxybutyrate) J. Bacteriol. 183 2001 301 308
    • (2001) J. Bacteriol. , vol.183 , pp. 301-308
    • Han, M.J.1
  • 17
    • 0142072824 scopus 로고    scopus 로고
    • Engineering Escherichia coli for increased production of serine-rich proteins based on proteome profiling
    • M.J. Han Engineering Escherichia coli for increased production of serine-rich proteins based on proteome profiling Appl. Environ. Microbiol. 69 2003 5772 5781
    • (2003) Appl. Environ. Microbiol. , vol.69 , pp. 5772-5781
    • Han, M.J.1
  • 18
    • 0010143371 scopus 로고    scopus 로고
    • Introduction to functional analysis of the yeast genome
    • A.J.P. Brown M. Tuite Academic Press
    • S.G. Oliver Introduction to functional analysis of the yeast genome A.J.P. Brown M. Tuite Methods in Microbiology 1998 Academic Press 1 13
    • (1998) Methods in Microbiology , pp. 1-13
    • Oliver, S.G.1
  • 19
    • 0034811345 scopus 로고    scopus 로고
    • Modeling and experimental design for metabolic flux analysis of lysine-producing Corynebacteria by mass spectrometry
    • C. Wittmann, and E. Heinzle Modeling and experimental design for metabolic flux analysis of lysine-producing Corynebacteria by mass spectrometry Metab. Eng. 3 2001 173 191
    • (2001) Metab. Eng. , vol.3 , pp. 173-191
    • Wittmann, C.1    Heinzle, E.2
  • 20
    • 0036273832 scopus 로고    scopus 로고
    • Genomics to fluxomics and physiomics - Pathway engineering
    • K. Sanford Genomics to fluxomics and physiomics - pathway engineering Curr. Opin. Microbiol. 5 2002 318 322
    • (2002) Curr. Opin. Microbiol. , vol.5 , pp. 318-322
    • Sanford, K.1
  • 21
    • 0037473189 scopus 로고    scopus 로고
    • Combined transcriptome and proteome analysis of Escherichia coli during high Cell density culture
    • S.H. Yoon Combined transcriptome and proteome analysis of Escherichia coli during high Cell density culture Biotechnol. Bioeng. 81 2003 753 767
    • (2003) Biotechnol. Bioeng. , vol.81 , pp. 753-767
    • Yoon, S.H.1
  • 22
    • 0041836104 scopus 로고    scopus 로고
    • Global analyses of transcriptomes and proteomes of a parent strain and an L-threonine-overproducing mutant strain
    • J.H. Lee Global analyses of transcriptomes and proteomes of a parent strain and an L-threonine-overproducing mutant strain J. Bacteriol. 185 2003 5442 5451
    • (2003) J. Bacteriol. , vol.185 , pp. 5442-5451
    • Lee, J.H.1
  • 23
    • 0037316031 scopus 로고    scopus 로고
    • Integrating transcriptional and metabolite profiles to direct the engineering of lovastatin-producing fungal strains
    • M. Askenazi Integrating transcriptional and metabolite profiles to direct the engineering of lovastatin-producing fungal strains Nat. Biotechnol. 21 2003 150 156
    • (2003) Nat. Biotechnol. , vol.21 , pp. 150-156
    • Askenazi, M.1
  • 24
    • 1542376957 scopus 로고    scopus 로고
    • In-depth profiling of lysine-producing Corynebacterium glutamicum by combined analysis of the transcriptome, metabolome, and fluxome
    • J.O. Krömer In-depth profiling of lysine-producing Corynebacterium glutamicum by combined analysis of the transcriptome, metabolome, and fluxome J. Bacteriol. 186 2004 1769 1784
    • (2004) J. Bacteriol. , vol.186 , pp. 1769-1784
    • Krömer, J.O.1
  • 25
    • 4544227574 scopus 로고    scopus 로고
    • Toward large-scale modeling of the microbial cell for computer simulation
    • N. Ishii Toward large-scale modeling of the microbial cell for computer simulation J. Biotechnol. 113 2004 281 294
    • (2004) J. Biotechnol. , vol.113 , pp. 281-294
    • Ishii, N.1
  • 26
    • 9544253891 scopus 로고    scopus 로고
    • Genome-scale models of microbial cells: Evaluating the consequences of constraints
    • N.D. Price 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
  • 27
    • 0033031386 scopus 로고    scopus 로고
    • E-CELL: Software environment for whole-cell simulation
    • M. Tomita E-CELL: software environment for whole-cell simulation Bioinformatics 15 1999 72 84
    • (1999) Bioinformatics , vol.15 , pp. 72-84
    • Tomita, M.1
  • 28
    • 0035812464 scopus 로고    scopus 로고
    • Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions
    • A.P. Burgard, and C.D. Maranas Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions Biotechnol. Bioeng. 74 2001 364 375
    • (2001) Biotechnol. Bioeng. , vol.74 , pp. 364-375
    • Burgard, A.P.1    Maranas, C.D.2
  • 29
    • 0037069467 scopus 로고    scopus 로고
    • Analysis of optimality in natural and perturbed metabolic networks
    • D. Segre Analysis of optimality in natural and perturbed metabolic networks Proc. Natl. Acad. Sci. U. S. A. 99 2002 15112 15117
    • (2002) Proc. Natl. Acad. Sci. U. S. A. , vol.99 , pp. 15112-15117
    • Segre, D.1
  • 30
    • 0242487787 scopus 로고    scopus 로고
    • Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization
    • A.P. Burgard 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
  • 31
    • 0027370376 scopus 로고
    • GEPASI: A software package for modeling the dynamics, steady states and control of biochemical and other systems
    • P. Mendes GEPASI: a software package for modeling the dynamics, steady states and control of biochemical and other systems Comput. Appl. Biosci. 9 1993 563 571
    • (1993) Comput. Appl. Biosci. , vol.9 , pp. 563-571
    • Mendes, P.1
  • 32
    • 0032825010 scopus 로고    scopus 로고
    • Mathematical simulation and analysis of cellular metabolism and regulation
    • I. Goryanin Mathematical simulation and analysis of cellular metabolism and regulation Bioinformatics 15 1999 749 758
    • (1999) Bioinformatics , vol.15 , pp. 749-758
    • Goryanin, I.1
  • 33
    • 0347511691 scopus 로고    scopus 로고
    • Next generation simuylation tools: The Systems Biology Workbench and BioSPICE integration
    • H.M. Sauro Next generation simuylation tools: the Systems Biology Workbench and BioSPICE integration OMICS 7 2003 355 372
    • (2003) OMICS , vol.7 , pp. 355-372
    • Sauro, H.M.1
  • 34
    • 0346250869 scopus 로고    scopus 로고
    • BioSPICE: Access to the most current computational tools for biologists
    • T.D. Garvey BioSPICE: access to the most current computational tools for biologists OMICS 7 2003 411 420
    • (2003) OMICS , vol.7 , pp. 411-420
    • Garvey, T.D.1
  • 35
    • 0242475329 scopus 로고    scopus 로고
    • MetaFluxNet: The management of metabolic reaction information and quantitative metabolic flux analysis
    • D-Y. Lee MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis Bioinformatics 19 2003 2144 2146
    • (2003) Bioinformatics , vol.19 , pp. 2144-2146
    • Lee, D.-Y.1
  • 36
    • 6944224154 scopus 로고    scopus 로고
    • Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes
    • S.S. Fong, and B.O. Palsson 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
  • 37
    • 2342648924 scopus 로고    scopus 로고
    • Integrating high-throughput and computational data elucidates bacterial networks
    • M.W. Covert Integrating high-throughput and computational data elucidates bacterial networks Nature 429 2004 92 96
    • (2004) Nature , vol.429 , pp. 92-96
    • Covert, M.W.1
  • 38
    • 5044220423 scopus 로고    scopus 로고
    • The genome sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens
    • S.H. Hong The genome sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens Nat. Biotechnol. 22 2004 1275 1281
    • (2004) Nat. Biotechnol. , vol.22 , pp. 1275-1281
    • Hong, S.H.1
  • 39
    • 10044291609 scopus 로고    scopus 로고
    • Genomes back-to-back: When sequencing race is a good thing
    • M.Y. Galperin Genomes back-to-back: when sequencing race is a good thing Environ. Microbiol. 6 2004 1205 1209
    • (2004) Environ. Microbiol. , vol.6 , pp. 1205-1209
    • Galperin, M.Y.1
  • 40
    • 5044237367 scopus 로고    scopus 로고
    • Exploiting biological complexity for strain improvement through systems biology
    • G. Stephanopoulos Exploiting biological complexity for strain improvement through systems biology Nat. Biotechnol. 22 2004 1261 1267
    • (2004) Nat. Biotechnol. , vol.22 , pp. 1261-1267
    • Stephanopoulos, G.1
  • 41
    • 0032025439 scopus 로고    scopus 로고
    • Simplification of mathematical models of chemical reaction systems
    • M.S. Okino, and M.L. Mavrovouniotis Simplification of mathematical models of chemical reaction systems Chem. Rev. 98 1998 391 408
    • (1998) Chem. Rev. , vol.98 , pp. 391-408
    • Okino, M.S.1    Mavrovouniotis, M.L.2
  • 42
    • 0041387671 scopus 로고    scopus 로고
    • Genome-wide analysis of the L-methionine biosynthetic pathway in Corynebacterium glutamicum by targeted gene deletion and homologous complementation
    • C. Ruckert Genome-wide analysis of the L-methionine biosynthetic pathway in Corynebacterium glutamicum by targeted gene deletion and homologous complementation J. Biotechnol. 104 2003 213 228
    • (2003) J. Biotechnol. , vol.104 , pp. 213-228
    • Ruckert, C.1
  • 43
    • 0037898149 scopus 로고    scopus 로고
    • Efficient 40 degrees C fermentation of L-lysine by a new Corynebacterium glutamicum mutant developed by genome breeding
    • J. Ohnishi Efficient 40 degrees C fermentation of L-lysine by a new Corynebacterium glutamicum mutant developed by genome breeding Appl. Microbiol. Biotechnol. 62 2003 69 75
    • (2003) Appl. Microbiol. Biotechnol. , vol.62 , pp. 69-75
    • Ohnishi, J.1
  • 44
    • 0347132481 scopus 로고    scopus 로고
    • Transcriptional analysis of product-concentration driven changes in cellular programs of recombinant Clostridium acetobutylicum strains
    • S.B. Tummala Transcriptional analysis of product-concentration driven changes in cellular programs of recombinant Clostridium acetobutylicum strains Biotechnol. Bioeng. 84 2003 842 854
    • (2003) Biotechnol. Bioeng. , vol.84 , pp. 842-854
    • Tummala, S.B.1
  • 45
    • 0042162814 scopus 로고    scopus 로고
    • Fermentation characteristics and protein expression patterns in a recombinant Escherichia coli mutant lacking phosphoglucose isomerase for poly(3-hydroxybutyrate) production
    • M.M. Kabir, and K. Shimizu Fermentation characteristics and protein expression patterns in a recombinant Escherichia coli mutant lacking phosphoglucose isomerase for poly(3-hydroxybutyrate) production Appl. Microbiol. Biotechnol. 62 2003 244 255
    • (2003) Appl. Microbiol. Biotechnol. , vol.62 , pp. 244-255
    • Kabir, M.M.1    Shimizu, K.2
  • 46
    • 0036203308 scopus 로고    scopus 로고
    • Intracellular carbon fluxes in riboflavin-producing Bacillus subtilis during growth on two-carbon substrate mixtures
    • M. Dauner Intracellular carbon fluxes in riboflavin-producing Bacillus subtilis during growth on two-carbon substrate mixtures Appl. Environ. Microbiol. 68 2002 1760 1771
    • (2002) Appl. Environ. Microbiol. , vol.68 , pp. 1760-1771
    • Dauner, M.1
  • 47
    • 0034625143 scopus 로고    scopus 로고
    • The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities
    • J.S. Edwards, and B.Ø. Palsson The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities Proc. Natl. Acad. Sci. U. S. A. 97 2000 5528 5533
    • (2000) Proc. Natl. Acad. Sci. U. S. A. , vol.97 , pp. 5528-5533
    • Edwards, J.S.1    Palsson B.Ø2
  • 48
    • 0344328817 scopus 로고    scopus 로고
    • An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
    • J.L. Reed An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR) Genome Biol. 4 2003 R54
    • (2003) Genome Biol. , vol.4 , pp. 54
    • Reed, J.L.1
  • 49
    • 0033580813 scopus 로고    scopus 로고
    • Systems properties of the Haemophilus influenzae Rd metabolic genotype
    • J.S. Edwards, and B.Ø. Palsson Systems properties of the Haemophilus influenzae Rd metabolic genotype J. Biol. Chem. 274 1999 17410 17416
    • (1999) J. Biol. Chem. , vol.274 , pp. 17410-17416
    • Edwards, J.S.1    Palsson B.Ø2
  • 50
    • 0036330798 scopus 로고    scopus 로고
    • Genome-scale metabolic model of Helicobacter pylori 26695
    • C.H. Schilling Genome-scale metabolic model of Helicobacter pylori 26695 J. Bacteriol. 184 2002 4582 4593
    • (2002) J. Bacteriol. , vol.184 , pp. 4582-4593
    • Schilling, C.H.1
  • 51
    • 0037313750 scopus 로고    scopus 로고
    • Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network
    • J. Forster Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network Genome Res. 13 2003 244 253
    • (2003) Genome Res. , vol.13 , pp. 244-253
    • Forster, J.1
  • 52
    • 3843128481 scopus 로고    scopus 로고
    • Reconstruction and validation of Saccharomyces scerevisiae iND750, a fully compartmentalized genome-scale metabolic model
    • N.C. Duarte Reconstruction and validation of Saccharomyces scerevisiae iND750, a fully compartmentalized genome-scale metabolic model Genome Res. 14 2004 1298 1309
    • (2004) Genome Res. , vol.14 , pp. 1298-1309
    • Duarte, N.C.1


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