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Volumn 21, Issue 1, 2010, Pages 21-26

Analyzing metabolic variations in different bacterial strains, historical perspectives and current trends - example E. coli

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL STRAINS; BIOCHEMICAL METHODS; CURRENT TRENDS; E. COLI; GENOMIC METHODS; HISTORICAL PERSPECTIVE; INDIVIDUAL COMPONENTS; MATHEMATICAL METHOD; METABOLIC ACTIVITY; METABOLIC FLUX; PRODUCTION PROPERTIES;

EID: 77950630135     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.copbio.2010.01.001     Document Type: Review
Times cited : (19)

References (43)
  • 1
    • 13344294402 scopus 로고    scopus 로고
    • Effect of glucose supply strategy on acetate accumulation, growth, and recombinant protein production by Escherichia coli BL21 (λDE3) and Escherichia coli JM109
    • Shiloach J., Kaufman J., Guillard A.S., Fass R. Effect of glucose supply strategy on acetate accumulation, growth, and recombinant protein production by Escherichia coli BL21 (λDE3) and Escherichia coli JM109. Biotechnol Bioeng 1996, 49:421-428.
    • (1996) Biotechnol Bioeng , vol.49 , pp. 421-428
    • Shiloach, J.1    Kaufman, J.2    Guillard, A.S.3    Fass, R.4
  • 2
    • 0026566666 scopus 로고
    • Optimal selection of metabolic fluxes for in vivo measurement. II. Application to Escherichia coli and hybridoma cell metabolism.
    • Savinell J.M., Palsson B.O. Optimal selection of metabolic fluxes for in vivo measurement. II. Application to Escherichia coli and hybridoma cell metabolism. J Theor Biol 1992, 155:215-242.
    • (1992) J Theor Biol , vol.155 , pp. 215-242
    • Savinell, J.M.1    Palsson, B.O.2
  • 3
    • 0032484705 scopus 로고    scopus 로고
    • Proposed mechanism of acetate accumulation in two recombinant Escherichia coli strains during high density fermentation
    • van de Walle M., Shiloach J. Proposed mechanism of acetate accumulation in two recombinant Escherichia coli strains during high density fermentation. Biotechnol Bioeng 1998, 57:71-78.
    • (1998) Biotechnol Bioeng , vol.57 , pp. 71-78
    • van de Walle, M.1    Shiloach, J.2
  • 4
    • 0001985853 scopus 로고
    • Flux determination in cellular bioreaction networks: applications to lysine fermentations
    • CRC Press, Boca Raton Florida, S.K. Sikdar, M. Bier, P. Todd (Eds.)
    • Vallino J.J., Stephanopoulos G. Flux determination in cellular bioreaction networks: applications to lysine fermentations. Frontiers in Bioprocessing 1990, 205-219. CRC Press, Boca Raton Florida. S.K. Sikdar, M. Bier, P. Todd (Eds.).
    • (1990) Frontiers in Bioprocessing , pp. 205-219
    • Vallino, J.J.1    Stephanopoulos, G.2
  • 8
    • 19944421092 scopus 로고    scopus 로고
    • Glucose metabolism at high density growth of E. coli B and E. coli K: differences in metabolic pathways are responsible for efficient glucose utilization in E. coli B as determined by microoarrays and northern blot analyses
    • Phue J.N., Noronha S.B., Hattacharyya R., Wolfe A.J., Shiloach J. Glucose metabolism at high density growth of E. coli B and E. coli K: differences in metabolic pathways are responsible for efficient glucose utilization in E. coli B as determined by microoarrays and northern blot analyses. Biotechnol Bioeng 2005, 90:805-820.
    • (2005) Biotechnol Bioeng , vol.90 , pp. 805-820
    • Phue, J.N.1    Noronha, S.B.2    Hattacharyya, R.3    Wolfe, A.J.4    Shiloach, J.5
  • 9
    • 1842582933 scopus 로고    scopus 로고
    • Transcription levels of key metabolic genes are the cause for different glucose utilization pathways in E. coli B (BL21) and E. coli K (JM109)
    • Phue J.N., Shiloach J. Transcription levels of key metabolic genes are the cause for different glucose utilization pathways in E. coli B (BL21) and E. coli K (JM109). J Biotechnol 2004, 109:21-30.
    • (2004) J Biotechnol , vol.109 , pp. 21-30
    • Phue, J.N.1    Shiloach, J.2
  • 10
    • 33846107981 scopus 로고    scopus 로고
    • Evaluating microarrays using a semiparametric approach: application to the central carbon metabolism of Escherichia coli BL21 and JM109
    • Phue J.N., Kedem B., Jaluria P., Shilocah J. Evaluating microarrays using a semiparametric approach: application to the central carbon metabolism of Escherichia coli BL21 and JM109. Genomics 2007, 89:300-305.
    • (2007) Genomics , vol.89 , pp. 300-305
    • Phue, J.N.1    Kedem, B.2    Jaluria, P.3    Shilocah, J.4
  • 11
    • 0004218135 scopus 로고    scopus 로고
    • Academic Press, G.N. Stephanopoulos, J. Nielsen, Aristidou A (Eds.)
    • Metabolic Engineering: Principles and Methodologies 1998, Academic Press. G.N. Stephanopoulos, J. Nielsen, Aristidou A (Eds.).
    • (1998) Metabolic Engineering: Principles and Methodologies
  • 13
    • 33748784390 scopus 로고    scopus 로고
    • Simultaneous quantitative analysis of metabolites using ion-pair liquid chromatographyelectrospray ionization mass spectrometry
    • Coulier L., Bas R., Jespersen S., Verheij E., van der Werf M.J., Hankemeier T. Simultaneous quantitative analysis of metabolites using ion-pair liquid chromatographyelectrospray ionization mass spectrometry. Anal Chem 2006, 78:6573-6582.
    • (2006) Anal Chem , vol.78 , pp. 6573-6582
    • Coulier, L.1    Bas, R.2    Jespersen, S.3    Verheij, E.4    van der Werf, M.J.5    Hankemeier, T.6
  • 16
    • 33746606019 scopus 로고    scopus 로고
    • Separation and quantitation of water soluble cellular metabolites by hydrophilic interaction chromatography- tandem mass spectrometry
    • Bajad S.U., Lu W., Kimball E.H., Yuan J., Peterson C., Rabinowitz J.D. Separation and quantitation of water soluble cellular metabolites by hydrophilic interaction chromatography- tandem mass spectrometry. J Chromatogr A 2006, 1125:76-88.
    • (2006) J Chromatogr A , vol.1125 , pp. 76-88
    • Bajad, S.U.1    Lu, W.2    Kimball, E.H.3    Yuan, J.4    Peterson, C.5    Rabinowitz, J.D.6
  • 17
    • 0028834386 scopus 로고
    • Single-run separation and detection of multiple metabolic intermediates by anion-exchange high-performance liquid chromatography and application to cell pool extracts prepared from Escherichia coli
    • Bhattacharya M., Fuhrman L., Ingram A., Nickerson K.W., Conway T. Single-run separation and detection of multiple metabolic intermediates by anion-exchange high-performance liquid chromatography and application to cell pool extracts prepared from Escherichia coli. Anal Biochem 1995, 232:98-106.
    • (1995) Anal Biochem , vol.232 , pp. 98-106
    • Bhattacharya, M.1    Fuhrman, L.2    Ingram, A.3    Nickerson, K.W.4    Conway, T.5
  • 18
    • 0036298294 scopus 로고    scopus 로고
    • Metabolomics: quantification of intracellular metabolite dynamics
    • Buchholz A., Hurlebaus J., Wandrey C., Takors R. Metabolomics: quantification of intracellular metabolite dynamics. Biomol Eng 2002, 19:5-15.
    • (2002) Biomol Eng , vol.19 , pp. 5-15
    • Buchholz, A.1    Hurlebaus, J.2    Wandrey, C.3    Takors, R.4
  • 19
    • 68049100110 scopus 로고    scopus 로고
    • Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli
    • Bennett B.D., Kimball E.H., Gao M., Osterhout R., Van Dien S.J., Rabinowitz J.D. Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat Chem Biol 2009, 5. pp. 593-559.
    • (2009) Nat Chem Biol , vol.5 , pp. 593-559
    • Bennett, B.D.1    Kimball, E.H.2    Gao, M.3    Osterhout, R.4    Van Dien, S.J.5    Rabinowitz, J.D.6
  • 20
    • 33144485880 scopus 로고    scopus 로고
    • Microbial metabolomics with gas chromatography/mass spectrometry
    • Koek M.M., Muilwijk B., van der Werf M.J., Hankemeier T. Microbial metabolomics with gas chromatography/mass spectrometry. Anal Chem 2006, 78:1272-1281.
    • (2006) Anal Chem , vol.78 , pp. 1272-1281
    • Koek, M.M.1    Muilwijk, B.2    van der Werf, M.J.3    Hankemeier, T.4
  • 21
    • 0037115531 scopus 로고    scopus 로고
    • Pressure-assisted capillary electrophoresis electrospray ionization mass spectrometry for analysis of multivalent anions
    • Soga T., Ueno Y., Naraoka H., Matsuda K., Tomita M., Nishioka T. Pressure-assisted capillary electrophoresis electrospray ionization mass spectrometry for analysis of multivalent anions. Anal Chem 2002, 74:6224-6229.
    • (2002) Anal Chem , vol.74 , pp. 6224-6229
    • Soga, T.1    Ueno, Y.2    Naraoka, H.3    Matsuda, K.4    Tomita, M.5    Nishioka, T.6
  • 22
    • 4344622634 scopus 로고    scopus 로고
    • Qualitative and quantitative analysis of amino acids by capillary electrophoresis-electrospray ionization-tandem mass spectrometry
    • Soga T., Kakazu Y., Robert M., Tomita M., Nishioka T. Qualitative and quantitative analysis of amino acids by capillary electrophoresis-electrospray ionization-tandem mass spectrometry. Electrophoresis 2004, 25:1964-1972.
    • (2004) Electrophoresis , vol.25 , pp. 1964-1972
    • Soga, T.1    Kakazu, Y.2    Robert, M.3    Tomita, M.4    Nishioka, T.5
  • 23
    • 34447276204 scopus 로고    scopus 로고
    • Direct measurement of isotopomer of intracellular metabolites using capillary electrophoresis time-of-flight mass spectrometry for efficient metabolic flux analysis
    • Toya Y., Ishii N., Hirasawa T., Naba M., Hirai K., Sugawara K., Igarashi S., Shimizu K., Tomita M., Soga T. Direct measurement of isotopomer of intracellular metabolites using capillary electrophoresis time-of-flight mass spectrometry for efficient metabolic flux analysis. J Chromatogr A 2007, 1159:134-141.
    • (2007) J Chromatogr A , vol.1159 , pp. 134-141
    • Toya, Y.1    Ishii, N.2    Hirasawa, T.3    Naba, M.4    Hirai, K.5    Sugawara, K.6    Igarashi, S.7    Shimizu, K.8    Tomita, M.9    Soga, T.10
  • 24
    • 17144387903 scopus 로고    scopus 로고
    • From stationary to instationary metabolic flux analysis
    • Wiechert W., Noh K. From stationary to instationary metabolic flux analysis. Adv Biochem Eng Biotechnol 2005, 92:145-172.
    • (2005) Adv Biochem Eng Biotechnol , vol.92 , pp. 145-172
    • Wiechert, W.1    Noh, K.2
  • 25
    • 16544366784 scopus 로고    scopus 로고
    • 13C-labeling experiments and integration of the information with gene and protein expression patterns
    • 13C-labeling experiments and integration of the information with gene and protein expression patterns. Adv Biochem Eng Biotechnol 2004, 91:1-49.
    • (2004) Adv Biochem Eng Biotechnol , vol.91 , pp. 1-49
    • Shimizu, K.1
  • 26
    • 0034741983 scopus 로고    scopus 로고
    • 13C metabolic flux analysis
    • 13C metabolic flux analysis. Metab Eng 2001, 3:195-206.
    • (2001) Metab Eng , vol.3 , pp. 195-206
    • Wiechert, W.1
  • 27
    • 50349092706 scopus 로고    scopus 로고
    • Kinetic flux profiling for quantitation of cellular metabolic fluxes
    • Yuan J., Bennett B.D., Rabinowitz J.D. Kinetic flux profiling for quantitation of cellular metabolic fluxes. Nat Protoc 2008, 3:1328-1340.
    • (2008) Nat Protoc , vol.3 , pp. 1328-1340
    • Yuan, J.1    Bennett, B.D.2    Rabinowitz, J.D.3
  • 29
    • 34447502083 scopus 로고    scopus 로고
    • Determination of metabolic flux ratios from 13C-experiments and gas chromatography-mass spectrometry data: protocol and principles
    • Nanchen A., Fuhrer T., Sauer U. Determination of metabolic flux ratios from 13C-experiments and gas chromatography-mass spectrometry data: protocol and principles. Methods Mol Biol 2007, 358:177-197.
    • (2007) Methods Mol Biol , vol.358 , pp. 177-197
    • Nanchen, A.1    Fuhrer, T.2    Sauer, U.3
  • 30
    • 0031555498 scopus 로고    scopus 로고
    • Comparative studies of Escherichia coli strains using different glucose uptake systems: Metabolism and energetics
    • Chen R., Yap W.M., Postma P.W., Bailey J.E. Comparative studies of Escherichia coli strains using different glucose uptake systems: Metabolism and energetics. Biotechnol Bioeng 1997, 56:583-590.
    • (1997) Biotechnol Bioeng , vol.56 , pp. 583-590
    • Chen, R.1    Yap, W.M.2    Postma, P.W.3    Bailey, J.E.4
  • 31
    • 38349132197 scopus 로고    scopus 로고
    • Role of GldA in dihydroxyacetone and methylglyoxal metabolism of Escherichia coli K12
    • Subedi K.P., Kim I., Kim J., Min B., Park C. Role of GldA in dihydroxyacetone and methylglyoxal metabolism of Escherichia coli K12. FEMS Microbiol Lett 2008, 279:180-187.
    • (2008) FEMS Microbiol Lett , vol.279 , pp. 180-187
    • Subedi, K.P.1    Kim, I.2    Kim, J.3    Min, B.4    Park, C.5
  • 32
    • 0033107827 scopus 로고    scopus 로고
    • Glucose catabolism of Escherichia coli strains with increased activity and altered regulation of key glycolytic enzymes
    • Emmerling M., Bailey J.E., Sauer U. Glucose catabolism of Escherichia coli strains with increased activity and altered regulation of key glycolytic enzymes. Metab Eng 1999, 1:117-127.
    • (1999) Metab Eng , vol.1 , pp. 117-127
    • Emmerling, M.1    Bailey, J.E.2    Sauer, U.3
  • 34
    • 71349087596 scopus 로고    scopus 로고
    • Enhancement of glutathione production with a tripeptidase-deficient recombinant Escherichia coli
    • Sep3
    • Lin J., Liao X., Zhang J., Du G., Chen J. Enhancement of glutathione production with a tripeptidase-deficient recombinant Escherichia coli. J Ind Microbiol Biotechnol 2009, Sep3.
    • (2009) J Ind Microbiol Biotechnol
    • Lin, J.1    Liao, X.2    Zhang, J.3    Du, G.4    Chen, J.5
  • 35
    • 61849139041 scopus 로고    scopus 로고
    • From proteome to genome for functional characterization of pH-dependent outer membrane proteins in Escherichia coli
    • Wu L., Lin X.M., Peng X.X. From proteome to genome for functional characterization of pH-dependent outer membrane proteins in Escherichia coli. J Proteome Res 2009, 8:1059-1070.
    • (2009) J Proteome Res , vol.8 , pp. 1059-1070
    • Wu, L.1    Lin, X.M.2    Peng, X.X.3
  • 37
    • 34447500551 scopus 로고    scopus 로고
    • Comparative genomic hybridization and physiological characterization of environmental isolates indicate that significant (eco-) physiological properties are highly conserved in the species Escherichia coli
    • Ihssen J., Grasselli E., Bassin C., Francois P., Piffaretti J.C., Koster W., Schrenzel J., Egli T. Comparative genomic hybridization and physiological characterization of environmental isolates indicate that significant (eco-) physiological properties are highly conserved in the species Escherichia coli. Microbiology 2007, 153:2052-2066.
    • (2007) Microbiology , vol.153 , pp. 2052-2066
    • Ihssen, J.1    Grasselli, E.2    Bassin, C.3    Francois, P.4    Piffaretti, J.C.5    Koster, W.6    Schrenzel, J.7    Egli, T.8
  • 38
    • 58249087221 scopus 로고    scopus 로고
    • The effect of heating rate on Escherichia coli metabolism, physiological stress, transcriptional response, and production of temperature-induced recombinant protein: a scale-down study
    • Caspeta L., Flores N., Perez N.O., Bolivar F., Ramirez O.T. The effect of heating rate on Escherichia coli metabolism, physiological stress, transcriptional response, and production of temperature-induced recombinant protein: a scale-down study. Biotechnol Bioeng 2009, 102:468-482.
    • (2009) Biotechnol Bioeng , vol.102 , pp. 468-482
    • Caspeta, L.1    Flores, N.2    Perez, N.O.3    Bolivar, F.4    Ramirez, O.T.5
  • 39
    • 0141429051 scopus 로고    scopus 로고
    • Gene expression patterns for metabolic pathway in pgi knockout Escherichia coli with and without phb genes based on RT-PCR
    • Kabir Md, Shimizu K. Gene expression patterns for metabolic pathway in pgi knockout Escherichia coli with and without phb genes based on RT-PCR. J Biotechnol 2003, 105:11-31.
    • (2003) J Biotechnol , vol.105 , pp. 11-31
    • Kabir, M.1    Shimizu, K.2
  • 40
    • 0344328817 scopus 로고    scopus 로고
    • An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
    • Reed J.L., Vo T.D., Schilling C.H., Palsson B.O. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol 2003, 4:R54.
    • (2003) Genome Biol , vol.4
    • Reed, J.L.1    Vo, T.D.2    Schilling, C.H.3    Palsson, B.O.4
  • 41
    • 0025866296 scopus 로고
    • Network rigidity and metabolic engineering in metabolite over production
    • Stephanopoulos G., Vallino J.J. Network rigidity and metabolic engineering in metabolite over production. Science 1991, 252:1675-1681.
    • (1991) Science , vol.252 , pp. 1675-1681
    • Stephanopoulos, G.1    Vallino, J.J.2
  • 43
    • 60349084386 scopus 로고    scopus 로고
    • Characterizing Escherichia coli DH5α growth and metabolism in a complex medium using genome-scale flux analysis
    • Selvarasu S., Ow D.S., Lee S.Y., Lee M.M., Oh S.K.W., Karimi I.A., Lee D.Y. Characterizing Escherichia coli DH5α growth and metabolism in a complex medium using genome-scale flux analysis. Biotechnol Bioeng 2009, 102:923-934.
    • (2009) Biotechnol Bioeng , vol.102 , pp. 923-934
    • Selvarasu, S.1    Ow, D.S.2    Lee, S.Y.3    Lee, M.M.4    Oh, S.K.W.5    Karimi, I.A.6    Lee, D.Y.7


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