메뉴 건너뛰기




Volumn 135, Issue 1, 2008, Pages 34-44

Monitoring of transcriptome and proteome profiles to investigate the cellular response of E. coli towards recombinant protein expression under defined chemostat conditions

Author keywords

E. coli; Ettan DIGE; MALDI; Microarray; Monitoring; Recombinant proteins; Stress response; Two dimensional gel electrophoresis

Indexed keywords

CHEMOSTATS; ELECTROPHORESIS; ESCHERICHIA COLI; GENE EXPRESSION; METABOLISM; STRESS ANALYSIS;

EID: 43049096460     PISSN: 01681656     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2008.02.013     Document Type: Article
Times cited : (45)

References (44)
  • 1
    • 8344256552 scopus 로고    scopus 로고
    • Recombinant protein folding and misfolding in Escherichia coli
    • Baneyx F., and Mujacic M. Recombinant protein folding and misfolding in Escherichia coli. Nat. Biotechnol. 22 (2004) 1399-1407
    • (2004) Nat. Biotechnol. , vol.22 , pp. 1399-1407
    • Baneyx, F.1    Mujacic, M.2
  • 2
    • 0028067436 scopus 로고
    • Inhibition of lipid biosynthesis induces the expression of the pspA gene
    • Bergler H., Abraham D., Aschauer H., and Turnowsky F. Inhibition of lipid biosynthesis induces the expression of the pspA gene. Microbiology 140 (1994) 1937-1944
    • (1994) Microbiology , vol.140 , pp. 1937-1944
    • Bergler, H.1    Abraham, D.2    Aschauer, H.3    Turnowsky, F.4
  • 3
    • 15444350252 scopus 로고    scopus 로고
    • The complete genome sequence of Escherichia coli K-12
    • 5331
    • Blattner F.R., Plunkett III G., Bloch C.A., Perna N.T., Burland V., et al. The complete genome sequence of Escherichia coli K-12. Science 5 277 (1997) 1453-1474 5331
    • (1997) Science , vol.5 , Issue.277 , pp. 1453-1474
    • Blattner, F.R.1    Plunkett III, G.2    Bloch, C.A.3    Perna, N.T.4    Burland, V.5
  • 4
    • 0031729344 scopus 로고    scopus 로고
    • Off-line quantitative monitoring of plasmid copy number in bacterial fermentation by capillary electrophoresis
    • Breuer S., Marzban G., Cserjan-Puschman M., Dürrschmid E., and Bayer K. Off-line quantitative monitoring of plasmid copy number in bacterial fermentation by capillary electrophoresis. Electrophoresis 19 14 (1998) 2474-2478
    • (1998) Electrophoresis , vol.19 , Issue.14 , pp. 2474-2478
    • Breuer, S.1    Marzban, G.2    Cserjan-Puschman, M.3    Dürrschmid, E.4    Bayer, K.5
  • 5
    • 0025731898 scopus 로고
    • Control of ColE1 plasmid replication by antisense RNA
    • Cesareni G., Helmer-Citterich M., and Castagnoli I. Control of ColE1 plasmid replication by antisense RNA. Trends Genet. 7 7 (1991) 230-235
    • (1991) Trends Genet. , vol.7 , Issue.7 , pp. 230-235
    • Cesareni, G.1    Helmer-Citterich, M.2    Castagnoli, I.3
  • 6
    • 0036069537 scopus 로고    scopus 로고
    • Gene expression profiling of Escherichia coli growth transitions: an expanded stringent response model
    • Chang D., Smalley D.J., and Conway T. Gene expression profiling of Escherichia coli growth transitions: an expanded stringent response model. Mol. Microbiol. 45 (2002) 289-306
    • (2002) Mol. Microbiol. , vol.45 , pp. 289-306
    • Chang, D.1    Smalley, D.J.2    Conway, T.3
  • 7
    • 0033565832 scopus 로고    scopus 로고
    • Role of accurate mass measurement (+-10 ppm) in protein identification strategies employing MS or MS/MS and database searching
    • Clauser K.R., Baker P., and Burlingame A.L. Role of accurate mass measurement (+-10 ppm) in protein identification strategies employing MS or MS/MS and database searching. Anal. Chem. 71 (1999) 2871-2882
    • (1999) Anal. Chem. , vol.71 , pp. 2871-2882
    • Clauser, K.R.1    Baker, P.2    Burlingame, A.L.3
  • 8
    • 26444526644 scopus 로고    scopus 로고
    • Sensor combination and chemometric modelling for improved process monitoring in recombinant E. coli fed-batch cultivations
    • Clementschitsch F., Jürgen F., Pötschacher F., and Bayer K. Sensor combination and chemometric modelling for improved process monitoring in recombinant E. coli fed-batch cultivations. J. Biotechnol. 120 (2005) 183-196
    • (2005) J. Biotechnol. , vol.120 , pp. 183-196
    • Clementschitsch, F.1    Jürgen, F.2    Pötschacher, F.3    Bayer, K.4
  • 10
    • 22644441730 scopus 로고    scopus 로고
    • The phage-shock-protein response
    • Darwin A.J. The phage-shock-protein response. Mol. Microbiol. 57 (2005) 621-628
    • (2005) Mol. Microbiol. , vol.57 , pp. 621-628
    • Darwin, A.J.1
  • 11
    • 0037269348 scopus 로고    scopus 로고
    • Monitoring shifts in quantitative protein patterns upon recombinant protein production in E.coli-a rational basis for process optimization
    • Dürrschmid K., Marzban G., Dürrschmid E., Striedner G., Clementschitsch F., Cserjan-Puschmann M., and Bayer K. Monitoring shifts in quantitative protein patterns upon recombinant protein production in E.coli-a rational basis for process optimization. Electrophoresis 24 1 (2003) 303-310
    • (2003) Electrophoresis , vol.24 , Issue.1 , pp. 303-310
    • Dürrschmid, K.1    Marzban, G.2    Dürrschmid, E.3    Striedner, G.4    Clementschitsch, F.5    Cserjan-Puschmann, M.6    Bayer, K.7
  • 13
    • 17644376529 scopus 로고    scopus 로고
    • Transcriptome profiles for high-cell density recombinant and wildtype Escherichia coli
    • Haddadin F.T., and Harcum S.W. Transcriptome profiles for high-cell density recombinant and wildtype Escherichia coli. Biotechnol. Bioeng. 90 2 (2004) 127-153
    • (2004) Biotechnol. Bioeng. , vol.90 , Issue.2 , pp. 127-153
    • Haddadin, F.T.1    Harcum, S.W.2
  • 14
    • 0027909877 scopus 로고
    • Response dynamics of 26-, 34-, 39-, 54-, and 80 kDa proteases in induced cultures of recombinant Escherichia coli
    • Harcum S.W., and Bentley W.E. Response dynamics of 26-, 34-, 39-, 54-, and 80 kDa proteases in induced cultures of recombinant Escherichia coli. Biotechnol. Bioeng. 42 (1993) 675-685
    • (1993) Biotechnol. Bioeng. , vol.42 , pp. 675-685
    • Harcum, S.W.1    Bentley, W.E.2
  • 15
    • 33745127048 scopus 로고    scopus 로고
    • The Escherichia coli proteome: past, present, and future prospects
    • Han M., and Lee S.Y. The Escherichia coli proteome: past, present, and future prospects. Microbiol. Mol. Biol. Rev. 70 (2006) 362-439
    • (2006) Microbiol. Mol. Biol. Rev. , vol.70 , pp. 362-439
    • Han, M.1    Lee, S.Y.2
  • 16
    • 0141831778 scopus 로고    scopus 로고
    • A proteomic view of cell physiology of Bacillus subtilis-bringing the genome sequence to life
    • Hecker M. A proteomic view of cell physiology of Bacillus subtilis-bringing the genome sequence to life. Adv. Biochem. Eng. Biotechnol. 83 (2003) 57-92
    • (2003) Adv. Biochem. Eng. Biotechnol. , vol.83 , pp. 57-92
    • Hecker, M.1
  • 18
    • 0036198628 scopus 로고    scopus 로고
    • Recent insights into the general stress response regulatory network in Escherichia coli
    • Hengge-Aronis R. Recent insights into the general stress response regulatory network in Escherichia coli. J. Mol. Microbiol. Biotechnol. 4 3 (2002) 341-346
    • (2002) J. Mol. Microbiol. Biotechnol. , vol.4 , Issue.3 , pp. 341-346
    • Hengge-Aronis, R.1
  • 19
    • 2942755215 scopus 로고    scopus 로고
    • Stress induced by recombinant protein production in Escherichia Coli
    • Hoffmann F., and Rinas U. Stress induced by recombinant protein production in Escherichia Coli. Adv. Biochem. Eng./Biotechnol. 89 (2004) 73-92
    • (2004) Adv. Biochem. Eng./Biotechnol. , vol.89 , pp. 73-92
    • Hoffmann, F.1    Rinas, U.2
  • 20
    • 34247107662 scopus 로고    scopus 로고
    • Effect of Cy-Dye minimum labeling in DIGE on the reliability of protein identification
    • Hrebicek T., Dürrschmid K., Auer N., Bayer K., and Rizzi A. Effect of Cy-Dye minimum labeling in DIGE on the reliability of protein identification. Electrophoresis 28 (2007) 1161-1169
    • (2007) Electrophoresis , vol.28 , pp. 1161-1169
    • Hrebicek, T.1    Dürrschmid, K.2    Auer, N.3    Bayer, K.4    Rizzi, A.5
  • 21
    • 33746361219 scopus 로고    scopus 로고
    • Induction and function of the phage-shock-protein (Psp) extracytoplasmic stress response in Escherichia coli
    • Jovanovic G., Lloyd L.J., Stumpf M.P.H., Mayhew A.J., and Buck M. Induction and function of the phage-shock-protein (Psp) extracytoplasmic stress response in Escherichia coli. J. Biol. Chem. 281 30 (2006) 21147-21161
    • (2006) J. Biol. Chem. , vol.281 , Issue.30 , pp. 21147-21161
    • Jovanovic, G.1    Lloyd, L.J.2    Stumpf, M.P.H.3    Mayhew, A.J.4    Buck, M.5
  • 22
    • 0034693456 scopus 로고    scopus 로고
    • Monitoring of genes that respond to overproduction of an insoluble recombinant protein in E. coli fed-batch fermentations
    • Jürgen B., Lin H.Y., Riemschneider S., Scharf C., Neubauer P., Schmid R., Hecker M., and Schweder T. Monitoring of genes that respond to overproduction of an insoluble recombinant protein in E. coli fed-batch fermentations. Biotechnol. Bioeng. 70 2 (2000) 217-224
    • (2000) Biotechnol. Bioeng. , vol.70 , Issue.2 , pp. 217-224
    • Jürgen, B.1    Lin, H.Y.2    Riemschneider, S.3    Scharf, C.4    Neubauer, P.5    Schmid, R.6    Hecker, M.7    Schweder, T.8
  • 23
    • 0024289037 scopus 로고
    • Laser desorption ionization of proteins with molecular masses exceeding 10 000 daltons
    • Karas M., and Hillenkamp F. Laser desorption ionization of proteins with molecular masses exceeding 10 000 daltons. Anal. Chem. 60 20 (1988) 2299-2301
    • (1988) Anal. Chem. , vol.60 , Issue.20 , pp. 2299-2301
    • Karas, M.1    Hillenkamp, F.2
  • 24
    • 0016637146 scopus 로고
    • Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues- a novel approach to testing for induced point mutations in mammals
    • Klose J. Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues- a novel approach to testing for induced point mutations in mammals. Humangenetik 26 (1975) 231-243
    • (1975) Humangenetik , vol.26 , pp. 231-243
    • Klose, J.1
  • 26
    • 1842478364 scopus 로고    scopus 로고
    • Recombinant proteins and host cell physiology
    • Lotti M., Porro D., and Srienc F. Recombinant proteins and host cell physiology. J. Biotechnol. 109 (2004) 1-2
    • (2004) J. Biotechnol. , vol.109 , pp. 1-2
    • Lotti, M.1    Porro, D.2    Srienc, F.3
  • 27
    • 0242386460 scopus 로고    scopus 로고
    • Identifying global regulators in transcriptional regulatory networks in bacteria
    • Martinez-Antonio A., and Collado Vides J. Identifying global regulators in transcriptional regulatory networks in bacteria. Curr. Opin. Microbiol. 6 (2003) 482-489
    • (2003) Curr. Opin. Microbiol. , vol.6 , pp. 482-489
    • Martinez-Antonio, A.1    Collado Vides, J.2
  • 28
    • 0142125283 scopus 로고    scopus 로고
    • Small heat shock proteins, ClpB and the DnaK system form a functional triade in reversing protein aggregation
    • Mogk A., Deuerline E., Vorderwülbecke S., Vierling E., and Bukau B. Small heat shock proteins, ClpB and the DnaK system form a functional triade in reversing protein aggregation. Mol. Microbiol. 50 2 (2003) 585-595
    • (2003) Mol. Microbiol. , vol.50 , Issue.2 , pp. 585-595
    • Mogk, A.1    Deuerline, E.2    Vorderwülbecke, S.3    Vierling, E.4    Bukau, B.5
  • 30
    • 0842346041 scopus 로고    scopus 로고
    • Evaluation of the GFP signal and its aptitude for novel on-line monitoring strategies of recombinant fermentation processes
    • Reischer H., Schotola I., Striedner G., Pötschacher F., and Bayer K. Evaluation of the GFP signal and its aptitude for novel on-line monitoring strategies of recombinant fermentation processes. J. Biotechnol. 108 2 (2004) 115-125
    • (2004) J. Biotechnol. , vol.108 , Issue.2 , pp. 115-125
    • Reischer, H.1    Schotola, I.2    Striedner, G.3    Pötschacher, F.4    Bayer, K.5
  • 31
    • 33645467362 scopus 로고    scopus 로고
    • Comparative proteome analysis of Staphylococcus aureus biofilm and planktonic cells and correlation with transcriptome profiling
    • Resch A., Leicht S., Saric M., Paszto L., et al. Comparative proteome analysis of Staphylococcus aureus biofilm and planktonic cells and correlation with transcriptome profiling. Proteomics 6 (2006) 1867-1877
    • (2006) Proteomics , vol.6 , pp. 1867-1877
    • Resch, A.1    Leicht, S.2    Saric, M.3    Paszto, L.4
  • 32
    • 0031861223 scopus 로고    scopus 로고
    • Genes and proteins of E. coli K-12 (GenProtEC)
    • Riley M. Genes and proteins of E. coli K-12 (GenProtEC). Nucleic Acids Res. 26 1 (1998) 54
    • (1998) Nucleic Acids Res. , vol.26 , Issue.1 , pp. 54
    • Riley, M.1
  • 33
    • 0025330210 scopus 로고
    • Estimation of cellular DNA content in cell lysates suitable for RNA isolation
    • Rymaszewski Z., Abplanalp W.A., Cohen R.M., and Chomczynski P. Estimation of cellular DNA content in cell lysates suitable for RNA isolation. Anal. Biochem. 188 1 (1990) 91-96
    • (1990) Anal. Biochem. , vol.188 , Issue.1 , pp. 91-96
    • Rymaszewski, Z.1    Abplanalp, W.A.2    Cohen, R.M.3    Chomczynski, P.4
  • 35
    • 0027427986 scopus 로고
    • DnaK, DnaJ. GrpE form a cellular chaperone machinery capable of repairing heat-induced protein damage
    • Schröder H., Langer T., Hartl F.-U., and Bukau B. DnaK, DnaJ. GrpE form a cellular chaperone machinery capable of repairing heat-induced protein damage. EMBO J. 12 (1993) 4137-4144
    • (1993) EMBO J. , vol.12 , pp. 4137-4144
    • Schröder, H.1    Langer, T.2    Hartl, F.-U.3    Bukau, B.4
  • 36
    • 0029927505 scopus 로고    scopus 로고
    • Mass spectrometric sequencing of proteins from silver-stained polyacrylamide gels
    • Shevchenko A., Wilm M., Vorm O., and Mann M. Mass spectrometric sequencing of proteins from silver-stained polyacrylamide gels. Anal Chem. 68 5 (1996) 850-858
    • (1996) Anal Chem. , vol.68 , Issue.5 , pp. 850-858
    • Shevchenko, A.1    Wilm, M.2    Vorm, O.3    Mann, M.4
  • 37
    • 0343376097 scopus 로고    scopus 로고
    • Difference gel electrophoresis: a single gel method for detecting changes in protein extracts
    • Ünlü M., Morgan M.E., and Minden J.S. Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 18 (1997) 2071-2077
    • (1997) Electrophoresis , vol.18 , pp. 2071-2077
    • Ünlü, M.1    Morgan, M.E.2    Minden, J.S.3
  • 38
    • 0000094029 scopus 로고
    • Improved resolution and very high sensitivity in MALDI TOF of matrix surfaces made by fast evaporation
    • Vorm O., Roepstorff P., and Mann M. Improved resolution and very high sensitivity in MALDI TOF of matrix surfaces made by fast evaporation. Anal. Chem. 66 (1994) 3281-3287
    • (1994) Anal. Chem. , vol.66 , pp. 3281-3287
    • Vorm, O.1    Roepstorff, P.2    Mann, M.3
  • 39
    • 3142678124 scopus 로고    scopus 로고
    • Molecular components of physiological responses in Escherichia Coli
    • Wick L.M., and Egli T. Molecular components of physiological responses in Escherichia Coli. Adv. Biochem. Eng./Biotechnol. 89 (2004) 1-45
    • (2004) Adv. Biochem. Eng./Biotechnol. , vol.89 , pp. 1-45
    • Wick, L.M.1    Egli, T.2
  • 41
    • 0036907867 scopus 로고    scopus 로고
    • Fluorescence two-dimensional difference gel electrophoresis and mass spectrometry based proteomic analysis of Escherichia coli
    • Yan J.X., Devenish A.T., Wait R., Stone T., Lewis S., and Fowler S. Fluorescence two-dimensional difference gel electrophoresis and mass spectrometry based proteomic analysis of Escherichia coli. Proteomics 2 (2002) 1682-1698
    • (2002) Proteomics , vol.2 , pp. 1682-1698
    • Yan, J.X.1    Devenish, A.T.2    Wait, R.3    Stone, T.4    Lewis, S.5    Fowler, S.6
  • 42
    • 1342294092 scopus 로고    scopus 로고
    • Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation
    • Yang Y.H., Dudoit S., Luu P., Lin D.M., Peng V., Ngai J., and Speed T.P. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30 4 (2002) e15
    • (2002) Nucleic Acids Res. , vol.30 , Issue.4
    • Yang, Y.H.1    Dudoit, S.2    Luu, P.3    Lin, D.M.4    Peng, V.5    Ngai, J.6    Speed, T.P.7
  • 43
    • 0024293671 scopus 로고
    • What does the homology between E. coli tRNAs and RNAs controlling ColE1 plasmid replication mean?
    • Yavachev L., and Ivanov I. What does the homology between E. coli tRNAs and RNAs controlling ColE1 plasmid replication mean?. J. Theor. Biol. 131 2 (1988) 235-241
    • (1988) J. Theor. Biol. , vol.131 , Issue.2 , pp. 235-241
    • Yavachev, L.1    Ivanov, I.2
  • 44
    • 0037473189 scopus 로고    scopus 로고
    • Combined transcriptome and proteome analysis of Escherichia Coli during high cell density culture
    • Yoon S.H., Han M.J., Lee S.Y., Jeong K.J., and Yoo J. Combined transcriptome and proteome analysis of Escherichia Coli during high cell density culture. Biotechnol. Bioeng. 81 7 (2003) 753-767
    • (2003) Biotechnol. Bioeng. , vol.81 , Issue.7 , pp. 753-767
    • Yoon, S.H.1    Han, M.J.2    Lee, S.Y.3    Jeong, K.J.4    Yoo, J.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.