Biochemistry, Genetics and Molecular Biology » "Advances in Applied Biotechnology", book edited by Marian Petre, ISBN 978-953-307-820-5, Published: January 20, 2012 under CC BY 3.0 license

Chapter 6

Increasing Recombinant Protein Production in E. coli by an Alternative Method to Reduce Acetate

By Hendrik Waegeman and Marjan De Mey
DOI: 10.5772/30726

  1. A. M. Abdallah, N. C. G. van Pittius, P. A. D. Champion, J. Cox, J. Luirink, C. M. J. E. Vandenbroucke-Grauls, B. J. Appelmelk, W. Bitter, 2007 Type VII secretion-mycobacteria show the way. Nat Rev Microbiol, 5 883 891

  2. M. Abu-Qarn, J. Eichler, N. Sharon, 2008 Not just for Eukarya anymore: protein glycosylation in Bacteria and Archaea. Curr Opin Struct Biol, 18 544 550

  3. M. Akesson, P. Hagander, J. P. Axelsson, 2001a Avoiding acetate accumulation in Escherichia coli cultures using feedback control of glucose feeding. Biotechnology and Bioengineering, 73 223 230

  4. M. Akesson, P. Hagander, J. P. Axelsson, 2001b Probing control of fed-batch cultivations: analysis and tuning. Control Engineering Practice, 9 709 723

  5. M. Akesson, E. N. Karlsson, P. Hagander, J. P. Axelsson, A. Tocaj, 1999 On-line detection of acetate formation in Escherichia coli cultures using dissolved oxygen responses to feed transients. Biotechnology and Bioengineering, 64 590 598

  6. S. Alexeeva, K. J. Hellingwerf, M. J. T. de Mattos, 2003 Requirement of ArcA for redox regulation in Escherichia coli under microaerobic but not anaerobic or aerobic conditions. J Bacteriol, 185 204 209

  7. K. B. Andersen, K. von Meyenburg, 1980 Are growth rates of Escherichia coli in batch cultures limited by respiration? J Bacteriol, 144 114 123

  8. W. E. Bentley, N. Mirjalili, D. C. Andersen, R. H. Davis, D. S. Kompala, 1990 Plasmid-encoded protein: the principal factor in the "metabolic burden" associated with recombinant bacteria. Biotechnol Bioeng, 35 668 681

  9. X. Chen, P. Cen, J. Chen, 2005 Enhanced production of human epidermal growth factor by a recombinant Escherichia coli integrated with in situ exchange of acetic acid by macroporous ion-exchange resin. Journal of Bioscience and Bioengineering, 100 579 581

  10. J. H. Choi, S. Y. Lee, 2004 Secretory and extracellular production of recombinant proteins using Escherichia coli. Appl Microbiol Biotechnol, 64 625 635

  11. C. H. Chou, G. N. Bennett, K. Y. San, 1994 Effect of modified glucose uptake using genetic engineering techniques on high-level recombinant protein production in Escherichia coli dense cultures. Biotechnol Bioeng, 44 952 960

  12. C. P. Chou, 2007 Engineering cell physiology to enhance recombinant protein production in Escherichia coli. Appl Microbiol Biotechnol, 76 521 532

  13. S. N. Cohen, A. C. Chang, H. W. Boyer, R. B. Helling, 1973 Construction of biologically functional bacterial plasmids in vitro. Proc Natl Acad Sci U S A, 70 3240 3244

  14. J. Contiero, C. Beatty, S. Kumari, C. De Santi, W. Strohl, A. Wolfe, 2000 Effects of mutations in acetate metabolism on high-cell-density growth of Escherichia coli. J Ind Microbiol Biotechnol, 24 421 430

  15. J. C. Cortay, D. Nègre, A. Galinier, B. Duclos, G. Perrière, A. J. Cozzone, 1991 Regulation of the acetate operon in Escherichia coli: purification and functional characterization of the IclR repressor. EMBO J, 10 675 679

  16. A. J. Cozzone, 1998 Regulation of acetate metabolism by protein phosphorylation in enteric bacteria. Annu Rev Microbiol, 52 127 164

  17. R. De Anda, A. R. Lara, V. Hernández, V. Hernández-Montalvo, G. Gosset, F. Bolívar, O. T. Ramírez, 2006 Replacement of the glucose phosphotransferase transport system by galactose permease reduces acetate accumulation and improves process performance of Escherichia coli for recombinant protein production without impairment of growth rate. Metab Eng, 8 281 290

  18. A. de Marco, 2009 Strategies for successful recombinant expression of disulfide bond-dependent proteins in Escherichia coli. Microb Cell Fact, 8 26

  19. M. De Mey, G. J. Lequeux, J. J. Beauprez, J. Maertens, E. Van Horen, W. K. Soetaert, P. A. Vanrolleghem, E. J. Vandamme, 2007a Comparison of different strategies to reduce acetate formation in Escherichia coli. Biotechnol Prog, 23 1053 1063

  20. M. De Mey, G. J. Lequeux, J. J. Beauprez, J. Maertens, H. J. Waegeman, I. N. Van Bogaert, M. R. Foulquie-Moreno, D. Charlier, W. K. Soetaert, P. A. Vanrolleghem, E. J. Vandamme, 2010 Transient metabolic modeling of Escherichia coli MG1655 and MG1655 DeltaackA-pta, DeltapoxB Deltapppc ppc-p37 for recombinant beta-galactosidase production. J Ind Microbiol Biotechnol, 37 793 803

  21. M. De Mey, S. D. Maeseneire, W. Soetaert, E. Vandamme, 2007b Minimizing acetate formation in E. coli fermentations. J Ind Microbiol Biotechnol, 34 689 700

  22. A. L. Demain, P. Vaishnav, 2009 Production of recombinant proteins by microbes and higher organisms. Biotechnol Adv, 27 297 306

  23. J. C. Diaz-Ricci, L. Regan, J. E. Bailey, 1991 Effect of alteration of the acetic acid synthesis pathway on the fermentation pattern of Escherichia coli. Biotechnol Bioeng, 38 1318 1324

  24. C. R. Dittrich, R. V. Vadali, G. N. Bennett, K.-Y. San, 2005 Redistribution of metabolic fluxes in the central aerobic metabolic pathway of E. coli mutant strains with deletion of the ackA-pta and poxB pathways for the synthesis of isoamyl acetate. Biotechnol Prog, 21 627 631

  25. H. Dong, L. Nilsson, C. G. Kurland, 1995 Gratuitous overexpression of genes in Escherichia coli leads to growth inhibition and ribosome destruction. J Bacteriol, 177 1497 1504

  26. Y. Durocher, M. Butler, 2009 Expression systems for therapeutic glycoprotein production. Curr Opin Biotechnol, 20 700 707

  27. M. A. Eiteman, E. Altman, 2006 Overcoming acetate in Escherichia coli recombinant protein fermentations. Trends in Biotechnology, 24 530 533

  28. E. M. El-Mansi, W. H. Holms, 1989 Control of carbon flux to acetate excretion during growth of Escherichia coli in batch and continuous cultures. J Gen Microbiol, 135 2875 2883

  29. M. El-Mansi, A. J. Cozzone, J. Shiloach, B. J. Eikmanns, 2006 Control of carbon flux through enzymes of central and intermediary metabolism during growth of Escherichia coli on acetate. Curr Opin Microbiol, 9 173 179

  30. W. R. Farmer, J. C. Liao, 1997 Reduction of aerobic acetate production by Escherichia coli. Appl Environ Microbiol, 63 3205 3210

  31. N. Ferrer-Miralles, J. Domingo-Espín, J. L. Corchero, E. Vázquez, A. Villaverde, 2009 Microbial factories for recombinant pharmaceuticals. Microb Cell Fact, 8 17

  32. E. Fischer, U. Sauer, 2003 A novel metabolic cycle catalyzes glucose oxidation and anaplerosis in hungry Escherichia coli. J Biol Chem, 278 46446 46451

  33. A. C. Fisher, C. H. Haitjema, C. Guarino, E. Çelik, C. E. Endicott, C. A. Reading, J. H. Merritt, A. C. Ptak, S. Zhang, M. P. De Lisa, 2011 Production of secretory and extracellular N-linked glycoproteins in Escherichia coli. Appl Environ Microbiol, 77 871 881

  34. C. Fuchs, D. Koster, S. Wiebusch, K. Mahr, G. Eisbrenner, H. Markl, 2002 Scale-up of dialysis fermentation for high cell density cultivation of Escherichia coli. Journal of Biotechnology, 93 243 251

  35. R. T. Gill, J. J. Valdes, W. E. Bentley, 2000 A comparative study of global stress gene regulation in response to overexpression of recombinant proteins in Escherichia coli. Metab Eng, 2 178 189

  36. Global Industry Analysts, I. 2011 Global Industrial Enzymes, In: PRWeb, July 20, 2011, Available from: http://www.prweb.com/releases/industrial_enzymes/proteases_carbohydrases/prweb8121185.htm.

  37. S. Gottesman, 1984 Bacterial regulation: global regulatory networks. Annu Rev Genet, 18 415 441

  38. S. Gottesman, 1989 Genetics of proteolysis in Escherichia coli. Annu Rev Genet, 23 163 198

  39. S. Gottesman, 1996 Proteases and their targets in Escherichia coli. Annu Rev Genet, 30 465 506

  40. S. Gottesman, M. R. Maurizi, 1992 Regulation by proteolysis: energy-dependent proteases and their targets. Microbiol Rev, 56 592 621

  41. J. Hodgson, 1994 The changing bulk biocatalyst market. Nat Biotechnol, 12 789 790

  42. F. Hoffmann, U. Rinas, 2004 Stress induced by recombinant protein production in Escherichia coli. Adv Biochem Eng Biotechnol, 89 73 92

  43. W. H. Holms, 1986 The central metabolic pathways of Escherichia coli: relationship between flux and control at a branch point, efficiency of conversion to biomass, and excretion of acetate. Curr Top Cell Regul, 28 69 105

  44. S. Iuchi, E. C. Lin, 1988 arcA (dye), a global regulatory gene in Escherichia coli mediating repression of enzymes in aerobic pathways. Proc Natl Acad Sci U S A, 85 1888 1892

  45. S. Iuchi, Z. Matsuda, T. Fujiwara, E. C. Lin, 1990 The arcB gene of Escherichia coli encodes a sensor-regulator protein for anaerobic repression of the arc modulon. Mol Microbiol, 4 715 727

  46. E. B. Jensen, S. Carlsen, 1990 Production of recombinant human growth hormone in Escherichia coli: expression of different precursors and physiological effects of glucose, acetate, and salts. Biotechnol Bioeng, 36 1 11

  47. W. S. P. Jong, A. Saurí, J. Luirink, 2010 Extracellular production of recombinant proteins using bacterial autotransporters. Curr Opin Biotechnol, 21 646 652

  48. B. Jürgen, A. Breitenstein, V. Urlacher, K. Büttner, H. Lin, M. Hecker, T. Schweder, P. Neubauer, 2010 Quality control of inclusion bodies in Escherichia coli. Microb Cell Fact, 9 41

  49. I. M. Keseler, J. Collado-Vides, A. Santos-Zavaleta, M. Peralta-Gil, S. Gama-Castro, L. Muniz-Rascado, C. Bonavides-Martinez, S. Paley, M. Krummenacker, T. Altman, P. Kaipa, A. Spaulding, J. Pacheco, M. Latendresse, C. Fulcher, M. Sarker, A. G. Shearer, A. Mackie, I. Paulsen, R. P. Gunsalus, P. D. Karp, 2011 EcoCyc: a comprehensive database of Escherichia coli biology. Nucleic Acids Research, 39 D583 D590

  50. C.-H. Ko, C.-H. Tsai, P.-H. Lin, K.-C. Chang, J. Tu, Y.-N. Wang, C.-Y. Yang, 2010 Characterization and pulp refining activity of a Paenibacillus campinasensis cellulase expressed in Escherichia coli. Bioresour Technol.

  51. C. G. Kurland, H. Dong, 1996 Bacterial growth inhibition by overproduction of protein. Mol Microbiol, 21 1 4

  52. M. Lotti, D. Porro, F. Srienc, 2004 Recombinant proteins and host cell physiology. J Biotechnol, 109 1 2

  53. R. P. Maharjan, P.-L. Yu, S. Seeto, T. Ferenci, 2005 The role of isocitrate lyase and the glyoxylate cycle in Escherichia coli growing under glucose limitation. Res Microbiol, 156 178 183

  54. S. C. Makrides, 1996 Strategies for achieving high-level expression of genes in Escherichia coli. Microbiol Rev, 60 512 538

  55. J. C. March, M. A. Eiteman, E. Altman, 2002 Expression of an anaplerotic enzyme, pyruvate carboxylase, improves recombinant protein production in Escherichia coli. Appl Environ Microbiol, 68 5620 5624

  56. A. Martinez-Antonio, J. Collado-Vides, 2003 Identifying global regulators in transcriptional regulatory networks in bacteria. Curr Opin Microbiol, 6 482 489

  57. K. Nakano, M. Rischke, S. Sato, H. Märkl, 1997 Influence of acetic acid on the growth of Escherichia coli K12 during high-cell-density cultivation in a dialysis reactor. Appl Microbiol Biotechnol, 48 597 601

  58. D. Noack, M. Roth, R. Geuther, G. Muller, K. Undisz, C. Hoffmeier, S. Gaspar, 1981 Maintenance and genetic stability of vector plasmids pBR322 and pBR325 in Escherichia coli K12 strains grown in a chemostat. Mol Gen Genet, 184 121 124

  59. S. B. Noronha, H. J. Yeh, T. F. Spande, J. Shiloach, 2000 Investigation of the TCA cycle and the glyoxylate shunt in Escherichia coli BL21 and JM109 using (13)C-NMR/MS. Biotechnol Bioeng, 68 316 327

  60. D. A. Parsell, R. T. Sauer, 1989 Induction of a heat shock-like response by unfolded protein in Escherichia coli: dependence on protein level not protein degradation. Genes Dev, 3 1226 1232

  61. A. Perrenoud, U. Sauer, 2005 Impact of global transcriptional regulation by ArcA, ArcB, Cra, Crp, Cya, Fnr, and Mlc on glucose catabolism in Escherichia coli. J Bacteriol, 187 3171 3179

  62. J.-N. Phue, S. B. Noronha, A. J. Ritabrata Wolfe, J. Shiloach, 2005 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 microarrays and Northern blot analyses. Biotechnol Bioeng, 90 805 820

  63. K. Rittinger, D. Negre, G. Divita, M. Scarabel, C. Bonod-Bidaud, R. S. Goody, A. J. Cozzone, J. C. Cortay, 1996 Escherichia coli isocitrate dehydrogenase kinase/phosphatase. Eur J Biochem, 237 247 254

  64. K. Ryu, K.-H. Kim, S.-Y. Yoo, E.-Y. Lee, K.-H. Lim, M.-K. Min, H. Kim, S. I. Choi, B. L. Seong, 2010 Production and characterization of active hepatitis C virus RNA-dependent RNA polymerase. Protein Expr Purif, 71 147 152

  65. S. Sahdev, S. K. Khattar, K. S. Saini, 2008 Production of active eukaryotic proteins through bacterial expression systems: a review of the existing biotechnology strategies. Mol Cell Biochem, 307 249 264

  66. K. A. Salmon, S.-p. Hung, N. R. Steffen, R. Krupp, P. Baldi, G. W. Hatfield, R. P. Gunsalus, 2005 Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA. J Biol Chem, 280 15084 15096

  67. J. Shiloach, J. Kaufman, A. S. Guillard, R. Fass, 1996 Effect of glucose supply strategy on acetate accumulation, growth, and recombinant protein production by Escherichia coli BL21 ($\lambda$DE3) and Escherichia coli JM109. Biotechnol Bioeng, 49 421 428

  68. R. Siguenza, N. Flores, G. Hernandez, A. Martinez, F. Bolivar, F. Valle, 1999 Kinetic characterization in batch and continuous culture of Escherichia coli mutants affected in phosphoenolpyruvate metabolism: differences in acetic acid production. World J Microbiol Biotechnol, 15 587 592

  69. G. Striedner, I. Pfaffenzeller, L. Markus, S. Nemecek, R. Grabherr, K. Bayer, 2010 Plasmid-free T7-based Escherichia coli expression systems. Biotechnol Bioeng, 105 786 794

  70. C. M. Szymanski, R. Yao, C. P. Ewing, T. J. Trust, P. Guerry, 1999 Evidence for a system of general protein glycosylation in Campylobacter jejuni. Mol Microbiol, 32 1022 1030

  71. K. Terpe, 2006 Overview of bacterial expression systems for heterologous protein production: from molecular and biochemical fundamentals to commercial systems. Appl Microbiol Biotechnol, 72 211 222

  72. T.-T. Tseng, B. M. Tyler, J. C. Setubal, 2009 Protein secretion systems in bacterial-host associations, and their description in the Gene Ontology. BMC Microbiol, 9 S2

  73. A. Varma, B. W. Boesch, B. O. Palsson, 1993a Biochemical production capabilities of Escherichia coli. Biotechnol Bioeng, 42 59 73

  74. A. Varma, B. W. Boesch, B. O. Palsson, 1993b Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates. Appl Environ Microbiol, 59 2465 2473

  75. S. Ventura, A. Villaverde, 2006 Protein quality in bacterial inclusion bodies. Trends Biotechnol, 24 179 185

  76. M. Wacker, D. Linton, P. G. Hitchen, M. Nita-Lazar, S. M. Haslam, S. J. North, M. Panico, H. R. Morris, A. Dell, B. W. Wren, M. Aebi, 2002 N-linked glycosylation in Campylobacter jejuni and its functional transfer into E. coli. Science, 298 1790 1793

  77. H. Waegeman, J. Beauprez, H. Moens, J. Maertens, M. De Mey, M. R. Foulquie-Moreno, J. J. Heijnen, D. Charlier, W. Soetaert, 2011a Effect of iclR and arcA knockouts on biomass formation and metabolic fluxes in Escherichia coli K12 and its implications on understanding the metabolism of Escherichia coli BL21 (DE3). BMC Microbiol, 11 70

  78. H. Waegeman, S. De Lausnay, J. Beauprez, J. Maertens, M. De Mey, W. Soetaert, 2011b Increasing recombinant protein production in Escherichia coli K12 through metabolic engineering. New Biotechnology, submitted

  79. H. Waegeman, J. Maertens, J. Beauprez, M. De Mey, W. Soetaert, 2011c Effect of iclR and arcA deletion on physiology and metabolic fluxes in Escherichia coli BL21(DE3). Biotechnology Progress, in press

  80. H. Waegeman, W. Soetaert, 2011 Increasing recombinant protein production in Escherichia coli through metabolic and genetic engineering. Journal of Industrial Microbiology and Biotechnology, accepted

  81. G. Walsh, 2010 Post-translational modifications of protein biopharmaceuticals. Drug Discov Today, 15 773 780

  82. M. S. Wong, S. Wu, T. B. Causey, G. N. Bennett, K.-Y. San, 2008 Reduction of acetate accumulation in Escherichia coli cultures for increased recombinant protein production. Metab Eng, 10 97 108

  83. K. Yamamoto, A. Ishihama, 2003 Two different modes of transcription repression of the Escherichia coli acetate operon by IclR. Mol Microbiol, 47 183 194

  84. Y. T. Yang, A. A. Aristidou, K. Y. San, G. N. Bennett, 1999 Metabolic flux analysis of Escherichia coli deficient in the acetate production pathway and expressing the Bacillus subtilis acetolactate synthase. Metab Eng, 1 26 34