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Applied Microbiology and Biotechnology

, Volume 67, Issue 3, pp 289–298 | Cite as

RETRACTED ARTICLE: Strategies for efficient production of heterologous proteins in Escherichia coli

  • S. Jana
  • J. K. DebEmail author
Mini-Review

Abstract

In recent years, the number of recombinant proteins used for therapeutic applications has increased dramatically. Production of these proteins has a remarkable demand in the market. Escherichia coli offers a means for the rapid and economical production of recombinant proteins. These advantages, coupled with a wealth of biochemical and genetic knowledge, have enabled the production of such economically therapeutic proteins such as insulin and bovine growth hormone. These demands have driven the development of a variety of strategies for achieving high-level expression of protein, particularly involving several aspects such as expression vectors design, gene dosage, promoter strength (transcriptional regulation), mRNA stability, translation initiation and termination (translational regulation), host design considerations, codon usage, and fermentation factors available for manipulating the expression conditions, which are the major challenges is obtaining the high yield of protein at low cost.

Keywords

Codon Codon Usage Recombinant Protein Production Plasmid Copy Number Rare Codon 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. Allen LH, Christopher KC, Roy C (2002) Construction of transcriptional and translational lacZ gene reporter plasmids for use in Streptococcus mutans. J Microbiol Methods 49:163–171CrossRefGoogle Scholar
  2. Aristidou AA, San KY, Bennett GN (1995) Metabolic engineering of Escherichia coli to enhance recombinant protein production through acetate reduction. Biotechnol Prog 11:475–478PubMedCrossRefGoogle Scholar
  3. Aristidou AA, Yu P, San K-Y (1993) Effects of glycine supplement on protein production and release in recombinant Escherichia coli. Biotechnol. Lett 15:331–336CrossRefGoogle Scholar
  4. Arsène F, Tomoyasu T, Bukau B (2000) The heat shock response of Escherichia coli. Int J Food Microbiol 55:3–9PubMedCrossRefGoogle Scholar
  5. Baneyx F (1999) Recombinant protein expression in Escherichia coli. Curr Opin Biotechnol 10:411–421PubMedCrossRefGoogle Scholar
  6. Bentley WE, Mirjalili N, Andersen DC, Davis RH, Kompala DS (1990) Plasmid-encoded protein: the principal factor in the “metabolic burden” associated with recombinant bacteria. Biotechnol Bioeng 35:668–681PubMedCrossRefGoogle Scholar
  7. Billman-Jacobe H, Hodgson ALM, Lightowlers M, Wood PR, Radford AJ (1994) Expression of ovine gamma interferon in Escherichia coil and Corynebacterium glutamicum. Appl Environ Microbiol 60:1641–1645PubMedCentralPubMedGoogle Scholar
  8. Bird PI, Pak SC, Worrall DM, Stephen P, Bottomley SP (2004) Production of recombinant serpins in Escherichia coli. Methods 32:169–176PubMedCrossRefGoogle Scholar
  9. Bowers LM, LaPoint K, Anthony L, Pluciennik A, Filutowicz M (2004) Bacterial expression system with tightly regulated gene expression and plasmid copy number. Gene (in press)Google Scholar
  10. Brurberg MB, Haandrikrnan AJ, Leenhouts KJ, Venema G, Nes IF (1994) Expression of a chitinase gene from Serratia marcesens in Lactococcus lactis and Lactobacillus plantarum. Appl Microbiol Biotechnol 42:108–115PubMedCrossRefGoogle Scholar
  11. Chadd HE, Chamow SM (2001) Therapeutic antibody expression technology. Curr Opin Biotechnol 12:188–194PubMedCrossRefGoogle Scholar
  12. Chen GFT, Inouye M (1994) Role of the AGA/AGG codons, the rarest codons in global gene expression in Escherichia coli. Genes Dev 8:2641–2652PubMedCrossRefGoogle Scholar
  13. Chen HC, Hwang CF, Mou DG (1992) High-density Escherichia coli cultivation process for hyperexpression of recombinant porcine growth hormone. Enzyme Microb Technol 14:321–326PubMedCrossRefGoogle Scholar
  14. Chou C-H, Bennett GN, San K-Y (1994) Effect of modified glucose uptake using genetic engineering techniques on high-level recombinant protein production in Escherichia coli dense cultures. Biotechnol Bioeng 44:952–960PubMedCrossRefGoogle Scholar
  15. Chou C-H, Aristidou AA, Meng SY, Bennett GN, San KY (1995) Characterization of a pH-inducible promoter system for high-level expression of recombinant proteins in Escherichia coli. Biotechnol Bioeng 47:186–192PubMedCrossRefGoogle Scholar
  16. Chu L, Robinson DK (2001) Industrial choices for protein production by large-scale cell culture. Curr Opin Biotechnol 12:180–187PubMedCrossRefGoogle Scholar
  17. Corisdeo S, Baiyang Wang B (2004) Functional expression and display of an antibody Fab fragment in Escherichia coli: study of vector designs and culture conditions. Protein Exp Purif 34:270–279CrossRefGoogle Scholar
  18. Cruz-Vera LR, Magos-Castro MA, Zamora-Romo E, Guarneros G (2004) Ribosome stalling and peptidyl-tRNA drop-off during translational delay at AGA codons. Nucleic Acids Res 32:4462–4468PubMedCentralPubMedCrossRefGoogle Scholar
  19. da Costa PN, Teixeira M, Saraiva LM (2003) Regulation of the flavorubredoxin nitric oxide reductase gene in Escherichia coli: nitrate repression, nitrite induction, and possible post-transcription control. FEMS Microbiol Lett 218:85–393CrossRefGoogle Scholar
  20. Das A (1990) Overproduction of proteins in Escherichia coli: vectors, hosts, and strategies. Methods Enzymol 182:93–112PubMedCrossRefGoogle Scholar
  21. Doran P (2000) Foreign protein production in plant tissue cultures. Curr Opin Biotechnol 11:199–204PubMedCrossRefGoogle Scholar
  22. Duilio A, Tutino ML, Marino G (2004) Recombinant protein production in Antarctic gram-negative bacteria. Methods Mol Biol 267:225–238PubMedGoogle Scholar
  23. Etchegaray J-P, Inouye M (1999) Translational enhancement by an element downstream of the initiation codon in Escherichia coli. J Biol Chem 274:10079–10085PubMedCrossRefGoogle Scholar
  24. Farmer WR, Liao JC (1997) Reduction of aerobic acetate production by Escherichia coli. Appl Environ Microbiol 63:3205–3210PubMedCentralPubMedGoogle Scholar
  25. Flores N, Xiao J, Berry A, Bolivar F, Valle F (1996) Pathway engineering for the production of aromatic compounds in Escherichia coli. Nat Biotechnol 14:620–623PubMedCrossRefGoogle Scholar
  26. Frey AD, Bailey JE, Kallio PT (2000) Expression of Alcaligenes eutrophus flavohemoprotein and engineered Vitreoscilla hemoglobin-reductase fusion protein for improved hypoxic growth of Escherichia coli. Appl Env Microbiol 66:98–104CrossRefGoogle Scholar
  27. Gao W, Rzewski A, Sun H, Robbins PD, Gambotto A (2004) UpGene: application of a Web-based DNA codon optimization algorithm. Biotechnol Prog 20:443–448PubMedCrossRefGoogle Scholar
  28. Goodrick JC, Xu M, Finnegan R, Schilling BM, Schiavi S, Hoppe H, Wan NC (2001) High-level expression and stabilization of recombinant human chitinase produced in a continuous constitutive Pichia pastoris expression system. Biotechnol Bioeng 74:492–497PubMedCrossRefGoogle Scholar
  29. Goldstein MA, Doi RH (1995) Prokaryotic promoters in biotechnology. Biotechnol Annu Rev 1:105–128PubMedCrossRefGoogle Scholar
  30. Gschaedler A, Robas N, Boudrant J, Branlant C (1999) Effects of pulse addition of carbon sources on continuous cultivation of Escherichia coli containing a recombinant E. coli gapA gene. Biotechnol Bioeng 63:712–720PubMedCrossRefGoogle Scholar
  31. Gupta P, Sahai V, Rakesh Bhatnagar R (2001) Enhanced expression of the recombinant lethal factor of Bacillus anthracis by fed-batch culture. Biochem Biophys Res Com 285:1025–1033PubMedCrossRefGoogle Scholar
  32. Guzman L-M, Belin D, Carson MJ, Beckwith J (1995) Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter. J Bacteriol 177:4121–4130PubMedCentralPubMedGoogle Scholar
  33. Hägg P, de Pohl JW, Abdulkarim F, Isaksson LA (2004) A host/plasmid system that is not dependent on antibiotics and antibiotic resistance genes for stable plasmid maintenance in Escherichia coli. J Biotechnol 111:17–30PubMedCrossRefGoogle Scholar
  34. Hall MN, Gabay J, De’barbouille M, Schwartz M (1982) A role for mRNA secondary structure in the control of translation initiation. Nature 295:616–618PubMedCrossRefGoogle Scholar
  35. Hasan N, Szybalski W (1995) Construction of lacIts and lacIqts expression plasmids and evaluation of the thermosensitive lac repressor. Gene 163:35–40PubMedCrossRefGoogle Scholar
  36. Hewitt L, McDonnell JM (2004) Screening and optimizing protein production in E. coli. Methods Mol Biol 278:1–16PubMedGoogle Scholar
  37. Hienonen E, Rantakari A, Romantschuk M, Taira S (2004) The bacterial type III secretion system-associated pilin HrpA has an unusually long mRNA half-life. FEBS Lett 571:217–220PubMedCrossRefGoogle Scholar
  38. Iost I, Dreyfus M (1994) mRNAs can be stabilized by DEAD-box proteins. Nature 372:193–196PubMedCrossRefGoogle Scholar
  39. Jana S, Karan G, Deb JK (2004) Purification of recombinant streptomycin adenylyltransferase from E. coli. Protein Express Purif (in press)Google Scholar
  40. Jiang X, Nakano H, Kigawa T, Yabuki T, Yokoyama S, Clark DS, Yamane T (2001) Dosage effect of minor arginyl- and isoleucyl-tRNAs on protein synthesis in an Escherichia coli in vitro couple transcription/translation system. J Biosci Bioeng 91:53–57PubMedGoogle Scholar
  41. Joliffe LK, Doyle RI, Streips UN (1980) Extracellular proteases modify cell wall turnover in Bacillus subtilis. J Bacteriol 141:1199–1208Google Scholar
  42. Jones KL, Keasling JD (1998) Construction and characterization of F plasmid-based expression vectors. Biotechnol Bioeng 59:659–665PubMedCrossRefGoogle Scholar
  43. Jones KL, Kim SW, Keasling JD (2000) Low-copy plasmids can perform as well as or better than high-copy plasmids for metabolic engineering of bacteria. Metab Eng 2:328–338PubMedCrossRefGoogle Scholar
  44. Kane JF (1995) Effect of rare codon clusters on high-level expression of heterologous proteins in Escherichia coli. Curr Opin Biotechnol 6:494–500PubMedCrossRefGoogle Scholar
  45. Kim D-M, Swartz JR (2001) Regeneration of adenosine triphosphate from glycolytic intermediates for cell-free protein synthesis. Biotechnol Bioeng 74:309–316PubMedCrossRefGoogle Scholar
  46. Larrick JW, Thomas DW (2001) Producing proteins in transgenic plant and animals. Curr Opin Biotechnol 12:411–418PubMedCrossRefGoogle Scholar
  47. Leenhouts KJ, Bolhuis A, Ledeboer A, Venerna G, Kok J (1995) Production of secreted quar α-galactosidase by Lactococcus lactis. Appl Microbiol Biotechnol 44:75–80CrossRefGoogle Scholar
  48. Liang ST, Bipatnath M, Xu YC, Chen SL, Dennis P, Ehrenberg M, Bremer H (1999) Activities of constitutive promoters in Escherichia coli. J Mol Biol 292:19–37PubMedCrossRefGoogle Scholar
  49. Lim J, Thomas T, Cavicchioli R (2000) Low temperature regulated DEAD-box RNA helicase from the Antarctic archaeon, Methanococcoides burtonii. J Mol Biol 297:553–567PubMedCrossRefGoogle Scholar
  50. Lindsley D, Gallant J (1993) On the directional specificity of ribosome frameshiffing at a ‘hungry’ codon. Proc Natl Acad Sci USA 90:5469–5473PubMedCentralPubMedCrossRefGoogle Scholar
  51. Lopez PJ, Marchand I, Joyce SA, Dreyfus M (1999) The C-terminal half of RNase E, which organizes the Escherichia coli degradosome, participates in mRNA degradation but not rRNA processing in vivo. Mol Microbiol 33:188–199PubMedCrossRefGoogle Scholar
  52. Love CA, Lilley PE, Dixon NE. (1996) Stable high-copy-number bacteriophage λ promoter vectors for overproduction of proteins in Escherichia coli. Gene 176:49–53PubMedCrossRefGoogle Scholar
  53. Luli GW, Strohl WR (1990) Comparison of growth, acetate production and acetate inhibition of Escherichia coli strains in batch and fed-batch fermentations. Appl Environ Microbiol 56:1004–1011PubMedCentralPubMedGoogle Scholar
  54. Ma J, Campbell A, Karlin S (2002) Correlations between Shine–Dalgarno sequences and gene features such as predicted expression levels and operon structures. J Bacteriol 184:5733–5745PubMedCentralPubMedCrossRefGoogle Scholar
  55. Massé E, Escorcia FE, Gottesman S (2003) Coupled degradation of a small regulatory RNA and its mRNA targets in Escherichia coli. Genes Dev 17:2374–2383PubMedCentralPubMedCrossRefGoogle Scholar
  56. Moll I, Afonyushkin T, Vytvytska O, Kaberdin VR, Blasi U (2003) Coincident Hfq binding and RNase E cleavage sites on mRNA and small regulatory RNAs. RNA 9:1308–1314PubMedCentralPubMedCrossRefGoogle Scholar
  57. Morita M, Asami K, Tanji Y, Unno H (2001) Programmed Escherichia coli cell lysis by expression of cloned T4 phage lysis genes. Biotechnol Prog 17:573–576PubMedCrossRefGoogle Scholar
  58. Nakashima N, Tamura T (2004) A novel system for expressing recombinant proteins over a wide temperature range from 4 to 35°C. Biotechnol Bioeng 86:136–148PubMedCrossRefGoogle Scholar
  59. Nierlich DP, Murakawa GJ (1996) The decay of bacterial messenger RNA. Prog Nucleic Acid Res 52:153–216CrossRefGoogle Scholar
  60. Nilsson M, Kallio PT, Bailey JE, Bulow L, Wahlund K-G (1999) Expression Vitreoscilla hemoglobin in Escherichia coli enhances ribosome and tRNA levels: a flow field-flow fractionation study. Biotechnol Prog 15:158–163PubMedCrossRefGoogle Scholar
  61. Nogueira T, de Smit M, Graffe M, Springe M (2001) The relationship between translational control and mRNA degradation for the Escherichia coli threonyl-tRNA synthetase gene. J Mol Biol 310:709–722PubMedCrossRefGoogle Scholar
  62. Peixoto L, Fernandez V, Musto H (2004) The effect of expression levels on codon usage in Plasmodium falciparum. Parasitology 128:245–251PubMedCrossRefGoogle Scholar
  63. Piao Y, Kawaraichi N, Asegawa R, Kiatpapan P, Ono H, Yamashita M, Murooka Y (2004) Molecular analysis of promoter elements from Propionibacterium freudenreichii. J Biosci Bioeng 97:310–316PubMedCrossRefGoogle Scholar
  64. Qing G, Xia B, Inouye M (2003) Enhancement of translation initiation by A/T-rich sequences downstream of the initiation codon in Escherichia coli. J Mol Microbiol Biotechnol 6:133–144PubMedCrossRefGoogle Scholar
  65. Qiu J, Swartz J-R, Georgiou G (1998) Expression of active human tissue-type plasminogen activator in Escherichia coli. Appl Environ Microbiol 64:4891–4896PubMedCentralPubMedGoogle Scholar
  66. Rao XC, Li S, Hu JC, Jin XL, Hu XM, Huang JJ, Chen ZJ, Zhu JM, Fu Q. Hu FQ (2004) A novel carrier molecule for high-level expression of peptide antibiotics in Escherichia coli. Protein Express Purif 36:11–18CrossRefGoogle Scholar
  67. Richardson JP (1993) Transcription termination. Crit Rev Biochem Mol Biol 28:1–30PubMedCrossRefGoogle Scholar
  68. Ringquist S, Shinedling S, Barrick D, Green L, Binkley J, Stormo GD, Gold L (1992) Translation initiation in Escherichia coli: sequences within the ribosome-binding site. Mol Microbiol 6:1219–1229PubMedCrossRefGoogle Scholar
  69. Ross J (1995) mRNA stability in mammalian cells. Microbiol Rev 59:423–450PubMedCentralPubMedGoogle Scholar
  70. Saier MH Jr (1995) Differential codon usage: a safeguard against inappropriate expression of specialized genes? FEBS Lett 362:1–4PubMedCrossRefGoogle Scholar
  71. Schmidt T, Friehs K, Flaschel E (1996) Rapid determination of plasmid copy number. J Biotechnol 49:219–229PubMedCrossRefGoogle Scholar
  72. Shatzman AR (1995) Expression systems. Curr Opin Biotechnol 6:491–493CrossRefGoogle Scholar
  73. Sharp JM, Doran PM (2001) Characterization of monoclonal antibody fragments produced by plant cells. Biotechnol Bioeng 73:338–346PubMedCrossRefGoogle Scholar
  74. Siegele DA, Hu JC (1997) Gene expression from plasmids containing araBAD promoter at subsaturating inducer concentrations represents mixed populations. Proc Natl Acad Sci USA 94:8168–8172PubMedCentralPubMedCrossRefGoogle Scholar
  75. Simmons LC, Yansura DG (1996) Translational level is a critical factor for the secretion of heterologous proteins in Escherichia coli. Nat Biotechnol 14:629–634PubMedCrossRefGoogle Scholar
  76. Sirnonen M, Palva I (1993) Protein secretion in Bacillus species. Microbiol Rev 57:109–137Google Scholar
  77. Sipley J, Goldman E (1993) Increased ribosomal accuracy increases a programmed translational frameshift in Escherichia coli. Proc Natl Acad Sci USA 90:2315–2319PubMedCentralPubMedCrossRefGoogle Scholar
  78. Sprengart ML, Porter AG (1997) Functional importance of RNA interactions in selection of translation initiation codons. Mol Microbiol 24:19–28PubMedCrossRefGoogle Scholar
  79. Srivastava P, Deb JK (2002) Construction of fusion vectors of Corynebacteria: expression of glutathione-s-transferase fusion protein in acetoacidophilum ATCC 21476. FEMS Microbiol Lett: 212:209–216PubMedCrossRefGoogle Scholar
  80. Steidler L, Wells JM, Raemaekers A, Vandekerckhove J, Fiers W, Remalt E (1995) Secretion of biologically active murine interleukin-2 by Lactococcus lactis subsp. lactis. Appl Environ Microbiol 61:1627–1629PubMedCentralPubMedGoogle Scholar
  81. Storz G, Opdyke JA, Zhang A (2004) Controlling mRNA stability and translation with small, noncoding RNAs. Curr Opin Microbiol 7:140–144PubMedCrossRefGoogle Scholar
  82. Swartz JR (2001) Advances in Escherichia coli production of therapeutic proteins. Curr Opin Biotechnol 12:195–201PubMedCrossRefGoogle Scholar
  83. Toivonen JM, Manjiry S, Touraille S, Alziari S, O’Dell KMC, Howard T, Jacobs HTD (2003) Gene dosage and selective expression modify phenotype in a Drosophila model of human mitochondrial disease. Mitochondrion 3: 83–96PubMedCrossRefGoogle Scholar
  84. Toksoy E, Onsan ZI, Kirdar B (2002) High-level production of TaqI restriction endonuclease by three different expression systems in Escherichia coli cells using the T7 phage promoter. Appl Microbiol Biotechnol 59:239–245PubMedCrossRefGoogle Scholar
  85. Valešová R, Hollerová-Sobotková L, Štěpánek V, Kyslík P (2004) Optimization of the host–plasmid interaction in the recombinant Escherichia coli strains overproducing penicillin G acylase. Enzyme Microbial Technol 35:74–80CrossRefGoogle Scholar
  86. Wang Y, Liang Z-H, Zhang Y-S, Yao S-Y, Xu Y-G, Tang Y-H, Zhu S-Q, Cui D-F, Feng Y-M (2001) Human insulin from a precursor overexpressed in the methylotrophic yeast Pichia pastoris and a simple procedure for purifying the expression product. Biotechnol Bioeng 73:74–79PubMedCrossRefGoogle Scholar
  87. Wells JM, Wilson PW, Norton PM, Gasson MJ, Le Page RWF (1993) Lactococcus laces: High-level expression of tetanus toxin fragment C and protection against lethal challenge. Mol Microbiol 8:1155–1162PubMedCrossRefGoogle Scholar
  88. Wild J, Szybalski W (2004) Copy-control tightly regulated expression vectors based on pBAC/oriV. Methods Mol Biol 267:155–168PubMedGoogle Scholar
  89. Wilms B, Hauck A, Reuss M, Syldatk C, Mattes R, Siemann M, Altenbuchner J (2001) High-cell-density fermentation for production L-N-carbamoylase using an expression system based on the Escherichia coli rhaBAD promoter. Biotechnol Bioeng 73:95-103PubMedCrossRefGoogle Scholar
  90. Wu X, Jornvall H, Berndt KD, Oppermann U (2004) Codon optimization reveals critical factors for high level expression of two rare codon genes in Escherichia coli: RNA stability and secondary structure but not tRNA abundance. Biochem Biophys Res Commun 313:89–96PubMedCrossRefGoogle Scholar
  91. Yabuta M, Miura-Onai S, Ohsuye K (1995) Thermo-inducible expression of a recombinant fusion protein by Escherichia coil lac repressor mutants. J Biotechnol 39:67–73PubMedCrossRefGoogle Scholar
  92. Yee L, Blanch HW (1992) Recombinant protein expression in high cell density fed-batch cultures of Escherichia coli. Bio/Technology 10:1550–556PubMedCrossRefGoogle Scholar
  93. Zhang S, Zubay G, Goldman E (1991) Low-usage codons in Escherichia coil, yeast, fruit fly, and primates. Gene 105:61–72PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2005

Authors and Affiliations

  1. 1.Department of Biochemical Engineering and BiotechnologyIndian Institute of Technology-DelhiHauz KhasIndia

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