Skip to main content

Expression in Bacteria and Refolding

  • Protocol
  • First Online:
Advanced Methods in Structural Biology

Part of the book series: Springer Protocols Handbooks ((SPH))

Abstract

Production of proteins by bacterial expression is common due to straightforwardness and inexpensiveness. In this chapter, we focus on the expression system using Escherichia coli and refolding of inclusion bodies formed with insoluble protein materials. In the first half, several steps required to produce soluble proteins as much amount as possible, in E. coli, are described. Here, the choice of either vector or bacterial strains, induction, extraction, fusion of solubilizing tags, and strategies to facilitate disulfide bond formation are included. In the second half, strategies to get soluble proteins from inclusion bodies are described. Here, the mechanism of protein refolding, the isolation of inclusion bodies, the choice of solubilizing materials, the refolding step, and the effects of additives while refolding are included. The selection of various strategies in these steps is discussed.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

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

    Article  CAS  PubMed  Google Scholar 

  2. Zerbs S, Frank AM, Collart FR (2009) Bacterial systems for production of heterologous proteins. Methods Enzymol 463:149–168

    Article  CAS  PubMed  Google Scholar 

  3. Sørensen HP, Mortensen KK (2005) Advanced genetic strategies for recombinant protein expression in Escherichia coli. J Biotechnol 115:113–128

    Article  PubMed  Google Scholar 

  4. Studier FW, Moffatt BA (1986) Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J Mol Biol 189:113–130

    Article  CAS  PubMed  Google Scholar 

  5. Correa A, Oppezzo P (2011) Tuning different expression parameters to achieve soluble recombinant proteins in E. coli: advantages of high-throughput screening. Biotechnol J 6:715–730

    Article  CAS  PubMed  Google Scholar 

  6. Waegeman H, Soetaert W (2011) Increasing recombinant protein production in Escherichia coli through metabolic and genetic engineering. J Ind Microbiol Biotechnol 38:1891–1910

    Article  CAS  PubMed  Google Scholar 

  7. Baca AM, Hol WG (2000) Overcoming codon bias: a method for high-level overexpression of plasmodium and other AT-rich parasite genes in Escherichia coli. Int J Parasitol 30:113–118

    Article  CAS  PubMed  Google Scholar 

  8. Studier FW (1991) Use of bacteriophage T7 lysozyme to improve an inducible T7 expression system. J Mol Biol 219:37–44

    Article  CAS  PubMed  Google Scholar 

  9. Miroux B, Walker JE (1996) Over-production of proteins in Escherichia coli: mutant hosts that allow synthesis of some membrane proteins and globular proteins at high levels. J Mol Biol 260:289–298

    Article  CAS  PubMed  Google Scholar 

  10. Wagner S, Klepsch MM, Schlegel S et al (2008) Tuning Escherichia coli for membrane protein overexpression. Proc Natl Acad Sci U S A 105:14371–14376

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Schlegel S, Löfblom J, Lee C et al (2012) Optimizing membrane protein overexpression in the Escherichia coli strain Lemo21(DE3). J Mol Biol 423:648–659

    Article  CAS  PubMed  Google Scholar 

  12. Song JM, An YJ, Kang MH et al (2012) Cultivation at 6–10 °C is an effective strategy to overcome the insolubility of recombinant proteins in Escherichia coli. Protein Expr Purif 82:297–301

    Article  CAS  PubMed  Google Scholar 

  13. Shih Y, Kung W, Chen J et al (2002) High-throughput screening of soluble recombinant proteins. Protein Sci 11:1714–1719

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Hammarstrom M, Hellgren N, van den Berg S et al (2002) Rapid screening for improved solubility of small human proteins produced as fusion proteins in Escherichia coli. Protein Sci 11:313–321

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Bird LE (2011) High throughput construction and small scale expression screening of multi-tag vectors in Escherichia coli. Methods 55:29–37

    Article  CAS  PubMed  Google Scholar 

  16. Vincentelli R, Cimino A, Geerlof A et al (2011) High-throughput protein expression screening and purification in Escherichia coli. Methods 55:65–72

    Article  CAS  PubMed  Google Scholar 

  17. Bell MR, Engleka MJ, Malik A, Strickler JE (2013) To fuse or not to fuse: what is your purpose? Protein Sci 22:1466–1477

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Wang D, Huang XY, Cole PA (2001) Molecular determinants for Csk-catalyzed tyrosine phosphorylation of the Src tail. Biochemistry 40:2004–2010

    Article  CAS  PubMed  Google Scholar 

  19. Haacke A, Fendrich G, Ramage P, Geiser M (2009) Chaperone over-expression in Escherichia coli: apparent increased yields of soluble recombinant protein kinases are due mainly to soluble aggregates. Protein Expr Purif 64:185–193

    Article  CAS  PubMed  Google Scholar 

  20. Thomas JG, Ayling A, Baneyx F (1997) Molecular chaperones, folding catalysts, and the recovery of active recombinant proteins from E. coli. To fold or to refold. Appl Biochem Biotechnol 66:197–238

    Article  CAS  PubMed  Google Scholar 

  21. Salinas G, Pellizza L, Margenat M et al (2011) Tuned Escherichia coli as a host for the expression of disulfide-rich proteins. Biotechnol J 6:686–699

    Article  CAS  PubMed  Google Scholar 

  22. De Marco A (2009) Strategies for successful recombinant expression of disulfide bond-dependent proteins in Escherichia coli. Microbiol Cell Fact 8:26

    Article  Google Scholar 

  23. Mergulhão FJM, Summers DK, Monteiro GA (2005) Recombinant protein secretion in Escherichia coli. Biotechnol Adv 23:177–202

    Article  PubMed  Google Scholar 

  24. Zalucki YM, Beacham IR, Jennings MP (2011) Coupling between codon usage, translation and protein export in Escherichia coli. Biotechnol J 6:660–667

    Article  CAS  PubMed  Google Scholar 

  25. Prinz WA, Ǻslund F, Holmgren A, Beckwith J (1997) The role of the thioredoxin and glutaredoxin pathways in reducing protein disulfide bonds in the Escherichia coli cytoplasm. J Biol Chem 272:15661–15667

    Article  CAS  PubMed  Google Scholar 

  26. Bessette PH, Ǻslund F, Beckwith J, Georgiou G (1999) Efficient folding of proteins with multiple disulfide bonds in the Escherichia coli cytoplasm. Proc Natl Acad Sci U S A 96:13703–13708

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Baneyx F, Mujacic M (2004) Recombinant protein folding and misfolding in Escherichia coli. Nat Biotechnol 22:1399–1408

    Article  CAS  PubMed  Google Scholar 

  28. Anfinsen CB, Scheraga HA (1975) Experimental and theoretical aspects of protein folding. Adv Protein Chem 29:205–300

    Article  CAS  PubMed  Google Scholar 

  29. Tanford C (1997) How protein chemists learned about the hydrophobic factor. Protein Sci 6:1358–1366

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Rudolph R, Lilie H (1996) In vitro folding of inclusion body proteins. FASEB J 10:49–56

    CAS  PubMed  Google Scholar 

  31. Clark E (1998) Refolding of recombinant proteins. Curr Opin Biotechnol 9:157–163

    Article  PubMed  Google Scholar 

  32. Singh SM, Panda AK (2005) Solubilization and refolding of bacterial inclusion body proteins. J Biosci Bioeng 99:303–310

    Article  CAS  PubMed  Google Scholar 

  33. Bhavesh NS, Panchal SC, Mittal R, Hosur RV (2001) NMR identification of local structural preferences in HIV-1 protease tethered heterodimer in 6 M guanidine hydrochloride. FEBS Lett 509:218–224

    Article  CAS  PubMed  Google Scholar 

  34. Markossian KA, Kurganov BI (2004) Protein folding, misfolding, and aggregation. Formation of inclusion bodies and aggresomes. Biochem Mosc 69:971–984

    Article  CAS  Google Scholar 

  35. Umetsu M, Tsumoto K, Ashish K et al (2004) Structural characteristics and refolding of in vivo aggregated hyperthermophilic archaeon proteins. FEBS Lett 557:49–56

    Article  CAS  PubMed  Google Scholar 

  36. Kopito RR (2000) Aggresomes, inclusion bodies and protein aggregation. Trends Cell Biol 68:524–530

    Article  Google Scholar 

  37. Fink AL (1998) Protein aggregation: folding aggregates, inclusion bodies and amyloid. Fold Des 3:R9–R23

    Article  CAS  PubMed  Google Scholar 

  38. Kudou M, Yumioka R, Ejima D et al (2011) A novel protein refolding system using lauroyl-l-glutamate as a solubilizing detergent and arginine as a folding assisting agent. Protein Expr Purif 75:46–54

    Article  CAS  PubMed  Google Scholar 

  39. Tsumoto K, Umetsu M, Kumagai I et al (2003) Solubilization of active green fluorescent protein from insoluble particles by guanidine and arginine. Biochem Biophys Res Commun 312:1383–1386

    Article  CAS  PubMed  Google Scholar 

  40. Tsumoto K, Ejima D, Kumagai I, Arakawa T (2003) Practical considerations in refolding proteins from inclusion bodies. Protein Expr Purif 28:1–8

    Article  CAS  PubMed  Google Scholar 

  41. Burgess RR (2009) Refolding solubilized inclusion body proteins. Methods Enzymol 463:259–282

    Article  CAS  PubMed  Google Scholar 

  42. Welker E, Wedemeyer WJ, Narayan M, Scheraga HA (2001) Coupling of conformational folding and disulfide-bond reactions in oxidative folding of proteins. Biochemistry 40:9059–9064

    Article  CAS  PubMed  Google Scholar 

  43. Tsumoto K, Shinoki K, Kondo H et al (1998) Highly efficient recovery of functional single-chain Fv fragments from inclusion bodies overexpressed in Escherichia coli by controlled introduction of oxidizing reagent—application to a human single-chain Fv fragment. J Immunol Methods 219:119–129

    Article  CAS  PubMed  Google Scholar 

  44. Li M, Su Z-G, Janson J-C (2004) In vitro protein refolding by chromatographic procedures. Protein Expr Purif 33:1–10

    Article  PubMed  Google Scholar 

  45. Jungbauer A, Kaar W, Schlegl R (2004) Folding and refolding of proteins in chromatographic beds. Curr Opin Biotechnol 15:487–494

    Article  CAS  PubMed  Google Scholar 

  46. Geng X, Wang C (2007) Protein folding liquid chromatography and its recent developments. J Chromatogr B 849:69–80

    Article  CAS  Google Scholar 

  47. Freydell EJ, van der Wielen L, Eppink M, Ottens M (2010) Ion-exchange chromatographic protein refolding. J Chromatogr A 1217:7265–7274

    Article  CAS  PubMed  Google Scholar 

  48. Freydell EJ, van der Wielen LAM, Eppink MHM, Ottens M (2010) Size-exclusion chromatographic protein refolding: fundamentals, modeling and operation. J Chromatogr A 1217:7723–7737

    Article  CAS  PubMed  Google Scholar 

  49. Matsumoto M, Misawa S, Tsumoto K et al (2003) On-column refolding and characterization of soluble human interleukin-15 receptor α-chain produced in Escherichia coli. Protein Expr Purif 31:64–71

    Article  CAS  PubMed  Google Scholar 

  50. Yamaguchi S, Yamamoto E, Mannen T, Nagamune T (2013) Protein refolding using chemical refolding additives. Biotechnol J 8:17–31

    Article  CAS  PubMed  Google Scholar 

  51. Zardeneta G, Horowitz PM (1994) Detergent, liposome, and micelle-assisted protein refolding. Anal Biochem 223:1–6

    Article  CAS  PubMed  Google Scholar 

  52. Arakawa T, Ejima D, Tsumoto K et al (2007) Suppression of protein interactions by arginine: a proposed mechanism of the arginine effects. Biophys Chem 127:1–8

    Article  CAS  PubMed  Google Scholar 

  53. Expert-Bezançon N, Rabilloud T, Vuillard L, Goldberg ME (2003) Physical-chemical features of non-detergent sulfobetaines active as protein-folding helpers. Biophys Chem 100:469–479

    Article  PubMed  Google Scholar 

  54. De Bernardez Clark E, Hevehan D, Szela S, Maachupalli-Reddy J (1998) Oxidative renaturation of hen egg-white lysozyme. Folding vs aggregation. Biotechnol Prog 14:47–54

    Article  PubMed  Google Scholar 

  55. Altamirano MM, García C, Possani LD, Fersht AR (1999) Oxidative refolding chromatography: folding of the scorpion toxin Cn5. Nat Biotechnol 17:187–191

    Article  CAS  PubMed  Google Scholar 

  56. Teshima T, Kohda J, Kondo A et al (2000) Preparation of Thermus thermophilus microspheres with high ability to facilitate protein refolding. Biotechnol Bioeng 68:184–190

    Article  CAS  PubMed  Google Scholar 

  57. Tsumoto K, Umetsu M, Yamada H et al (2003) Immobilized oxidoreductase as an additive for refolding inclusion bodies: application to antibody fragments. Protein Eng 16:535–541

    Article  CAS  PubMed  Google Scholar 

  58. Preston NS, Baker DJ, Bottomley SP, Gore MG (1999) The production and characterisation of an immobilised chaperonin system. Biochim Biophys Acta 1426:99–109

    Article  CAS  PubMed  Google Scholar 

  59. Machida S, Ogawa S, Xiaohua S et al (2000) Cycloamylose as an efficient artificial chaperone for protein refolding. FEBS Lett 486:131–135

    Article  CAS  PubMed  Google Scholar 

  60. Daugherty DL, Rozema D, Hanson PE, Gellman SH (1998) Artificial chaperone-assisted refolding of citrate synthase. J Biol Chem 273:33961–33971

    Article  CAS  PubMed  Google Scholar 

  61. Nomura Y, Ikeda M, Yamaguchi N et al (2003) Protein refolding assisted by self-assembled nanogels as novel artificial molecular chaperone. FEBS Lett 553:271–276

    Article  CAS  PubMed  Google Scholar 

  62. Chiku H, Kawai A, Ishibashi T et al (2006) A novel protein refolding method using a zeolite. Anal Biochem 348:307–314

    Article  CAS  PubMed  Google Scholar 

  63. Sakono M, Kawashima Y, Ichinose H et al (2004) Direct refolding of inclusion bodies using reversed micelles. Biotechnol Prog 20:1783–1787

    Article  CAS  PubMed  Google Scholar 

  64. Kim Y-S, Randolph TW, Seefeldt MB, Carpenter JF (2006) High-pressure studies on protein aggregates and amyloid fibrils. Methods Enzymol 413:237–253

    Article  CAS  PubMed  Google Scholar 

  65. Lee S, Carpenter JF, Chang BS et al (2006) Effects of solutes on solubilization and refolding of proteins from inclusion bodies with high hydrostatic pressure. Protein Sci 15:304–313

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Baker D (2000) A surprising simplicity to protein folding. Nature 405:39–42

    Article  CAS  PubMed  Google Scholar 

  67. Ferguson N, Fersht AR (2003) Early events in protein folding. Curr Opin Struct Biol 13:75–81

    Article  CAS  PubMed  Google Scholar 

  68. Chow MKM, Amin AA, Fulton KF et al (2006) REFOLD: an analytical database of protein refolding methods. Protein Expr Purif 46:166–171

    Article  CAS  PubMed  Google Scholar 

  69. Rathore AS, Bade P, Joshi V et al (2013) Refolding of biotech therapeutic proteins expressed in bacteria: review. J Chem Technol Biotechnol 88:1794–1806

    Article  CAS  Google Scholar 

  70. Basu A, Li X, Leong SSJ (2011) Refolding of proteins from inclusion bodies: rational design and recipes. Appl Microbiol Biotechnol 92:241–251

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Kouhei Tsumoto .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer Japan

About this protocol

Cite this protocol

Akiba, H., Tsumoto, K. (2016). Expression in Bacteria and Refolding. In: Senda, T., Maenaka, K. (eds) Advanced Methods in Structural Biology. Springer Protocols Handbooks. Springer, Tokyo. https://doi.org/10.1007/978-4-431-56030-2_1

Download citation

  • DOI: https://doi.org/10.1007/978-4-431-56030-2_1

  • Published:

  • Publisher Name: Springer, Tokyo

  • Print ISBN: 978-4-431-56028-9

  • Online ISBN: 978-4-431-56030-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics