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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
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
Zerbs S, Frank AM, Collart FR (2009) Bacterial systems for production of heterologous proteins. Methods Enzymol 463:149–168
Sørensen HP, Mortensen KK (2005) Advanced genetic strategies for recombinant protein expression in Escherichia coli. J Biotechnol 115:113–128
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
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
Waegeman H, Soetaert W (2011) Increasing recombinant protein production in Escherichia coli through metabolic and genetic engineering. J Ind Microbiol Biotechnol 38:1891–1910
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
Studier FW (1991) Use of bacteriophage T7 lysozyme to improve an inducible T7 expression system. J Mol Biol 219:37–44
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
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
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
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
Shih Y, Kung W, Chen J et al (2002) High-throughput screening of soluble recombinant proteins. Protein Sci 11:1714–1719
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
Bird LE (2011) High throughput construction and small scale expression screening of multi-tag vectors in Escherichia coli. Methods 55:29–37
Vincentelli R, Cimino A, Geerlof A et al (2011) High-throughput protein expression screening and purification in Escherichia coli. Methods 55:65–72
Bell MR, Engleka MJ, Malik A, Strickler JE (2013) To fuse or not to fuse: what is your purpose? Protein Sci 22:1466–1477
Wang D, Huang XY, Cole PA (2001) Molecular determinants for Csk-catalyzed tyrosine phosphorylation of the Src tail. Biochemistry 40:2004–2010
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
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
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
De Marco A (2009) Strategies for successful recombinant expression of disulfide bond-dependent proteins in Escherichia coli. Microbiol Cell Fact 8:26
Mergulhão FJM, Summers DK, Monteiro GA (2005) Recombinant protein secretion in Escherichia coli. Biotechnol Adv 23:177–202
Zalucki YM, Beacham IR, Jennings MP (2011) Coupling between codon usage, translation and protein export in Escherichia coli. Biotechnol J 6:660–667
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
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
Baneyx F, Mujacic M (2004) Recombinant protein folding and misfolding in Escherichia coli. Nat Biotechnol 22:1399–1408
Anfinsen CB, Scheraga HA (1975) Experimental and theoretical aspects of protein folding. Adv Protein Chem 29:205–300
Tanford C (1997) How protein chemists learned about the hydrophobic factor. Protein Sci 6:1358–1366
Rudolph R, Lilie H (1996) In vitro folding of inclusion body proteins. FASEB J 10:49–56
Clark E (1998) Refolding of recombinant proteins. Curr Opin Biotechnol 9:157–163
Singh SM, Panda AK (2005) Solubilization and refolding of bacterial inclusion body proteins. J Biosci Bioeng 99:303–310
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
Markossian KA, Kurganov BI (2004) Protein folding, misfolding, and aggregation. Formation of inclusion bodies and aggresomes. Biochem Mosc 69:971–984
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
Kopito RR (2000) Aggresomes, inclusion bodies and protein aggregation. Trends Cell Biol 68:524–530
Fink AL (1998) Protein aggregation: folding aggregates, inclusion bodies and amyloid. Fold Des 3:R9–R23
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
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
Tsumoto K, Ejima D, Kumagai I, Arakawa T (2003) Practical considerations in refolding proteins from inclusion bodies. Protein Expr Purif 28:1–8
Burgess RR (2009) Refolding solubilized inclusion body proteins. Methods Enzymol 463:259–282
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
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
Li M, Su Z-G, Janson J-C (2004) In vitro protein refolding by chromatographic procedures. Protein Expr Purif 33:1–10
Jungbauer A, Kaar W, Schlegl R (2004) Folding and refolding of proteins in chromatographic beds. Curr Opin Biotechnol 15:487–494
Geng X, Wang C (2007) Protein folding liquid chromatography and its recent developments. J Chromatogr B 849:69–80
Freydell EJ, van der Wielen L, Eppink M, Ottens M (2010) Ion-exchange chromatographic protein refolding. J Chromatogr A 1217:7265–7274
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
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
Yamaguchi S, Yamamoto E, Mannen T, Nagamune T (2013) Protein refolding using chemical refolding additives. Biotechnol J 8:17–31
Zardeneta G, Horowitz PM (1994) Detergent, liposome, and micelle-assisted protein refolding. Anal Biochem 223:1–6
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
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
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
Altamirano MM, GarcÃa C, Possani LD, Fersht AR (1999) Oxidative refolding chromatography: folding of the scorpion toxin Cn5. Nat Biotechnol 17:187–191
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
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
Preston NS, Baker DJ, Bottomley SP, Gore MG (1999) The production and characterisation of an immobilised chaperonin system. Biochim Biophys Acta 1426:99–109
Machida S, Ogawa S, Xiaohua S et al (2000) Cycloamylose as an efficient artificial chaperone for protein refolding. FEBS Lett 486:131–135
Daugherty DL, Rozema D, Hanson PE, Gellman SH (1998) Artificial chaperone-assisted refolding of citrate synthase. J Biol Chem 273:33961–33971
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
Chiku H, Kawai A, Ishibashi T et al (2006) A novel protein refolding method using a zeolite. Anal Biochem 348:307–314
Sakono M, Kawashima Y, Ichinose H et al (2004) Direct refolding of inclusion bodies using reversed micelles. Biotechnol Prog 20:1783–1787
Kim Y-S, Randolph TW, Seefeldt MB, Carpenter JF (2006) High-pressure studies on protein aggregates and amyloid fibrils. Methods Enzymol 413:237–253
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
Baker D (2000) A surprising simplicity to protein folding. Nature 405:39–42
Ferguson N, Fersht AR (2003) Early events in protein folding. Curr Opin Struct Biol 13:75–81
Chow MKM, Amin AA, Fulton KF et al (2006) REFOLD: an analytical database of protein refolding methods. Protein Expr Purif 46:166–171
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
Basu A, Li X, Leong SSJ (2011) Refolding of proteins from inclusion bodies: rational design and recipes. Appl Microbiol Biotechnol 92:241–251
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights 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