Skip to main content

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 896))

Abstract

Cell-free protein synthesis based on E. coli cell extracts has been described for the first time more than 50 years ago. To date, cell-free synthesis is widely used for the preparation of toxic proteins, for studies of the translation process and its regulation as well as for the incorporation of artificial or labeled amino acids into a polypeptide chain. Many efforts have been directed towards establishing cell-free expression as a standard method for gene expression, with limited success. In this chapter we will describe the state-of-the-art of cell-free expression, extract preparation methods and recent examples for successful applications of cell-free synthesis of macromolecular complexes.

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

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 199.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
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. Borsook H (1950) Protein turnover and incorporation of labeled amino acids into tissue proteins in vivo and in vitro. Physiol Rev 30(2):206–219

    CAS  PubMed  Google Scholar 

  2. Winnick T (1950) Studies on the mechanism of protein synthesis in embryonic and tumor tissues. I. Evidence relating to the incorporation of labeled amino acids into protein structure in homogenates. Arch Biochem 27(1):65–74

    CAS  PubMed  Google Scholar 

  3. Palade GE (1955) A small particulate component of the cytoplasm. J Biophys Biochem Cytol 1(1):59–68

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Tissieres A, Schlessinger D, Gros F (1960) Amino acid incorporation into proteins by Escherichia coli ribosomes. Proc Natl Acad Sci U S A 46(11):1450–1463

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Nirenberg MW (1963) Cell-free protein synthesis directed by messenger RNA. Methods Enzymol 6:17–23

    Article  CAS  Google Scholar 

  6. Nirenberg MW, Matthaei JH (1961) The dependence of cell-free protein synthesis in E. coli upon naturally occurring or synthetic polyribonucleotides. Proc Natl Acad Sci U S A 47:1588–1602

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Zubay G (1973) In vitro synthesis of protein in microbial systems. Annu Rev Genet 7:267–287

    Article  CAS  PubMed  Google Scholar 

  8. Pratt JM (1984) Coupled transcription–translation in prokaryotic cellfree systems. In: Hemes BD, Higgins SJ (eds) Current protocols. IRL Press, Oxford, pp 179–209

    Google Scholar 

  9. Lesley SA (1995) Preparation and use of E. coli S-30 extracts. Methods Mol Biol 37:265–278

    CAS  PubMed  Google Scholar 

  10. Spirin AS (1991) Cell-free protein synthesis bioreactor. Front Bioprocess II:31–43

    Google Scholar 

  11. Spirin AS, Baranov VI, Ryabova LA, Ovodov SY, Alakhov YB (1988) A continuous cell-free translation system capable of producing polypeptides in high yield. Science 242(4882):1162–1164

    Article  CAS  PubMed  Google Scholar 

  12. Kigawa T et al (1999) Cell-free production and stable-isotope labeling of milligram quantities of proteins. FEBS Lett 442(1):15–19

    Article  CAS  PubMed  Google Scholar 

  13. Kigawa TIM, Aoki M, Matsuda T, Yabuki T, Seki E, Harada T, Watanabe S, Yokoyama S (2008) The use of the Escherichia coli cell-free protein synthesis for structural biology and structural proteomics. In: Spirin AS, Swartz JR (eds) Cell-free protein synthesis: methods and protocols. Wiley, New York, pp 99–109

    Google Scholar 

  14. Vinarov DA et al (2004) Cell-free protein production and labeling protocol for NMR-based structural proteomics. Nat Methods 1(2):149–153

    Article  CAS  PubMed  Google Scholar 

  15. Yokoyama S et al (2000) Structural genomics projects in Japan. Nat Struct Biol 7(Suppl):943–945

    Article  CAS  PubMed  Google Scholar 

  16. He F et al (2009) Structural and functional characterization of the NHR1 domain of the Drosophila neuralized E3 ligase in the notch signaling pathway. J Mol Biol 393(2):478–495

    Article  CAS  PubMed  Google Scholar 

  17. Koglin A et al (2006) Combination of cell-free expression and NMR spectroscopy as a new approach for structural investigation of membrane proteins. Magn Reson Chem 44 Spec No:S17–S23

    Google Scholar 

  18. Maslennikov I et al (2010) Membrane domain structures of three classes of histidine kinase receptors by cell-free expression and rapid NMR analysis. Proc Natl Acad Sci U S A 107(24):10902–10907

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Yokoyama S (2003) Protein expression systems for structural genomics and proteomics. Curr Opin Chem Biol 7(1):39–43

    Article  CAS  PubMed  Google Scholar 

  20. Hanes J, PlĂ¼ckthun A (1997) In vitro selection and evolution of functional proteins by using ribosome display. Proc Natl Acad Sci U S A 94(10):4937–4942

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Klammt C et al (2007) Cell-free production of G protein-coupled receptors for functional and structural studies. J Struct Biol 158(3):482–493

    Article  CAS  PubMed  Google Scholar 

  22. Chen YJ et al (2007) X-ray structure of EmrE supports dual topology model. Proc Natl Acad Sci U S A 104(48):18999–19004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Deniaud A, Liguori L, Blesneac I, Lenormand JL, Pebay-Peyroula E (2010) Crystallization of the membrane protein hVDAC1 produced in cell-free system. Biochim Biophys Acta 1798(8):1540–1546

    Article  CAS  PubMed  Google Scholar 

  24. Boland C et al (2014) Cell-free expression and in meso crystallisation of an integral membrane kinase for structure determination. Cell Mol Life Sci 71(24):4895–4910

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Kim TW et al (2006) Simple procedures for the construction of a robust and cost-effective cell-free protein synthesis system. J Biotechnol 126(4):554–561

    Article  CAS  PubMed  Google Scholar 

  26. Yang HL, Zubay G (1973) Synthesis of the arabinose operon regulator protein in a cell-free system. Mol Gen Genet 122(2):131–136

    Article  CAS  PubMed  Google Scholar 

  27. Ryabova LA, Desplancq D, Spirin AS, PlĂ¼ckthun A (1997) Functional antibody production using cell-free translation: effects of protein disulfide isomerase and chaperones. Nat Biotechnol 15(1):79–84

    Article  CAS  PubMed  Google Scholar 

  28. Iskakova MB, Szaflarski W, Dreyfus M, Remme J, Nierhaus KH (2006) Troubleshooting coupled in vitro transcription-translation system derived from Escherichia coli cells: synthesis of high-yield fully active proteins. Nucleic Acids Res 34(19), e135

    Article  PubMed  PubMed Central  Google Scholar 

  29. Shimizu Y et al (2001) Cell-free translation reconstituted with purified components. Nat Biotechnol 19(8):751–755

    Article  CAS  PubMed  Google Scholar 

  30. Fedorov AN, Baldwin TO (1998) Protein folding and assembly in a cell-free expression system. Methods Enzymol 290:1–17

    Article  CAS  PubMed  Google Scholar 

  31. Von Loeffelholz O, Botte M, Schaffitzel C (2011) Escherichia coli cotranslational targeting and translocation. ELS. doi:10.1002/9780470015902.a0023170

    Google Scholar 

  32. Walter P, Blobel G (1983) Preparation of microsomal membranes for cotranslational protein translocation. Methods Enzymol 96:84–93

    Article  CAS  PubMed  Google Scholar 

  33. MĂ¼ller M, Blobel G (1984) In vitro translocation of bacterial proteins across the plasma membrane of Escherichia coli. Proc Natl Acad Sci U S A 81(23):7421–7425

    Article  PubMed  PubMed Central  Google Scholar 

  34. Schulze RJ et al (2014) Membrane protein insertion and proton-motive-force-dependent secretion through the bacterial holo-translocon SecYEG-SecDF-YajC-YidC. Proc Natl Acad Sci U S A 111(13):4844–4849

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Yi L, Celebi N, Chen M, Dalbey RE (2004) Sec/SRP requirements and energetics of membrane insertion of subunits a, b, and c of the Escherichia coli F1F0 ATP synthase. J Biol Chem 279(38):39260–39267

    Article  CAS  PubMed  Google Scholar 

  36. Schaffitzel C, Ban N (2007) Generation of ribosome nascent chain complexes for structural and functional studies. J Struct Biol 158(3):463–471

    Article  CAS  PubMed  Google Scholar 

  37. Giudice E, Mace K, Gillet R (2014) Trans-translation exposed: understanding the structures and functions of tmRNA-SmpB. Front Microbiol 5:113

    Article  PubMed  PubMed Central  Google Scholar 

  38. Bischoff L, Berninghausen O, Beckmann R (2014) Molecular basis for the ribosome functioning as an L-tryptophan sensor. Cell Rep 9(2):469–475

    Article  CAS  PubMed  Google Scholar 

  39. Merz F et al (2008) Molecular mechanism and structure of Trigger Factor bound to the translating ribosome. EMBO J 27(11):1622–1632

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Schaffitzel C et al (2006) Structure of the E. coli signal recognition particle bound to a translating ribosome. Nature 444(7118):503–506

    Article  CAS  PubMed  Google Scholar 

  41. Estrozi LF, Boehringer D, Shan SO, Ban N, Schaffitzel C (2011) Cryo-EM structure of the E. coli translating ribosome in complex with SRP and its receptor. Nat Struct Mol Biol 18(1):88–90

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. von Loeffelholz O et al (2013) Structural basis of signal sequence surveillance and selection by the SRP-FtsY complex. Nat Struct Mol Biol 20(5):604–610

    Article  Google Scholar 

  43. Zhang X, Schaffitzel C, Ban N, Shan SO (2009) Multiple conformational switches in a GTPase complex control co-translational protein targeting. Proc Natl Acad Sci U S A 106(6):1754–1759

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Frauenfeld J et al (2011) Cryo-EM structure of the ribosome-SecYE complex in the membrane environment. Nat Struct Mol Biol 18(5):614–621

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Kohler R et al (2009) YidC and Oxa1 form dimeric insertion pores on the translating ribosome. Mol Cell 34(3):344–353

    Article  CAS  PubMed  Google Scholar 

  46. Clark PL, Ugrinov KG (2009) Measuring cotranslational folding of nascent polypeptide chains on ribosomes. Methods Enzymol 466:567–590

    Article  CAS  PubMed  Google Scholar 

  47. Hsu ST et al (2007) Structure and dynamics of a ribosome-bound nascent chain by NMR spectroscopy. Proc Natl Acad Sci U S A 104(42):16516–16521

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Hsu ST, Cabrita LD, Fucini P, Christodoulou J, Dobson CM (2009) Probing side-chain dynamics of a ribosome-bound nascent chain using methyl NMR spectroscopy. J Am Chem Soc 131(24):8366–8367

    Article  CAS  PubMed  Google Scholar 

  49. O’Brien EP, Christodoulou J, Vendruscolo M, Dobson CM (2012) Trigger factor slows co-translational folding through kinetic trapping while sterically protecting the nascent chain from aberrant cytosolic interactions. J Am Chem Soc 134(26):10920–10932

    Article  PubMed  Google Scholar 

  50. Roberts RW, Szostak JW (1997) RNA-peptide fusions for the in vitro selection of peptides and proteins. Proc Natl Acad Sci U S A 94(23):12297–12302

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Hanes J, Schaffitzel C, Knappik A, Pluckthun A (2000) Picomolar affinity antibodies from a fully synthetic naive library selected and evolved by ribosome display. Nat Biotechnol 18(12):1287–1292

    Article  CAS  PubMed  Google Scholar 

  52. Schaffitzel C et al (2001) In vitro generated antibodies specific for telomeric guanine-quadruplex DNA react with Stylonychia lemnae macronuclei. Proc Natl Acad Sci U S A 98(15):8572–8577

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Wada A, Hara S, Osada H (2014) Ribosome display and photo-cross-linking techniques for in vitro identification of target proteins of bioactive small molecules. Anal Chem 86(14):6768–6773

    Article  CAS  PubMed  Google Scholar 

  54. Kanamori T, Fujino Y, Ueda T (2014) PURE ribosome display and its application in antibody technology. Biochim Biophys Acta 1844(11):1925–1932

    Article  CAS  PubMed  Google Scholar 

  55. Klammt C et al (2004) High level cell-free expression and specific labeling of integral membrane proteins. Eur J Biochem 271(3):568–580

    Article  CAS  PubMed  Google Scholar 

  56. Elbaz Y, Steiner-Mordoch S, Danieli T, Schuldiner S (2004) In vitro synthesis of fully functional EmrE, a multidrug transporter, and study of its oligomeric state. Proc Natl Acad Sci U S A 101(6):1519–1524

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Sansuk K et al (2008) GPCR proteomics: mass spectrometric and functional analysis of histamine H1 receptor after baculovirus-driven and in vitro cell free expression. J Proteome Res 7(2):621–629

    Article  CAS  PubMed  Google Scholar 

  58. Klammt C et al (2005) Evaluation of detergents for the soluble expression of alpha-helical and beta-barrel-type integral membrane proteins by a preparative scale individual cell-free expression system. FEBS J 272(23):6024–6038

    Article  CAS  PubMed  Google Scholar 

  59. Park KH et al (2007) Fluorinated and hemifluorinated surfactants as alternatives to detergents for membrane protein cell-free synthesis. Biochem J 403(1):183–187

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Matthies D et al (2011) Cell-free expression and assembly of ATP synthase. J Mol Biol 413(3):593–603

    Article  CAS  PubMed  Google Scholar 

  61. Matsubayashi H, Kuruma Y, Ueda T (2014) In vitro synthesis of the E. coli Sec translocon from DNA. Angew Chem Int Ed Engl 53(29):7535–7538

    Article  CAS  PubMed  Google Scholar 

  62. Asahara H, Chong S (2010) In vitro genetic reconstruction of bacterial transcription initiation by coupled synthesis and detection of RNA polymerase holoenzyme. Nucleic Acids Res 38(13), e141

    Article  PubMed  PubMed Central  Google Scholar 

  63. Fujiwara K, Katayama T, Nomura SM (2013) Cooperative working of bacterial chromosome replication proteins generated by a reconstituted protein expression system. Nucleic Acids Res 41(14):7176–7183

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Shin J, Noireaux V (2010) Efficient cell-free expression with the endogenous E. Coli RNA polymerase and sigma factor 70. J Biol Eng 4:8

    Article  PubMed  PubMed Central  Google Scholar 

  65. Maeda YT et al (2012) Assembly of MreB filaments on liposome membranes: a synthetic biology approach. ACS Synth Biol 1(2):53–59

    Article  CAS  PubMed  Google Scholar 

  66. Noireaux V, Libchaber A (2004) A vesicle bioreactor as a step toward an artificial cell assembly. Proc Natl Acad Sci U S A 101(51):17669–17674

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Shin J, Jardine P, Noireaux V (2012) Genome replication, synthesis, and assembly of the bacteriophage T7 in a single cell-free reaction. ACS Synth Biol 1(9):408–413

    Article  CAS  PubMed  Google Scholar 

  68. Karzbrun E, Tayar AM, Noireaux V, Bar-Ziv RH (2014) Synthetic biology. Programmable on-chip DNA compartments as artificial cells. Science 345(6198):829–832

    Article  CAS  PubMed  Google Scholar 

  69. Watanabe M et al (2010) Cell-free protein synthesis for structure determination by X-ray crystallography. Methods Mol Biol 607:149–160

    Article  CAS  PubMed  Google Scholar 

  70. Hendrickson TL, de Crecy-Lagard V, Schimmel P (2004) Incorporation of nonnatural amino acids into proteins. Annu Rev Biochem 73:147–176

    Article  CAS  PubMed  Google Scholar 

  71. Noren CJ, Anthony-Cahill SJ, Griffith MC, Schultz PG (1989) A general method for site-specific incorporation of unnatural amino acids into proteins. Science 244(4901):182–188

    Article  CAS  PubMed  Google Scholar 

  72. Wang K et al (2014) Optimized orthogonal translation of unnatural amino acids enables spontaneous protein double-labelling and FRET. Nat Chem 6(5):393–403

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Chin JW (2014) Expanding and reprogramming the genetic code of cells and animals. Annu Rev Biochem 83:379–408

    Article  CAS  PubMed  Google Scholar 

  74. Kim CH, Axup JY, Schultz PG (2013) Protein conjugation with genetically encoded unnatural amino acids. Curr Opin Chem Biol 17(3):412–419

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Alkalaeva EZ, Pisarev AV, Frolova LY, Kisselev LL, Pestova TV (2006) In vitro reconstitution of eukaryotic translation reveals cooperativity between release factors eRF1 and eRF3. Cell 125(6):1125–1136

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

C.S. acknowledges funding by the European Research Council Starting grant (ComplexNMD, 281331); and by a Sinergia grant from the Swiss National Science Foundation (CRSII3_136254/1).

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Aurélien Deniaud or Christiane Schaffitzel .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer International Publishing Switzerland

About this chapter

Cite this chapter

Botte, M., Deniaud, A., Schaffitzel, C. (2016). Cell-Free Synthesis of Macromolecular Complexes. In: Vega, M. (eds) Advanced Technologies for Protein Complex Production and Characterization. Advances in Experimental Medicine and Biology, vol 896. Springer, Cham. https://doi.org/10.1007/978-3-319-27216-0_6

Download citation

Publish with us

Policies and ethics